Κυριακή 12 Ιανουαρίου 2020

GSE



GSE143490 Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors. [exp2]
Contributor : Bartłomiej TomasikSeries Type : Expression profiling by RT-PCROrganism : Homo sapiensThe samples were drawn from patients with diagnosed oropharyngeal cancer. We used blood samples (10ml) collected from patients after diagnosis, before treatment. Blood was centrifuged for 10 min, after which serum was aspirated, aliquoted in RNAse-free tubes, stored at −80°C until required for further processing and did not undergo more than two freeze-thaw cycles. MicroRNA was extracted from 200 μL...
GEO series published today
55m
GSE116928 Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of step-wise in vitro induction/differentiation of human presomitic mesoderm and its derivatives
Contributors : Yoshihiro Yamanaka ; Maya Uemura ; Satoko Sakurai ; Takuya Yamamoto ; Cantas AlevSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types experimental model systems that can recapitulate more complex biological features...
GEO series published today
55m
GSE143489 Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors. [exp1]
Contributor : Bartłomiej TomasikSeries Type : Expression profiling by RT-PCROrganism : Homo sapiensThe samples were drawn from patients with diagnosed oropharyngeal cancer treated with irradiation. We used blood samples (10ml) collected from patients 7 days after receiving 20Gy dose of irradiation. Blood was centrifuged for 10 min, after which serum was aspirated, aliquoted in RNAse-free tubes, stored at −80°C until required for further processing and did not undergo more than two freeze-thaw cycles....
GEO series published today
55m
GSE116935 Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
55m
GSE143486 Contradictory of gene expression signatures for clinical prognostic prediction caused by update of reference genome and annotation
Contributor : Lishuang QiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGene expression estimates detected by RNA-sequencing technology vary with the updates of reference genome and gene annotation, which might confound existing expression-based prognostic signatures, making them inapplicable to clinical practice. In this study, we proposed a method to decrease these effects and developed a qualitative signature for stage I lung adenocarcinoma, whose classification...
GEO series published today
55m
GSE143491 Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors.
Series Type : Expression profiling by RT-PCROrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
55m
GSE143485 nsp1 acts on HEK-293T
Contributor : Zhou ShenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIdenrify the function of NSP1
GEO series published today
55m
GSE120542 Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [RNA-seq]
Contributors : H C Aegerter ; S Crotta ; J Kulikauskaite ; H Patel ; E M Hessel ; S Beinke ; A WackSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate transcriptomic differences using RNA-seq in macrophages from a BM origin (CD45.1) and embryonic origin (CD45.2) in influenza-experienced, and naive lungs - at baseline and following stimulation
GEO series published today
55m
GSE143484 IRF-1 expressed in the early blastocyst inner cell mass of pigs enhances the pluripotency of induced pluripotent stem cells
Contributors : Bingbo Shi ; Dengfeng GaoSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Sus scrofaNaïve porcine stem cells is supposed to rely on the regulation of unique transcription factor in the early inner cell mass. The expression of Interferon regulatory factor 1 (IRF-1) were detected in aggregation in d6~7 somatic cell nuclear transfer blastocysts, which was supposed to regulate the pluripotency...
GEO series published today
55m
GSE116930 Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of healthy control (WT) and knock-out reporter lines of segmentation clock genes HES7, DLL3, LFNG and MESP2.
Contributors : Yoshihiro Yamanaka ; Maya Uemura ; Satoko Sakurai ; Takuya Yamamoto ; Cantas AlevSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types experimental model systems that can recapitulate more complex biological features...
GEO series published today
55m
GSE143480 Characterization of the Late Response of Neisseria gonorrhoeae F62 to Iron and Fur
Contributors : Ryan McClure ; Caroline A GencoSeries Type : Expression profiling by high throughput sequencingOrganism : Neisseria gonorrhoeae F62In this study wild-type, fur mutant, and complemented fur mutant strains of the human pathogen Neisseria gonorrhoeae F62 were grown under high (100 uM iron) or low (100 uM desferal) iron conditions to identify genes whose expression was regulated by iron and/or Fur. This study looked at the response 3 hours after the addition of iron or desferal.
GEO series published today
55m
GSE93760 Transcript profile of Trichoderma-induced response in Zea mays against Fusarium verticillioides infection
Contributors : Valeria A Campos-Bermudez ; Sebastian P Rius ; Romina B Agostini ; Agustina Postigo ; Gabriel E Rech ; Walter A VargasSeries Type : Expression profiling by high throughput sequencingOrganism : Zea maysIn the present study we have assessed, by transcriptional profiling, the systemic defense response of Zea mays plants to the ear rotting pathogen Fusarium verticilioides induced by the beneficial fungus Trichoderma atroviride
GEO series published today
55m
GSE143477 Expression data from SOX9 knockdown in HCC cells
Contributors : Mengchao Wang ; Gang HuangSeries Type : Expression profiling by arrayOrganism : Homo sapiensSorafenib is a multi-kinase blocker and one of the few suggested drug treatments for aggressive hepatocellular carcinoma (HCC) patients. However, drug resistance to sorafenib may often occur over time and cause further tumor aggression. Recently, cancer stem cells were found in HCC and were speculated to be involved in tumor progression. SOX9 is highly expressed in HCC cancer stem cells and...
GEO series published today
55m
GSE131252 Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [RNA-seq 2]
Contributors : H C Aegerter ; S Crotta ; J Kulikauskaite ; H Patel ; E M Hessel ; S Beinke ; A WackSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate transcriptomic differences using RNA-seq. This was done in macrophages isolated from a busulfan chimera, using congenic markers (CD45.1 for a BM origin, and CD45.2 for a host origin) in influenza-experienced, and naive lungs - at baseline and following Pam3CSK4 stimulation
GEO series published today
55m
GSE141299 The effects of chromosomal copy number variations (CNV) on transcriptional programs at single cell resolution in multiple myeloma
Contributors : Ali M Shirayeh ; Rodger E TiedemannSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensChromosome copy number variations (CNV) are a near-universal feature of cancer however their specific effects on cellular function are poorly understood. Single-cell RNA sequencing (scRNA-seq) can reveal cellular gene expression however cannot directly link this to CNVs. Here we report scRNA-seq normalization methods that improve inter-cellular expression...
GEO series published today
55m
GSE120543 Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
55m
GSE140241 Zebrafish periderm at 4-somite stage
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Danio rerioThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
55m
GSE120540 Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [ATAC-seq]
Contributors : H C Aegerter ; S Crotta ; J Kulikauskaite ; H Patel ; E M Hessel ; S Beinke ; A WackSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTo investigate differences in the chromatin accessibility using ATAC-seq. This was done in macrophages from a BM origin (CD45.1) and embryonic origin (CD45.2) in influenza-experienced, and naive lungs - at baseline and following Pam3CSK4 stimulation
GEO series published today
55m
GSE140240 ATAC-seq profile of zebrafish periderm at 4-somite stage
Contributors : Huan Liu ; Robert A CornellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Danio rerioIn order to profile periderm-specific nucleosome free regions of zebrafish periderm cells at 4-somite stage, we isolated the equal number of GFP-positive cells and GFP-negative cells from Tg(krt4:GFP) embryos and perform ATAC-seq. This study revealed the landscape of zebrafish periderm-specific nucleosome free regions at 4-somite stage.
GEO series published today
55m
GSE116934 Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq-based comparison of patient and isogenic rescue / healthy control iPSC lines during in vitro differentiation of human presomitic mesoderm and its derivatives
Contributors : Yoshihiro Yamanaka ; Maya Uemura ; Satoko Sakurai ; Takuya Yamamoto ; Cantas AlevSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types experimental model systems that can recapitulate more complex biological features...
GEO series published today
55m
GSE139808 mRNA profile of zebrafish periderm at 4-somite stage
Contributors : Huan Liu ; Robert A CornellSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioIn order to compare the transcriptome and tissue-specific nucleosome free regions of zebrafish periderm cells at 4-somite stage, we isolated the RNA from sorted GFP-positive cells of Tg(krt4:GFP) embryos and perform low-input RNA-seq. This study revealed periderm-specific transcriptome at 4-somite stage. Moreover, comparing with ATAC-seq from the same tissue, we confirmed...
GEO series published today
55m
GSE116929 Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of in vitro induced human presomitic mesoderm (PSM) and identification of components of the human segmentation clock [Oscillation_Hs]
Contributors : Mitsuhiro Matsuda* (equal contribution) ; Yoshihiro Yamanaka* (equal contribution) ; Maya Uemura ; Satoko Sakurai ; Miki Ebisuya ; Takuya Yamamoto ; Cantas AlevSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types...
GEO series published today
55m
GSE138711 Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
55m
GSE132811 Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of in vitro induced human presomitic mesoderm (PSM) and identification of components of the human segmentation clock [Oscillation_Mm]
Contributors : Mitsuhiro Matsuda* (equal contribution) ; Yoshihiro Yamanaka* (equal contribution) ; Maya Uemura ; Satoko Sakurai ; Miki Ebisuya ; Takuya Yamamoto ; Cantas AlevSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types,...
GEO series published today
55m
GSE93710 miR363-3p Mediates Maintenance and Chemoresistance of Breast Cancer Stem Cells
Contributor : Stéphanie RenaudSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensThere is increasing evidence that cancer recurrence and resistance to chemotherapy are linked to a subset of cancer stem cells. However, detecting these cells specifically and targeting them therapeutically remain challenging. As microRNAs (miRNAs) are emerging as key players in cancer biology, we set up to identify miRNAs involved in chemoresistance of breast cancer stem cells. In this study, we...
GEO series published today
55m
GSE137833 Androgen Receptor Degraders Overcome Common Resistance Mechanisms Developed During Prostate Cancer Treatment
Contributors : Steven Kregel ; Arul ChinnaiyanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-sequencing of VCaP and LNCaP, LNCaP-EnzR, or LNCaP AR-V7 overexpressing prostate cancer cell lines treated with AR degrader ARD-61.
GEO series published today
8h
GSE126985 PRC1 facilitates stage-specific enhancer-promoter contacts during Drosophila development
Contributors : V Loubiere ; G L Papadopoulos ; Q Szabo ; A-M M Martinez ; G CavalliSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Drosophila melanogasterPolycomb repressive complexes 1 and 2 (PRC1 and PRC2) are highly conserved epigenetic factors that collaborate at multiple levels to maintain their target genes in a repressed state. However, recent reports suggest that PRC1 binds a subset of...
GEO series published today
9h
GSE133527 miR-221-3p drives the Shift of M2-Macrophage to a Pro-Inflammatory Function by Modulating JAK3/STAT3 Signaling and is Increased in Rheumatoid Arthritis
Contributors : Lilian Quero ; Diego KyburzSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed a transcriptome analysis of M2 macrophages generated in vitro from monocytes isolated from peripheral blood of healthy donors, and studied the effect of miR-221-3p mimic transfection and stimulation with LPS.
GEO series published today
1d
GSE93550 Next Generation Sequencing of miRNome of G-CSF treated huCD34+ HSPCs
Contributors : Jens-Uwe Hartmann ; Gerhard BehreSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensMicroRNAs (miRNAs) are a class of small non coding RNAs (ncRNAs) with 19-25 nucleotides in length, which can inhibit the translation or induce the destabilization and/or degradation of their mRNA targets, usually by binding in an incomplete manner to the 3`untranslated region (3`UTR) of their respective targets. We were interested in miRNAs that are regulated...
GEO series published today
1d
GSE132289 Mouse ovarian cancer models recapitulate the human tumor microenvironment and patient response to treatment
Contributors : Eleni Maniati ; Chiara Berlato ; Ganga Gopinathan ; Owen Heath ; Frances BalkwillSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusAlthough there are many prospective targets in the tumor microenvironment (TME) of high-grade serous ovarian cancer (HGSOC), pre-clinical testing is challenging especially as there is limited information on the murine TME. Here, we have characterized the TME of six orthotopic, transplantable syngeneic...
GEO series published today
1d
GSE93665 Differential gene expression between feminized C. elegans male and female germlines
Contributors : Tamara Mikeladze-Dvali ; Sevinc Ercan ; Sarah E AlbrittonSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansWith the aim to determine the extent of germline feminization in feminized male worms, we performed differential gene expression profiling of isolated gonads and whole worms between fog-1(q253) XO males and XX females.
GEO series published today
1d
GSE93883 Gene expression-based, individualized outcome prediction for osteoporosis with vertebral fracture
Contributor : Mengge SunSeries Type : Expression profiling by arrayOrganism : Homo sapiens ; Mus musculus ; Rattus norvegicusThis study aims to identify specific miRNAs profiles in osteoporotic patients with and without vertebral fractures. MiRNAs array analysis was performed on the plasma samples including a pool of 6 miRNA samples from osteoporotic patients with vertebral fractures, a pool of 6 miRNA samples from osteoporotic patients without fracture and another pool of 6 miRNA samples from nonosteoporotic...
GEO series published today
1d
GSE93549 Identification of miR-143 mRNA-targets by AGO-RIP in the myeloid cell line K562
Contributors : J-U Hartmann ; Gerhard BehreSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMiR-143 is a miRNA commonly found to be downregulated in a variety of cancers. The goal of this study is the identifacation of miR-143 target mRNAs by next generation sequencing (NGS) in myeloid cells after overxpression of miR-143.
GEO series published today
1d
GSE132865 Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance
Series Type : Genome binding/occupancy profiling by genome tiling array ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Schizosaccharomyces pombeThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
1d
GSE132797 Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-chip_C50]
Contributors : Sahana Holla ; H D Folco ; Jothy Dhakshnamoorthy ; Vanivilasini Balachandran ; Hua Xiao ; David Wheeler ; Martin Zofall ; Shiv I GrewalSeries Type : Genome binding/occupancy profiling by genome tiling arrayOrganism : Schizosaccharomyces pombeOccupancy profiling of FLAG-tagged H3 in fission yeast.
GEO series published today
1d
GSE132862 Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-chip_C300]
Contributors : Sahana Holla ; H D Folco ; Jothy Dhakshnamoorthy ; Vanivilasini Balachandran ; Hua Xiao ; David Wheeler ; Martin Zofall ; Shiv I GrewalSeries Type : Genome binding/occupancy profiling by genome tiling arrayOrganism : Schizosaccharomyces pombeOccupancy profiling of GFP-tagged Rix1, Las1, Ipi1, Crb3 proteins in fission yeast.Occupancy profiling of lysine 9 trimethylated histone H3 in fission yeast.
GEO series published today
1d
GSE141070 Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-seq]
Contributors : Sahana Holla ; H D Folco ; Jothy Dhakshnamoorthy ; Vanivilasini Balachandran ; Hua Xiao ; David Wheeler ; Martin Zofall ; Shiv I GrewalSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Schizosaccharomyces pombeOccupancy profiling of GFP-tagged Rix1 protein in fission yeast.
GEO series published today
1d
GSE140134 The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter
Contributors : Selamawit A Woldemeskel ; Allison K Daitch ; Laura Alvarez ; Gaël Panis ; Rilee Zeinert ; Diego Gonzalez ; Erika Smith ; Justine Collier ; Peter Chien ; Felipe Cava ; Patrick H Viollier ; Erin D GoleySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Caulobacter vibrioidesBacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes...
GEO series published today
1d
GSE127723 Hippocampus RNA-seq in CD x Gtf2i*
Contributors : Nathan D Kopp ; Joseph D DoughertySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWilliams syndrome is a neurodevelopmental disorder caused by a 1.5-1.8Mbp deletion on chromosome 7q11.23, affecting the copy number of 26-28 genes. Phenotypes of Williams syndrome include cardiovascular problems, craniofacial dysmorphology, deficits in visual spatial cognition, and a characteristic hypersocial personality. There are still no genes in the region that...
GEO series published today
1d

GSE142774 Systemic HIV/SIV latency reversal via non-canonical NF-κB signaling in vivo
Contributors : Corbin D Jones ; Richard M Dunham ; Chahroudi Ann ; J V Garcia ; Angela WahlSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMolecules mimicking the active N-terminal tetrapeptide of the second mitochondrial-derived activator of caspases (SMACm) potently reverse HIV latency in vitro and ex vivo without the pleotropic cellular effects seen with other LRAs. We verified that SMACm facilitate latency reversal through activation of the non-canonical...
GEO series published today
1d
GSE137326 Transcriptional Profiling of Lumbar Spinal Cord in a Rat Model of Bone Cancer Pain
Contributors : Xinran Hou ; Yingqi Weng ; Jian Wang ; Jiajia Dai ; Zhuofeng Ding ; Zongbin Song ; Qulian GuoSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Rattus norvegicusBone cancer pain (BCP), in which the majority is caused by metastasis from other cancer sites, is the most common type of chronic cancer pain. Bone cancer pain is developed accompanied by changes of numerous genes expression, from peripheral...
GEO series published today
1d
GSE125022 STAT3 Signaling Pathway in Keloid Pathogenesis Implicated by Preliminary Transcriptome and ATAC Analyses
Contributors : Yun-Shain Lee ; Ya-Chen Liang ; Ping Wu ; David A Kulber ; Kylie Tanabe ; Cheng-Ming Chuong ; Randall Widelitz ; Tai-Lan TuanSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensKeloids are wounding-induced fibroproliferative human tumor–like skin scars of complex genetic makeup and poorly defined pathogenesis. Fibroblasts are the principal mediator of fibroproliferative disorders....
GEO series published today
2d
GSE93587 Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells II
Contributors : Hadassa C Santos ; Renato M Ramos ; Lucas G Ferreira ; Silvia Y Bando ; Fernanda B Bertonha ; Leandro R Ferreira ; Carlos A Moreira-Filho ; Cecília M Abe ; Ana R Moreno ; Marina B MartinezSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial...
GEO series published today
2d
GSE143462 Omipalisib Inhibits Esophageal Cancer Growth through PI3K/AKT/mTOR Signalling Pathway Disruption
Contributors : Dong-shan Zhu ; Jing-yao Dong ; Yao-yao Xu ; Xin-tong Zhang ; Shi-bo Fu ; Wei LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEsophageal squamous cell carcinoma (OSCC) is a lethal digestive tract malignancy with limited effective interventions. This study aims to explore a new potential inhibitor on OSCC and investigate the underlying mechanisms. Based on a drug screen of an FDA-proven library consisting of 1404 compounds, we demonstrated...
GEO series published today
2d
GSE124730 Gene expression and chromatin accessibility of iLSCs vs iBlasts cells
Contributors : Eirini Papapetrou ; Michael Kharras ; Christina Leslie ; Josephine Wesely ; Andriana Kotini ; Han Yuan ; Hanzhi LuoSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe identified two phenotypically and functionally distinct populations in AML-iPSC lines upon hematopoietic differentiation. A cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent...
GEO series published today
2d
GSE143443 Joint Location-Specific JAK-STAT Signaling in Rheumatoid Arthritis Fibroblast-like Synoviocytes
Contributors : D Hammaker ; G Nygaard ; A Kuhs ; R Ai ; D L Boyle ; W Wang ; G S FiresteinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRheumatoid arthritis (RA) fibroblast‐like synoviocytes (FLS) derived from hip and knee have distinctive DNA methylation and transcriptome patterns in interleukin (IL)‐6 signaling and Janus kinase (JAK)–signal transducers and activators of transcription (STAT) pathways. To determine the functional effects of these joint‐specific...
GEO series published today
2d
GSE143467 Genome-wide CRISPR/Cas9 library screening identifies genes regulating the IFN signalling pathways.
Contributors : Guo Deyin ; Hou PanpanSeries Type : OtherOrganism : Homo sapiensInnate immunity is a non-specific host immune response against pathogen invasion. It exists widely in most of cells and is considered as the first line of defense against pathogen infection. Upon virus infection, the natural immune system is activated to generate immune response, thereby exerting the antiviral effect and effectively inhibiting the spread of virus in the body. With recent decades of research, people have...
GEO series published today
2d
GSE143437 Single-cell transcriptomic atlas of the mouse regenerating muscle tissue
Contributors : Benjamin D Cogrove ; Andrea J De MicheliSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology.
GEO series published today
2d
GSE124966 Gene expression and chromatin accessibility of iLSCs vs iBlasts cells
Contributors : Eirini Papapetrou ; Michael Kharras ; Christina Leslie ; Josephine Wesely ; Andriana Kotini ; Han Yuan ; Hanzhi LuoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe identified two phenotypically and functionally distinct populations in AML-iPSC lines upon hematopoietic differentiation. A cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth (iLSCs =samples A) and a fraction of more differentiated...
GEO series published today
2d
GSE143435 Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells
Contributors : Benjamin D Cogrove ; Andrea J De MicheliSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology.
GEO series published today
2d
GSE93881 Estrogen Receptor α (ERα)-mTOR signaling crosstalk rewires cancer cell metabolism providing a mechanism underlying obesity-associated postmenopausal breast cancer
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
2d
GSE143430 Muscle-type specific transcriptomic expression patterns in Drosophila
Contributors : Maria L Spletter ; Frank Schnorrer ; Assa Yeroslaviz ; Bianca Habermann ; Alexander StarkSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTo complement our existing data on developmental gene expression changes in flight muscle (IFM) development in Drosophila (GSE107247, GSE63707), we performed mRNA-Seq on dissected leg samples at three stages during pupal development (30, 50 and 72h APF). We further sequenced an additional timepoint...
GEO series published today
2d
GSE93510 Estrogen Receptor α (ERα)-mTOR signaling crosstalk rewires cancer cell metabolism providing a mechanism underlying obesity-associated postmenopausal breast cancer [ChIP-seq]
Contributor : Zeynep Madak-ErdoganSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensObesity is a risk factor for postmenopausal ERα (+) breast cancer. The metabolites from serum that contribute to this risk and how these factors affect ERα signaling are not known. Using whole metabolite profiling and a detection panel for proteins, we identified biomarkers that were differentially present in serum from obese vs. non-obese postmenopausal women, and...
GEO series published today
2d
GSE143423 Single-Cell Map of Diverse Immune Phenotypes in the Metastatic Brain Tumor Microenvironment of Non Small Cell Lung Cancer and triple negative breast cancer
Contributors : Liang Wang ; Jinxiang Dai ; Runrun Han ; Weilin JinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo shed light on the complexity of tumor-infiltrating immune cells in non-small cell lung cancer (NSCLC) patients and triple negative breast cancer (TNBC) patients with a metastatic brain tumor, we performed massively-parallel single-cell RNA sequencing on 12,196 cells,including 2,012 myeloid cells from 3 surgically removed brain lesions of treatment-naïve...
GEO series published today
2d
GSE142315 Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
2d
GSE143421 Comparision of hepatic gene expression between HFHS diet-fed WT and CREBH-Tg mice
Contributor : Yoshimi NakagawaSeries Type : Expression profiling by arrayOrganism : Mus musculusTo determine CREBH-mediated hepatic gene expression changes in hifh-fat high-sucrose (HFHS) dit feeding, we employed the microarray analysis. We collected the livers from male WT and CREBH-Tg mice fed with HFHS diet for 12 weeks from 6 weeks old.
GEO series published today
2d
GSE124967 Gene expression and chromatin accessibility of iLSCs vs iBlasts cells
Contributors : Eirini Papapetrou ; Michael Kharras ; Christina Leslie ; Josephine Wesely ; Andriana Kotini ; Han Yuan ; Hanzhi LuoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe identified two phenotypically and functionally distinct populations in AML-iPSC lines upon hematopoietic differentiation. A cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth (iLSCs =samples A) and a fraction of more...
GEO series published today
2d
GSE143420 Comparision of hepatic gene expression between fasted and fed ad lib states in C57B6J (WT) and CREBH KO mice
Contributor : Yoshimi NakagawaSeries Type : Expression profiling by arrayOrganism : Mus musculusTo determine hepatic gene expression changes in fasted state, we employed the microarray analysis. We collected the livers from 8-weeks-old male WT and CREBH KO mice in both fasted and fed ad lib states.
GEO series published today
2d
GSE124963 Suppression of oncogenic super enhancers in MYC-dependent AMLs by NR4A Nuclear Receptors
Contributors : S G Call ; O M ConneelySeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensNR4A nuclear receptors are tumor suppressors of acute myeloid leukemia (AML) that are silenced in AML at the level of transcription elongation. Using RNA-Seq, we show that NR4As inhibit leukemic cell growth largely through suppression of MYC pathway genes. MYC is highly expressed in AML and contributes to AML...
GEO series published today
2d

GSE143418 Expression analysis of mouse embryonic fibroblasts (MEFs) and Thymidine treatment-induced MEFs (induced cells).
Contributors : Buqing Ye ; Benyu Liu ; Zusen FanSeries Type : Expression profiling by arrayOrganism : Mus musculusInvestigation of differentially expressed genes in thymidine treatment-induced MEFs. Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin...
GEO series published today
2d
GSE109066 miR-182 and miR-183 act as GDNF mimics in midbrain neurons
Contributors : Anna-Elisa Roser ; Lucas C Gomes ; Rashi Halder ; Gaurav Jain ; Fabian Maass ; Lars Tönges ; Lars Tatenhorst ; Mathias Bähr ; André Fischer ; Paul LingorSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusWe found in primary midbrain neurons the expression of miR-182 and miR-183 is increased with the treatment of GDNF. Further we showed that the transfaction with these two miRNA mimics resulted into the increased neurite length and regeneration...
GEO series published today
2d
GSE142980 Altered expression in sika deer skeletal muscle with age
Series Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Cervus nipponThis SuperSeries is composed of the SubSeries listed below.
GEO series published today
2d
GSE93588 Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells III
Contributors : Hadassa C Santos ; Renato M Ramos ; Lucas G Ferreira ; Silvia Y Bando ; Fernanda B Bertonha ; Leandro R Ferreira ; Carlos A Moreira-Filho ; Cecília M Abe ; Ana R Moreno ; Marina B MartinezSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial...
GEO series published today
2d
GSE142978 Altered miRNA expression in sika deer skeletal muscle with age
Contributors : Boyin Jia ; Dongdong Liu ; Fuhe YangSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Cervus nipponStudies of the miRNA expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of miRNAs from skeletal muscle tissues...
GEO series published today
2d
GSE93525 Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells I
Contributors : Hadassa C Santos ; Renato M Ramos ; Lucas G Ferreira ; Silvia Y Bando ; Fernanda B Bertonha ; Leandro R Ferreira ; Carlos A Moreira-Filho ; Cecília M Abe ; Ana C Moreno ; Marina B MartinezSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial...
GEO series published today
2d
GSE142977 Altered mRNA expression in sika deer skeletal muscle with age
Contributors : Boyin Jia ; Dongdong Liu ; Fuhe YangSeries Type : Expression profiling by high throughput sequencingOrganism : Cervus nipponStudies of the gene expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of unigenes from skeletal muscle tissues...
GEO series published today
2d
GSE93505 Estrogen Receptor α (ERα)-mTOR signaling crosstalk rewires cancer cell metabolism providing a mechanism underlying obesity-associated postmenopausal breast cancer [RNA-seq]
Contributor : Zeynep Madak-ErdoganSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensObesity is a risk factor for postmenopausal ERα (+) breast cancer. The metabolites from serum that contribute to this risk and how these factors affect ERα signaling are not known. Using whole metabolite profiling and a detection panel for proteins, we identified biomarkers that were differentially present in serum from obese vs. non-obese postmenopausal women, and we validated...
GEO series published today
2d
GSE100437 Upregulated heme biosynthesis, an exploitable vulnerability in MYCN-driven leukemogenesis
Contributors : Yu Fukuda ; Geoffrey Neale ; Gerard Grosveld ; John SchuetzSeries Type : Expression profiling by arrayOrganism : Mus musculusThe increased heme biosynthesis long observed in leukemia was previously of unknown significance. Heme, synthesized from porphyrin precursors, plays a central role in oxygen metabolism and mitochondrial function, yet little is known about its role in leukemogenesis. Here we show increased expression of heme biosynthetic genes, including UROD, only in pediatric...
GEO series published today
2d
GSE143291 Alpha/Beta Mouse TCR Sequencing of CD4+ thymic regulatory and conventional T-cells
Contributors : Annette Ko ; Alvin Shi ; Thomas NguyenSeries Type : OtherOrganism : Mus musculusThymic regulatory T cells (tTreg) are critical in maintenance of normal T cell immunity and tolerance. The role of TCR in tTreg cell selection remains incompletely understood. Here we assessed TCRa and TCRb sequences of tTreg and conventional thymic CD4+ T (Tconv) cells by high throughput sequencing. We identified ab TCR sequences that were unique to either tTreg or Tconv cells and found that these...
GEO series published today
2d
GSE141499 Homeostasis and transitional activation of regulatory T cells require c-Myc
Contributors : Jordy Saravia ; Hu Zeng ; Yogesh Dhungana ; Geoffrey Neale ; Peter Carmeliet ; Hongbo ChiSeries Type : Expression profiling by arrayOrganism : Mus musculusRegulatory T (Treg) cell activation and expansion during neonatal life and in response to inflammation are critical for immunosuppression, yet the mechanisms governing these events are incompletely understood. We report that the oncogene and transcriptional regulator c-Myc (Myc) controls immune homeostasis through regulation...
GEO series published today
2d
GSE141054 Transcriptional profilling of pathogen-specific T helper cells
Contributors : Chandrashekhar Pasare ; Yajing GaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntroduction: We reported a in vitro pathogen-specific priming system to using pathogen lysate stimulated splenic CD11c+ DCs to differentiate pathogen-specific murine T helper cells. This method allowed us to compare side-by-side transcriptional profiles of bulk T helper cells that are specific to distinct pathogens and to study their composition and functionality.Method:...
GEO series published today
2d
GSE141062 Transcriptional profilling of In vitro-primed C.rodentium-specific WT or Caspase-1 deficient Th cells
Contributors : Chandrashekhar Pasare ; Yajing GaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntroduction: We reported that caspase-1 is highly expressed in in vitro-primed C.rodentium-specific Th cells. Caspase-1 deficient (Casp1d10) naïve T cells differentiate into pathogen-specific Th17 cells at an suboptimal level and fail to protect against C.rodentium infection. To gain insight into the regulatory pathways exerted by caspase-1 in Th cells, we performed...
GEO series published today
2d
GSE141061 Transcriptional profilling of In vitro-primed C.rodentium-specific Th17 cells, cytokine-differentiated Th17 cells and ex vivo Th17 cells following C.rodentium infection
Contributors : Chandrashekhar Pasare ; Yajing GaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntroduction: We reported a in vitro pathogen-specific priming system to using pathogen lysate stimulated splenic CD11c+ DCs to differentiate pathogen-specific murine T helper cells. This method allowed us to compare side-by-side transcriptional profiles of bulk T helper cells that are specific to distinct pathogens and to study their composition and functionality....
GEO series published today
2d
GSE128177 Skeletal Muscle Transcriptional Networks Linked to Motor Unit Remodeling in Human Parkinson’s Disease
Contributors : Kaleen M Lavin ; Stuart C Sealfon ; Merry-Lynn N McDonald ; Brandon M Roberts ; Katarzyna Wilk ; Venugopalan D Nair ; Yongchao Ge ; Preeti L Kumar ; Samuel T Wndham ; Marcas M BammanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed transcriptional profiling to test the hypothesis that type I grouping severity in Parksino's disease link to distinct gene expression networks
GEO series published today
2d
GSE136991 A white to opaque like phenotypic switch in the yeast Torulaspora microellipsoides
Contributors : Cedric A Brimacombe ; Thomas Sierocinski ; Matthew DahabiehSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Torulaspora microellipsoidesTorulaspora microellipsoides is a unicellular budding yeast of the Saccharomycetaceae family and is primarily associated with viticulture, however it has not been studied with regards to growth morphology or phenotypic switching. We discovered that T. microellipsoides undergoes a low-frequency morphological switch...
GEO series published today
2d
GSE132107 RNA-seq of Laser Captured Microdissected high-grade serous ovarian tumors
Contributors : Mara Artibani ; Salma El-Sahhar ; Zhiyuan Hu ; Garry Mallett ; Christopher Yau ; Ahmed A AhmedSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe inter-differentiation between cell states promotes cancer cell survival under stress and fosters non-genetic heterogeneity (NGH). NGH is, therefore, a surrogate of tumor resilience but its quantification is confounded by genetic heterogeneity. Here we show that NGH can be accurately measured when...
GEO series published today
2d
GSE139079 Single-cell RNA sequencing of human fallopian tubes from benign donors
Contributors : Zhiyuan Hu ; Christopher Yau ; Ahmed A AhmedSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe inter-differentiation between cell states promotes cancer cell survival under stress and fosters non-genetic heterogeneity (NGH). NGH is, therefore, a surrogate of tumor resilience but its quantification is confounded by genetic heterogeneity. Here we show that NGH can be accurately measured when informed by the molecular signatures of the normal...
GEO series published today
2d
GSE132149 Single-cell RNA sequencing of human fallopian tubes
Contributors : Zhiyuan Hu ; Christopher Yau ; Ahmed A AhmedSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe inter-differentiation between cell states promotes cancer cell survival under stress and fosters non-genetic heterogeneity (NGH). NGH is, therefore, a surrogate of tumor resilience but its quantification is confounded by genetic heterogeneity. Here we show that NGH can be accurately measured when informed by the molecular signatures of the normal...
GEO series published today
2d
GSE141466 Transcriptomic and proteomic response of the organohalide respiring bacterium Desulfoluna spongiiphila to growth with 2,6-dibromophenol as electron acceptor
Contributors : Jie Liu ; Max M HäggblomSeries Type : Expression profiling by high throughput sequencingOrganism : Desulfoluna spongiiphilaWe compared the global transcriptomic analysis of Desulfoluna spongiiphila strain AA1, an organohalide-respiring Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which...
GEO series published today
2d

GSE136766 DNA methylation alternations in the offspring liver from inulin early intervention dams
Contributors : Qian Zhang ; Xinhua Xiao ; Jia Zheng ; Ming Li ; Miao Yu ; Fan Ping ; Tong Wang ; Xiaojing WangSeries Type : Methylation profiling by genome tiling arrayOrganism : Mus musculusMaternal high fat diet may disturb susceptibility in offspring. liver from maternal inulin early intervention has CpG sites that exhibit differential DNA methylationregulated compared to high fat diet.
GEO series published today
2d
GSE141105 Bulk and single cell transcriptomic data indicate that a dichotomy between inflammatory pathways in peripheral blood and arthritic joints complicates biomarker discovery
Contributors : Eun Lee ; Sandra Lilja ; Xinxiu Li ; Samuel Schäfer ; Huan Zhang ; Mikael BensonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBackground: Unbiased studies using different genome-wide methods have identified several promising novel biomarkers for diagnosis and treatment response in Rheumatoid Arthritis (RA). However, clinical translation has proven difficult. Here, we hypothesized that one reason could be that inflammatory responses in...
GEO series published today
2d

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