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...
35m
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...
35m
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...
35m
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,...
35m
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 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
1h
Series Type : Expression profiling by RT-PCROrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
1h
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...
1h
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...
1h
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....
1h
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
1h
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...
1h
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
1h
Contributor : Zhou ShenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIdenrify the function of NSP1
1h
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
1h
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...
1h
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...
1h
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.
1h
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
1h
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...
1h
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.
1h
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...
1h
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
1h
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.
1h
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.
1h
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...
1h
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.
9h
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...
9h
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.
1d
Contributors : Jens-Uwe Hartmann ; Gerhard BehreSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : MicroRNAs (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 during G-CSF...
1d
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...
1d
Contributors : Tamara Mikeladze-Dvali ; Sevinc Ercan ; Sarah E AlbrittonSeries Type : Expression profiling by high throughput sequencingOrganism : With 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.
1d
Contributor : Mengge SunSeries Type : Expression profiling by arrayOrganism : This 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 patients to identify regulated miRNAs...
1d
Contributors : J-U Hartmann ; Gerhard BehreSeries Type : Expression profiling by high throughput sequencingOrganism : MiR-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.
1d
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.
1d
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.
1d
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.
1d
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.
1d
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...
1d
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...
1d
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...
1d
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...
1d
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....
2d
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...
2d
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...
2d
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...
2d
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...
2d
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...
2d
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.
2d
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...
2d
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.
2d
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.
2d
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...
2d
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...
2d
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...
2d
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.
2d
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.
2d
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...
2d
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.
2d
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...
2d
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...
2d
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...
2d
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.
2d
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...
2d
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...
2d
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...
2d
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...
2d
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...
2d
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...
2d
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...
2d
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...
2d
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:...
2d
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...
2d
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....
2d
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
2d
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...
2d
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...
2d
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...
2d
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...
2d
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...
2d
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.
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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...
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