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Sequencing-based assays page 16
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GSE89917: Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [RNA-Seq KO]
Targeting the activation function-1 (AF-1) at the N-terminus of the androgen receptor (AR) is an att...
GSE81285: mTor inhibition induces a paused pluripotent state
Cultured pluripotent stem cells are a cornerstone of regenerative medicine due to their ability to g...
GSE94784: RNASeq of adipocytes from ROSA vs BMPR2 DELX mice
We sequenced RNA from adipocytes of ROSA and BMPR2 DELX transgenic mice SOURCE: James West (j.west@v...
GSE108688: GR cistromes reprogramming by High Fat Diet [RNA-seq]
We mapped the genome-wide binding profiles of GR throughout the day/night cycle (ZT0-ZT4-ZT8-ZT12-ZT...
GSE99707: RSK2-regulated gene signature associates with ER+ breast cancer
We used CRISPR RSK2 knock-out MCF-7 cells to identify RSK2-regulated genes. SOURCE: Deborah Lannigan...
GSE131299: The role of CIC in brain development and neuronal differentiation (RNA-Seq)
RNA_seq analysis for Nes Cre;CIC+/+ vs.Nes Cre;CICflox/flox mouse brain SOURCE: Jihye Paik (Jep2025@...
GSE98860: Mtor knockout in PDAC cells
A pancreatic ductal adenocarcinoma cell line was isolated from a Pdx1-Flp, FSF-KRasG12D/+, Rosa26-Cr...
GSE94840: ALOX5 exhibits anti-tumor and drug-sensitizing effects in MLL-rearranged leukemia
MLL-rearranged acute myeloid leukemia (AML) remains a fatal disease with a high rate of relapse and ...
GSE81286: Transcriptional profiles of skeletal muscles in mice exposed to acute hypoxia
To understand the underlying gene changes in in vivo muscles during acute hypoxic exposure, we studi...
GSE89020: Parallel transcriptional programs driving early-starting inheritable lineage bias of myeloid, lymphoid and dendritic cells are initiated by distinct dosage of PU.1 and IRF8 in HSCs
In the traditional model of hematopoiesis, blood lineages diversify from HSCs through a sequential p...
GSE84517: Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk [RNA-Seq]
The M1 and the M2 macrophage polarization programs (activated by IFN and IL-4, respectively) lie at ...
GSE105070: RNA sequencing of control and CTCF-null embryonic day 14 telencephalon
The goals of this study are to evaluate differences in transcriptome profiles of E14 mouse telenceph...
GSE98585: Gene expression profiling of continuous growth hormone infused (cGH) adult male mouse liver by RNA-seq analysis of rRNA-depleted liver RNA. [G137_G138]
rRNA-depleted RNA isolated from livers of intact male and female mice and from male mice treated wit...
GSE100026: Transcriptome characterization of chronic myeloid leukemia by RNA sequencing
To determine differentially expressed and spliced transcripts in chronic myeloid leukemia, a high th...
GSE100827: Analysis of transcriptome profiling in liver tissues of wild-type and SREBP1c knockout mice using RNA-seq
Sterol regulatory element-binding protein 1c (SREBP1c) plays important roles in lipid metabolism and...
GSE99231: ZFR coordinates crosstalk between RNA decay and transcription in innate immunity
Identification of RNAs differentially expressed upon ZFR knockdown in THP1 and HEK-293TO cells. SOUR...
GSE89495: Efficient Mammary Gland Involution Requires c-Jun N-terminal kinase
Involution returns the lactating mammary gland to a quiescent state after weaning. The mechanism of ...
GSE98950: Transcriptomics profiling of CD141+ dendritic cells isolated from peripheral blood or synovial fluid of arthritis patients
Total RNA sequencing was performed on CD141+ DC isloated from peripheral blood of healthy individual...
GSE98559: Expression Profiling of Cisplatin Resistant SKOV3 Cell Lines vs. Wild Type SKOV3 Cell Lines
Ovarian cancer SKOV3 cells were studied to profile the expression of wild type (WT, Cisplatin Suscep...
GSE102881: Transcriptomic analysis of healthy donor and Sickle Cell Disease (SCD) hematopoietic stem/progenitor cells
Human hematopoietic stem/progenitor cells (HSPCs) were either collected from bone marrow or mobilize...
GSE92770: Tissue-specific histone variant exchange during transcriptional activation and the link with pre-mRNA splicing factors
ChIP-seq, CLIP-seq, and mRNA-seq from mouse hippocampal tissues and testes to study the role of hi...
GSE112365: A SIRT1-centered Circuitry Regulates Breast Cancer Stemness and Metastasis
Deficiency of deacetylase SIRT1 or its downstream target PRRX1 promotes breast cancer stemness and m...
GSE89226: Analysis of gene expression (RNAseq) from shTP53:RB1 LNCaP/AR cell lines
Some cancers evade targeted therapies through a mechanism known as lineage plasticity, whereby tumor...
GSE111347: RNA-sequencing of Adult Mouse Pillar and Deiters Supporting Cells of the Organ of Corti
To understand the basic biological properties of supporting cells of the mammalian inner ear, we exa...
GSE99824: Molecular pathogenesis of human prostate basal cell hyperplasia reveals a keratinocyte metaplasia
The incidence of basal cell hyperplasia (BCH) has been reported at 8-10%, but a molecular and cellul...
GSE106885: Epigenome-wide Effects of Vitamin-D on Bronchial Epithelial Cells using ATAC-Seq and RNA-seq
Vitamin D has been associated with viral respiratory infections, the main cause of severe asthma exa...
GSE100402: Mouse natural killer cells response to DKK2 treatment
Analysis of mouse primary natural killer (NK) cells and NK cells treated with DKK2 for 24 hours.Sequ...
GSE100859: mRNA-Seq profiling of human developing kidney
To characterize the molecular features of human kidney development, and to capture timing of emergen...
GSE89365: DDX54 regulates transcriptome dynamics during DNA damage response [4SU-seq]
The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveil...
GSE106984: SOX10 Single Transcription Factor Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells
We report the use of a single transcription factor, SOX10, for the generation of oligodendrocytes fr...
GSE100576: Subcellular RNA fractions of HSV-1 infected primary human fibroblasts
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain...
GSE114966: Transcriptional change of THP-1 after HSV-1UL37WT or HSV-1UL37C819S
we reporter the transcritional difference after THP-1 cells were infected with HSV-1UL37WT virus or ...
GSE99381: AR-independent prostate cancer is sustained through FGF signaling
Androgen receptor (AR) signaling is a distinctive feature of prostate cancer (PC) and represents the...
GSE100501: The dynamics of cellular response to therapeutic perturbation using multiplexed quantification of the proteome and transcriptome at single-cell resolution
We developed a scalable assay permitting the simultaneous quantification of hundreds of proteins and...
GSE99659: WT Pik3ca2X basal cell expression profile
WT Pik3caH1047R/H1047R basal cell RNASeq SOURCE: Slobodan Beronja (beronja@fredhutch.org) - Beronja ...
GSE100610: Genome-wide expression of mRNAs and microRNAs in response to ERI2 knockdown
Here we describe the biological properties of new member of the Enhancer of RNAi (ERI) subfamily of ...
GSE89767: Enhancer and transcription factor dynamics within the granulocytic-monocytic lineage reveal an early differentiation block in Cebpa null progenitors
Myeloid cells of the granulocytic-monocytic (GM) lineage develop in a process orchestrated mainly by...
GSE100244: Transient Notch Activation Induces Long-term Gene Expression Changes Leading to Sick Sinus Syndrome in Mice
We are reporting RNA-seq data from doxycycline induced myocyte specific Notch signaling (iNICD) in a...
GSE97990: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (RNA-Seq)
We generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell d...
GSE85335: A non-cell autonomous mechanism of beige adipocyte renaissance in subcutaneous adipose tissue
Two types of UCP1 positive cells-brown and beige adipocytes exist in mammals. Beige adipocytes are v...
GSE101241: Epigenetic enhancer changes during oncogenic transformation [RNA-seq]
Identification of differential enhancers active during oncogenic transformation, using RNA-seq with ...
GSE94304: Interrogation of functional cell surface markers identifies CD151 dependency in high-grade serous ovarian cancer
The high degree of genetic aberrations characteristic of high-grade serous ovarian cancer (HGSC) mak...
GSE90497: Steatohepatitis progresses to cancer via immunosuppression of HCC directed CD8+ T cells
We show that chronic inflammation and fibrosis in mice with non-alcoholic fatty liver disease (NASH...
GSE96685: 2.5 dpc female HPG axis RNASeq of Kdm4a wildtype and knockout mice
Purpose: We performed RNA-Seq on 2.5dpc mouse hypothalamus, pituitary, ovary and uterus of 8-10 week...
GSE130052: RNA-seq analysis of mouse normal penile epithelium and penile squamous cell carcinoma
We aim to detect differential gene expression using RNA-seq between normal penile epithelial tissue ...
GSE95079: The effect of Abl kinases,or Ponatinib challenging on breast cancer cells' global transcriptome
To gain insight into the signaling pathway(s) required for ABL1/ABL2-kinase activity or effected by ...
GSE89970: Genome-wide map of HAEC chromatin landscape under resting and TNFa, IL1b, and OxPAPC stimulation, with corresponding transcription factor binding and RNA expression
We report the dynamic enhancer landscape of HAEC at baseline and under inflammatory stimulation, and...
GSE99787: Global mRNA translational landscapes in mouse bone-marrow-derived-macrophage-mediated response to LPS (lipopolysaccharide)
We performed ribosome profiling and RNA-seq on mouse bone marrow derived macrophages (BMDMs) treated...
GSE126887: RNA-seq analysis of high fat diet-induced changes in macrophage transcriptome
Systemic low-grade inflammation associated with obesity and the metabolic syndrome is also a strong ...
GSE100278: Next-generation sequencing measuring genome-wide RNA decay by s4U Seq in nave CD4+ T cells from Mettl3 WT and KO mice
Nave T cells of Mettl3 KO and WT were pulse labeled by s4U for 15 min before and after IL-7 stimulat...
GSE85197: RNA-seq of N2a cells treated with 100 nM Dexamethasone for 4 hours +/- siARGLU1
ARGLU1 was identified in a screen for new modulators of glucocorticoid signaling in the CNS. RNA-seq...
GSE100099: p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics
Investigation of mechanism of gene regulation in response to pulses in p53 protein level induced by ...
GSE103354: A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
Airways conduct gases to the lung and are disease sites of asthma and cystic fibrosis. Here we study...
GSE112832: SETD2 regulates the maternal epigenome and embryonic development [RNA-seq]
Mammalian oocyte epigenome plays critical roles in gametogenesis and embryogenesis. Yet, how it is e...
GSE101503: Transcriptome analysis of V336Y mutant mitochondrial ribosomal protein in human HEK293 cell line
Analysis of HEK293 cells lines expressing V336Y mutant mitochondrial ribosomal protein. SOURCE: Ge T...
GSE113073: Transcription Factor SOX30 Is a Key Regulator of Mouse Spermiogenesis
As Sox30 knockout arrests spermatogenesis at the step 3 round spermatid (rST) stage, we performed RN...
GSE104820: Opposing roles of dendritic cells subsets in experimental GN
Classical dendritic cells (DCs) are key players at the interface between innate and adaptive immunit...
GSE121118: Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development
How de novo DNA methylation over heterochromatin is introduced in mouse gonocyte remains obscure. We...
GSE100082: Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon
To understand the extent of Smad-mediated gene regulation in the colon, we isolated colon epithelium...
GSE101415: Intestinal IKKa is required for tumor initiation in APC mutant mice
We have generated a mouse model for tumor initiation carrying a mutation in APC and lacking IKK in i...
GSE93897: Preclinical Evaluation of Dual mTOR inhibitor, AZD2014, and Castration in Prostate Cancer
Purpose: RNA sequence analysis identified active proliferation of T cells in the combination therapy...
GSE90463: Age-Related Gene Expression Changes in Prostate Cancer Patients [RNA-Seq]
Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients SOURCE: Susan NeuhausenYuan D...
GSE93678: A Novel Alzheimer's Disease Drug Candidate Targeting Inflammation and Fatty Acid Metabolism
CAD-31 has potent neuroprotective properties in six distinct nerve cell assays that mimic toxicities...
GSE123463: Total uterus transcriptome after depletion of regulatory T cells at E8 of murine pregnancy
Regulatory T cells (Tregs) contribute to successful pregnancy by promoting maternal-fetal tolerance....
GSE106281: Transriptome profiling of mutant p53 skin deficient in AURORA-A KINASE
We performed next-generation sequencing of RNA to determine the transcriptional changes in hyperplas...
GSE106312: Genome-wide RNA-seq from c-MYC-depleted and rescued MDA-MB-231BrM cells
Purpose: To identify downstream signaling pathways that mediate functions of c-MYC; Methods: RNAs is...
GSE103021: Targeting KRAS mutant cancers with a covalent G12C-specific inhibitor
We report RNAseq gene expression data following ARS-1620 treatment and shKRAS expressing cells (NCI-...
GSE104964: mRNA profiling of Asns-silenced murine 4T1-T breast cancer cells grown in the presence and absence of Asparagine
Murine 4T1-T breast cancer cells were infected with an shRNA targeting Asparagine Synthetase (Asns) ...
GSE106295: Transcriptome of cardiac tissue from WT mice, cardiac macrophages depleted mice, and mice deficient for Mertk and LxR
Our study aims to analyze the effect in whole cardiac transcriptome of cardiac macrophage depletion ...
GSE99548: Biomodal role of H3.3 in safe-guarding and establishing cell identities during reprogramming [RNA-Seq]
Determination of transcriptome rewiring during cellular reprogramming using RNA-Seq SOURCE: Chadi EL...
GSE83580: RNA-sequencing of Fes KO and WT melanomas
Publication abstract: An incomplete view of the (epi)genetic events that drive melanoma initiation a...
GSE89689: Role of Hmgb1 in hepatocarcinogenesis
The gene expression of normal and tumor tissues isolated from WT mice were compared with tumor tissu...
GSE82294: RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response
The transcriptional response to many widely used drugs and its modulation by genetic variability is ...
GSE93069: Transcriptome sequencing (RNA-Seq) of non-tumor kidney tissues from 36 patients undergoing nephrectomy for exploring the metabolic mechanism of sorafenib and identifying the major transcriptional regulation factors in sorafenib metabolism in kidney
The multi-kinase inhibitor drug sorafenib is used as first line treatment for hepatocellular carcino...
GSE101550: Essential roles of mitochondria biogenesis regulator Nrf1 in retina development and homeostasis
Purpose: RNA-seq analysis for E13.5 wildtype vs. Nrf1-flox/flox:Six3-Cre retinas SOURCE: Chai-An Mao...
GSE106634: ETS1 acts as a tumor suppressor in breast cancer by inhibiting growth-related factors
To characterize the effect of Core regulatory element (CRE) deletion in breast cancer cell line (MDA...
GSE90461: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha (Mouse ChIP-seq, RNA-seq, and DNase-seq)
We profiled transcriptome and chromatin landscapes in jejunal mouse intestinal epithelial cells (IEC...
GSE100403: A kinome-wide high-content siRNA screen identifies MEK5-ERK5 signaling as critical for breast cancer cell EMT and metastasis
We have employed a high-content microscopy screen in combination with a kinome and phosphatome-wide ...
GSE91062 (human): Epigenetic Therapy Increases Therapeutic Efficacy in Myeloproliferative Neoplasms Through Inhibition of Aberrant Inflammatory Signaling
The mechanisms that mediate transformation in MPN are not fully delineated and clinically utilized J...
GSE93976: In vivo analysis of injury sites presenting full or attenuated pericyte-derived scarring after spinal cord injury (SCI)
A subpopulation of pericytes expressing the Glast-CreERT2 transgene (Type A pericytes) has recently ...
GSE111294: An exploratory study to examine the effects of maternal choline supplementation during mouse pregnancy on placental epigenetic markers (mRNA-seq data set)
This study sought to explore the effects of 4X maternal choline supplementation (MCS) on mRNA and mi...
GSE101610: Transcriptional and epigenetic profiling of aged mouse SVZ-derived neural stem / progenitor cells
Here we analyse histone modifications, DNA methylation and transcriptome profiles of SVZ-derived neu...
GSE100425: Heterogeneous responses of hematopoietic stem cells to inflammatory stimuli are altered with age - bulk
This includes bulk RNA-seq samples for sorted LT-HSCs, ST-HSCs, and MPPs stimulated (or not) with LP...
GSE95672: Response in the NGF withdrawal model
RNA was purified from DRG neurons grown for 4 days in culture.; ; The "SAMPLE_ID" sample characteris...
GSE109841: Heterogeneous maintenance of human tissue resident memory T cells based on efflux capacities
Tissue-resident memory T cells (TRM) accelerate pathogen clearance through rapid and enhanced functi...
GSE108383: SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [Fluidiam scRNA-Seq]
The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populatio...
GSE96760: H-STS NET cell line perturbed with small molecule compounds
Expression profile of H-STS NET cell line at 6h and 24h after perturbation with small molecule compo...
GSE93256: LIN28A Over-expression RNAseq
To explore the effects of LIN28Ain human erythroid cell development, lentiviral transduction was use...
GSE102973: Identification of Latrophilin-2, a Specific Cell-surface Marker for Cardiac Progenitor Cells, and its Functional Significance in Heart Development [RNA-Seq]
Background: Identification of a lineage-specific marker plays a pivotal role in understanding develo...
GSE101833: ETS1 induction by the omental microenvironment promotes ovarian cancer metastasis [RNA-Seq]
ETS1 expression is induced by the microenvironment of ovarian metastasis and this expression allows ...
GSE120366: Comparative gene expression analysis between wild-type (WT) and Cables2-deficient epiblast-like cells (EpiLCs).
We found that Cables2 physically interacts with Smad2 and beta-catenin, and enhances their transcrip...
GSE90710: Mediator complex component MED13 regulates zygotic genome activation and is required for postimplantation development
Understanding the factors that regulate the transition from oocyte to embryo is critical for determi...
GSE90885: Defined IFNg levels improve anti-tumor and preclinical testing of immunotherapy in hosts with cancer and underlying autoimmunity
Most immunotherapies benefit only subsets of cancer patients, except those with autoimmune diseases ...
GSE89981: RNA-seq of FACS sorted neurons overexpressing miR-203 in wild-type mice
Purpose: The goal of this study was to assess gene expression changes in neurons overexpressing miR-...
GSE89448: Global reduction in H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas
A subgroup of Posterior fossa ependymomas show reduced H3K27me3, global DNA hypomethylation, are mo...
GSE83636: miR-17-92 cluster regulates adult hippocampal neurogenesis, anxiety and depression
Emerging evidence has shown that noncoding RNAs, particularly microRNAs (miRNAs), contribute to the ...
GSE95743: ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing (RNA-seq)
We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate th...
GSE89479: Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche
In this work, we generated early human amnion-like tissues by culturing human pluripotent stem cells...
GSE90715: Hijacking of stress response machinery by oncogenes in acute leukaemia [RNA-seq]
Our data demonstrate binding of NOTCH1 on the promoters of HSF1 and HSF1 targets. We performed RNA-s...
GSE83127: Effect of 24h treatment with 100nM GSK2879552 on the murine T-ALL cell with and without Zeb2 overexpression
RNA sequencing was performed on biological triplicates of p53 null T-ALL cells with ZEB2 overexpress...