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Sequencing-based assays (Page 130)
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GSE99215: TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency
Transition from primed to naive pluripotency is associated with dynamic changes in transposable elem...
GSE119449: Septin 9 over expression in MCF7
Septin 9 (SEPT9), a member of the septin gene family, is strongly linked to cancer, particularly bre...
GSE129407: Gene Specific Activation Driven by Small Molecules
Differing levels of chromatin compaction throughout the genome contribute to cell specificity and fu...
GSE99637 (human): Universal alternative splicing of noncoding exons
The human transcriptome is so large, diverse and dynamic that, even after a decade of investigation ...
GSE102910: The hepatitis C viral protein NS5A stabilizes growth-regulatory human transcripts
Numerous mammalian proto-oncogene and other growth-regulatory transcripts are upregulated in maligna...
GSE98509: MYOD Remodeling of the Genome Architecture during Myogenic Conversion of Somatic Cells
We provide here an unprecedented analysis of the three-dimensional re-organization of the genome dur...
GSE99074 (human): Transcriptomic analysis of purified human cortical microglia reveals age-associated changes
Purpose: Microglia are essential for central nervous system (CNS) homeostasis and innate neuroimmune...
GSE99794: Activation of the p53 transcriptional program sensitizes cancer cells to Cdk7 inhibitors
Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors th...
GSE98288: Progressive motor neuron pathology and the role of astrocytes in a human stem cell model of VCP-related ALS
Motor neurons (MNs) and astrocytes (ACs) are implicated in the pathogenesis of amy...
GSE98476: YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction [RNA-seq]
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal d...
GSE99469: RNA-Seq profiling of days 0, 7 and 18 kidney organoids differentiated from three separate vials of starting material
The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid ...
GSE100338: Expression profiling of lncRNAs, miRNAs and mRNAs and their differential expression in leiomyoma using next generation RNA sequencing
Total RNA was isolated from leiomyoma and paired myometrium (N=8) and samples from three pairs were ...
GSE98867: Gene expression changes upon drug withdrawal (Mel888 cell line)
In this study we investigate the mechanism of drug addiction SOURCE: Oscar Krijgsman (o.krijgsman@nk...
GSE98411: A comparative study of endoderm differentiation in humans and chimpanzees
There is substantial interest in the genetic regulatory framework that is established in early human...
GSE98422: Identification of long noncoding RNA RP11-2B6.2 as a positive regulator of type I interferon pathway in lupus nephritis
Methods and Materials The high throughput RNA sequencing (RNA-seq) data from kidney biopsies of LN ...
GSE125862: Gene expression profile in response to HIF-1 inhibition together with PPAR activation and the postnatal factors (T3, IGF-1 and dexamethasone) in hiPSC-CMs
Methods: RNA-seq libraries were prepared using the Illumina TruSeq technology. The libraries were qu...
GSE99583: Human iPSC derived glomeruli facilitate accurate modelling of podocytopathy
Podocytes are the highly specialised cells within the glomeruli of the kidney that maintain the filt...
GSE106534: Long noncoding RNA LNMAT1 promotes lymphatic metastasis in bladder cancer
Long non-coding RNAs (lncRNAs) are a large class of non-protein-coding transcripts that are over 200...
GSE131276: Preclinical Model of ER-positive breast cancer treated with thyroid hormone with or without tamoxifen
Here, we treated a nove ER-positive PDX (UCD12) supplemented with estrogen (E2) with or without thyr...
GSE100132: Gene expression analysis upon mtDNA depletion [RNA-seq]
The goal of the study was to understand whether mitochondrial-driven epigenetic changes regulate gen...
GSE102498: JCAD/KIAA1462, a coronary artery disease-associated gene product, regulates endothelial function
Recent genome-wide association studies (GWAS) have identified gene variants associated with coronary...
GSE100040: Human TFIIH kinase CDK7 regulates transcription-associated epigenetic modification
CDK7 phosphorylates the RNA polymerase II (pol II) CTD and activates the P-TEFb- associated kinase, ...
GSE102469: Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines (RNA-seq)
Current approaches to menopausal hormone therapy consist of compounds which provide tissue specific ...
GSE100075: Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [RNA-Seq]
We report the first discovery of naturally occurring ESR1Y537C and ESR1Y537S mutations in MCF7 and S...
GSE126788: Cell cycle dynamics of human pluripotent stem cells primed for differentiation
Understanding the molecular properties of the cell cycle of human pluripotent stem cells (hPSCs) is ...
GSE99795: Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell cycle-related transcription and attenuated androgen response
Increasing evidence indicates that minor subpopulations intrinsic to androgen-independence are prese...
GSE100118: Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing [RNA-seq]
Despite their fundamental biological and clinical importance, the molecular mechanisms that regulate...
GSE100066: Transcriptome sequencing analysis of BRAF-mutant melanoma metastases.
Melanoma patients carry a high risk of developing brain metastases, and improvements in survival are...
GSE109979: Single-Cell RNA Sequencing Reveals Metallothionein Heterogeneity during hESC Differentiation to Definitive Endoderm [scRNA-Seq]
Differentiation of human pluripotent stem cells toward definitive endoderm (DE) is the critical firs...
GSE129982: A USP28-Np63 axis is a druggable vulnerability of squamous tumour formation and maintenance
The oncoprotein Np63 is an essential transcriptional master- and cell identity regulator in squamous...
GSE102025: Early transcriptome profiling of microRNA-mediated neuronal reprogramming [RNA-seq timecourse]
Neuronal microRNAs, miR-9/9* and miR-124 (miR-9/9*-124), exert reprogramming activities to direct ce...
GSE98206: MALT1 Inhibition Is Efficacious in Both Nave and Ibrutinib-Resistant Chronic Lymphocytic Leukemia.
The clinical efficacy displayed by ibrutinib in chronic lymphocytic leukemia (CLL) has been challeng...
GSE99821: Transcriptional profile of human iPSC and HIOs with APC mutations
Background and Aims: mutations in the gene Adenomatous Polyposis Coli or APC appear in most sporadic...
GSE101234: CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL3.shR6.RNAseq.lg]
The death receptor CD95/Fas can be activated by immune cells to kill cancer cells. However, most siR...
GSE103938: Transcriptome analysis of OSKM- or RAS-induced senescent IMR90 fibroblasts treated with Rapamycin.
Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram soma...
GSE120886: Inherent DNA binding specificities of the HIF-1 and HIF-2 transcription factors in chromatin (RNA-seq)
Hypoxia inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypox...
GSE100007: Widespread translational remodeling during human neuronal differentiation
Faithful cellular differentiation requires precise coordination of changes in gene expression. Howev...
GSE100344: Determination of dynamic changes in chromatin accessibility during cellular reprogramming [scRNA]
Understanding the heterogeneity of cellular reprogramming process at a single-cell high resolution l...
GSE104926: RNA-seq of exosomes identifies lncRNA profiles that distinguish early-stage esophageal squamous cell carcinoma (ESCC) from non-malignant esophagitis
We report the application of RNA sequencing technology for high-throughput profiling of transcriptom...
GSE100223: Assessing the developmental and malignant potential of human pluripotent stem cells by RNA-seq analysis of Teratomas
The International Stem Cell Initiative compared three common approaches for assessing pluripotent st...
GSE101451: Transcripotome analysis of different locations of hair follicles (bulb, bulge) in androgenetic alopecia
To fully interrogate location-specific variations of the hair follicle in AGA and normal persons, we...
GSE101571: Analysis of chromatin landscapes in early human development reveals epigenetic transition during ZGA
Upon fertilization, drastic chromatin reorganization occurs during human preimplantation development...
GSE106602: Expression profile of early and mid-secretory human endometrium revealed by RNA-seq: a paired-sample cohort study
Inner uterine lining or endometrium is a unique constantly self-renewed adult tissue that is vital f...
GSE100266: The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin Remodeling Complexes
BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxica...
GSE104856: SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA
The number of known long noncoding RNA (lncRNA) functions is rapidly growing, but how those function...
GSE101594: Profiling of differential RNAs in SORBS2-depleted ovarian cancer cells and control cells
In this study, we examined the differential RNA profile of SORBS2-depleted ovarian cancer cells comp...
GSE102633: Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects [Ex vivo Blood RNA-Seq]
Metformin, the most widely administered diabetes drug, has been proposed as a candidate for host dir...
GSE99843: Progressive motor neuron pathology and the role of astrocytes in a human stem cell model of VCP-related ALS [terminally differentiated iPSC-derived astrocytes]
Motor neurons (MNs) and astrocytes (ACs) are implicated in the pathogenesis of amy...
GSE104982: WNK1 kinase and the termination factor PCF11 connect nuclear mRNA export with transcription
Transcription termination and mRNA export from the nucleus are closely regulated and coordinated pro...
GSE102481: Temporal alterations in the HSAEC transcriptome following infection by virulent and attenuated strains of Rift Valley Fever Virus
Rift Valley fever virus (RVFV) causes major outbreaks among livestock, characterized by abortion sto...
GSE100009: The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation
Recognition of post-translational modifications on histones by epigenetic readers is a fundamental m...
GSE103001: Stranded RNASeq of human mammary primary tumors ER+ and paired adjacent healthy tissues
Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of ...
GSE102069: Unraveling cis-regulatory elements by mapping structural changes in mRNAs
mRNA molecules are generally thought to be messengers of genetic information in the cell. Stretches ...
GSE101871: A unified activation mechanism for mRNA 3 end processing and splicing mediated by SR superfamily proteins
Alternative mRNA processing is a critical mechanism for proteome expansion and gene regulation in hi...
GSE106640: Extracellular matrix components HAPLN1, lumican and collagen I cause hyaluronic acid-dependent folding of the developing human neocortex
Neocortical expansion, thought to underlie the cognitive traits unique to humans, is accompanied by ...
GSE100400: Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx
In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular...
GSE131049: Purity Independent Subtyping of Tumors (PurIST), a clinically robust single sample classifier for tumor subtyping in pancreatic cancer (NanoString)
We assess three major subtype classification schemas in the context of results from two clinical tri...
GSE106589: Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with signatures from post mortem adult brains
Whereas highly penetrant variants have proven well-suited to human induced pluripotent stem cell (hi...
GSE103919: Single cell transcriptomic profiling of pluripotent stem cell-derived SCGB3A2+ airway epithelium reveals fate plasticity I
Many lung diseases involve alterations in the cellular identity of the lung epithelium. Improved ins...
GSE109809: Transcriptome profiling of HCC1937 vector and wtBRCA1 cell lines which were treated with OTX-015
Purpose: To compare the transcriptomes of HCC1937 vector and wtBRCA1 cells which were treated with O...
GSE111366: APOE-mediated dysfunction in human iPSC-derived endothelial cells
Brain endothelial cells play a crucial role in the brain by forming a network of tight junctions to ...
GSE100568: Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2 to tumor suppression
Neuroblastoma is a pediatric cancer characterized by variable outcomes ranging from spontaneous regr...
GSE102638: Chromatin landscape of human visceral and subcutaneous adipocytes
Obesity is characterized by the excess of body fat leading to impaired health. Abdominal fat is part...
GSE106540: Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis [scRNA-seq]
CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several vira...
GSE138475: Quantitative analysis of transcriptomes in control and mTORC2-suppressed glioblastoma cells
We herein demonstrate that mammalian target of rapamycin complex 2 (mTORC2), a critical core compone...
GSE102505: Transcriptional changes in glioma cells following treatment with 1-Benzyl-3-cetyl-2-methylimidazolium iodide (NH125), Tunicamycin, and 0.1% DMSO (in media)
Purpose: Evaluate transcriptional changes in glioma derived stem cells, U251, and normal human astro...
GSE106392: RNA-seq analysis of THP-1 cell line upon knockdown of CHD4
Epigenetic alterations contribute to leukemogenesis in childhood acute myeloid leukemia (AML). We us...
GSE102676: Transcription factors and stress response gene alterations in human keratinocytes following Solar Simulated Ultra Violet Radiation
Ultraviolet radiation (UVR) from sunlight is the major effector for skin aging and carcinogenesis. H...
GSE100483: RNA-seq of MDA-MB-231 cells with TET1 knockout
DNA hypermethylation is known to contribute to the formation of cancer. However, DNA hypomethylatio...
GSE103510: Pharmacologic inhibition of STAT5 in AML
The transcription factors STAT5A and STAT5B are essential downstream mediators of many tyrosine kina...
GSE107006: Antibodies That Convert Bone Marrow Into Trafficking Microglia-Like Cells Reduce Brain Amyloid
One goal of regenerative medicine is to repair damaged tissue. This requires not only generating new...
GSE103356: SPINK7 transcriptome
RNA sequencing data of SPINK7 gene silencing (SPINK7) as compared to Non silencing control (NSC) tr...
GSE101880: RNA-sequencing of neonatal monocyte responses to E. coli and S. epidermidis
Newborns, particularly those born prematurely, are extremely vulnerable to sepsis and this has been ...
GSE102616: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters
We performed ChIP-seq in four cancer cell lines to identify ZFX binding sites throughout the human g...
GSE105083: Targeting multiple effector pathways in pancreatic ductal adenocarcinoma with a G-quadruplex-binding small molecule
Human pancreatic ductal adenocarcinoma (PDAC) involves the dysregulation of multiple signalling path...
GSE126794: RalA and RalB are potential therapeutic targets in multiple myeloma which mediate cell survival independently of oncogenic RAS
NRAS and KRAS are frequently mutated oncogenic drivers in multiple myeloma, however, their use as d...
GSE112356: A genomic study of the contribution of DNA methylation to regulatory evolution in primates
A long-standing hypothesis is that changes in gene regulation play an important role in adaptive evo...
GSE100855: Transcriptional Consequences of XPA Disruption in Human Cell Lines
Purpose: Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum grou...
GSE102677: Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects [PBMC RNA-Seq]
Metformin, the most widely administered diabetes drug, has been proposed as a candidate for host dir...
GSE102744: Gene expression profiles of ibrutinib-responsive and ibrutinib non-responsive cells in ERBB4 expressing cancer cell lines
By using a unique functional protein microarray platform, we found that the FDA approved drug ibrut...
GSE100891: Identification of downstream genes regulated by YAP1 through knockdown and overexpression of YAP1 in U251 cell with a stably expression of mutant APP
Upstream regulator genes are central hub nodes in a network and their expression may response to up...
GSE103068: Synergistic activity of BET inhibitor BI 894999 with PLK inhibitor volasertib in AML in vitro and in vivo
Interactions between a new potent Bromodomain and extraterminal domain (BET) inhibitor BI 894999 and...
GSE102683: RNA sequencing based comparative analysis of human hepatic progenitor cells and their niche from alcoholic steatohepatitis livers
Hepatic progenitor cells (HPCs) are small cells with a relative large oval nucleus and a scanty cyto...
GSE111301 (human): mRNA sequencing of the mouse and human Hep-Orgs, Chol-Orgs and primary hepatocytes
The mammalian liver possesses a remarkable regenerative ability. 1) The 'oval cell' response emanate...
GSE100905: Human CD11b+ macrophages - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages
The human aged hematopoietic system is prone to dysfunction and clonal selection. Aged hematopoietic...
GSE100796: Human-specific features of special gene expression and regulation in eight brain regions
Despite the substantial efforts made to compile the molecular maps of the human brain, they do not f...
GSE101642: O-glcnAc reprograms cellular energetics
Dysfunctional mitochondria and generation of reactive oxygen species (ROS) promote chronic diseases,...
GSE107273: Role of CD133 molecule in WNT response and renal repair
Renal repair after injury is dependent on clonal expansion of proliferation competent cells. In the ...
GSE105439: Effects of the novel PI3K / inhibitor RP6530 on global gene expression in Hodgkin Lymphoma cell lines.
Tumor-associated macrophages (TAMs) are involved in the pathogenesis of Hodgkin lymphoma (HL) and co...
GSE102730: C/EBP overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1 [RNA-seq]
Acute myeloid leukemia (AML) is a heterogeneous disease caused by recurrent mutations in the transcr...
GSE102746: Transcriptome-analysis of patient-derived normal and ulcerative colitis intestinal epithelial organoids
Purpose: The objective of this study is to compare the transcriptome profile of intestinal epithelia...
GSE101076: In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [LN-521 or LN-521+LN-221]
Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no metho...
GSE101419: The phosphatidylinositol 3-kinase pathway as a potential therapeutic target in bladder cancer
Activation of the phosphatidylinositol 3-kinase (PI3K) pathway occurs in over 40% of bladder urothel...
GSE101934: Distinct gene expression profile of Huh7 cell lines stably overexpressing CRABP1 or 2
The metabolism of ROL to the biogenesis of ATRA occurs in the cytoplasms of hepatocytes, which in tu...
GSE102183: Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [RNA-seq C-terminal mutant]
Targeting the activation function-1 (AF-1) at the N-terminus of the androgen receptor (AR) is an att...
GSE102209 (human): Cooperation between TLX1 and the NUP214-ABL1/STAT5 signaling in T-cell acute lymphoblastic leukemia
The NUP214-ABL1 fusion is a constitutively activated tyrosine kinase that is significantly associate...
GSE104908: A novel non-canonical signaling pathway mediates TGF-1-induced glucocorticoid insensitivity in epithelial cells
Limited therapeutic responses to glucocorticoids in chronic inflammatory disease are partly attribut...
GSE102741: RiboZero Gold paired-end RNA-seq data from postmortem tissue of the dorsolateral prefrontal cortex of autism spectrum disorder samples and healthy control samples
Purpose: The goals of this study was to compare the expression of histamine related genes in ASD pat...
GSE102762: CSL RNA-Seq on HKC and SCC cell lines
Down-modulation or loss-of-function mutations of the Notch 1 and 2 genes are associated with develop...
GSE127444: Role of the mRNA-binding protein HuR in the global transcriptomic status of cells stimulated with electrophiles and oxidants
HuR has been implicated as a stress-responsive protein: cytoplasmic translocation of HuR is promoted...