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Sequencing-based assays (Page 51)
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GSE120071: CDK12 catalytic activity is rate-limiting for RNAPII processivity on core DNA replication genes and G1/S progression (nuclear RNA)
In this study we characterized the importance of CDK12-kinase activity in cell cycle regulation, usi...
GSE81977: E-cadherin loss induces autocrine activation of oncogenic growth factor signalling in metastatic lobular breast cancer.
Background: Despite the fact that loss of E-cadherin is causal to the development and progression of...
GSE137795: Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes
In this study, we express an activated form of Notch1 in the mouse mammary luminal lineage and analy...
GSE115813: Metabolic labeling of Hek293 cells using 4-thiouracil
Hek293 cells were metabolically labelled using 4-thiouracil as described in (Schwalb et al, Science....
GSE115137: The transcriptome of human endometrial mesenchymal stem cells under TGFR inhibition reveals improved potential for cell-based therapies
Mesenchymal stem/stromal cells (MSCs) are multipotent cells with favorable properties for cell thera...
GSE123462: Transcriptional profiling of stem cell-derived polarized hepatocytes
Human stem cell-derived hepatocyte-like cells (HLCs) offer an attractive platform to study liver dis...
GSE87647: Molecular codes for cell type specification in Brn3 Retinal Ganglion Cells
Visual information is conveyed from the eye to the brain by distinct types of Retinal Ganglion Cells...
GSE135861: Transcriptome analysis of methylparaben treated H1299 lung carcinoma cells
Purpose: finding differential transcripts usage in environmentally harzardous chemical, methylparabe...
GSE108017: Transcriptional profiling of mouse prostate tumors with conditional mutations in the Pten, Apc, or Tgfbr2 genes
We report the changes in gene expression in mouse prostate comparing normal wild type prostate to tu...
GSE87183: RNAseq in primary pituitary cells
Deployment of a cell-specifying enhancer repertoire by the pioneer factor Pax7; The establishment an...
GSE105781: RNA-seq expression profiling of Grhl2-deficient and control murine lung epithelium at embryonic day E16.5
Epithelial (CD31-CD45-EpCAM+) cells were isolated by FACS from Grhl2-deficient (Shh-Cre;Grhl2f/-) an...
GSE129826: Global analysis of enhancer targets: Mosaic-seq
Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment o...
GSE123477: RNA-seq of WT and Nocturnin knockout A549 cells
mRNA regulation by the circadian protein Nocturnin in A549 cells. SOURCE: Alexei Korennykh (akorenny...
GSE101637: RNA-Seq analysis of the impact of a kinase NIK inhibitor (DMBP5) on the human melanoma cell line A375 (replicate 1)
Introduction: there is growing evidence that the IFN--related cytokine signature plays a major role ...
GSE123822: Stat1-induced NAMPT sustains NAD levels to regulate gene expression in classically activated macrophages
We identify gene regulation patterns that influence inflammation and metabolism during interferon tr...
GSE121535: RNA-seq analyisis of PUM2 knockout cells
Expression analysis in HeLa stable cell clones expressing a control shRNA (SCR) or two independent s...
GSE123532: Analysis of the polyA+ RNA of LPS-treated human CD14+ monocytes
This study aims to investigate the profile and the role of lncRNAs in the IFN response initiated by ...
GSE123509: Global brain transcriptome analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model
We analyzed expression changes in the Tpp1-/- forebrain/midbrain and cerebellum of 4 mo. mutants com...
GSE140026 (mouse): GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment [RNA-Seq]
The purpose of our study was to examine the role of GCN2 in the function of immunosuppressive cells ...
GSE123514: Transcriptome of Dp1Tyb and wild-type mouse embryonic fibroblasts [ERCC spike-ins]
Purpose: to identify the effects of the Dp1Tyb mutation on the transcriptome of mouse embryonic fibr...
GSE124583: Expression changes in the prefrontal cortex after neurotransmission blocking of nucleus accumbens pathways
GSEA using both edgeR and voom statistics revealed that the ES of two types of corticothalamic neuro...
GSE124946: Striatum transcriptome analysis of Shank3 knock-out/heterozygous mice
Shank3 is a core excitatory postsynaptic protein expressed in multiple brain regions including the m...
GSE83918: Mouse model of RHOA G17V mutation in Peripheral T-Cell Lymphoma
Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive lymphoid tumor derived from malignant tra...
GSE142684: RNA-seq analysis of Wildtype and Prdm16 cKO ventricular zone tissue during cortex development in mouse
Purpose: To explore the mechanisms by which PRDM16 regulates reactive oxygen species levels and oxid...
GSE132281: Laminin-binding integrins are essential for the maintenance of functional secretory epithelium in lactation
Integrin dimers 3/1, 6/1 and 6/4 are the mammary epithelial cell receptors for laminins, which are m...
GSE132198: LSD1 regulates the plasmablast transcriptome
To understand the role of LSD1 in marginal zone B cell development, CD93+ transitional B cells were ...
GSE104785: Salmonella persisters undermine host immune defences during antibiotic treatment
Many bacterial infections are hard to treat and tend to relapse, possibly due to the presence of ant...
GSE107009: Study on the circular RNA expression profile of articular chondrocytes in an IL-1-induced mouse model of osteoarthritis
Circular RNA expression profiling by high-throughput sequencing SOURCE: zhibin zhou (zhouzhibin@smmu...
GSE117644: Genome-wide transcript structure resolution in murine gammaherpesvirus 68: 3T12 deepCAGE
deepCAGE was used in conjunction with Pacific Biosciences Iso-Seq and Illumina RNA-Seq to globally r...
GSE134428: RNAseq analysis of prostate cancer stem cells
Prostate cancer stem cells were isolated from PC3 cells by fluorescence activated cell sorting using...
GSE125267: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [lnc-Nr2f1 overexpression]
The goal is to examine the global transcriptomic changes upon lnc-Nr2f1 overexpression in human neur...
GSE134082: Transcriptomic analysis of Clec12A-deficient BMDCs stimulated with RIG-I agonist
Innate immune receptors rely on the detection of diverse immunological cues and intensive crosstalk ...
GSE129715: Total and newly transcribed (4sU-RNA) RNA of primary human fibroblasts infected with the vhs-null mutant of HSV-1
Primary human foreskin fibroblasts (HFF) were infected with vhs-null mutant of HSV-1 strain 17 at a ...
GSE132706: Systemic approaches reveal anti-adipogenic signals at the onset of obesityrelated inflammation in white adipose tissue [RNA-seq]
HFD feeding induces a rapid adipocyte progenitors (APs) proliferation in visceral adipose tissue (vW...
GSE128917: Gene expression of human myoblasts with ectopic DUXB
RNA-seq of MB135 myoblasts with inducible DUXB, comparing uninduced and induced myoblasts SOURCE: Gu...
GSE138618: Impact of ZFAND3 knockdown on whole-genome gene expression in GBM cells
ZFAND3 was beforehand identified to be invasion essentiel in GBM cells using genome-wide shRNA libra...
GSE102478: Timeseries analysis of gene expression in Adrb2+/+ and Adrb2-/- Clone4-transgenic CD8+ T cells responding to Vesicular Stomatitis Virus expressing hemagglutinin from influenza A PR/8.
RNA sequencing was performed to elucidate the role of beta2-adrenergic receptor (Adrb2) signaling on...
GSE133101: circRNAs in human brains of Parkinson's disease
total RNA sequencing of Parkinson's disease 3 regions of human brain SOURCE: Hermona Soreq (hermona....
GSE121051: Transcriptomic profiling of LPS-induced adrenal inflammation in WT mice
Although of the utmost importance for our survival, the activation of the adrenal gland is often imp...
GSE107590: Hyperactive mTOR and MNK1 phosphorylation of eIF4E confer tamoxifen resistance and estrogen independence through selective mRNA translation reprogramming
Tamoxifen resistant translational reprogramming is shown to be mediated by increased expression of e...
GSE135538: mRNA sequencing of clinical-grade neural stem cells derived from human ES cells
We report the transcriptome profile of human neural stem cells derived from ES cells. Cells were tr...
GSE128951: 5-hydroxymethylcytosine Promotes Productive Transcription and Inhibits Spurious Promoters
Covalent DNA modifications play vital roles during animal development. While 5-methylcytosine (5mC) ...
GSE130892: MeRIP-seq for heat shock in B-cell lymphoma cells
We ran MeRIP-seq on RNA from heat shocked (43 C for 1 hr) and untreated cells to compare to previous...
GSE133903: Transcriptome analyses of human pancreatic islets and pseudoislets
We have observed an improvement of glucose-stimulated insulin secretion upon the formation of pseudo...
GSE136657: RNAseq analysis of total skin from control or JunBdep mice
RNA was isolated from total skin of control or JunBdep mice at 6-7 months of age when the skin of mu...
GSE128526: Aberrant expression of select piRNA-pathway genes does not reactivate piRNA silencing in cancer cells
Analysis of PIWIL1 function in COLO205 [ATCC CCL-222] colon adenocarcinoma cancer cell culture model...
GSE128101 (mouse): Subcellular pathways shared by afflicted patients and mutant mice identify a new drug treatment for aortic aneurysm in Marfan syndrome
We analyzed differentially expressed genes in smooth muscle cells derived from the thoracic aorta of...
GSE142334: Gene expression profiling in follicular lymphoma (FL) samples and paired transformed follicular lymphoma (tFL) (n=6 samples)
Follicular lymphoma (FL) is the second most common forms of B cell lymphoma that result from the ex...
GSE132245: Deep sequencing of an AML cell line, with and without p53, treated with vehicle control, BETi, MDM2i, or a drug combination
Gene expression changes were compared in human OCI-AML3 cells, with or without p53 knock down, that ...
GSE129891: Mice modeling human CNVs associated with psychiatric disorders
139 samples from cortex and hipocampus of the mice modeling human CNVs associatted with schizophreni...
GSE134875: Transcriptome analysis of CD4+ T cells differentiated from wild-type and tumor bearing C57BL/6J mice
We report a crosstalk between T follicular helper (Tfh) and Th2 cells mediated by the Prostaglandin ...
GSE141842: Change in translation efficiency in mouse eyes at P0.5 by RNG140 knockout
RNG140 is an RNA-binding protein that increases in expression during eye lens differentiation and is...
GSE132008: Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (RNA-sequencing)
Sequences within 5' untranslated regions (UTRs) dictate the site and efficiency of translation initi...
GSE132785: Transcriptome analysis upon Nipbl, Brd2 and Brd4 knockdown in P19 cells
Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin lo...
GSE121359: Sphingosine kinase 2 signaling modulates altered expression profile of host genome in a murine model of Pseudomonas aeruginosa pneumonia.
We present the set of pseudomonas responsive genes activated in the WT mice in comparison with Sphk2...
GSE135012: Stau2 knockdown in human bcCML cells (K562)"
STAU2 knockdown in human K562 cells SOURCE: Michael Hamilton (mihamilton@ucsd.edu) - UCSD
GSE133738: LSD1 inhibition promotes epithelial differentiation through derepression of fate- determining transcription factors [proliferation vs differentiation]
Genome-wide gene expression changes triggered by Ca2+-induced differentiation of epidermal progenito...
GSE111091: Establishing a preclinical model of squamous lung cancer to investigate of novel chemopreventive approaches in high risk individuals with bronchial premalignant lesion
Lung cancer is the leading cause of cancer mortality due to limited diagnosis and interception of di...
GSE124641: Study evaluating striatal and hippocampal tissues between Helios full knockout and wild type mice
Striatal and hippocampal tissues were dissected out from wild type and helios knockout mice to perfo...
GSE119906: Decoding aging and maturation related transcriptome and methylome dynamics in mouse oocytes by single cell parellel sequencing technology
We applied the modified single-cell parallel sequencing (scM&T) technology to generate the transcrip...
GSE132799: RNA sequencing of periheral CD4+ T cells and Mucosal associated invariant T cells (MAIT) cells from periphery blood
MAIT cells and CD8+ T cells from periphery blood were analysed and revealed altered transcriptome of...
GSE134907: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1, H1 derived APLNR+ cells, CD31+CD34+ cells and CD43+ cells during human early hematopoietic differentiation
Purpose: The goals of this study are to verify the dynamic changes of MAGs in H1 derived different p...
GSE114749: Bulk RNA sequencing of NCR- ILC3s from the murine spleen and the small intestine
Splenic and intestinal NCR- ILC3s have been shown to be phenotypically and functional different. The...
GSE120983: Post-developmental deletion of adipocytes autophagy
Autophagy is a homeostatic cellular process involved in the degradation of long-lived/damaged cellul...
GSE139452: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of bone marrow granulocyte-macrophage progenitors (GMP)
Induction of trained immunity by beta-glucan affects myeloid cells and their bone marrow progenitors...
GSE123357: Mouse Estrogen Treatment Study Analysis of Peri-prostatic Fat
Obesity is associated with an increased incidence of high grade prostate cancer (PC) and worse progn...
GSE139573: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of lack of autophagy on sorted mouse lung ILC2 Transcriptomes
Atg5, a key gene of the autophagy can affect ILC2 effector functions ex vivo. Increased ILC2 activat...
GSE141203: Transcriptional profiling of cells in the dorsal striatum and accumbens nucleus of older Drd1-TRAP (CP73) mice
Using translational profiling we obtained RNA-Seq data from total RNA present in the dorsal striatum...
GSE145288: Transcriptomes of small intestinal WT and Tph1-deficient ILC2s
RNA sequencing of small intestinal ILC2s sorted from Il7rCre/+ Tph1flox/flox or Il7rCre/+ control mi...
GSE127244: RNA-seq dynamic transcriptomic pipeline
Purpose: Develop an analytical pipeline for dynamic RNA-seq experiments and highlight the importance...
GSE124517: Regulation of neuronal commitment in mouse embryonic stem cells by the Reno/Bahcc1 locus
Regulation of neuronal commitment in mouse embryonic stem cells by the Reno/Bahcc1 locus SOURCE: Igo...
GSE138270: scRNASeq analysis of cycling cardiomyocytes
Cardiomyocytes with true mitotic potential were enriched by means of CDC20 and SPG20 molecular beaco...
GSE133809: Regulation of intestinal gene expression by Turicibacter sanguinis colonization in mice
The objective of this study is to determine whether monocolonization of germ-free mice with Turiciba...
GSE136134: The effect of insulin on mRNA transcription of human pluripotent stem cells
RNA-seq mRNA transcriptome profiling of human induced pluripotent stem (hiPSCs) cells to identify th...
GSE112717: Enhancer-dependence of gene expression increases with developmental age
How overall principles of gene regulation (the "logic") may change during ontogeny is largely unexpl...
GSE124716: Comparison of Prox1 expressing and Prox1 knockout intestinal tumors and the effect of A2V+CD40
Control or A2V+CD40 treated Prox1-proficient (AP) and Prox1-deficient (APP) tumors SOURCE: Tatiana P...
GSE124463: Promoter capture Hi-C identifies long-range promoter contact dynamics in response to diet and the development of non-alcoholic fatty liver disease
We profiled the chromatin interactions in liver from mice fed either an obesogenic or control diet. ...
GSE123977: Recurrent Group A Streptococcus Tonsillitis
To determine differences in GC Tfh cells isolated from the tonsils of children who have undergone to...
GSE95029: The developmental and metabolic roles of the diabetes candidate gene TCF7L2 in adipose tissue
The gene encoding for transcription factor 7-like 2 (TCF7L2) is the strongest type 2 diabetes (T2DM)...
GSE125287: Gene expression analysis of mouse alveolar macrophages infected with Mycobacterium tuberculosis
The aim of this study was to measure the immune response of alveolar macrophages (AMs) to intracellu...
GSE108917: LncRNAs and open chromatin regions constitute midbrain dopaminergic neuron- specific molecular signatures
Midbrain dopaminergic (DA) neurons are involved in diverse neurological functions, including control...
GSE145081: Long non-coding RNA MANCR is a target of BET bromodomain protein BRD4 and plays a critical role for cellular migration and invasion abilities of prostate cancer
Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) is highly aggressive and...
GSE114067: Tissue tuft cell mRNA sequencing
The goal of the study was to sequence mRNA from tuft cells (identified as CD45-;EpCAM+;IL-25+ using ...
GSE142481: Combined targeting of the BRD4-NUT-p300 axis in NUT midline carcinoma by dual selective bromodomain inhibitor, NEO2734
NUT midline carcinoma (NMC) is a rare, aggressive subtype of squamous carcinoma that is driven by th...
GSE121976: HOXC6 affects the malignant phenotype of esophageal squamous cell carcinoma cells
HOXC6 is a member of the HOX family, and its aberrant expression has been verified in a variety of c...
GSE139506: Acute Kidney Injury Transcriptional Profiles:Single Cell RNA Sequencing reveals Injury induced Renal Developmental programreactivation and Lineage Infidelity in adult kidney
Acute Kidney Injury (AKI) is a rapid renal function decline associated with pronounced morbidity and...
GSE128933: scRNA sequencing of 2 leukemia patients in remission after T cell therapy
peripheral blood samples of two leukemia patients in remission were profiled by single cell RNA sequ...
GSE148397: Darolutamide antagonizes androgen signaling by blocking enhancer and super-enhancer activation [RNA-seq]
The androgen receptor (AR) antagonist darolutamide has very recently been approved for the treatment...
GSE120261 (mouse): In situ 10-cell RNA sequencing in tissue and tumor biopsy samples
We combined the tissue preservation and single-cell resolution of laser capture with an improved pre...
GSE139390: Multi-colour lineage tracing reveals intra-stage proliferative heterogeneity during mammary tumour progression
We have assessed clonal heterogeneity within individual primary tumours and metastasis and also duri...
GSE153499: Protein synthesis inhibitors stimulate MondoA transcriptional activity by driving accumulation of glucose 6-phosphate
BACKGROUND: Protein synthesis is regulated by the availability of amino acids, the engagement of gro...
GSE118963: The p30 isoform of CEBPA uncovers a silent enhancer to drive the expression of the tumor promotive factor CD73 in CEBPA mutant AML
CEBPA is a key hematopoietic transcription factor (TF), found mutated in 5-14% of all acute myeloid ...
GSE142380: Comprehensive analysis of soluble RNAs in human embryo culture media
Spent culture media was collected on day 5 after in vitro fertilization from 5 human blastocysts tha...
GSE134412: Siah2 control on tumor environment
Understanding mechanisms underlying anti-tumor immunity is pivotal for improving immune-based cancer...
GSE99646: RNASeq to identify the in vivo mechanism of anti-Ox40 mAb treatment exacerbated lupus in NZB/W F1 Mice
We've recently shown that we can accelerate disease in a model of SLE (the NZB/W F1 model) using an ...
GSE100861: Single cell transcriptomics reveal an essential role for Hippo signaling in cell state transitions during cardiac fibroblast development
We usesingle cell RNA-sequencing (Drop-seq) to profile cardiac cells(excluded atria) fromcontrol (Wt...
GSE104736: Non-synchronized cell cycle transcriptomics in U2OS and HeLa cancer cells
Sorting U2OS and HeLa cells genetically modified with the Fucci System allowed us to separate cells ...
GSE116256: Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity
Acute myeloid leukemia (AML) is a heterogeneous disease that resides within a complex microenvironme...
GSE89520: Lamins organize the three dimensional genome from nuclear periphery in ES cells
Lamins are the major structural components of the nuclear lamina (NL) beneath the inner nuclear memb...
GSE93306: Genome-wide mRNA expression analyses revealed dysregulation of genes important for sympathetic neuron development in isl1 cko and hypomorphic mutant embryos.
Understanding factors that drive development and function of the sympathetic neuron is crucial to d...