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Sequencing-based assays page 25
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GSE99121: Analysis of DNA polymerase function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance
Whole genome transcriptome analysis by RNAseq was performed to determine whether Poln disruption inf...
GSE100572: Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands [RNA-seq]
The addressable pocket of a target protein is often not functionally relevant. This is particularly ...
GSE100743: Gene Expression Profiling of SPOP Knocked Down Cell
SPOP is one of the most frequent mutated genes in prostate cancer. In the current study, we identifi...
GSE112383: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq]
Analysis of human embryonic stem cells and induced pluripotent stem cells depleted for DDX6. Results...
GSE38148: The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation
Enhancers play a central role in precisely regulating the spatiotemporal expression of developmental...
GSE43296: Polysome-associated mRNA profiling of cancer cells in response to CXCL12 and IGF1
CXCL12 and IGF1 are key secreting molecules produced by cancer-associated fibroblasts in breast canc...
GSE57980: Skeletal muscle gene expression in the wild type and the GAA knock-out mice, a model of Pompe disease
Pompe disease is a Lysosomal glycogen storage disorder due to the deficiency of acid alpha glucosida...
GSE108745: WNT-signaling cells polarize inhibitors to protect their identity and fate
We demonstrated that during development WNT signaling cells produce their own inhibitors polarizing ...
GSE42805: Chronic cocaine-regulated epigenome in mouse [RNA-Seq]
Increasing evidence supports a role for altered gene expression in mediating the lasting effects of ...
GSE113855: Inhibition of 2-AG hydrolysis differentially regulates blood brain barrier permeability after injury
Here we demonstrate that the neurovasculature exhibits a unique transcriptional signature following ...
GSE42951: Genome-wide maps of WT and over-expressing CenH3/CENP-A in Human HeLa S3 cells
Centromeres are essential to ensure proper chromosome segregation in eukaryotes. Their definition re...
GSE42662: UC San Diego Friedmann Kang Neuronal Differentiation DSD3 SNM
The gene expression pattern of spherical neural masses (SNM) derived from HPRT knockdown murine D3 s...
GSE72986: Expression profiles of cultured human epididymis cells reveal the functional diversity of caput, corpus and cauda regions.
Purpose: To compare the transcriptome profiles (RNA-seq) of cultured human epididymis cells and tiss...
GSE42100: Stabilization competency signature
Comparison of gene expresion profile of 4 SC clones and 4 SI clones at different time points defined...
GSE84336: Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells [Toxin]
We report the response of Caco-2 cells to infection by C. concisus strains or exposure to C. concisu...
GSE43070: Genome-wide Analysis of Chromatin Interactions in Human Cells
Millions of cis-regulatory sequences have recently been found in the human genome, but the function ...
GSE54098: Spontaneous tumor regression is driven by Wnt/Retinoic Acid signaling cross-talk
We have identified by RNA sequencing the molecular signaling pathways that are involved in skin tumo...
GSE44061: KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy [Seq]
A multilayered transcription regulatory system is unveiled, where protein- and RNA-based repressors ...
GSE114686: Total RNA profiles in response to four tyrosine kinase inhibitors in human induced pluripotent stem cell-derived cardiomyocytes
To define molecular markers of tyrosine kinase inhibitor-induced cardiotoxicity, we measured transcr...
GSE126969: Comparative bulk RNAseq analysis of CXCL12-abundant reticular (CAR) cells, fetal perichondrium-derived CAR cells and chondrocyte-derived CAR cells.
We revealed the unique molecular signature characterizing fetal perichondrium-derived and chondrocyt...
GSE41090: Mouse CD4+/CD8+ thymocytes from miR-181a1/b1 KO vs WT
miR-181a1/b1, miR-181a2/b2, and miR-181c/d belong to a highly conserved family of microRNA clusters,...
GSE40978: Long non-coding RNAs act as novel mediators of Innate Immunity
Recent advances in genome technologies have uncovered thousands of long non-coding RNAs (lncRNAs) wh...
GSE46980: Quantitative single-cell RNA-seq
Purpose: We applied cDNA molecule counting using unique molecular identifiers combined with high-thr...
GSE41637: Evolutionary dynamics of gene and isoform regulation in mammalian tissues
Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of...
GSE42960: The effect of nicotinamide on dysregulated genes associated with frataxin deficiency in FRDA.
To investigate the efficacy of nicotinamide treatment using our ex-vivo primary lymphocyte model, we...
GSE54066: Human Hepatocytes with Drug Metabolic Function Induced from Fibroblasts by Lineage Reprogramming
We generated induced human hepatocyte by transduction of several lineage specific transcription fact...
GSE119411: Comparison of transcriptome in gonads and somatic tissues in mice
RNA from female gonads (C57/BL6xDBA/2 background) at different developmental stages (11.5dpc, 12.5dp...
GSE44229: The Neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory.
We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: ...
GSE44976: Global analysis of alternative splicing regulated by RBM10
RBM10 is an RNA binding protein that was identified as a component of spliceosome complex, suggestin...
GSE113313: Nascent RNA sequencing in IMR-32 cells treated with THZ531 or DMSO
We performed RNA-seq analsysis of nascent transcripts obtained by 4sU labeling in IMR-32 cells treat...
GSE48552: Alteration of the microRNA network during the progression of Alzheimers disease
We report the high-throughput profiling of microRNAs (miRNAs) from the prefrontal cortex of controls...
GSE43153: Antiviral RNA interference in mammalian cells
Plants and invertebrates protect themselves from viruses through RNA interference (RNAi), yet it rem...
GSE47966: Global epigenomic reconfiguration during mammalian brain development
Whole-genome single-base resolution methylcytosine and hydroxymethylcytosine maps reveal profound ch...
GSE121272: Gene expression profile of a FLT3-ITD acute myeloid leukemia cell line treated with FLT3 inhibitors for six and twelve hours
Adaptive resistance is an important mechanism of resistance to tyrokine kinase inhibitors in cancer....
GSE84271: Next Generation Sequencing of Control and Pbx Mutant Spinal Motor Neuron Transcriptomes
Purpose: Conducted expression profiling by RNA-seq as unbiased screen to identify genes that are alt...
GSE119983: SMARTer single cell total RNA sequencing [SK-N-BE-2C]
single cell polyA+ and total RNA-seq data was generated for NGP, SK-N-BE-2C and SHSY5Y-MYCN-TR cells...
GSE43194: Spatial Transcriptional Profile of the Chick and Mouse Endocardial Cushions Identify Novel Regulators of Endocardial EMT in vitro
Objective: We developed an unbiased strategy to identify genes important in endocardial epithelial-t...
GSE44775: Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.
The degradation of TNF mRNA is critical for restricting TNF synthesis and involves a constitutive de...
GSE96560: Effect of BET bromodomain inhibition with JQ1 in stressed human derived iPS cardiomyocytes
Gene expression profile of endothelin-1 (ET-1) stressed human derived iPS cardiomyocytes (from Cellu...
GSE45152: Interrogating translating RNAs and cell-type specific gene expression using Cre-activated translating ribosome affinity purification
We characterize a Cre-activated TRAP allele (Rosa26fsTRAP) to show that endothelium-specific activat...
GSE43143: RNA-Seq analysis of neurons derived from induced pluripotent stem cells reprogrammed from dental pulp
In this study, we investigated its suitability for disease modeling by carrying out gene expression ...
GSE53928: Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (RNA-Seq)
Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. W...
GSE47817: Epigenetic and genetic changes during mouse hematopoietic stem cell aging [RNA-Seq]
To investigate the global transcriptome changes in mouse hematopoietic stem cell aging, we performed...
GSE50534: Function of MLL4 in mouse embryonic stem cells and somatic cell reprogramming
Enhancers control cell type-specific gene expression and direct cell fate transition. Enhancers are ...
GSE48230: Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer
This paper shows, for the first time, a novel function of the OVO-like proteins (OVOL1and OVOL2) as ...
GSE54112: ZNF804A transcriptome networks in differentiating human neurons derived from induced pluripotent stem cells
The goal of this project is to study transcriptome change by knocking down ZNF804A, a schizophrenia ...
GSE116456: Transcriptome analysis on TDP-43 downstream genes in Tardbp KO mice by Next Generation Sequencing
TDP-43 has been reported to be RNA-binding proteins; however their roles in mammary gland developmen...
GSE46953: Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (RNA-Seq)
To understand what dictates the emerging patterns of de novo DNA methylation, we mapped DNA methylat...
GSE110673: Glucagon contributes to liver zonation in mice [Gcg infusion]
Liver zonation characterizes the separation of metabolic pathways along the lobules and is required ...
GSE115849: RNA seq comparison between scrambled and shGRP78 cells
Pancreatic cancer cells transduced with sh knockdown of GRP78 SOURCE: Patricia Dauer (dauer010@umn.e...
GSE45760: Identification of dysregulated genes after deletion of miR-1-1 and miR-1-2
Purpose: The goals of this study are to identify dysregulated mRNAs in the heart after deletion of m...
GSE48286: High-throughput sequencing of PROMPT-enriched samples.
Sequencing of 5' and 3'ends and RNA-seq of PROMPT and mRNA molecules from control and exosome-deplet...
GSE57501: The epigenetic reader protein SPIN1 controls proliferation and survival of liposarcoma by modulating the RET signaling pathway [RNA-Seq]
The aim of this study is to identify the SPIN1 target genes in liposarcoma cells SOURCE: Henriette F...
GSE45254: mRNA profiling of GGT-HIF2aM3 (gamma-HIF2alphaM3) kidney cortex
The complete transcriptomes of kidney cortex from 3 -HIF2M3 18 month old TG+ male mice and 3 age mat...
GSE63424: Sequencing of First-strand cDNA Library Reveals Full-length Transcriptomes
We developed a new method of preparing libraries for strand-specific RNA sequencing (ssRNA-Seq). It ...
GSE63609: Effect of REST-003 downregulation on cancer invasiveness in MDA-MB-231 cells using RNA-sequencing (RNA-seq) analysis .
Fifty six genes from DESeq were differentially expressed in the treated versus control samples. Mor...
GSE142340: Optimized high-order low-dose drug mixtures boost selectivity and efficacy of colorectal carcinoma treatment
Colorectal carcinoma is currently treated with a combination of chemotherapeutics, often supplemente...
GSE41985: Transcriptome analysis in mouse late spermatocyte deficient in pachytene piRNAs (Miwi+/- and -/-)
In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-trans...
GSE56292: Expression profiling by high throughput sequencing
Innate immune cells control acute eosinophilic lung inflammation induced by cystein proteases. Here ...
GSE63577: RNA-seq of human fibroblasts during replicative senescence
Senescent human fibroblasts were compared to young proliferating fibroblasts. Five different cell li...
GSE47926: In vivo development, differentiation and function of brown fat proceeds in the absence of miRNAs 193b and 365-1
Brown adipose (BAT) development and function are unaffected by the absence of miR-193b/365-1 SOURCE:...
GSE49608: Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells
We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative...
GSE45930: TRIM28 silences endogenous retroviruses in neural progenitor cells
Here we show that in neural progenitor cells (NPCs) TRIM28 silences transcription of two groups of e...
GSE59283: Genome-wide mapping of Rad21 binding sites and gene expression profiling in wild type mouse small intestinal epithelial crypts and Apc Min adenomas
To investigate the role of RAD21 in the transcriptional regulation of global gene expression at earl...
GSE48109: RNA-seq analysis of gene expression in male and female mouse liver
Gene expression in adult male and female mouse liver assayed by RNA-seq, as part of a study on chrom...
GSE53655: Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion
In this study we aimed to assess technical variability associated with globin depletion in addition ...
GSE90712: RNA sequencing of CDH1+/THY1+ and CDH1-/THY1+ germline stem cells
To futher understand the properties of CDH1+ GSCs and CDH1- GSCs, flow cytometry was used to sort th...
GSE40436: Next Generation Sequencing Facilitates Quantitative Analysis of Cyp26b1-/-skin and En1cre;Cyp26b1f/- epidermal and dermal Transcriptomes
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular path...
GSE45284: Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery (RNA-Seq)
Protein Arginine MethylTransferase 5 (PRMT5) is known to mediate epigenetic control on chromatin and...
GSE118026: Telomeres suppress the activity of retrotransposons in pluripotent stem cells [exp2]
Telomeres, which locate at the end of chromosomes protect chromosomes from fusion and deterioration....
GSE45803: Genome-wide RNA probing reveals mRNA structures are far less common in vivo than in vitro
We use Dimethyl Sulfate to probe the structure of rRNA and mRNA in yeast in vivo, in vitro, and at d...
GSE46434: Expression data from GFP-labeled c-Kit+ mouse APL cells and normal Lin-Sca-1-c-Kit+ mouse bone marrow cells
To characterize the differentially expressed genes between leukemic and normal myeloid progenitors S...
GSE56087: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
Mammals have evolved an XY sex chromosome system, resulting in dosage imbalance not only between sex...
GSE112540: RNA deep sequencing from murine BALB/c WT and IL-2-KO bulk CD8 T cells
Our goal was to identify early genetic changes in the development of autoimmune dysfunction. WT and ...
GSE40823: RNA-Seq profiling unveils a non-canonical Wnt signalling signature in pancreas versus liver fate decision
Understanding how distinct cell types arise from common multipotent progenitor cells is a major ques...
GSE120115: HantavaxTM vaccinated peripheral blood mononuclear cells (PBMCs) and sera analyses by transcriptomic and metabolomic profilings
Purpose: To annotate vaccine-induced protective immunity following vaccination and identify the dyna...
GSE47395: RNA Seq analysis of Mefs Isolated from STC1+/+ and STC1-/- mice
Evaluation of X-linked gene expression in MEFs isolated from STC1 wild type and knock out mice; X ch...
GSE50595: Argonaute-bound small RNAs from promoter-proximal RNA Polymerase II
Argonaute (Ago) proteins mediate post-transcriptional gene repression by binding guide microRNAs (m...
GSE46224: Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNA in Failing Human Heart and Remodeling with Mechanical Circulatory Support
Complete transcriptome profiling in human failing and non-failing control hearts using next-gen sequ...
GSE52912: Differential expression of human parthenogenic stem cells, neural stem cells and DA progenitors.
Neural stem cells (NSC) derived from human parthenogenic stem cells (hpSC) have been observed to sho...
GSE101595: Profiling of differential RNAs in alpha amanitin treated SORBS2-depleted ovarian cancer cells and control-treated SORBS2-depleted
In this study, we examined the differential RNA profile of alpha amanitin-treated SORBS2-depleted o...
GSE47774: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium
We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the Un...
GSE123989: Functional Significance of U2AF1 S34F Mutation in Lung Adenocarcinomas
We conducted RNA-Seq and iCLIP for dox-inducible constructs of FLAG-HA tagged U2AF1 in the wild-type...
GSE45358: Gene expression analysis of murine peritoneal macrophages deficient for SAMHD1 and IFNAR
To investigate the contribution of type-1 IFN signalling to the upregulation of IFN- stimulated gene...
GSE66928: GRO-seq analysis of control and Myc-induced U2OS cells
We used GRO-seq to examine the effect of Myc activation on RNA transcription in U2OS cells. SOURCE: ...
GSE55391: TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma
Analysis of 5-hydroxymethylcytosine changes in hypoxia in neuroblastoma cells SOURCE: Christopher Ma...
GSE46597: Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed ...
GSE57514: Transcriptome profile of oocytes expressing a catalytically inactive knock-in allele of Ago2
The RNase III enzyme DICER generates both microRNAs (miRNAs) and endogenous short interfering RNAs (...
GSE103345: RNAseq of FACS Drd1 and Drd2 receptor expressing medium spiny neurons (direct and indirect medium spiny neurons) from 5-6 month Q175 Huntington's disease model mice, compared to WT littermates.
mRNAseq for baseline transcriptional profiling of D1 and D2 receptor-expressing medium spiny neurons...
GSE43520 (mouse): The evolution of lncRNA repertoires and expression patterns in tetrapods
Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary...
GSE47708: Genome wide expression analysis of Ctbp2 knock down mouse F9 cells
Using an RNA interference-based genetic screen in mouse F9 cells we identify the transcriptional cor...
GSE45822: Functional Importance of eRNAs for Estrogen-dependent Gene Transcriptional Activation
The functional importance of gene enhancers in regulated gene expression is well established. In add...
GSE46038: The effects of dietary selenium on selenocysteine incorporation and selenoprotein expression
The goal of this study was to determine the effects of dietary selenium levels on translational cont...
GSE47399: mRNA sequencing identifies differential gene expresssion profiles between ASCC3 knock-down cells and control cells
We sequenced mRNAs from HeLa cells transduced with either scrambled shRNA or shRNA targeting ASCC3. ...
GSE60005: Genome-wide maps of chromatin state in HSC, Pro B and mature B cells
We have used a genome-wide ChIP-sequencing approach to define and investigate the dynamics of the ci...
GSE46494: Natural genetic variation perturbs collaborative transcription factor binding required for enhancer selection and function
Natural genetic variation between two mouse strains was used as a natural mutagenesis screen to test...
GSE118246: RNA sequencing of genetically engineered mouse model lung tumors and normal mouse lung.
Genetically engineered mouse models (GEMM) of cancer are powerful tools to study multiple aspects of...
GSE47480: The star-nosed mole reveals clues to the molecular basis of mammalian touch.
Little is known about the molecular mechanisms underlying mammalian touch transduction. To identify ...
GSE44402: Next-generation sequencing identifies mRNAs targets that experience significant changes in alternative splicing upon PQBP1 knockdown in mouse embryonic cortical neurons
PQBP1 is a highly conserved protein closely related to neurodegenerative disorders. We identified PQ...
GSE112697: RNA-seq analysis from epididymis and testis of ArKI mice
We generated a mouse model (ArKI) in which the two conserved SUMO acceptor lysines of androgen recep...