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Sequencing-based assays page 70
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GSE120415: RNAseq in BAP1 KO primary mouse mesothelial cells
Malignancies arising from mutation of tumor suppressor genes display an unexplained tissue proclivit...
GSE118809: Synergy of Nras mutation and Nup98-Hoxa10HD gene fusion efficiently preserves the stemness of single hematopoietic stem cells after feeder-free culture
Hematopoietic stem cell (HSC) gives rise to all the hematopoietic cells. The stemness of HSC is stri...
GSE114948: Signal sequences in the viral genome regulate the generation of copy-back defective viral genomes
We developed VODKA (Viral Opensource DVG Key Algorithm) to identify cbDVGs from RNA-Seq data from in...
GSE123999: Next-generation sequencing analysis of Abcg2-expressing vascular endothelial stem cells and mature endothelial cells
We have identified that ATP binding Cassette Subfamily G Member 2 (Abcg2) lables vascular endothelia...
GSE115579: RNA-Seq analysis of hearts from NBCe1 Na-HCO3 cotransporter cardiac conditional knockout (K) vs wild-type (W) mice
The purpose of this study was to investigate the hypothesis that cardiomyocyte-specific loss of the ...
GSE105806: STAT4 and T-bet control follicular helper T cells development in viral infections [RNA-seq]
Follicular helper T (Tfh) cells promote germinal center (GC) B cell survival and proliferation, and ...
GSE129653: HNF1A deficiency impairs -cell fate, granule maturation and function (scRNA-seq of 271 hESC-derived cells: Differentiation day 25)
Mutations in HNF1A cause Maturity Onset Diabetes of the Young type 3, the second most frequent form ...
GSE106097: Gene expression changes in fibroblasts with constitutively active Nrf2 reflect a senescence-associated secretory phenotype (SASP)
Nrf2 is a key regulator of the cellular antioxidant defense system, and pharmacological Nrf2 activat...
GSE110239: Differential Gene expression in the mouse mammary tumors of PyMT-Malat1 wild-type (WT), PyMT-Malat1 knockout (KO) and PyMT-Malat1 knockout with Malat1 transgene expression (TG)
Previously, lncRNA Malat1 knockout mice were generated by insertional inactivation. By crossing this...
GSE114434: Tissue-resident macrophages in the intestine are long-lived and defined by Tim-4 and CD4 expression
A defining feature of resident gut macrophages is their high replenishment rate from blood monocytes...
GSE114789 (human): UPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking
Assuming that functional lncRNAs form larger ribonucleoprotein complex and thus are easily crosslink...
GSE147790: Vascularcontribution to 16p11.2 deletion autism syndrome modeled in mice
While the neuronal underpinnings of autism spectrum disorders (ASD) are being unraveled, vascular co...
GSE116713: Maternal Eed knockout causes loss of H3K27me3 imprinting and random X-inactivation in the extra-embryonic cells
Genomic imprinting is essential for mammalian development. Recent studies have revealed that materna...
GSE115339: Transcriptional profile of Th17 cells: The role of glycolysis
The aim of this study is to investigate a role of glycolysis in transcriptional programing of Th17 c...
GSE142229: Continued Bcl6 expression prevents the transdifferentiation of established Tfh cells into Th1 cells during acute viral infection
By using a temporally-controlled system for the ablation of Bcl6 and Cxcr5 speficially in CD4 T cell...
GSE123080: Mus musculus Gata2 +9.5 Ets C>T transition untreated and 10 days post 5-FU LSK cells
The development and function of stem and progenitor cells that produce blood cells are vital in phys...
GSE122465: Single-cell RNA-seq of frequent and rare populations in mouse bone marrow
This data set contains single-cell RNA sequencing data of mature immune cells, hematopoietic and imm...
GSE117127: Long noncoding RNA signatures induced by TLR7 and type I IFN signaling in activated human plasmacytoid dendritic cells
Using genome-wide sequencing approaches we viewed the contributions of Toll-like receptor 7 (TLR7) a...
GSE120268: RNA-seq of MDA-MB-231 siCt and siAXL
Triple-Negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is associated wi...
GSE117106: Gene expression changes in THP1 cells at day 2 and 4 following shRNA knock-down of RUVBL2
We used an inducible shRNA system and RNA-Seq to examine gene expression changes in acute myeloid le...
GSE118663: iNKT cells RNA-Seq (WT vs SFR KO)
RNA transcriptome difference between WT and SFR KO iNKT cells; To understand how SLAM family recepto...
GSE107655: A comprehensive map coupling distribution of histone modifications with gene regulation in adult in vivo midbrain dopamine neurons [RNA-Seq]
The adult brain is composed of hundreds of different neuronal subtypes, which retain their different...
GSE113146: Inhibition of EGFR signaling downregulates K-RAS mutated activity
KRAS mutations are the ost abundand driver mutations found in lung adenocarcinoma patients. Unfortun...
GSE115451: Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [RNA-Seq]
Total RNA was extracted at different stages of somatic cell reprogramming of OG2-MEFs to induced plu...
GSE121292: Sex chromsomes affect gene expression of autoantigen specific CD4+ T cells
To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throu...
GSE115576: WDR68 is essential for the PRC1-AUTS2 complex activating role and for stem cell differentiation
Recent studies on Polycomb repressive complexes (PRC) reveal a surprising role in transcriptional ac...
GSE123133: Transcriptonal and epigenetic changes of adult liver cells in vivo and in vitro
RNA profile, TET1 and H3K4me3 occupancy in adult ductal cells grown as organoids in vitro; RNA profi...
GSE117129: Identification of an Early Unipotent Neutrophil Progenitor with Pro-Tumoral Activity in Mouse and Human Bone Marrow
Neutrophils are short-lived immune cells that play important roles in a variety of diseases. The oli...
GSE106174: Enhanced glucose uptake in adipocytes despite deteriorating insulin signaling and increased autophagic flux with high fat feeding in mice
Background: Systemic glucose homeostasis is affected by adipose cell function. Still, the cellular e...
GSE121332: Estrogen receptor beta enhances chemotherapy response of GBM cells by down regulating DNA damage response pathways
We examined the transcriptional changes modulated by estrogen receptor beta (ER) by performing globa...
GSE106790: G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst
Early mouse development is regulated and accompanied by dynamic changes in chromatin modifications, ...
GSE119962: Twist1-Haploinsufficiency Selectively Enhances the Osteoskeletal Capacity of Mesoderm-derived Parietal Bone through Downregulation of Fgf23
Purpose: This study investigates the postnatal impact of Twist1 haploinsufficiency on the osteoskele...
GSE121607: Global gene expression analysis of human monocyte-derived dendritic cells (DCs) treated with HMGN1 (N1) and R848 alone or in combination.
RNA-seq data demonstrate that N1 plus R848 at the global gene expression level synergistically promo...
GSE110265: Single cell RNA Sequencing Analysis of Gene Expression Profile in Dgcr8 Conditional KO Embryonic Hearts
Purpose: To compare the single cell transcriptome of wild type and Mesp1Cre+/Dgcr8-/- embryonic hea...
GSE127234: Transcriptome profiling of CD8+ T cells exposed to vehicle or IL-1b treatment in vivo
RNA sequencing analysis is capable of quantitatively analyzing transcriptome of a cell population at...
GSE115403: Inflammation-produced TNF protects hematopoietic stem cells from necroptosis and promotes hematopoietic regeneration
To gain molecular insights into the differential effect of TNF between hematopoietic stem cells (HSC...
GSE115237: A transcription factor addiction imposed by an oncogene promoter sequence [RNA-seq]
Transcriptome analysis by high throughput sequencing SOURCE: Olaf Klingbeil (klingbe@cshl.edu) - Co...
GSE129687: RNA-seq assessment of quadriceps muscle and brown adipose tissue in PPARGC1A uORF-TAA mice
We report a mutant mouse in which the uORF encoded by the PPARGC1A gene is disrupted via mutation of...
GSE106369: The histone acetyl-tranferase MOF is required for metabolic function in the liver .
Purpose: Conditional MOF deletion in mouse livers resulted in acute hepatic necrosis. The goal of t...
GSE113983: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [RNA-seq]
In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs)...
GSE110300: Next Generation Sequencing Provides Transcriptional Analysis for Estradiol Effects in Skeletally Immature (7-weeks old) Female WT and Estrogen Receptor Alpha Knockout Mice
Temporomandibular joint degenerative disease (TMJ-DD) is a chronic form of TMJ disorder that specifi...
GSE120393: Polycomb Mediated Chromatin Organization Reveals Transcriptional Silencers Required for Embryonic Development
Polycomb repressive complex 2 (PRC2), a key regulator of metazoan development, induces transcription...
GSE115244: Gamma entrainment binds higher order brain regions and alleviates neurodegeneration
We report the RNA-Seq data of microglia from CK-p25 mice visual cortex SOURCE: Li-Huei Tsai (lhtsai_...
GSE117510: Lin28/let-7 axis regulates the timig of cession of nephrogenesis
To study role of Lin28/let-7 axis on nephrogenesis, we profiled kidney transcriptom of LIN28 OE, let...
GSE106365: The transcriptome difference analysis after overexpression of lncRNA-smad7 in skeletal muscle damage
Long noncoding RNAs (lncRNAs) have been demonstrated to play important roles in skeletal muscle deve...
GSE115698: Histone deacetylase inhibitors in alveolar rhabdomyosarcoma
Multiple histone deacetylase inhibitors were tested on multiple alveolar rhabdomyosarcoma cell lines...
GSE115670: yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [mouse]
Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study i...
GSE113474: RNA Sequencing of adult high grade glioblastoma tumors
RNA extracted from fresh frozen adult high grade glioblastomas were sequenced for transcriptomic ana...
GSE114464: Mesoderm-derived PDGFRA+ cells regulate emergence of hematopoietic stem cells in the dorsal aorta
During embryonic development, the first hematopoietic stem cells (HSCs) arise from a transient popul...
GSE123165: Codon and amino acid identity are major determinants of mRNA stability in humans
To investigate the effects of the coding sequence on mRNA decay, we globally analyzed the stability ...
GSE113980: CD47 expression in natural killer cell regulates homeostasis and modulates immune response to lymphocytic choriomeningitis virus
CD47 is a ubiquitous cell surface receptor that limits cell clearance by phagocytes that express its...
GSE113221: RNAseq of Wild Type and Prdm1/c-Maf cDKO CD8+ Tumor infiltrating lymphocytes isolated from B16F10 melanoma
Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechani...
GSE130009: RNA sequencing of single LN cells sorted from virus-activated CD4 T clusters
PA-GFP mice were infected subcutaneously with either rVSV or rLCMV viruses. Two days upon infection,...
GSE115477: In vivo replacement of damaged bladder urothelium by Wolffian duct epithelial cells
The bladders remarkable regenerative capacity in response to injury had been thought to reside excl...
GSE115240: FGF2 induces migration of human bone marrow stromal cells by increasing core-fucosylations on N-glycans of integrins
RNAseq analysis of human bone marrow derived stromal cells (MSCs) treated for 24 hours with or wihou...
GSE114514: Modulation of SF3B1 causes global intron retention and downregulation of the B-cell receptor pathway in chronic lymphocytic leukemia
Splicing factor SF3B1 is frequently mutated in chronic lymphocytic leukemia (CLL) patients and has b...
GSE106462: The transcription factor c-Maf is a positive regulator of IL-10 with context-specific roles in CD4+ T cell effector function and in vivo consequences [RNA-seq in vivo]
CD4+ T cells differentiate into distinct subsets which produce unique patterns of cytokines to eradi...
GSE122688: Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (RNAseq)
Despite the ever-increasing speed of detecting fusion transcripts in cancer, it remains formidable t...
GSE116765: Pleiotropic impact of DNA-PK in cancer and implications to therapeutic strategies
DNA-dependent protein kinase catalitic subunit (DNA-PK) is associated with aggressive disease. DNA-P...
GSE129701: Super-enhancer redistribution as a mechanism of broad gene dysregulation in repeatedly drug-treated cancer cells [dataset 2]
We provide a series of chromatin and transcriptomic profiles to establish the short-term and long-te...
GSE115612: scSLAM-seq reveals core features of transcription dynamics in single cells
Single cell RNA sequencing so far only depicts cellular transcriptomes at a single time point with l...
GSE120973: Single-cell RNA-seq Reveals a Developmental Hierarchy and Oncogenic Networks for Initiation of Medulloblastoma [RNA-Seq]
By utilizing single-cell analysis at different stages of tumorigenesis, we demonstrated a developmen...
GSE122380: Dynamic genetic regulation of gene expression during cellular differentiation
The impact of genetic regulatory elements on gene expression can change during differentiation and a...
GSE121148: Three Transcription Factor Functions Empower Progression from Nave to Formative Pluripotency [RNA-Seq]
The gene regulatory network in nave mouse embryonic stem cells (ESCs) must be reconfigured for linea...
GSE115686: Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria
Human cytotoxic T cell subsets were sorted based on cytotoxic molecule expression and RNA sequencing...
GSE110263: Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency [RNA-seq]
Chemical induction of pluripotency (CIP) is an ideal way to reprogram cell fate, but remains poorly ...
GSE118654: Human pluripotent stem cell-derived brain tumor model uncovered embryonic stem cell signature as a key driver in atypical teratoid/rhabdoid tumor (RNA-Seq)
Atypical teratoid/rhabdoid tumor (AT/RT), which harbors INI1 mutation and exhibits a characteristic ...
GSE106427: BATF regulates the expression of Nfil3, Wnt10a and miR155hg for efficient induction of antibody class switch recombination
BATF functions in both T cells and B cells to control the host response to antigen and promote the p...
GSE118951: A novel CD4+ T cell population expanded in SLE blood provides B cell help through IL10 and succinate
A better understanding of the mechanisms involved in human plasma cell differentiation will accelera...
GSE119508: The ovulatory signal precipitates LRH-1 transcriptional switching mediated by differential chromatin accessibility.
In the ovary, follicular growth and maturation are complicated processes that involve a series of mo...
GSE129637 (mouse): MLL-Menin inhibition reverses pre-leukemic progenitor self-renewal induced by NPM1c mutations [RNA-Seq]
Menin binding to MLL1 is required to maintain self-renewal properties of NPM1c progenitors at differ...
GSE115649: Gene expression profiling of Dermal Papilla (DP) cells isolated from wild type (WT) and DP-specific Smo gain-of-function (Smo*) mutant mice during both telogen (at P20) and anagen (at P28).
Gene expression analysis revealed that the DP transcriptome is altered in the Smo* mutant. At P28 t...
GSE116744: RNA-Seq analysis of long-term estrogen-deprived (LTED) MDA-MB-134VI (MM134) and SUM44PE (SUM44) ILC cell lines
Background: Invasive lobular breast carcinoma (ILC) is a histological subtype of breast cancer that ...
GSE134596: RNA-seq analysis of the transcriptional profile of SiHa cells with CNN3 interference.
Transcriptome variation of SiHa cells transfected with si-CNN3 or si-NC were detected by RNA-seq. S...
GSE107759: ADAM17 is required for EGF-R induced intestinal tumors via IL-6 trans-signaling
Colorectal cancer is treated with antibodies blocking epidermal growth factor receptor (EGF-R) but t...
GSE106423: Epitranscriptomic m6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System
N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental tra...
GSE117485: RNA-Seq in two Ewing sarcoma cell lines: A673 and SKNMC
As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiat...
GSE116130: A human TH17 population with a tissue-resident signature in healthy and inflamed oral mucosal tissues [10x]
T cells in mucosal tissues fulfill a complex array of duties to ensure maintenance of barrier immuni...
GSE148516: Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment
In this study, we use small RNA sequencing to investigate the effect of a null mutation of RNase 1 o...
GSE106495: Glutamine 5 serotonylation on histone H3 is a permissive modification that functions combinatorialy with H3K4me3 to potentiate TFIID interactions
Chemical modifications of histone proteins, along with the ?writers,? ?erasers? and ?readers? of the...
GSE116230: RNA-Seq: Smad4-iECKO vs Smad4f/f P7 isolated retinal endothelial cells (iECKO=inducible, endothelial cell specific knockout)
To understand how loss of Smad4 leads to arteriovenous malformation development, we performed RNA-Se...
GSE104182: CNS-draining lymphatics play a key role in age-dependent cognitive decline and Alzheimers disease pathology [2 of 3]
Aging is a major risk factor for many neurological pathologies, including Alzheimers disease (AD). H...
GSE118964: Progression of progenitor B cell leukemia is associated with alterations of the bone marrow micro-environment
Many of the clinical manifestations of B-lymphoid leukemia is a consequence of disrupted formation o...
GSE127699: Bulk RNA-Seq analysis of WT and Bach2-deficient Foxp3+ Treg cells
These are the FastQ files used for the RNA-seq analysis of WT and Bach2-deficient splenic Foxp3+ Tre...
GSE127788: Gene expression changes in HT-22 cells with or without PGC-1 overexpression upon OGD stimulation
PGC-1 overexpression in neurons protects against chronic cerebral hypoperfusion-induced cognitive im...
GSE110303: Next Generation Sequencing Provides Transcriptional Analysis for Estradiol Effects in Skeletally Mature (17-week old) Female WT and Estrogen Receptor Alpha Knockout Mice
Temporomandibular joint degenerative disease (TMJ-DD) is a chronic form of TMJ disorder that specifi...
GSE120084: Macrophage Ad5f35 PhenoMap
Human monocyte derived macrophages (GM-CSF differentiated) were stimulated with control media, IFNy/...
GSE129609: Genome-wide analysis of the transcriptional profile of the CNS during EAE in B6 mice by scRNA-seq [scRNA-seq]
We identify cellular heterogeneity during EAE in B6 mice.; ; Multiple sclerosis (MS) is an autoimmun...
GSE116690: Gene expression analysis of E16.5 Stk11-sufficient control and Sk11-/- lungs
Functional properties of mucosal surfaces are dependent on establishing the correct proportions of s...
GSE117115: PPARg Deficiency Suppresses the Release of IL-1b and a in Macrophages via a Type 1 Interferon Dependent Mechanism
TG elicited Peritoneal macrophages from WT and PPARgamma KO mice were treated with control or lipid ...
GSE121170: Transcriptomic Profiles of Immortalized Human Hepatocytes Overexpressing Intracellular Domain of NOTCH1
To investigate the effect of hyperactivation of Notch signaling in hepatocytes, an immortalized huma...
GSE115499: The lncRNA locus Handsdown regulates cardiac gene programs and is essential for early mouse development
WT and Handsdown mutant ESC were differentatied into the meosdermal cell lineage and harvested at de...
GSE118645: BCL6 confers KRAS-mutant NSCLCs resistance to BET inhibitors
We report that OTX015 upregulates BCL6 in KRAS-mutant NSCLC cells. Considering that both BCL6 and BE...
GSE116120: The Zmiz1-Notch1 interaction induces Myc expression to drive steady state and stress thymopoiesis [ETP and DN3]
Notch1 signaling ramps up to very high levels in order to drive CD4-CD8- double-negative (DN) thymoc...
GSE106853: Mutant p53R270H drives altered metabolism and increased invasion in pancreatic ductal adenocarcinoma
Pancreatic cancer is characterized by nearly universal activating mutations in KRAS. Among other som...
GSE120038: Effect of miR-92a-3p and/or miR-489-3p inhibition on aorta endothelium of Apoe-/-;5/6Nx
The role of endothelial miR-92a-3p and miR-489-3p in CKD-associated atherosclerosis was examined by ...
GSE117133: RNA-seq after siRNA targeting DDX24 applied to iHUVECs cell lines
DDX24 Mutations Associated with Vascular Malformations SOURCE: Pengfei Pang (huxiaoj5@mail.sysu.edu....
GSE135951: Phenotype and function of ex vivo expanded liver progenitor-like cells through liver parenchymal and non-parenchymal reversion
The cellular source for hepatocyte transplantation and liver regeneration in chronically hepatic dis...
GSE130095: B cell HVEM interaction with T cell BTLA restrains the help delivered to germinal center B cells
Gene expression of HVEM-deficient versus WT germinal center (GC) B cells. SOURCE: Michelle,Amy,Mintz...
GSE121241: Long non-coding RNAs are central regulators of the IL-1b-induced inflammatory response in human lung fibroblasts
There is accumulating evidence to indicate that long non-coding RNAs (lncRNAs) are important regulat...