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Links from GEO DataSets

Items: 19

1.

Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity: ChIP-Seq

(Submitter supplied) Smad3 co-occupies DNA binding sites with master transcription factors.
Organism:
Mus musculus; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9250 GPL9115
21 Samples
Download data: TXT, WIG
Series
Accession:
GSE21614
ID:
200021614
2.

Chip-seq of H3 in murine embryonic stem cells, myotubes and pro-B cells.

(Submitter supplied) Nucleosome remodeling results in loss of histone occupancy. To gain insight into variations in H3 occupancy in different murine cell types, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine genome wide occupancy of H3 in ES cells, myotubes and pro-B cells.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9250
4 Samples
Download data: TXT
Series
Accession:
GSE23830
ID:
200023830
3.

Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL4134 GPL9250 GPL9115
22 Samples
Download data: TXT, WIG
Series
Accession:
GSE21621
ID:
200021621
4.

Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity: Gene Expression

(Submitter supplied) Smad3 co-occupies DNA binding sites with master transcription factors.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL4134
6 Samples
Download data: TXT
Series
Accession:
GSE21608
ID:
200021608
5.

Switch Enhancer Elements Control Cell Fate in Human Embryonic Stem Cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13938 GPL10999
14 Samples
Download data
Series
Accession:
GSE52440
ID:
200052440
6.

Switch Enhancer Elements Control Cell Fate in Human Embryonic Stem Cells (BeadChip)

(Submitter supplied) A small toolkit of morphogens is used repeatedly to direct development, raising the question of how context dictates interpretation of the same cue. One example is the TGFβ pathway that in human embryonic stem cells fulfills two opposite functions: pluripotency maintenance and mesendoderm (ME) specification. Using proteomics coupled to analysis of genome occupancy, we uncover a regulatory complex comprised of transcriptional effectors of the Hippo pathway (TAZ/YAP/TEAD), the TGFβ pathway (SMAD2/3) and the pluripotency regulator OCT4 (TSO). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL13938
6 Samples
Download data: TXT
Series
Accession:
GSE52439
ID:
200052439
7.

Switch Enhancer Elements Control Cell Fate in Human Embryonic Stem Cells (ChIP-Seq)

(Submitter supplied) A small toolkit of morphogens is used repeatedly to direct development, raising the question of how context dictates interpretation of the same cue. One example is the TGFβ pathway that in human embryonic stem cells fulfills two opposite functions: pluripotency maintenance and mesendoderm (ME) specification. Using proteomics coupled to analysis of genome occupancy, we uncover a regulatory complex comprised of transcriptional effectors of the Hippo pathway (TAZ/YAP/TEAD), the TGFβ pathway (SMAD2/3) and the pluripotency regulator OCT4 (TSO). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
8 Samples
Download data: BED
Series
Accession:
GSE52437
ID:
200052437
8.

Gene expression profiling in murine Smad-deficient CD4+ T cells stimulated with TGF-b

(Submitter supplied) TGF-b is an important pleiotropic cytokine with potent immunoregulatory properties. Although many previous reports have been proposed for the immunoregulatory functions of TGF-b on T cells, such as the suppression of cell proliferation, cytokine production and cytokine signaling, as well as the induction of apoptosis, it is not well elucidated whether the each effect of TGF-b on T cells is dependent on Smad signaling or Smad-independent other signaling pathways. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
8 Samples
Download data: CEL, CHP
Series
Accession:
GSE19601
ID:
200019601
9.

RNAseq & Smad and Foxh1 ChIpseq in pluripotent mESC and EBs

(Submitter supplied) Smad2, Smad3, Smad4 and Foxh1 ChIPseq performed in pluripotent mESC and embryonic bodies (EBs). RNAseq were performed in WT mESCs and Ebs of WT, Smad2KO, Smad3KO and Smad2/3DKO.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
24 Samples
Download data: TDF, TXT
Series
Accession:
GSE125116
ID:
200125116
10.

TGF-beta/Smad2/3 signaling directly regulates several miRNAs in mouse ES Cells and early embryos

(Submitter supplied) Purpose: We aimed to identify miRNAs which are induced by the Activin/Nodal effectors, P-Smad2/3, in order to further our understanding of how P-Smad2/3 controls downstream gene expression in mouse ES cells to regulate crucial biological processes. Methods: We used a previously developed Tetracycline-On (Tet-On) system (TAG1) to manipulate the levels of P-Smad2/3 in mouse ES cells and performed an Illumina deep-sequencing screen to identify miRNAs which followed the P-Smad2/3 pathway. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9250
3 Samples
Download data: TXT
Series
Accession:
GSE39994
ID:
200039994
11.

Fibroblast-specific genetic dissection of TGFβ-Smad2/3 signaling in cardiac fibrosis

(Submitter supplied) Overall goal: To elucidate fibroblast-specific role of TGFβ-Smad2/3 signaling in fibroblast activation and their differentiation to myofibroblasts. Purpose of analysis: To generate transcriptional profile of Smad2/3 and TGFβreceptors1/2-deficient fibroblasts in the context of pathological cardiac fibrosis.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
8 Samples
Download data: TXT
Series
Accession:
GSE101772
ID:
200101772
12.

TGF-beta-induced gene expression data and Smad2/3 binding sites of HaCaT keratinocytes

(Submitter supplied) Smad2/3 are transcription factors that engage in TGF-beta-induced transcription. Here we analyzed the effect of identified Smad2/3 binding sites to transcription. We used expression microarrays to compare the Smad2/3 binding sites identified by ChIP-chip to TGF-beta-induced gene expressions. Keywords: time course We also examined the effect of either ETS1/TFAP2A/SMAD2/SMAD3 siRNAs on TGF-beta-induced gene expression change.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL570 GPL7026
20 Samples
Download data: CEL
Series
Accession:
GSE11710
ID:
200011710
13.

β-catenin regulates primitive streak induction through collaborative interactions with SMAD2/3 and OCT4

(Submitter supplied) Canonical Wnt and Nodal signaling are both required for induction of the primitive streak (PS), which guides organization of the early embryo. The Wnt effector β-catenin is thought to function in these early lineage specification decisions via transcriptional activation of Nodal signaling. Here, we demonstrate a broader role for β-catenin in PS formation by analyzing its genome-wide binding in a human embryonic stem cell model of PS induction. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: TXT, WIG
Series
Accession:
GSE58476
ID:
200058476
14.

Gene expression profiling of human musculoskeletal tissue samples

(Submitter supplied) We profiled gene expression of purified cell types isolated from 5 musculoskeletal tissues: tendon, bone, muscle, cartilage and ligament. We then performed WGCNA to identify tissue-specific transcription factors, signaling pathways and cell surface receptors. The sequencing data for muscle cells is made available here.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
35 Samples
Download data: XLSX
Series
Accession:
GSE106292
ID:
200106292
15.

TGF-b signaling and response

(Submitter supplied) This work evaluates new and specific therapeutic targets and molecular diagnostic markers connected to the TGF-b response system in chronic fibrotic diseases. Keywords: other
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL362
74 Samples
Download data
Series
Accession:
GSE579
ID:
200000579
16.

AECOM 9K mouse array; 6M-8M print series

(Submitter supplied) cDNA spotted microarray; 8,976 cDNAs from Incyte GEM1 mouse cloneset; chip layout in 4(tips)X51(columns)X44(rows).
Organism:
Mus musculus
1 Series
74 Samples
Download data
Platform
Accession:
GPL362
ID:
100000362
17.

Expression data from C2C12 cells with or without Smad3 overexpression

(Submitter supplied) The goal of this study was to identify genes in C2C12 myoblasts whose expression was altered by overexpression of Smad3.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
4 Samples
Download data: CEL
Series
Accession:
GSE30459
ID:
200030459
18.

Mediator condensates localize signaling factors to key cell identity genes

(Submitter supplied) The gene expression programs that define each cell’s identity are controlled by master transcription factors (TFs) that bind cell-type specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here we present evidence that signaling factors for the WNT, TGF-β and JAK/STAT pathways employ their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
5 Samples
Download data: WIG
Series
Accession:
GSE134387
ID:
200134387
19.

Transcriptomic Analysis of Differentiating Primary Myoblasts treated or not with TGFB1 recombinant protein or ITD-1 compound.

(Submitter supplied) Transforming Growth Factor beta (TGFβ) signaling cascade plays a fundamental role during muscle development and regeneration. Previous reports proposed several roles for the TGFβ superfamily members and generally they are considered negative regulators of myogenic differentiation. However, the activation of this signaling pathway has been shown to be essential to obtain a correct muscle tissue repair process. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL24557
9 Samples
Download data: CEL
Series
Accession:
GSE123425
ID:
200123425
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