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Chromatin accessibility of GIST48, GIST882 and GIST-T1 cells with ETV1 or FOXF1 knockdown

ABSTRACT: Chromatin accessibility of GIST48, GIST882 and GIST-T1 cells with ETV1 or FOXF1 knockdown

PROVIDER: PRJNA417537 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6265800_1.fastq.gz	Fastqsanger.gz
	SRR6265800_2.fastq.gz	Fastqsanger.gz
	SRR6265801_1.fastq.gz	Fastqsanger.gz
	SRR6265801_2.fastq.gz	Fastqsanger.gz
	SRR6265802_1.fastq.gz	Fastqsanger.gz

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Chromatin accessibility of GIST48, GIST882 and GIST-T1 cells with ETV1 or FOXF1 knockdown

Project description:Chromatin accessibility of GIST48, GIST882 and GIST-T1 cells with ETV1 or FOXF1 knockdown

| PRJNA417537 | ENA

ETV1 and FOXF1 cistrome in wildtype GIST48, GIST-T1, MDA-PCa2b, and ETV1 or FOXF1 knocked-down GIST48 cells

Project description:ETV1 and FOXF1 cistrome in wildtype GIST48, GIST-T1, MDA-PCa2b, and ETV1 or FOXF1 knocked-down GIST48 cells

| PRJNA417539 | ENA

ETV1 knockdown in GIST cell lines

2010-10-13 | GSE19396 | GEO

ETV1 knockdown in GIST cell lines

Project description:ETV1 is highly expressed in GIST cells and required for their survival and growth. To identify genes and pathways regulated by ETV1 in GIST, we performed expression profiles of GIST cells after ETV1 knockdown. Two GIST cell lines (GIST48 and GIST882) were infected in duplicate with three shRNA viruses (Scrambled, ETV1sh1-B11TRCN0000013923, ETV1sh2-TRCN0000013925). Four days after infection, RNA was harvested for expression profiling.

2010-10-13 | E-GEOD-19396 | biostudies-arrayexpress

ETV1 binding sites in GIST and Melanoma cells

Project description:ETV1 is an oncogene in GIST and melanoma and a downstream transcriptional effector of MAP kinase signaling. Here, mapped the ETV1 binding sites in GIST and melanoma cell lines using ChIP-seq.

2018-04-15 | GSE80443 | GEO

Mapping of ETV1 genomic binding sites in gastrointestinal stromal tumor (GIST).

2010-10-14 | GSE22441 | GEO

RNA-Seq of murine GIST-like tumors after Etv1 ablation

Project description:We used a mouse expressing three alleles 1) KitV558Delta/+ activating allele that develop GIST-like tumors in the cecum, 2) Etv1 flox/flox conditional knockout allele and 3) Rosa26-CreERT2 tamoxifen activated Cre allele. Mice were treated with either Tamoxifen (to delete Etv1) or corn oil (control). Cecal tumors were isolated for gene expression profiling by RNA-Seq. Expression profile mouse cecal GIST tumor with or without Etv1 ablation was generated by RNA-Seq

2015-01-01 | E-GEOD-64608 | biostudies-arrayexpress

Mapping of ETV1 genomic binding sites in gastrointestinal stromal tumor (GIST).

Project description:ETV1 is highly expressed in GIST and their presumed precursors--the interstitial cells of Cajal. ETV1 is required for survival for both GIST and ICC and regulates GIST signature genes. Here, using Illumina-Solexa based next-generation sequencing of ETV1 chromatin immunoprecipates (ChIP-Seq), we define ETV1 binding sites in the GIST48 cell line. Crosslinked ChIP using input control ETV1 ChIP in GIST48 cells. Details: GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with anti-ETV1 antibody (Abcam Ab81086, Lot 787879), washed, eluted, reverse cross-linked, and purified. Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR, and sequenced on Solexa Genome Analyzer. All reads (~36-bp) from ChIP-Seq were aligned to the human genome (build 36, or hg18) using the ELAND alignment software within the Illumina Analysis Pipeline. Unique reads mapped to a single best-matching location with no more than two mismatches were kept and used to generate genome-wide distribution of ETV1-binding and for peak identification. Redundant reads were considered once.

2010-10-14 | E-GEOD-22441 | biostudies-arrayexpress

RNA-Seq of murine GIST-like tumors after Etv1 ablation

2015-01-01 | GSE64608 | GEO

Gene expression signatures in GIST-T1 cells transfected with a miR-186 inhibitor molecule

Project description:To clarify the role of miR-186 in GIST, we carried out a gene expression microarray analysis using GIST-T1 cells transfected with a miR-186 inhibitor or a negative control. We found that 253 probe sets (229 unique genes) were upregulated (>1.5-fold) by inhibition of miR-186 in GIST-T1 cells.

2017-01-01 | GSE85613 | GEO

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