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SRX13171720: GSM5695599: hASPS_input; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina MiSeq) run: 10.1M spots, 1.3G bases, 438.1Mb downloads

Submitted by: NCBI (GEO)
Study: ASPSCR1-TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma [ChIP-seq]
show Abstracthide Abstract
Alveolar soft part sarcoma (ASPS) is a rare soft part malignancy affecting adolescents and young adult. ASPS is characterized by its alveolar structure consisting of tumor cells and highly integrated vascular network, and its high metastatic potential indicates the importance of the prominent angiogenic activity of ASPS. Here we find that the expression of ASPSCR1-TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance but required for in vivo tumor development via angiogenesis. ASPSCR1-TFE3 frequently associates with active enhancers including super-enhancers (SE) upon its DNA binding, and the loss of its expression induces dynamic modification of SE distribution related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical target genes associated with reduced enhancer activities due to the ASPSCR1-TFE3 loss. ASPSCR1-TFE3 thus orchestrates higher ordered angiogenesis via enhanced intracellular trafficking of angiogenic factors. Overall design: Mouse ASPS was induced by expressing ASPSCR1-TFE3 in embryonic mesenchymal cells followed by subcutaneous transplantation into nude mice. Subcutaneous tumors were subjected to cell culture. Human ASPS cell lines were used for gene knockdown experiments.
Sample: hASPS_input
SAMN23297133 • SRS11101650 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina MiSeq
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Experiment attributes:
GEO Accession: GSM5695599
Links:
Runs: 1 run, 10.1M spots, 1.3G bases, 438.1Mb
Run# of Spots# of BasesSizePublished
SRR1698094010,075,9161.3G438.1Mb2023-01-17

ID:
17984441

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