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Status |
Public on Apr 19, 2024 |
Title |
ASPS_Tumor-1_H3K27ac |
Sample type |
SRA |
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Source name |
ASPS Tumor
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Organism |
Homo sapiens |
Characteristics |
tissue: ASPS Tumor cell type: ASPS chip antibody: H3K27ac (Abcam, ab4729)
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Treatment protocol |
None
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Growth protocol |
Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin
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Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries for paired-end 37 bp sequencing on an Illumina NextSeq 550 were prepared with a ThruPLEX DNA-seq Kit (Takara).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
All Chip-Seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html) Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp). Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination. Assembly: hg19 Supplementary files format and content: Processed ChIP-Seq data files are in wiggle format
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Submission date |
Jun 26, 2023 |
Last update date |
Apr 19, 2024 |
Contact name |
Matthew Hemming |
E-mail(s) |
matthew.hemming@umassmemorial.org
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Organization name |
UMass Medical School
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Street address |
364 Plantation Street
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City |
Worcester |
State/province |
MA |
ZIP/Postal code |
01605 |
Country |
USA |
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Platform ID |
GPL18573 |
Series (2) |
GSE235737 |
Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [ChIP-Seq] |
GSE235739 |
ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs |
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Relations |
BioSample |
SAMN35984367 |
SRA |
SRX20777224 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7508707_ASPS_Tumor-1_H3K27ac.wig.gz |
92.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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