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Sample GSM7508708 Query DataSets for GSM7508708
Status Public on Apr 19, 2024
Title ASPS_Tumor-1_input
Sample type SRA
 
Source name ASPS Tumor
Organism Homo sapiens
Characteristics tissue: ASPS Tumor
cell type: ASPS
chip antibody: none
Treatment protocol None
Growth protocol Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin
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).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
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
 
Submission date Jun 26, 2023
Last update date Apr 19, 2024
Contact name Matthew Hemming
E-mail(s) matthew.hemming@umassmemorial.org
Organization name UMass Medical School
Street address 364 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
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
Relations
BioSample SAMN35984366
SRA SRX20777225

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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