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Sample GSM3959419 Query DataSets for GSM3959419
Status Public on Jun 24, 2020
Title ATAC-seq_shCtrl-1
Sample type SRA
 
Source name shCtrl
Organism Mus musculus
Characteristics cell line: AML12 cells
genotype/variation: shCtrl
Growth protocol AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
Extracted molecule genomic DNA
Extraction protocol The ATAC-seq was performed as described (Buenrostro et al., 2015) with minor modifications: starting with 30,000 AML12 cells and transposition reaction at 37°C for 45 min.
Illumina sequencing library were prepared according to the standard Illumina protocol.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing Paired-end reads were aligned to the mouse genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012) with parameters “-X 2000”.
Mitochondrial and PCR duplicate reads were removed after alignment.
Peaks were identified using MACS2 (Zhang et al., 2008) with a q value threshold of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ATAC-seq signal for each replicate.
 
Submission date Jul 22, 2019
Last update date Jun 26, 2020
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Street address 130 Dongan Rd.
City ShangHai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21273
Series (2)
GSE134619 TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [ATAC-seq]
GSE134624 TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes
Relations
BioSample SAMN12333900
SRA SRX6484412

Supplementary file Size Download File type/resource
GSM3959419_shCtrl-1.bigwig 85.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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