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Sample GSM4889011 Query DataSets for GSM4889011
Status Public on May 03, 2021
Title C2C12_ATAC_rep1
Sample type SRA
 
Source name C2C12_ATAC
Organism Mus musculus
Characteristics strain background: C3H
cell line: C2C12
cell type: skeletal muscle cell line
genotype: WT
Treatment protocol none
Growth protocol C2C12 control and C2C12 Hira KO cell lines were collected when grown in high serum medium at low density (proliferating conditions)
Extracted molecule genomic DNA
Extraction protocol C2C12 cells were harvested and cell pellets were resuspended in lysis buffer, pelleted and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing alignment: BWA algorithm (mem mode; default settings)
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file and with the –nomodel option
Genome_build: mm10
Supplementary_files_format_and_content: Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program
 
Submission date Nov 08, 2020
Last update date May 03, 2021
Contact name Joana Esteves de Lima
E-mail(s) joanaesteveslima@gmail.com
Organization name INSERM
Department IMRB INSERM U955
Lab Team RELAIX
Street address 8 rue du general sarrail
City Creteil
ZIP/Postal code 94000
Country France
 
Platform ID GPL19057
Series (2)
GSE161053 Genome-wide changes in chromatin accessibility in myoblasts lacking Hira [ATAC-seq]
GSE161056 ATAC-seq, ChIP-seq and RNA-seq studies in myoblasts lacking Hira
Relations
BioSample SAMN16706613
SRA SRX9460289

Supplementary file Size Download File type/resource
GSM4889011_C2C12_ATAC_rep1.bw 184.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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