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Sample GSM1552830 Query DataSets for GSM1552830
Status Public on Jul 23, 2015
Title PM_ATAC-Seq
Sample type SRA
Source name Primary proliferating myoblasts
Organism Mus musculus
Characteristics cell type: primary
days in culture: 3
strain: C57BL/6
chip antibody: No antibody
Treatment protocol Cell were treated with transposase (Illumina #FC-121-1030)
Growth protocol We isolatedf SC from gastrocnemius muscles of 2-3 weeks old C57bl/6 WT or Runx1f/f mice. Cells were grown at 37°C, 5% CO2 on GHR MatrigelTM (BD Biosciences, USA) in proliferation medium (BIOAMF-2, Biological Industries, Israel), which was replaced daily.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to previous protocol (Buenrostro et al., 2013) using KAPA HiFi PCR kit (KAPA biosystems, # KK2601)
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description ATAC-seq of WT PM
Data processing Library strategy: ATAC (assay for transposase-accessible chromatin)
Basecalls were obtained using CASAVA version 1.8.4.
Illumina adaptors were removed using a custom python script, reads were treamed to 50 bp.
Reads were aligned to the mm9 genome assembly using Bowtie2 with default options, mitochondrial reads were removed from the analysis .
Replicated reads were removed using Picard tools, MarkDuplicates.
Reads with insert size smaller than 140 bases were selected for peak detectection, that was performed using the MACS2 callpeak function for broad peaks.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS2.
Submission date Nov 24, 2014
Last update date May 15, 2019
Contact name kfir baruch Umansky
Phone 97289342318
Organization name Weizmann Institute
Street address POB 25
City Rehovot
State/province Rehovot
ZIP/Postal code 76100
Country Israel
Platform ID GPL17021
Series (2)
GSE56131 Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation
GSE63573 Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ATAC-Seq]
BioSample SAMN03217766
SRA SRX766230

Supplementary file Size Download File type/resource
GSM1552830_clipped_ATAC_peaks.broadPeak.gz 981.8 Kb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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