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Sample GSM2396549 Query DataSets for GSM2396549
Status Public on Dec 12, 2016
Title mTEC Hi ATAC-Seq 2
Sample type SRA
Source name Mature mTECs from WT mice
Organism Mus musculus
Characteristics cell type: Thymic EpCAM+Ly51-MHCIIhi
strain: C57BL/6
age: 6 weeks-old
Growth protocol Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2
Extracted molecule genomic DNA
Extraction protocol Cells were FACS sorted into MACS buffer and the open chromatin was profiled by the ATAC-seq protocol developed by (Buenrostro et al., 2013) with modifications described by (Lara-Astiaso et al., 2014).
protocol developed by (Buenrostro et al., 2013).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing fastq using bcl2fastq
alignment using bowtie2 (--local, mm9)
filter out reads that align to same place and sequence on R2 from nucleotides #1 to #15 are identical
makeTagDirectory -tbp
makeUCSCfile -bigWig -fsize 1e20
Genome_build: mm9
Submission date Nov 18, 2016
Last update date May 15, 2019
Contact name Jakub Abramson
Organization name Weizmann Institute
Department Immunology
Street address Herzl 234
City Rehovot
ZIP/Postal code 76100
Country Israel
Platform ID GPL19057
Series (2)
GSE90048 Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells [ATAC-Seq]
GSE90050 Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells
BioSample SAMN06039813
SRA SRX2359708

Supplementary file Size Download File type/resource
GSM2396549_mTEC_high_rep2.bigWig 53.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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