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Sample GSM2396553 Query DataSets for GSM2396553
Status Public on Dec 12, 2016
Title cTEC ATAC-Seq 2
Sample type SRA
 
Source name Cortical TECs from WT mice
Organism Mus musculus
Characteristics cell type: Thymic EpCAM+Ly51+
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
E-mail(s) jakub.abramson@weizmann.ac.il
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
Relations
BioSample SAMN06039809
SRA SRX2359712

Supplementary file Size Download File type/resource
GSM2396553_cTEC_rep2.bigWig 61.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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