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Sample GSM2396554 Query DataSets for GSM2396554
Status Public on Dec 12, 2016
Title Irf8 iChIP mTEC Hi
Sample type SRA
Source name Mature mTECs from WT mice
Organism Mus musculus
Characteristics cell type: Thymic EpCAM+Ly51-MHCIIhi
mouse strain: C57BL/6
chip antibody: Irf8 (Bethyl A303-BL12058)
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 crosslinked and FACS sorted into MACS buffer and Chromatin was analysed using iChIP (Lara-Aatiaso et al.) with our new modification iChIP-IVT
protocol developed by (Lara-Astiaso et al.)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing bcl2fastq/
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108). In case of paired end samples if single end protocol was used a short read in R2 was used as a UMI
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
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)
GSE90049 Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells [ChIP-Seq]
GSE90050 Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells
BioSample SAMN06039816
SRA SRX2359705

Supplementary file Size Download File type/resource
GSM2396554_mTEChigh-Irf8.bigWig 48.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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