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Sample GSM5478659 Query DataSets for GSM5478659
Status Public on Jul 30, 2021
Title Aire_KO_CTCF_Rep_2 [ChIP-seq]
Sample type SRA
 
Source name Thymus
Organism Mus musculus
Characteristics strain background: C57Bl/6
genotype: Aire-/-
tissue: Thymus
cell type: mTECs
Extracted molecule genomic DNA
Extraction protocol Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as mTECs.
IPed chromatin was eluted from the Protein G beads, treated with DNase-free RNase and proteinase K followed by reverse cross-linking. DNA from reverse cross-linked material was purified with SPRI beads; and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification were performed to prepare the ChIP-seq library for each sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description LIB027574_CHS00092745_S12
Data processing Low-quality reads were trimmed using sickle1.2, and short reads (50bp, single end) were aligned to the mouse reference genome (mm10) using bowtie aligner version 2.2.4.
Unmapped reads and reads with multiple alignments were removed with samtools (v1.1) followed by de-duplication with picard (v1.130) MarkDuplicates command.
Peaks in ChIPseq data were identified with HOMER (v4.6) package’s findPeaks command with the ‘histone’ parameter for SMC1 and MED1, while ‘factor’ parameter for CTCF ChIP-seq.
To visualize individual ChIP-seq data on Integrative Genomics Viewer (IGV), bam output files from picard were converted into normalized bigwig format using the bamCoverage function in deepTools (v1.6).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
 
Submission date Jul 27, 2021
Last update date Jul 30, 2021
Contact name CBDM Lab
E-mail(s) cbdm@hms.harvard.edu
Phone 617-432-7747
Organization name Harvard Medical School
Department Microbiology and Immunobiology
Lab CBDM
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL19057
Series (2)
GSE180934 Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [ChIP-seq]
GSE180937 Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers
Relations
BioSample SAMN20436979
SRA SRX11570194

Supplementary file Size Download File type/resource
GSM5478659_Aire_KO_CTCF_Rep_2.mapped_1align.sorted.uniq.RPKM.bigWig 21.9 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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