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| Status |
Public on Jul 30, 2021 |
| Title |
WT_MED1_Rep_2 [ChIP-seq] |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6
genotype: Aire+/+
tissue: Thymus
cell type: mTECs
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
LIB027574_CHS00092737_S4
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| 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
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| Submission date |
Jul 27, 2021 |
| Last update date |
Jul 30, 2021 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
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| Phone |
617-432-7747
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| Organization name |
Harvard Medical School
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| Department |
Microbiology and Immunobiology
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| Lab |
CBDM
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN20436990 |
| SRA |
SRX11570196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5478649_WT_MED1_Rep_2.mapped_1align.sorted.uniq.RPKM.bigWig |
165.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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