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| Status |
Public on Jun 06, 2019 |
| Title |
H3K4me3_CD8SP-EomesTG |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
cell type: Thymocytes
Stage: CD8SP EomesTG
strain: BALB/c
chip antibody: H3K4me3 (Merck, 17-614)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD8SP from pooled thymus were isolated and crosslinked with formaldehyde 1% for 10min at room temperature before staining. Crosslinking was stopped with 0.125 M glycine. Cells then were washed twice by ice-cold PBS and sorted. Each sorted cell-population was resuspended with ChIP-lysis buffer (10mM Tris pH8, 140mM NaCl, 1mM EDTA, 1% Triton x-100, 0.5% SDS, 0.1% Na-Deoxycholate) for 10min on ice supplemented with PIC (proteinase inhibitors cocktail) and sheared to have a fragments size range between 200-600bp. After clearance by centrifugation at 4°C, sheared chromatin used for each immunoprecipitation of histone marks or transcription factors.
For histones marks, library preparation was performed using TruSeq ChIP library Preparation kit using 3-6ng of ChIPed DNA. For transcription factors, the library preparation was done with MicroPlex Library Preparation kit with 0.5ng od ChIPed DNA
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Peak calling was performed with MACS2 callpeak, using standard parameters, except for : H3K4me3, H3K4me1, H3K27ac for which we used a q-value threshold=0.01 ; Eomes for which we used a p-value threshold=0.001 ; Runx3 for which we used a p-value threshold=0.01
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal
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| Submission date |
Jan 10, 2019 |
| Last update date |
Jun 08, 2019 |
| Contact name |
Stanislas Goriely |
| E-mail(s) |
stgoriel@ulb.ac.be
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| Phone |
+3226509586
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| Organization name |
Université Libre de Bruxelles
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| Lab |
IMI
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| Street address |
Rue Adrienne Bolland 8
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| City |
Gosselies |
| ZIP/Postal code |
B-6041 |
| Country |
Belgium |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE124912 |
EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits (ChIP-Seq) |
| GSE124914 |
EOMES-dependent epigenetic reprogramming during CD8 T cell development leads to acquisition of memory traits |
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| Relations |
| BioSample |
SAMN10721902 |
| SRA |
SRX5236585 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3559318_H3K4me3_CD8SP-EomesTG_peaks.broadPeak.gz |
329.7 Kb |
(ftp)(http) |
BROADPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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