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Sample GSM5701996 Query DataSets for GSM5701996
Status Public on Nov 26, 2021
Title H3K27Ac.HiChIP.WTGFP#1
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics cell type: Treg
strain: C57BL/6
tissue: spleen
genotype: wt
epitope: H3K27Ac
chip antibody: H3K27Ac (Abcam ab4729)
Treatment protocol HiChIP was optimized and performed in biological replicates for all conditions. Briefly, 5 x 10^6 Tregs were crosslinked for each FoxP3 HiChIP replicate, 2 x 10^6 million cells for H3K27Ac and Yy1 HiChIPs respectively. Additionally, 5 x 10^6 million Tregs and Tconvs were crosslinked to include a negative IgG isotype control HiChIP samples. Low input H3K27Ac HiChIP was performed on 2 x 10^5 crosslinked WT-GFP and KO-GFP Tregs respectively. DNA sonication of fragments to 200-600 bp following MboI digestion was performed using the Covaris M220. Sonicated DNA was pre-cleared using Protein A magnetic beads followed by overnight chromatin immunoprecipitations with 3 ug H3K27Ac (Abcam ab4729), 5 ug FoxP3 (Abcam ab150743), 3 ug Yy1 (Abcam ab109237) and 5 ug rabbit IgG (Cell Signaling 2729S), in a final concentration 0.07% SDS.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared using Illumina Nextera DNA library preparation kit, size-selected using low-melt gel extraction and paired-end sequenced using NextSeq 500 Illumina platform.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: HiChIP
HiChIP paired-end reads were aligned to the mm10 genome using the HiC-Pro pipeline. Default settings were used for removal of duplicated reads, assignment to MboI restriction fragments and filtering for valid interactions.
Non-uniquely mapped reads were discarded.
HiChIP HiC-Pro valid pairs of replicates and processed as .hic files using the hicpro2juicebox function.
Genome_build: mm10
Supplementary_files_format_and_content: .hic contact matrix
 
Submission date Nov 23, 2021
Last update date Nov 26, 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)
GSE189442 FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression [HiChIP]
GSE190057 FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression
Relations
BioSample SAMN23413023
SRA SRX13211197

Supplementary file Size Download File type/resource
GSM5701996_H3K27Ac_WTGFP_R1.hic 423.2 Mb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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