|
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
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|
|
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 |