|
Status |
Public on Oct 13, 2020 |
Title |
H3 ChIP centroblast Cγ1-cre 1 |
Sample type |
SRA |
|
|
Source name |
germinal center centrocytes from spleen
|
Organism |
Mus musculus |
Characteristics |
cell type: germinal center centrocytes from spleen genotype: Cgamma1-cre+/- strain: C57BL/6J age: 3-4 months littermate: mixed litters chip antibody: H3
|
Treatment protocol |
Mice were immunized with sheep red blood cells (SRBC) 8 days before extraction of spleens
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Mint-ChIP was performed using H3K27Ac antibody (Cat#39133, lot 31814008) from Active Motif following the protocol from the Berstein lab. Briefly, 50,000 FACS sorted centrocytes, in triplicates, were processed with MNase to fragment native chromatin. Barcoded adapters were ligated to every sample and samples were multiplexed for chromatin immunoprecipitation (ChIP). After ChIP, material was linearly amplified by RNA in vitro transcription in the presence of RNAse inhibitor RNAseOUT (Invitrogen 10777019). Fragments were reverse-transcribed and amplified as a library
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
cells sorted: DAPI-, B220+, FAS+, CD38-, CXCR4-, CD86+
|
Data processing |
The split reads were aligned using bwa mem to mm10. Duplicate marking and removal was done by Picard. Peaking calling were preformed using two methods. The H3K27Ac peaks were called against H3 total as input uisng Homer package with following command: findPeaks <K27Tag> -style histone 1000 -C 0 -o auto -i <H3_Tag>. A consensus peaks were called using Genrich packages. All H3K27ac aligned files is provided as sample and H3 aligned files were provided as input to creat a concensus peak file. Genome_build: mm10 Supplementary_files_format_and_content: Normalized and scaled bigwigs and narrowpeak file
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|
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Submission date |
Mar 10, 2020 |
Last update date |
Oct 13, 2020 |
Contact name |
Cem Meydan |
Organization name |
Weill Cornell Medical College
|
Department |
Physiology & Biophysics
|
Lab |
Melnick Lab & Mason Lab
|
Street address |
1305 York
|
City |
New York |
State/province |
New York |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE143852 |
Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation |
GSE146753 |
Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation (Mint-ChIP) |
|
Relations |
BioSample |
SAMN14349583 |
SRA |
SRX7889693 |