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Sample GSM4405420 Query DataSets for GSM4405420
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
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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