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Sample GSM6704267 Query DataSets for GSM6704267
Status Public on Nov 02, 2022
Title Gata3-ChIPseq_2
Sample type SRA
 
Source name Splenic TH2 cell subsets expanded in vitro
Organism Mus musculus
Characteristics cell type: Splenic TH2 cell subsets expanded in vitro
chip antibody: anti-GATA3 ((D13C9)
Extracted molecule genomic DNA
Extraction protocol Chromatin extracts from in vitro expanded ILC2 (10 million) were prepared using truChIP Chromatin Shearing kit (Covaris), with 5 min of crosslink and optimized shearing conditions (peak power 75, duty factor 10.0, cycles/burst 200, duration 300 sec) to obtain fragments of ~500bp
Chromatin-antibody-bead complexes were then subjected to tagmentation, followed by DNA elution, and libraries amplification and purification, as described previously (Schmidl et al., 2015)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing Pooled libraries were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequenced reads were aligned to the mouse genome (GRCm38) using Bowtie2 (v2.3.5.1) with default parameters
reads that could not be uniquely mapped were removed from further analysis
Peak calling analysis was performed using Macs2 (v2.1.2)
Supplementary files format and content: GRCm38
Supplementary files format and content: macs2 output files with peak calling data
 
Submission date Nov 01, 2022
Last update date Nov 02, 2022
Contact name Alastair Crisp
Organization name MRC Laboratory of Molecular Biology
Street address Francis Crick Avenue
City Cambridge
ZIP/Postal code CB2 0QH
Country United Kingdom
 
Platform ID GPL21103
Series (2)
GSE179210 Genome-wide CRISPR screen reveals a key role for integrin avb3 in TH2 cell polarisation.
GSE217054 An avb3 integrin checkpoint is critical for efficient TH2 cytokine polarisation and potentiating antigen-specific immunity [ChIP-seq]
Relations
BioSample SAMN31561970
SRA SRX18113531

Supplementary file Size Download File type/resource
GSM6704267_ChIPseq_13_CD4cre_GATA3_TH2_702503.filtered.sorted.dedup.bed.gz 373.6 Mb (ftp)(http) BED
GSM6704267_ChIPseq_13_CD4cre_GATA3_TH2_702503.peaks_peaks.xlsx 1.5 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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