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Sample GSM5514713 Query DataSets for GSM5514713
Status Public on Aug 11, 2022
Title Day 45 H3K4me3 ChIP-seq WT 2
Sample type SRA
Source name Mouse beta cells with S2 cell spike-in
Organisms Drosophila melanogaster; Mus musculus
Characteristics strain: PdxCreER mTmG
cell type: Mouse beta cells with S2 cell spike-in
genotype/variation: CTRL
chip antibody: H3K4me3 (Abcam, ab1012, lot GR158530-14)
Extracted molecule genomic DNA
Extraction protocol FACS-enriched beta cells were pooled with a 50% spike-in of drosophila S2 cells. Chromatin was fragmented with MNase and histone-DNA complexes were extracted using antibodies
ChIP libraries were prepared using NEBNext II Ultra DNA library prep kit for Illumina (E7645)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Illumina NextSeq Control Software v2.2.0.4 for base calling
Reads aligned to GRCm38/mm10 using Bowtie2 v2.3.4.1 with options ‘--very-sensitive --no-unal --no-discordant’
Multi-mapped reads, reads with mapping quality MAPQ < 20, and suspected PCR-duplicates were discarded using Samtools
bw files were generated using BEDtools, adjusted using the Drosphila read fraction, and bedGraphToBigWig
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwigs showing genome enrichment scores, adjusted by drosophila cell spike-in read fraction
Submission date Aug 12, 2021
Last update date Aug 11, 2022
Contact name Brad Hoffman
Organization name University of British Columbia
Street address Room A4-151 950 W28 Ave
City Vancouver
State/province BC
ZIP/Postal code V5Z 2B3
Country Canada
Platform ID GPL25537
Series (2)
GSE181949 H3K4 Methylation in β-cells prevents transcriptional downregulation and variance associated with type 2 diabetes [ChIP-seq]
GSE181951 H3K4 Methylation in β-cells prevents transcriptional downregulation and variance associated with type 2 diabetes.
BioSample SAMN20721341
SRA SRX11725630

Supplementary file Size Download File type/resource 404.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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