|
| 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 |
| E-mail(s) |
brad.hoffman@ubc.ca
|
| 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. |
|
| Relations |
| BioSample |
SAMN20721341 |
| SRA |
SRX11725630 |
