|
| Status |
Public on Jul 01, 2016 |
| Title |
crypts-WT-H3K27ac_Sample#2 |
| Sample type |
SRA |
| |
|
| Source name |
crypts-WT-H3K27ac
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
age: 6 weeks
treated with: beta-naphthoflavone for 6 weeks
cell type: small intestinal crypts
chip antibody: anti-H3K27Ac; Abcam, cat.# ab4729, lot #254707-01
|
| Treatment protocol |
After treating 6 weeks old mice with beta-naphthoflavone for 6 weeks, crypts were isolated from the small intestine by scraping off villi and EDTA chelation, after which they were washed. Crypts were then lysed in TRIzol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein A-G magnetic beads (Dynabeads, Thermo Fisher Scientific) were used to pull down immunocomplexes.
Illumina compatible libraries were prepared using Diagenode's MicroPlex v2 Library Preparation™ kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
description; output; software name version; parameters
base calling; $fastq; bcl2fastq2 2.17.1.14; --mask-short-adapter-reads 0 --runfolder-dir $runfolder --output-dir $outputdir --interop-dir $outputdir/InterOp --sample-sheet $samplesheet
alignment; pipe; bwa 0.7.10; mem -t 14 Mus_musculus.GRCm38.dna.primary_assembly.fa $fastq
single end sam; pipe; bwa 0.7.10; samse -r $readgroup Mus_musculus.GRCm38.dna.primary_assembly.fa - $fastq
sam to bam; pipe; samtools 0.1.19; view -Sbu -
sort; $bam; samtools 0.1.19; sort -m 3000000000 - $basename
view; pipe; samtools 0.1.19; view -bu $bam
genomecov; pipe; bedtools 2-2.20.1; genomecov -bg -ibam -
fix for downstream analysis; $bedGraph; GNU sed 4.1.5; -n -r "/^([0-9]+|[XY]|MT)/{s/^MT/M/;s/^/chr/;p}" > $bedGraph
fetchChromSizes; mm10.chrom.sizes; UCSC genome browser 'kent' bioinformatic utilities FetchChromSizes v1.2; mm10 > mm10.chrom.sizes
bedGraphToBigWig; $bigWig; bedGraphToBigWig v4; $bedGraph mm10.chrom.sizes
Genome_build: Ensembl GRCm38, primary assembly
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
May 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martijn Koppens |
| E-mail(s) |
[email protected]
|
| Organization name |
NKI-AVL
|
| Department |
Molecular Genetics
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE81577 |
Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [ChIP-seq] |
| GSE81578 |
Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts |
|
| Relations |
| BioSample |
SAMN05007711 |
| SRA |
SRX1771659 |
