|
| Status |
Public on Jul 27, 2021 |
| Title |
D30_IMQ_H3K4me1_Mint-ChIPseq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
Sex: female
cell type: Epidermal Stem Cells
strain: C57BL/6
genotype: wildtype
facs markers: ITGA6+, ITGB1+, Sca1+, CD34-
treatment: Imiquimod for 6 days
chip antibody: H3K4me1
|
| Treatment protocol |
2-3 postnatal day 60 murine backskin was treated with Imiquimod for 6 consecutive days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.031
NEBNext Ultra II DNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PCR amplified library from genomic DNA
|
| Data processing |
MINT-ChIP reads were processed as shown in van Galen et al (doi::10.1016/j.molcel.2015.11.003) with appropriate modifications made for the T7 barcode adaptor in read2 instead read 1 (van Galen et al). Reads were first demultiplexed by Illumina’s bcl2fastq2 and further demultiplexed using the additional the T7 barcode in read2 (van Galen et al). These demultiplexed reads were aligned to the mm10 genome from the Bsgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0) using Rsubread's align method in paired-end mode with fragments between 1 to 5000 base-pairs considered properly paired (Liao Y et al). Normalized, fragment signal bigWigs were created using the rtracklayer package. For Homer peak calling, reads were filtered as shown in van Galen et al., with the appropriate modifications for the T7 barcode in read2. First reads where both pairs are multi mapping and improperly paired are removed and following this fragment duplicates and read pairs with T7 (read 2) duplicates are filtered (van Galen et al). Homer tag directories were created from the filtered BAM files and peak calls made using the Homer’s findPeaks with parameters (-region , -size 1000, -minDist 2500).
Genome_build: mm10
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Samantha B Larsen |
| Organization name |
NYU School of Medicine
|
| Street address |
435 East 30th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE171596 |
Establishment, Maintenance and Recall of Inflammatory Memory |
|
| Relations |
| BioSample |
SAMN18642147 |
| SRA |
SRX10528538 |
