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| Status |
Public on Dec 03, 2019 |
| Title |
Mi2_ATAC_rep1 |
| Sample type |
SRA |
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| Source name |
adult epidermis
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell types: keratinocytes
genotype: Chd4-/-
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dorsal epidermis was separated from the dermis by digestion with 0.25% trypsin overnight at 4C to obtain a single cell suspension. ITGA6+, CD45-, CD34- cells were sorted with FACS Aria.
Nextera DNA sample prep kit (Illumina)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls were performed using bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) or hg19 (human genome) assembly using the genome mappers Bowtie2 for ATACseq and STAR for RNAseq and ChIPseq.
For RNA-seq, read normalization, RPKM and differential gene expression, were performed using the HOMER scripts analyzeRepeats.pl and getDiffExpression.pl with implementation of DESeq2 through R.
Peak calling for ATAC-seq was perfomed using MACS2 call peaks with --keep-dup all --nomodel --shift 37 --extsize 73.
Peak calling for ChIP-seq was performed using the Homer findPeaks algorithm.
Genome_build: mm10, hg19
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| Submission date |
Oct 31, 2019 |
| Last update date |
Dec 03, 2019 |
| Contact name |
Katia Georgopoulos |
| E-mail(s) |
[email protected]
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| Phone |
617-7264445
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| Organization name |
Harvard Medical School
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| Department |
CBRC
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| Lab |
Georgopoulos
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| Street address |
1st and 13th St
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| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE139685 |
Functional interactions between Mi-2β and AP1 complexes control response and recovery from barrier disruption |
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| Relations |
| BioSample |
SAMN13173355 |
| SRA |
SRX7082258 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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