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| Status |
Public on Nov 12, 2015 |
| Title |
BAF_ChIP_63i |
| Sample type |
SRA |
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| Source name |
human keratinoctyes with p63 siRNA
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary human neonatal keratinocytes
knockdown: p63
chip antibody: J1 (gift from the Crabtree Lab (Khavari et al. Nature 1993))
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| Treatment protocol |
To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 1nM of siRNA for each target were nucleofected (Lonza to keratinocytes)
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| Growth protocol |
neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq, around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition. For ChIP-seq, a mininum of 2 million cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipiated with antibodies recognizing Brg1/Brm (J1), H3K27Ac, H3K27me3, H3K4me1, p300, pol II, and p63.
For ATAC-seq, sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit. For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina were use for library construction
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ChIP-seq in differentiated keratinocytes with p63 knockdown
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| Data processing |
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.ATACseq peaks were called using the MACS2 algorithm,ChIPseq peaks were called using MACS14.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in standard bed/whole bed format
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| Submission date |
Mar 27, 2015 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Douglas Porter |
| Organization name |
Stanford
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| Department |
Dermatology
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| Lab |
Khavari
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE67382 |
BAF controls genome accessibility |
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| Relations |
| BioSample |
SAMN03450219 |
| SRA |
SRX971583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1645712_J1_63i_total_peaks.bed.gz |
78.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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