|
| Status |
Public on Jan 28, 2019 |
| Title |
AP2Cd7On_2 |
| Sample type |
SRA |
| |
|
| Source name |
early surface ectoderm differentiation from hESC
|
| Organism |
Homo sapiens |
| Characteristics |
originating cell line: H9
cell type: surface ectoderm progenitor cells
genotype/variation: TetO-TFAP2C
treatment and stage: Dox+ for 7 days
|
| Growth protocol |
In vitro differentiation of TetO-TFAP2C H9 hESCs: To study the function of TFAP2C in surface ectoderm differentiation, TetO-TFAP2C H9 hESCs were induced with 2 mg/ml Doxycycline (Dox) in E6 medium without RA/BMP4 for 7 days. The resulting cells were imaged and collected for subsequent analysis. To study long term epidermal differentiation ability, TetO-TFAP2C H9 hESCs were first induced into surface ectodermal cells by activation of TFAP2C expression with Dox in E6 medium for 7 days; and then were transitioned to DKSFM with Dox for 14 days and then maintained in DKSFM only until keratinocyte colony was formed. The differentiated keratinocytes were passed and maintained onto collagen coated plates (CELLstar) in DKSFM, and collected for additional analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.
Peaks were called using the HOTSPOT algorithm.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig file
|
| |
|
| Submission date |
Dec 18, 2017 |
| Last update date |
Jan 28, 2019 |
| Contact name |
Anthony Oro |
| E-mail(s) |
oro@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Oro
|
| Street address |
269 Campus Drive, CCSR 2145c
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE108248 |
Epigenome regulation during epidermal lineage commitment [ATAC-seq, RNA-seq] |
| GSE122385 |
Epigenome regulation during epidermal lineage commitment |
|
| Relations |
| BioSample |
SAMN08200557 |
| SRA |
SRX3481053 |
