|
| Status |
Public on Jan 28, 2019 |
| Title |
AP2Cd7Off_2 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
TetO-TFAP2C hESC differentiation at Day7 without Dox
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: early epidemal differentiated cell
genotype: TetO-TFAP2C
treatment and stage: early differentiaiton without 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 |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNeasy Plus (Qiagen) from the samples reported in this research. Ribosomal RNA was removed from each RNA extraction using Ribo-Zero Gold rRNA Removal kit (Illumina).
The RNA-seq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
total RNA with ribosomal RNA depleted
RNA-seq
|
| Data processing |
Alignment was performed using tophat. RPKM values were called using cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
May 11, 2018 |
| 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 |
SAMN09199019 |
| SRA |
SRX4075321 |
