|
| Status |
Public on Jan 28, 2019 |
| Title |
D21b |
| Sample type |
SRA |
| |
|
| Source name |
progenitor cells from hESC-epidermal differentiation
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Epidermal differentitation at Day 21
genotype: Differentiation from wild type hESC
treatment and stage: Differentiation at Day 21
|
| Growth protocol |
In vitro differentiation of hESC into keratinocyte :H9 hESCs were passed on to Matrigel coated plate and maintained in Essential 8 media. To induce differentiation into keratinocyte, the cells were first fed with “differentiation medium 1” containing 5ng/ml BMP4 and 1 μM RA in Essential 6 media (Life Technologies) for seven days; thus forming surface ectodermal progenitor cells. After seven days, the medium was changed to “differentiation medium 2”, i.e. Defined Keratinocyte Serum Free Medium (DKSFM) with growth supplements containing EGF and FGF (Life Technologies), and the cells underwent selection and expansion for 2 months to get maturation into keratinocyte. The resulting keratinocyte colonies were passed onto Corning PureCoat™ ECM Mimetic 6-well Collagen I Peptide Plate (Corning) and expanded in DKSFM medium.
|
| 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 |
hESC_lineH9_Differentiation_D21
|
| Data processing |
Alignment was called using tophat. FPKM values were called using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file. FPKM values
|
| |
|
| Submission date |
Nov 09, 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) |
| GSE122383 |
Epigenome regulation during epidermal lineage commitment [RNA-seq] |
| GSE122385 |
Epigenome regulation during epidermal lineage commitment |
|
| Relations |
| BioSample |
SAMN10406585 |
| SRA |
SRX4999877 |
