|
| Status |
Public on Jan 28, 2019 |
| Title |
H9_2 [ATAC-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
undifferentiated human embryonic stem cell line H9
|
| Organism |
Homo sapiens |
| Characteristics |
originating cell line: H9
cell type: hESC line H9, differentiation at Day 0
treatment and stage: Differentiation at Day 0
|
| 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 |
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 |
| |
|
| Description |
hESC_lineH9_Differentiation_D0
Differentiation from wild type hESC
genomic DNA from open chromatin region
H9.fdr0.01.pks.bed
|
| Data processing |
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard.
peaks called using HOTSPOT
Genome_build: hg19
Supplementary_files_format_and_content: bed file, peaks
|
| |
|
| Submission date |
May 18, 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 |
SAMN09225063 |
| SRA |
SRX4099759 |
