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| Status |
Public on Jan 28, 2019 |
| Title |
ipsKC_2: iPSC_Differentiation_mature keratinocytes(KC) (ATAC-Seq) |
| Sample type |
SRA |
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| Source name |
mature keratinocyte from iPSC-epidermal differentiation
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| Organism |
Homo sapiens |
| Characteristics |
cell type: mature keratinocyte differentiated from iPSC
genotype: Differentiation from wild type iPSC
Stage: mature keratinocyte from terminal differentiation
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| Growth protocol |
The iPSC line was derived by sendai virus vector-mediated reprogramming in human fibroblast from Invitrogen (Macarthur et al., Stem Cells Int 2012, 564612.). The cells were differentiated into keratinocyte using a protocol revised from Sebastiano et al. 2014 (Science translational medicine 6, 264ra163). Briefly, the iPSCs were first formed into embryo bodies, using AggreWell 400 plates and AggreWell medium (STEMCELL Technologies) supplemented with 1mg/ml RA and 10 mM ROCK inhibitor (STEMCELL Technologies) for 24 hours. Embryoid bodies were collected and cultured in suspension for 2 days and then plated onto gelatin-coated dishes in FAD medium (Itoh et. al. 2011, Proc. Natl. Acad. Sci. U.S.A. 108, 8797–8802) for 4 days and then in N2 medium (Metallo et. al. 2008, Stem Cells 26(2):372-80) for 3 days. During this 7-day differentiation, the media were supplemented with RA (1 mg/ml) and human recombinant BMP4 (25 ng/ml). The medium was then changed to either N2 or DKSFM (Life Technologies), and the cells underwent selection and expansion for 2 months. The resulting keratinocyte colonies were passed onto Corning PureCoat™ ECM Mimetic 6-well Collagen I Peptide Plate (Corning) and expanded in DKSFM medium.
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| 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 by following the published ATAC-seq protocols (NHK samples: Buenrostro et al., 2013, Nat Methods 10, 1213-1218; iPSC samples: Corces et. al. Nat Methods 14, 959-962.) using a modified version of the Illumina Nextera DNA Sample prep kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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: bigwig, bed
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| Submission date |
Oct 23, 2018 |
| Last update date |
Jan 28, 2019 |
| Contact name |
Anthony Oro |
| E-mail(s) |
oro@stanford.edu
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| Organization name |
Stanford University
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| Department |
Dermatology
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| Lab |
Oro
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| Street address |
269 Campus Drive, CCSR 2145c
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE108248 |
Epigenome regulation during epidermal lineage commitment [ATAC-seq, RNA-seq] |
| GSE122385 |
Epigenome regulation during epidermal lineage commitment |
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| Relations |
| BioSample |
SAMN10282706 |
| SRA |
SRX4925285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3444163_ipsKC-rep2.norm.bw |
266.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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