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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 27, 2016 |
| Title |
246G1 |
| Sample type |
SRA |
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| Source name |
induced pluripotent stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: undifferentiated induced pluripotent stem cells
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| Treatment protocol |
Human iPSC/ESCs were culture on mitomycin C-treated SNL feeder cells in Primate ES cell medium (ReproCELL) containing 4 ng/mL recombinant bFGF (Wako) unless mentioned otherwise. One ESC sample (sample name: SAMPLE 28, khES3 with 100 ng/ml bFGF) was cultured with increased concentration of bFGF (100 ng/ml) for 1 week. The human fibroblasts were cultured with Dulbecco's Modified Eagle Medium with 10% fetal bovine serum. The peripheral blood were freshly drawn from a volunteer, and subject to the analysis. The keratinocyte was purchased from ATCC, and cultured with Keratinocyte-SFM (1X), Liquid (Life Technologies).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: The sequencing library preparation including barcoding was conducted using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN). The Illumina libraries were sequenced with the TruSeq SBS kit v3 (Illumina) in 51-cycle Single-End mode of HiSeq 2500 (Illumina).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Methyl-seq: Methyl-seq data were aligned using Bismark(v0.14.1) with Bowtie2 (version 2.2.5) allowing up to 1 mismatches (-N 1). The methylation calls at CpG sites were performed by bismark_methylation_extractor in the Bismark (v0.14.1) software. Methylation calls are deposited in processed data files. We used CpGs represented by at least 10 sequencing reads.
ATAC-seq: Mapping was performed by BWA (version 0.6.2) , allowing up to 2 mismatches, using the reference human genome, NCBI build 37 (hg19) .
ChIP-seq: Mapping was performed by BWA (version 0.6.2) , allowing up to 2 mismatches, using the reference human genome, NCBI build 37 (hg19) .
Genome_build: hg19
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| Submission date |
Nov 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Akira Watanabe |
| E-mail(s) |
a.watanabe@cyberomix.com
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| Organization name |
CyberomiX Inc
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| Street address |
Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
602-8407 |
| Country |
Japan |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE74967 |
Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells |
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| Relations |
| BioSample |
SAMN04263532 |
| SRA |
SRX1430071 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1939269_Sample_MS92_R1.fastq.gz_bismark_bt2_pe.bismark.zero.cov.txt.gz |
46.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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