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Sample GSM1548432 Query DataSets for GSM1548432
Status Public on Jul 16, 2015
Title 14dd_DOX_plus_SSEA3_neg_Rep1
Sample type SRA
 
Source name reprogramming intermediates of hiF-T cells
Organism Homo sapiens
Characteristics surface antigen enrichment: SSEA3-
treatment: DOX days 0-14
Treatment protocol Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript.
Growth protocol hiF-T fibroblasts were expanded on gelatin-coated dishes in hiF medium composed of basal medium (DMEM-F12 Glutamax, 1X MEM-NEAA, 1X beta-ME, 0.2X P/S) supplemented with 10% ES-FBS and 16 ng/ml FGFbasic. HUES64 and hIPSC-T were expanded in feeder-free conditions using Essential 8 (E8) medium. The attachment matrix for PSC was either Matrigel (MTG) or Vitronectin (VTN) with no significant differences.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with the QIAamp DNA Mini Kit (QIAGEN)
Reduced Representation Bisulfite Sequencing (RRBS) Illumina libraries were prepared according to a standard gel-free pipeline(Boyle et al., 2012) starting from 10ng of genomic DNA.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
Description 123
Data processing Reads were aligned on build hg19 of the human genome with MAQ(Li, Ruan, & Durbin, 2008) in bisulfite alignment mode.
The methylation level at single CpGs was calculated as the fraction of reads with unconverted cytosines over the total number of reads at that position. The methylation level for promoters was calculated as the mean of the methylation levels of the CpGs within the promoter weighted by the number of reads covering each CpG.
Differentially methylated promoters were defined as those exhibiting a methylation difference of 0.2 or greater between any two conditions and used for standard k-means clustering.
Genome_build: hg19
Supplementary_files_format_and_content: chrom, chromstart, chromend, 'number methylated cytosines/number total cytosines', score, strand
 
Submission date Nov 18, 2014
Last update date May 15, 2019
Contact name Shannan J Ho Sui
E-mail(s) shosui@hsph.harvard.edu
Organization name Harvard T.H. han Scholol of Public Health
Department Biostatistics
Street address 655 Huntington Ave, Building 2, Rm 437A
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL16791
Series (2)
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
GSE63419 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [RRBS]
Relations
BioSample SAMN03199520
SRA SRX763124

Supplementary file Size Download File type/resource
GSM1548432_14dd_dox_SSEA3Neg.bed.gz 22.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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