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Sample GSM1533229 Query DataSets for GSM1533229
Status Public on Jul 16, 2015
Title 20dd_DOX_plus_TRA_plus_Rep2_mRNA
Sample type SRA
Source name reprogramming intermediates of hiF-T cells
Organism Homo sapiens
Characteristics surface antigen enrichment: TRA-1-60+
treatment: DOX days 0-20
Growth protocol Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript.
Extracted molecule total RNA
Extraction protocol Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
RNA-Seq Illumina libraries for mRNA profiling were prepared from 100 ng total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Reads were mapped with TopHat version 2.0.7 and Bowtie version 2.1.0 with default parameters against build hg19 of the human genome, and build 13 of the GENCODE human genome annotation
Samples were quantified with the Cufflinks package version 2.2.0.
Differential expression was performed using Cuffdiff 2.2.0 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Submission date Oct 28, 2014
Last update date May 15, 2019
Contact name Shannan J Ho Sui
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)
GSE62772 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [mRNA-Seq]
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
BioSample SAMN03145543
SRA SRX745190

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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