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Sample GSM1825832 Query DataSets for GSM1825832
Status Public on Jul 17, 2015
Title shRNA_hiF-T_Rep2
Sample type SRA
 
Source name shRNA infected hiF-T cell
Organism Homo sapiens
Characteristics cell type: shRNA infected hiF-T cell
Treatment protocol Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript. http://www.cell.com/cell/pdf/S0092-8674(15)00700-X.pdf
Growth protocol Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript. http://www.cell.com/cell/pdf/S0092-8674(15)00700-X.pdf
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with the QIAamp DNA Mini Kit (QIAGEN)
shRNA sequences were retrieved by PCR from genomic DNA with the direct inclusion of illumina sequencing adapters. Strezoska et al., 2012
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description 91
Data processing Custom perl software was used to analyze the resulting fastq sequencing files. Each read harbors a unique variable sequence that corresponds to one of the hairpin sequences listed in the processed data table. We simply counted the number of reads harboring individual hairpin sequences and then normalized by the total number of reads in each sample.
Supplementary_files_format_and_content: tab-delimited text file: TRC hairpin ID, hairpin sequence, target genes, sequencing depth normalized read counts for each sample
 
Submission date Jul 17, 2015
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 GPL15520
Series (2)
GSE62777 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
GSE71035 Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [shRNA]
Relations
BioSample SAMN03876659
SRA SRX1099992

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

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