|
| Status |
Public on Jul 17, 2015 |
| Title |
shRNA_hiF-T_Rep1 |
| 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 |
90
|
| 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 Ho Sui |
| E-mail(s) |
shosui@hsph.harvard.edu
|
| Organization name |
Harvard T.H. Chan School of Public Health
|
| Department |
Biostatistics
|
| Street address |
401 Park Drive, Level 3 East
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| 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 |
SAMN03876658 |
| SRA |
SRX1099991 |
