|
| Status |
Public on Jul 17, 2015 |
| Title |
15dd_DOX_shRNA_plus_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
reprogramming of shRNA infected hiF-T cell
|
| Organism |
Homo sapiens |
| Characteristics |
surface antigen enrichment: TRA-1-60+
treatment: DOX days 0-15
cell type: reprogramming of 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 |
104
|
| 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 |
SAMN03876660 |
| SRA |
SRX1099993 |
