|
| Status |
Public on Jul 16, 2015 |
| Title |
2dd_DOX_plus_Rep2_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
reprogramming intermediates of hiF-T cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: DOX days 0-2
|
| 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 |
| 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) |
| 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 |
|
| Relations |
| BioSample |
SAMN03145526 |
| SRA |
SRX745176 |
