|
| Status |
Public on Jan 29, 2014 |
| Title |
13271-100mers-GM12878-220_pool_split_4 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
labexpid: 13271
cell line: GM12878
|
| Growth protocol |
http://genome.ucsc.edu/ENCODE/protocols/cell/human/GM12878_protocol.pdf
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Reads of length 100 bp were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequence. Reads were mapped using TopHat 1.4.1 and the GENCODE V13 annotation (using the "--GTF" option in TopHat). Quantification was carried out using Cufflinks 2.0.2
|
| |
|
| Submission date |
Dec 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Diane E Trout |
| Organization name |
California Institute of Technology
|
| Department |
Biology
|
| Lab |
Wold
|
| Street address |
1200 E California Blvd M/C 156-29
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN02487057 |
| SRA |
SRX403415 |
