|
| Status |
Public on May 14, 2014 |
| Title |
ABRF-PRO-NCI-D-1 |
| Sample type |
SRA |
| |
|
| Source name |
ABRF-PRO-NCI-D
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pooled Tumor
reference rna: Agilent Universal Human Reference RNA
reference rna cat. #: #740000
reference rna 2: FirstChoice® Human Brain Reference Total RNA
reference rna 2 cat. #: #6050
reference rna 2 lot #: 105P055201A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
NA
Poly A; Libraries were prepared from 1 ug of MAQC A, B, C, and D RNA containing ERCC controls using either polyA enrichment (as described for PGM) or ribo-depletion using Ribo-Zero Magnetic Kit (MRZH11124, Epicentre). After enrichment, 8-9 ng of polyA mRNA or 150 ng of ribo-depleted RNA was used for ligation reactions. The size selection step was adjusted to 220 bp using a standard Pippin Prep protocol, generating library competent molecules with a template insert size of approximately 150 bp. The Ion Total RNA-seq Kit v2 (4476286 Rev D, Life Technologies) was used to prepare the MAQC libraries for sequencing. The resulting material was quantified using the Agilent Bioanalyzer High Sensitivity Chip.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Pooled RNA Sample of 1/4 ABRF Sample A and 3/4 ABRF Sample B
|
| Data processing |
STAR Aligner v2.3.0 long
Read counts were calculated using the Rmake pipeline (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/) with Gencode v12 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Counts table
|
| |
|
| Submission date |
Jun 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher E Mason |
| E-mail(s) |
chm2042@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Physiology and Biophysics
|
| Lab |
Christopher Mason Lab
|
| Street address |
1305 York Ave
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE46876 |
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq. |
| GSE48034 |
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Ion Torrent Proton] |
|
| Relations |
| BioSample |
SAMN02205212 |
| SRA |
SRX307053 |
