|
Status |
Public on May 14, 2014 |
Title |
ABRF-PRO-NCI-A-1 |
Sample type |
SRA |
|
|
Source name |
ABRF-PRO-NCI-A
|
Organism |
Homo sapiens |
Characteristics |
tissue: Pooled Tumor reference rna: Agilent Universal Human Reference RNA reference rna cat. #: #740000
|
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 |
Pure Human Reference RNA Sample from Agilent, Inc.
|
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 |
SAMN02205205 |
SRA |
SRX307050 |