|
| Status |
Public on May 14, 2014 |
| Title |
ABRF-PGM-MSK-F-2 |
| Sample type |
SRA |
| |
|
| Source name |
ABRF-PGM-MSK-F
|
| Organism |
synthetic construct |
| Characteristics |
tissue: Synthetic
reference rna: Reference ERCC 2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
NA
Poly A; Whole transcriptome library preparation was performed using 5-10 ng of fragmented enriched polyA RNA according to the manufacturer’s protocol (Ion Total RNA-Seq Kit V2 protocol #4476286B Life Technologies). Size selection of a 315 bp product was performed using a standard Pippin prep protocol (Sage Science) followed by purification with AMPure beads (Beckman-Coulter Genomics). The synthetic ERCC 1 and ERCC 2 control RNA library construction was performed directly from 30 ng of the non-polyA enriched sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
Reference ERCC spike-ins
|
| 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 |
GPL17302 |
| Series (2) |
| GSE46876 |
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq. |
| GSE48033 |
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Ion Torrent PGM] |
|
| Relations |
| BioSample |
SAMN02205249 |
| SRA |
SRX307031 |
