|
Status |
Public on May 14, 2014 |
Title |
ABRF-PGM-MSK-B-1 |
Sample type |
SRA |
|
|
Source name |
ABRF-PGM-MSK-B
|
Organism |
Homo sapiens |
Characteristics |
tissue: Brain reference rna: FirstChoice® Human Brain Reference Total RNA reference rna cat. #: #6050 reference rna lot #: 105P055201A
|
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 |
Pure Human Brain Reference RNA Sample from Ambion, 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 |
GPL17301 |
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 |
SAMN02205245 |
SRA |
SRX307026 |