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Sample GSM1166063 Query DataSets for GSM1166063
Status Public on May 14, 2014
Title ABRF-PRO-MSK-B-2
Sample type SRA
 
Source name ABRF-PRO-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; 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 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 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 SAMN02205208
SRA SRX307048

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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