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Sample GSM1166036 Query DataSets for GSM1166036
Status Public on May 14, 2014
Title ABRF-454-UI-B-1
Sample type SRA
 
Source name ABRF-454-UI-B
Organism Homo sapiens
Characteristics tissue: Brain
reference rna: FirstChoice® Human Brain Reference Total RNA, Lot #105P055201A, Cat #6050
reference rna cat. #: #6050
reference rna lot #: 105P055201A
Extracted molecule polyA RNA
Extraction protocol NA
Poly A; Library synthesis and sequencing was performed with MAQC A and MAQC B samples at three core laboratory sites. Each site constructed one cDNA library from each of the polyA-enriched RNA samples. Enriched RNA (200 ng) was reduced to 19 µl in a vacuum centrifuge at 60 oC, followed by library construction using the Roche cDNA Rapid Library Preparation Method Manual XL+ (May 2011) with the following modifications: (1) RNA Fragmentation Reagent kit (AM#8740, Life Technologies) was used in place of the RNA Fragmentation Solution; (2) all magnetic particle concentrator (MPC) pelleting steps were held for 2 minutes; (3) Roche rapid library multiplex identifier (RL-MIDs) adaptors were used for the adaptor ligation step; (4) the final libraries were quantified using a Qubit fluorometer (Life Technologies) and average fragment sizes were determined by analyzing 1 µl of the libraries on the Agilent Bioanalyzer 2100 using a High-Sensitivity DNA LabChip; and (5) the library concentrations were determined using the average fragment size from the Bioanalyzer analysis. Final samples were diluted to 1x108 molecules/µl in Tris-HCl pH 8 buffer with 0.001% Tween-20.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model 454 GS FLX Titanium
 
Description Pure Human Brain Reference RNA Sample from Ambion, Inc.
Data processing STAR Aligner v2.3.0 Regular
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 GPL14603
Series (2)
GSE46876 The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq.
GSE48032 The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [454 GS FLX Titanium]
Relations
BioSample SAMN02205244
SRA SRX307019

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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