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Sample GSM1166103 Query DataSets for GSM1166103
Status Public on May 14, 2014
Title ABRF-ILMN-RIBO-C-3
Sample type SRA
 
Source name ABRF-ILMN-RIBO-C
Organism Homo sapiens
Characteristics tissue: Pooled tumor
reference rna: Agilent Universal Human Reference RNA
reference rna cat. #: #740000
reference rna 2: FirstChoice® Human Brain Reference Total RNA
reference rna 2 cat. #: #6050
reference rna 2 lot #: 105P055201A
Extracted molecule total RNA
Extraction protocol NA
Ribo-Depleted; Following ribo-depletion, all recovered RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit v2 protocol at the “elute-fragment-prime” step, followed by the standard TruSeq protocol. Completed libraries were evaluated by DNA quantitation and Bioanalyzer analysis, and then submitted to a single core laboratory site for sequencing. Sequencing libraries were constructed with barcodes to allow multiplexing of 12 samples per lane, pooled to target 200 million clusters per channel and 100 million reads per library, and distributed over multiple channels of three flow cells to normalize for lane and run variability. Sequencing was carried out on Illumina HiSeq 2500 instruments using protocols HCS 1.5.15.1 and RTA 1.13.48.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Agilent Universal Human Reference RNA, Catalog #740000 and FirstChoice® Human Brain Reference Total RNA, Lot #105P055201A, Cat #6050
Pooled RNA Sample of 3/4 ABRF Sample A and 1/4 ABRF Sample B
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 GPL16791
Series (2)
GSE46876 The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq.
GSE48035 The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Illumina HiSeq 2500]
Relations
BioSample SAMN02205293
SRA SRX307091

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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