|
Status |
Public on Sep 28, 2015 |
Title |
pure reference RNA (AGO) CT |
Sample type |
SRA |
|
|
Source name |
Original Agilent Human Universal Reference RNA
|
Organism |
Homo sapiens |
Characteristics |
cell type: mixture of multiple cell lines
|
Treatment protocol |
None
|
Growth protocol |
Samples used in the study are commercially available RNAs derived from mixture of multiple cell lines and RNAs extracted from patient bone marrow specimens
|
Extracted molecule |
total RNA |
Extraction protocol |
Samples used in the study are commercially available RNAs derived from mixture of multiple cell lines and RNAs extracted from patient bone marrow specimens The library preparation protocol was oligo-d(T)-priming based Clontech SMARTer Ultra Low RNA Kit for Illumina® Sequencing from Clontech (a Takara Bio Company, hereafter labeled as “ClonTech”). A starting amount of 10 ng RNAs was processed in ClonTech assays, amplified cDNA was sheared using a Covaris E210 instrument. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample. In pooling of multiple libraries for running on a single lane, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 5 RNA libraries. Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Illumina Casava1.8+ software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensembl release version 72 (R72) of human whole genome and transcriptome with TopHat version 2.0.8 using Bowtie2 version 2.1.0. Both exon- and gene-level count data were generated by HTSeq (Anders et al. 2015) for differential expression analysis, and the raw count data at exon- and gene-levels were normalized by library size with a R package “edgeR” from Bioconductor (Robinson et al. 2010; Robinson and Oshlack 2010). As a result, the count per million (cpm) values were produced for calculation of fold-changes. Genome_build: Ensembl release version R72 human reference genome Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample.
|
|
|
Submission date |
Mar 05, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Jinsheng Yu |
E-mail(s) |
jyu@wustl.edu
|
Organization name |
Washington University School of Medicine
|
Department |
Genetics
|
Lab |
GTAC Lab
|
Street address |
660 S. Euclid Ave.
|
City |
St. Louis |
State/province |
MO |
ZIP/Postal code |
63110 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (2) |
GSE66592 |
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology (RNA-seq_ClonTech) |
GSE66649 |
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology |
|
Relations |
BioSample |
SAMN03392970 |
SRA |
SRX906151 |