|
| Status |
Public on Sep 28, 2015 |
| Title |
pure bone marrow RNA (BMO) CT |
| Sample type |
SRA |
| |
|
| Source name |
Original Bone Marrow RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human bone marrow sample
|
| 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 |
SAMN03392996 |
| SRA |
SRX906155 |
