|
| Status |
Public on Sep 28, 2015 |
| Title |
1:4 mixture of AGO and BMO |
| Sample type |
SRA |
| |
|
| Source name |
Mixed RNA of both (1:4)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mixed sample of both (1:4)
|
| 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 random priming based Ribo-Zero™ rRNA Removal Kits from Epicentre (an Illumina company, labeled as “RiboZero”). 1 ug were input with RiboZero protocol, RiboZero depleted RNA was chemically fragmented, then made into cDNA with Superscript III (Life Technologies) and random hexamers followed by a second strand reaction. 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) |
| GSE66590 |
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology (RNA-seq_RiboZero) |
| GSE66649 |
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology |
|
| Relations |
| BioSample |
SAMN03392914 |
| SRA |
SRX906147 |
