|
| 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 |
