|
| Status |
Public on May 14, 2014 |
| Title |
ABRF-454-UI-A-1 |
| Sample type |
SRA |
| |
|
| Source name |
ABRF-454-UI-A
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pooled Tumor Tisue
reference rna: Agilent Universal Human Reference RNA
reference rna cat. #: #740000
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
NA
Poly A; Library synthesis and sequencing was performed with MAQC A and MAQC B samples at three core laboratory sites. Each site constructed one cDNA library from each of the polyA-enriched RNA samples. Enriched RNA (200 ng) was reduced to 19 µl in a vacuum centrifuge at 60 oC, followed by library construction using the Roche cDNA Rapid Library Preparation Method Manual XL+ (May 2011) with the following modifications: (1) RNA Fragmentation Reagent kit (AM#8740, Life Technologies) was used in place of the RNA Fragmentation Solution; (2) all magnetic particle concentrator (MPC) pelleting steps were held for 2 minutes; (3) Roche rapid library multiplex identifier (RL-MIDs) adaptors were used for the adaptor ligation step; (4) the final libraries were quantified using a Qubit fluorometer (Life Technologies) and average fragment sizes were determined by analyzing 1 µl of the libraries on the Agilent Bioanalyzer 2100 using a High-Sensitivity DNA LabChip; and (5) the library concentrations were determined using the average fragment size from the Bioanalyzer analysis. Final samples were diluted to 1x108 molecules/µl in Tris-HCl pH 8 buffer with 0.001% Tween-20.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX Titanium |
| |
|
| Description |
Pure Human Reference RNA Sample from Agilent, Inc.
|
| Data processing |
STAR Aligner v2.3.0 Regular
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 |
GPL14603 |
| Series (2) |
| GSE46876 |
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq. |
| GSE48032 |
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [454 GS FLX Titanium] |
|
| Relations |
| BioSample |
SAMN02205236 |
| SRA |
SRX307017 |
