|
| Status |
Public on Sep 12, 2011 |
| Title |
RNA Capture sequencing 9 (454) |
| Sample type |
SRA |
| |
|
| Source name |
Fetal lung (FL) fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary fetal lung fibroblasts
sample type: RNA Capture sequencing
|
| Growth protocol |
Primary human female fetal lung fibroblasts and human male foot fibroblasts in DMEM supplemented with 10% FBS at 37 °C with 5% CO2 as previously described (J. L. Rinn et. al., PLoS Genet, 2006).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
454 GS-FLX Titanium Sequencing libraries from c45 and FL fibroblast cDNA were constructed using the 454 LifeSciences GSFLX Titanium Kit according to manufacturers instructions. All single-stranded DNA product from library preparation was utilized as template in a Pre-Hybridization Linker Mediated PCR reaction to ensure that the plurality of the molecules contained adapters on both sides of the putative cDNA inserts. The amplified material was recovered with a Qiaquick column and DNA evaluated electrophoretically by an Agilent Bioanalyzer 2100. Library fragment sizes were found to be between 500-700 bp. Samples were purified and combined with C0T-1 DNA, enhancing oligos, NimbleGen hybridization buffer and Component A prior to capture. Hybridisation and post-hybridisation LMPCR were performed with identical conditions. The resulting post capture enriched sequencing libraries were sequenced on 454 Genome Sequencer FLX System using Titanium chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX Titanium |
| |
|
| Data processing |
Roche 454 reads were firstlycombined and aligned to the human genome (hg19) using Blat (http://www.soe.ucsc.edu/~kent) with the following non-default parameters; minIdentity=90, minScore=100. Resultant *.psl files were converted into *.sam files using bedTools and samtools.
|
| |
|
| Submission date |
May 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim R. Mercer |
| Organization name |
Garvan
|
| Lab |
Prof. John Mattick
|
| Street address |
384 Victoria Street Darlinghurst NSW 2010
|
| City |
Sydney |
| State/province |
New South Wales |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL14603 |
| Series (2) |
| GSE29040 |
RNA Capture-Seq resolves the deep complexity of the human transcriptome (454) |
| GSE29041 |
RNA Capture-Seq resolves the deep complexity of the human transcriptome |
|
| Relations |
| SRA |
SRX060826 |
| BioSample |
SAMN00263086 |
