 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 17, 2013 |
| Title |
Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides.
Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching.
|
| |
|
| Overall design |
Jurkat T-cell mRNA was analyzed on an Illumina HiSeq2000. ~80 million paired end reads (2x200bp, ~350bp lengths) were collected.
|
| |
|
| Contributor(s) |
Sheynkman G, Smith L |
| Citation(s) |
23629695 |
| Submission date |
Mar 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gloria Sheynkman |
| E-mail(s) |
gloria.kreitinger@gmail.com
|
| Organization name |
UW-Madison
|
| Department |
Chemistry
|
| Lab |
Lloyd Smith
|
| Street address |
1101 University Ave.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (3) |
|
| Relations |
| BioProject |
PRJNA193719 |
| SRA |
SRP019939 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45428_Jurkat_RSEM_TPMs.txt.gz |
432.5 Kb |
(ftp)(http) |
TXT |
| GSE45428_Jurkat_tophatJunctions.bed.gz |
5.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
