|
| Status |
Public on Nov 15, 2018 |
| Title |
TcRBP7 targets rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Epimastigotes
|
| Organism |
Trypanosoma cruzi |
| Characteristics |
strain: Dm28c
tissue: GFP-TcRBP7 transfected epimastigotes
|
| Growth protocol |
T. cruzi Dm28c epimastigotes were grown in liver infusion tryptose (LIT) medium supplemented with 10% heat-inactivated fetal bovine serum at 28 ºC. Experiments were carried out at the exponential growth phase when the culture density was approximately 3x107 parasites/mL. Selected transfectants were confirmed for the tagged protein expression.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RBPs were co-immunoprecipitated with magnetic beads mobilized with anti-GFP. After proper wash, mRNAs were isolated with RNeasy Extraction Kit from Qiagen.
Sequencing libraries were prepared with the SOLiD Total RNA-Seq Kit (Applied Biosystems), selecting for fragments of 150-250 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
RBP-bound fraction
|
| Data processing |
sequence were mapped against T. cruzi Sylvio X/10 genome v. 9., using bowtie v1.2.1.1 with parameters -f -Q -n 3 -C --best.
Enrichment analysis was performed in the EdgeR package from R software consisted of genes above 2-fold enrichment and p<0.01
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Saloe Bispo Poubel |
| E-mail(s) |
saloebispo@gmail.com
|
| Organization name |
Lund University
|
| Street address |
Building 404:B3 Scheelevägen 2
|
| City |
Lund |
| State/province |
skane |
| ZIP/Postal code |
223 81 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23054 |
| Series (1) |
| GSE106934 |
Ribonomic identification of mRNAs associated with RNA binding proteins TcRBP7 and TcRBP40 from Trypanosoma cruzi |
|
| Relations |
| BioSample |
SAMN08028270 |
| SRA |
SRX3394554 |
