|
| Status |
Public on Mar 01, 2015 |
| Title |
Delta_8aa_Dox-_2 |
| Sample type |
SRA |
| |
|
| Source name |
MDS-L
|
| Organism |
Homo sapiens |
| Characteristics |
individual: MDS patient
tissue: bone marrow
cell line: MDS-derived cell line (MDS-L)
treatment: srsf2-shRNA + Delta_8aa srsf2
|
| Treatment protocol |
Doxycycline 2.5 ug/ml (for sh only cells) or 1.0 ug/ml (for other cells) were added (Dox+) or not added (Dox-) to the cells every day for 3 days.
|
| Growth protocol |
MDS-L cells transduced with pTRIPZ vectors containing shRNA against endogenous SRSF2 with/without wild type (WT), P95H or 8-amino-acid deletion (Delta_8aa) mutant of human SRSF2 cDNA were cultured in triplicate in RPMI supplemented with 10% fetal bovine serum, penicillin/streptomycin and 10 ng/ml human IL-3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using Trizol reagent (Life technologies).
RASL library was constructed according to Li H, et al protocol published Current Protocols in Molecular Biology.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
srsf2-shRNA + Delta_8aa srsf2 without dox rep2
|
| Data processing |
library strategy: RASL-Seq
The sequenced 40 bases were mapped to the oligo pool sequences with Bowtie by allowing 1 mismatch in each of the donor and acceptor sequences.
Genome_build: hg18
Supplementary_files_format_and_content: The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
|
| |
|
| Submission date |
Sep 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiang-Dong Fu |
| Organization name |
UC San Diego
|
| Department |
CMM
|
| Lab |
George Palade Laboratories
|
| Street address |
9500 Gilman Drive, Room 231
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0651 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE61052 |
SRSF2 is essential for hematopoiesis and its myelodysplastic syndromes-related mutations dysregulate alternative pre-mRNA splicing |
|
| Relations |
| BioSample |
SAMN03018353 |
| SRA |
SRX694793 |
