|
| Status |
Public on Sep 21, 2011 |
| Title |
u87_adar_kd |
| Sample type |
SRA |
| |
|
| Source name |
Glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87MG
treatment: ADAR1 siRNA
|
| Treatment protocol |
50ng of ADAR1 siRNA and control siRNA were transfected respectively with lipofectamine RNAiMAX into 5x104 U87MG cells per single well of 6-well plate via reverse transfection and cells were harvested 48h following transfection. Total RNA was isolated using the RNeasy micro kit.
|
| Growth protocol |
U87MG cells were maintained in DMEM high glucose medium supplemented with pyruvate, L-glutamine, and 10% fetal bovine serum (FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used the standard Illumina protocol to prepare libraries for RNA-Seq (http://www.illumina.com/support/documentation.ilmn). Briefly, 10ug total RNA was first processed via poly-A selection and fragmentation. We generated first-strand cDNA using random hexamer-primed reverse transcription and subsequently used it to generate second-strand cDNA using RNase H and DNA polymerase. Sequencing adapters were ligated using the Illumina Paired-End sample prep kit. Fragments of ~200 bp were isolated by gel electrophoresis, amplified by 15 cycles of PCR and sequenced.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
cDNA with ADAR siRNA treatment
|
| Data processing |
The sequence reads are aligned to the genome and transcriptome using blat, bowtie and tophat allowing at most 12 mismatches. Unique pair of the alignments of a pair of reads is accepted if both ends have less than 6 mismatches.
|
| |
|
| Submission date |
Mar 18, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Gang Li |
| E-mail(s) |
gl@ucla.edu
|
| Organization name |
UCLA
|
| Street address |
611 Charles E. Young Drive Rm. 660
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE28040 |
Accurate Identification of A-to-I RNA editing in human by transcriptome sequencing |
|
| Relations |
| SRA |
SRX110673 |
| SRA |
SRX110674 |
| BioSample |
SAMN00764115 |
