|
| Status |
Public on Apr 15, 2012 |
| Title |
RPE1_PABPN1kd2_3seq |
| Sample type |
SRA |
| |
|
| Source name |
RPE-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hTERT-immortalized retinal pigment epithelial
cell line: RPE-1 cells
transfection: PABPN1 - si#2
|
| Growth protocol |
U2OS osteosarcoma cells and RPE-1 (hTERT-immortalized retinal pigment epithelial) cells were either transfected with two different scrambled control siRNAs (siC1 and siC2), pcDNA5 vector (vecC1 and vecC2) or two different siRNAs against PABPN1. 72 hours after transfection the cells were harvested and further processed for construction of the 3’Seq libraries
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from either U2OS or RPE-1 cells. mRNA was isolated, heat fragmented and the fragmented mRNA was then converted to single-stranded cDNA using SuperScript III reverse transcriptase and P7-t25-vn oligo-dT primer. This was followed by second-strand cDNA synthesis and end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. After purification, a P5-splinkerette was ligated and the splikerette-ligated cDNA was size-selected for approximately 220 bp long cDNA fragments using the E-Gel iBase Power System from Invitrogen. The final 3'Seq libraries were then generated by PCR amplification of the linker-ligated cDNA with P5 and P7 primers. After a last purification step the 3'Seq libraries were sequenced on the Illumina Genome Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
3'-Seq in RPE-1 cells transfected with PABPN1 - si#2
hg18
|
| Data processing |
Reads were aligned to the hg18 using bowtie. Wig files summarize read coverage at each genomic ccordinate (hg18)
|
| |
|
| Submission date |
Feb 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Ran Elkon |
| Organization name |
Tel Aviv University
|
| Department |
Human Genetics
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| ZIP/Postal code |
69494 |
| Country |
Israel |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE27452 |
Genome-wide maps of polyadenylation sites in control and PABPN1kd cells |
| GSE32303 |
PABPN1 role in regulation of alternative cleavage and polyadenylation |
|
| Relations |
| SRA |
SRX085425 |
| BioSample |
SAMN00690320 |
