|
| Status |
Public on Nov 25, 2015 |
| Title |
Vector_PARN_OE |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
construct: Vector_PARN_OE
|
| Treatment protocol |
For siRNA knockdown, cells were treated twice (two or three day interval) with 20 nM or 40 nM siRNA using Dharmafect I (Dharmacon). For PARN overexpression, PARN-pCMV6-XL (Origene, SC325208 ) was transfected into HeLa cells using Fugene HD (Promega) for 72 hours.
|
| Growth protocol |
HeLa cells were cultured in Dulbecco’s modified eagle medium (Life Technologies 11995-065) containing 10% fetal bovine serum (Sigma) at 37°C, 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed once with Dulbecco’s phosphate-buffered saline and collected in Trizol reagent (Ambion, Life Technologies) according to manufacturer’s instructions, followed by treatment with DNase I (New England Biolabs) at 37°C for 30 min. RNA was extracted with phenol/chloroform equilibrated with 50 mM NaOAc (pH 5.0) and ethanol precipitated.
Library preparation was modified from the protocol which published by Goldfard and Cech (Goldfarb and Cech 2013). The samples were sequenced on the Illumina HiSeq using RapidSeq-100bp single-end reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: RLM-RACE-seq
Reads were filtered for non-hTR and hTR with sequencing error. Reads were kept if an exact match to at least 28 nucleotides of the 3' end of the hTR sequence was found.
Reads were binned and counted based on their hTR sequence. The counts were normalized to library size.
Supplementary_files_format_and_content: Percentages of hTR forms per sample.
|
| |
|
| Submission date |
Oct 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Baumann |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE73776 |
Human telomerase RNA processing and quality control |
|
| Relations |
| BioSample |
SAMN04147514 |
| SRA |
SRX1308344 |
