|
| Status |
Public on Mar 05, 2013 |
| Title |
HeLa mitochondrial RNA |
| Sample type |
SRA |
| |
|
| Source name |
cervical adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: 31 year adult female
tissue: cervix
disease/cell type: transformed with adenovirus 5 DNA
cell line: HeLa
|
| Treatment protocol |
Mitochondria were prepared from HEK293 and HeLa cells using Qproteome Mitochondria Isolation Kit (Qaigen, USA). The purity of mitochondria was confirmed by western blotting using different antibodies. RNA was isolated from mitochondria using miRCURYTM RNA Isolation Kit (Exiqon, Germany) according to manufacturer's instructions. RNA integrity was checked by Agilent 2100 Bioanalyzer (Ambion, USA).
|
| Growth protocol |
Dulbecco's Modified Eagle's Medium (DMEM, Lonza, Switzerland) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Lonza, Switzerland) and 1% penicillin, streptomycin and amphotericin B (PSA) antibiotic mixture (Lonza, Switzerland). Maintained cells were used to prepare various plates and disc as per requirement.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
sRNAs ranging from 18 to 30-nt were gel-purified and ligated to the 3' adaptor and 5' adaptor. The ligated products were used for cDNA synthesis, purified by acrylamide gel electrophoresis and then amplified to generate small RNA libraries.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The data cleaning of 50nt sequence tags was done to exclude the low quality tags and all contaminants. The 3' adaptor sequences, 5' contaminants and polyA reads were removed using a dynamic programming algorithm. The remaining sequences were mapped to human genome using SOAP with the following options: soap -v 0 -r 2 -s 7 -p 7 -a.
|
| |
|
| Submission date |
Sep 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Rajesh Singh |
| E-mail(s) |
rsingh@iiar.res.in
|
| Fax |
917930514241
|
| URL |
http://www.iiar.res.in
|
| Organization name |
Indian Institute of Advanced Research
|
| Department |
Cell Biology
|
| Lab |
Cell Biology
|
| Street address |
Koba Inst Area
|
| City |
Gandhinagar |
| State/province |
GJ |
| ZIP/Postal code |
382007 |
| Country |
India |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE32185 |
Human mitochondria hub of small RNAs: Analysis by deep Sequencing |
|
| Relations |
| SRA |
SRX097599 |
| BioSample |
SAMN00718911 |
