|
| Status |
Public on Sep 01, 2017 |
| Title |
SKOV_FAV_pcDNA3 |
| Sample type |
SRA |
| |
|
| Source name |
SKOV3ip1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Ovarian serous cystadenocarcinoma
treatment: Lipofectamine 2000 treated, empty pcDNA3 vector transfected
|
| Growth protocol |
grown in DMEM/F12 (50/50) medium (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine. Cell propagation and passaging were as recommended by ATCC (American Type Culture Collection). Cells were trypsinized and collected in 5X106 pellets resuspended in 700ul TRIzol (Ambion) and kept at -80°C until RNA extraction
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA library produced with retroviral RT
The poly(A) RNA was isolated and purified from 5ug DNA-free total RNA using NEBNext Poly (A) mRNA Isolation Module (New England Biolabs) according to the manufacturer protocol.
Library preparations were performed using the NEBNext Ultra directional RNA library Prep Kit for Illumina (New England Biolabs) in order to generate RNA-seq library from 100 ng of purified RNA. The RNA and library quality were verified using Agilent Bioanalyzer (Agilent Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
poly-A RNA, fragmented (200nt)
|
| Data processing |
Reads were treated with Cutadapt (using parameters -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG --minimum-length 2) and Trimmomatic (with TRAILING:30)
The resulting reads were aligned to the build hg38 using STAR (--outSAMprimaryFlag AllBestScore, --alignIntronMax 1250000), unmapped reads being re-aligned with Bowtie2 (-q -I 13).
CoCo (http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco) was used to produce read counts per genes and associated CPM and TPM values from the Ensembl (v87) annotation modified with CoCo.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated-value (csv) files holding the name of every gene and their abundance value (raw counts, CPM or TPM) for each dataset
|
| |
|
| Submission date |
May 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michelle S Scott |
| E-mail(s) |
michelle.scott@usherbrooke.ca
|
| Organization name |
University of Sherbrooke
|
| Department |
Biochemistry
|
| Street address |
3201 Jean Mignault
|
| City |
Sherbrooke |
| State/province |
Quebec |
| ZIP/Postal code |
J1E 4K8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE99065 |
Simultaneous detection and relative quantification of coding and non-coding RNA using a single sequencing reaction |
|
| Relations |
| BioSample |
SAMN07140771 |
| SRA |
SRX2833975 |
