|
| Status |
Public on Mar 03, 2016 |
| Title |
A673 |
| Sample type |
SRA |
| |
|
| Source name |
EWS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A673
cell type: Ewing's sarcoma cell line
|
| Growth protocol |
All Ewing’s sarcoma cell lines were kept in RPMI1640 medium supplemented with 10% FCS. The MSC lines 4+v and 5H [PMID:20466760] were grown in MesenCult MSC basal medium supplemented with 10% MesencCult stimulatory supplements (Stemcell Technologies)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted from each cell line using Trizol RNA extraction reagent (Life Technologies), according to manufacturer’s recommendations and 75 µg was used in two rounds of polyA selection to purify the mRNA.
The mRNA was reverse transcribed into cDNA and made into dsDNA using Just cDNA Double Stranded cDNA Synthesis Kit (Stratagene). The double stranded products were fragmented using Covaris S2 System, size selected using Ampure XP beads (Beckman Coulter), then sequencing libraries prepared before single end deep sequencing was carried out with an Illumina GA IIx to obtain 80bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
a673
|
| Data processing |
Read trimming with Trim Galore, default settings
Alignment and transcript abundance estimation with Sailfish, default settings
Differential expression with DESeq2, default settings
Genome_build: human cDNA, Ensembl version 75
Supplementary_files_format_and_content: CSV, estimated transcripts per million (Sailfish estimate), cell type mean, standard deviation and log fold change (estimated by DESeq2)
|
| |
|
| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Helio Pais |
| E-mail(s) |
helio.pais@imm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Weatherall Institute of Molecular Medicine
|
| Street address |
Jonh Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE73610 |
RNA-Seq profiling of Ewing's sarcoma and MSC cell lines |
|
| Relations |
| BioSample |
SAMN04123613 |
| SRA |
SRX1297097 |
