|
| Status |
Public on Feb 09, 2017 |
| Title |
HeLa WT + IDO 48hr |
| Sample type |
SRA |
| |
|
| Source name |
IDO1-transduced HeLa cells cultured for 48h
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human cervical cancer cells (HeLa)
|
| Growth protocol |
HeLa cells were cultured at the concentration of 100,000 cells per ml in 1.5ml complete Minimum Essential Medium per well of a 12-well plate for 48h or 72h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from frozen cell pellets using the Ambion miRvana RNA isolation kit.
Sequencing library was made by following standard protocol: http://www.illumina.com/documents/products/technotes/technote-truseq-rna-access.pdf. Superscript III reverse transcriptase (Life Technologies) and Illumina’s TruSeq Stranded Total RNA Sample Prep Kit (Illumina) were used for making the cDNA library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
OC12
|
| Data processing |
x100 bp reads were produced with the Illumina Hi-seq sequencer.
After quality and adaptor trimming, an average of ~115 million reads were generated for each sample of which there was a single replicate.
Reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned with TopHat version 1.1.4.
Reads were aligned to the GRCh37/hg19 human reference genome build and quantified by Cufflinks as RPKM (reads per kilobase million).
|
| |
|
| Submission date |
Dec 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Taylor |
| E-mail(s) |
stephen.taylor@imm.ox.ac.uk
|
| Phone |
+44 1865 222640
|
| Organization name |
CBRG
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE75956 |
HeLa transcriptome induction by IFN gamma and indoleamine 2,3-dioxygenase (IDO) |
|
| Relations |
| BioSample |
SAMN04334797 |
| SRA |
SRX1479531 |
