|
Status |
Public on Feb 09, 2017 |
Title |
HeLa WT 72hr |
Sample type |
SRA |
|
|
Source name |
Untreated WT HeLa cells cultured for 72h
|
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 |
OC13
|
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 |
SAMN04334798 |
SRA |
SRX1479532 |