|
| Status |
Public on Jun 22, 2016 |
| Title |
RIS_rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 cells
|
| Organism |
Homo sapiens |
| Characteristics |
sample group: Vec_Tam
n11cd factor: No
4oht factor: Yes
vec factor: Yes
|
| Treatment protocol |
Control: vehicle-treated, control vector transduced ER:RAS IMR90 cells; RIS: 4OHT-treated, control vector transduced ER:RAS IMR90 cells; NIS: vehicle-treated, N1ICD-FLAG transduced ER:RAS IMR90 cells; RNIS: 4OHT-treated, N1ICD-FLAG transduced ER:RAS IMR90 cells.
|
| Growth protocol |
Cells were grown in DMEM media with 10% FBS at 37C in a 5% O2 / 5% CO2 atmosphere
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (RNEasy Plus kit, Qiagen) from the cultured cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts
|
| |
|
| Submission date |
Aug 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE72404 |
NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence [N1ICD] |
| GSE72409 |
NOTCH1 mediates a reciprocal switch between two distinct secretomes during senescence |
|
| Relations |
| BioSample |
SAMN04012756 |
| SRA |
SRX1165058 |
