|
| Status |
Public on Apr 24, 2018 |
| Title |
Growing_shHMGA1_R2 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
agent: none
vector 1: ER:HRAS(G12V)
vector 2: MSCV miR30 shHMGA1
passage: 23-28
cell line: IMR90
|
| Treatment protocol |
Cells were retrovirally infected with ER:HRAS(G12V) and either MSCV vector or MSCV miR30 shHMGA1. For RIS samples, cells are treated for 6 days with 4OHT.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Qiagen RNeasy plus kit (74136, Qiagen) according to the manufacturer’s instructions and reverse-transcribed to cDNA using the Applied Biosystems High-Capacity Reverse Transcription Kit (43-688-13, Thermo Fischer).
Libraries were prepared from 6 biological replicates of each condition using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturers instructions and sequenced using the HiSeq-2500 platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to the Human reference genome hg19 with the STAR (version 2.5.0b) aligner
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0)
Read counting was performed using Bioconductor package Rsubread and differential expression analysis with edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts per gene calculated using Rsubread.
|
| |
|
| Submission date |
Apr 12, 2018 |
| Last update date |
Apr 25, 2018 |
| Contact name |
Shamith Samarajiwa |
| Organization name |
Imperial College London
|
| Department |
Genetics and Genomics Section Department of Metabolism, Digestion and Reproduction
|
| Lab |
Computational Biology & Data Science
|
| Street address |
ICTEM Building, Hammersmith Campus, Du Cane Road,
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE103590 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence |
| GSE113060 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN08920051 |
| SRA |
SRX3928555 |
