|
| Status |
Public on Jan 04, 2021 |
| Title |
Trf1f/f Ad-GFP biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Trf1f/f MEFs
treatment: Ad-GFP infected
|
| Treatment protocol |
Where applicable, cells were treated with 10uM TMPyP4 48 hours prior to the RNA collection.
|
| Growth protocol |
MEFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (Invitrogen), L-glutamine, and penicillin-streptomycin, at 37 °C in 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The total RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent, Santa Clara, CA, USA) to insure RNA integrity and concentration before starting the procedure. mRNA libraries were generated using the KAPA mRNA Hyper Prep Kit (Roche) following manufacturer’s instructions. Library QC was reperformed on the BioAnalyser 2100 followed by sequencing on the Illumina HiSeq 2500 to generate 101bp strand-specific single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TRF1_FF_GFP_R2,
|
| Data processing |
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 19th February 2016. The parameters used were “--star-output-genome-bam --forward-prob 0 --paired-end”.
Differential expression analysis was performed with the DESeq2 package (version 1.28.0) (Love et al., 2014) within the R programming environment (version 4.0.0) (http://www.R-project.org/). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study
|
| |
|
| Submission date |
May 04, 2020 |
| Last update date |
Jan 04, 2021 |
| Contact name |
Simon J Boulton |
| E-mail(s) |
simon.boulton@crick.ac.uk
|
| Organization name |
The Francis Crick Institute
|
| Lab |
DSB Repair Metabolism Lab
|
| Street address |
1 Midland Rd
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE149850 |
Comparative genome-wide transcriptional profile after RTEL1 depletion and G4 stabilisation. |
| GSE161597 |
RTEL1 regulates G4/R-loops to avert replication-transcription collisions |
|
| Relations |
| BioSample |
SAMN14829595 |
| SRA |
SRX8246241 |
