 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 14, 2021 |
| Title |
Merb 30 min rep1 |
| Sample type |
SRA |
| |
|
| Source name |
retinal pigment epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hTERT RPE-1
genotype/variation: wild type
treatment: Merbarone, 30 min
|
| Treatment protocol |
RPE-1 cells were treated with vehicle (DMSO) for 30 minutes or merbarone (200μM) for 30 or 120 minutes.
|
| Growth protocol |
RPE-1 cells were serum starved by 48h incubation in Dulbecco's Modified Eagle’s Medium (DMEM) F-12 (Sigma) supplemented with penicillin, streptomycin and 0.1% Fetal Bovine Serum (FBS) (Sigma) at 37ºC in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNeasy kit from Qiagen following instructions from the manufacturer.
cDNA libraries were prepared with TruSeq Stranded mRNA (Illumina) using 150ng of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.0 with parameter -m 1.
Differentially expressed genes were identified using DEseq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample and were computed using custom R scripts that made use of the Bioconductor libraries bamsignals and edgeR.
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage function from deepTools v2.4.1 with parameters --binSize 50 –normalizeUsingRPKM. Refs: Mammana A, Helmuth J (2019). bamsignals: Extract read count signals from bam files. R package version 1.18.0, https://github.com/lamortenera/bamsignals . McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. doi: 10.1093/nar/gks042. Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
Apr 14, 2021 |
| Contact name |
Felipe Cortés Ledesma |
| E-mail(s) |
fcortes@cnio.es
|
| Organization name |
CNIO
|
| Department |
Molecular Oncology
|
| Lab |
Topology and DNA breaks
|
| Street address |
Melchor Fernández Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE141799 |
Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling [RNA-seq] |
| GSE141800 |
Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling |
|
| Relations |
| BioSample |
SAMN13528539 |
| SRA |
SRX7341870 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4213401_rna_seq_RPE_Merb_30min_1.bigWig |
12.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM4213401_rna_seq_RPE_Merb_30min_1_RPKM.txt.gz |
201.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
