|
| Status |
Public on Mar 06, 2023 |
| Title |
RMC2C_48hr_1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line derived from human renal medullary carcinoma (RMC2C); see (Msaouel et al., 2020)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RMC-2C
treatment: doxycycline
tissue: Kidney
time after treatment: 48 hours
|
| Treatment protocol |
Genetically modified cells were cultured in adequate media supplemented with G418 (50uM) for selection. Reexpression experiments were done using 2uM doxycycline for the indicated amount of time.
|
| Growth protocol |
Fresh RMC219 were cultured for maximum 10 passages at a dilution of 1:1,5 in DMEM/F12 + 10% FCS + Glutamine 2mM + AANE + PS. Fresh RMC2C were cultured for maximum 10 passages at a dilution of 1:2 in MEM + 10% FCS + AANE + PS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA-seq libraries were generated using TruSeq Stranded Total RNA Library Prep Kit from Illumina.
RNA isolation was performed according to standard procedure (Macherey Nagel Nucleospin RNA Plus).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing log2(fold-changes) and p-values computed by DESeq2 for SMARCB1 versus NEG comparisons at both timepoints in RMC219 and RMC-2C cells.
|
| |
|
| Submission date |
Jul 28, 2021 |
| Last update date |
Mar 06, 2023 |
| Contact name |
Guillaume Davidson |
| E-mail(s) |
davidsoy@igbmc.fr
|
| Organization name |
IGBMC
|
| Street address |
1 Rue Laurent Fries
|
| City |
Strasbourg |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE180999 |
SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. [RNAseq] |
| GSE181001 |
SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. |
|
| Relations |
| BioSample |
SAMN20456177 |
| SRA |
SRX11582722 |
