|
| Status |
Public on Jan 19, 2022 |
| Title |
Parental H295R cells rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Adrenocortical carcinoma (ACC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H295R
cell type: adrenocortical carcinoma cells
cell population: Parental ACC cells
|
| Treatment protocol |
None
|
| Growth protocol |
Parental H295R cells and Ptch1 positive H295R were cultured in DMEM/F12 supplemented with 2% NuSerum (BD), 1% ITS+ (BD) and penicillin/streptomycin (Invitrogen) at 37°C in a 5% CO2/95% air water-saturated atmosphere.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the RNA extraction kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.
Truseq Stranded Total RNA Libraries were generated from 500ng of total RNAs using Truseq Stranded Total RNA kit (Illumina). Libraries were then quantified with Qubit and pooled. 4nM of this pool were loaded on a High Output Flowcell and sequenced on a NextSeq500 platform (Illumina) with 2x75bp paired-end chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WT 3001
|
| Data processing |
Quality control of reads using fastQC and Fastq-scren analysis
Genome mapping with STAR_2.4.0a versus hg38 following ENCODE RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20"
Transcripts counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCh38.76 release.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts.txt : tab-delimited text file with gene counting using featureCount
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE189424 |
Comparison of gene expression between parental adrenocortical carcinoma cells and a subpopulation overexpressing Ptch1 |
|
| Relations |
| BioSample |
SAMN23410829 |
| SRA |
SRX13209634 |
