|
| Status |
Public on Dec 29, 2021 |
| Title |
M238P Lenti-miR-143/-145_2 |
| Sample type |
SRA |
| |
|
| Source name |
human melanoma M238P cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: M238P
cell type: human melanoma
genotype/variation: miR-143/-145
|
| 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 |
miR-143/145
|
| Data processing |
Mapping with STAR_2.4.0a versus hg19 folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20". Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options.
Genome_build: hg19
Supplementary_files_format_and_content: featurecounts.txt:
|
| |
|
| Submission date |
Apr 12, 2021 |
| Last update date |
Dec 29, 2021 |
| 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 (2) |
| GSE171881 |
RNA-Seq analysis of human M238P melanoma cells transduced with a lentivirus expressing the miR-143/145 cluster or a control lentivirus |
| GSE171883 |
Blockade of the pro-fibrotic reaction mediated by the miR-143/-145 cluster enhances the responses to targeted therapy in melanoma |
|
| Relations |
| BioSample |
SAMN18714206 |
| SRA |
SRX10578988 |
