 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 12, 2024 |
| Title |
H1650, Scramble, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
H1650
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1650
cell type: Lung
genotype: WT
treatment: Scramble SSO
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For RNA extraction, 1M cells were collected with 750 µL of RLT lysis buffer supplemented with 1% β-mercaptoethanol. Total RNA was extracted from cell lines using RNeasy Mini Kit (Qiagen) following manufacturer instructions. For sequencing purposes, RNA interrogation number (RIN) was measured using a Bioanalyzer RNA 6000 nano assay (Agilent) to verify a RIN >7.
Libraries were generated from 500 ng or 1000 ng of total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit. PolyA enrichment was done using magnetic beads and then, RNA was fragmented. cDNA was synthetized from the resulting fragments, and after dA-tailing, they were ligated to TruSeq indexed adapters, and amplified by PCR (12-15 cycles). Sequencing was performed (paired-end reads, 100 nucleotide length) on a Novaseq 6000 system with a demanded depth of 200 million reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw RNA-seq files were aligned using STAR (v2.5.3a) two-pass modes. Bam files were processed by featureCounts to quantify gene expression84. Gene read counts were uploaded to R and converted to Transcript per million (TPM) using tpm function from drfun R package. Only raw gene counts from genes with TPM >0.5 were submitted to differential expression analysis using DESeq2 R package85.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include featureCounts output
|
| |
|
| Submission date |
Jul 31, 2024 |
| Last update date |
Dec 12, 2024 |
| Contact name |
Yago A Arribas |
| E-mail(s) |
yago.arribas-de-sandoval@curie.fr
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE234223 |
Transposable element exonization by non-canonical splicing generates a diversity reservoir of functional protein isoforms |
|
| Relations |
| BioSample |
SAMN42956015 |
| SRA |
SRX25535827 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8433924_D1722T113_counts_reduced.txt.gz |
372.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
