|
| Status |
Public on Jun 26, 2023 |
| Title |
U2OS_RNAseq_siGAR1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: Human bone osteosarcoma
treatment: siGAR1
|
| Treatment protocol |
Cells were transfected for 48 hours with 15 nM siRNA using RNAiMAX (Thermo Fisher Scientific) according to manufacturer’s instructions.
|
| Growth protocol |
DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Cells were harvested and subjected to nuclear fractionation. Nuclear RNA was extracted using Trizol (Thermo Fisher Scientific) according to manufacturer’s instructions.
Libraries were generated using the RiboCop rRNA depletion kit followed by the CORALL Total RNA-Seq library preparation kit (both from Lexogen), following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing quality checks were performed on all experiments using FastQC (v0.11.9).
Adaptor sequences were removed using TrimGalore (v0.6.4_dev) with default parameters.
Reads were filtered against human rRNA and tRNA sequences obtained from the NCBI using Bowtie2 (v2.4.1) with the option --sensitive-local.
Reads that failed to align were used as input for STAR (v2.7.0e) and were mapped to the human reference genome (GRCh38/hg38) using GENCODE (v27) gene annotation as reference, with the following parameters: --twopassMode Basic --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMultimapNmax 1 --outFilterType BySJout --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
PCR duplicates were removed using Picard MarkDuplicates (v2.18.11) with default parameters.
Transcript expression quantification was carried out using Salmon (v1.2.0) in pseudo-alignment mode, with library type (-l ISR) and correction of sequence-specific (--seqBias) and position-specific (--posBias) biases, and the GENCODE (v27) annotation and corresponding transcriptome as references.
Assembly: GRCh38/hg38
Supplementary files format and content: Salmon quantification file, tab-separated file with a single header line
|
| |
|
| Submission date |
Aug 14, 2022 |
| Last update date |
Jun 26, 2023 |
| Contact name |
Federico Agostini |
| E-mail(s) |
[email protected]
|
| Organization name |
Science for Life Laboratories
|
| Street address |
Tomtebodavägen 23a
|
| City |
Solna |
| State/province |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE211200 |
Co-transcriptional pseudouridylation of mRNAs by the H/ACA complex controls translational efficiency [RNA-seq] |
| GSE211202 |
Co-transcriptional pseudouridylation of mRNAs by the H/ACA complex controls translational efficiency. |
|
| Relations |
| BioSample |
SAMN30308429 |
| SRA |
SRX17062493 |
