 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 29, 2024 |
| Title |
A549 RSV-infected, total RNA 3 |
| Sample type |
SRA |
| |
|
| Source name |
A549
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: lung epithelial
genotype: WT
treatment: RSV-infection
|
| Treatment protocol |
Cells were either Mock or RSV-infected (MOI 0.1) for 48h, then the cells were lysed and 1/10 was used for total RNA, 9/10 were used for AGO2 IP
|
| Growth protocol |
Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using miRNeasy kit (Qiagen) with on-column DNase digest (Qiagen)
Libraries were generated using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina and the NEBNext rRNA Depletion kit (Human/Mouse/Rat) according manufacture's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
RSV IN 3
|
| Data processing |
adapter trimming and quality filters with trimmomatic PE -phred33 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
alignment to the genome with hisat2 --non-deterministic in paired-end mode
samtools to convert to bam file, sort and index alignments
counted reads in features with featureCounts implemented in Rsubread 2.12.3 R package, with params: GTFattrType="gene_id", isPairedEnd = TRUE, primaryOnly = FALSE, countMultiMappingReads = TRUE, isGTFAnnotationFile = TRUE, allowMultiOverlap = FALSE, fraction=TRUE, fracOverlap =0, largestOverlap=TRUE, requireBothEndsMapped=FALSE, checkFragLength=FALSE, minOverlap=1, strandSpecific = 2
Assembly: GRCh38.primary_assembly.genome.fa taken from Gencode 34
Supplementary files format and content: csv containing gene_symbol, biotype, chr, gene_id and counts for each gene or regulatory region in the genome
|
| |
|
| Submission date |
May 05, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
José Roberto Bermúdez-Barrientos |
| E-mail(s) |
roberto89bermudez@gmail.com, beto.bermudez@ed.ac.uk, sarah.ressel@ed.ac.uk
|
| Organization name |
The University of Edinburgh
|
| Department |
Institute of Immunology & Infection
|
| Lab |
Buck Lab
|
| Street address |
Charlotte Auerbach Rd
|
| City |
Edinburgh |
| State/province |
Lothian |
| ZIP/Postal code |
EH9 3AZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE231788 |
Respiratory Syncytial virus (RSV) directly binds host microRNAs and de-regulates host gene targets [RNA-seq] |
| GSE232687 |
Respiratory Syncytial virus (RSV) |
|
| Relations |
| BioSample |
SAMN34718269 |
| SRA |
SRX20233206 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
