|
| Status |
Public on Feb 14, 2018 |
| Title |
HTLV1_TAX_PBM_RNA_seq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HTLV infected T cells
|
| Organism |
Homo sapiens |
| Characteristics |
host organism: hu-mice
cell type: T cell
infected with: Human T-lymphotropic virus type 1 (HTLV-1)
virus genotype: Tax delta_PBM
|
| Treatment protocol |
Cells (5x10^6) were then washed with ice-cold PBS, centrifuged at 500g for 5 min at 4°C and lysed in 1 mL of lysis buffer (10mM Tris-HCl pH7.5, 5mM MgCl2, 100mM KCl, 2mM DTT, protease inhibitor EDTA-free Roche, 1% Triton X-100). Lysates were gently homogenized and incubated at 4 °C for 10 min, centrifuged at 1,300g for 10 min at 4 °C and the supernatant (corresponding to the cytoplasmic fraction) was recovered.
|
| Growth protocol |
T lymphocytes isolated from the spleen of WT or ∆PBM infected hu-mice were cultured in complete RPMI medium containing IL2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cytoplasmic extracts using Trizol
Libraries were constructed following the SmartSeq2 protocol (Picelli S 2013 Nature Methods)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LRPS7
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were first split with respect to their dual barcode sequences. After this, 3′-adaptor sequences were removed from reads when present. Reads were then aligned to a custom set of sequences corresponding to ribosomal RNA and tRNA sequences using Bowtie2 v1.1.1 with parameters -fast -fr in order to remove contaminants. Remaining reads were aligned to the human genome and transcriptome (hg19 assembly) using TopHat2 v2.0.13 with parameters --library-type fr-secondstrand --no-coverage-search --b2-sensitive -i 30 -m 0 -g 10 --max-coverage-intron 1000000
Read counts per gene were obtained using HTSeq v0.6.1p1 with parameters -s yes -m intersection-strict --type=exon –idattr=gene_id (using the UCSC hg19 annotation file).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include exon gene counts values for each Sample. Bedgraphs files for each biological replicate.
|
| |
|
| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Emiliano P Ricci |
| E-mail(s) |
emiliano.ricci@ens-lyon.fr
|
| Organization name |
INSERM
|
| Department |
Centre International de Recherche en Infectiologie
|
| Street address |
46 allée d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE102220 |
Transcriptome-wide analysis of the role of HTLV-1 Tax PBM in T-Cells from infected humanized-mice (hu-Mice) |
|
| Relations |
| BioSample |
SAMN07446734 |
| SRA |
SRX3058388 |
