|
| Status |
Public on Apr 28, 2022 |
| Title |
TBJ360_DP1 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4 T-cell
timer phase: DP
clone: TBJ 3.60
|
| Treatment protocol |
Sub-populations (DN, Blue, DP and Red) of timer protein-expressing cells were flow cytometry sorted.
|
| Growth protocol |
Two naturally infected T-cell clones isolated from non-malignant HTLV-1 positive individuals were stably transduced with a Tax-responsive fluorescent timer protein reporter cassette. Transduced cells were cultured in T75 flasks at 1-2 million cells per millilitre in RPMI-1640 and 20% fetal bovine serum supplemented twice weekly with 100 IU/ml human interleukin 2, 10 µM Raltegravir and 1 µg/ml Puromycin Dihydrochloride.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from flow cytometry sorted cells using Qiagen RNeasy Micro Kit (Catalogue number 74034).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
150 bp poly-A enriched stranded RNA-seq. All samples were sequenced in two lanes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw fastq files for the same sample from different sequencing lanes were concatenate.
Trim-galore with parameteres –paired –length 30 –stringency 3 was used.
STAR aligner was used with to create genome index with custom gtf and genome, which included the Timer construct sequence and HTLV-1 genome (GenBank: AB513134).
STAR aligner was used to align fastq files. Important parameters: --outSAMtype BAM SortedByCoordinate –quantMode TranscriptomeSam Genecounts
RSEM was used to quantify transcript abundances. Parameters: -p 30 –paired-end –forward-prob 0 –calc-pme
Genome_build: GRCh38/hg38;GenBank: AB513134
Supplementary_files_format_and_content: Tab-delimited text files of RSEM output including expected raw readcounts, TPM, FPKM.
|
| |
|
| Submission date |
Feb 21, 2022 |
| Last update date |
Apr 28, 2022 |
| Contact name |
Charles R. M. Bangham |
| E-mail(s) |
c.bangham@imperial.ac.uk
|
| Phone |
+44 20 7594 3730
|
| Organization name |
Imperial College London
|
| Department |
Infectious Disease
|
| Lab |
Bangham Lab
|
| Street address |
Norfolk Place
|
| City |
London |
| ZIP/Postal code |
W2 1PG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE197110 |
Time-course of host cell transcription during the HTLV-1 transcriptional burst |
|
| Relations |
| BioSample |
SAMN26136633 |
| SRA |
SRX14240129 |
