|
| Status |
Public on Oct 15, 2019 |
| Title |
SND1 Scramble Rep1 Lytic |
| Sample type |
SRA |
| |
|
| Source name |
SND1 Scramble Lytic, KSHV-infected B-lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: BCBL1 cells
infection: KSHV
shRNA: Scramble shRNA (Addgene plasmid # 1864)
|
| Treatment protocol |
For virus reactivation, TREx BCBL1-Rta cells were induced using 2 μg/mL doxycycline hyclate (Sigma-Aldrich) and BCBL1 cells were induced using 2 nM
|
| Growth protocol |
BCBL1 cells were grown in RPMI1640 growth medium with glutamine (Gibco) supplemented with 10% (v/v) FCS (Gibco) and 1% (v/v) P/S (Gibco). TREx BCBL1-Rta cells were grown in RPMI1640 growth medium with glutamine (Gibco) supplemented with 10% (v/v) FCS, (Gibco), 1% P/S (v/v) (Gibco) and 100 μg/mL hygromycin B (Thermo Scientific). sodium butyrate (Sigma-Aldrich).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was used for m6A-seq and RNA-seq. For SND1-seq, input libraries were made from total RNA isolated with TRIzol (Thermo Fisher) and RIP libraries were made from sonicated SND1 enriched RNA which had been purified with TRIzol LS (Thermo Scientific).
m6A-seq libraries were made using NEBNext Ultra kit (NEB) according to the manufacturer’s protocol. RIP-seq and RNA-seq libraries were made using TruSeq Stranded Total RNA library production kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
processed data file: RAW_READ_COUNTS_SND1_KO_BCBL.xlsx
processed data column header: S0HLyticSND1
|
| Data processing |
Raw Reads were trimmed using Cutadapt software for Illumina adapter sequences and poor quality bases
Reads were aligned against hg38 analysis set reference genome and KSHV genome sequences using STAR aligner
Duplicates were marked using Picard Tools
Peaks were called using m6aViewer software
Raw read counts were obtained using Rsubread featureCounts software
Size-factor normalisation was performed using DESeq2 r package
Genome_build: hg38
Supplementary_files_format_and_content: [m6A peak calls.xlsx] Excel spreadsheet with m6A peak calls
[SND1_RIP_RAW_COUNTS.txt] tab delimited raw read counts
[RAW_READ_COUNTS_SND1_KO_TREX.txt] tab delimited raw read counts
[RAW_READ_COUNTS_SND1_KO_BCBL.xlsx] Excel spreadsheed with raw read counts
|
| |
|
| Submission date |
Aug 24, 2018 |
| Last update date |
Oct 15, 2019 |
| Contact name |
Agne Antanaviciute |
| E-mail(s) |
umaan@leeds.ac.uk
|
| Organization name |
University of Leeds
|
| Street address |
University of Leeds, St. James’s University Hospital
|
| City |
leeds |
| ZIP/Postal code |
LS9 7TF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE119026 |
m6A-RNA mapping, SND1-RNA binding profile mapping and SND1-depletion in KSHV-infected B-lymphocytes |
|
| Relations |
| BioSample |
SAMN09910100 |
| SRA |
SRX4607573 |
