NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3356768 Query DataSets for GSM3356768
Status Public on Oct 15, 2019
Title SND1 INPUT Rep2 8H
Sample type SRA
 
Source name SND1 INPUT 8H, KSHV-infected B-lymphocytes
Organism Homo sapiens
Characteristics cell type: TREx BCBL1-Rta cells
infection: KSHV
ip antibody: none
time: 8H
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 RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Description processed data file: SND1_RIP_RAW_COUNTS.txt
processed data column header: run3_8HInput
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 SAMN09910106
SRA SRX4607567

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap