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Series GSE119026 Query DataSets for GSE119026
Status Public on Oct 15, 2019
Title m6A-RNA mapping, SND1-RNA binding profile mapping and SND1-depletion in KSHV-infected B-lymphocytes
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary We have mapped m6A sites and endogenous SND1 binding sites in the viral and cellular transcriptome using TREx BCBL1-Rta cells. In addition, we have depleted SND1 in TREx BCBL1-Rta cells and BCBL1 cells and analyzed their RNA expression profile both during latency and lytic replication.
Overall design Identification of m6A sites in TREx BCBL1-Rta cells at 0h, 8 and 20 h post-lytic reactivation. SND1 transcriptome-wide binding profile in TREx BCBL1-Rta cells at 0h, 8 and 20 h post-lytic reactivation. RNA expression profile in scramble and SND1-depleted cells in both latent and reactivated TREx BCBL1-Rta cells for 24 h. Same RNA expression profile in shRNA scramble and shRNA SND1-depleted BCBL1 cells.
Contributor(s) Baquero-Perez B, Antanaviciute A, Carr I, Whitehouse A
Citation(s) 31647415
Submission date Aug 24, 2018
Last update date Nov 04, 2019
Contact name Agne Antanaviciute
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
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (43)
GSM3356744 m6A IP Rep1 0H
GSM3356745 m6A IP Rep1 8H
GSM3356746 m6A IP Rep1 20H
BioProject PRJNA487788
SRA SRP158777

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Supplementary file Size Download File type/resource
GSE119026_RAW_READ_COUNTS_SND1_KO_BCBL.xlsx 9.9 Mb (ftp)(http) XLSX
GSE119026_RAW_READ_COUNTS_SND1_KO_TREX.txt.gz 3.7 Mb (ftp)(http) TXT
GSE119026_SND1_RIP_RAW_COUNTS.txt.gz 3.9 Mb (ftp)(http) TXT
GSE119026_m6A_peak_calls.xlsx 10.1 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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