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Sample GSM5828122 Query DataSets for GSM5828122
Status Public on Jan 23, 2022
Title iSLK-UR
Sample type SRA
 
Source name iSLK.219 cells
Organism Homo sapiens
Characteristics cell type: iSLK.219 cells
treatment: --
Treatment protocol Lytic reactivation cells were induced by the addition of 0.2 μg/ml doxycycline (BD Biosciences) and 110 μg/ml sodium butyrate for 48 h
Growth protocol ISLK.219 cells were grown were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS), and were harvested in their latent phase or 48h post reactivation.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using TRIzol according to the manufacturer's protocol. Samples were sent to Eclipse Bio for m6A eCLIP enrichment then subsequent RNA seq and processing
samples were processed by EclipseBio as described in their user guide, performing 150 Paired End run on NovaSeq6000 on was PolyA selected RNA
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description m6A eCLIP-RNA seq
Data processing Only the forward (R1" reads were used for the analysis.
Bam and bigWig files for each of the IP and input libraries to vizualize read alignment, KSHV genome is added as an extra genome for comparison
Eclipse used PureCLIP (https://pureclip.readthedocs.io/en/latest/) to identify m6A sites with a single nucleotide resolution. This algorithm identifies crosslink sites in eCLIP experiments, and it is not specifically trained to call m6A sites or required to ensure that crosslink site calls correspond to Adenosines. Therefore, as a part of the evaluation, we assessed enrichment of DRACH motif relative to reads starts in IP and input libraries, as well as calculated what fraction of identified crosslink sites are positioned on DRACH
Supplementary_files_format_and_content: Two files containing the PureCLIP start and stop locations of m6A sites. Labeled with the chromosome, strand, gene, Ensembl ID and feature. It also features the read start fold change. One file are the UR iSLK.219s and the other the 48R iSLK.219 sample
 
Submission date Jan 20, 2022
Last update date Jan 24, 2022
Contact name Daniel MacVeigh-Fierro
E-mail(s) dmacveighfie@umass.edu
Organization name UMass Amherst
Department Microbiology
Lab Muller Lab
Street address 639 N Pleasant St, Morrill Iv North
City Amherst
State/province MA
ZIP/Postal code 01003
Country USA
 
Platform ID GPL24676
Series (1)
GSE194100 The m6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay
Relations
BioSample SAMN25144803
SRA SRX13845827

Supplementary file Size Download File type/resource
GSM5828122_G_iSLK-UR_R1.CombinedID.merged.r2.norm.neg.bw 20.7 Mb (ftp)(http) BW
GSM5828122_G_iSLK-UR_R1.CombinedID.merged.r2.norm.pos.bw 21.8 Mb (ftp)(http) BW
GSM5828122_G_iSLK-UR_R1_01.basedon.peaks.l2inputnormnew.bed.compressed.bed.gz 1.5 Mb (ftp)(http) BED
GSM5828122_TABLE_S2_ISLK_UR.xlsx 18.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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