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Sample GSM6048101 Query DataSets for GSM6048101
Status Public on Nov 19, 2022
Title Rep A-Input-P1
Sample type SRA
 
Source name HCT116 with ORF59 reporter
Organism Homo sapiens
Characteristics cell line: HCT116 colorectal line derivative
treatment: PNUTS siRNA, siP1
chip antibody: none
Treatment protocol Cells were treated with 30nM of indicated siRNA 96 hrs prior to harvesting.
Growth protocol All cell lines were grown at 37°C with 5% CO2, with 1X penicillin-streptomycin (Sigma), and 2mM L-glutamine (Fisher) in DMEM (Sigma) supplemented with 10% FBS (Sigma);
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 0.5% formaldehyde at RT for 10 min then quenched with 150 mM glycine at room temperature, 5 min. Cells were harvested by scraping in cold 1X PBS and pelleted at 1000 x g, 5 min at 4°C. Harvested cells were lysed for 30 min at 4°C in Farnham lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X protease inhibitor cocktail (PIC)). Additional details of Dna shearing, and IP are given in Devlin et al. 2022.
For ChIP-seq library preparations, 4 ng of ChIP or input DNA was processed using the KAPA Hyper Prep Kit according to the manufacturer’s protocol (Roche KK8504).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Single end sequenced reads were trimmed for adaptor sequence and filtered for quality with trim galore/0.6.4, and aligned to synthetic genome assembly (ORF59_reporter integatred into GRCh38 and dm6) using Bowtie2/2.3.2
The aligned reads were subsequently filtered for mapping quality (MAPQ 30) and PCR duplicates by SAMtools/1.6 and Picard. Uniquely mappable reads were retained for further analysis.
SpikeIN normalizations were performed after calculating scaling factor for each data set.
MACS2 was used for peak calling and generation of Input normalized (subtracted) coverage tracks.
Assembly: chimera genome assembly (ORF59_reporter integrated into chr19:55,115,766-55,121,825 of GRCh38)
Supplementary files format and content: Normalized Bigwig files
 
Submission date Apr 18, 2022
Last update date Nov 19, 2022
Contact name Nicholas K Conrad
E-mail(s) nicholas.conrad@utsouthwestern.edu
Phone 2146480795
Organization name UT Southwestern Medical Center
Department Microbiology
Street address 6000 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75063
Country USA
 
Platform ID GPL16791
Series (2)
GSE200992 The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication [ChIP-seq]
GSE201046 The PNUTS-protein phosphatase 1 complex acts as an intrinsic barrier to KSHV replication
Relations
BioSample SAMN27622635
SRA SRX14894049

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

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