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Sample GSM4481346 Query DataSets for GSM4481346
Status Public on Apr 17, 2021
Title 0h (1)
Sample type SRA
 
Source name osteosarcoma
Organism Homo sapiens
Characteristics tissue: bone
cell line: U2OS
developmental stage: 0h
antibody: gamma tubulin
Treatment protocol Cells were subjected to dubble thymidine syncronization and released for 0h, 3h, 5h, 7h, 9h prior to harvest. Alternatively, cells were kept in confluency 48 h before harvesting.
Growth protocol U2OS osteosarcoma epitelial cells were grown in McCoy'5A medium supplemented with 5% fetal calf serum and 1% PEST.
Extracted molecule genomic DNA
Extraction protocol Nuclei were lysed and sonicated. Nuclei were cleared and gamma-tubulin-DNA-complexes or PCNA-DNA-complexes were isolated with antibody.
Libraries were prepared according to AB libray builder system instructions accompanying the DNA Sample Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB 5500 Genetic Analyzer
 
Description gTub_0h.bedgraph
Data processing SOLiD XSQ files were converted into color based fastq file using XSQConvertor version v10:03-07-2013
ChIP-seq reads were aligned to the hg19 genome assembly using BFAST version 0.70a
Peaks were called using PeakSeq version 1.31 with FDR cutoff of 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated; Scores represent signal values
 
Submission date Apr 16, 2020
Last update date Apr 17, 2021
Contact name Maria Alvarado-Kristensson
Organization name Lund University
Street address 59 Jan Waldenstr ms street
City Lund
ZIP/Postal code 20502 Malm
Country Sweden
 
Platform ID GPL16558
Series (1)
GSE148798 The g-tubulin meshwork assists to the transport of cytosolic PCNA to chromatin in mammalian cells
Relations
BioSample SAMN14608473
SRA SRX8127309

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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