|
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 |