|
| Status |
Public on Apr 17, 2021 |
| Title |
9h (1) |
| Sample type |
SRA |
| |
|
| Source name |
osteosarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone
cell line: U2OS
developmental stage: 9h
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_9h.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 |
SAMN14608487 |
| SRA |
SRX8127318 |
