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| Status |
Public on Aug 01, 2023 |
| Title |
ZBTB33/KAISO-ChIP |
| Sample type |
SRA |
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| Source name |
T98G
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| Organism |
Homo sapiens |
| Characteristics |
cell line: T98G
cell type: Brain-Glioblastoma
chip antibody: KAISO(6F8, Santa Cruz, sc-23871)
treatment: untreated
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| Treatment protocol |
For cell transduction, the virus was added to the medium with the cells in suspension, and replaced with fresh complete DMEM 24 h after infection and seeding. Selection of infected cells was performed by adding 1.25 mg/ml of puromycin (Sigma) for 48-72 h, and cells were allowed to recover in the absence of puromycin for 24 h.
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| Growth protocol |
Human cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and antibiotics (100 U/ml penicillin and 100 µg/ml streptomycin). mESCs were maintained in 0.1% gelatin (Millipore ES-006-B)-coated plates mESC medium, which consisted of DMEM supplemented with 15% FBS, L– glutamine (2 mM), penicillin (100 U/ml), streptomycin (100 µg/ ml), sodium pyruvate (1 mM), non-essential amino acid (NEAA) (0,1 mM), 2-mercaptoethanol (0,5 mM) and ESGRO mLif (1000 U/ml).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
DNA libraries were generated by using the OvationÒ Ultralow Library System V2 (NuGEN) following the manufacturer’s instructions. To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference (or to the mm9 mouse genome reference) using Bowtie and aligning parameters of unique- ness (-S –m1 –v2 –t –q).
p values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38 or mm9
Supplementary_files_format_and_content: peak text files and bigwig files
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| Submission date |
Aug 06, 2020 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Chiara Di Vona |
| E-mail(s) |
chiara.divona@crg.eu
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| Organization name |
CRG
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| Department |
Gene Regulation, Stem Cells and Cancer
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| Lab |
Gene Function
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| Street address |
Carrer Dr. Aiguader 88
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| City |
Barcelona |
| State/province |
Spain |
| ZIP/Postal code |
08011 |
| Country |
Spain |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE155807 |
The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells [ChIP-seq] |
| GSE155809 |
The DYRK1A protein kinase is recruited to a subset of ribosomal protein gene promoters in human and mouse cells |
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| Relations |
| BioSample |
SAMN15748038 |
| SRA |
SRX8899553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4712420_ZBTB33_LB11_peaks.txt.gz |
2.5 Kb |
(ftp)(http) |
TXT |
| GSM4712420_ZBTB33_LB11_poissP.bigwig |
245.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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