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| Status |
Public on Sep 29, 2022 |
| Title |
Input, rep1 |
| Sample type |
SRA |
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| Source name |
U2OS cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS-derived UTA6 cells
cell type: osteosarcoma cell
clone: U2OS-derived UTA6 clone
chip antibody: none
treatment: untreated
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| Treatment protocol |
experiments were carried out in 2 independent replicates for JUNB and input
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| Growth protocol |
U20S-derived UTA6 cells (Englert C, Hou X, Maheswaran S, Bennett P, Ngwu C, Re G G, Garvin A J, Rosner M R, Haber D A. WT1 suppresses synthesis of the epidermal factor receptor and induces apoptosis. EMBO J. 1995;14:4662–4675) were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and JUNB complexes were isolated with the appropriate antibodies.
ChIP-seq libraries were prepared using the TruSeq ChIP sample reparation kit from Illumina by the MGX sequencing Platform (Montpellier, France) ChIP-seq - Instrument model : Illumina HiSeq 2500 (MGX Platform, Montpellier France).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
UTD6 input 10 11a
macs14_UTD6_I_10_11a_vs_UTD6_input_10_11a_model-s_peaks.bed
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| Data processing |
Reads were aligned to the human genome (hg19) using CASAVA (Illumina)
Peak calling was performed using MACS2 and p-value cutoff 1.00e-05, setting as control the input samples.
Only peaks found across biological replicates (BEDtools (Quinlan, A.R. and I.M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 2010. 26(6): p. 841-2.)), 1 bp minimum overlapping, were considered as binding sites for downstream analysis. BED files from biological replicates were merged.
Genome_build: Hg19
Supplementary_files_format_and_content: bed
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| Submission date |
Feb 02, 2022 |
| Last update date |
Sep 29, 2022 |
| Contact name |
Rosa Farràs |
| E-mail(s) |
rfarras@cipf.es
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| Phone |
+34963289680
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| Organization name |
Centro de Investigación Príncipe Felipe
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| Street address |
Eduardo Primo Yúfera, 12
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| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46012 |
| Country |
Spain |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE195991 |
JUNB ChIP-seq |
| GSE195993 |
JUNB transcriptional regulation in cell cycle control and tumorigenic cell invasion |
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| Relations |
| BioSample |
SAMN25600056 |
| SRA |
SRX14024457 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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