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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2016 |
| Title |
Input virus |
| Sample type |
SRA |
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| Source name |
3T3-L1_Input virus
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| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3-L1
cell type: Preadipocyte cell line
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| Treatment protocol |
Two days post confluency (day 0), 3T3-L1 cells were induced to differentiate using a standard cocktail of adipogenic inducers (dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and fetal bovine serum). Two days post induction (day 2), medium was changed to DMEM supplemented with fetal bovine serum and insulin. Cells were maintained in DMEM supplemented with fetal bovine serum for the remainder of the differentiation. For knock down experiments, pre-confluent 3T3-L1 cells were transduced 4 days before induction of differentiation by incubation for 24 hours at 37°C with medium containing lentiviral constructs (shKDM5A/B/C or control shLuc) and 6 μg/mL polybrene (Sigma). After 24 hours the medium was changed to normal growth medium.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed in 3T3-L1 cells essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
For normalization of H3K4me3 and matching input libraries a two-stage normalization was used. First, genome-scale normalization on background reads were done by counting tags in 10kb windows throughout the genome as described in (Lun and Smyth, 2014, Nucleic Acid Res. 42:1-11) and normalized using a relative log expression (RLE) method normalization (Love et al., 2014, Genome Bio. 15: 550). Second, the signal in peaks was normalized for each condition over time, but not across conditions.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: H3K4me3_promoter_peaks_tags.txt: Table containing promoter H3K4me3 binding sites, including normalized tag counts for H3K4me3 libraries
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C libraries
RNA_all_genes_log2_tags_kb.txt: Table containing gene expression data for all RNA-seq libraries (reported as log2(tags/kb))
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| Submission date |
Jul 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ann-Sofie Bøgh Brier |
| E-mail(s) |
a.boegh@me.com
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| Phone |
+4522969284
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| Organization name |
University of Southern Denmark, Odense
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| Department |
Department of Biochemistry and Molecular Biology
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| Lab |
Mandrup lab
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| Street address |
Campusvej 55
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| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE84410 |
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation |
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| Relations |
| BioSample |
SAMN05391996 |
| SRA |
SRX1949132 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2233355_SM455_GTCCGC_3T3-L1_INPUT_D0_Virus.TD.ucsc.bedGraph.gz |
32.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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