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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2012 |
| Title |
IgG_shFbxl10 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
chip antibody: IgG (Thermo scientific, 23212, lot LI150449)
cell type: embryonic stem cells
transfection/genotype: shFbxl10
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| Treatment protocol |
Cells were either untransfected or transfected with a scrambled or Fbxl10 specific shRNA
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| Growth protocol |
Mouse ES cells were cultured feeder-free on 0.1% gelatin-coated plates in 2i medium (Dulbecco’s modified Eagle’s medium [DMEM; Hi-Glucose]/Neuralbasel medium 1:1, non-essential amino acids, L-glutamine, b-mercaptoethanol, penicillin/streptomycin, sodium pyruvate, N2, B27 and leukemia inhibitory factor (LIF), GSK3β and MEK1 inhibitors. All cell cultures were maintained at 37 °C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation assays (ChIP) were performed and analysed as previously described {Pasini et al. (2010). Nature. 2010 Mar 11;464(7286):306-10. ES cell DNA was sonicated to an average size between 200-400 bp. The sequencing libraries were constructed using the NEBNext™ DNA Sample Prep Master Mix, NEB combined with Illumina adaptors. The DNA was purified using a Qiaquick PCR purification kit (Qiagen) and amplified by 18 cycles of PCR. The amplified DNA from ChIP-seq experiments was analyzed by Solexa/Illumina high-throughput sequencing. The tags were mapped to the mouse genome (assembly mm9) with the Bowtie alignment tool and the Solexa Analysis Pipeline.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA version 1.8.2 – except: version 1.8.0 for FLAG_HA_IgG, version 1.7.0 for FLAG_HA_FH_Fbxl10
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with parameters: -p 20 -S -m 1 mm9 <FILE>. For “FLAG_HA_FH_Fbxl10” the quality-score was specified by adding the “--solexa1.3-quals” flag
SAM-files were converted to BAM using the “samtools view” command from “Samtools” version 0.1.18, and
BAM-files were converted to BED-files using the “bamToBed” command from “bedtools” version 2.15.0
Genome_build: mm9
Supplementary_files_format_and_content: BED files (BED6)
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| Submission date |
May 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Xudong Wu |
| E-mail(s) |
[email protected]
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| Organization name |
Biotech Research and Innovation Centre
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| Street address |
Ole Maaløes Vej 5
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE37930 |
Fbxl10 regulates PRC1 recruitment to CpG islands and H2A ubiquitination |
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| Relations |
| SRA |
SRX147766 |
| BioSample |
SAMN00993304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM930146_IgG_shFbxl10.bed.gz |
454.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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