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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 19, 2015 |
| Title |
chr11_reciprocal_Asic2_vp_LacR_4C-Seq_R1 |
| Sample type |
SRA |
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| Source name |
LacO transgenic embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: LacO transgenic embryonic stem cells
tissue/cell line: cell line
strain: F1s from 129/Sv x C57BL/6
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| Treatment protocol |
cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS
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| Growth protocol |
Mouse embryonic stem cells C57Bl/6-129/Sv were cultured on gelatin-coated plates in BRL (buffalo–rat liver cells)-conditioned DMEM (Hooper et al., 1987)(high glucose, Gibco) with 15% FBS, 1x non-essential amino acids (NEAA; Gibco), 1x penicillin–streptomycin (Gibco), 1:1000 b-mercaptoethanol (Invitrogen), 1x L-glutamine (Gibco) and 1000 U ml-1 leukaemia inhibitory factor (LIF; Gibco).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Cells are cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with HindIII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (DpnII or NlaIII). After a second re-ligation step, the sample is purified and a 4C PCR is performed.
4C PCR
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII sites (4C fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome mm9.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle tracks contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located. Scores represent the number of reads mapping to a HindIII restriction fragment end.
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| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Geert Geeven |
| E-mail(s) |
geertgeeven@yahoo.com
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| Organization name |
Hubrecht Institute
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| Department |
Biomedical Genomics
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| Lab |
Wouter de Laat
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE76174 |
Cause and consequence of tethering a sub-TAD to different nuclear compartments |
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| Relations |
| BioSample |
SAMN04351340 |
| SRA |
SRX1492075 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1975791_chr11_reciprocal_Asic2_vp_LacR_4C-Seq_R1_mapped_reads_cis.wig.gz |
256.1 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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