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| Status |
Public on May 27, 2019 |
| Title |
5C_WT #1 |
| Sample type |
SRA |
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| Source name |
mouse ES cells E14Tg2a
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| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola, XY
genotype: WT
capture-c viewpoint: NA
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| Treatment protocol |
NA
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| Growth protocol |
Feeder-independent male mouse ESCs (E14Tg2a.4, Sanger) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged every 48h. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative. E14Tg2a.4 cells were transfected with CRISPR plasmids or TALENs to generate targeted inversions or deletions. Generated clones were validated by PCR and Sanger sequencing.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates and scraped off; For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate; For RAP cells were fixed and lysed.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using NEBNext kit; RNA-seq libraries were generated using the TruSeq Stranded mRNA kit (Illumina); RAP libraries were genrated using NEBNext kit.
5C, Capture-C, RNA-seq, RAP
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
5C
E14_B100_A836
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| Data processing |
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Genome_build: mm9
Supplementary_files_format_and_content: 5C processed data files represent the contact counts between each pairs of 5C primers (reverse/forward)
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| Submission date |
Aug 30, 2018 |
| Last update date |
May 27, 2019 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
Nicolas.Servant@curie.fr
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| Organization name |
Institut Curie
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| Street address |
26 rue d'ulm
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| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE111205 |
The bipartite TAD organization of the X-inactivation centre ensures opposing developmental regulation of Tsix and Xist |
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| Relations |
| BioSample |
SAMN09939174 |
| SRA |
SRX4626848 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3368768_B100_E14_bwt2_rf.matrix.gz |
941.7 Kb |
(ftp)(http) |
MATRIX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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