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Sample GSM3368768 Query DataSets for GSM3368768
Status Public on May 27, 2019
Title 5C_WT #1
Sample type SRA
 
Source name mouse ES cells E14Tg2a
Organism Mus musculus
Characteristics strain: 129/Ola, XY
genotype: WT
capture-c viewpoint: NA
Treatment protocol NA
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.
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
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description 5C
E14_B100_A836
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)
 
Submission date Aug 30, 2018
Last update date May 27, 2019
Contact name Nicolas Servant
E-mail(s) Nicolas.Servant@curie.fr
Organization name Institut Curie
Street address 26 rue d'ulm
City Paris Cedex 05
ZIP/Postal code 75248
Country France
 
Platform ID GPL17021
Series (1)
GSE111205 The bipartite TAD organization of the X-inactivation centre ensures opposing developmental regulation of Tsix and Xist
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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