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Sample GSM1982235 Query DataSets for GSM1982235
Status Public on Dec 29, 2015
Title wt_TCC_st10.5_rep2
Sample type SRA
 
Source name whole embryo
Organism Xenopus laevis
Characteristics tissue: whole embryo
harvest time/stage: Stage 10.5
injected mrna: none
Treatment protocol Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.
Growth protocol Whole embryos or animal caps (ectoderm) dissected from embryos at stage 10 were cultured in 0.5x MMR.
Extracted molecule genomic DNA
Extraction protocol Embryos were fixed in 1% paraformaldehyde in PBS for 30 minutes at 22 degrees and fix was quenched with 0.125M glycine. TCC was performed as described (PMID: 22198700) with the following modifications: Tissue was thawed, rinsed in PBS, and lysed directly in 250 ul ice-cold wash buffer with SDS added (50 mM Tris.HCl pH=8.0, 50 mM NaCl, 1 mM EDTA, 0.56% SDS) rather than using lysis buffer.
Following sonication of ligated fragments, we polished and adenylated ends (NEB End-It and A-tailing modules) and ligated Truseq v2 adapters (Illumina).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description Proximity-ligated genomic DNA
Data processing Library strategy: Proximity ligation (TCC/HiC)
TCC reads were aligned to X. laevis genome build v9.1 or v7.1 with bwa mem (PMID: 19451168)
Reads trimmed to nearest mboI site (homerTools, PMID: 20513432)
Reads were combined into tag directories and TADs called with HOMER (PMID: 20513432, 23064439)
Proximity ligation data were used to assemble chromosomes from scaffolds in genome build v7.1 with either Lachesis (PMID: 24185095) or HighRise (arXiv:1502.05331)
Genome_build: X. laevis build v9.1 or v7.1 (http://www.xenbase.org/)
Supplementary_files_format_and_content: Bed file of TADs from all 9h timepoints (stage 18 ectoderm)
 
Submission date Dec 28, 2015
Last update date May 15, 2019
Contact name Ian K Quigley
E-mail(s) iquigley@salk.edu
Phone 858-453-4100
Organization name Salk Institute
Department Molecular Neurobiology Lab
Lab Kintner
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL18936
Series (1)
GSE76363 3D chromosomal capture of X. laevis
Relations
BioSample SAMN04372340
SRA SRX1503160

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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