|
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 |