|
| Status |
Public on Dec 29, 2015 |
| Title |
mcidas_TCC_9h |
| Sample type |
SRA |
| |
|
| Source name |
animal cap (dissected ectoderm)
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: animal cap (dissected ectoderm)
harvest time/stage: 9h @ 22 deg after mid-11 (stage 18)
injected mrna: Mcidas-HGR
|
| 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 |
SAMN04372338 |
| SRA |
SRX1503158 |
