|
| Status |
Public on Apr 15, 2021 |
| Title |
ChIP-seq for Lim1/Lhx1 |
| Sample type |
SRA |
| |
|
| Source name |
early gastrula embryo (st 10.5)
|
| Organism |
Xenopus tropicalis |
| Characteristics |
strain: Nigerian A
chip antibody: Lim1-Lhx1 (Sudou et al., 2012)
tissue: early gastrula embryo
Stage: st 10.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei of 2000-3000 fixed embryos and protein-DNA complexes were isolated by antibody.
Libraries were prepared for the Illumina GAIIx according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Raw reads were mapped xenopus tropicalis (v9.1) genome using CSBB-v3.0 (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists)
Mapped reads in Bam format were used to call peaks using MACS2.
Mapped reads in Bam format were used to bigwigs using deeptools
Genome_build: xenopus tropicalis v9.1
Supplementary_files_format_and_content: bigwigs and bed
|
| |
|
| Submission date |
Apr 14, 2021 |
| Last update date |
Apr 15, 2021 |
| Contact name |
Aaron Zorn |
| E-mail(s) |
ZornLab1@gmail.com, Aaron.Zorn@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital and Medical Center
|
| Department |
Developmental Biology
|
| Lab |
Zorn Lab
|
| Street address |
240 Albert Sabin Way, Bld S
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24898 |
| Series (1) |
| GSE172076 |
Occupancies of tissue-specific cis-regulatory modules by Spemann-Mangold organizer-specific transcription factors for embryonic head specification |
|
| Relations |
| SRA |
DRX001274 |
| BioSample |
SAMD00009338 |
