|
| Status |
Public on Jul 19, 2022 |
| Title |
WT-in-control_3 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine at stage 54, wild type, no T3 treatment
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage: stage 54
tissue: Intestine
genotype: wild type
treatment: no T3
|
| Treatment protocol |
When tadpoles reached to around stage 54, tadpoles of T3 groups were treated with 10nM T3 for 18 hours.
|
| Growth protocol |
Intestinal samples were collected from WT and TRα (-/-) tadpoles which born from same parents.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Intestinal chromatin DNA was extracted and IP was performed with TR antibody. After purification of ChIP-DNA, all purified DNA was used for the construction of sequencing libraries.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Short reads mapping (Bowtie2 v2.3.4.1)
Peak calling (MACS2 v2.1.1.20160309)
Genome_build: Ensembl Xenopus_tropicalis.JGI_4.2 and Xenbase v9.1
Supplementary_files_format_and_content: peak text files
|
| |
|
| Submission date |
Nov 18, 2020 |
| Last update date |
Mar 16, 2023 |
| Contact name |
Ryan Dale |
| E-mail(s) |
dalerr@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Child Health and Human Development
|
| Lab |
Bioinformatics and Scientific Programming Core
|
| Street address |
Rm 10D39, 10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21875 |
| Series (1) |
| GSE161718 |
Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway |
|
| Relations |
| BioSample |
SAMN16826907 |
| SRA |
SRX9527554 |
