|
| Status |
Public on Feb 28, 2017 |
| Title |
HG noHS rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
HG_noHS
|
| Organism |
Xenopus laevis |
| Characteristics |
Stage: NF20
tissue: Hindgut explants
genotype/variation: wild type
treatment: no Heatshock
|
| Treatment protocol |
Small molecule inhibitors were dissolved in DMSO and embryos were cultured from stages NF12-20 with either DMSO vehicle in 0.1XMBS or 40 μM DMH1 (TOCRIS) or BIO (60 μM; TOCRIS). To activate the hsp:Dkk1GFP transgene, we gave a pulse of 30min in 37C followed by incubation at 13C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from two or three independent biological replicates using the Nucleo-spin RNA kit (Machery-Nagel).
Libraries were constructed with TruSeq Stranded mRNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality check and trimming of raw reads was performed using FastQC and Trimmomatic, respectively at default parameters. Quality trimmed Reads were mapped to the X. laevis genome 9.1 and quantified using RSEM at default parameters.
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Matrix with genes and samples providing expression of genes in each sample in TPM(Transcripts per Million). File is in .xlsx format
|
| |
|
| Submission date |
Oct 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron M Zorn |
| E-mail(s) |
aaron.zorn@cchmc.org
|
| Phone |
636 3770
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Develpomental Biology
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45236 |
| Country |
USA |
| |
|
| Platform ID |
GPL18936 |
| Series (2) |
| GSE87653 |
Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [RNA-seq] |
| GSE87654 |
Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors |
|
| Relations |
| BioSample |
SAMN05864172 |
| SRA |
SRX2213260 |
