|
| Status |
Public on Mar 31, 2021 |
| Title |
vagalton#2019_Tri |
| Sample type |
SRA |
| |
|
| Source name |
Dio1KO/Dio2KO/Pax8KO_Vehicle_Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6J
age: Postnatal day 14
genotype: Dio1KO/Dio2KO/Pax8KO
treatment: Vehicle
tissue: Liver
|
| Treatment protocol |
Mice were injected every other day with thyroid hormones or vehicle starting at postnatal day 2 until sacrifice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver samples were frozen on dry ice and total RNA was extracted using TRIzol solution from Invitrogen according to the manufacturer's instructions
Library synthesis for RNA-Seq was performed with 1 ug of high quality RNA [RIN 7.5 or higher] using the Illumina TruSeq mRNA Stranded library synthesis as described by the manufacturer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
vagalton_T4_20141104_2019_Tri_Male
|
| Data processing |
Illumina bcl2fastq used for basecalling
Sequences were trimmed of adaptor sequences, bases <Q15, and length >50bp using Trimmomatic
Reads passing QC were mapped to the human genome (GRCh38, version 38, Ensembl 78) using bwa 0.7.10
A counts matrix was made using DESeq's summarizedExperiment
Genome_build: GRCh38 version 38 Ensembl 78
Supplementary_files_format_and_content: raw counts at the gene level for each sample
|
| |
|
| Submission date |
Jul 09, 2020 |
| Last update date |
Mar 31, 2021 |
| Contact name |
Valerie Anne Galton |
| E-mail(s) |
val.galton@dartmouth.edu
|
| Organization name |
Dartmouth Geisel School of Medicine
|
| Department |
Physiology and Neurobiology
|
| Street address |
1 Medical Center Drive
|
| City |
Lebanon |
| State/province |
New Hampshire |
| ZIP/Postal code |
03756 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE154156 |
The Intrinsic Activity of Thyroxine is Critical for Survival and Growth and Regulates Gene expression in Neonatal Liver |
|
| Relations |
| BioSample |
SAMN15499031 |
| SRA |
SRX8703741 |
