|
Status |
Public on Mar 31, 2021 |
Title |
vagalton#43_Tri_T4 |
Sample type |
SRA |
|
|
Source name |
Dio1KO/Dio2KO/Pax8KO_T4_Liver
|
Organism |
Mus musculus |
Characteristics |
strain background: C57Bl/6J age: Postnatal day 14 genotype: Dio1KO/Dio2KO/Pax8KO treatment: T4 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_43_Tri_T4
|
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 |
SAMN15499025 |
SRA |
SRX8703747 |