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Sample GSM4665170 Query DataSets for GSM4665170
Status Public on Mar 31, 2021
Title vagalton#69_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_69_Tri_T4_Female
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 SAMN15499021
SRA SRX8703751

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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