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Sample GSM6598565 Query DataSets for GSM6598565
Status Public on Oct 13, 2023
Title 1-KTD-M80-2-L
Sample type SRA
 
Source name Liver tissue
Organism Mus musculus
Characteristics sample group: Plin2+/+ Fed
strain: C57BL/6N
timepoint: 15-week old
Growth protocol Female 15-week old Plin2+/+ and Plin2-/- mice on C57BL/6N background fed chow or fasted for 24h.
Extracted molecule total RNA
Extraction protocol RNA was isolated with a NucleoSpin RNA mini kit (Machery-Nagel), according to the manufacturer’s instructions.
Strand-Specific TruSeqTM mRNA-seq library preparation
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing 50 bp paired end reads were sequenced on an Illumina Novaseq 600 intrument
BBDuk (BBMap v34.56) was used to remove/trim low-quality reads and adapter sequences
Reads were mapped to a human reference genome/transcriptome (ENSEMBL release 101, GRCh38.101) using HiSat2 v.1.2.1
Read counting was done with FeatureCounts v1.4.6-p1
Assembly: GRCh38.101
Supplementary files format and content: Normalized_gene_counts_TPM.csv is a csv file that containes normalised counts (TPM), for all samples, annotated to ensembl/entrez/hgnc. Unnormalised_feature_counts.csv is a csv file containing unnormalised counts for all samples, annotated to ensembl, generated in HiSat2 v.1.2.1
 
Submission date Sep 23, 2022
Last update date Oct 13, 2023
Contact name Atanaska Doncheva
Organization name University of Oslo
Street address Songsvannveien
City Oslo
ZIP/Postal code 0371
Country Norway
 
Platform ID GPL24247
Series (1)
GSE214064 Altered hepatic lipid droplet morphology and lipid metabolism in fasted Plin2 null mice
Relations
BioSample SAMN30986036
SRA SRX17682681

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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