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Sample GSM6598566

Query DataSets for GSM6598566

Status

Public on Oct 13, 2023

Title

2-KTD-M80-3-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