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Status |
Public on Oct 13, 2023 |
Title |
1-KTD-M80-2-L |
Sample type |
SRA |
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Source name |
Liver tissue
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Organism |
Mus musculus |
Characteristics |
sample group: Plin2+/+ Fed strain: C57BL/6N timepoint: 15-week old
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Growth protocol |
Female 15-week old Plin2+/+ and Plin2-/- mice on C57BL/6N background fed chow or fasted for 24h.
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Sep 23, 2022 |
Last update date |
Oct 13, 2023 |
Contact name |
Atanaska Doncheva |
Organization name |
University of Oslo
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Street address |
Songsvannveien
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City |
Oslo |
ZIP/Postal code |
0371 |
Country |
Norway |
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Platform ID |
GPL24247 |
Series (1) |
GSE214064 |
Altered hepatic lipid droplet morphology and lipid metabolism in fasted Plin2 null mice |
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Relations |
BioSample |
SAMN30986036 |
SRA |
SRX17682681 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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