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| Status |
Public on Jul 18, 2024 |
| Title |
CD6 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: C57/BL6J
diet: CD
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from snap-frozen (liquid nitrogen) samples of maternal liver at late gestation using the RNeasy Mini plus kit (Qiagen, UK), in accordance with the manufacturer’s instructions. RNA was treated with QIAseq FastSelect -rRNA HMR, to prevent any rRNA present from being converted into the sequencing library
Stranded RNA-seq libraries were prepared from 500 ng of total RNA per sample, using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (NEB; E7760) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Pairs) (NEBNext; E6440). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (ThermoFisher Scientific; Q32854). Library fragment-length distributions were analysed using the Agilent 4200 TapeStation and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent; 5067-5584 and 5067-5585). Libraries were pooled in equimolar amounts and final library quantification was performed using the KAPA Library Quantification Kit for Illumina (Roche; KK4824). The library pool was sequenced on the Illlumina NextSeq500 over three NextSeq500 High Output 150 cycle kits (Illumina; 20024907), to generate over 40 million pairs of 75-bp paired-end reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw reads were trimmed of Illumina adapters and low quality (Q <20) nucleotides using TrimGalore (v 0.6.7). Reads shorter than 15 bp were discarded.
Trimmed reads were aligned to the Mus musculus reference genome GRCm39 using HISAT2 (v 2.2.1).
StringTie (v 2.2.1) was used to assemble genes and calculate gene abundance. Differential expression analysis was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-deliminated txt file with normalised counts for each samples
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| Submission date |
Apr 24, 2024 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Hannah L Morgan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Nottingham
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| Department |
School of Medicine
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| Street address |
Queens Medical Centre
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| City |
Nottingham |
| ZIP/Postal code |
NG7 2UH |
| Country |
United Kingdom |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE265783 |
Sub-optimal paternal diet at the time of mating perturbs maternal adaptations in the late gestation mouse |
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| Relations |
| BioSample |
SAMN41073906 |
| SRA |
SRX24357600 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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