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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2023 |
| Title |
metanephros-10% fat+fiber-NZO/HlLtJ-M (ORSAM8984) |
| Sample type |
SRA |
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| Source name |
metanephros
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| Organism |
Mus musculus |
| Characteristics |
tissue: metanephros
diet: 10% fat + fiber
strain: NZO/HlLtJ
Sex: Male
genotype: WT
treatment: None
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| Treatment protocol |
Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at fifteen weeks of age.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
100 bp paired-end to a targeted read depth of 30 million read pairs
ORSAM8984
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| Data processing |
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv
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| Submission date |
Jun 14, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Gary Churchill |
| E-mail(s) |
Gary.Churchill@jax.org
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| Phone |
207-288-6000
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| Organization name |
The Jackson Laboratory
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| Street address |
600 Main St
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| City |
Bar Harbor |
| State/province |
Maine |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE234957 |
Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [kidney] |
| GSE235498 |
Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models |
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| Relations |
| BioSample |
SAMN35739719 |
| SRA |
SRX20683957 |
| 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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