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| Status |
Public on Nov 18, 2024 |
| Title |
N4wK (A038) |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
strain: C57BL/6J
genotype: WT
treatment: Control
timepoint: 4 weeks
Sex: male
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| Treatment protocol |
mice were treated with 2DG (6g/L) through water or just water for 96 hours or 4 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bulk RNA of the 9 excised tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) (4 samples per treatment and time combination) was isolated with the QIAGEN miRNeasy mini extraction kit (QIAGEN) and cDNA was synthesized with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2.
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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 |
Bulk RNA of the 9 excised tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) (4 samples per treatment and time combination) was isolated with the QIAGEN miRNeasy mini extraction kit (QIAGEN) and cDNA was synthesized with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). RNA quality was assessed with a Bioanalyzer 2100 (Agilent Technologies). Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2. RNA-seq was performed in a 150-bp paired-end format with a minimum of 40 million reads per sample on the Illumina HiSeq platform according to the manufacturer’s instructions. RNA-seq reads were filtered and trimmed for quality scores >30 using a custom python script. The filtered reads were aligned to Mus musculus GRCm38 using RSEM (v1.2.12) (58) with Bowtie2 (v2.2.0)(21) (command: rsem-calculate-expression -p 12--phred33-quals --seed-length 25 --forward-prob 0 --time --output-genome-bam -- bowtie2).RSEM calculates expected counts and transcript per million (TPM). The expected counts from RSEM were used in the Bioconductor edgeR 3.20.9 package(22-24) to determine differentially expressed genes.
Assembly: Mus musculus GRCm38
Supplementary files format and content: .Rdata contains FPKM counts
Supplementary files format and content: tab-delimited text file contains expected count, TPM, and FPKM
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| Submission date |
Nov 29, 2023 |
| Last update date |
Nov 18, 2024 |
| Contact name |
Chih-Hao Chang |
| E-mail(s) |
[email protected]
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| Organization name |
The Jackson Laboratory
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| Street address |
600 Main Street
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE248967 |
Transcriptome Analysis Reveals Organ-Specific Effects of 2-Deoxyglucose Treatment in Healthy Mice |
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| Relations |
| BioSample |
SAMN38504940 |
| SRA |
SRX22684591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7923747_A038_R003-P3-8-F05_S38_L003.txt.gz |
804.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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