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| Status |
Public on May 03, 2023 |
| Title |
2517-RP-57 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Cavia porcellus |
| Characteristics |
breed: Hartley
tissue: Kidney
Sex: male
time point: 33 h
agent: High (1.50 mg/kg HgCl2)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen whole kidney samples were powdered in liquid nitrogen, since these organs are histologically heterogeneous. Total RNA was isolated from powdered kidney, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Treatment
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| Data processing |
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Cavia porcellus (Cavpor3.0) transcriptome downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample" $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Assembly: Cavia porcellus transcriptome (Cavpor3.0)
Supplementary files format and content: tab-delimited text files, including abundance measurements
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| Submission date |
Feb 28, 2023 |
| Last update date |
May 03, 2023 |
| Contact name |
Himanshu Goel |
| E-mail(s) |
hgoel@bhsai.org
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| Organization name |
Biotechnology HPC Software Applications Institute (BHSAI)
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| Street address |
2405 Whittier Drive, Suite 200
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| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
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| Platform ID |
GPL28437 |
| Series (2) |
| GSE226312 |
Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments [in vivo] |
| GSE226313 |
Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments |
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| Relations |
| BioSample |
SAMN33548549 |
| SRA |
SRX19533248 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7072856_T.57_lh33.txt.gz |
395.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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