|
| Status |
Public on May 03, 2023 |
| Title |
2818-RP-4 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Cavia porcellus |
| Characteristics |
breed: Hartley
tissue: Renal tube epithelial cells
time point: 12 h
agent: Vehicle
|
| Growth protocol |
We cultured renal cells for 48 hours before expososure to mercuric chloride or vehicle (Hepatocyte Maintenance Medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific) and further purifed from the aqueous phase of TRIzol using RNeasy Plus Mini kit (Qiagen) and eliminated genomic DNA by in-column DNase I digestion. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Control
|
| 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
|
| |
|
| Submission date |
Feb 28, 2023 |
| Last update date |
May 03, 2023 |
| Contact name |
Himanshu Goel |
| E-mail(s) |
hgoel@bhsai.org
|
| Organization name |
Biotechnology HPC Software Applications Institute (BHSAI)
|
| Street address |
2405 Whittier Drive, Suite 200
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL28437 |
| Series (2) |
| GSE226311 |
Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments [in vitro] |
| GSE226313 |
Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments |
|
| Relations |
| BioSample |
SAMN33527604 |
| SRA |
SRX19530678 |
