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Status |
Public on Jun 17, 2024 |
Title |
VM09 Adjacent Kidney |
Sample type |
SRA |
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Source name |
Adjacent Kidney
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Organism |
Homo sapiens |
Characteristics |
tissue: Adjacent Kidney
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated using Trizol (Thermo Fisher Scientific, Cat. No. 15596018) and an Rneasy Mini Kit (Qiagen, Cat. No. 74106). Total RNA was quantified using a Qubit fluorometer and the Invitrogen Qubit RNA High Sensitivity kit (Invitrogen, Cat. No. Q32852). Samples were diluted in ultrapure water prior to sequencing. RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library prep kit with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. No. E7490L, E7760L) according to manufacturer’s instructions. Libraries were stranded using standard N.E.B indices according to manufacturer’s instructions (New England Biolabs, Cat. No. E7730L, E7335L, E7500L).
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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 |
Ends of sequences were trimmed with remaining adapter or quality scores <25. Sequencing reads were aligned to the human reference genome (hg19) by STAR 2.7.3.a with default parameters in the 2-pass mod. Counts for each gene were generated using htseq-count v0.6.1. DEGs were identified by DESeq2 v1.14.1. Ends of sequences were trimmed with remaining adapter or quality scores <25. Sequence less than 35bp after trimming were removed. The trimmed Fastq files were aligned to the GRCh38 using HiSAT272 and duplicates were marked with SAMBAMBA. Features (genes, transcripts and exons) were counted using featureCounts73. Differential expression analysis was performed using EdgeR74 and DESeq75. Genes with 0 values for all samples were trimmed from the processed data. Assembly: hg19 Supplementary files format and content: Excel file includes log2CPM counts for each Sample
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Submission date |
Dec 22, 2023 |
Last update date |
Jun 17, 2024 |
Contact name |
Divya Bezwada |
E-mail(s) |
divya.bezwada@utsouthwestern.edu, dbezwada@scripps.edu
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Organization name |
University of Texas Southwestern Medical Center
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Lab |
Ralph DeBerardinis, MD, PhD
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Street address |
5323 Harry Hines Blvd
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City |
Dallas |
State/province |
Texas |
ZIP/Postal code |
75390 |
Country |
USA |
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Platform ID |
GPL18573 |
Series (1) |
GSE251905 |
Mitochondrial complex I promotes kidney cancer metastasis |
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Relations |
BioSample |
SAMN39081837 |
SRA |
SRX23006365 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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