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Sample GSM7989721 Query DataSets for GSM7989721
Status Public on Jun 17, 2024
Title VM54 Adjacent Kidney
Sample type SRA
 
Source name Adjacent Kidney
Organism Homo sapiens
Characteristics tissue: Adjacent Kidney
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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
 
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
Organization name University of Texas Southwestern Medical Center
Lab Ralph DeBerardinis, MD, PhD
Street address 5323 Harry Hines Blvd
City Dallas
State/province Texas
ZIP/Postal code 75390
Country USA
 
Platform ID GPL18573
Series (1)
GSE251905 Mitochondrial complex I promotes kidney cancer metastasis
Relations
BioSample SAMN39081840
SRA SRX23006362

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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