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Sample GSM7989742

Query DataSets for GSM7989742

Status

Public on Jun 17, 2024

Title

VM26 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