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Sample GSM7462035 Query DataSets for GSM7462035
Status Public on Feb 07, 2024
Title 13732BO
Sample type SRA
 
Source name esophageal tissue
Organism Homo sapiens
Characteristics tissue: Barretts esophagus
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen lung tissues using TRIzol (Invitrogen) according to the manufacturer’s protocol. Only RNA samples with RNA sufficient RNA were included for analysis.
Libraries suitable for paired-ended sequencing were generated using Illumina’s TruSeq Stranded Total RNA Library Prep Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg38, using STAR in two-pass mode with GENCODE v19 annotation
Gene expression levels were quantified using TPM.
Assembly: hg38
 
Submission date Jun 06, 2023
Last update date Feb 07, 2024
Contact name Joshua Stone
E-mail(s) josh.stone@nih.gov
Organization name NIH
Street address 37 Convent Drive Room 3050
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL18573
Series (1)
GSE234304 Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue
Relations
BioSample SAMN35652615
SRA SRX20608068

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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