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| Status |
Public on Feb 07, 2024 |
| Title |
13732BO |
| Sample type |
SRA |
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| Source name |
esophageal tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Barretts esophagus
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| 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.
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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 |
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
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| Submission date |
Jun 06, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Joshua Stone |
| E-mail(s) |
josh.stone@nih.gov
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| Organization name |
NIH
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| Street address |
37 Convent Drive Room 3050
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE234304 |
Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue |
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| Relations |
| BioSample |
SAMN35652615 |
| SRA |
SRX20608068 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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