GSM5033946: Patient tumor sample_2_baseline; Homo sapiens; RNA-Seq - SRA

SRX9932092: GSM5033946: Patient tumor sample_2_baseline; Homo sapiens; RNA-Seq
5 ILLUMINA (Illumina HiSeq 4000) runs: 88.1M spots, 5.1G bases, 1.7Gb downloads

Submitted by: NCBI (GEO)

Study: RNA sequencing of the phase II PERFECT trial combining a PD-L1 inhibitor (atezolizumab) with neoadjuvant chemoradiotherapy in resectable esophageal adenocarcinoma patients.

PRJNA694637 • SRP303154 • All experiments • All runs

show Abstracthide Abstract

We performed bulk RNA sequencing of tumor biopsies from patients before treatment, on-treatment and in case a poor response was suspected from the resection specimen. At baseline we found in responding patients a higher six-gene IFNy score compared to non-responders. On-treatment non-responders showed either high expression of co-inhibitory checkpoints with a high number of cytotoxic lymphocytes or low expression and a low number of cytotoxic lymphocytes. Overall design: RNA sequencing of esophageal tumor biopsies at baseline from patients, on-treatment (3rd week) and at resection.

Sample: Patient tumor sample_2_baseline

SAMN17528639 • SRS8107536 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: Snap frozen tumor biopsies were cut into smaller pieces on the cryostat. One section was used for haematoxylin and eosin staining to determine the tumor cell percentage in the biopsy, which was performed by an experienced pathologist. Total RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA universal kit. The NanoDrop (Thermo Fisher) was used to measure RNA concentration (ng/ul). Biopsies were sent for bulk RNA sequencing in case the tumor % was ≥ 30% and RNA concentration was not lower than 20 ng/ul. RNA libraries were prepared for sequencing using standard Illumina protocols

Experiment attributes:

GEO Accession: GSM5033946

Links:

NCBI link: NCBI Entrez (gds)

Runs: 5 runs, 88.1M spots, 5.1G bases, 1.7Gb

Run	# of Spots	# of Bases	Size	Published
SRR13521095	4,129,876	239.5M	82.4Mb	2021-02-04
SRR13521096	32,390,596	1.9G	654.5Mb	2021-02-04
SRR13521097	11,403,087	661.4M	226.9Mb	2021-02-04
SRR13521098	24,171,350	1.4G	486.1Mb	2021-02-04
SRR13521099	15,995,618	927.7M	328.1Mb	2021-02-04

ID:: 12992643

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