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| Status |
Public on Oct 06, 2022 |
| Title |
CE38_Mlung |
| Sample type |
SRA |
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| Source name |
Lung metastasis
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung metastasis
tumor type: uterine adenocarcinoma
tumor area: invasive tumor front
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from 5µm FFPE tissue sections of microdissected ITF using the Agencourt FormaPure kit (A33341; Beckman Coulter, Indianapolis, IN, USA) and following the manufacturer’s instructions. RNA concentration was determined with Qubit 4 Fluorometer and Qubit® RNA HS Reagent (Thermo Fisher Scientific, Waltham, MA, USA).
HTG EdgeSeq Chemistry was employed to synthetize the RNA-Seq library. Briefly, target capture was performed by hybridizing the mRNA with Nuclease Protection Probes (NPPs). The S1 nuclease was added to the mix, producing a stoichiometric amount of target mRNA/NPP duplexes. This reaction was blocked by enzyme heat denaturation of S1. The samples were randomized before inclusion in the HTG EdgeSeq system to reduce potential biases in the run. Each hybridized sample was used as template to set up PCR reactions with specially designed tags, sharing common sequences that are complementary to both 5’-end and 3’-sequences of the probes, and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode used for sample identification and multiplexing. After PCR amplification, a clean-up procedure was performed using Agencourt AMPure XP (Beckman Coulter). The library was quantified by quantitative PCR, using KAPA Library Quantification (Roche), according to the manufacturer’s instructions. All samples and controls were quantified in triplicate and no template control was included in any run.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Base-calling: Illumina Basespace
Generation of read counts: HTG Edgeseq Parser v. 5,2,823,5648
Normalization : R Bioconductor DESeq2 v. 1,28,1
Assembly: hg19
Supplementary files format and content: Table with median transformation normalized counts
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Oct 04, 2022 |
| Last update date |
Oct 06, 2022 |
| Contact name |
Juan Diaz-Martin |
| E-mail(s) |
jdiaz-ibis@us.es
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| Organization name |
IBiS
|
| Street address |
Av Manuel Siurot
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| City |
Seville |
| ZIP/Postal code |
41013 |
| Country |
Spain |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE214779 |
Towards Optimization of Precision Oncology in Metastatic Uterine Tumors |
| GSE214780 |
Invasive tumor front (ITF) of uterine adenocarcinomas and leiomyosarcomas. Primary and metastatic specimens |
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| Relations |
| BioSample |
SAMN31151653 |
| SRA |
SRX17795977 |
| 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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