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| Status |
Public on May 18, 2022 |
| Title |
Tumor 5T |
| Sample type |
SRA |
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| Source name |
pancreas_tumor
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| Organism |
Homo sapiens |
| Characteristics |
subject status: pancreatic ductal adenocarcinoma (PDAC) patient
Sex: Male
age: 77
tissue: PDAC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Surgical fragments of PDAC and peritumoral nonmalignant tissues were collected and snap frozen in liquid nitrogen. RNA was isolated using the Trizol reagent (ThermoFisher) and purified according to the manufacturer’s protocol.
RNA-Seq libraries were generated using the Illumina TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (Cat# RS-122-2001) according to the standard manufacturer’s protocol (Part no. 15031048 Rev. D April 2013).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
5T_AGTCAA_L001
patient 30
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| Data processing |
Quality control of reads was performed using FastQC v0.10.1. Adapters and low quality sequences were filtered out with Trimmomatic (sliding window 4:15, minlen: 35). Reads were aligned against the human genome reference (hg19 version) using TopHat2 software. Tumor and non-tumor samples were assembled separately using SringTie and merged with Cuffmerge to generate a final pancreatic transcriptome reference. Gene and transcript abundance levels in each sample were estimated using RSEM. Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Length, effective length, expected count, TPM and FPKM values for each sample
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| Submission date |
May 03, 2019 |
| Last update date |
May 20, 2022 |
| Contact name |
Eduardo Moraes Reis |
| E-mail(s) |
emreis@iq.usp.br
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| Phone |
+55-11-30912173
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| Organization name |
University of São Paulo
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| Department |
Biochemistry
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| Street address |
Av. Prof. Lineu Prestes, 748
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| City |
São Paulo |
| State/province |
SP |
| ZIP/Postal code |
05508-900 |
| Country |
Brazil |
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| Platform ID |
GPL18460 |
| Series (1) |
| GSE130688 |
Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma |
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| Relations |
| BioSample |
SAMN11569865 |
| SRA |
SRX5785821 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3747767_5T_rsem.txt.genes.results.txt.gz |
808.5 Kb |
(ftp)(http) |
TXT |
| GSM3747767_5T_rsem.txt.isoforms.results.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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