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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 07, 2024 |
| Title |
PDT39 |
| Sample type |
SRA |
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| Source name |
Bladder
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Bladder
cell type: Patient-derived tumoroids
cell line: PDT39
disease state: Bladder Cancer
treatment: -
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| Treatment protocol |
-
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| Growth protocol |
Tumoroids and organoids were cultured in a culture medium containing Ad+++ supplemented with 1 × B-27 (Gibco), 1.25 mM N-acetylcysteine (Sigma), 10 mM nicotinamide, 20μM TGFβ receptor inhibitor A83-01, 100ng/ml recombinant human FGF10 (Peprotech), 25 ng/ml recombinant human FGF7 (Peprotech), 12.5 ng/ml recombinant human FGF2 (Peprotech), 10μM Y27632 Rho Kinase (ROCK) Inhibitor (Sigma) and conditioned media for recombinant Rspondin (2.5% v/v), and Wnt3A (2.5% v/v)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Protocol for Phenol/Chloroform RNA Extraction
QuantSeq-LEXOGEN (3’ mRNA-seq Library Prep Kit for Ion Torrent)
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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 was performed using bcl2fastq software.
Fastq files were mapped to the Genome Reference Consortium Human Build 37 (GRCh37), using a two-step alignment process. Firstly, reads were mapped with hisat2, using default parameters. Next, the unmapped reads were mapped with bowtie2 using the --local and --very-sensitive parameters.
Counting the reads on the 3’ UTRs was performed with metaseqR2 and were normalized with DESEQ. For the ARID1A KD comparisons, we employed the PANDORA algorithm within the metaseqR2 package by integrating the DESEQ, DESEQ2, edgeR, limma, NBPSeq, and NOISeq algorithms. Differentially expressed genes were identified based on a meta p-value threshold of < 0.05 and a log2 fold change > 1.
Assembly: hg19
Supplementary files format and content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for Quant-Seq data.
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| Submission date |
Jul 05, 2024 |
| Last update date |
Nov 07, 2024 |
| Contact name |
Tokameh Mahmoudi |
| E-mail(s) |
[email protected]
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| Organization name |
Erasmus MC Cancer Institute
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| Department |
Department of Urology, Department of Biochemistry, Department of Pathology
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| Lab |
Mahmoudi Lab
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| Street address |
Dr. Molewaterplein 40
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| City |
Rotterdam |
| ZIP/Postal code |
3015 GD |
| Country |
Netherlands |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE271565 |
Integrative analysis of patient-derived tumoroids and ex vivo organoid modeling of ARID1A loss in bladder cancer reveals therapeutic molecular targets |
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| Relations |
| BioSample |
SAMN42337262 |
| SRA |
SRX25218649 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8379812_MS9.txt.gz |
199.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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