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Understanding the dosage-dependent role of Dicer1 in thyroid tumorigenesis

GSE273129 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/10/09 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Thyroid cancerThis series is part of our curated briefing on it.
Samples
18 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Understanding the Dosage-Dependent Role of Dicer1 in Thyroid TumorigenesisInternational journal of molecular sciences · 2024
Summary (written by the submitters)
Multiple studies suggest Dicer1 as a haploinsufficient tumor suppressor gene: while the loss of one allele promotes tumorigenesis, the complete loss of Dicer1 prevents tumor formation. To study the impact of Dicer1 partial or total loss in papillary thyroid carcinoma cells in vitro, we generated stable Dicer1 (+/-) cell lines by CRISPR-Cas9 from TPC1 cell line.
Read the full summary ↓
No Dicer1 (-/-) cell lines could be generated. Therefore, siRNA against Dicer1 was transfected into Dicer1 (+/-) cell lines to further decrease its expression. RNA sequencing and transcriptomic analysis revealed alterations in proliferation, cell cycle and cell locomotion. BrdU staining revealed a slow-down of the cell cycle, with lower percentages of cells in S-phase and higher percentages of cells in G0-G1-phase. Furthermore, transwell invasion and migration assays showed a decrease of invasive and migrating cells following transfection of Dicer1 siRNA. These results were confirmed in two supplementary thyroid cell lines, BCPAP and H-Tori3. Additionally, to achieve high protein levels, we performed Dicer1 plasmid transfection and we observed reduced proliferation and invasion as well as increased apoptosis. Globally, our results allow us to better understand the function of Dicer1 in thyroid cancer tumorigenesis and suggest Dicer1 as an attractive target for novel therapeutic strategies.
Published in
Understanding the Dosage-Dependent Role of Dicer1 in Thyroid Tumorigenesis
Rojo-Pardillo M, Godefroid L, Dom G et al. · International journal of molecular sciences 2024 · PMID 39409030 · doi:10.3390/ijms251910701
This dataset
Open GSE273129 in finder → Find more human RNA-seq datasets → Thyroid cancer landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE273129_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1140219 and SRA study SRP522244. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39409030) ↗
Study design
6 conditions, mostly in triplicate
TPC1 NON TRANSFECTED REPLICATA ×3 TPC1 NEGATIVE CONTROL REPLICATA ×3 TPC1 Dicer1 siRNA TRANSFECTED REPLICATA ×3 D11 NON TRANSFECTED REPLICATA ×3 D11 NEGATIVE CONTROL REPLICATA ×3 D11 Dicer1 siRNA TRANSFECTED REPLICATA ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
More Thyroid cancer datasets

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