GEO series
Small RNA Analysis within Human Trophoblast-Derived Extracellular Vesicles and Effect of These Structures on the Transcriptome Profile of Human Neural Progenitor Cells [bulk RNAseq]
GSE226979
Homo sapiens (human)
RNA-seq (gene expression)
12 samples
Submitted 2024/11/30
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 12 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)
- Samples
- 12 samples: 4 × NPC_Control vs 4 × NPC_iPS_EV vs 4 × NPC_TB_EVGroups 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
- Small and Long Non-Coding RNA Analysis for Human Trophoblast-Derived Extracellular Vesicles and Their Effect on the Transcriptome Profile of Human Neural Progenitor CellsCells · 2024
Summary (written by the submitters)
The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis.
Read the full summary ↓
We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. We isolated EV from human trophoblast (TB) differentiated in vitro and the parental induced pluripotent stem cells (iPSC) from which the TB was derived, and small RNAseq was done to characterize small RNA profiles within these EV. Human neural progenitor cells (NPC) generated from the same iPSC were exposed to EV derived from TB or iPSC or only treated with control media. Results indicate EV derived from human TB cells contain unique profiles of miRNA and long non-coding RNA (lncRNA) relative to EV isolated from parental iPS cells. Human TB-derived EV readily internalized by human NPC. EV from TB cells induce transcripts in NPC associated with forebrain formation and neurogenesis, suggesting that such EV might program early fetal brain development. Results shed light on the inner workings of the placenta-brain axis. Understanding how contents of TB-derived EV, namely small RNA, affect NPC might yield new insights and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASD). The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis. We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. We isolated EV from human trophoblast (TB) differentiated in vitro and the parental induced pluripotent stem cells (iPSC) from which the TB was derived, and small RNAseq was done to characterize small RNA profiles within these EV. Human neural progenitor cells (NPC) generated from the same iPSC were exposed to EV derived from TB or iPSC or only treated with control media. Results indicate EV derived from human TB cells contain unique profiles of miRNA and long non-coding RNA (lncRNA) relative to EV isolated from parental iPS cells. Human TB-derived EV readily internalized by human NPC. EV from TB cells induce transcripts in NPC associated with forebrain formation and neurogenesis, suggesting that such EV might program early fetal brain development. Results shed light on the inner workings of the placenta-brain axis. Understanding how contents of TB-derived EV, namely small RNA, affect NPC might yield new insights and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASD).
Published in
Kinkade JA, Singh P, Verma M et al.
· Cells 2024
· PMID 39594615
· doi:10.3390/cells13221867
This dataset
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.
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 GSE226979_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA942355 and SRA study SRP426336. Searching any of these in the dataset finder brings you back here.
Study design
4 × NPC_Control vs 4 × NPC_iPS_EV vs 4 × NPC_TB_EV
Supports a between-group comparison across 12 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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
- GSM7089317 NPC_Control_1 NPC_Control
- GSM7089318 NPC_Control_2 NPC_Control
- GSM7089319 NPC_Control_3 NPC_Control
- GSM7089320 NPC_Control_4 NPC_Control
- GSM7089321 NPC_iPS_EV_1 NPC_iPS_EV
- GSM7089322 NPC_iPS_EV_2 NPC_iPS_EV
- GSM7089323 NPC_iPS_EV_3 NPC_iPS_EV
- GSM7089324 NPC_iPS_EV_4 NPC_iPS_EV
- GSM7089325 NPC_TB_EV_1 NPC_TB_EV
- GSM7089326 NPC_TB_EV_2 NPC_TB_EV
- GSM7089327 NPC_TB_EV_3 NPC_TB_EV
- GSM7089328 NPC_TB_EV_4 NPC_TB_EV
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Share this dataset
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