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Study on the mechanism of TSC22D3 regulating the stability of P53 to promote the quiescence of hematopoietic stem cells

GSE179123 Homo sapiens (human) RNA-seq (gene expression) 28 samples Submitted 2024/06/28 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 28 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
28 samples: 8 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
In adults, human hematopoietic stem cells (HSCs) are mostly in a quiescent state (G0 stage) and show multilineage reconstruction. When the cell cycle is activated, HSCs gradually lose the hematopoietic reconstruction ability. It indicates that the maintenance of the quiescent state of HSPCs has very important physiological significance.
Read the full summary ↓
However, the maintenance and regulation mechanism of the quiescent state of HSCs has not yet been clarified. We found that TSC22D3 was highly enriched in quiescent state HSCs but downregulated in culture with the activation of the cell cycle. We further confirmed that stabilizing TSC22D3 expression in HSCs could promote the maintenance of the quiescent state and provide balanced multilineage reconstitution in primary mouse recipients.We found that overexpression of TSC22D3 can promote the maintenance of the resting state of HSCs and the ability of hematopoietic reconstitution by inhibiting the expression of cell cycle-related kinases. Also we confirmed that TSC22D3 can promote the accumulation of p53 protein in cells and up-regulate the expression of p21, p27 and other proteins by qPCR and western blot. Therefore, we speculate that TSC22D3 can promote the resting state of HSCs by regulating the stability of p53. It remains elusive that how TSC22D3 plays a role in the regulation of the maintenance of HSCs in vitro, therefore, further investigations are required to depict its underlying mechanism. On this basis, We firstly plan to analyze the potential downstream targets of TSC22D3 in the maintenance of HSCs in vitro through RNA-seq based transcriptome comparison; then, we will verify the predicted targets of TSC22D3 through Co-IP, gene overexpression, gene knockdown, and signaling pathway activation/inhibition. Our project could contribute to an in-depth understanding of the quiescent maintenance mechanisms of HSPCs in vitro and provide ideas for the treatment of leukemia and other malignant hematological diseases.
This dataset
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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 GSE179123_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 PRJNA742366 and SRA study SRP325990. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly with about 4 replicates each
PB_0h_rp ×4 PB_96h_rp ×4 CB_0h_rp ×4 CB_96h_rp ×4 HPC_D6_rp ×3 HPC_D10_rp ×3 GFP+ Hematopoietic Stem Cell rp ×3 TSC22D3/GFP+ Hematopoietic Stem Cell_rp ×3

Supports a between-group comparison across 28 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 28 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
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