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Isolation, identification and osteogenic capability analysis of mesenchymal stem cells derived from different layers of human maxillary sinus membrane

GSE240641 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/06/30 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)
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.
Summary (written by the submitters)
Mesenchymal stem cells (MSCs) from different tissue sources have different biological processes and differentiation abilities. Although previous studies confirm that MSCs derived from human maxillary sinus membrane (hMSM) can be cultured in vitro, it cannot confirm whether they belong to the same type and possess the same differentiation ability.
Read the full summary ↓
In this study, lamina propria layer derived MSCs (hLMSCs) and periosteum layer derived MSCs (hPMSCs) from hMSM are isolated and expanded using explant cell culture method and the biological characteristics of hLMSCs and hPMSCs are compared using RNA sequencing. According to RNA sequencing and subsequent functional verification, hLMSCs and hPMSCs are identified as CD171+/CD90+ and CD171-/CD90+ phenotypes separately. This study suggests that two different types of MSCs can be identified and isolated from hMSMs. Both cells serve as good MSCs potential candidates for bone regeneration. It also indicates that hLMSCs and hPMSCs are valuable in vitro tools for preclinical studies and future exploration of the origin osteogenesis machenism in maxillary sinus region.
This dataset
Open GSE240641 in finder → Find more human RNA-seq datasets →
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 GSE240641_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 PRJNA1004538 and SRA study SRP454612. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
LMSCs, ×3 PMSCs, ×3 LMSCs,control group, ×3 iLMSCs,osteogenic induction group, ×3 PMSCs,control group, ×3 iPMSCs,osteogenic induction group, ×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
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.