Gene expression of human bone marrow-derived stem cells on liquid crystalline self-assembed hydroxyapatite nanorods for bone regeneration
RNA-seq (gene expression) · human · 15 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
- 15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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
- Liquid Crystalline Hydroxyapatite Nanorods Orchestrate Hierarchical Bone-Like MineralizationSmall (Weinheim an der Bergstrasse, Germany) · 2024
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE210696_RAW.tar (it can run to tens of gigabytes).
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 PRJNA867161 and SRA study SRP390392. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. 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.
- GSM6435617 Control_1, Day 21
- GSM6435618 Control_2, Day 21
- GSM6435619 Control_3, Day 21
- GSM6435620 HAp_short_1, Day 21
- GSM6435621 HAp_short_2, Day 21
- GSM6435622 HAp_short_3, Day 21
- GSM6435623 HAp_long_1, Day 21
- GSM6435624 HAp_long_2, Day 21
- GSM6435625 HAp_long_3, Day 21
- GSM6435626 Tb_HAp_short_1, Day 21
- GSM6435627 Tb_HAp_short_2, Day 21
- GSM6435628 Tb_HAp_short_3, Day 21
- GSM6435629 Tb_HAp_long_1, Day 21
- GSM6435630 Tb_HAp_long_2, Day 21
- GSM6435631 Tb_HAp_long_3, Day 21
- GSE311899 Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [biopsies] 35 samples shares marrow-derived, bone
- GSE261696 Transcriptional characteristics of human primary, bone marrow-derived and iPSC-derived monocytes and macrophages [RNA-Seq] 19 samples shares marrow-derived, bone
- GSE281162 The Impact of PPARβ/ agonism/antagonism on human bone-marrow-derived Mesenchymal Stromal Cells 18 samples shares marrow-derived, bone
- GSE294487 A strategy for challenging tumorous bone regeneration by utilizing borosilicate bioactive glass synchronously boosting osteosarcoma combating and osteogenesis promotion of moderate magnetic hyperthermia 12 samples shares regeneration, bone
- GSE309449 Transcriptomic profiling of osteoblasts on hydroxyapatite-coated surfaces reveals enhanced osteogenic and angiogenic processes relevant to accelerated bone healing. 12 samples shares hydroxyapatite, bone
- GSE294322 A strategy for challenging tumorous bone regeneration by utilizing borosilicate bioactive glass synchronously boosting osteosarcoma combating and osteogenesis promotion of moderate magnetic hyperthermia 12 samples shares regeneration, bone
- GSE311897 Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [organoids] 9 samples shares marrow-derived, bone
- GSE217506 Bone Marrow-Derived Mesenchymal Stem Cell Secretome Alters Gene Expression and Upregulates Motility of Human Endometrial Stromal Cells 9 samples shares marrow-derived, bone
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.