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| Status |
Public on Jan 15, 2025 |
| Title |
MSC 125 3D |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell line: primary cells
cell type: mesencymal stromal cells
genotype: wild type
treatment: 3D
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| Treatment protocol |
For 3D culture, ceramic scaffolds were seeded with mesenchymal stromal cells and cultured for seven days in standard culture conditions. As a control, the same biological donors were kept in a 2D monolayer culture (DMEM; 10%FCS; 1% Penicillin–Streptomycin).
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| Growth protocol |
Mesenchymal stromal cells were isolated from femoral heads and propagated in standard culture conditions (DMEM; 10%FCS; 1% Penicillin–Streptomycin).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
whole RNA was isolated by the Nucleo Spin RNA Kit (Macherey & Nagel)
for samples from Donor 125 and 135: The indexed cDNA library was generated using the TruSeq Stranded mRNA LT Sample Prep Kit 24 (Illumina), according to the TruSeq Stranded mRNA Sample PreparaCon Protocol LS (Illumina). The inital quantity of total RNA was 800 ng for bone marrow stromal cells for samples from donor 351 and 355: Total RNA samples were quantified using a Qubit Fluorometer, and RNA integrity was checked on a TapeStation (Agilent). Double-indexed stranded mRNA-Seq libraries were prepared using the ILMN Stranded mRNA Library Prep Kit (Illumina, #20040534), starting from 500 ng of input material according to the manufacturer’s instructions.
for samples from donor 125 and 135: Libraries were quality checked by qPCR and equimolarly pooled based concentration measurements (nanodrop). The sequencing was performed on the Illumina MiSeq System. for sampls from donor 351 and 355: Libraries were equimolarly pooled based on Qubit concentration measurements and TapeStation size distributions. The loading concentration of the pool was determined using a qPCR assay (Roche, #7960573001). Libraries were then sequenced on the Illumina NovaSeq X Plus platform using PE100 sequencing mode, with a target of 50 million reads per library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
RAW data were demultiplexed and processed on the Galaxy Project Platorm, using the FASTQ Groomer tool to convert the output data into Sanger sequencing data. Fragments were then mapped against the human genome (hg38) to detect splice junctons between exons by HISAT2. Mapped reads were processed by the FeatureCount tool. The Galaxy Community. [The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update,; Nucleic Acids Research, Volume 52, Issue W1, 5 July 2024, Pages W83–W94, https://doi.org/10.1093/nar/gkae410; https://usegalaxy.org/]
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts and GeneID for each sample
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| Submission date |
Sep 13, 2024 |
| Last update date |
Jan 15, 2025 |
| Contact name |
Mark Rosowski |
| E-mail(s) |
mark.rosowski@tu-berlin.de
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| Organization name |
TU Berlin
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| Street address |
Gusav-Meyer-Allee 25
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| City |
Berlin |
| ZIP/Postal code |
13355 |
| Country |
Germany |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE277163 |
Effect of 3D cultivation of human mesenchymal stomal cells to emulate the bone marrow niche microenvironment |
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| Relations |
| BioSample |
SAMN43762827 |
| SRA |
SRX26080958 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8515667_MSC_125_3D_raw_counts.txt.gz |
111.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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