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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 05, 2024 |
| Title |
hMSC WT, DMSO, Activin A, 3 |
| Sample type |
SRA |
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| Source name |
bone marrow derived
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| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow derived
cell line: hMSC
cell type: hMSC
genotype: transduced ACVR1-WT
treatment: DMSO, Activin A
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| Treatment protocol |
Overnight serum starvation was performed with DMEM (Gibco) without any supplements. The cells were pre-treated with 1uM BYL719 or DMSO for 30 minutes in DMEM (Gibco) prior to 1 hour stimulation with Activin A (50 ng/ml) or BMP6 (50 ng/ml) (both R&D).
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| Growth protocol |
The hMSCs (overexpressed with ACVR1-WT or -R206H) were cultured in AMEM (Gibco) supplemented with 10% FBS, 1 ng/ml bFGF (ReproTech) and 100U/ml P/S
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| Extracted molecule |
total RNA |
| Extraction protocol |
ReliaPrep RNA Miniprep Systems (Promega)
mRNA was purified from tRNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTPs. Subsequent A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification and purification was performed to construct the directional library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
processed counts, column 16
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| Data processing |
The raw reads were processed by removing adapters, ploy-N and other low quality reads. Subsequent quality control was performed and further down-stream analyses were based on the clean data with high quality.
The clean reads were mapped to the GRCh38/hg38 reference genome using Hisat2 v2.0.5.
The total counts per gene were quantified using featureCounts v1.5.0-p3. These are the processed data supplied in the processed data file matrix.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data file format is .csv and consists of the following columns gene_id, WT1_1, WT1_2, WT1_3, WT1_4, WT2_1, WT2_2, WT2_3, WT2_4, WT3_1, WT3_2, WT3_3, WT3_4, WT5_1, WT5_2, WT5_3, WT5_4, WT6_1, WT6_2, WT6_3, WT6_4, RH1_1, RH1_2, RH1_4, RH2_1, RH2_2, RH2_3, RH2_4, RH3_1, RH3_2, RH3_3, RH3_4, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family
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| Submission date |
Nov 15, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Gonzalo Sánchez-Duffhues |
| E-mail(s) |
g.s.duffhues@cinn.es
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| Organization name |
Nanomaterials and Nanotechnology Research Center (CINN-CSIC)
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| Lab |
Tissue-specific BMP signalling
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| Street address |
Avda. de Roma, s/n
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| City |
Oviedo |
| State/province |
Asturias |
| ZIP/Postal code |
33011 |
| Country |
Spain |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE237512 |
PI3Kα inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification |
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| Relations |
| BioSample |
SAMN38265355 |
| SRA |
SRX22533421 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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