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| Status |
Public on Jan 31, 2019 |
| Title |
mRNA from flight cells, Osteogenic medium, biological replicate 1_RNA-seq |
| Sample type |
SRA |
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| Source name |
hBMSCs on board the ISS cultured in osteogenic medium
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| Organism |
Homo sapiens |
| Characteristics |
cell type: bone marrow mesenchymal stem cells
medium: osteogenic
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| Growth protocol |
Standard Medium (SM): DMEM (Dulbecco’s Modified Eagle’s medium) supplemented with 12.5 mM HEPES, 10 U/mL heparin, 200 mM glutamine, 500 μg/mL streptomycin sulphate, 600 μg/mL penicillin.
Osteogenic Medium (OM): SM added with 0.1 M ascorbic acid, 10 mM b-glycerophosphate, and 10-8 M 1,25(OH)2D3 (Vit D3).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were preserved in RNAlater; resuspended by scraping in Trizol (Thermo Fisher Scientific) for total RNA extraction. 100ng of total RNA were used to purify mRNA and to synthesize cDNA in one tube (Thermo Fisher Scientific -Dynabeads mRNA DIRECT Micro Kit), using RCC RNA Spike-In Control Mixes (Thermo Fisher Scientific) as a control.
Ion Total RNA-Seq Kit v2 to construct the whole transcriptome libraries, using oligo-dT primers.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
FM_OM_1
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| Data processing |
Pre processing: Sickle trimmer was used to remove low quality ends of the raw reads (using a quality threshold of 20, with option –q 20) and to remove short reads (using a minimum length threshold of 30, with option –l 30); Adapters were removed using CUTADAPT
Mapping: Reads were firstly aligned to reference genome with TopHat2 (v2.1.1); unmapped reads were re-aligned with Bowtie2 (v2.2.9) in local mode. Alignments were joined with picard tools (v1.119)
Feature count: Gene count data were obtained with htsseq-count command in HTSeq framework (v0.6.0)
Differential expression analysis: performed using the edgeR (v3.16.5) package in R. After library normalization, the genewise exact tests for differences in the mean between the two groups of negative-binomially distributed counts was calculated with command exactTest. Significantly differentially expressed genes (DE-genes) between the two conditions (FMOM vs FMSM), without adjustment for multiple testing, were identified and exported for further analysis.
Genome_build: ENSEMBLE GRCh38.p5 Human Genome assembly
Supplementary_files_format_and_content: text file with mRNA count data.
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| Submission date |
Jul 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Bradamante |
| E-mail(s) |
[email protected]
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| Phone |
+390264485030
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| Organization name |
CNR-ISTM, Institute of Molecular Science and Technology
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| Street address |
Via Golgi 19
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| City |
Milan |
| ZIP/Postal code |
20133 |
| Country |
Italy |
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| Platform ID |
GPL17303 |
| Series (2) |
| GSE100931 |
SCD – Stem Cell Differentiation on board the International Space Station [RNA-seq] |
| GSE100933 |
SCD – Stem Cell Differentiation on board the International Space Station: the problem of human bone loss |
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| Relations |
| BioSample |
SAMN07333453 |
| SRA |
SRX2990436 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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