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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 22, 2014 |
| Title |
MVth1_RNASeq |
| Sample type |
SRA |
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| Source name |
Microvesicles derived from Neural Progenitor Cells cultured in Th1 conditions
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| Organism |
Mus musculus |
| Characteristics |
cell type: Microvesicles
strain: SJL
culturing conditions: Th1 cytokines supplemented medium (500 IU/ml recombinant mouse IFN-γ, BD Biosciences; 200 UI/ml recombinant mouse TNF-α, Pepro Tech Inc.; 100 UI/ml recombinant mouse IL-1β, Euroclone)
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| Treatment protocol |
NPCs were plated in complete growth medium (CGM) with or without either Th1 (500 IU/ml recombinant mouse IFN-γ, BD Biosciences; 200 UI/ml recombinant mouse TNF-α, Pepro Tech Inc.; 100 UI/ml recombinant mouse IL-1β, Euroclone) or Th2 (10 ng/ml recombinant murine IL-4, R&D; 10 ng/ml recombinant mouse IL-5, R&D; 10 ng/ml recombinant mouse IL-13, R&D) cytokine mixes for 16 hours in vitro, as described (Pluchino et al., 2008). At the end of the conditioning, NPCs were harvested and the supernatants processed for the collection of either MVs or EXOs.
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| Growth protocol |
NPCs lines were prepared from the subventricular zone (SVZ) of 7-12 week old female SJL mice (18-20 gr. Charles River), as described (Pluchino et al., Nature, 2005).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA purity and integrity was firstly confirmed by BioAnalyzer (Agilent,). Deep sequencing of the isolated polyA RNA was performed by Eastern Sequence and Informatics Hub (EASIH; University of Cambridge, UK) on the Illumina GAIIx platform (Illumina, CA) according to the Illumina RNA-Seq protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Reads were mapped to the mouse genome (mm9) using Tophat. Transcripts were then assembled using Cufflinks using UCSC annotation as reference.
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| Submission date |
Nov 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefano Pluchino |
| E-mail(s) |
spp24@cam.ac.uk
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| Organization name |
University of Cambridge
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| Department |
Brain Repair Centre
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| Lab |
Pluchino laboratory
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| Street address |
Forvie Site, Robinson Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0PY |
| Country |
United Kingdom |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE33527 |
Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signalling in target cells |
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| Relations |
| SRA |
SRX104910 |
| BioSample |
SAMN00750290 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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