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| Status |
Public on May 22, 2018 |
| Title |
mock 2 (SC1_Vehicle) |
| Sample type |
SRA |
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| Source name |
Schwann cells
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
age: adult
tissue: Schwann cells
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| Treatment protocol |
Starved Schwann cells were stimulated for 6 hours in "starving medium" containing 10 nM recombinant soluble NRG1β1 (#396-HB), purchased from R&D systems. Control mock samples were stimulated with the same volume of ligand resuspension buffer (PBS containing 1% bovine serum albumin, BSA, Sigma).
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| Growth protocol |
Primary Schwann cells were routinely cultured on poly-L-lysine (PLL, Sigma)-coated plate, in complete medium consisting of DMEM (Sigma #D5671) supplemented with 10% heat-inactivated foetal bovine serum (FBS, Invitrogen), 100 units/mL penicillin, 0.1 mg/mL streptomycin, 1 mM sodium pyruvate, 2 mM L-glutamine, 63 ng/mL glial growth factor (GGF, #369-HB, R&D Systems) and 10 µM forskolin (Sigma) and incubated at 37°C in 5% CO2.
Confluent Schwann cells were starved overnight (18 hours) in "starving medium" consisting in: DMEM (Sigma #D5671) supplemented with 2% heat-inactivated foetal bovine serum, 100 units/mL penicillin, 0.1 mg/mL streptomycin, 1 mM sodium pyruvate, 2 mM L-glutamine, and 10 µM forskolin
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| Extracted molecule |
total RNA |
| Extraction protocol |
Deep RNA sequencing was performed on three mock samples and three stimulated samples obtained in three independent experiments. RNA quality was assessed on an Agilent 2100 Bioanalyzer. All samples had RIN ≥ 9. For RNA-Seq library preparation, approximately 2 μg of total RNA were subjected to poly(A) selection and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Sequencing was performed on the Illumina NextSeq 500 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were mapped to the Rattus norvegicus rn5 reference assembly using TopHat v2.0.10 (D. Kim et al., 2013) ts were generated using htseq and the refseq transcriptome. Genes with RPKM > 1 in all 3 replicates were considered expressed in each condition.
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| Submission date |
Sep 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Elio Grazio |
| E-mail(s) |
elio.grazio@unito.it
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| Organization name |
University of Turin
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| Street address |
Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10
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| City |
Orbassano |
| ZIP/Postal code |
10043 |
| Country |
Italy |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE104324 |
Soluble Neuregulin1 is a negative regulator of myelination |
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| Relations |
| BioSample |
SAMN07710198 |
| SRA |
SRX3220874 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2795459_SC1-Vehicle_counts.txt.gz |
67.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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