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| Status |
Public on Oct 22, 2020 |
| Title |
NIC1_S6: NPCs grown inside the Nichoid |
| Sample type |
SRA |
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| Source name |
Sub Ventricular Zone
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| Organism |
Mus musculus |
| Characteristics |
cell type: Neural Precursor Stem Cells (NPCs)
treatment: nichioid
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| Treatment protocol |
NIC samples were harvested, collected by centrifugation (123xg for 10 minutes), mechanically dissociated and counted with trypan blue reagent (Sigma Aldrich). 10 000 cells were seeded at the centre of the Nichoid in a single drop of 35 μL NSCs medium. The multi-well was kept in the incubator for 1 hour to allow cells to enter the 3D niches and then 465μL of NSCs medium were added.
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| Growth protocol |
NSCs were maintained in culture in Neurobasal Medium (GIBCOTM, Life Technologies) containing 2% B-27 supplement (Life Technologies), 2% L-Glutamine (Euroclone), 1% penicillin and streptomycin (Euroclone), b-FGF (human recombinant, 20 ng/mL) and hEGF (human recombinant, 20 ng/mL).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Neural Precursors Cells (NPCs) expressing green fluorescent protein (GFP) were isolated 6 h post-mortem from adult C57BL/6-Tg(UBC-GFP)30Scha/J mice weighing 25–30 g (Charles River)
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 200-ng total RNA (Illumina). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.
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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 |
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA was performed using R package DESeq2
Genome_build: M24
Supplementary_files_format_and_content: RSEM output: transcript_id, gene_id, length, effective_length, expected_count, TPM, FPKM
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| Submission date |
May 18, 2020 |
| Last update date |
Oct 22, 2020 |
| Contact name |
Stella Gagliardi |
| E-mail(s) |
stella.gagliardi@mondino.it
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| Organization name |
IRCCS Mondino Foundation
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| Department |
GPG center
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| Street address |
Via Mondino, 2
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| City |
Pavia |
| State/province |
Pavia |
| ZIP/Postal code |
27100 |
| Country |
Italy |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE150767 |
Dissecting the effect of a 3D micro-scaffold on the transcriptome of Neural Stem Cells with computational genomics |
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| Relations |
| BioSample |
SAMN14945271 |
| SRA |
SRX8358238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4558309_NIC1_S6.gtf_annotated_genes.results.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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