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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 04, 2024 |
| Title |
NPCs, EU treatment, Rep1 |
| Sample type |
SRA |
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| Source name |
embryonic brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic brain
cell type: Neural progenitor cells
treatment: EU
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| Treatment protocol |
NPCs were treated with EU (250 µM) one day after induction of quiescence and RNA was isolated on day 8 after induction of quiescence.
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| Growth protocol |
Quiescent neural progenitor cells (NPCs) were maintained in DMEM/F12 supplemented with N2, B27, FGF2 (10 ng/ml), Bmp4 (20 ng/ml) at 37°C in a humified incubator.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol and genomic DNA was removed with Dnase I. EU-labelled RNA was purified using Biotin-Click reaction and Streptavidin beads (Life Technologies). PBS-treated samples underwent the same extraction protocol.
Libraries were prepared using Universal Plus Total RNA-seq kit (TECAN).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Fragments were demultiplexed using bcl2fastq2 (v2.20.0). Because the libraries contain UMI information, a separate file was created per library which contains the UMIs per sequenced fragment. Next, the UMI information was added to the files, which contain the sequenced fragments, using UMI-tools (v1.1.2, umi_tools extract). Afterwards, fragments were aligned to the mouse reference GRCm39 with the support of Ensembl gene annotation version 104 using the STAR aligner (v2.7.10b). Deduplication of the aligned fragments based on UMIs and mapping coordinate was done with umi_tools (umi_tools dedup). Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: Tab separated Excel Table from featureCounts. The rows are genes and the columns provide gene information and list of samples.
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| Submission date |
Nov 17, 2023 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Tomohisa Toda |
| E-mail(s) |
tomohisa.toda@fau.de
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| Organization name |
DZNE
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| Street address |
Tatzberg 41
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| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE248099 |
Life-long persistence of nuclear RNAs in the mouse brain [NPCs] |
| GSE248101 |
Life-long persistence of nuclear RNAs in the mouse brain |
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| Relations |
| BioSample |
SAMN38299093 |
| SRA |
SRX22556965 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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