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| Status |
Public on Aug 12, 2022 |
| Title |
Con + FK866 - 2 [X427DS_FK] |
| Sample type |
SRA |
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| Source name |
astrocyte
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| Organism |
Mus |
| Characteristics |
cell type: astrocyte
genotype: WT
treatment: Con + FK867
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with a GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, # PLN70)
RNA libraries for RNA-seq were prepared using using the MARS-seq protocol [H. Keren-Shaul, et al., Nat Protoc 14, 1841–1862 (2019)]
Libraries were normalized, pooled, and sequenced on a single lane of an Illumina NovaSeq. Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt and resulting reads shorter than 30 bp were discarded. The remaining reads were mapped onto 3’ UTR regions (1000 bases) of the M. musculus, mm10 genome according to Refseq annotations, using STAR (77) with the EndToEnd option and with outFilterMismatchNoverLmax set to 0.05. Deduplication was accomplished by flagging all reads that were mapped to the same gene and had the same UMI.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
427DS_FK_S25
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| Data processing |
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt; resulting reads shorter than 30bp were discarded
Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the M. musculus, mm10 genome according to Refseq annotations, using STAR] with EndToEnd option and outFilterMismatchNoverLmax was set to 0.05.
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Counts for each gene were quantified using htseq-count, using the gtf above and corrected for UMI saturation
Assembly: M. musculus, mm10 genome
Supplementary files format and content: NOT PROVIDED
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| Submission date |
Jun 12, 2022 |
| Last update date |
Aug 12, 2022 |
| Contact name |
Lior Mayo |
| Organization name |
Tel Aviv Unoversity
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| Street address |
Britannia Bldg. Room 204, Tel Aviv univeristy
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| City |
Tel Aviv |
| State/province |
Israel |
| ZIP/Postal code |
69978 |
| Country |
Israel |
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| Platform ID |
GPL31136 |
| Series (1) |
| GSE205944 |
Effect of NAMPT inhibition on gene expression in LPS/IFNg-stimulated primary mouse astrocytes |
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| Relations |
| BioSample |
SAMN29005111 |
| SRA |
SRX15683032 |
| 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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