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| Status |
Public on Apr 26, 2024 |
| Title |
Mouse6_LarynxNE_BioRep3 |
| Sample type |
SRA |
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| Source name |
Larynx
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| Organism |
Mus musculus |
| Characteristics |
tissue: Larynx
cell type: tdTomato+ Cell
genotype: Ascl1CreERT2/Ai14
treatment: tamoxifen
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were sorted directed into Takara Smart Seq lysis buffer and then flash frozen. See Seeholzer and Julius 2024 for further details.
We performed cDNA synthesis with Smart-Seq v4 kit according to the protocol recommendatioons (Takara Bio, 634890). cDNA library was generated by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024). See Seeholzer and Julius 2024 for further details.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Quality was checked with fastqc and adapter/low quality reads were trimmed with Cutadapt via TrimGalore
Assembly: mm10 containing exogenous sequence for tdTomato
Supplementary files format and content: Reads were aligned to reference genome using StarAlign
Supplementary files format and content: Processed data file is a normalized read count for each sample, which was generated using rsem-calculate-expression function of RSEM-1.3.3 in Rstudio
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| Submission date |
Feb 20, 2024 |
| Last update date |
Apr 26, 2024 |
| Contact name |
David Julius |
| Organization name |
UCSF
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| Street address |
600 16th St
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| City |
San Francisc |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE256180 |
Neuroendocrine cells initiate protective upper airway reflexes |
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| Relations |
| BioSample |
SAMN40001304 |
| SRA |
SRX23671443 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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