NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8087023 Query DataSets for GSM8087023
Status Public on Apr 26, 2024
Title Mouse4_TracheaEpithelialCell_BioRep1
Sample type SRA
 
Source name Trachea
Organism Mus musculus
Characteristics tissue: Trachea
cell type: EpCam+/tdTomto- Cell
genotype: Ascl1CreERT2/Ai14
treatment: tamoxifen
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
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
 
Submission date Feb 20, 2024
Last update date Apr 26, 2024
Contact name David Julius
Organization name UCSF
Street address 600 16th St
City San Francisc
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL21103
Series (1)
GSE256180 Neuroendocrine cells initiate protective upper airway reflexes
Relations
BioSample SAMN40001308
SRA SRX23671439

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap