NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6754312 Query DataSets for GSM6754312
Status Public on Jan 31, 2023
Title CD49f+NGFR+ cells rep 3
Sample type SRA
 
Source name primary epithelia
Organism Mus musculus
Characteristics tissue: airway epithelia
strain: C57BL/6
genotype: wt
cell type: basal
Treatment protocol Cultures were trypsinized and sorted into CD49f+NGFR+ (Basal Cells), CD49f-NGFR- SiRTubulin + (ciliated) and CD49f-NGFR- SiRTubulin - (secretory) subsets
Growth protocol Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Cells were collected at day 10 post air-exposure.
Extracted molecule total RNA
Extraction protocol RNA was isolated from sorted cells , using the Qiagen RNeasy mini kit
RNA (200 ng) was used to prepare cDNA libraries using the NEBNext_Low_Input_w_NEB_Ultra_II_FS Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description ALI t10 sorted
Data processing fastq files were processed with nf-core/rnaseq pipeline v 3.8.1
pipeline was run using STAR and RSEM for alignment and quantification
Differential expressed genes were obtained from DESeq2 v1.34.0 within an R 4.1.1 environment
Genes are considered significant when padj < 0.05
Assembly: Mus_musculus, ensembl,GRCm38,release-95
Supplementary files format and content: rsem output, counts and TPMs per gene per sample as tab separate file
 
Submission date Nov 23, 2022
Last update date Feb 01, 2023
Contact name Andreas Wack
E-mail(s) andreas.wack@crick.ac.uk
Organization name The Francis Crick Institute
Lab Immunoregulation Laboratory
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platform ID GPL24247
Series (1)
GSE218663 Repair of airway epithelia requires metabolic rewiring towards fatty acid oxidation
Relations
BioSample SAMN31853215
SRA SRX18366946

Supplementary file Size Download File type/resource
GSM6754312_SC254_3.genes.results.gz 1.1 Mb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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