|
| Status |
Public on Jan 31, 2023 |
| Title |
CD49f-NGFR- Sir Tubulin - cells rep1 |
| Sample type |
SRA |
| |
|
| Source name |
primary epithelia
|
| Organism |
Mus musculus |
| Characteristics |
tissue: airway epithelia
strain: C57BL/6
genotype: wt
cell type: secretory
|
| 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 |
SAMN31853214 |
| SRA |
SRX18366947 |
