|
| Status |
Public on Sep 02, 2023 |
| Title |
RNA_Z5_NfiABXko_K5CreER_INP_r2 |
| Sample type |
SRA |
| |
|
| Source name |
tdTomato +(dim) cells from the regenerating olfactory epithelium: immediate neuronal progenitors (INP)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: tdTomato +(dim) cells from the regenerating olfactory epithelium: immediate neuronal progenitors (INP)
genotype: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl; K5CreER*/+; Rosa-CAG-tdtomfl/fl
|
| Treatment protocol |
Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then tdTomato + (dim) cells were isolated with FAC-sorting
|
| Growth protocol |
Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 8 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA-seq libraries were prepared using Ovation RNA-Seq System 1-16 for Model Organisms (Nugen 0348)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). Reads were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads
|
| |
|
| Submission date |
Sep 01, 2023 |
| Last update date |
Sep 02, 2023 |
| Contact name |
Elizaveta Bashkirova |
| E-mail(s) |
evbashkirova@gmail.com
|
| Organization name |
Columbia University
|
| Department |
Biochemistry
|
| Lab |
Lomvardas
|
| Street address |
3227 Broadway
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10027 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE158730 |
NFI transcription factors regulate zonal olfactory receptor expression |
|
| Relations |
| BioSample |
SAMN37231087 |
| SRA |
SRX21591734 |
