|
| Status |
Public on Aug 03, 2023 |
| Title |
P19 cells, D0, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
P19
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19
cell type: Embryonal carcinoma
genotype: WT
treatment: Day 0
|
| Treatment protocol |
To induce neuronal differentiation, 3x105 cells were seeded in poly-L-lysine-coated 6-well plates in the presence TaKaRa NDiff® 227 Medium and 500 nM retinoic acid. Media was changed daily up to 6 days after induction.
|
| Growth protocol |
Mouse embryonal carcinoma P19 cells (ATCC) were maintained in Dulbecco's modified Eagle's medium with 4,500 mg/L of glucose supplemented with 100 units/mL penicillin/streptomycin (Life Technologies) and 10% fetal bovine serum (FBS, Gemini Bio-Products).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol. Poly(A) RNAs were purified using Dynabeads™ Oligo(dT)25 (ThermoFisher).
Total RNA libraries were prepared with the Nanopore direct RNA-seq kit.
Libraries were run on a Nanopore R9 chip on a MinIon instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
Direct RNA-seq
DESeq2_annotated_all.csv
master.polya.tsv
|
| Data processing |
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Assembly: mm10 assembly annotated with GENCODE vM17 genes and repetitive elements.
Supplementary files format and content: Comma-separated value file with polyA tail length, mapping transcript, and replicate information for each read.
Supplementary files format and content: DESeq results comparing Day 0 expression levels to Day 2, Day 4, and Day 6 expression levels.
|
| |
|
| Submission date |
Oct 05, 2022 |
| Last update date |
Aug 03, 2023 |
| Contact name |
Marcos Morgan |
| Organization name |
NIEHS
|
| Street address |
111 TW Alexander Dr
|
| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL24973 |
| Series (2) |
| GSE214874 |
Post-transcriptional regulation of Ribosome Biogenesis during differentiation [dRNA-seq] |
| GSE214875 |
Post-transcriptional regulation of Ribosome Biogenesis during differentiation |
|
| Relations |
| BioSample |
SAMN31169192 |
| SRA |
SRX17808095 |
