|
| Status |
Public on Aug 03, 2023 |
| Title |
T1_undiff_ana_58 |
| Sample type |
SRA |
| |
|
| Source name |
P19 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19 cells
cell type: Embryonal carcinoma
genotype: WT
treatment: Undifferentiated
treatment assay: anabolic
treatment time: 1
|
| 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 |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol.
Libraries were constructed following the SLAM-seq catabolic and anabolic protocols using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling was done with Illumina NovaSeq software.
We used the SLAMdunk pipeline to map the reads and calculate the conversion rate due to the incorporation of 4sU.
The decay or synthesis half-life for each transcript was estimated by fitting a first-order exponential.
Assembly: mm10 assembly annotated with GENCODE vM17 genes
Supplementary files format and content: SlamDunk output as a tab-separated value table with conversion rates.
Library strategy: SLAM-seq
|
| |
|
| 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 |
GPL24247 |
| Series (2) |
| GSE214860 |
Post-transcriptional regulation of Ribosome Biogenesis during differentiation [SLAM-seq] |
| GSE214875 |
Post-transcriptional regulation of Ribosome Biogenesis during differentiation |
|
| Relations |
| BioSample |
SAMN31165810 |
| SRA |
SRX17804755 |
