|
| Status |
Public on Jun 29, 2023 |
| Title |
NtermRBD_2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: Human Embryonic Kidney
genotype: N-term RBD
|
| Growth protocol |
HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol reagent (Ambion) according to manufacturer protocol.PolyA RNA was isolated total RNA using the Poly(A)Purist MAG Kit (Invitrogen) according to manufacturer protocol.
cDNA libraries were created with Nanopore Direct cDNA sequeuncing kit using Native Barcoding according to manufacturer protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Sequences were basecalled using the high accuracy basecalling setting and default parameters for quality, barcode identification and trimming.
Passed reads were mapped using MinMap2 to Human Hg38 genome with the Oxford Nanopore read to reference mapping option enabled (minimap2 -x map-ont --q-occ-frac 0.01 -t 6 -a)
Reads were quantified using featureCounts and differential expression determined with DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file with normalized read counts for all genes in all samples/replicate
|
| |
|
| Submission date |
Nov 03, 2022 |
| Last update date |
Jun 29, 2023 |
| Contact name |
Kyle D. Mansfield |
| E-mail(s) |
[email protected]
|
| Organization name |
East Carolina University, Brody School of Medicine
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
600 Moye Blvd, MS622
|
| City |
Greenville |
| State/province |
NC |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE217192 |
RNA Methyltransferase METTL16's Protein Domains Have Differential Functional Effects on Cell Processes |
|
| Relations |
| BioSample |
SAMN31583855 |
| SRA |
SRX18156643 |
