|
| Status |
Public on Jun 20, 2022 |
| Title |
SNB19 EV Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SNB19 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Glioblastoma cell
transduced: Empty vector (EV)
cell line: SNB19
|
| Treatment protocol |
SNB19 cells were transduced with lentiviral particles expressing specific proteins (EV, ZBTB18, ZBTB18-mut, ZBTB18 SF, ZBTB18 SF-mut)
|
| Growth protocol |
SNB19 cells were grown in DMEM +10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent. We then performed mRNA purification from total RNA samples using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, Carlsbad, USA).
Library was prepared using the Low Input by PCR Barcoding Kit and the cDNA-PCR Sequencing Kit (Oxford Nanopore Technologies, Oxford, United Kingdom) as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
BC2
|
| Data processing |
Basecalling was performed by Albacore implemented in the nanopore software.
Postprocessing was performed using the NanoPoreSeq pipeline, available at github (https://github.com/heilandd/NanoPoreSeq)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 28, 2021 |
| Last update date |
Jun 20, 2022 |
| Contact name |
Maria Stella Carro |
| E-mail(s) |
[email protected]
|
| Phone |
0049 76127054400
|
| Organization name |
Freiburg University Medical Center
|
| Lab |
Neuro-oncology
|
| Street address |
Breisacherstraße 64
|
| City |
Freiburg |
| ZIP/Postal code |
79211 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE184890 |
Analysis of gene expression changes upon ZBTB18 full length (FL), ZBTB18 full length-mutant (FL-mut), ZBTB18 short form Nte (SF-Nte) and ZBTB18 short form Nte (SF-mut) in SNB19 glioblastoma cell line |
|
| Relations |
| BioSample |
SAMN21877887 |
| SRA |
SRX12381786 |
