|
| Status |
Public on Nov 22, 2023 |
| Title |
SKMES_shZNF714_rep2 [S4_2] |
| Sample type |
genomic |
| |
|
| Source name |
lung squamous cell carcinoma cell line, knocked-down ZNF714 expression
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKMES
histopathological subtype: squamous cell carcinoma
genotype: shZNF714
|
| Treatment protocol |
shZNF714 and shLUC cancer cells were transduced with lentiviral vectors carrying shRNA sequences complementary to ZNF714 mRNA or complementary to luciferase (5’-CAGCGATGACGAAATTCTTAG-3’) as a control (respectively). We used a mix of two different shZNF714 sequences (5’-ACACCTACATCAACATAAAAG-3’; 5’-CAAATGTGGTTGAGTGTAAGG-3’) to obtain the most efficient level of gene knockdown (shZNF714). Lentiviral particles were prepared by 2nd generation system in HEK-293T cells, using psPAX2 and pMD2.G packaging plasmid and pLV-THEM-GP transfer vector.
|
| Growth protocol |
Lung cancer cells received DMEM F-12 medium (Biowest, Nuaillé, France) with 10% FBS (EURx, Gdansk, Poland) and 1% penicillin-streptomycin (Biowest, Nuaillé, France). The cells were cultured in a suitable incubator at 37°C in 5% CO2. Trypsin (Biowest, Nuaillé, France) at the appropriate concentration was used to detach the cells during passaging.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from 3 biological replicates of H2073 and SKMES cells (WT, shLUC, shZNF714) was isolated with Cell Culture DNA Purification Kit (EurXEURx, Gdansk, Poland) according to the manufacturer’s protocol.
|
| Label |
not provided
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC BeadChIP using standard Illumina protocol
|
| Scan protocol |
Standard Illumina procedures using Illumina iScan scanner
|
| Data processing |
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0). The ß-value reflects the methylation level of each CpG site. A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.
matrix processed value definition: Average Beta
|
| |
|
| Submission date |
Jul 24, 2023 |
| Last update date |
Nov 22, 2023 |
| Contact name |
Marta Machnik |
| E-mail(s) |
[email protected]
|
| Organization name |
Poznan University of Medical Sciences
|
| Department |
Chair of Medical Biotechnology
|
| Street address |
Rokietnicka 8
|
| City |
Poznan |
| State/province |
Wielkopolska |
| ZIP/Postal code |
60-806 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE238088 |
ZNF714 – a novel oncogene in lung cancer cells |
|
