|
| Status |
Public on Jul 01, 2024 |
| Title |
(-Glc) KO1 RNAseq exp1 |
| Sample type |
SRA |
| |
|
| Source name |
SCC23 HNSCC cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SCC23 HNSCC cells
cell type: HNSCC
genotype: KMT2D Knockout
treatment: KO
|
| Treatment protocol |
To generate KMT2D knockout cell lines, SCC23 and SCC1 cells were transfected with pSpCas9(BB)-2A-GFP plasmid (Addgene, Cat#48138) containing sgRNA targeting either LacZ or KMT2D for 24 hours.
|
| Growth protocol |
Human HNSCC cell line SCC23 was obtained from the University of Michigan, SCC46 and SCC74A cells were from Dr. Zhong Chen’s lab (National Institutes of Health) with permission from Dr. Thomas E. Carey (University of Michigan). These cell lines were maintained in high glucose DMEM (Thermo Fisher Scientific, Cat#11995065) containing 10% FBS and 1% antibiotics at 37°C in a 5% CO2 atmosphere.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by RNAeasy kit(Thermo)
Neb UTRL2 RNAseq with PolyA mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Low Glucose condition
|
| Data processing |
FASTQ sequences were mapped to human genome hg38(GRCh38) by Hisat2.
For the uniquely mapped reads, FeatureCounts were used to count the reads mapped to each gene
Supplementary files format and content: raw gene count
|
| |
|
| Submission date |
Jul 14, 2023 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Cunyu Wang |
| E-mail(s) |
cwang@dentistry.ucla.edu
|
| Phone |
3108256317
|
| Organization name |
UCLA
|
| Department |
School of Dentistry
|
| Lab |
CHS 56-200
|
| Street address |
10833 Le Conte Ave
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE234716 |
KMT2D regulates gene expression through regulating promoters/enhances upon glucose deprivation. |
| GSE237454 |
Gene regulation profiling by KMT2D under different glucose conditions in HNSCC (RNAseq) |
|
| Relations |
| BioSample |
SAMN36459505 |
| SRA |
SRX21031813 |
