|
| Status |
Public on Oct 26, 2022 |
| Title |
Fadu_EpEX 6h_4 |
| Sample type |
SRA |
| |
|
| Source name |
hypopharynx
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Fadu
tissue: hypopharyngeal carcinoma
treatment: EpEX
timepoint: 6h
|
| Treatment protocol |
Treatements were all performed under serum-starvation conditions. Cells were plated in FCS-containing medium and were serum-starved 24h later for additional 24h before adding EGF or EpEX-Fc. EGF and EpEX-Fc treatment was performed for 6h and 72h before collecting samples.
|
| Growth protocol |
Kyse30 and FaDu (ATCC, Manassas, VA, USA) were passaged in DMEM or RPMI, 10% FCS, 1% penicillin/streptomycin, 5% CO2 atmosphere at 37°C. Treatment with EGF (PromoCell PromoKine, Heidelberg, Germany), EpEX-Fc (Pan et al. PMID: 30261040) were conducted under serum-free conditions for 6h and 72h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from cell pellets using the Qiagen AllPrep DNA/RNA Micro Kit according to the kit manual.
RNA libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina kit following the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 07, 2022 |
| Last update date |
Oct 26, 2022 |
| Contact name |
Kristian Unger |
| E-mail(s) |
[email protected]
|
| Organization name |
LMU University Hospital
|
| Department |
Department of radiation oncology
|
| Lab |
AI-assisted therapy decisions in oncology
|
| Street address |
Marchioninistr. 15
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE200421 |
A Transcriptomic Map of EGFR-induced Epithelial-to-Mesenchymal Transition Identifies Prognostic and Therapeutic Targets for Head and Neck Cancer |
|
| Relations |
| BioSample |
SAMN27404621 |
| SRA |
SRX14777125 |
