|
| Status |
Public on Nov 08, 2023 |
| Title |
RNAseq_E6_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
primary keratinocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary keratinocytes
treatment: HPV16 E6
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Quick-RNA MiniPrep (Zymo Research)
TruSeq Stranded Total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Assembly: hg38
Supplementary files format and content: diff_gene_expr_paired.txt = tab-delimited text file containing differential gene expression results form DESeq2
|
| |
|
| Submission date |
Jun 23, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Susanna Chiocca |
| E-mail(s) |
[email protected]
|
| Organization name |
European Institute of Oncology, IEO
|
| Street address |
Via Adamello 16
|
| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE235662 |
c-MYC-dependent transcriptional inhibition of autophagy is implicated in Cisplatin sensitivity in HPV-positive Head and Neck Cancer |
|
| Relations |
| BioSample |
SAMN35881849 |
| SRA |
SRX20765641 |
