|
| Status |
Public on Apr 21, 2023 |
| Title |
CDK13_R860Q_oe_R159 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Melanoma
cdk13 status: R860Q
|
| Growth protocol |
p53-/-; mitfa:BRAFV600E;Na-/- one-cell embryos were injected with either 20ng/uL control or experimental MiniCoopR (MCR) DNA along with tol2 in vitro transcribed RNA for integration. In all experiments, 20 zebrafish were raised per tank to control for density effects. Zebrafish were scored for the emergence of raised melanoma lesions as published. Zebrafish were sacrificed on ice and the tumors were dissected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library prepped with random priming (NEBNext Ultra RNA Library Prep Kit for Illumina, E7530), fragmentation time of 15min, 12 PCR cycles, and sequenced on an Illumina HiSeq 2000 (100bp paired end reads).
Melanomas were homogenized in RLT buffer, subjected to QIAshredder columns (Qiagen, 79656), and then RNA was isolated with a column based method with genomic DNA column removal (Qiagen, 74134). RNA was ribodepleted (Illumina Ribozero Gold, MRZG12324). Ribodepletion was confirmed with Agilent 4200 Tapestation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to a custom version of the danRer10 genome that also contained the human CDK13 gene sequence using bowtie with parameters --library-type fr-unstranded --no-novel-juncs and -G set revision 90 of the Ensembl GRCz10 genes
Expression of revision 90 GRCz10 genes was quantified using htseq-count with parameters -r name -I gene_name --stranded=no -m intersection-strict
Supplementary_files_format_and_content: Counts files contain gene names and htseq-determined read counts
|
| |
|
| Submission date |
May 16, 2019 |
| Last update date |
Apr 21, 2023 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE131333 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (zfRNAseq) |
| GSE131334 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance |
|
| Relations |
| BioSample |
SAMN11659651 |
| SRA |
SRX5846425 |
