|
| Status |
Public on Apr 21, 2023 |
| Title |
Zebrafish_melanoma_CDK13_R860Q_3pSeq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma
|
| Organism |
Danio rerio |
| Characteristics |
tissue: melanoma
treatment: CDK13R860Q injection
|
| Growth protocol |
Melanomas generated from CDK13R860Q (n=3) or EGFP (n=3) injected into p53-/-; mitfa:BRAFV600E; mitfa-/- zebrafish were isolated and approximately equal cell numbers were gathered.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Poly-A selection was undertaken (NEB, E7490). Tissue was disrupted (Qiagen, 79654), DNA was removed, and RNA was isolated (Qiagen, 741134).
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina, 016.24
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA 3' end sequencing
|
| Data processing |
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013)
Custom Python script to filter reads from each bam file based on the following parameters: 1) Proper mate pairing; 2) orientation of the putative 3’ cleavage end corresponding to the direction of transcription for the gene to which reads mapped; 3) concordant mapping to known chromosomes; 4) no soft clippings; 5) skipped regions must be longer than 70 nucleotides.
Bedtools cluster tool version 2.26.0 (Quinlan and Hall, 2010) and custom Python scripts were used to generate read clusters by grouping any 3’ end coordinates that fell within 40 nucleotides of one another into a single cluster.
Clusters present in >1 replicate were considered to be true termination sites (high confidence termination sites). High confidence termination site reads were reclusters to define a complete and non-redundant 3' cleavage map for all conditions.
3' cleavage site reads were quantified using DEX-seq (Anders et al, 2012).
Assembly: GRCz11
Supplementary files format and content: 3pSeq counts tables contain gene coordinates, a unique polyA-site identifier, strand, and read counts
|
| |
|
| Submission date |
Jan 27, 2023 |
| 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) |
| GSE131334 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance |
| GSE223889 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [zf3primeseq] |
|
| Relations |
| BioSample |
SAMN32941384 |
| SRA |
SRX19200263 |
