GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM6998359 Query DataSets for GSM6998359
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
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]
BioSample SAMN32941384
SRA SRX19200263

Supplementary file Size Download File type/resource
GSM6998359_Zebrafish_PAS_raw_counts_CDK13_R860Q_R1.txt.gz 1021.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap