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Sample GSM6703391 Query DataSets for GSM6703391
Status Public on Nov 30, 2022
Title (Bulk RNA-Seq) 5dpf Ift88 KO Replicate #2
Sample type SRA
 
Source name whole embryos
Organism Danio rerio
Characteristics tissue: whole embryos
genotype: Ift88 KO
time point: Day 5
Extracted molecule total RNA
Extraction protocol 30-35 2-dpf or 5-dpf zebrafish embryos were pooled to extract RNA with Qiagen Rneasy Plus Mini Kit
The library was prepared with Illumina RNA with PolyA selection package and sequenced with Illumina HiSeq 2x150bp, single index
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing RNA-seq raw reads were trimmed with TrimGalore 0.4.4
Trimmed reads were aligned to Danio rerio GRCz11 with Star 2.7.3a with default setting
Expression counts were calculated with HTSeq-count 0.12.3 with default setting
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each sample
 
Submission date Nov 01, 2022
Last update date Dec 01, 2022
Contact name John M Parant
Organization name University of Alabama at Birmingham
Street address 1670 University Blvd
City Birmingham
State/province AL
ZIP/Postal code 35233
Country USA
 
Platform ID GPL14875
Series (1)
GSE217001 Variable phenotypes and penetrance between and within different zebrafish transition zone mutants
Relations
BioSample SAMN31557292
SRA SRX18108804

Supplementary file Size Download File type/resource
GSM6703391_5dpf_ift88_mutant_R2_HTSeq.count.txt.gz 128.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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