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Sample GSM7673070 Query DataSets for GSM7673070
Status Public on Dec 05, 2023
Title xl_els_flx_HDP4
Sample type SRA
 
Source name embryo
Organism Xenopus laevis
Characteristics lifestage: els
tissue: embryo
chemical: flx
concentration: HIGH
Extracted molecule total RNA
Extraction protocol RNA was extracted from Japanese quail and Double-crested cormorant samples using the Qiagen RNeasy mini kits; RNA was extracted from the fathead minnow, rainbow trout, African-clawed frog and the northern leopard frog using the Qiagen RNeasy Universal Mini kit.
Library was prepared according to Illumina instructions for NovaSeq 6000 S4 PE100 or HiSeq 4000 PE100 101-bp paired-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description xl_els_flx.txt
Data processing Reads were aligned using the Seq2Fun algorithm which translates raw reads to protein orthologs and maps them to a high-resolution protein-ortholog database - EcoOmicsDB available at www.expressanalyst.ca. The filtering parameters are provided below
Filtering: N. of amino acid mismatches was set at 2
Filtering: Minimum matching length was set at 19
Filtering: Minimum matching score was set at 80
Assembly: Mapping was species agnostic. Translated reads were mapped to the Vertebrate database
Raw fastq files were filtered as mentioned above and provided count matrices. These were analyzed for gene expression and pathway enrichment analysis.
Raw files and count files are provided as fastq files and .txt files, respectively.
Supplementary files format and content: Files here are from 49 datasets (datasets column below). Each dataset has a processed file which contains the counts for all samples within that dataset. Hence all samples (with unique title) from a dataset is present in the corresponding processed file. The title of the raw file for each sample is provided below as well. Some exposures were conducted together and hence had a common control exposure. Hence while 776 libraries are listed, they will correspond to fewer fastq files. But all fastq files are present.
 
Submission date Aug 01, 2023
Last update date Dec 05, 2023
Contact name Niladri Basu
E-mail(s) niladri.basu@mcgill.ca
Organization name McGill University
Street address 21,1111 Lakeshore Blvd, Apt #2
City Sainte-Anne-de-Bellevue
State/province Quebec
ZIP/Postal code H9X3V9
Country Canada
 
Platform ID GPL28901
Series (1)
GSE239776 EcoToxChip 2016 LSARP RNASeq database
Relations
BioSample SAMN36787153
SRA SRX21216631

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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