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Status |
Public on Dec 05, 2023 |
Title |
xl_els_tb_HBP2 |
Sample type |
SRA |
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Source name |
embryo
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Organism |
Xenopus laevis |
Characteristics |
lifestage: els tissue: embryo chemical: tb concentration: HIGH
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
xl_els_tb.txt
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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.
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Submission date |
Aug 01, 2023 |
Last update date |
Dec 05, 2023 |
Contact name |
Niladri Basu |
E-mail(s) |
niladri.basu@mcgill.ca
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Organization name |
McGill University
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Street address |
21,1111 Lakeshore Blvd, Apt #2
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City |
Sainte-Anne-de-Bellevue |
State/province |
Quebec |
ZIP/Postal code |
H9X3V9 |
Country |
Canada |
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Platform ID |
GPL28901 |
Series (1) |
GSE239776 |
EcoToxChip 2016 LSARP RNASeq database |
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Relations |
BioSample |
SAMN36787112 |
SRA |
SRX21216427 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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