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| Status |
Public on Jul 01, 2021 |
| Title |
adult whole brain B8 |
| Sample type |
SRA |
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| Source name |
adult whole brain
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| Organism |
Danio rerio |
| Characteristics |
strain: AB line
generation: F1
Sex: M
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fish were euthanized, brains were dissected and flash frozen in liquid nitrogen, and DNA was extracted using TriPrep extraction kit (Macherey-Nagel). 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE, University of Perpignan, France, for pair-ended or single ended RRBS
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| Library strategy |
Bisulfite-Seq |
| Library source |
transcriptomic |
| Library selection |
Reduced Representation |
| Instrument model |
NextSeq 550 |
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| Description |
corrected_matrix.csv ID: B8
library pool: P4-6
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| Data processing |
Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1
Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L,0,-0.6". Rk due to batch effects described below, PE sequences were analyzed as SE.
methyl calling using Bismark extractor, cov >= 5 (processed data files)
batch correction using ComBat (see supplementary data corrected_matrix.csv)
identification of DMRs using Methylkit R v1.12; (300 bp tiles with at least 4 C included and >=10% differential methylation)
Genome_build: DanRer11
Supplementary_files_format_and_content: methyl call (cov >= 5) from bismark methyl extractor. *.tabular files (before correction) and corrected_matrix.csv (after correction)
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| Submission date |
Jul 10, 2020 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Mélanie Blanc |
| Organization name |
INRAE
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| Department |
UMR MARBEC
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| Street address |
Route de Maguelone
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| City |
Palavas |
| ZIP/Postal code |
34250 |
| Country |
France |
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| Platform ID |
GPL25922 |
| Series (1) |
| GSE154206 |
Epigenomic (RRBS) analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring after early-life exposure to permethrin 10 microg/L |
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| Relations |
| BioSample |
SAMN15504349 |
| SRA |
SRX8707743 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4666889_Galaxy36-_Filter_on_B8_.tabular.txt.gz |
8.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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