|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jul 01, 2021 |
Title |
adult whole brain C1 |
Sample type |
SRA |
|
|
Source name |
adult whole brain
|
Organism |
Danio rerio |
Characteristics |
strain: AB line generation: F2 Sex: F
|
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
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
transcriptomic |
Library selection |
Reduced Representation |
Instrument model |
NextSeq 550 |
|
|
Description |
corrected_matrix.csv ID: C1 library pool: P6-3
|
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)
|
|
|
Submission date |
Jul 10, 2020 |
Last update date |
Jul 01, 2021 |
Contact name |
Mélanie Blanc |
Organization name |
INRAE
|
Department |
UMR MARBEC
|
Street address |
Route de Maguelone
|
City |
Palavas |
ZIP/Postal code |
34250 |
Country |
France |
|
|
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 |
|
Relations |
BioSample |
SAMN15504314 |
SRA |
SRX8707720 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4666866_Galaxy21-_Filter_on_data_82_C1_.tabular.txt.gz |
5.4 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 |
|
|
|
|
|