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SRX26112229: epiGBS pool blood Parus major
1 ILLUMINA (HiSeq X Ten) run: 459.1M spots, 137.7G bases, 65.7Gb downloads

Design: The sequencing libraries each contained DNA extracted from 36 blood samples (216 samples in total). Each library consisting of three samples from 12 Parus major nestlings (12 x 3 = 36), collected on day 7, day 9 and day 14 after hatching . DNA methylation was assessed using the reduced-representation bisulfite sequencing method epiGBS2 (Gawehns et al., 2022). EpiGBS2 library preparations were conducted at the NIOO-KNAW following the laboratory protocol described in the Supporting Information of Sepers et al. (2023). 800 ng DNA per sample was extracted using the FavorPrep 96-Well Genomic DNA Extraction Kit (Favorgen) and digested with the restriction enzyme MspI (NEB). The fragments were ligated to a unique barcode combination for each sample and the fragments from 36 samples were pooled (i.e. multiplexed). To be able to differentiate methylated cytosines from unmethylated cytosines, unmethylated cytosines were converted to thymines using sodium bisulfite. Sequencing was performed by Novogene (Novogene (HK) Company Limited, Hong Kong) on an Illumina HiSeq X (150 bp from paired-end, directional reads). PhiX DNA was spiked-in (12%).
Submitted by: Netherlands Institute of Ecology (NIOO-KNAW)
Study: Parus major Genome sequencing and assembly
show Abstracthide Abstract
Seasonal timing is a key life-history trait with major fitness consequences. The small songbird Parus major (great tit) for decades has been a model to study fitness traits like e.g. avian timing of reproduction. The research is closely linked to the impact of global climate change on timing and its consequences. Linking quantitative genetic variation in life-history traits with polymorphisms in specific genes is essential for better understanding the causes and consequences of the diversity in these traits. Genetic variation in life-history traits in wild songbirds has been demonstrated in many, often long-term, studies throughout the world. Linking this variation to genomic information requires the development of the necessary genomics tools specifically aimed at these non-model species. The assembly and annotation of the genome of the great tit will greatly enhance the further use of the great tit as a model species in this research field.
Sample:
SAMN43807016 • SRS22676359 • All experiments • All runs
Organism: Parus major
Library:
Name: B13
Instrument: HiSeq X Ten
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: Reduced Representation
Layout: PAIRED
Runs: 1 run, 459.1M spots, 137.7G bases, 65.7Gb
Run# of Spots# of BasesSizePublished
SRR30694708459,127,931137.7G65.7Gb2024-09-18

ID:
35231179

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