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SRX18523282: epiGBS pool blood Parus major
1 ILLUMINA (HiSeq X Ten) run: 463.4M spots, 139G bases, 59.4Gb downloads

Design: Each of the eight sequencing libraries contained 36-37 samples: 64 parental samples and 222 nestling samples from 20 cross-foster pairs. We assessed genome-wide DNA methylation levels using epiGBS2 (Gawehns et al., 2022), with some improvements. Sequencing libraries were prepared at the NIOO-KNAW. DNA was isolated from 2 to 5 L blood per sample using the FavorPrep 96-Well Genomic DNA Extraction Kit (Favorgen). 800 ng DNA per sample was digested with MspI. Large fragments were removed using beads (0.8x AMPure XP beads). The fragments were ligated to a unique barcoded adapter combination for each sample within a sequencing library, after which the fragments of all 36 to 37 samples were pooled into one sequencing library. The pooled fragments were exposed to sodium bisulfite, which converts unmethylated cytosines (Cs) into uracils, which will later be amplified as thymines. Bisulfite-PCR amplification was conducted with 15 PCR cycles and the KAPA HIFI Uracil + hotstart ready mix. The amplified libraries were sequenced on an Illumina HiSeq X (150 bp, paired-end, directional) by Novogene (Novogene (HK) Company Limited, Hong Kong).
Submitted by: Netherlands Institute of Ecology (NIOO-KNAW) (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: B3
SAMN32085371 • SRS15991149 • All experiments • All runs
Organism: Parus major
Library:
Name: B3
Instrument: HiSeq X Ten
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: Reduced Representation
Layout: PAIRED
Runs: 1 run, 463.4M spots, 139G bases, 59.4Gb
Run# of Spots# of BasesSizePublished
SRR22559865463,425,178139G59.4Gb2023-04-05

ID:
25575761

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