epiGBS individual blood Parus major - SRA

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SRX10994460: epiGBS individual blood Parus major
1 ILLUMINA (HiSeq X Ten) run: 6M spots, 1.7G bases, 758.2Mb downloads

Design: For detailed methods on sample collection and DNA isolation see Sepers et al., 2021. Several major improvements were made to the original epiGBS laboratory protocol (Boquete et al., 2020). In short, the genomic DNA was digested with the restriction enzymes MspI and NsII. A random three letter oligonucleotide (UMI) was placed in the adapter sequence (Moorsel, et al., 2019). Furthermore, a control nucleotide (CN, an un-methylated cytosine) was placed after the barcode followed by the sequence of the RE overhang (Moorsel, et al., 2019). The cytosines of the oligonucleotides adapter BA-I and adapter CO-I were 5-C methylated. The oligonucleotides of the opposite strands (adapter BA-II and adapter CO-II) contained un-methylated cytosines only and are 5-de-phosphorylated. After annealing the respective BA-I and BA-II and CO-I and CO-II adapter oligonucleotides and ligating them with the enzyme digested DNA fragment, only adapter 3 ends and fragment 5 ends ligate. The nick between adapter 5 ends and fragment 3 ends was repaired by using dNTPs that contained 5-meCs and that directly translated all 5-3 nucleotides starting from the nick. This resulted in fully methylated adapters that were ligated to the digested DNA fragment and a complementary 3-nucleotide short UMI sequence. As the four samples were pooled with 44 other samples, this resulted in a single, multiplexed sequencing library containing 48 barcoded samples. Library construction was conducted at the NIOO-KNAW. The final epiGBS2 library was sequenced on an Illumina HiSeq X Ten (150 bp from paired-end reads) by Novogene (Novogene (HK) Company Limited, Hong Kong, China) in 2019. The resulting epiGBS2 library was paired-end and directional, all four different bisulfite strands were present in the sequenced library: the original top strand (Watson), the complementary Watson strand, the original bottom strand (Crick), and the complementary Crick strand.

Submitted by: Netherlands Institute of Ecology (NIOO-KNAW) (NIOO-KNAW)

Study: Parus major Genome sequencing and assembly

PRJNA208335 • SRP055861 • All experiments • All runs

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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: S4

SAMN19349308 • SRS9068549 • All experiments • All runs

Organism: Parus major

Library:

Name: S4

Instrument: HiSeq X Ten

Strategy: Bisulfite-Seq

Source: GENOMIC

Selection: Reduced Representation

Layout: PAIRED

Runs: 1 run, 6M spots, 1.7G bases, 758.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR14655965	6,005,050	1.7G	758.2Mb	2022-02-04

ID:: 14622630

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