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| Status |
Public on Jun 16, 2021 |
| Title |
P144_BSseq |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Polistes canadensis |
| Characteristics |
tissue: Brain
experiment: Queen removal
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Heads were cut off and immediately placed in RNA later solution (Ambion) and kept at -20°C until brain dissection.
Genomic DNA was extracted from single brains using the QIAGEN All Prep DNA/RNA Mini Kit according to the man- ufacturer’s instructions.
Between 200 ng and 500 ng of input genomic DNA was used per library and spiked with unmethylated lambda DNA to provide an esti- mation of BS conversion efficiency. DNA was end-repaired, A-tailed, and ligated with a methylation Adaptor Oligo Kit (Illumina) using the NEB Next kit according to the manufacturer’s instructions. The adaptor-ligated DNA was treated with sodium-BS using an Imprint DNA Modification Kit from Sigma–Aldrich according to the manufacturer’s instructions for the two-step protocol. BS-treated DNA was amplified using KAPA HiFi Uracil + DNA Polymerase (KAPA Biosystems) with 15 cycles. Size selection and cleaning between steps were performed with an AMPure XP system (Agencourt) to select DNA fragments between 250 bp and 500 bp.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence were trimmed to remove both poor quality calls and adapters using Trim Galore (version 0.3.5 with default parameters, www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were then aligned to genome assembly (EVM/PASA; Patalano et al. PNAS, 2015) using Bismark (version 0.12.2, with the parameters: --bowtie2 --score_min L,0,−0.4).
Genome_build: Polistes canadensis GCF_001313835.1
Bisulfite-Seq
Quantification was done in SeqMonk over probes which contain 50 CpGs each with a minimum read count of 4. Only 10bb to 3kbp probes overlapping genes were kept.
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| Submission date |
Jan 28, 2020 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Felix Krueger |
| E-mail(s) |
[email protected]
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| Organization name |
Altos Labs
|
| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL28086 |
| Series (2) |
| GSE144407 |
Specialisation and plasticity in a primitive social insect (Bisulfite-Seq) |
| GSE144409 |
Specialisation and plasticity in a primitive social insect |
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| Relations |
| BioSample |
SAMN13938005 |
| SRA |
SRX7644377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4287572_P144_BSseq.cov.gz |
66.3 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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