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| Status |
Public on Aug 09, 2018 |
| Title |
MethylC-seq_heads of newly eclosed, orphaned bees rep3 |
| Sample type |
SRA |
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| Source name |
Huntlab_C_calcarata_PBE09_methyl
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| Organism |
Ceratina calcarata |
| Characteristics |
ecotype: Collected in their nests (stems of Rhus typhina) from Durham, NH in June 2015 at 8am and brought to the lab. Mother was removed and offspring were reared to adulthood
tissue: 9 pooled heads
age: newly eclosed adult
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| Treatment protocol |
N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
mRNA (for RNA-seq) was extracted and prepared using the Truseq library preparation protocol. Bisulfite conversion and illumina sequencing was performed by the Beijing Genomics Institute.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
bisulfite-treated DNA from heads of newly eclosed, orphaned bees rep3
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| Data processing |
Data were mapped to the Ceratina calcarata v1.1 genome
For RNA-seq data:RNA-seq reads were checked for biases using FastQC (v0.11.4) (Andrews, 2010) and then trimmed using Trimmomatic (v0.32) (Bolger, Lohse, & Usadel, 2014). Reads were then aligned to the C. calcarata reference assembly (v1.1) (Rehan et al., 2016) using Tophat (Trapnell et al., 2012) with parameters “--no-mixed --no-discordant” to filter out read pairs that did not have both reads mapping or had a read pair mapping discordantly. Aligned reads were counted against annotated gene models (Rehan et al. 2016) using Rsubread. Gene models were generated previously as described in Rehan et al. 2016.
For Bisulfite-sequencing data: We trimmed adapters and removed low-quality reads using Trimmomatic (v0.32) (Bolger et al., 2014). Reads were then aligned to the reference genome using Bismark (v0.14.5) (Krueger & Andrews, 2011). Bismark was also used to remove duplicate reads and to extract and quantify the per-site methylation level.
Genome_build: Ceratina calcarata v1.1 reference genome
Supplementary_files_format_and_content: For RNA-seq data: Tab delimited file: <gene_symbol> <aligned reads count>.
For Bisulfite-sequencing data: <chromosome/scaffold> <position> <strand> <reads mapped> <% methylated C> <% unmethylated C>
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| Submission date |
Mar 08, 2018 |
| Last update date |
Aug 10, 2018 |
| Contact name |
Brendan G. Hunt |
| E-mail(s) |
[email protected]
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| Phone |
(770) 412-4093
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| Organization name |
University of Georgia
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| Department |
Entomology
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| Lab |
Brendan G. Hunt Lab
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| Street address |
125 Redding Building, Griffin Campus, 1109 Experiment Street
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| City |
Griffin |
| State/province |
GA |
| ZIP/Postal code |
30223 |
| Country |
USA |
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| Platform ID |
GPL24713 |
| Series (1) |
| GSE111611 |
The Effect of Maternal Care on Gene Expression and DNA Methylation in Ceratina calcarata |
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| Relations |
| BioSample |
SAMN08663760 |
| SRA |
SRX3776766 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3035126_PBE09_CpG.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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