#Oly_Oyster_DNA_Methylation
This repository includes data and analysis scripts to accompany:
Authors:
Journal:
Link:
Description:
High-throughput sequencing, and analysis, of Olympia oyster (Ostrea lurida), MBD-enriched and bisulfite-treated DNA from two parent populations (Hood Canal=HC, and Osyter Bay=South Sound=SS), both grown out in Clam Bay (Manchester, WA):
Populations
Hood Canal (HC=Hood Canal)
Oyster Bay (SS=South Sound)
DNA extracted with Omega E.Z.N.A. Mollusc DNA Kit
Methylation Enrichment
Library Prep and Sequencing
- Libraries were prepped by ZymoResearch
- Sequencing was Illumina 50bp, single read
- Total reads generated for this project: 1,481,836,875
Received: 20160108
Total Number of Files: 108
Format: FASTQ (Illumina HiSeq2500)
Location: http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq/
The 18 samples were MBD-enriched and then sent to ZymoResearch for bisulfite conversion, multiplex library construction, and subsequent sequencing. The library (multiplex of all samples) was sequenced in a single lane, three times. Thus, we would expect 54 FASTQ files. However, ZymoResearch was dissatisfied with the QC of the initial sequencing run (completed on 20160129), so they re-ran the samples (completed on 20160202). This created two sets of data, resulting in a total of 108 FASTQ files.
Filenames containing s1, s2, or s3 are from initial sequencing run.
Filenames containing s4, s5, or s6 are from second sequencing run.
| FILENAME | READS | SAMPLE |
|---|---|---|
| zr1394_10_s1_R1.fastq.gz | 12129726 | ss2_9B |
| zr1394_10_s2_R1.fastq.gz | 11482874 | ss2_9B |
| zr1394_10_s3_R1.fastq.gz | 10547199 | ss2_9B |
| zr1394_10_s4_R1.fastq.gz | 26306980 | ss2_9B |
| zr1394_10_s5_R1.fastq.gz | 26573036 | ss2_9B |
| zr1394_10_s6_R1.fastq.gz | 26384567 | ss2_9B |
| zr1394_11_s1_R1.fastq.gz | 7893266 | ss2_14B |
| zr1394_11_s2_R1.fastq.gz | 7495554 | ss2_14B |
| zr1394_11_s3_R1.fastq.gz | 6775729 | ss2_14B |
| zr1394_11_s4_R1.fastq.gz | 18477911 | ss2_14B |
| zr1394_11_s5_R1.fastq.gz | 18305906 | ss2_14B |
| zr1394_11_s6_R1.fastq.gz | 18325711 | ss2_14B |
| zr1394_12_s1_R1.fastq.gz | 9669005 | ss2_18B |
| zr1394_12_s2_R1.fastq.gz | 9147875 | ss2_18B |
| zr1394_12_s3_R1.fastq.gz | 8338418 | ss2_18B |
| zr1394_12_s4_R1.fastq.gz | 20188420 | ss2_18B |
| zr1394_12_s5_R1.fastq.gz | 20006134 | ss2_18B |
| zr1394_12_s6_R1.fastq.gz | 19958692 | ss2_18B |
| zr1394_13_s1_R1.fastq.gz | 9840016 | ss3_3B |
| zr1394_13_s2_R1.fastq.gz | 9358447 | ss3_3B |
| zr1394_13_s3_R1.fastq.gz | 8578615 | ss3_3B |
| zr1394_13_s4_R1.fastq.gz | 21598254 | ss3_3B |
| zr1394_13_s5_R1.fastq.gz | 21823361 | ss3_3B |
| zr1394_13_s6_R1.fastq.gz | 21660067 | ss3_3B |
| zr1394_14_s1_R1.fastq.gz | 13367447 | ss3_14B |
| zr1394_14_s2_R1.fastq.gz | 12782967 | ss3_14B |
| zr1394_14_s3_R1.fastq.gz | 11914441 | ss3_14B |
| zr1394_14_s4_R1.fastq.gz | 29782244 | ss3_14B |
| zr1394_14_s5_R1.fastq.gz | 29515814 | ss3_14B |
| zr1394_14_s6_R1.fastq.gz | 29473848 | ss3_14B |
| zr1394_15_s1_R1.fastq.gz | 10879464 | ss3_15B |
| zr1394_15_s2_R1.fastq.gz | 10267923 | ss3_15B |
| zr1394_15_s3_R1.fastq.gz | 9425665 | ss3_15B |
| zr1394_15_s4_R1.fastq.gz | 23084106 | ss3_15B |
| zr1394_15_s5_R1.fastq.gz | 22853637 | ss3_15B |
| zr1394_15_s6_R1.fastq.gz | 22920249 | ss3_15B |
| zr1394_16_s1_R1.fastq.gz | 11242167 | ss3_16B |
| zr1394_16_s2_R1.fastq.gz | 10639584 | ss3_16B |
| zr1394_16_s3_R1.fastq.gz | 9717312 | ss3_16B |
| zr1394_16_s4_R1.fastq.gz | 25050434 | ss3_16B |
| zr1394_16_s5_R1.fastq.gz | 25317275 | ss3_16B |
| zr1394_16_s6_R1.fastq.gz | 25082606 | ss3_16B |
| zr1394_17_s1_R1.fastq.gz | 6292243 | ss3_20 |
| zr1394_17_s2_R1.fastq.gz | 5878505 | ss3_20 |
| zr1394_17_s3_R1.fastq.gz | 5300767 | ss3_20 |
| zr1394_17_s4_R1.fastq.gz | 14329557 | ss3_20 |
| zr1394_17_s5_R1.fastq.gz | 14186344 | ss3_20 |
| zr1394_17_s6_R1.fastq.gz | 14214584 | ss3_20 |
| zr1394_18_s1_R1.fastq.gz | 8197198 | ss5_18 |
| zr1394_18_s2_R1.fastq.gz | 7871675 | ss5_18 |
| zr1394_18_s3_R1.fastq.gz | 6898091 | ss5_18 |
| zr1394_18_s4_R1.fastq.gz | 18627445 | ss5_18 |
| zr1394_18_s5_R1.fastq.gz | 18447543 | ss5_18 |
| zr1394_18_s6_R1.fastq.gz | 18484693 | ss5_18 |
| zr1394_1_s1_R1.fastq.gz | 6768171 | hc1_2B |
| zr1394_1_s2_R1.fastq.gz | 7088611 | hc1_2B |
| zr1394_1_s3_R1.fastq.gz | 6127974 | hc1_2B |
| zr1394_1_s4_R1.fastq.gz | 15875631 | hc1_2B |
| zr1394_1_s5_R1.fastq.gz | 15747941 | hc1_2B |
| zr1394_1_s6_R1.fastq.gz | 15775841 | hc1_2B |
| zr1394_2_s1_R1.fastq.gz | 7073025 | hc1_4B |
| zr1394_2_s2_R1.fastq.gz | 6596118 | hc1_4B |
| zr1394_2_s3_R1.fastq.gz | 6079643 | hc1_4B |
| zr1394_2_s4_R1.fastq.gz | 15635185 | hc1_4B |
| zr1394_2_s5_R1.fastq.gz | 15492802 | hc1_4B |
| zr1394_2_s6_R1.fastq.gz | 15538451 | hc1_4B |
| zr1394_3_s1_R1.fastq.gz | 7293076 | hc2_15B |
| zr1394_3_s2_R1.fastq.gz | 6737811 | hc2_15B |
| zr1394_3_s3_R1.fastq.gz | 6144269 | hc2_15B |
| zr1394_3_s4_R1.fastq.gz | 16379997 | hc2_15B |
| zr1394_3_s5_R1.fastq.gz | 16260168 | hc2_15B |
| zr1394_3_s6_R1.fastq.gz | 16286455 | hc2_15B |
| zr1394_4_s1_R1.fastq.gz | 6649632 | hc2_17 |
| zr1394_4_s2_R1.fastq.gz | 6270620 | hc2_17 |
| zr1394_4_s3_R1.fastq.gz | 5813100 | hc2_17 |
| zr1394_4_s4_R1.fastq.gz | 15241034 | hc2_17 |
| zr1394_4_s5_R1.fastq.gz | 15080117 | hc2_17 |
| zr1394_4_s6_R1.fastq.gz | 15090774 | hc2_17 |
| zr1394_5_s1_R1.fastq.gz | 7149560 | hc3_1 |
| zr1394_5_s2_R1.fastq.gz | 6855766 | hc3_1 |
| zr1394_5_s3_R1.fastq.gz | 6226422 | hc3_1 |
| zr1394_5_s4_R1.fastq.gz | 16122713 | hc3_1 |
| zr1394_5_s5_R1.fastq.gz | 15952921 | hc3_1 |
| zr1394_5_s6_R1.fastq.gz | 15974422 | hc3_1 |
| zr1394_6_s1_R1.fastq.gz | 6614004 | hc3_5 |
| zr1394_6_s2_R1.fastq.gz | 6355162 | hc3_5 |
| zr1394_6_s3_R1.fastq.gz | 5529830 | hc3_5 |
| zr1394_6_s4_R1.fastq.gz | 15735916 | hc3_5 |
| zr1394_6_s5_R1.fastq.gz | 15596312 | hc3_5 |
| zr1394_6_s6_R1.fastq.gz | 15612183 | hc3_5 |
| zr1394_7_s1_R1.fastq.gz | 7571742 | hc3_7 |
| zr1394_7_s2_R1.fastq.gz | 7125072 | hc3_7 |
| zr1394_7_s3_R1.fastq.gz | 6436872 | hc3_7 |
| zr1394_7_s4_R1.fastq.gz | 16920844 | hc3_7 |
| zr1394_7_s5_R1.fastq.gz | 16731051 | hc3_7 |
| zr1394_7_s6_R1.fastq.gz | 16747458 | hc3_7 |
| zr1394_8_s1_R1.fastq.gz | 6146166 | hc3_10 |
| zr1394_8_s2_R1.fastq.gz | 5775399 | hc3_10 |
| zr1394_8_s3_R1.fastq.gz | 5262335 | hc3_10 |
| zr1394_8_s4_R1.fastq.gz | 13117656 | hc3_10 |
| zr1394_8_s5_R1.fastq.gz | 12994067 | hc3_10 |
| zr1394_8_s6_R1.fastq.gz | 13024791 | hc3_10 |
| zr1394_9_s1_R1.fastq.gz | 11259296 | hc3_11 |
| zr1394_9_s2_R1.fastq.gz | 11063708 | hc3_11 |
| zr1394_9_s3_R1.fastq.gz | 9830662 | hc3_11 |
| zr1394_9_s4_R1.fastq.gz | 26183621 | hc3_11 |
| zr1394_9_s5_R1.fastq.gz | 25958649 | hc3_11 |
| zr1394_9_s6_R1.fastq.gz | 26004238 | hc3_11 |
- Genome Data
- 20160512 - Ostrea_lurida.scafSeq file was trimmed to retain reads >10k to reduce small repeated fragments that prevent mapping of bisulfite reads.
The directory containing the analysis results, figures, tables, and supplementary material.