Tag Archives: ss3_3B

Data Received – Ostrea lurida MBD-enriched BS-seq

Received the Olympia oyster, MBD-enriched BS-seq sequencing files (50bp, single read) from ZymoResearch (submitted 20151208). Here’s the sample list:

  • E1_hc1_2B
  • E1_hc1_4B
  • E1_hc2_15B
  • E1_hc2_17
  • E1_hc3_1
  • E1_hc3_5
  • E1_hc3_7
  • E1_hc3_10
  • E1_hc3_11
  • E1_ss2_9B
  • E1_ss2_14B
  • E1_ss2_18B
  • E1_ss3_3B
  • E1_ss3_14B
  • E1_ss3_15B
  • E1_ss3_16B
  • E1_ss3_20
  • E1_ss5_18


The 18 samples listed above had previously been 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.

ZymoResearch data portal does not allow bulk download of files. However, I ended up using Chrono Download Manager extension for Google Chrome to allow for automated downloading of each file (per ZymoResearch recommendation).

After download, the files were moved to their permanent storage location on Owl: http://owl.fish.washington.edu/nightingales/O_lurida/20160203_mbdseq

The readme.md file was updated to include project/file information.

The file manipulations were performed in a Jupyter notebook (see below).


Total reads generated for this project: 1,481,836,875


Jupyter Notebook file: 20160203_Olurida_Zymo_Data_Handling.ipynb

Notebook Viewer: 20160203_Olurida_Zymo_Data_Handling.ipynb


MBD Enrichment – Sonicated Olympia Oyster gDNA

Olympia oyster gDNA that had previously been sonicated and fragmented was enriched for the methylated fragments using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen).

Prepared the following components:

  • 20mL 1x Bind/Wash Buffer (4mL 5x Bind/Wash Buffer + 16mL H2O)
  • 640μL of beads (35μL of beads x 18 samples )
  • 200μL MBD-Biotin Protein (63μL MBD-Biotin Protein + 137μL 1x Bind/Wash Buffer)

Followed the manufacturer’s protocol for input DNA quantities 1μg – 10μg.

Used single fraction, high salt elution.

Neglected to account for the control reaction during initial set up and did not have sufficient quantities of beads to run a control reaction.

The table below provides the individual sample volumes and the volumes of the buffer, beads, H2O for the MBD capture reactions.

Samples listed with “NA” were not processed because they did not fragment during sonication.

Sample Volume (μL) Buffer/Beads (μL) H2O (μL) Total (μL)
hc1_2B 75 135 290 500
hc1_4B 90 135 275 500
hc2_15B 75 135 290 500
hc2_17 75 135 290 500
hc3_1 75 135 290 500
hc3_5 75 135 290 500
hc3_7 70 135 295 500
hc3_9 NA NA NA NA
hc3_10 70 135 295 500
hc3_11 70 135 295 500
ss2_9B 190 135 175 500
ss2_14B 195 135 170 500
ss2_18B 195 135 170 500
ss3_3B 190 135 175 500
ss3_4B NA NA NA NA
ss3_14B 195 135 170 500
ss3_15B 195 135 170 500
ss3_16B 195 135 170 500
ss3_20 135 135 230 500
ss5_18 75 135 290 500


Non-captured & wash fractions were pooled into single samples and stored @ -20C.

MBD fraction was EtOH precipitated according to the manufacturer’s protocol and incubate O/N @ -80C.



DNA Sonication – Oly gDNA for MBD

In preparation for MBD enrichment, fragmented Olympia oyster gDNA with a target size of ~350bp.

Genomic DNA samples were isolated and provided to us by Katherine Silliman at UIC. Selected samples will compare Hood Canal (HC) and Oyster Bay (SS, South Sound) populations.

Used the Seeb Lab’s Bioruptor 300 (Diagenode) sonicator.

After sonication, samples were run on a the Seeb Lab’s 2100 Bioanalyzer (Agilent) on DNA 12000 chips.





More detailed analysis (including average fragment size for each samples) will be coming soon…