title: Sample 94
organism: Caenorhabditis elegans
description: Protocols: The Caenorhabditis elegans nematodes were grown on petri-dishes with nematode growth medium, feeding off Escherichia coli OP50. A new population was started by transferring clean eggs to a fresh dish. After 72 hours at 20°C, nematodes were collected by washing off with M9 buffer. Pellets with nematodes were allowed to settle by gravity and washed three times to remove external bacteria. Pellets were flash-frozen in liquid nitrogen and stored at -80°C until further processing. DNA was extracted using the DNeasy® 96 Blood & Tissue Kit (QIAGEN, Germany) according to the manufacturers specifications. For each sample 0.75 ng of DNA was combined with 2.5 µl 1/35th diluted transposome (Illumina; # FC-121-1011), and 1X Tris Buffer in a 10 µl final volume on ice. This reaction was incubated at 55°C for 10 minutes. Subsequently the DNA was amplified. This reaction contained for each sample (final concentrations): 1X ExTaq Buffer, 0.2 mM dNTPs, 1 Unit ExTaq (Takara, catalog #RR001A), 0.2 µM primer 1, 0.2 µM primer 2, and 5 µl of tagmentation material from the previous step in a 25 µl total volume. Each sample had a unique pair of indexed primers. Amplification was carried out in a thermocycler with the following conditions: 72°C for 3 minutes (1X); 95°C for 30 seconds (1X); 95°C 10 seconds, 62°C 30 seconds, 72°C 3 minutes (20X); 10°C hold. Then, 16 µl from each amplification reaction was used to generate a pool of 48 libraries. Amplicons were gel extracted in the size range of 500-700 bp, and gel purified the sample with Qiagen's Gel Purification Kit (catalog #28706).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-06-30T00:24:15Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-06-30T00:24:15Z
attributes.tag: External Id
attributes.value: SAMEA112483517
attributes.tag: INSDC center alias
attributes.value: Wageningen University and Research
attributes.tag: INSDC center name
attributes.value: Wageningen University and Research
attributes.tag: INSDC first public
attributes.value: 2023-06-30T00:24:15Z
attributes.tag: INSDC last update
attributes.value: 2023-06-30T00:24:15Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-12575:Sample 94
attributes.tag: age
attributes.value: 72
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: genotype
attributes.value: WN610
attributes.tag: individual
attributes.value: WN610
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: whole organism
attributes.tag: sample name
attributes.value: E-MTAB-12575:Sample 94
attributes.tag: scientific_name
attributes.value: Caenorhabditis elegans
attributes.tag: sex
attributes.value: hermaphrodite
attributes.tag: strain
attributes.value: WN610