title: ICC21_control_L2
organism: Oryza sativa Indica Group
description: Protocols: The sample material was 12 pooled fourth leaves of individual plants for the control line and the epiline LR2, which belongs to the 4th selfing of the EUE selection pedigree. LR2 and the control line were grown in soil in a growth chamber at 26 C / 21 C (day / night) for 24 days with a 16 h light/8 h dark regime (light intensity was 300 mol m-2 sec-1, the relative humidity was kept at 71%) DNA isolation was performed using the CTAB (cetyltrimethyl/ammonium bromide) standard protocol For WGBS, paired-end bisulfite sequencing libraries were constructed by Alpha Biolaboratory, Inc. Saratoga, CA as described previously (Ibarra et al., 2012) with modifications. About 300 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon, Huntsville, AL) according to the manufacturer's (Illumina, San Diego, CA) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen, Hilden, Germany) as outlined in the manufacturer's instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 µL of 10 x Extaq reaction buffer, 25 µM dNTPs, 1 µL primer 1.1, 1 µl primer 2.1 in a 50 µL reaction. The thermocyling conditions were as follows: 95°C for 3 min, then 12-14 cycles of 95°C for 30 s, 65°C for 30 s and 72°C for 60 s. The enriched libraries were purified twice with solid phase reversible immobilization (SPRI) method using 0.8 x v/v AM-Pure beads (Beckman Coulter, Brea, CA) prior to quantification with a Bioanalyzer (Agilent Technologies, Santa Clara, CA).
attributes.tag: ENA first public
attributes.value: 2017-12-14
attributes.tag: ENA last update
attributes.value: 2016-08-10
attributes.tag: External Id
attributes.value: SAMEA4378192
attributes.tag: INSDC center alias
attributes.value: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium
attributes.tag: INSDC center name
attributes.value: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium
attributes.tag: INSDC first public
attributes.value: 2017-12-14T17:02:59Z
attributes.tag: INSDC last update
attributes.value: 2016-08-10T17:43:34Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-5002:ICC21_control_L2
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: long-grained rice
attributes.tag: organims part
attributes.value: leaf
attributes.tag: sample name
attributes.value: E-MTAB-5002:ICC21_control_L2
attributes.tag: selfing
attributes.value: 4
attributes.tag: sequencing run
attributes.value: 275
attributes.tag: strain
attributes.value: control_11_D