title: Sample 45
organism: Arabidopsis thaliana
description: Protocols: Arabidopsis thaliana rosette leaves collected from 5-week-old plants and frozen (-20 degres celsius) Arabidopsis thaliana grown under long day conditions (16 hr light) and 20 degrees Celcius. Genotypes: HEI10 overexpression line - HEI10 was amplified from Col or Ler genomic DNA using primers HEI10-XbaI and HEI10-BamHI (Supplemental Table S29). Amplification products were cloned into the pGREEN-0029 binary vector using XbaI and BamHI restriction enzymes. Promoter swap constructs were generated using XbaI/PacI digestion and vector religation. These vectors were transformed into Col-420 FTL hemizygous plants using Agrobacterium strain GV3101 and floral dipping.( text taken from doi: 10.1101/gad.295501.116 Ziolkowski et al, 2017) and recq4a recq4b mutant lines recq4a-4 (N419423) recq4b-2 (N511130) (mutation described in paper: doi: 10.1073/pnas.0705998104 reference. Text taken from doi: 10.1073/pnas.1423107112 Seguela-Arnaud et al, 2015) Standard CTAB DNA extraction. DNA was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al. 2015; Yelina et al. 2015) with the following modifications. DNA was extracted from three rosette leaves of 5-wk-old plants, and 150 ng of DNA was used as input for each library. DNA was sheared for 20 min at 37°C with 0.4 U of DNA Shearase (Zymo research). Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Text taken from: doi: 10.1101/gad.295501.116 TruSeq DNA sample prep kit. Illumina sequencing: DNA was extracted from three rosette leaves of 5-wk-old plants, and 150 ng of DNA was used as input for each library. DNA was sheared for 20 min at 37°C with 0.4 U of DNA Shearase (Zymo research). Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). (text taken from doi: 10.1101/gad.295501.116 Ziolkowski et al, 2017)
attributes.tag: ENA first public
attributes.value: 2018-03-17
attributes.tag: ENA last update
attributes.value: 2018-03-07
attributes.tag: External Id
attributes.value: SAMEA104668346
attributes.tag: INSDC center alias
attributes.value: PDRA, Bioinformatician
attributes.tag: INSDC center name
attributes.value: PDRA, Bioinformatician
attributes.tag: INSDC first public
attributes.value: 2018-03-17T17:02:02Z
attributes.tag: INSDC last update
attributes.value: 2018-03-07T13:11:47Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-6577:Sample 45
attributes.tag: age
attributes.value: 5
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: thale cress
attributes.tag: cultivar
attributes.value: Col-0/Ler-0 F2
attributes.tag: developmental stage
attributes.value: leaf production stage
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: individual
attributes.value: 45
attributes.tag: organism part
attributes.value: rosette leaf
attributes.tag: sample name
attributes.value: E-MTAB-6577:Sample 45
attributes.tag: time
attributes.value: 10/2016