Arabidopsis thaliana
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 loss of function 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)
ENA first public
2017-11-30
ENA last update
2017-11-20
External Id
SAMEA104392421
INSDC center alias
Bioinfromatician, Postdoc
INSDC center name
Bioinfromatician, Postdoc
INSDC first public
2017-11-30T17:01:56Z
INSDC last update
2017-11-20T11:33:22Z
INSDC status
public
Submitter Id
E-MTAB-5949:Sample 316
age
5
broker name
ArrayExpress
common name
thale cress
ecotype
Col-0 x Ler-0 F2
genotype
Recq4a Recq4b Hei10
growth condition
16 hours light at 20 degrees celsius
organism part
rosette leaf
phenotype
loss of function mutation in Recq4a and Recq4b; overexpression of Hei10
sample name
E-MTAB-5949:Sample 316