NASCArrays Information at The BAR

Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the experiment number. To download the CEL files, please click on the ftp link.

Experiment:	647
Title:	Identification of genes that are directly regulated by NMD in Arabidopsis
Date:	2012-12-07
Description:	To understand the way NMD mediates responses it is important to distinguish between direct and indirect targets. We will accomplish this using a global analysis of mRNA stability in wild type and NMD mutant backgrounds. Direct NMD targets show enhanced stability exclusively in NMD mutants. We will use cordycepin to interrupt transcription in wild type and NMD mutant three week old seedlings and analyse samples at time intervals following treatment. We will take timepoints at 0hrs, 1hr, 3hrs and 6hrs. We will analyse global mRNA stability in seedlings of four of our NMD mutant lines (upf1-5, UPF2 (6-11E5), upf3-1 and smg7-1) and wild type. This experiment will generate a list of mRNAs that are directly destabilised by NMD, which can be compared and analysed for features that make them targets of NMD. Three crucial questions will be addressed by this experiment. Firstly, the mRNA decay data will allow us to identify the genes that are directly targeted by each subset of the NMD pathway. For example, targets that are independent of UPF3 will appear to have altered stability only in the upf1 and smg7 mutant backgrounds. Secondly, it will allow us to test the association of specific NMD trigger signals with subsets of NMD. Finally, the list of direct targets will facilitate identification and dissection of the downstream regulated processes.
ftp Link:	ftp Link

Slide Information:

Slide ID	Slide Name	Genetic Background	Tissue	Stock Code	Cel File
Rayson_647-10_upf1-5_NMD_1hr_cordycepin_Rep1_ATH1	7781106	Col-0	Aerial tissues	N9902	Rayson_647-10_upf1-5_NMD_1hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-10_upf1-5_NMD_1hr_cordycepin_Rep1_ATH1	Treatment: Time = 1 hour Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-11_upf1-5_NMD_3hr_cordycepin_Rep1_ATH1	7781105	Col-0	Aerial tissues	N9902	Rayson_647-11_upf1-5_NMD_3hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-11_upf1-5_NMD_3hr_cordycepin_Rep1_ATH1	Treatment: Time = 3 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-12_upf1-5_NMD_6hr_cordycepin_Rep1_ATH1	7781104	Col-0	Aerial tissues	N9902	Rayson_647-12_upf1-5_NMD_6hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-12_upf1-5_NMD_6hr_cordycepin_Rep1_ATH1	Treatment: Time = 6 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-13_UPF2(6-11E5)_NMD_0hr_cordycepin_Rep1_ATH1	7781103		Aerial tissues		Rayson_647-13_UPF2(6-11E5)_NMD_0hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-13_UPF2(6-11E5)_NMD_0hr_cordycepin_Rep1_ATH1	Treatment: Time = 0 Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-14_UPF2(6-11E5)_NMD_1hr _cordycepin_Rep1_ATH1	7781102		Aerial tissues		Rayson_647-14_UPF2(6-11E5)_NMD_1hr _cordycepin_Rep1_ATH1.CEL
Rayson_647-14_UPF2(6-11E5)_NMD_1hr _cordycepin_Rep1_ATH1	Treatment: Time = 1 hour Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-15_UPF2(6-11E5)_NMD_3hr _cordycepin_Rep1_ATH1	7781101		Aerial tissues		Rayson_647-15_UPF2(6-11E5)_NMD_3hr _cordycepin_Rep1_ATH1.CEL
Rayson_647-15_UPF2(6-11E5)_NMD_3hr _cordycepin_Rep1_ATH1	Treatment: Time = 3 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-16_UPF2(6-11E5)_NMD_6hr _cordycepin_Rep1_ATH1	7781100		Aerial tissues		Rayson_647-16_UPF2(6-11E5)_NMD_6hr _cordycepin_Rep1_ATH1.CEL
Rayson_647-16_UPF2(6-11E5)_NMD_6hr _cordycepin_Rep1_ATH1	Treatment: Time = 6 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-17_upf3-1_NMD_0hr_cordycepin_Rep1_ATH1	7781099	Col-0	Aerial tissues	N9900	Rayson_647-17_upf3-1_NMD_0hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-17_upf3-1_NMD_0hr_cordycepin_Rep1_ATH1	Treatment: Time = 0 Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-18_upf3-1_NMD_1hr _cordycepin_Rep1_ATH1	7781098	Col-0	Aerial tissues	N9900	Rayson_647-18_upf3-1_NMD_1hr _cordycepin_Rep1_ATH1.CEL
Rayson_647-18_upf3-1_NMD_1hr _cordycepin_Rep1_ATH1	Treatment: Time = 1 hour Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-19_upf3-1_NMD_3hr _cordycepin_Rep1_ATH1	7781097	Col-0	Aerial tissues	N9900	Rayson_647-19_upf3-1_NMD_3hr _cordycepin_Rep1_ATH1.CEL
Rayson_647-19_upf3-1_NMD_3hr _cordycepin_Rep1_ATH1	Treatment: Time = 3 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-1_WT_0hr_cordycepin_Rep1_ATH1	7781115	Col-0 (Columbia)	Aerial tissues	N60000	Rayson_647-1_WT_0hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-1_WT_0hr_cordycepin_Rep1_ATH1	Treatment: Time = 0 (no cordycepin) Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-20_upf3-1_NMD_6hr _cordycepin_Rep1_ATH1	7781096	Col-0	Aerial tissues	N9900	Rayson_647-20_upf3-1_NMD_6hr _cordycepin_Rep1_ATH1.CEL
Rayson_647-20_upf3-1_NMD_6hr _cordycepin_Rep1_ATH1	Treatment: Time = 6 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-2_WT_1hr_cordycepin_Rep1_ATH1	7781114	Col-0 (Columbia)	Aerial tissues	N60000	Rayson_647-2_WT_1hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-2_WT_1hr_cordycepin_Rep1_ATH1	Treatment: Time = 1 hour Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-3_WT_3hr_cordycepin_Rep1_ATH1	7781112	Col-0 (Columbia)	Aerial tissues	N60000	Rayson_647-3_WT_3hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-3_WT_3hr_cordycepin_Rep1_ATH1	Treatment: Time = 3 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-4_WT_6hr_cordycepin_Rep1_ATH1	7781113	Col-0 (Columbia)	Aerial tissues	N60000	Rayson_647-4_WT_6hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-4_WT_6hr_cordycepin_Rep1_ATH1	Treatment: Time = 6 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.
Rayson_647-5_smg7-1_NMD_0hr_cordycepin_Rep1_ATH1	7781111	Col-0 (Columbia, N60000)	Aerial tissues	N573354	Rayson_647-5_smg7-1_NMD_0hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-5_smg7-1_NMD_0hr_cordycepin_Rep1_ATH1	Treatment: Time = 0 Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0. One leaf was taken for genotyping 1 week prior to treatment. Only confirmed homozygotes were used.
Rayson_647-6_smg7-1_NMD_1hr_cordycepin_Rep1_ATH1	7781110	Col-0 (Columbia, N60000)	Aerial tissues	N573354	Rayson_647-6_smg7-1_NMD_1hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-6_smg7-1_NMD_1hr_cordycepin_Rep1_ATH1	Treatment: Time = 1hour Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0. One leaf was taken for genotyping 1 week prior to treatment. Only confirmed homozygotes were used.
Rayson_647-7_smg7-1_NMD_3hr_cordycepin_Rep1_ATH1	7781109	Col-0 (Columbia, N60000)	Aerial tissues	N573354	Rayson_647-7_smg7-1_NMD_3hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-7_smg7-1_NMD_3hr_cordycepin_Rep1_ATH1	Treatment: Time = 3 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0. One leaf was taken for genotyping 1 week prior to treatment. Only confirmed homozygotes were used.
Rayson_647-8_smg7-1_NMD_6hr_cordycepin_Rep1_ATH1	7781108	Col-0 (Columbia, N60000)	Aerial tissues	N573354	Rayson_647-8_smg7-1_NMD_6hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-8_smg7-1_NMD_6hr_cordycepin_Rep1_ATH1	Treatment: Time = 6 hours Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0. One leaf was taken for genotyping 1 week prior to treatment. Only confirmed homozygotes were used.
Rayson_647-9_upf1-5_NMD_0hr_cordycepin_Rep1_ATH1	7781107	Col-0	Aerial tissues	N9902	Rayson_647-9_upf1-5_NMD_0hr_cordycepin_Rep1_ATH1.CEL
Rayson_647-9_upf1-5_NMD_0hr_cordycepin_Rep1_ATH1	Treatment: Time = 0 Aerial tissues were harvested into incubation buffer (IB: 1 mM Pipes, 1 mM Sodium citrate, 1 mM Potassium chloride, 15 mM Sucrose). After 30 minutes in IB, all except the time (T) = 0 samples were transferred to IB with cordycepin (150 Âµg ml-1). The T = 0 samples were transferred to fresh IB without cordycepin. All flasks (including the T = 0) were transferred to a bell jar and vacuum infiltrated. Immediately post-infiltration was classed as T =0.