title: No pulse_0nM GnRH_0hT_collect_pulse3_270minET_rep2 [020116data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep1 [011416_2data]

status: Public on Apr 07 2017

type: RNA

city: New York

first: Frederique

last: Ruf-Zamojski

state: NY

address: 1468 Madison Avenue

department: Neurology

country: USA

institute: Mount Sinai Medical Center

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 24

data_processing:
Results were exported as cycle threshold (Ct) values, and Ct values of target genes were normalized to those of housekeeping gene (HKG) RPS11 (ribosomal protein S11; NM_013725.4). Data were expressed as relative Copy numbers by using the formula, Copy Number = 2500 X 1.93(Ct value of Rps11 - Ct value of gene of interest). No fold changes were calculated.
In the non-normalized data matrix, each Biological Sample N appears in 3 columns with the headers 'SAMPLE N-1', 'SAMPLE N-2', and 'SAMPLE N-3', which correspond to 3 qPCR replicates.
In the Sample data tables, the Copy Number of each Biological Sample was derived from the median Ct value of its 3 qPCR replicates.

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: pituitary gonadotrope-derived cells

label_protocol: After reverse-transcription of 1 mg of RNA with the Affinity Script reverse-transcriptase (Agilent, Santa Clara, CA), samples were diluted 1:20 in molecular biology grade H2O (Cellgro, Manassas, VA). Later, SYBR Green qPCR assays were performed (40 cycles) in an ABI Prism 7900HT thermal cycler (Applied Biosystems, Foster City, CA) using 5ml of cDNA template and 5ml of master mix containing the specific primers for the targeted gene, Platinum®Taq DNA polymerase, and the required qPCR buffer, according to manufacturer’s recommendations. Three technical qPCR replicates were run for each biological replicate.

growth_protocol: LβT2 cells were seeded on each tissue culture-treated coverslip and were grown for two days in DMEM supplemented with 10% FBS. Cells were incubated in DMEM supplemented with 2% charcoal-treated FBS and 20mM HEPES overnight before the pulse experiment.

extract_protocol: Coverslips were collected with forceps directly in the chamber and placed immediately in 360 ml guanidium thiocyanate RNA lysis buffer (4M guanidium thiocyanate, 25mM sodium citrate pH 7, 0.5% sarcosyl [N-lauroyl sarcosine], and 0.1M 2-mercaptoethanol). Total RNA was isolated with the “Absolutely RNA 96 microprep” kit (Agilent, Santa Clara, CA) according to the manufacturer's protocol, subjected to an ethanol precipitation to remove salts, and resuspended in elution buffer (Agilent, Santa Clara, CA). RNA concentrations were determined with Quant-iT RiboGreen RNA reagent (Invitrogen, Carlsbad, CA) using a fluorescence microplate reader (SpectraMax M3, Molecular Devices, Sunnyvale, CA).

treatment_protocol: Coverslips were placed in inert coverslip racks and pulse patterns were achieved by moving racks among GnRH, wash and resting solutions in chambers maintained at 37°C in a water bath.

tag: cell line

tag: cell type

value: immortalized gonadotrope cells


title: No pulse_0nM GnRH_0hT_collect_pulse3_270minET_rep4 [020116data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: No pulse_0nM GnRH_0hT_collect_pulse2_210minET_rep2 [020116data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: No pulse_0nM GnRH_0hT_collect_pulse2_150minET_rep1 [020116data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 1


title: No pulse_0nM GnRH_0hT_collect_pulse2_150minET_rep2 [020116data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 2


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 23


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 27


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 32


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 22


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 31


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 29


title: No pulse_0nM GnRH_0hT_collect_pulse3_330minET_rep1 [020116data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 21


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 26


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 18


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 20


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 13


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 16


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 25


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 15


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 17


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 28


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 4


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 9


title: No pulse_0nM GnRH_0hT__480minET_rep3 [011416_2data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 3


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 6


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 7


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep1 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 12


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep2 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 19


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep2 [011416_1data]


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 27


title: No pulse_0nM GnRH_0hT__480minET_rep2 [011416_2data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 2


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 24


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 29


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep3 [011416_2data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 14


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep3 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 23


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 21


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 22


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 16


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep3 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep3 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 17


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 18


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep3 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep2 [011416_1data]


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep3 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 20


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 4


title: No pulse_0nM GnRH_0hT__480minET_rep2 [011416_1data]


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 12


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 19


title: No pulse_0nM GnRH_0hT__480minET_rep1 [011416_2data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 1


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 28


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 13


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 15


title: No pulse_0nM GnRH_0hT__480minET_rep1 [011416_1data]


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 9


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 6


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep2 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep1 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 26


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 42


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 45


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 41


title: No pulse_0nM GnRH_0hT__480minET_rep3 [011416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 3


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 40


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 39


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 43


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 36


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 33


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 32


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 34


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 31


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep2 [010516data]


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 30


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 44


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep3 [011416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 14


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 29


title: No pulse_0nM GnRH_0hT__480minET_rep3 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 15


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 16


title: No pulse_0nM GnRH_0hT__480minET_rep1 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 13


title: No pulse_0nM GnRH_0hT__450minET_rep3 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 12


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 23


title: No pulse_0nM GnRH_0hT__450minET_rep2 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11


title: No pulse_0nM GnRH_0hT__420minET_rep2 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 38


title: No pulse_0nM GnRH_0hT__390minET_rep2 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: No pulse_0nM GnRH_0hT__360minET_rep3 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 3


title: No pulse_0nM GnRH_0hT__360minET_rep2 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 2


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 25


title: No pulse_0nM GnRH_0hT__360minET_rep1 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 1


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 31


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 33


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 37


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 30


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 24


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 21


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 28


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 20


title: No pulse_0nM GnRH_0hT__480minET_rep2 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 14


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 22


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep1 [010516data]


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 17


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep2 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 35


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 27


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 26


title: No pulse_0nM GnRH_0hT__420minET_rep1 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 7


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep1 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 19


title: No pulse_0nM GnRH_0hT__390minET_rep3 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 6


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 36


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 34


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep1 [010416_1data]


title: No pulse_0nM GnRH_0hT__450minET_rep1 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep3 [010516data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 18


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 32


title: No pulse_0nM GnRH_0hT__420minET_rep3 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 9


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep2 [010416_1data]


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep3 [010416_1data]


title: 254706910124_b1 - fit-3_3 vs FIT-GFP_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Transcriptomical changes in transgenic plants that carry a point mutation in FIT.

hyb_protocol: FIT-GFP_3 Cy5 / fit-3_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media: Hoagland Agar hygrometry : NA Temperature: 21°C / 19°C Light: 16h Light / 8h Dark

extract_protocol: FIT-GFP_3:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype/variation

value: mutant

tag: age

tag: dev stage (boyes et al. plant cell 2001)

extract_protocol: fit-3_3:100mg. (Qiagen_RNeasy.pdf)


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep1 [010416_1data]


title: No pulse_0nM GnRH_0hT__390minET_rep1 [010516data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 4


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 29


title: 254706910124_b4 - mFIT-GFP_3 vs fit-3_3

hyb_protocol: fit-3_3 Cy5 / mFIT-GFP_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: mFIT-GFP_3:100mg. (Qiagen_RNeasy.pdf)


title: 254706910123_b4 - FIT-GFP_2 vs fit-3_2

hyb_protocol: fit-3_2 Cy5 / FIT-GFP_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: fit-3_2:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: FIT-GFP_2:100mg. (Qiagen_RNeasy.pdf)


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 16


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 20


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 25


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 21


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 15


title: 254706910123_b1 - fit-3_1 vs FIT-GFP_1

hyb_protocol: FIT-GFP_1 Cy5 / fit-3_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: FIT-GFP_1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: fit-3_1:100mg. (Qiagen_RNeasy.pdf)


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 23


title: 254706910124_b2 - FIT-GFP_3 vs fit-3_3

hyb_protocol: fit-3_3 Cy5 / FIT-GFP_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep3 [010416_1data]


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 24


title: 254706910123_b3 - fit-3_2 vs FIT-GFP_2

hyb_protocol: FIT-GFP_2 Cy5 / fit-3_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910124_b3 - fit-3_3 vs mFIT-GFP_3

hyb_protocol: mFIT-GFP_3 Cy5 / fit-3_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 12


title: 254706910122_b2 - mFIT-GFP_2 vs FIT-GFP_2

hyb_protocol: FIT-GFP_2 Cy5 / mFIT-GFP_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: mFIT-GFP_2:100mg. (Qiagen_RNeasy.pdf)


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 13


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 14


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 17


title: 254706910121_b4 - mFIT-GFP_1 vs FIT-GFP_1

hyb_protocol: FIT-GFP_1 Cy5 / mFIT-GFP_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: mFIT-GFP_1:100mg. (Qiagen_RNeasy.pdf)


title: 254706910121_b2 - FIT-GFP_3 vs Col-0_3

hyb_protocol: Col-0_3 Cy5 / FIT-GFP_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col-0_3:100mg. (Qiagen_RNeasy.pdf)


title: 254706910120_b4 - FIT-GFP_2 vs Col-0_2

hyb_protocol: Col-0_2 Cy5 / FIT-GFP_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col-0_2:100mg. (Qiagen_RNeasy.pdf)


title: No pulse_0nM GnRH_0hT__480minET_rep5 [010416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: 254706910122_b1 - FIT-GFP_2 vs mFIT-GFP_2

hyb_protocol: mFIT-GFP_2 Cy5 / FIT-GFP_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910121_b3 - FIT-GFP_1 vs mFIT-GFP_1

hyb_protocol: mFIT-GFP_1 Cy5 / FIT-GFP_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: No pulse_0nM GnRH_0hT__480minET_rep1 [010416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 1


title: 254706910123_b2 - FIT-GFP_1 vs fit-3_1

hyb_protocol: fit-3_1 Cy5 / FIT-GFP_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep3 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 9


title: 254706910122_b3 - FIT-GFP_3 vs mFIT-GFP_3

description: Transcriptomical changes in transgenic plants that carry a point mutation in FIT.

hyb_protocol: mFIT-GFP_3 Cy5 / FIT-GFP_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: 254706910121_b1 - Col-0_3 vs FIT-GFP_3

hyb_protocol: FIT-GFP_3 Cy5 / Col-0_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep1 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 7


title: 254706910122_b4 - mFIT-GFP_3 vs FIT-GFP_3

hyb_protocol: FIT-GFP_3 Cy5 / mFIT-GFP_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: No pulse_0nM GnRH_0hT__480minET_rep4 [010416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 4


title: No pulse_0nM GnRH_0hT__480minET_rep3 [010416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 3


title: No pulse_0nM GnRH_0hT__0minET_rep5 [2hFreq_ReanalysisLISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 65


title: No pulse_0nM GnRH_0hT__0minET_rep4 [2hFreq_ReanalysisLISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 64


title: No pulse_0nM GnRH_0hT__0minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 63


title: No pulse_0nM GnRH_0hT__480minET_rep6 [010416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 6


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep2 [010416_1data]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8


title: No pulse_0nM GnRH_0hT__0minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 61


title: 254706910118_b3 - Col-0_3 vs fit-3_3

hyb_protocol: fit-3_3 Cy5 / Col-0_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: No pulse_0nM GnRH_0hT__480minET_rep2 [010416_1data]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 2


title: 254706910118_b2 - fit-3_2 vs Col-0_2

hyb_protocol: Col-0_2 Cy5 / fit-3_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910118_b4 - fit-3_3 vs Col-0_3

hyb_protocol: Col-0_3 Cy5 / fit-3_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: No pulse_0nM GnRH_0hT__0minET_rep6 [2hFreq_ReanalysisLISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 66


title: 254706910120_b3 - Col-0_2 vs FIT-GFP_2

hyb_protocol: FIT-GFP_2 Cy5 / Col-0_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse5_540minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 59


title: 5min pulse_0nM GnRH_2hT_collect_pulse5_540minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 58


title: 5min pulse_0nM GnRH_2hT_collect_pulse5_510minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 57


title: 5min pulse_0nM GnRH_2hT_collect_pulse5_510minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 56


title: 254706910119_b4 - mFIT-GFP_2 vs fit-3_2

description: Transcriptomical changes in transgenic plants that carry a point mutation in FIT.

hyb_protocol: fit-3_2 Cy5 / mFIT-GFP_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910119_b3 - fit-3_2 vs mFIT-GFP_2

hyb_protocol: mFIT-GFP_2 Cy5 / fit-3_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910119_b2 - mFIT-GFP_1 vs fit-3_1

hyb_protocol: fit-3_1 Cy5 / mFIT-GFP_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910117_b1 - Col-0_3 vs mFIT-GFP_3

hyb_protocol: mFIT-GFP_3 Cy5 / Col-0_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910120_b1 - Col-0_1 vs FIT-GFP_1

hyb_protocol: FIT-GFP_1 Cy5 / Col-0_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col-0_1:100mg. (Qiagen_RNeasy.pdf)


title: 254706910120_b2 - FIT-GFP_1 vs Col-0_1

hyb_protocol: Col-0_1 Cy5 / FIT-GFP_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910119_b1 - fit-3_1 vs mFIT-GFP_1

hyb_protocol: mFIT-GFP_1 Cy5 / fit-3_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 53


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 50


title: No pulse_0nM GnRH_0hT__0minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 62


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 48


title: 5min pulse_0nM GnRH_2hT_collect_pulse5_510minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 55


title: 254706910116_b2 - mFIT-GFP_1 vs Col-0_1

hyb_protocol: Col-0_1 Cy5 / mFIT-GFP_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 47


title: 254706910116_b4 - mFIT-GFP_2 vs Col-0_2

hyb_protocol: Col-0_2 Cy5 / mFIT-GFP_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 54


title: 254706910117_b3 - Col-0_1 vs fit-3_1

hyb_protocol: fit-3_1 Cy5 / Col-0_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 49


title: 254706910118_b1 - Col-0_2 vs fit-3_2

hyb_protocol: fit-3_2 Cy5 / Col-0_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_450minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 51


title: 254706910117_b2 - mFIT-GFP_3 vs Col-0_3

hyb_protocol: Col-0_3 Cy5 / mFIT-GFP_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_420minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 46


title: 254706910117_b4 - fit-3_1 vs Col-0_1

hyb_protocol: Col-0_1 Cy5 / fit-3_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse5_540minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 60


title: 254706910116_b3 - Col-0_2 vs mFIT-GFP_2

hyb_protocol: mFIT-GFP_2 Cy5 / Col-0_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 45


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_480minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 52


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 40


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 43


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_330minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 39


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 41


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_360minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 42


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_330minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 37


title: 254706910116_b1 - Col-0_1 vs mFIT-GFP_1

description: Transcriptomical changes in transgenic plants that carry a point mutation in FIT.

hyb_protocol: mFIT-GFP_1 Cy5 / Col-0_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_300minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 36


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_300minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 35


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_300minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 34


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 44


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_330minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 38


title: COS1_S211A+MDFIC_Dex6hr_rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

organism: Chlorocebus aethiops

source_name: COS1 cells_S211A+MDFIC_100nM Dex-treated_6 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced per manufacturer’s protocol.

growth_protocol: COS-1 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated FBS, 50 U/mL penicillin, 50 g/mL streptomycin, and 2 mM L-glutamine.  Cells were transfected using FuGENE6 (Promega).  The day after transfection, medium was replaced with new medium supplemented with 10% charcoal-stripped FBS.

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from 3 biological replicates of vehicle-treated S211A cells, Dex-treated S211A cells, vehicle-treated S211A+MDFIC cells, and Dex-treated S211A+MDFIC cells.

treatment_protocol: Cells were stimulated with either vehicle (control) or 100nM Dex for 6 hours.

value: African green monkey kidney cell line

tag: morphhology

value: fibroblast-like

tag: transfected with

tag: treated with

value: 100nM Dex for 6hrs


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_270minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 33


title: COS1_S211A+MDFIC_Con6hr_rep3

value: vehicle for 6hrs


title: COS1_S211A+MDFIC_Dex6hr_rep3


title: 5min pulse_2nM GnRH_2hT_collect_pulse5_540minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 30


title: 5min pulse_2nM GnRH_2hT_collect_pulse5_540minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 28


title: COS1_S211A+MDFIC_Dex6hr_rep1


title: COS1_S211A+MDFIC_Con6hr_rep2


title: COS1_S211A_Con6hr_rep3


title: COS1_S211A_Dex6hr_rep1

source_name: COS1 cells_S211A_100nM Dex-treated_6 hours


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_270minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 32


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 24


title: 5min pulse_2nM GnRH_2hT_collect_pulse5_510minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 25


title: COS1_GR+MDFIC_Dex6hr_rep3

description:
251485084528_1_4
Gene expression from COS1 cells, GR+MDFIC, 100nM Dex-treated, 6 hours

source_name: COS1_GR+MDFIC_100nM Dex-treated_6 hours

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from 3 biological replicates of vehicle-treated GR cells, Dex-treated GR cells, vehicle-treated GR+MDFIC cells, and Dex-treated GR+MDFIC cells.

tag: morphology

value: GR+MDFIC


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 23


title: 5min pulse_2nM GnRH_2hT_collect_pulse5_540minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 29


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 21


title: 5min pulse_2nM GnRH_2hT_collect_pulse5_510minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 26


title: COS1_GR+MDFIC_Con6hr_rep3

description:
251485084528_1_1
Gene expression from COS1 cells, GR+MDFIC, vehicle-treated, 6 hours

source_name: COS1_GR+MDFIC_vehicle-treated_6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 18


title: COS1_GR+MDFIC_Con6hr_rep1

description:
251485084527_1_3
Gene expression from COS1 cells, GR+MDFIC, vehicle-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse5_510minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 27


title: COS1_GR_Dex6hr_rep3

description:
251485084527_1_2
Gene expression from COS1 cells, GR, 100nM Dex-treated, 6 hours

source_name: COS1_GR_100nM Dex-treated_6 hours

value: GR


title: COS1_S211A_Dex6hr_rep2


title: COS1_S211A_Dex6hr_rep3


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 17


title: COS1_GR+MDFIC_Dex6hr_rep1

description:
251485084528_1_2
Gene expression from COS1 cells, GR+MDFIC, 100nM Dex-treated, 6 hours


title: COS1_S211A+MDFIC_Con6hr_rep1


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_480minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 22


title: COS1_S211A_Con6hr_rep2


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 14


title: 5min pulse_0nM GnRH_2hT_collect_pulse3_270minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 31


title: COS1_S211A_Con6hr_rep1


title: COS1_GR_Con6hr_rep1

description:
251485084526_1_1
Gene expression from COS1 cells, GR, vehicle-treated, 6 hours

source_name: COS1_GR_vehicle-treated_6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 20


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 15


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: COS1_GR+MDFIC_Dex6hr_rep2

description:
251485084528_1_3
Gene expression from COS1 cells, GR+MDFIC, 100nM Dex-treated, 6 hours


title: A549_MDFICsiRNA_Con6hr_rep3

description: Gene expression from A549 cells, MDFIC siRNA, vehicle-treated, 6 hours

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Homo sapiens

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: A549 were maintained in Dulbecco’s modified Eagle’s medium-F-12 (DMEM) supplemented with 10% heat-inactivated FBS, 50 U/mL penicillin, 50 g/mL streptomycin, and 2 mM L-glutamine.  The day before siRNA transfection, cells were plated in medium without antibiotics.  The day after siRNA transfection, cells were plated in medium with antibiotics. Prior to Dex treatment, cells were cultured overnight in medium supplemented with 10% charcoal-stripped FBS.

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from 3 biological replicates of vehicle-treated NTC cells, Dex-treated NTC cells, vehicle-treated MDFIC knockdown cells, and Dex-treated MDFIC knockdown cells.

value: lung carcinoma epithelial cell line

tag: gender

value: Caucasian male


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_330minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 9


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_450minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 19


title: A549_MDFICsiRNA_Dex6hr_rep2

description: Gene expression from A549 cells, MDFIC siRNA, 100nM Dex-treated, 6 hours


title: COS1_GR_Con6hr_rep3

description:
251485084526_1_3
Gene expression from COS1 cells, GR, vehicle-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_420minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 16


title: COS1_GR_Dex6hr_rep2

description:
251485084527_1_1
Gene expression from COS1 cells, GR, 100nM Dex-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_330minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 8


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_330minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 7


title: COS1_GR_Con6hr_rep2

description:
251485084526_1_2
Gene expression from COS1 cells, GR, vehicle-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 13


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_360minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 12


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_300minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 6


title: A549_MDFICsiRNA_Con6hr_rep1

source_name: A549 cells, MDFIC siRNA, vehicle-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_300minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 5


title: COS1_GR+MDFIC_Con6hr_rep2

description:
251485084527_1_4
Gene expression from COS1 cells, GR+MDFIC, vehicle-treated, 6 hours


title: A549_MDFICsiRNA_Dex6hr_rep1

source_name: A549 cells, MDFIC siRNA, 100nM Dex-treated, 6 hours


title: A549_NTCsiRNA_Dex6hr_rep3

description: Gene expression from A549 cells, NTC siRNA, 100nM Dex-treated, 6 hours


title: COS1_GR_Dex6hr_rep1

description:
251485084526_1_4
Gene expression from COS1 cells, GR, 100nM Dex-treated, 6 hours


title: A549_NTCsiRNA_Dex6hr_rep2

source_name: A549 cells, NTC siRNA, 100nM Dex-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_270minET_rep3 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 3


title: A549_MDFICsiRNA_Dex6hr_rep3


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_300minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 4


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_270minET_rep1 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 1


title: A549_NTCsiRNA_Con6hr_rep2

description: Gene expression from A549 cells, NTC siRNA, vehicle-treated, 6 hours


title: 5min pulse_2nM GnRH_2hT_collect_pulse3_270minET_rep2 [2hFreq_ReanalysisLISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 2


title: A549_NTCsiRNA_Dex6hr_rep1


title: A549_MDFICsiRNA_Con6hr_rep2

description: Gene expression from A549 cells, MDFIC siRNA, vehicle-treated, 6 hours


title: No pulse_0nM GnRH_0hT__0minET_rep5 [2hFreq_LISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 17

source_name: pituitary gonadotrope-derived cells, no pulse


title: No pulse_0nM GnRH_0hT__0minET_rep6 [2hFreq_LISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 18


title: KO sham2

city: Kanazawa

first: Soichiro

last: Usui

address: 13-1 Takaramachi

department: Department of System Biology

country: Japan

institute: Kanazawa University, Graduate School of Medical Sciences

description: MAFbxKO

hyb_protocol: RNA samples were hybridizaed with Affymetrix expression arrays offering whole-transcript coverage. After hybridization, non-specific binding was washed off according to the manufacturer's protocol.

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner.

data_processing: In the Expression Console software, hybridization intensity data were normalized using the Robust Multichip Average (RMA) method.

label: biotin

source_name: mouse heart

label_protocol: Biotinylated cRNA were prepared from total RNA as described by Affymetrix.

extract_protocol: Total RNA was isolated from mouse hearts using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Chatsworth, CA) according to manufacturer's instructions.

tag: tissue

value: heart

tag: genotype

value: MAFbxKO

tag: condition

value: sham


title: LM MI d1_1

description: WT

value: WT

value: MI


title: No pulse_0nM GnRH_0hT__0minET_rep2 [2hFreq_LISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 14

extract_protocol: Coverslips were collected with forceps directly in the chamber and placed immediately in 360 ml guanidium thiocyanate RNA lysis buffer (4M guanidium thiocyanate, 25mM sodium citrate pH 7, 0.5% sarcosyl [N-lauroyl sarcosine], and 0.1M 2-mercaptoethanol). Total RNA was isolated with the “Absolutely RNA 96 microprep” kit (Agilent, Santa Clara, CA) according to the manufacturer's protocol, subjected to an ethanol precipitation to remove salts, and resuspended in elution buffer (Agilent, Santa Clara, CA). RNA concentrations were determined with Quant-iT RiboGreen RNA reagent (Invitrogen, Carlsbad, CA) using a fluorescence microplate reader (SpectraMax M3, Molecular Devices, Sunnyvale, CA).


title: M. truncatula root_mtpt4-1_colonized with Gigaspora gigantea_replicate_1

city: Ithaca

first: Maria

middle: J.

last: Harrison

state: New York

address: 533 Tower Road

institute: Boyce Thompson Institute

description:
gene expression in mtpt4-1 mutant roots colonized with Gigaspora gigantea
M. truncatula mtpt4-1/G. gigantea root_ 1

hyb_protocol: 10ug of biotinylated cRNA was fragmented and hybridized to the Medicago Affymetrics Medicago Genome Array according to Affymetrix protocols and processed by an Affymetrix GeneChip Fluidics Station 450. Hybridization protocol-EukGE-WS2v5_450.

scan_protocol: GeneChips were scanned using an Affymetrics GeneChip Scanner, protocol  Scan-M10.

data_processing:
The images were analyzed by Microarray Suite version 5.0 (MAS 5.0) algorithm (Affymetrix). The data was normalized per array using GeneSpring version 7.3 software (Agilent).
Algorithm: ExpressionStat 5.0

organism: Medicago truncatula

source_name: Mycorrhizal Roots_mtpt4-1 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: See Floss et al., Current Biology

extract_protocol: RNA was isolated from roots using the Qiagen RNeasy Micro Kit and the quantity and quality assessed with an Agilent BioAnalyser 2100

treatment_protocol: See Floss et al., Current Biology

value: mtpt4-1 mutuant

value: root colonized with Gigaspora gigantea


title: No pulse_0nM GnRH_0hT__0minET_rep1 [2hFreq_LISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 13

value: immortalized gonadotrope cells


title: No pulse_0nM GnRH_0hT__0minET_rep4 [2hFreq_LISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 16


title: LM sham2

description: WT


title: A549_NTCsiRNA_Con6hr_rep3

source_name: A549 cells, NTC siRNA, vehicle-treated, 6 hours


title: KO sham1

description: MAFbxKO


title: KO MI d1_2

description: MAFbxKO


title: KO MI d1_1

description: MAFbxKO


title: LM MI d1_2

description: WT


title: M. truncatula root_A17_colonized with Gigaspora gigantea_replicate 3

description:
gene expression in wild-type roots colonized with Gigaspora gigantea
M. truncatula A17/G. gigantea root_3

source_name: Mycorrhizal Roots_Wild Type

value: Wild type


title: LM sham1

description: WT


title: A549_NTCsiRNA_Con6hr_rep1


title: M. truncatula root_mtpt4-1_colonized with Gigaspora gigantea_replicate_2

description:
gene expression in mtpt4-1 mutant roots colonized with Gigaspora gigantea
M. truncatula mtpt4-1/G. gigantea root_2


title: M. truncatula root_A17_colonized with Gigaspora gigantea_replicate 2

description:
gene expression in wild-type roots colonized with Gigaspora gigantea
M. truncatula A17/G. gigantea root_2


title: M. truncatula root_mtpt4-1_colonized with Gigaspora gigantea_replicate_3

description:
gene expression in mtpt4-1 mutant roots colonized with Gigaspora gigantea
M. truncatula mtpt4-1/G. gigantea root_3


title: M. truncatula root_A17_colonized with Gigaspora gigantea_replicate 1

description:
gene expression in wild-type roots colonized with Gigaspora gigantea
M. truncatula A17/G. gigantea root_ 1


title: No pulse_0nM GnRH_0hT__0minET_rep3 [2hFreq_LISAdata]

description:
Control; each biological sample represents 3 qPCR assay replicates.
SAMPLE 15


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep5 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 11

source_name: pituitary gonadotrope-derived cells, vehicle-pulsed, 2h period, 4-pulse collection


title: T6E R1984A-DMSO-rep 2

city: Boston

first: Eric

middle: A

last: Severson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The .CEL files were imported into R using the oligo package. Data were analyzed in R and batch effects were corrected with ComBat. Differential expression was assessed in R using the limma package.

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

treatment_protocol: Cells were treated with DMSO or 1 uM of Compound E, a gamma secretase inhibitor, for 6 hours.

value: dimerization-defective intracellular Notch 1(R1984A)

value: DMSO for 6hrs


title: T6E R1984A-DMSO-rep 3


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep6 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 12


title: T6E R1984A-GSI-rep 3

value: gamma secretase inhibitor (GSI) for 6hrs


title: T6E R1984A-GSI-rep 2


title: T6E ICN1-GSI-rep 3

value: intracellular Notch 1 (ICN1)


title: T6E ICN1-GSI-rep 1


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep4 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 10


title: T6E R1984A-GSI-rep 1


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep6 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 6

source_name: pituitary gonadotrope-derived cells, GnRH-pulsed, 2h period, 4-pulse collection


title: 5min pulse_0nM GnRH_2hT_collect_pulse4_390minET_rep1 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 7


title: 5min pulse_2nM GnRH_2hT_collect_pulse4_390minET_rep4 [2hFreq_LISAdata]

description:
Test; each biological sample represents 3 qPCR assay replicates.
SAMPLE 4