title: 1yr, pineal, night, rep4

status: Public on Oct 27 2009

type: RNA

city: Bethesda

first: Reiko

last: Toyama

state: MD

address: Bldg.6B, Room 420, 9000 Rockville Pike

department: NICHD

country: USA

institute: NIH

description: Biological replicate 4 of 4

hyb_protocol: 2.2 micrograms of labeled cDNA was hybridized to the Affymetrix zebrafish GeneChip at 45 degrees C for 18 hrs. Post-hybridization, staining, and washing were performed using a Fluidics Station 450 (Affymetrix) with protocol EukGE-WS2v4_450.

scan_protocol: The hybridized chips were scanned by Affymetrix GeneChip Scanner 3000 and then processed with GeneChip Operating Software (GCOS).

data_processing: Global scaling was employed for analysis and the target Intensity value (TGT) was set as 500 following the manufacturer's (Affymetrix) recommendations. GeneChip Operating Software (Affymetrix) was used to create CEL files from each experiment.  Further statistical analysis was done using JMP, the statistical Discovery Software (http://www.jmp.com).

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: 1-2yr old, pineal gland, night-time

label_protocol: Biotinylated cDNA was prepared using the Ovation Biotin system kit (NeuGen) according to the manufacturer's instructions.

growth_protocol: Adults and embryos were kept at 28.5oC under a 14-hr-light/10-hr-dark cycle.

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: Adult


title: 1yr, brain, day, rep2

description: Biological replicate 2 of 3

source_name: 1-2yr old, brain, day-time


title: 1yr, brain, night, rep3

description: Biological replicate 3 of 3

source_name: 1-2yr old, brain, night-time


title: 1yr, brain, day, rep1

description: Biological replicate 1 of 3


title: 1yr, brain, night, rep2

description: Biological replicate 2 of 3


title: 1yr, pineal, day, rep4

description: Biological replicate 4 of 4

source_name: 1-2yr old, pineal gland, day-time


title: 3mo, brain, night, rep3

description: Biological replicate 3 of 3

source_name: 3mo old, brain, night-time


title: 1yr, brain, night, rep1

description: Biological replicate 1 of 3


title: 1yr, pineal, night, rep1

description: Biological replicate 1 of 4


title: 1yr, pineal, night, rep2

description: Biological replicate 2 of 4


title: 1yr, pineal, night, rep3

description: Biological replicate 3 of 4


title: 1yr, pineal, day, rep3

description: Biological replicate 3 of 4


title: 1yr, brain, day, rep3

description: Biological replicate 3 of 3


title: 3mo, brain, night, rep2

description: Biological replicate 2 of 3


title: 1yr, pineal, day, rep1

description: Biological replicate 1 of 4


title: 3mo, pineal, night, rep2

description: Biological replicate 2 of 3

source_name: 3mo old, pineal gland, night-time


title: 3mo, brain, day, rep3

description: Biological replicate 3 of 3

source_name: 3mo old, brain, day-time


title: 1yr, pineal, day, rep2

description: Biological replicate 2 of 4


title: 3mo, brain, day, rep1

description: Biological replicate 1 of 3


title: 3mo, brain, night, rep1

description: Biological replicate 1 of 3


title: 3mo, pineal, night, rep3

description: Biological replicate 3 of 3


title: 3mo, pineal, day, rep3

description: Biological replicate 3 of 3

source_name: 3mo old, pineal gland, day-time


title: 3mo, brain, day, rep2

description: Biological replicate 2 of 3


title: 3mo, pineal, night, rep1

description: Biological replicate 1 of 3


title: 3mo, pineal, day, rep2

description: Biological replicate 2 of 3


title: 10d, pineal, night, rep2

description: Biological replicate 2 of 4

source_name: 10d old, pineal gland, night-time

tag: Embryo


title: 10d, brain, day, rep3

description: Biological replicate 3 of 3

source_name: 10d old, brain, day-time


title: 10d, pineal, day, rep2

description: Biological replicate 2 of 4

source_name: 10d old, pineal gland, day-time


title: 10d, pineal, night, rep3

description: Biological replicate 3 of 4


title: 10d, brain, day, rep1

description: Biological replicate 1 of 3


title: 10d, brain, night, rep2

description: Biological replicate 2 of 4

source_name: 10d old, brain, night-time


title: 10d, brain, night, rep3

description: Biological replicate 3 of 4


title: 10d, pineal, night, rep4

description: Biological replicate 4 of 4


title: 10d, brain, night, rep1

description: Biological replicate 1 of 4


title: 10d, pineal, day, rep4

description: Biological replicate 4 of 4


title: 10d, pineal, day, rep1

description: Biological replicate 1 of 4


title: 10d, brain, night, rep4

description: Biological replicate 4 of 4


title: 5d, pineal, night, rep4

description: Biological replicate 4 of 4

source_name: 5d old, pineal gland, night-time


title: 10d, pineal, night, rep1

description: Biological replicate 1 of 4


title: 5d, brain, night, rep2

description: Biological replicate 2 of 2

source_name: 5d old, brain, night-time


title: 3mo, pineal, day, rep1

description: Biological replicate 1 of 3


title: 10d, pineal, day, rep3

description: Biological replicate 3 of 4


title: 10d, brain, day, rep2

description: Biological replicate 2 of 3


title: 5d, brain, night, rep1

description: Biological replicate 1 of 2


title: 5d, pineal, night, rep2

description: Biological replicate 2 of 4


title: 5d, pineal, night, rep1

description: Biological replicate 1 of 4


title: 5d, brain, day, rep3

description: Biological replicate 3 of 3

source_name: 5d old, brain, day-time


title: 5d, pineal, night, rep3

description: Biological replicate 3 of 4


title: 5d, brain, day, rep2

description: Biological replicate 2 of 3


title: 5d, brain, day, rep1

description: Biological replicate 1 of 3


title: 5d, pineal, day, rep4

description: Biological replicate 4 of 5

source_name: 5d old, pineal gland, day-time


title: 5d, pineal, day, rep5

description: Biological replicate 5 of 5


title: 5d, pineal, day, rep2

description: Biological replicate 2 of 5


title: 5d, pineal, day, rep3

description: Biological replicate 3 of 5


title: 3d, pineal, night, rep2

description: Biological replicate 2 of 4

source_name: 3d old, pineal gland, night-time


title: 3d, pineal, night, rep3

description: Biological replicate 3 of 4


title: 5d, pineal, day, rep1

description: Biological replicate 1 of 5


title: 3d, pineal, night, rep4

description: Biological replicate 4 of 4


title: 3d, brain, night, rep3

description: Biological replicate 3 of 4

source_name: 3d old, brain, night-time


title: 3d, pineal, night, rep1

description: Biological replicate 1 of 4


title: 3d, brain, night, rep2

description: Biological replicate 2 of 4


title: 3d, brain, day, rep3

description: Biological replicate 3 of 3

source_name: 3d old, brain, day-time


title: 3d, brain, night, rep4

description: Biological replicate 4 of 4


title: 3d, pineal, day, rep1

description: Biological replicate 1 of 3

source_name: 3d old, pineal gland, day-time


title: 3d, brain, day, rep2

description: Biological replicate 2 of 3


title: 3d, pineal, day, rep3

description: Biological replicate 3 of 3


title: 3d, pineal, day, rep2

description: Biological replicate 2 of 3


title: 3d, brain, night, rep1

description: Biological replicate 1 of 4


title: 3d, brain, day, rep1

description: Biological replicate 1 of 3


title: Susceptible_YHV_Day2_Organism4

status: Public on Oct 23 2009

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

description: no additional information

hyb_protocol: The slides were initially washed (0.2% SDS for 2 minutes, boiling MilliQ water for 2 minutes and 70% ethanol for 2 minutes).  They were incubated for 1 hour at 50ºC in a rocker at 10 rpm with 90 mL of preheated (50ºC) pre-hybridization solution (29.5 mL of H2O, 31.5 mL of formamide, 18 mL of 20X SSPE, 4.5 mL of 10% SDS, 5.6 mL of 40X Denhardt's solution, 0.9 mL of salmon sperm DNA).  The slides were washed in MiliQ water and the sample (10 mg of the labeled aRNA (28mL), 2 mL of blocking solution and 60 mL of hybridization solution (2.25 mL of H20, 30 mL of formamide, 12 mL of 20X SSPE, 12 mL of 10% SDS, 3.75 mL of 40X Denhardt's solution) boiled for 1 minute and incubated for 1 hour at 50ºC) added.  The slides with the sample were placed in a dark incubation oven at 50ºC with a rocker at 10 rpm for 16 hours.

scan_protocol: The slides were scanned at 70PMT in a ScanArray Express (Perkin Elmer) and intensity quantification was carried out by the software ScanArray

data_processing: The data were background corrected using the normexp method.  A print-order loess normalization was carried out followed by a quantile within array normalization using a smooth spline.  Next, genes which the 4 replicates did not show intensity higher than three times the average intensity of the non-shrimp genes present in the slides  in at least 10% of the slides in the experiment were disregarded (the intensity of the probes that were disregarded are shown in the data matrix as null).  Last, the remaining data were variance stabilization normalized (vsn)

organism: Penaeus vannamei

source_name: Hepatopancreas, Susceptible, YHV, Day2

label_protocol: 20 mg of the amino allyl aRNA were labeled with the NHS ester Cy3 following the instruction in the Amino Allyl MessageAmp II aRNA kit (Ambion).

growth_protocol: The shrimp were kept in an indoor, semi-closed recirculating system composed of 25 transparent 10L tanks with particulate, biological and UV light filtration, and were allowed to acclimatize for one week prior to the experiment.  They were fed on average one food pellet per shrimp per day.

extract_protocol: Total RNA was extracted from approximatelly 1 mm3 of hepatopancreas using the Rneasy kit (Qiagen) with the on-column Dnase step.  Next, 1 mg the total RNA was reverse transcribed and in-vitro transcribed using the Amino Allyl MessageAmp II aRNA kit (Ambion).

treatment_protocol: At day 0 the shrimp were injected with 60uL of a shrimp extract made from shrimp previously injected with either a saline (1x10-4), Taura Syndrome Virus (1x10-5) or Yellow Head Virus (1x10-4).  The hepatopancreas was manual dissected and stored in RNAlater® (Ambion).

tag: Common name

value: Pacific Whiteleg Shrimp

tag: Group

value: Susceptible YHV

tag: Strain

value: Susceptible

tag: Injection

value: Extract of YHV infected shrimp

tag: Concentration of injection

tag: Tissue

value: Hepatopancreas

tag: Weight ± Standard Deviation of group

tag: Day sampled

value: Day 2

tag: Mortality of group at day 1

tag: Mortality of group at day 2

tag: Mortality of group at the end of experiment


title: Susceptible_YHV_Day2_Organism5

description: no additional information


title: Susceptible_YHV_Day2_Organism2

description: no additional information


title: Susceptible_YHV_Day2_Organism1

description: no additional information


title: Resistant_YHV_Day2_Organism5

description: no additional information

source_name: Hepatopancreas, Resistant, YHV, Day2

value: Resistant YHV

value: Resistant


title: Resistant_YHV_Day2_Organism4

description: no additional information


title: Resistant_YHV_Day2_Organism2

description: no additional information


title: Resistant_YHV_Day2_Organism3

description: no additional information


title: Resistant_YHV_Day2_Organism1

description: no additional information


title: Resistant_TSV_Day2_Organism3

description: no additional information

source_name: Hepatopancreas, Resistant, TSV, Day2

value: Resistant TSV

value: Extract of TSV infected shrimp


title: Susceptible_TSV_Day2_Organism2

description: no additional information

source_name: Hepatopancreas, Susceptible, TSV, Day2

value: Susceptible TSV


title: Resistant_TSV_Day2_Organism4

description: no additional information


title: Susceptible_YHV_Day2_Organism3

description: no additional information


title: Resistant_Control_Day2_Organism5

description: no additional information

source_name: Hepatopancreas, Resistant, Control, Day2

value: Resistant Control

value: Extract of SPF shrimp


title: Susceptible_TSV_Day2_Organism4

description: no additional information


title: Resistant_Control_Day2_Organism4

description: no additional information


title: Resistant_TSV_Day2_Organism1

description: no additional information


title: Susceptible_TSV_Day2_Organism5

description: no additional information


title: Susceptible_TSV_Day2_Organism1

description: no additional information


title: Resistant_Control_Day2_Organism3

description: no additional information


title: Resistant_Control_Day2_Organism1

description: no additional information


title: Susceptible_TSV_Day2_Organism3

description: no additional information


title: Resistant_TSV_Day2_Organism5

description: no additional information


title: Susceptible_Control_Day2_Organism2

description: no additional information

source_name: Hepatopancreas, Susceptible, Control, Day2

value: Susceptible Control


title: Susceptible_Control_Day2_Organism1

description: no additional information


title: Resistant_TSV_Day2_Organism2

description: no additional information


title: Susceptible_YHV_Day1_Organism5

description: no additional information

source_name: Hepatopancreas, Susceptible, YHV, Day1

value: Day 1


title: Susceptible_YHV_Day1_Organism2

description: no additional information


title: Resistant_YHV_Day1_Organism5

description: no additional information

source_name: Hepatopancreas, Resistant, YHV, Day1


title: Susceptible_YHV_Day1_Organism3

description: no additional information


title: Resistant_Control_Day2_Organism2

description: no additional information


title: Susceptible_Control_Day2_Organism5

description: no additional information


title: Susceptible_Control_Day2_Organism4

description: no additional information


title: Resistant_YHV_Day1_Organism2

description: no additional information


title: Susceptible_Control_Day2_Organism3

description: no additional information


title: Susceptible_YHV_Day1_Organism1

description: no additional information


title: Susceptible_TSV_Day1_Organism5

description: no additional information

source_name: Hepatopancreas, Susceptible, TSV, Day1


title: Resistant_YHV_Day1_Organism4

description: no additional information


title: Susceptible_TSV_Day1_Organism2

description: no additional information


title: Susceptible_YHV_Day1_Organism4

description: no additional information


title: Resistant_TSV_Day1_Organism4

description: no additional information

source_name: Hepatopancreas, Resistant, TSV, Day1


title: Resistant_TSV_Day1_Organism3

description: no additional information


title: Resistant_TSV_Day1_Organism1

description: no additional information


title: Resistant_Control_Day1_Organism1

description: no additional information

source_name: Hepatopancreas, Resistant, Control, Day1


title: Resistant_YHV_Day1_Organism3

description: no additional information


title: Resistant_YHV_Day1_Organism1

description: no additional information


title: Resistant_Control_Day1_Organism5

description: no additional information


title: Susceptible_Control_Day1_Organism5

description: no additional information

source_name: Hepatopancreas, Susceptible, Control, Day1


title: Susceptible_Control_Day1_Organism4

description: no additional information


title: Susceptible_TSV_Day1_Organism3

description: no additional information


title: Susceptible_TSV_Day1_Organism1

description: no additional information


title: Resistant_TSV_Day1_Organism5

description: no additional information


title: Susceptible_TSV_Day1_Organism4

description: no additional information


title: Susceptible_Control_Day1_Organism2

description: no additional information


title: Resistant_TSV_Day1_Organism2

description: no additional information


title: Susceptible_Control_Day1_Organism1

description: no additional information


title: Resistant_Control_Day1_Organism3

description: no additional information


title: Susceptible_Control_Day1_Organism3

description: no additional information


title: Resistant_Control_Day1_Organism4

description: no additional information


title: Susceptible_Control_Day0_Organism1

description: no additional information

source_name: Hepatopancreas, Susceptible, Control, Day0

value: Day 0


title: Susceptible_Control_Day0_Organism4

description: no additional information


title: Susceptible_Control_Day0_Organism5

description: no additional information


title: Resistant_Control_Day1_Organism2

description: no additional information


title: Resistant_Control_Day0_Organism4

description: no additional information

source_name: Hepatopancreas, Resistant, Control, Day0


title: Susceptible_Control_Day0_Organism3

description: no additional information


title: Resistant_Control_Day0_Organism2

description: no additional information


title: Susceptible_Control_Day0_Organism2

description: no additional information


title: Resistant_Control_Day0_Organism5

description: no additional information


title: Resistant_Control_Day0_Organism1

description: no additional information


title: Resistant_Control_Day0_Organism3

description: no additional information


title: RLDP-20wk_highfat_WistarKyoto-5RP

status: Public on Oct 21 2009

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

description: Gene expression data of the liver from WKY rat 5, feeded with HFD and sacrificed at 20 weeks

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230_2 plus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: MAS 5

organism: Rattus norvegicus

source_name: rat liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: RLDP-20wk_highfat_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_highfat_WistarKyoto-6RP

description: Gene expression data of the liver from WKY rat 6, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_normal_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_normal_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_normal_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_highfat_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_normal_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_highfat_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_normal_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_highfat_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_highfat_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_highfat_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with HFD and sacrificed at 20 weeks


title: RLDP-20wk_highfat_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with HFD and sacrificed at 20 weeks


title: RLDP-16wk_highfat_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with HFD and sacrificed at 16 weeks


title: RLDP-16wk_highfat_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with HFD and sacrificed at 16 weeks


title: RLDP-20wk_normal_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_normal_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_highfat_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with HFD and sacrificed at 20 weeks


title: RLDP-16wk_highfat_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with HFD and sacrificed at 16 weeks


title: RLDP-20wk_normal_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_normal_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_normal_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with ND and sacrificed at 20 weeks


title: RLDP-20wk_highfat_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with HFD and sacrificed at 20 weeks


title: RLDP-16wk_highfat_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with HFD and sacrificed at 16 weeks


title: RLDP-16wk_normal_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_highfat_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with HFD and sacrificed at 16 weeks


title: RLDP-16wk_normal_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_normal_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_highfat_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with HFD and sacrificed at 16 weeks


title: RLDP-12wk_normal_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with ND and sacrificed at 12 weeks


title: RLDP-12wk_highfat_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_highfat_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with HFD and sacrificed at 12 weeks


title: RLDP-16wk_highfat_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with HFD and sacrificed at 16 weeks


title: RLDP-16wk_normal_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_highfat_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with HFD and sacrificed at 16 weeks


title: RLDP-12wk_normal_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with ND and sacrificed at 12 weeks


title: RLDP-16wk_normal_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_normal_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_highfat_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with HFD and sacrificed at 16 weeks


title: RLDP-16wk_normal_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with ND and sacrificed at 16 weeks


title: RLDP-12wk_normal_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with ND and sacrificed at 12 weeks


title: RLDP-16wk_normal_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with ND and sacrificed at 16 weeks


title: RLDP-12wk_highfat_WistarKyoto-3RP

description: Gene expression data of the liver  from WKY rat 3, feeded with HFD and sacrificed at 12 weeks


title: RLDP-16wk_highfat_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with HFD and sacrificed at 16 weeks


title: RLDP-12wk_normal_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with ND and sacrificed at 12 weeks


title: RLDP-12wk_normal_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with ND and sacrificed at 12 weeks


title: RLDP-16wk_normal_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with ND and sacrificed at 16 weeks


title: RLDP-16wk_normal_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with ND and sacrificed at 16 weeks


title: RLDP-12wk_highfat_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_highfat_WistarKyoto-5RP

description: Gene expression data of the liver from WKYrat 5, feeded with HFD and sacrificed at 12 weeks

tag: liver from WKY rat 5, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_highfat_WistarKyoto-4RP

description: Gene expression data of the liver  from WKY rat 4, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_highfat_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_highfat_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_highfat_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with HFD and sacrificed at 12 weeks


title: RLDP-12wk_normal_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with ND and sacrificed at 12 weeks


title: RLDP-12wk_normal_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with ND and sacrificed at 12 weeks


title: RLDP-8wk_highfat_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_normal_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_normal_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_highfat_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_normal_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_normal_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with ND and sacrificed at 8 weeks


title: RLDP-12wk_normal_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with ND and sacrificed at 12 weeks


title: RLDP-12wk_normal_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with ND and sacrificed at 12 weeks


title: RLDP-8wk_normal_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_normal_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_highfat_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_highfat_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_highfat_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_highfat_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_normal_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_highfat_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_highfat_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with HFD and sacrificed at 8 weeks


title: RLDP-8wk_normal_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_normal_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with ND and sacrificed at 8 weeks


title: RLDP-8wk_normal_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with ND and sacrificed at 8 weeks


title: RLDP-12wk_normal_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with ND and sacrificed at 12 weeks


title: RLDP-8wk_highfat_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with HFD and sacrificed at 8 weeks


title: RLDP-4wk_highfat_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_highfat_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_highfat_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_highfat_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_highfat_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with HFD and sacrificed at 4 weeks


title: RLDP-12wk_highfat_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with HFD and sacrificed at 12 weeks


title: RLDP-4wk_normal_WistarKyoto-3RP

description: Gene expression data of the liver from WKY rat 3, feeded with ND and sacrificed at 4 weeks


title: RLDP-4wk_normal_WistarKyoto-2RP

description: Gene expression data of the liver from WKY rat 2, feeded with ND and sacrificed at 4 weeks


title: RLDP-4wk_normal_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with ND and sacrificed at 4 weeks


title: RLDP-4wk_highfat_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_normal_Goto-Kakizake-5RP

description: Gene expression data of the liver from GK rat 5, feeded with ND and sacrificed at 4 weeks


title: RLDP-4wk_highfat_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_highfat_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_highfat_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_normal_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with ND and sacrificed at 4 weeks


title: RLDP-4wk_normal_Goto-Kakizake-4RP

description: Gene expression data of the liver from GK rat 4, feeded with ND and sacrificed at 4 weeks


title: RLDP-4wk_highfat_Goto-Kakizake-3RP

description: Gene expression data of the liver from GK rat 3, feeded with HFD and sacrificed at 4 weeks


title: RLDP-4wk_normal_WistarKyoto-5RP

description: Gene expression data of the liver from WKY rat 5, feeded with ND and sacrificed at 4 weeks


title: RLDP-8wk_highfat_WistarKyoto-4RP

description: Gene expression data of the liver from WKY rat 4, feeded with HFD and sacrificed at 8 weeks


title: RLDP-4wk_normal_WistarKyoto-1RP

description: Gene expression data of the liver from WKY rat 1, feeded with ND and sacrificed at 4 weeks


title: RMDP-20wk_highfat_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with HFD and sacrificed at 20 weeks

source_name: rat gastrocnemius muscle


title: RMDP-20wk_highfat_WistarKyoto-6RP

description: Gene expression data of gastrocnemius muscle from WKY rat 6, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_normal_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_highfat_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_highfat_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with HFD and sacrificed at 20 weeks


title: RLDP-4wk_normal_Goto-Kakizake-2RP

description: Gene expression data of the liver from GK rat 2, feeded with ND and sacrificed at 4 weeks


title: RMDP-20wk_normal_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_normal_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_highfat_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_highfat_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_normal_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with ND and sacrificed at 20 weeks


title: RLDP-4wk_normal_Goto-Kakizake-1RP

description: Gene expression data of the liver from GK rat 1, feeded with ND and sacrificed at 4 weeks


title: RMDP-20wk_normal_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_normal_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_normal_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with ND and sacrificed at 20 weeks


title: RMDP-16wk_highfat_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with HFD and sacrificed at 16 weeks


title: RMDP-20wk_normal_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_highfat_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_normal_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_normal_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with ND and sacrificed at 20 weeks


title: RMDP-20wk_highfat_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_highfat_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with HFD and sacrificed at 20 weeks


title: RMDP-16wk_highfat_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_highfat_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_highfat_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with HFD and sacrificed at 16 weeks


title: RMDP-20wk_highfat_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with HFD and sacrificed at 20 weeks


title: RMDP-20wk_highfat_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with HFD and sacrificed at 20 weeks


title: RMDP-16wk_normal_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_highfat_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_normal_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_highfat_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_highfat_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_highfat_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat1, feeded with HFD and sacrificed at 16 weeks

tag: GK rat 1, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_highfat_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_normal_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_normal_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_normal_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_normal_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_highfat_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with HFD and sacrificed at 16 weeks


title: RMDP-16wk_normal_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_normal_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with ND and sacrificed at 16 weeks


title: RMDP-12wk_highfat_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_highfat_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with HFD and sacrificed at 12 weeks


title: RMDP-16wk_normal_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with ND and sacrificed at 16 weeks


title: RMDP-16wk_normal_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with ND and sacrificed at 16 weeks


title: RMDP-12wk_highfat_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_normal_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_normal_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_normal_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_normal_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_highfat_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_highfat_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_highfat_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_normal_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_highfat_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_highfat_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_highfat_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with HFD and sacrificed at 12 weeks


title: RMDP-12wk_normal_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_highfat_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with HFD and sacrificed at 12 weeks


title: RMDP-8wk_highfat_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with HFD and sacrificed at 8 weeks


title: RMDP-8wk_highfat_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with HFD and sacrificed at 8 weeks


title: RMDP-8wk_highfat_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with HFD and sacrificed at 8 weeks


title: RMDP-8wk_normal_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with ND and sacrificed at 8 weeks


title: RMDP-12wk_normal_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with ND and sacrificed at 12 weeks


title: RMDP-12wk_normal_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with ND and sacrificed at 12 weeks


title: RMDP-8wk_normal_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_normal_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_highfat_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with HFD and sacrificed at 8 weeks


title: RMDP-12wk_normal_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with ND and sacrificed at 12 weeks


title: RMDP-8wk_highfat_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with HFD and sacrificed at 8 weeks


title: RMDP-12wk_normal_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with ND and sacrificed at 12 weeks


title: RMDP-8wk_normal_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_highfat_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with HFD and sacrificed at 8 weeks


title: RMDP-8wk_highfat_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with HFD and sacrificed at 8 weeks


title: RMDP-8wk_normal_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_normal_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_highfat_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with HFD and sacrificed at 8 weeks


title: RMDP-8wk_normal_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_normal_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with ND and sacrificed at 8 weeks


title: RMDP-8wk_normal_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with ND and sacrificed at 8 weeks


title: RMDP-4wk_highfat_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with HFD and sacrificed at 4 weeks


title: RMDP-8wk_highfat_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with HFD and sacrificed at 8 weeks


title: RMDP-4wk_normal_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_highfat_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_highfat_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with HFD and sacrificed at 4 weeks


title: RMDP-8wk_normal_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with ND and sacrificed at 8 weeks


title: RMDP-4wk_highfat_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_highfat_WistarKyoto-3RP

description: Gene expression data of gastrocnemius muscle from WKY rat 3, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_normal_WistarKyoto-5RP

description: Gene expression data of gastrocnemius muscle from WKY rat 5, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_highfat_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_highfat_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_normal_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_highfat_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_highfat_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with HFD and sacrificed at 4 weeks


title: RMDP-4wk_normal_WistarKyoto-4RP

description: Gene expression data of gastrocnemius muscle from WKY rat 4, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_normal_WistarKyoto-1RP

description: Gene expression data of gastrocnemius muscle from WKY rat 1, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_normal_WistarKyoto-2RP

description: Gene expression data of gastrocnemius muscle from WKY rat 2, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_highfat_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with HFD and sacrificed at 4 weeks


title: RADP-20wk_highfat_WistarKyoto-6RP

description: Gene expression data of the adipose tissue from WKY rat 6, feeded with HFD and sacrificed at 20 weeks

source_name: rat adipose tissue


title: RMDP-4wk_normal_GotoKakizake-3RP

description: Gene expression data of gastrocnemius muscle from GK rat 3, feeded with ND and sacrificed at 4 weeks


title: RADP-20wk_highfat_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with HFD and sacrificed at 20 weeks


title: RMDP-4wk_normal_GotoKakizake-4RP

description: Gene expression data of gastrocnemius muscle from GK rat 4, feeded with ND and sacrificed at 4 weeks


title: RMDP-8wk_highfat_GotoKakizake-5RP

description: Gene expression data of gastrocnemius muscle from GK rat 5, feeded with HFD and sacrificed at 8 weeks


title: RMDP-4wk_normal_GotoKakizake-2RP

description: Gene expression data of gastrocnemius muscle from GK rat 2, feeded with ND and sacrificed at 4 weeks


title: RMDP-4wk_normal_GotoKakizake-1RP

description: Gene expression data of gastrocnemius muscle from GK rat 1, feeded with ND and sacrificed at 4 weeks


title: RADP-20wk_highfat_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_normal_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_normal_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_normal_WistarKyoto-2RP

description: Gene expression data of the livadipose tissueer from WKY rat 2, feeded with ND and sacrificed at 20 weeks

tag: adipose tissue from WKY rat 2, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_normal_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_normal_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_highfat_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_highfat_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_highfat_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_normal_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_highfat_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_normal_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_highfat_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_normal_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_highfat_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with HFD and sacrificed at 20 weeks


title: RADP-20wk_highfat_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with HFD and sacrificed at 20 weeks


title: RADP-16wk_highfat_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with HFD and sacrificed at 16 weeks


title: RADP-20wk_normal_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with ND and sacrificed at 20 weeks


title: RADP-20wk_highfat_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with HFD and sacrificed at 20 weeks


title: RADP-16wk_highfat_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_normal_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_highfat_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with HFD and sacrificed at 16 weeks


title: RADP-20wk_normal_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with ND and sacrificed at 20 weeks


title: RADP-16wk_normal_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_normal_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_highfat_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_highfat_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_normal_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_normal_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_highfat_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_highfat_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_normal_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_normal_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with ND and sacrificed at 16 weeks


title: RADP-16wk_highfat_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_highfat_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_highfat_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with HFD and sacrificed at 16 weeks


title: RADP-16wk_normal_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with ND and sacrificed at 16 weeks


title: RADP-12wk_highfat_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_normal_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_normal_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_normal_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_highfat_WistarKyoto-4RP

description: Gene expression data of the adipose tissue  from WKY rat 4, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_highfat_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKYrat 5, feeded with HFD and sacrificed at 12 weeks

tag: adipose tissue from WKY rat 5, feeded with HFD and sacrificed at 12 weeks


title: RADP-16wk_normal_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with ND and sacrificed at 16 weeks


title: RADP-12wk_normal_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_highfat_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_highfat_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_highfat_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_normal_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_highfat_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_normal_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_normal_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_highfat_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with HFD and sacrificed at 12 weeks


title: RADP-12wk_highfat_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with HFD and sacrificed at 12 weeks


title: RADP-8wk_highfat_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with HFD and sacrificed at 8 weeks


title: RADP-8wk_normal_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with ND and sacrificed at 8 weeks


title: RADP-16wk_normal_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with ND and sacrificed at 16 weeks


title: RADP-8wk_highfat_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with HFD and sacrificed at 8 weeks


title: RADP-8wk_highfat_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with HFD and sacrificed at 8 weeks


title: RADP-12wk_normal_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with ND and sacrificed at 12 weeks


title: RADP-12wk_normal_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with ND and sacrificed at 12 weeks


title: RADP-8wk_highfat_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with HFD and sacrificed at 8 weeks


title: RADP-8wk_normal_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with ND and sacrificed at 8 weeks


title: RADP-8wk_normal_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with ND and sacrificed at 8 weeks


title: RADP-8wk_highfat_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with HFD and sacrificed at 8 weeks


title: RADP-12wk_normal_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with ND and sacrificed at 12 weeks


title: RADP-8wk_highfat_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with HFD and sacrificed at 8 weeks


title: RADP-8wk_normal_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with ND and sacrificed at 8 weeks


title: RADP-8wk_highfat_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with HFD and sacrificed at 8 weeks


title: RADP-8wk_normal_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with ND and sacrificed at 8 weeks


title: RADP-8wk_normal_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with ND and sacrificed at 8 weeks


title: RADP-8wk_highfat_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with HFD and sacrificed at 8 weeks


title: RADP-4wk_highfat_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with HFD and sacrificed at 4 weeks


title: RADP-8wk_normal_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with ND and sacrificed at 8 weeks


title: RADP-8wk_normal_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with ND and sacrificed at 8 weeks


title: RADP-12wk_highfat_WistarKyoto-3RP

description: Gene expression data of the adipose tissue  from WKY rat 3, feeded with HFD and sacrificed at 12 weeks


title: RADP-8wk_highfat_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with HFD and sacrificed at 8 weeks


title: RADP-4wk_highfat_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with HFD and sacrificed at 4 weeks


title: RADP-8wk_normal_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with ND and sacrificed at 8 weeks


title: RADP-4wk_highfat_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with HFD and sacrificed at 4 weeks


title: RADP-8wk_normal_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with ND and sacrificed at 8 weeks


title: RADP-4wk_normal_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with ND and sacrificed at 4 weeks


title: RADP-4wk_normal_WistarKyoto-3RP

description: Gene expression data of the adipose tissue from WKY rat 3, feeded with ND and sacrificed at 4 weeks


title: RADP-4wk_highfat_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with HFD and sacrificed at 4 weeks


title: RADP-4wk_highfat_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with HFD and sacrificed at 4 weeks


title: RADP-4wk_highfat_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with HFD and sacrificed at 4 weeks


title: RADP-4wk_normal_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with ND and sacrificed at 4 weeks


title: RADP-4wk_highfat_WistarKyoto-2RP

description: Gene expression data of the adipose tissue from WKY rat 2, feeded with HFD and sacrificed at 4 weeks


title: RADP-4wk_highfat_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with HFD and sacrificed at 4 weeks


title: RADP-4wk_highfat_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with HFD and sacrificed at 4 weeks


title: RADP-4wk_normal_Goto-Kakizaki-5RP

description: Gene expression data of the adipose tissue from GK rat 5, feeded with ND and sacrificed at 4 weeks


title: RADP-4wk_normal_WistarKyoto-4RP

description: Gene expression data of the adipose tissue from WKY rat 4, feeded with ND and sacrificed at 4 weeks


title: RADP-4wk_normal_Goto-Kakizaki-4RP

description: Gene expression data of the adipose tissue from GK rat 4, feeded with ND and sacrificed at 4 weeks


title: RADP-4wk_normal_Goto-Kakizaki-3RP

description: Gene expression data of the adipose tissue from GK rat 3, feeded with ND and sacrificed at 4 weeks


title: RADP-8wk_highfat_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with HFD and sacrificed at 8 weeks


title: Cin85_brain_rep5

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

organism: Mus musculus

source_name: Kdn Cin85-/-

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Gender

value: Male

tag: Age

value: 15 weeks

tag: Mouse ID

source_name: Brain wt pool

value: wt


title: Cin85_brain_rep7


title: Cin85_brain_rep9


title: Cin85_brain_rep8


title: Cin85_brain_rep6


title: Cin85_brain_rep4


title: RADP-4wk_normal_Goto-Kakizaki-1RP

description: Gene expression data of the adipose tissue from GK rat 1, feeded with ND and sacrificed at 4 weeks


title: Cin85_brain_rep10


title: Cin85_brain_rep3


title: RADP-4wk_normal_Goto-Kakizaki-2RP

description: Gene expression data of the adipose tissue from GK rat 2, feeded with ND and sacrificed at 4 weeks


title: Cin85_brain_rep1


title: Cin85_brain_rep2


title: ccm biological rep 3

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

description: Gene expression data from_ccm

hyb_protocol: All in vivo cRNAs and 3 mg of in vitro cRNAs were hybridized to a custom Affymetrix GeneChip designed as previously described

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Coxiella burnetii

source_name: ccm

label_protocol: All RNA (~ 1 μg) samples were amplified using a MessageAmp II Bacteria kit (Applied Biosystem, Foster City, CA) according to the manufacturer’s recommendations. Briefly, RNA was concentrated and polyA-tailed using E. coli polyA polymerase. One microliter of RNA mixture of B. subtilis polyA tailed RNAs (lysA, trp, thrB, jojF) were spiked into each sample for quality control purposes. RNA was reverse transcribed in a reaction primed by a T7 Oligo(dT)VN anchored primer producing cDNA containing a T7 promoter. Resulting cDNAs were reverse transcribed into double stranded DNA, then transcribed to produce biotinylated complimentary RNA (cRNA) copies from the cDNA template. Labeled cRNA was purified in a 96-well format using a Qiagen RNeasy 96-well system as previously described (30). The yield of labeled cRNA was estimated by measuring absorbance at A260/A280 with a spectrophotometer. The average target size was evaluated using an Agilent 2100 Bioanalyzer. To get a qualitative estimate of the biotin-labeling efficiency of each target, samples were “shifted” using Streptavidin protein (Sigma) and labelling efficiency assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: For analysis of C. burnetii transcript profiles during intracellular growth, Vero cells at 90-95% confluency in T-75 cell culture flasks were infected with C. burnetii at a multiplicity of infection of 10 for 2 h at room temperature. The inoculum was removed, cell cultures washed to remove non-internalized bacteria, then 10 ml RPMI supplemented with 2% FBS added to the culture flasks

extract_protocol: Bacteria were transferred to a 1.5 ml Microfuge tube, pelleted by centrifugation, then Trizol reagent (1.0 ml) added to each tube. Samples were stored at -80 oC until further processing. All Trizol samples were homogenized twice for 40 sec at speed setting 5 using a FastPrep FP120A Instrument in FastRNA Pro Blue vials (MP Biomedicals, Irvine, CA) to release cellular RNA. Two hundred microliters of 1-bromo-3-chloropropane (Sigma-Alrich, St. Louis, MO) was added per ml Trizol, the mixture vortexed for 15 sec, then heated for 20 min at 65 oC. Trizol samples were centrifuged at 12,000 x g for 15 min at 4 oC to separate the aqueous RNA containing phase from the organic phase. The Trizol aqueous phase was removed and passed through a Qiagen QiaShredder (Qiagen, Valencia, CA) column to fragment genomic DNA. To each sample, 700 μl Qiagen RNeasy RLT buffer with 0.145 M β-mercaptoethanol and 700 μl 70% ethanol were added and RNA was extracted using a Qiagen RNeasy 96-well system as described previously (30). RNA yield was determined by spectrophotometry (A260/A280) and RNA integrity verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)To increase the relative level of C. burnetii RNA, a MicrobEnrich kit (Applied Biosystems, Foster City, CA) was used to remove Vero host cell ribosomal RNAs from the mixed RNA samples. RNA samples from C. burnetii cultured in CCM were treated identically to facilitate comparisons with RNA samples derived from Vero cell- propagated C. burnetii. Briefly, RNA was precipitated, resuspended in 30 μl of Tris-EDTA (TE) buffer, combined with binding buffer and capture oligos (2 μl per 5 μg RNA), denatured, then captured for 1 h at 37 oC. Captured host ribosomal RNA was removed with magnetic beads (25 μl per 5 μg RNA). Supernatants containing enriched bacterial RNA were precipitated and resuspended in 70 μl TE buffer. An aliquot of resuspended RNA was diluted 1:20 in water and RNA integrity analyzed using an Agilent 2100 Bioanalyzer.

treatment_protocol: At 5 d post infection, host cell cultures were washed with 10 ml of Hank’s buffered saline solution, then lysed with 3 ml of Trizol reagent (Invitrogen, Calsbad, CA). Samples were stored at -80 oC until further processing. For analysis of C. burnetii transcript profiles in CCM, 2.5 x 109 GE of C. burnetii were incubated in triplicate in 0.5 ml CCM in 24-well plates for 24 h.

tag: RSA439, clone 4


title: carryover biological rep 1

description: Gene expression data from_carryover

source_name: carryover


title: carryover biological rep 2

description: Gene expression data from_carryover


title: 5day infected biological rep 3

description: Gene expression data from_5day infected

source_name: 5day infected


title: ccm biological rep 2

description: Gene expression data from_ccm


title: Subependymal18_giant_cell_astrocytoma_grade_1

status: Public on Oct 18 2009

city: Richmond

first: Timothy

middle: E

last: Van Meter

state: VA

address: 1101 E. Marshall St.

department: Neurosurgery

institute: Virginia Commonwealth University

description: Subependymal giant cell astrocytoma, WHO grade 1

hyb_protocol: As per the Affymetrix protocol, 10 µg of fragmented cRNA were hybridized on the GeneChip® Human Genome U133A 2.0 (HG-U133A 2.0) array for 16 hours at 60 rpm in a 45°C hybridization oven. The arrays were washed and stained with streptavidin phycoerythrin (SAPE; Molecular Probes, Eugene, OR) in the Affymetrix fluidics workstation.  To amplify the fluorescent signal, SAPE solution was added twice with an antistreptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA) staining step in between.

scan_protocol: Every chip was scanned at a high resolution, with pixelations ranging from 2.5 µm down to 0.51 µm, by the Affymetrix GeneChip® Scanner 3000 according to the GeneChip® Expression Analysis Technical Manual procedures (Affymetrix, Santa Clara, CA).  After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the GeneChip® Operating Software version 1.4 (GCOS1.4) (Affymetrix, Santa Clara, CA).

data_processing: MAS5.0, scaled to 100

organism: Homo sapiens

label_protocol: The Affymetrix® protocol was used in this experiment. Briefly, starting from 5 µg of total RNA, we performed a single-strand cDNA synthesis primed with a T7- (dT24) oligonucleotide.  Second strand cDNA synthesis was performed with the E.coli DNA Polymerase I, using the GeneChip® One-Cycle cDNA Synthesis Kit (Manufactured by Invitrogen for Affymetrix).  The resulting cDNA was purified using the cDNA cleanup reagents from the GeneChip Sample Cleanup Module (Developed and manufactured by QIAGEN® specifically for GeneChip arrays).  Biotinylation of the cRNA was achieved by an in vitro transcription (IVT) reaction using the GeneChip IVT Labeling Kit. After a 37°C incubation for 16 hours, the labeled cRNA was purified using the cRNA cleanup reagents from the GeneChip Sample Cleanup Module.  The cRNA was then fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94°C.

extract_protocol: Specimens for analysis were obtained under a Virginia Commonwealth University Institutional Review Board-approved protocol and anonymized.  Tumor biopsies were collected at the time of surgery and transported within 5 minutes to the surgical pathology laboratory for immediate processing.  Residual tissue from each surgical pathology specimen was snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.  Histopathological scoring of standard features (tumor content, stroma contribution, presence of necrosis, and grade) was performed by a pathologist on hematoxylin and eosin stained frozen sections adjacent, above and below the tissue used for RNA isolation.  All samples used for this study contained more than 70% tumor.  To extract RNA, multiple 10 µm thick frozen sections of the tissue samples were placed directly in TRIZOL reagent (InvitrogenTM Life Technologies, Carlsbad, CA).  A subsequent cleanup process with RNeasy reagents (QIAGEN Inc., Valencia, CA) was performed according to the manufacturer’s protocol.  RNA purity was judged by spectrophotometry at 260, 270, and 280 nm.  RNA integrity as well as cDNA and cRNA synthesis products were assessed by running 1 µL of every sample in RNA 6000 Nano LabChips® on the 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).

tag: Frozen brain tumor biopsy


title: Ependymoma15_primary_posterior_fossa_grade_2

description: Primary posterior fossa ependymoma, WHO grade 2


title: 5day infected biological rep 2

description: Gene expression data from_5day infected


title: 5day infected biological rep 1

description: Gene expression data from_5day infected


title: Ependymoma16_recurrent_supratentorial_grade_3

description: Recurrent supratentorial ependymoma, WHO grade 3


title: carryover biological rep 3

description: Gene expression data from_carryover


title: RADP-4wk_normal_WistarKyoto-1RP

description: Gene expression data of the adipose tissue from WKY rat 1, feeded with ND and sacrificed at 4 weeks


title: ccm biological rep 1

description: Gene expression data from_ccm


title: Ependymoma11_primary_posterior_fossa_grade_2

source_name: Primary posterior fossa ependymoma, WHO grade 2


title: Ependymoma17_primary_myxopapillary_grade_1

description: Primary myxopapillary ependymoma, WHO grade 1


title: Ependymoma10_primary_posterior_fossa_grade_2


title: Ependymoma12_recurrent_posterior_fossa_grade_2

description: Recurrent posterior fossa ependymoma, WHO grade 2


title: Ependymoma8_primary_spinal_grade_2

description: Primary spinal ependymoma, WHO grade 2

source_name: Primary spinal ependymoma, WHO grade 2


title: Ependymoma4_primary_posterior_fossa_grade_2


title: 6 h bead+LPS, biological rep2

status: Public on Oct 16 2009

city: Nashville

first: David

middle: W

last: Wright

state: TN

address: SC Stevenson Center 7, Station B 351822

department: Chemistry

institute: Vanderbilt University

hyb_protocol: Arrays were hybridized as described in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual v4

scan_protocol: GeneChips were scanned using the The GeneChip Scanner as described in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual v4

data_processing: Signal intensities across microarrays were RMA normalized

source_name: 6 h bead+LPS

label_protocol: 10ug of cRNA is reverse transcribed to make ss cDNA of the correct sense to hybridize to the probes on the array.  A total of 5.5ug of this product is fragmented, and then labeled with Terminal Deoxy Transferase with Biotin

growth_protocol: Cells were cultured under standard incubation conditions (37 ºC, 5% CO2) and grown in RPMI supplemented with 5% FBS and 1μg/mL P/S

extract_protocol: Cells were harvested at 6 h using Versagene RNA purification and DNase treatment kits. Six wells of a 6-well plate were pooled for each biological replicate.

treatment_protocol: Samples were treated with 10μL of 0.05% latex bead (0.1μm) per 1x10^6 cells. Immediately following treatment, lipopolysaccharide (LPS) was added at a final concentration of 1 μg/mL

tag: RAW 264.7 cell line


title: Ependymoma9_primary_posterior_fossa_grade_2


title: Ependymoma14_primary_posterior_fossa_grade_2


title: 6 h BH+LPS, biological rep3

source_name: 6 h BH+LPS

treatment_protocol: Samples were treated with 0.1 mg/mL Beta-Hematin. Immediately following treatment, lipopolysaccharide (LPS) was added at a final concentration of 1 μg/mL


title: 6 h LPS, biological rep2

source_name: 6 h LPS

treatment_protocol: Samples were untreated. Lipopolysaccharide (LPS) was added at a final concentration of 1 μg/mL


title: Ependymoma5_primary_supratentorial_anaplastic_grade_3

description: Primary supratentorial anaplastic ependymoma, WHO grade 3


title: Ependymoma3_recurrent_supratentorial_grade_3

source_name: Recurrent supratentorial ependymoma, WHO grade 3


title: Ependymoma7_recurrent_spinal_grade_2

description: Recurrent spinal ependymoma, WHO grade 2


title: Ependymoma1_primary_posterior_fossa_grade_2


title: 6 h BH+LPS, biological rep2


title: 6 h HNE+LPS, biological rep2

source_name: 6 h HNE+LPS

treatment_protocol: Samples were treated with 35 μM 4-hydroxy-2-nonenal (HNE). Immediately following treatment, lipopolysaccharide (LPS) was added at a final concentration of 1 μg/mL


title: 6 h bead+LPS, biological rep1


title: 6 h LPS, biological rep3


title: 6 h bead+LPS, biological rep3


title: 6 h HNE+LPS, biological rep3


title: Ependymoma6_recurrent_grade_2

description: Recurrent ependymoma, WHO grade 2

source_name: Recurrent ependymoma, WHO grade 2


title: 6 h LPS, biological rep1


title: BH, biological rep3

hyb_protocol: All hybridization reagents, hybridization controls, wash reagents, and chemiluminescent reagents were provided in the ABI CL Detection Kit, part#4342142, and the manufacturer’s protocol was followed.  Briefly, the arrays were equilibrated to room temperature and then pre-hybridized with a 1ml volume for 60’ with agitation (100RPM) at 55C per manufacturer’s protocol.  During the pre-hybridization, the DIG-labelled targets were fragmented and then stored on ice until the pre-hyb was completed.  Once pre-hyb was completed the targets were mixed with the appropriate reagents, including Hybridization controls, and the 0.5ml target was added to the pre-hybridization through the port on the array chamber.  The arrays were immediately returned to the 55C Hybridization oven and agitated exactly 16 hours at 100RPM.  The arrays were then washed and incubated with Anti-Dig-APAntibody for 20 minutes.  Following antibody washes, the arrays were incubated with Chemiluminescence Enhancing Solution, washed a final time and then stored in the last wash buffer at room temperature. Substrate for the chemiluminescence reaction was added to each array individually and then the array was immediately imaged on the 1700 Chemiluminescent Analyzer.

scan_protocol: Following addition of the chemiluminescence reaction substrate, each array was immediately imaged on the 1700 Chemiluminescent Analyzer. Each imaging was completed in approximately 15 minutes and the images were assessed for QC/QA and a primary analysis was completed by the AB1700 Expression Array System Software (v 1.1.1).

data_processing: Signal intensities across microarrays were quantile normalized

label: Digoxigenin

source_name: BH

label_protocol: All RNA Preps were run on an Agilent 2100 Bioanalyzer to assess RNA integrity. Those samples meeting minimum requirements of RIN value of 7.0 and greater were used to generate targets for hybridization to ABI arrays. One (1) ug of Total RNA (30ng mRNA) was used to generate First Strand cDNA using the NanoAmp RT-IVT labeling kit according to manufacturer’s protocol (ABI, Cat#4365715).  Following first strand synthesis, second strand synthesis was completed.  The resulting cDNA was then purified using an ABI kit provided column and the entire reaction was used in an IVT reaction to generate DIG labeled cRNA.  The cRNA was then purified using a kit provided column and assessed for quality on an Agilent Bioanalyzer.  All reactions meeting ABI criteria in terms of quantity and size of target produced were fragmented and then hybridized to the appropriate array for 16 hours with agitation at 55C.

extract_protocol: Cells were harvested at 24 h using Versagene RNA purification and DNase treatment kits. Six wells of a 6-well plate were pooled for each biological replicate.


title: BH, biological rep2


title: HNE, biological rep1

source_name: HNE


title: 6 h BH+LPS, biological rep1


title: 6 h HNE+LPS, biological rep1

treatment_protocol: Samples were treated with 35 µM 4-hydroxy-2-nonenal (HNE). Immediately following treatment, lipopolysaccharide (LPS) was added at a final concentration of 1 µg/mL


title: HNE, biological rep3


title: Ependymoma2_recurrent_supratentorial_grade_3


title: HNE, biological rep2


title: RADP-4wk_highfat_WistarKyoto-5RP

description: Gene expression data of the adipose tissue from WKY rat 5, feeded with HFD and sacrificed at 4 weeks


title: bead, biological rep2

source_name: bead


title: BH, biological rep1


title: bead, biological rep3


title: bead, biological rep1


title: PBMC_CD3CD28Activated_IL23100ng/mlTreated_Rep5

status: Public on Oct 10 2009

city: London

first: Graham

last: Heap

address: 4 Newark Street

country: United Kingdom

institute: QMUL

description: Replicate 5 of 6

hyb_protocol: 1.5ug labelled cRNA Hybridized according to Illumina Standard protocol

scan_protocol: Scanned on Illumina BeadStation

data_processing: Data quantile normalised on Illumina BeadStudio Gene Expression Module v3.2.3

source_name: PBMC CD3 CD28 Stimulated IL23 100ng/ml

label_protocol: 250ng Total RNA amplified and labelled according to Ambion Illumina TotalPrep RNA Amplification Kit protocol

extract_protocol: Standard TRIZOL Extraction followed by Qiagen RNeasy Column Purification

tag: Cryopreserved PBMC


title: CD30V_rep3

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

hyb_protocol: llumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illuminas protocol

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment and Quantile normalisation was performed using the BeadExplorer package

source_name: HES2 infected with CD30 variant overexpressing lentivirus, replicate 3

label_protocol: Targets were prepared from 500 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: RNA samples were prepared using Qiagen RNeasy Micro Kit (Qiagen) and then assayed using the Agilent Systems Bioanalyzer 2100 to ensure that high-quality RNA was used for the array experiments.

tag: Embryonic Stem Cells


title: PBMC_CD3CD28Activated_IL23100ng/mlTreated_Rep6

description: Replicate 6 of 6


title: PBMC_CD3CD28Activated_IL23100ng/mlTreated_Rep3

description: Replicate 3 of 6


title: Mock Tranfected Raji cells, biological rep 1.

status: Public on Oct 15 2009

city: Memphis

first: Celia

last: Longhurst

address: 956 Court Avenue Room H300

department: Medicine

institute: UTHSC

description: Gene expression data from cells harvested during exponential growth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Raji human B cells stably expressing human CD9 transfected with PRVCMVCD9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Transfected Raji cells were grown in growth media consisting of RPMI 1640, 10% FBS and 1mg/ml G418

treatment_protocol: Transfected Raji cells were grown in growth media, harvested, reseeded in fresh growth media, Raji cells were harvested for total RNA extraction during exponential phase of growth.

tag: Raji human lymphoblast-like cells derived from Burkitts lymphoma 11year old black male.


title: GFP_rep3

source_name: HES2 infected with GFP overexpressing lentivirus, replicate 3


title: PBMC_CD3CD28Activated_IL23100ng/mlTreated_Rep2

description: Replicate 2 of 6

source_name: PBMC CD3 CD28 Simulated IL23 100ng/ml


title: PBMC_CD3CD28Activated_Rep5

description: Replicate 5 of 6

source_name: PBMC CD3 CD28 Stimulated


title: PBMC_CD3CD28Activated_Rep3

description: Replicate 3 of 6


title: PBMC_CD3CD28Activated_Rep1

description: Replicate 1 of 6


title: GFP_rep2

source_name: HES2 infected with GFP overexpressing lentivirus, replicate 2


title: CD9 Tranfected Raji cells, biological rep 2.

source_name: Stably transfected Raji human B cells with PRVCMV empty vector (MOCK)


title: PBMC_CD3CD28Activated_Rep4

description: Replicate 4 of 6


title: PBMC_CD3CD28Activated_IL23100ng/mlTreated_Rep4

description: Replicate 4 of 6


title: CD30V_rep1

source_name: HES2 infected with CD30 variant overexpressing lentivirus, replicate 1


title: PBMC_CD3CD28Activated_IL23100ng/mlTreated_Rep1

description: Replicate 1 of 6


title: CD30V_rep2

source_name: HES2 infected with CD30 variant overexpressing lentivirus, replicate 2


title: GFP_rep1

source_name: HES2 infected with GFP overexpressing lentivirus, replicate 1


title: CD9 Tranfected Raji cells, biological rep 1.


title: spleen, young, arthritic, biological replicate 1

status: Public on Oct 09 2009

city: Chicago

first: Tibor

middle: T

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.

scan_protocol: Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’.  Each array was analyzed for the following quality metrics:  total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.

data_processing: Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.).  Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003).  Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).

growth_protocol: Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis.  A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)

extract_protocol: Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.

treatment_protocol: Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.

tag: Strain

value: BALB/c

value: female

tag: Arthritic


title: Mock Tranfected Raji cells, biological rep 2.


title: spleen, old, non-arthritic, biological replicate 2

tag: Non-arthritic


title: PBMC_CD3CD28Activated_Rep6

description: Replicate 6 of 6


title: spleen, young, non-arthritic, biological replicate 3


title: PBMC_CD3CD28Activated_Rep2

description: Replicate 2 of 6


title: spleen, young, non-arthritic, biological replicate 4


title: spleen, young, non-arthritic, biological replicate 2


title: spleen, young, non-arthritic, biological replicate 1


title: spleen, young, arthritic, biological replicate 2


title: spleen, old, arthritic, biological replicate 1


title: spleen, old, non-arthritic, biological replicate 1


title: U937 Cells Sol B 1 hr-rep1

status: Public on Oct 01 2009

city: Jackson

first: Donna

middle: C.

last: Sullivan

state: MS

address: 2500 North State Street

institute: University of Mississippi Medical Center

description:
Results_SolB_1hr_1_12762745
Biological replicate 1 of 3.

hyb_protocol: The paired reactions were combined and purified with TE-30 columns (Clontech, Palo Alto, CA), suspended in 90 ul dH2O and precipitated with 2 ul glycogen, 60 ul 5 M NH4OAc, and 300 ul ethanol.  Labeled pellets were resuspended in 24 ul of hybridization buffer (5X SSC, 0.2% DSD, 1 mM DTT).  Probe was applied to the glass microarray and covered with a 22 mm2 glass coverslip.  Hybridization was performed at 60°C for 6.5 hours in a sealed humidified chamber (Corning Life Sciences; Acton, MA).

scan_protocol: Slides were scanned using a ChipReader microarray scanner (Virtek Vision Intl.). QuantArray Microarray Analysis software (Packark BioScience, Inc.) was used for image analysis and data visualization.  Scans for the two fluorescent probes were normalized to the signal intensity of actin and glyceraldehyde-3-phosphate dehydrogenase.

data_processing: The local background values were calculated from the area surrounding each spot and subtracted from the total spot signal values.  These adjusted values were used to determine differential gene expression (Cy3/Cy5 ratio) for each spot.  A normalization factor was applied to account for systematic differences in the probe labels by using the differential gene expression ratio to balance the Cy5 signals.  Each experiment included three sets of biological replicas of control and alkaloid-exposed samples.

source_name: Human cell line + Synthetic fire ant venom

label_protocol: RNA from control and drug-treated cells (biological replicates) were used in these studies to prepare three independent cDNA probe sets per time point (1 and 6 hours).  Reactions were incubated for 2 hours, 37oC, with 200 ng polyA RNA, 4 mM DTT, 1 unit RNAse inhibitor (Ambion, Austin, Tx), 0.5 mM each dATP, dGTP,  dCTP, and TTP (NEN Life Sciences; Boston, MA); and 2 ug Cy3 (alkaloid exposed cells)- or Cy5 (control cyclodextrin exposed cells)-labeled random 9-mers (Operon Technologies, Inc., Alameda, CA) in a buffer containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, and 3 mM MgCl2.

extract_protocol: RNA was isolated using protocols and reagents recommended by the manufacturer of the human microarray (University of Toronto Microarray Center/Clinical Genomics Center).

treatment_protocol: Cells were incubated for 1 hr, 37oC, with 13 micromolar solenopsin B.

tag: Human U937 cell line

source_name: Human cell line + cyclodextrin diluent

tag: Cells were incubated for 1 hr, 5% cyclodextrin diluent


title: U937 Cells Sol B 6 hr-rep3

description:
Results_SolB_6hr_3_12768620
Biological replicate 3 of 3.

treatment_protocol: Cells were incubated for 6 hr, 37oC, with 13 micromolar solenopsin B.


title: U937 Cells Sol B 1 hr-rep2

description:
Results_SolB_1hr_2_12768626
Biological replicate 2 of 3.


title: U937 Cells Sol B 6 hr-rep2

description:
Results_SolB_6hr_2_12768624
Biological replicate 2 of 3.


title: spleen, old, arthritic, biological replicate 2


title: U937 Cells Sol B 6 hr-rep1

description:
Results_SolB_6hr_1_12768629
Biological replicate 1 of 3.


title: U937 Cells Sol B 1 hr-rep3

description:
Results_SolB_1hr_3_12768630
Biological replicate 3 of 3.