title: AHX-treated rice seedling_2weeks_replicate2

city: Shizuoka

first: JAE-HOON

last: CHOI

address: 836 Ohya

department: Graduate School of Science and Technology

institute: Shizuoka University

description: dye swap of sample(Con-200AHX)

hyb_protocol: Sample RNA was hybridized on the two color Agilent human 4x44K arrays with reference RNA. Agilent Gene Expression Hybridization kit was used.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.6.1.1).

data_processing:
LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.
Genes showing a signal value below 300 in the control channel were excluded from the analysis. Feature extraction and image analysis software (version A.6.1.1; Agilent Technologies) were used to locate and delineate each spot in the array and to integrate each spot’s intensity, filtering, and normalization.

organism: Oryza sativa Japonica Group

source_name: rice seedling

label_protocol: Labeled with Agilent Low RNA Input Amplification kit following manufacturer's instructions.

extract_protocol: Total RNA was isolated from the seedlings using an RNeasy plant mini kit (Qiagen)

tag: cultivar

value: japonica

value: rice seedling

tag: agent

value: with 0.2 mM AHX (2weeks)

value: without AHX (2weeks)


title: g-MPX 12 hr FibroS100

status: Public on Apr 14 2011

type: RNA

city: Stanford

first: Patrick

middle: O

last: Brown

state: CA

address: Beckman Center b439

department: Department of biochemistry

country: USA

institute: Stanford university school of medicine

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55194.gif
Figure in article: 1

hyb_protocol: not provided

scan_protocol: scanner model: GenePix 4000A

data_processing: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA). Grids were manually aligned and features were found using the software feature extraction. Features were visually inspected for blemishes and removed from downstream analysis. Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/) and normalized using regression correlation. Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array. Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays. For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples. The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis. The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Universal Human Reference RNA

source_name: g-MPX 12 hr Primary Human SkinFibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

label_protocol: Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA  1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul:    mRNA 3-4ug  pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL  2. Heat to 65oC for 10 min and cool on ice.   3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture  5X first-strand buffer 6.0uL  0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL   4. Incubate at 42oC for 1 hr.   5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr.   6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min.   7. Neutralize by addition of 15uL of 0.1N HCl.  8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column.  Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon.  9. WASH 1: Spin 7-8 min. at 14,000g (=RCF).  Remove flow through and save to a separate tube.  10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube.  11.  WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL  polyA RNA (Sigma, #P9403) 2 uL 10ug/uL  tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane.  Make sure not to dry the membrane completely!  12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Kate,,Rubins

extract_protocol:
Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases.  Keep the samples cold or on ice as much as possible to prevent RNA degradation.   Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment.  2. Add 1mL of Trizol to the frozen PBMC pellet.   3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes.  4. Vortex and transfer to 1.5ml microfuge tubes if not already in them.  5. Add 0.2 mls chloroform per 1 ml Trizol.  Vortex or shake vigorously and incubate at room temp. for 2-3 minutes.  6. Centrifuge at 12,000g for 15 minutes at 4C.  7. Transfer the aqueous phase to a fresh tube.  (The volume will be about 60% of the volume of Trizol.)  Note:  If isolating DNA, save the organic phase.  Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low.  8. Add 0.5 mLs of isopropanol per 1 ml Trizol used.  Incubate at room temp. for 10 minutes.   9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C.    10. The RNA pellet will be visible at the bottom of the tube.  Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  11. WASH 1: Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  13. WASH 2:  Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes).  Do not overdry!  16. Resuspend the pellet in 20uls of DEPC H2O.  Store at ?80C.  17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Kate,,Rubins
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug  Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water  70oC for 10 min in a thermocycler with lid on, but not clamped down.   Centrifuge briefly.   Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly.  Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes.   Add to the master mix: Amount Reagent 1uL Reverse Transcriptase  Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting.   42oC for 2 hours in thermocycler with lid on, but not clamped down.   Centrifuge briefly, place on ice, and immediately proceed to next step  SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  16oC for 2 hours in thermocycler with lid completely off.    DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min.  Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through.  Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol.  Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column.   Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g.   Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat.   Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC.  IN VITRO TRANSCRIPTION  Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 6 hours in hybridization oven.  Add to each reaction: Amount Reagent 2uL DNaseI  Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 30min in hybridization oven   aRNA PURIFICATION  Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes.  Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min.  Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL.   Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing.  Apply entire sample to the equilibrated filter cartridge.  Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube.  Add 650uL aRNA Wash Buffer to each filter.   Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube.  Elute aRNA by adding 50uL preheated (50oC) water to center of column.  Incubate at room temperature for 2 min.  Centrifuge for 1 minute at 10,000 x g.  Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g.   Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Kate,,Rubins

tag: time

tag: infection

value: killed Monkeypox Virus

tag: cell type

value: Primary Human Dermal Fibroblast


title: MPX 48hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50489.gif
Figure in article: 1

scan_protocol: scanner model: GenePix 4000B

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

value: Monkeypox Virus

value: Primary Human Macrophage


title: Family8_WholeEmbryo_1

type: genomic

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix Fluidics Station 640, and scanned using the GeneChip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.

label: biotin

molecule: genomic DNA

source_name: Whole Embryo

label_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, and biotinylated according to the manufacturer's recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

extract_protocol: Biopsied trophectoderm and arrested whole embryo samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

tag: tissue

value: whole embryo

tag: family


title: Family8_WholeEmbryo_2

description: Hybridized to 250K_Nsp


title: g-MPX 0hr Pool Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55116.gif
Figure in article: 1

source_name: g-MPX 0hr Pool Primary Human Macrophages infected with Killed Monkeypox in vitro 7.29.04

value: 0 h


title: Family8_WholeEmbryo_8

description: Hybridized to 250K_Nsp


title: AHX-treated rice seedling_2weeks_replicate1

country: Japan

description: dye swap of sample(Con-50AHX)

value: with 0.05 mM AHX (2weeks)


title: VAC-NY 2hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50464.gif
Figure in article: 1

value: 2 h

value: Vaccinia NY


title: Family8_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: Blood_30weeks_female_1

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

description:
SC20_028
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old female miniature pig.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-020109 Porcine Gene Expression Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. Features flagged with not positive and significant or flagged with not above significant were considered as unexpressed genes. The quantile normalization method was used in our microarray analysis.

organism: Sus scrofa

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Whole blood RNA was extracted using the PAXgene RNA Isolation kit from whole blood preserved in Paxgene tubes (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Paxgene tube conservation at -80ºC

value: whole blood

tag: gender

value: male

tag: age


title: Blood_30weeks_male_3

description:
SC20_027
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old male miniature pig.


title: Blood_30weeks_female_3

description:
SC20_030
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old female miniature pig.

value: female


title: Family8_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: Blood_30weeks_female_2

description:
SC20_029
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old female miniature pig.


title: HUES-9_P33

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description: Blastocyst-derived ES cells

hyb_protocol: Hybridization and washing steps were using Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using DNA MicroArray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 9.5.3 and further analyzed using GeneSpring GX software version 11.0.2. Data were normalized to the 75 th percentile (median).

label_protocol: 250 ng of total RNA was labelled with Cy3 using the Low RNA Fluorecent Linear Amplification Kit PLUS, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Frozen pellets of human ESCs (HUESCs) were kindly gifted from Drs. C. Cowan and T. Tenzan (Harvard Stem Cell Institute, Harvard University, Cambridge, MA).

extract_protocol: Total RNA was extracted using the RNeasy mini kit from QIAGEN® according to the manufacturer's instructions.

tag: sample type

value: Embryonic stem cells

tag: disease state

value: normal

tag: cell line


title: non-treated rice seedling_2weeks_replicate2

description: dye swap of sample(200AHX-Con)

value: japonica

value: rice seedling

value: without AHX (2weeks)

value: with 0.2 mM AHX (2weeks)


title: MPX 1.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50476.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

value: Monkeypox Virus

value: Primary Human Macrophage


title: Mock 0.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50445.gif
Figure in article: 1

value: Mock infection


title: Blood_30weeks_male_2

description:
SC20_026
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old male miniature pig.


title: Family7_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: HUES-8_P24

description: Blastocyst-derived ES cells


title: Killed MPX 48hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50484.gif
Figure in article: 1

value: killed Monkeypox Virus


title: Family7_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: Family8_WholeEmbryo_3

description: Hybridized to 250K_Nsp

value: whole embryo


title: HUES-3_P29

description: Blastocyst-derived ES cells

value: male


title: Family7_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: 201B7_P18

description: Fibroblast-derived iPS cells established by Dr Yamanaka

growth_protocol: Human iPS were maintained on irradiated MEFs in iPSellon medium (Cardio Incorporated, Osaka, Japan) supplemented with 10 ng/ml recombinant human basic fibroblast growth factor (bFGF, Wako Pure Chemical Industries, Ltd., Osaka, Japan),

value: inducible pluripotent stem cells

value: female


title: Family7_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: Killed MPX 9hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50477.gif
Figure in article: 1

value: 9 h


title: UtE-iPS-11_P39

description: Endometrium cell line, UtE1104,-derived iPS cells

value: normal


title: Family7_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: Blood_30weeks_male_1

description:
SC20_025
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old male miniature pig.

value: whole blood


title: Blood_20weeks_female_2

description:
SC20_022
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old female miniature pig.


title: Blood_20weeks_female_4

description:
SC20_024
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old female miniature pig.


title: g-MPX 24 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55198.gif
Figure in article: 1

source_name: g-MPX 24 hr Primary Human Skin FibroblastsS100 infected with Vaccinia WR in vitro 7.29.04

value: Primary Human Dermal Fibroblast


title: VAC 12 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55207.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: VAC 12 hr Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04

value: Vaccinia WR


title: VAC-NY 48hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50470.gif
Figure in article: 1

value: Vaccinia NY

value: Primary Human Macrophage


title: Family7_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: VAC-NY 9hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50467.gif
Figure in article: 1


title: Blood_20weeks_female_3

description:
SC20_023
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old female miniature pig.


title: Family7_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: PAE-iPS-1_P8

description: Placental artery endothelial cell line, PAE551,derived iPS cells


title: AM-iPS-8_P28

description: Amnion cell line, AM936EP,-derived iPS cells


title: Blood_20weeks_male_4

description:
SC20_020
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old male miniature pig.


title: MPX 4 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55213.gif
Figure in article: 1

source_name: MPX 4 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04

value: 4 h

value: Monkeypox Virus


title: MRC-iPS-25_P37

description: Fetal lung fibroblast cell line, MRC5,-derived iPS cells


title: Blood_20weeks_female_1

description:
SC20_021
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old female miniature pig.


title: Blood_20weeks_male_3

description:
SC20_019
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old male miniature pig.


title: MRC-iPS-25_P30


title: non-treated rice seedling_2weeks_replicate1

description: dye swap of sample(50AHX-Con)

value: japonica

value: rice seedling

value: without AHX (2weeks)

value: with 0.05 mM AHX (2weeks)


title: Family7_maternal_gDNA

description: Hybridized to 250K_Nsp

value: maternal blood


title: UtE-iPS-11_P31

value: inducible pluripotent stem cells

value: female


title: Blood_20weeks_male_1

description:
SC20_017
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old male miniature pig.

value: male


title: Family7_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp

value: cryopreserved embryo


title: Family7_paternal_gDNA

description: Hybridized to 250K_Nsp

value: paternal blood


title: MRC-iPS-11_P4

value: normal


title: Blood_12weeks_female_4

description:
SC20_016
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old female miniature pig.

value: whole blood


title: Blood_20weeks_male_2

description:
SC20_018
gene expression analysis performed on a whole blood (PAXgene) preparation from a 20-weeks-old male miniature pig.


title: g-MPX 1 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55180.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: g-MPX 1 hr Primary Human Skin FibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 1 h

value: killed Monkeypox Virus

value: Primary Human Dermal Fibroblast


title: Edom-iPS-2_P42

description: Edom22-derived iPS cells


title: Edom-iPS-2_P31

description: Edom22-derived iPS cells


title: Blood_12weeks_female_3

description:
SC20_015
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old female miniature pig.


title: Family6_Buccal_gDNA

description: Hybridized to 250K_Nsp

value: bucca


title: Edom-iPS-2_P22

description: Edom22-derived iPS cells


title: Family6_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

value: enriched fetal DNA from maternal plasma


title: MPX 24hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50487.gif
Figure in article: 1

value: Monkeypox Virus

value: Primary Human Macrophage


title: Killed MPX 1.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50473.gif
Figure in article: 1


title: VAC-NY 24hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50469.gif
Figure in article: 1

value: Vaccinia NY


title: Blood_12weeks_female_2

description:
SC20_014
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old female miniature pig.


title: Blood_12weeks_female_1

description:
SC20_013
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old female miniature pig.


title: Blood_12weeks_male_4

description:
SC20_012
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old male miniature pig.


title: Family6_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Edom-iPS-3_P29

description: Edom22-derived iPS cells


title: Family6_TransferredEmbryo_1

description: Hybridized to 250K_Nsp

value: transferred embryo


title: Family6_TransferredEmbryo_2

description: Hybridized to 250K_Nsp


title: Edom22

description: Menstrual blood-derived cells

growth_protocol: Edom22 cells were maintained in the POWEREDBY 10 medium (MED SHIROTORI CO., Ltd, Tokyo, Japan).

value: Menstrual blood


title: Family6_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: Blood_fetus_female_4

description:
SC20_008
gene expression analysis performed on a whole blood (PAXgene) preparation from a female fetus miniature pig.

value: female

value: fetus


title: Blood_12weeks_male_2

description:
SC20_010
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old male miniature pig.

value: male


title: g-MPX 4 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55144.gif
Figure in article: 1

source_name: g-MPX 4 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 4 h


title: MPX 2 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55158.gif
Figure in article: 1

source_name: MPX 2 hr Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04

value: 2 h


title: Family6_CryopreservedEmbryo_6

description: Hybridized to 250K_Nsp

value: cryopreserved embryo


title: Blood_12weeks_male_3

description:
SC20_011
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old male miniature pig.

value: whole blood


title: Family6_paternal_gDNA

description: Hybridized to 250K_Nsp

value: paternal blood


title: Family5_TransferredEmbryo_2

description: Hybridized to 250K_Nsp


title: Blood_fetus_female_2

description:
SC20_006
gene expression analysis performed on a whole blood (PAXgene) preparation from a female fetus miniature pig.


title: Blood_fetus_female_1

description:
SC20_005
gene expression analysis performed on a whole blood (PAXgene) preparation from a female fetus miniature pig.


title: VAC 24 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55154.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

value: Stratagene Universal Human Reference RNA

source_name: VAC 24 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04

value: Vaccinia WR


title: Family5_EnrichedFetalDNA

description: Hybridized to 250K_Nsp


title: Blood_fetus_male_3

description:
SC20_003
gene expression analysis performed on a whole blood (PAXgene) preparation from a male fetus miniature pig.


title: Killed MPX 1hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50472.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

value: 1 h

value: killed Monkeypox Virus


title: Blood_12weeks_male_1

description:
SC20_009
gene expression analysis performed on a whole blood (PAXgene) preparation from a 12-weeks-old male miniature pig.


title: Family6_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: g-MPX 8 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55190.gif
Figure in article: 1

source_name: g-MPX 8 hr Primary Human Skin FibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 8 h

value: Primary Human Dermal Fibroblast


title: Family5_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: Blood_fetus_male_2

description:
SC20_002
gene expression analysis performed on a whole blood (PAXgene) preparation from a male fetus miniature pig.


title: Family5_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp


title: Blood_fetus_female_3

description:
SC20_007
gene expression analysis performed on a whole blood (PAXgene) preparation from a female fetus miniature pig.


title: Family5_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: VAC-WR 1.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50454.gif
Figure in article: 1

value: Primary Human Macrophage


title: Blood_fetus_male_1

description:
SC20_001
gene expression analysis performed on a whole blood (PAXgene) preparation from a male fetus miniature pig.


title: Blood_fetus_male_4

description:
SC20_004
gene expression analysis performed on a whole blood (PAXgene) preparation from a male fetus miniature pig.


title: Family5_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: Family5_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Family6_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp


title: VAC 4 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55205.gif
Figure in article: 1

source_name: VAC 4 hr Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04


title: Killed MPX 12hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50480.gif
Figure in article: 1


title: Family6_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: VAC 0 Pool Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55149.gif
Figure in article: 1

source_name: VAC 0 Pool Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04

value: 0 h


title: VAC 8 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55152.gif
Figure in article: 1

source_name: VAC 8 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04


title: MPX plus I+P at 4 Hrs PI 6 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65331.gif
Figure in article: 3

scan_protocol: scanner model: GenePix 4200A

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Mock 6 HeLa cells Mock Infected in vitro 5.5.05

value: 6 h

value: Mock infection

tag: compound based treatment

value: Ionomycin + PMA


title: 0hr 3a in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50443.gif
Figure in article: 1

source_name: 0hr 3a in vitro monocyte pox timecourse


title: Family6_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: VAC 2 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55150.gif
Figure in article: 1

source_name: VAC 2 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04


title: Family5_TransferredEmbryo_1

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: Family5_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: VAC-WR 4hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50458.gif
Figure in article: 1

value: 4 h


title: Family4_Buccal_gDNA

description: Hybridized to 250K_Nsp


title: MPX plus I+P at 4 Hrs PI 1 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65471.gif
Figure in article: 3

source_name: MPX plus I+P at 4 Hrs PI 1 NHDF inf w MPX plus I+P at 4 Hrs PI

value: Monkeypox Virus


title: Mock 1hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50447.gif
Figure in article: 1


title: MPX plus I+P at 4 Hrs PI 2 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65472.gif
Figure in article: 3

source_name: MPX plus I+P at 4 Hrs PI 2 NHDF inf w MPX plus I+P at 4 Hrs PI

value: 2 h


title: Family4_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: Family5_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: Family4_TransferredEmbryo_2

description: Hybridized to 250K_Nsp


title: MPX plus Poly [IC] at 4 Hrs PI 12 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65481.gif
Figure in article: 3

value: Stratagene Universal Human Reference RNA

source_name: MPX plus Poly [IC] at 4 Hrs PI 12 NHDF inf w MPX plus Poly [IC] at 4 Hrs PI

value: polyinosinic-polycytidylic acid


title: Mock 0 Mph a

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65328.gif
Figure in article: 3

source_name: Mock 0 HeLa cells Mock Infected in vitro 5.5.05

value: Pre infection


title: Mock 0b NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65451.gif
Figure in article: 3

source_name: Mock 0b NHDF Mock Infected

value: Primary Human Dermal Fibroblast


title: MPX 0 Pool Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55156.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: MPX 0 Pool Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04

value: Primary Human Macrophage


title: Family4_CryopreservedEmbryo_8

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: Family4_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: Family4_CryopreservedEmbryo_6

description: Hybridized to 250K_Nsp


title: Mock plus Poly [IC]at 4hrs PI 12 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65476.gif
Figure in article: 3

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Mock plus Poly [IC]at 4hrs PI 12 NHDF inf w Mock plus Poly [IC]at 4hrs PI


title: Family4_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Mock 0b Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65413.gif
Figure in article: 3

source_name: Mock 0b Mph cells Mock Infected in vitro 5.5.05

value: 0 h


title: Family4_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: MPX plus I+P at 4 Hrs PI 12 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65332.gif
Figure in article: 3

source_name: Mock 12 HeLa cells Mock Infected in vitro 5.5.05

value: Mock infection


title: Family4_CryopreservedEmbryo_7

description: Hybridized to 250K_Nsp


title: Mock 2hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50451.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX


title: Mock plus I+Pat 4hrs PI 12 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65469.gif
Figure in article: 3

source_name: Mock plus I+Pat 4hrs PI 12 NHDF inf w Mock plus I+Pat 4hrs PI

value: Ionomycin + PMA


title: MPX plus I+P at 4 Hrs PI 6 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65473.gif
Figure in article: 3

source_name: MPX plus I+P at 4 Hrs PI 6 NHDF inf w MPX plus I+P at 4 Hrs PI

value: 6 h


title: Family5_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: Mock 0 Mph b

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65334.gif
Figure in article: 3

source_name: Killed MPX 1 HeLa cells infected with Killed MPX in vitro 5.5.05


title: VAC 1 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55203.gif
Figure in article: 1

source_name: VAC 1 hr Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04

value: 1 h

value: Vaccinia WR


title: MPX 4 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55160.gif
Figure in article: 1

source_name: MPX 4 hr Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04

value: 4 h

value: Monkeypox Virus


title: Killed MPX 4hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50475.gif
Figure in article: 1

value: killed Monkeypox Virus


title: VAC-WR 9hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50461.gif
Figure in article: 1

value: 9 h


title: Family4_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: MPX plus I+P at 4 Hrs PI 2 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65430.gif
Figure in article: 3

value: Stratagene Universal Human Reference RNA

source_name: MPX + I+P 2 Mph cells inf w MPX plus I+P at 4 Hrs PI

value: 2 h


title: Family3_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: Family4_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: MPX 2hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50479.gif
Figure in article: 1

value: Primary Human Macrophage


title: Mock 0d NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65468.gif
Figure in article: 3

source_name: Mock 0d NHDF Mock Infected

value: Primary Human Dermal Fibroblast


title: Family4_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

value: cryopreserved embryo


title: Family4_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: Case4_blood

city: Helsinki

first: Eevi

last: Kaasinen

address: Haartmaninkatu 8

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

hyb_protocol: According to the standard Affymetrix procedures

data_processing: RMA processing of Affymetrix raw data files in R (affy package).

source_name: Blood

label_protocol: According to the standard Affymetrix protocol from 10ug of total RNA

extract_protocol: PAXgene Blood RNA Kit, Qiagen

value: blood

value: Finnish NLPHL family

tag: family member

value: Case 4

value: NLPHL

tag: genotype/variation

value: Heterozygous for the NPAT c.2437-2438delAG.


title: MPX plus Poly [IC] at 4 Hrs PI 1 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65478.gif
Figure in article: 3

source_name: MPX plus Poly [IC] at 4 Hrs PI 1 NHDF inf w MPX plus Poly [IC] at 4 Hrs PI

value: 1 h

value: polyinosinic-polycytidylic acid


title: Mock 0c Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65423.gif
Figure in article: 3

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Mock 0c Mph cells Mock Infected in vitro 5.5.05

value: 0 h

value: Mock infection


title: MPX plus Poly [IC] at 4 Hrs PI 6 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65480.gif
Figure in article: 3

source_name: MPX plus Poly [IC] at 4 Hrs PI 6 NHDF inf w MPX plus Poly [IC] at 4 Hrs PI

value: 6 h

value: Monkeypox Virus


title: Family4_maternal_gDNA

description: Hybridized to 250K_Nsp

value: maternal blood


title: Mock plus Poly [IC]at 4hrs PI 24 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65477.gif
Figure in article: 3

value: Stratagene Universal Human Reference RNA

source_name: Mock plus Poly [IC]at 4hrs PI 24 NHDF inf w Mock plus Poly [IC]at 4hrs PI


title: MPX 12hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50485.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX


title: Family3_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: MPX plus Poly [IC] at 4 Hrs PI 6 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65337.gif
Figure in article: 3

source_name: Killed MPX 12 HeLa cells infected with Killed MPX in vitro 5.5.05

value: killed Monkeypox Virus

value: Primary Human Macrophage


title: Mock 0a NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65433.gif
Figure in article: 3

source_name: Mock 0a NHDF Mock Infected

value: Primary Human Dermal Fibroblast


title: Case3_blood

scan_protocol: According to the standard Affymetrix procedures

value: blood

value: Case 3


title: MPX 12 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55215.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: MPX 12 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04


title: MPX plus I+P at 4 Hrs PI 1 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65429.gif
Figure in article: 3

source_name: MPX + I+P 1 Mph cells inf  MPX plus I+P at 4 Hrs PI

value: Ionomycin + PMA


title: Mock 1.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50449.gif
Figure in article: 1


title: MPX 8 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55162.gif
Figure in article: 1

source_name: MPX 8 hr Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04

value: 8 h


title: Family3_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: Killed MPX 24hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50482.gif
Figure in article: 1


title: Control2_blood

value: Finnish NLPHL family

value: Cousin to case 1, case 2, case 3 and case 4

value: Wild type for the NPAT c.2437-2438delAG.


title: Carrier1_blood

value: Mother to case 1 and case 2, and aunt to case 3 and case 4

value: Heterozygous for the NPAT c.2437-2438delAG.


title: Mock 4hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50453.gif
Figure in article: 1

value: 4 h

value: Mock infection


title: Family3_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: Family3_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Carrier3_blood

value: Mother to case 4, and aunt to case 1, case 2 and case 3


title: Case1_blood

value: Case 1

value: NLPHL


title: Carrier2_blood

value: Brother to case 4


title: Family3_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: MPX plus Poly [IC] at 4 Hrs PI 2 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65432.gif
Figure in article: 2

value: Stratagene Universal Human Reference RNA

source_name: MPX + Poly [IC] 2 Mph cells inf w MPX plus Poly [IC] at 4 Hrs PI

value: 2 h

value: Monkeypox Virus

value: polyinosinic-polycytidylic acid

value: Primary Human Macrophage


title: Family3_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: MPX plus I+P at 4 Hrs PI 24 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65475.gif
Figure in article: 3

source_name: MPX plus I+P at 4 Hrs PI 24 NHDF inf w MPX plus I+P at 4 Hrs PI

value: Ionomycin + PMA

value: Primary Human Dermal Fibroblast


title: Mock plus I+Pat 4hrs PI 24 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65330.gif
Figure in article: 3

source_name: Mock 2 HeLa cells Mock Infected in vitro 5.5.05


title: Family3_TransferredEmbryo_1

description: Hybridized to 250K_Nsp

value: transferred embryo


title: Control1_blood

source_name: Blood

value: blood

value: Finnish NLPHL family

value: Aunt to case 1, case 2, case 3 and case 4

value: Wild type for the NPAT c.2437-2438delAG.


title: Carrier5_blood

value: Heterozygous for the NPAT c.2437-2438delAG.


title: Mock plus I+Pat 4hrs PI 24 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65470.gif
Figure in article: 3

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Mock plus I+Pat 4hrs PI 24 NHDF inf w Mock plus I+Pat 4hrs PI

value: Mock infection


title: Mock plus I+Pat 4hrs PI 12 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65329.gif
Figure in article: 3

source_name: Mock 1 HeLa cells Mock Infected in vitro 5.5.05


title: Carrier4_blood


title: Control12_blood

tag: individual

value: control


title: Control11_blood


title: Family3_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: Mock 0a Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65408.gif
Figure in article: 3

source_name: Mock 0a Mph cells Mock Infected in vitro 5.5.05

value: 0 h


title: Family3_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: Family3_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp

value: cryopreserved embryo


title: MPX plus Poly [IC] at 4 Hrs PI 2 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65479.gif
Figure in article: 3

value: Stratagene Universal Human Reference RNA

source_name: MPX plus Poly [IC] at 4 Hrs PI 2 NHDF inf w MPX plus Poly [IC] at 4 Hrs PI

value: 2 h

value: Monkeypox Virus


title: Mock plus Poly [IC]at 4hrs PI 12 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65335.gif
Figure in article: 3

source_name: Killed MPX 2 HeLa cells infected with Killed MPX in vitro 5.5.05

value: 4 h

value: killed Monkeypox Virus

value: polyinosinic-polycytidylic acid

value: Primary Human Macrophage


title: Control10_blood

value: blood


title: OS_80 min

city: changsha

first: xueduan

last: liu

address: lushan south road

country: China

institute: central south university

description: Each gene was spotted on the arrays in three replicates.

hyb_protocol: The purified and fluorescently labeled probes were dissolved in 30μl of hybridization buffer containing 50% (v/v) formamide, 3×SSC (containing 0.45 mM NaCl and 0.045 mM sodium citrate), 20μg of unlabeled herring sperm DNA (Promega, USA), and 0.3% (v/v) sodium dodecyl sulfate (SDS). The hybridization mixture was heated at 98°C for 2 min, applied directly onto the microarray slide, then covered with a glass coverslip. After that the microarray was placed into a hybridization chamber (Corning, USA), and immersed into the preheated water bath (45°C) immediately for 10-12 h. After hybridization, each microarray slide was taken out, and washed sequentially in 1×SSC-0.2%SDS for 5 min, 0.1×SSC-0.2% SDS for 10 min and 0.1×SSC for 30 s. Drying of the microarray slide was necessary before data scanning.

scan_protocol: The microarrays were scanned with a GenePix 4000B Array Scanner (AXON instruments, Inc, U.S.A).The emitted fluorescent signal was detected by a photomultiplier tube (PMT) at 570 nm (Cy3). The scanned images were saved as 16-bit TIFF files, and each spot was quantified by using GenePix Pro 6.0 software (AXON instruments, Inc, USA).

data_processing: After hybridization, microarrays were scanned with a ScanArray 4100 Microarray Analysis System (AXON instruments, Inc, USA).The emitted fluorescent signal was detected by a photomultiplier tube (PMT) at 532 nm. After background subtraction, signal intensities for each spot were quantified using GenePix Pro version 6.0 (AXON instruments, Inc, USA). The SNRs from three replicate data sets were then averaged to represent the SNR for a particular probe. A commonly accepted criterion for the minimum signal (threshold) that can be accurately quantified is SNR ≥ 2. Spots that appeared to be lower than the threshold value were removed from the data set. The data sheet from GenePix Pro was then exported to Excel for further processing. Spot intensities and median values for each spot were normalized by average intensity of each slide to account for any difference in total intensity between the scanned images. The processed stress and non stress signal intensities for each spot were used for calculating the Log transformed expression ratio (log2 stress / non stress) (data provided as a supplementary GSE28538.txt file). Genes with a |log2 ratio| larger than 1 (|ratio| > 2) are considered differentially expressed.

source_name: Acidithiobacillus ferrooxidans bacterial cultures

label_protocol: RNA samples from A. ferrooxidans in non stress and stress conditions were labeled with Cy3-labeled dUTP during cDNA production. 10μg of total cellular RNA was mixed with 10μg of random primer at 70°C for 10 min, then immediately chilled by ice for 2 min. The labeling reaction mixture, which contains 5×reverse transcription buffer; 5 mM MgCl2; 5 mM each of dATP, dTTP, and dGTP; 2.5 mM dCTP (New England Biolabs, Beverly, Mass); 1 mM Cy3 dUTP (Amersham Pharmacia Biotech, Piscataway, USA); and 40 units of RNAase OUT (Invitrogen), was added to the RNA primer solution and then incubated at 25°C for 5 min. Superscript II reverse transcriptase (200 units, Invitrogen) was added to the solution and the mixture was incubated at 25°C for 10 min and then 42°C for 2 h. The labeled cDNA probes was treated with 1 mM NaOH to remove residual RNA, and purified with a Qiagen PCR puriﬁcation column, then concentrated in speedvac at 45°C for 30 min.

growth_protocol: Acidithiobacillus ferrooxidans ATCC 23270 obtained from American Type Culture Collection (ATCC) was cultivated at 30°C in medium containing 0.5 g/L MgSO4•7H2O, 3.0 g/L (NH4)2SO4, 0.5 g/L K2HPO4, 0.1 g/L KCl and 0.01g/L Ca(NO3)2. The medium (pH =2.0) was sterilized at 120°C for 20 min and added elemental sulfur to 10.0 g/L.

extract_protocol: Total cellular RNA from A. ferrooxidans grown in the presence and absence of Lix984n was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, USA) following the manufacturer’s instructions. RNA samples were treated with RNase-free DNaseI (QIAGEN, Carlsbad, USA) to digest residual chromosomal DNA and then purified with an RNeasy kit (Qiagen, Valencia, USA). Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Three replicates of purified RNA for each sample mixed and the mixed RNA served as the template for labeling.

treatment_protocol: For microarray analysis, when the cells were in mid-log phase (~95 h), eight volumes (400 ml) of bacterial culture were condensed to one volume (50 ml) by centrifugation (10, 000×g) for 10 min at 4°C in a 5804R centrifuge (Eppendorf, Wesbury, N.Y.) and re-suspended with sterilized fresh medium when the cells were in mid-log phase. Samples (cellular density is about 5.86×108 cells/ml) were collected from three independent experiments grown under 0% (non stress condition) and 1% (stress condition) Lix984n for 0 (control), 5, 20, 40, 80 min respectively, and centrifuged at 10, 000×g for 10 min at 4°C in a 5804R centrifuge (Eppendorf, Wesbury, N.Y.). The resulting twenty-seven pellets were frozen immediately in liquid nitrogen and stored at -80°C before RNA extraction.

tag: time point

value: 80 min

tag: medium

value: with 1% Lix984n stress


title: Control8_blood


title: Control9_blood


title: OS_40 min

organism: Acidithiobacillus ferrooxidans ATCC 23270

value: 40 min


title: Control7_blood


title: MPX plus Poly [IC] at 4 Hrs PI 1 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65431.gif
Figure in article: 2

tag: reference

source_name: MPX + Poly [IC] 1 Mph cells inf w MPX plus Poly [IC] at 4 Hrs PI

value: 1 h


title: Family2_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: MPX plus I+P at 4 Hrs PI 12 NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65474.gif
Figure in article: 3

source_name: MPX plus I+P at 4 Hrs PI 12 NHDF inf w MPX plus I+P at 4 Hrs PI

tag: time

value: Ionomycin + PMA

value: Primary Human Dermal Fibroblast


title: OS_20 min

value: 20 min


title: Control6_blood

value: control


title: Family2_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: OS_5 min

value: 5 min


title: NOS_80 min

value: without Lix984n stress


title: MPX plus I+P at 4 Hrs PI 24 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65333.gif
Figure in article: 3

value: Stratagene Universal Human Reference RNA

source_name: Mock 24 HeLa cells Mock Infected in vitro 5.5.05

tag: infection

value: Mock infection


title: Control4_blood


title: Mock 0c NHDF

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65462.gif
Figure in article: 3

source_name: Mock 0c NHDF Mock Infected

value: 0 h

tag: cell type


title: MPX plus Poly [IC] at 4 Hrs PI 12 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65338.gif
Figure in article: 3

source_name: Killed MPX 24 HeLa cells infected with Mock in vitro 5.5.05

value: killed Monkeypox Virus

value: polyinosinic-polycytidylic acid

value: Primary Human Macrophage


title: Family2_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

tag: tissue

value: cryopreserved embryo


title: Control3_blood

source_name: Blood

value: blood


title: Family2_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

tag: family


title: In vivo v. in vitro rep4

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

hyb_protocol: Dyed samples to be compared were combined and resuspended in 196µl Ambion SlideHyb buffer 1. Samples were added to Agilent gasket slides, sandwiched with a UV-crosslinked, blocked microarray slide and sealed inside an Agilent hybridization chamber. This was rotated at 54 degrees celsius for 18 hours to allow hybridization to the array before washing and scanning.

scan_protocol: Slides were scanned using a GenePix scanner and GenePix Pro 4.1 software. PMT values were adjusted to obtain approximately equal levels of signal from both wavelength channels.

data_processing: Data analysis done using R/LIMMA. Signal ratios were normalized using a global loess procedure. A least squares linear model was fit, and using false-discovery rate adjustment, P-values less than 0.05 were considered differentially expressed.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Camylobacter jejuni NCTC11168 RNA

label_protocol: 6-10µg RNA was reverse transcribed with random hexamer primers and an aminoallyl-dUTP/dNTP mix using Invitrogen SuperScriptIII. CyDyes 3 or 5 from New England Biolabs were used to dye aminoallyl-cDNA samples. Reactions were cleaned at each step using a QIAGEN QIAquick kit.

extract_protocol: Mouse cecal contents or pelleted Broth grown C. jejuni were stored in approximately 7ml RNALater (Ambion) on ice for approximately 2 hours before being stored at -80 degrees celsius. An equal volume of phosphate buffered saline plus a 1:100 volume of phenol (Invitrogen) was added directly to each tube. Tubes were vortexed before slow-speed centrifugation, supernatant extraction, and then high-speed centrifugation. RNA was then extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions. To remove proteins, fat, polysaccharides, proteoglycans, and insoluble materials, centrifugation after homogenization, and precipitation using a high salt solution and isopropanol was performed as described in the TRIzol reagent protocol. Samples were treated for vigorous DNA contamination with the TURBO DNA-free kit (Ambion) and then precipitated overnight with a 1:10 volume of 3M sodium acetate, pH 5.5, and 3 volumes of 100% ethanol.

tag: growth condition

value: C. jejuni grown in Bolton broth, shaking, 37 degrees celsius, 10% CO2 atmosphere to mid-exponential phase

value: C. jejuni grown inside the cecum of C57 BL/6 IL-10-/- germ-free mice 96 hours post infection


title: NOS_20 min


title: NOS_40 min

value: 40 min


title: Family2_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: Mock plus Poly [IC]at 4hrs PI 24 Mph

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65336.gif
Figure in article: 3

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Killed MPX 6 HeLa cells infected with Killed MPX in vitro 5.5.05

value: 4 h


title: Family2_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: In vivo v. in vitro rep3


title: NOS_5 min


title: NOS_0 min

description:
Each gene was spotted on the arrays in three replicates.
We combined the sample grown under 0% Lix984n for 0 min and sample grown under1% Lix984n for 0 min into one sample.

value: 0 min

value: with/without Lix984n stress


title: Family2_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: In vivo v. in vitro rep2


title: In vivo v. in vitro rep1


title: Control5_blood

value: control


title: Family_2_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: Family2_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: IL-exp6_VEGF trap_4.3-1

status: Public on Apr 13 2011

city: Tarrytown

first: Ivan

middle: B

last: Lobov

state: NY

address: 777 Old Saw Mill River Road,

department: Regeneron Pharmaceuticals

institute: Regeneron Pharmaceuticals

hyb_protocol: Each sample labeled in Cyanine 3 and common reference labeled in Cyanine 5 were hybridized to a custom Agilent mouse whole genome gene expression array.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner.

data_processing: Agilent Feature Extraction Software (v9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: IL-exp6_VEGF trap_4.3-1 sample

label_protocol: Cyanine labeled cRNA was produced from 2 microgram of total RNA using low RNA Input Linear Amplication Kit (Agilent).

growth_protocol: C57Bl6 mice were housed in normal conditions

extract_protocol: Retinas were extracted from mouse pups 24 hrs after treatment.  RNA was purified using Rneasy Mini Kit (Qiagen).

treatment_protocol: 8 day old pups were injected intravitreally (ITV) with 1 microgram VEGFA, 4 micrograms Dll4-Fc, or 4 micrograms hFc alone

tag: strain

value: retina

tag: treatment

value: VEGF Trap

source_name: IL-exp6 common reference

tag: description

value: pooled of equal amount of RNA from this experiment


title: IL-exp6_VEGF Trap_3.1-1

source_name: IL-exp6_VEGF Trap_3.1-1 sample


title: IL-exp6_VEGF Trap_3.2-1

source_name: IL-exp6_VEGF Trap_3.2-1 sample


title: IL-exp6_VEGF A_4.3-2

source_name: IL-exp6_VEGF A_4.3-2 sample

value: VEGFA


title: IL-exp6_VEGF A_3.4-1

source_name: IL-exp6_VEGF A_3.4-1 sample


title: Family2_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: SalivaryGlands_Fed_9days_rep3

city: PULLMAN

first: Ricardo

middle: Francisco

last: Mercado-Curiel

state: WA

address: BUSTAD 402

department: College Of Veterinary Medicine

institute: Washington State University

hyb_protocol: The procedure was carried out using the Hybridization, Sample Tracking Control, Wash Buffer and Array Processing Accessories kits (Roche NimbleGen) according to the manufacturer’s recommendations.

scan_protocol: One-Color array scanning was performed in a GenePix 4000B scanner (Molecular Devices) using default settings obtaining the desired histogram with 1e-5 normalized counts at 65,000 saturation (intensity level). The scanned images were imported to Roche NimbleScan software where quality controls of the experimental data were carried out including: 1) visual and software-generated Sample Tracking analysis and 2) Experimental Metrics Report provided by the software; and the .xys files from raw data were generated.

data_processing: Additional quality controls and statistical analysis of the raw data (.xys files) were carried out using R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org). These analysis included (1) Box plot, histogram and cluster analysis of raw data, (2) Robust Multi-array Average (RMA) normalization (background correction, quantile normalization, log transformation, summarization), (3) Box plot, histogram and cluster analysis of RMA normalized data.

organism: Rhipicephalus microplus

label_protocol: Labeling was carried out using One-Color DNA Labelling Kit (Roche NimbleGen) according to the manufacturer’s recommendations.

growth_protocol: R. microplus larvae ticks were applied to a naïve calf; as the nymphs molted they were removed from the calf and allowed to molt to adult stage in the incubator (26°C which humidity is maintained by KNO3 saturated solution).

extract_protocol: 10mg of high-quality total RNA were obtained from dissected tissues from all studied groups based on standard TRIzol method (Invitrogen). Quality of RNA samples was verified using denaturing agarose gel from reagents for northern blotting (Ambion) and quantified having A260/A280 ≥ 1.8 and a concentration ≥ 1.0mg/ml.

treatment_protocol: Midguts or salivary glands were dissected from 10 different tick groups; 2 groups of unfed newly hatched adult male ticks (one group for midguts and another for salivary glands) and 8 groups from two sets of ticks that were allowed to feed in an uninfected or in an A. marginale acute infected calf (2 groups for midguts at 2 days and 6 groups for salivary glands at 2, 6 and 9 days). Each group was analyzed in triplicates and each replicate consisted of 90 ticks.

tag: gender

value: Male

value: Salivary Glands

tag: blood fed

value: Yes

tag: time point (days)


title: IL-exp6_Dll4-Fc_2.2-1

source_name: IL-exp6_Dll4-Fc_2.2-1 sample


title: IL-exp6_VEGF A_4.2-2

source_name: IL-exp6_VEGF A_4.2-2 sample


title: IL-exp6_VEGF A_4.4-2

source_name: IL-exp6_VEGF A_4.4-2 sample


title: SalivaryGlands_Fed_9days_rep2


title: IL-exp6_Dll4-Fc_2.3-2

source_name: IL-exp6_Dll4-Fc_2.3-2 sample


title: IL-exp6_VEGF A_3.3-1

source_name: IL-exp6_VEGF A_3.3-1 sample


title: Family2_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: Family1_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: IL-exp6_Dll4-Fc_2.4-2

source_name: IL-exp6_Dll4-Fc_2.4-2 sample


title: Family1_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: Family1_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: SalivaryGlands_Infected_9days_rep3

value: A. marginale


title: IL-exp6_hFc_1.4-2

source_name: IL-exp6_hFc_1.4-2 sample

value: hFc


title: Family1_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: Family1_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: SalivaryGlands_Infected_9days_rep1


title: IL-exp6_hFc_1.2-2

source_name: IL-exp6_hFc_1.2-2 sample


title: IL-exp6_hFc_1.3-2

source_name: IL-exp6_hFc_1.3-2 sample

source_name: IL-exp6 common reference


title: SalivaryGlands_Fed_6days_rep3


title: Family1_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA


title: IL-exp6_hFc_1.2-1

source_name: IL-exp6_hFc_1.2-1 sample


title: WTH-WTT:Est

city: Vancouver

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: VALUE ratio in data table below represents Cy3/Cy5

hyb_protocol: Labelled cDNA hybridised using The 3DNA Array 350 kit (Genisphere).

scan_protocol: Arrays scanned using an Perkin Elmer Scan Array Express.

data_processing:
Data were analyzed using R-2.10.1 and nlme: Linear and Nonlinear Mixed Effects Models and qvalue: Q-value estimation for false discovery rate packages (version 1.22.0). R code is attached as a supplementary file on the Series record.
Each channel was background corrected by subtracting the lowest 10% of foreground signal intensities within each subgrid of the array. The two channels of each array were normalized to each other by Huber's variance stabilization algorithm (Huber et al., 2002). A linear mixed effects model was applied to the normalized data in each channel. A fixed effect was included for each array, for the dye by gene interaction and for each treatment/strain combination. Random effects were included for within-array variability (each gene appeared twice on each array), technical variability (replicate culture was hybridized twice) and biological variability (48 replicate cultures were employed). The pairwise changes between treatments within strain and the pairwise changes between strains with treatment were estimated with standard errors and p-values based Student t statistics; q-values were computed to adjust for the false discovery rate.

organism: Cryptococcus neoformans

source_name: low-iron + 10 uM Hemin

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Three biological replicates for each strain were grown in 25 ml of YPD overnight at 30C. Cells were washed twice with low-iron medium (LIM) followed by growth in LIM at 30C for an additional 16 hours in order to eliminate any iron carryover from the rich medium. Cultures were then harvested and washed twice with LIM. The cells were counted and transferred to 50 ml LIM + different iron sources. The cells were then grown at 30C for another 12 h and harvested for RNA extractions.

extract_protocol: RNA was purified with the RNeasy kit (Qiagen) and treated with DNAse (Qiagen) following the manufacturer’s recommendations. The quality of RNA was analyzed with an Agilent 2100 Bioanalyzer

treatment_protocol: Low-iron medium (LIM), LIM + 100 uM of FeCl3, LIM + 5 uM of Transferrin or LIM + 10 uM of Hemin.

tag: genotype/variation

value: WT

tag: treatment group

value: low-iron + 10 uM Hemin

source_name: low-iron + 5 uM Transferrin

value: low-iron + 5 uM Transferrin


title: Lxn (+) cells vs control cells, MGC803

city: Beijing

first: Jianqing

last: Zhao

address: 18 Life Science Parkway

institute: Capitalbio. Crop

description: the genomic influence of Lxn expression on MGC803 cells

hyb_protocol: standard Capitalbio Methods

scan_protocol: CapitalBio manual

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For test and control sample, one hybridizations were performed.

source_name: gastric epithelial cancer Lxn (-) cell line MGC803, vehicle-treated

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: RNA isolation was accomplished with RNA Isolation Solvent RNA-Bee (TEL-TEST, Texas, USA).

tag: cell line

value: Lxn (-) cell line MGC803

value: MGC803 gastric epithelial cancer cell line, vehicle-treated

source_name: gastric epithelial cancer cell line (C39-8), transformed with vector containing Lxn gene

value: Lxn (+) cell line C39-8

value: MGC803 gastric epithelial cancer cell line, transformed with vector containing Lxn gene


title: SalivaryGlands_Infected_6days_rep3


title: WTF-WTT:Est

description: VALUE ratio in data table below represents Cy5/Cy3

source_name: low-iron + 100 uM FeCl3

value: low-iron + 100 uM FeCl3


title: WTF-WTH:Est


title: Chlorinated solvent contaminated groundwater

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

description: Total RNA extracted from a groundwater contaminated with chlorinated solvents (PCE, TCE) after a biostimulation treatment

hyb_protocol: For each hybridization experiment, labeled antisenses RNA (Cy3) were vacuum dried and resuspended in 5.6 µL of water. Then, the hybridization mix (Roche NimbleGen) was realized according to the manufacturer's protocols. The arrays were hybridized on a 4-bay NimbleGen Hybridization System (Roche NimbleGen) at 42°C for 72 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Samples were scanned using a Scanner Innoscan 900AL (Innopsys, Carbonne, France) at 2 μm resolution. Individual array images were acquired independently, adjusting the PMT gain for each image as recommended using the software Mapix® (Innopsys). Then, for each array image, raw expression data had been extracted using the NimbleScan software v2.1. (Roche NimbleGen) and feature intensities were exported as .pair files.

data_processing: The background noise was then determined using random probes present on the microarrays (8,863 probes in our experiment). This background noise is defined by two components: the background median intensity (Bposition) and its dispersion (Bdispersion). Finally, a modified signal-to-noise ratio called SNR’ and based on the formula of Verdik (Verdick, D., Handran, S. and Pickett, S. (2002) In LLC, D. P. (ed.), In G. Kamberova (ed.), DNA array image analysis: nuts and bolts. Salem, MA., pp. p. 83-98) is calculated as follow in order to reduce-centralize our data: SNR’ = (probe signal intensity - Bposition)/ Bdispersion. However, spatial effect across array surface is a predominant within-slide experimental artifact that needs to be eliminated before any other normalization procedure (Wang, X., He, H., Li, L., Chen, R., Deng, X.W. and Li, S. (2006) NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics, 22, 2955-2957). That is why, for all array images obtained in this work, surface was segmented to 16 sub-squares according to probe position (X, Y) indicated in pair report. A Perl script was developed to calculate local background noise in all sub-squares and the median SNR’ retrieved from the three replicates of each probe. Finally, another Perl script was implemented to summarize each replicate probe treated and determine the median value between the three replicates. Positive hybridization was considered significant for probes having an SNR’ > 3 (value to avoid all false positives).

organism: uncultured organism

source_name: antisense mRNA from the contaminated groundwater (6µg)

label_protocol: Antisense mRNA obtained from rumen and groundwater samples were labelled with Cy3 fluorescent dye (CyDyeTM Post-Labeling Reactive Dye Packs, GE Healthcare) following the manufacturer's instructions. Antisense RNAs (aRNAs) from the three synthetic genes mmoC, tceA and vcrA were labelled with Cy3-ULS as described in the Kreatech ULS labelling procedure (Kreatech Diagnostics).

growth_protocol: Fresh samples of whole rumen content were withdrawn from a cannulated sheep, farmed at INRA of Clermont-Ferrand-Theix (France), by inertial pumping using a Perspex tube.   Groundwater sample was collected by SITA Remediation Company (Lyon, France) by direct pumping at 10 m depth in a piezometer bored near the contamination source and immediately stored on ice until processed.

extract_protocol: Rumen sample collected was filtered through nylon membrane of 250 µm porosity and 0.5 g of filtrate was recovered and centrifuged at 21 000 g. Total RNA extraction was performed from the pellet using the optimized protocol described by Culley (Culley, D.E., Kovacik, J.W.P., Brockman, F.J. and Zhang, W. (2006) Optimization of RNA isolation from the archaebacterium Methanosarcina barkeri and validation for oligonucleotide microarray analysis. Journal of Microbiological Methods, 67, 36-43). Groundwater sample was transferred to the laboratory, 300 to 500 mL were filtered under vacuum and collected onto a 47 mm TSTP Millipore filter (3 µm pore size). Filters were then cut in pieces and placed into 900 µL of nucleic extraction buffer (50 mM glucose, 10 mM EDTA, 25 mM Tris-HCl pH 8.0) as described by Vetriani (Vetriani, C., Tran, H.V. and Kerkhof, L.J. (2003) Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea. Appl. Environ. Microbiol., 69, 6481-6488). In this protocol, freeze-thaw cycles were replaced by beat betting 1 min at 30 Hz with 1 g of glass beads of ≤106 μm in diameter (Sigma-Aldrich). Total RNA were extracted using a standard phenol-chloroform-isoamyl alcohol (25:24:1) method followed by a second extraction with an equal volume of chloroform. Nucleic acids were then precipitated, washed in 70% ethanol and resuspended in nuclease free water. Co-extracted DNA was removed by digestion with 4U of (RNAse free) DNase I (DNA-free, Ambion) at 37°C for 35 min. 8-9 µg of total RNA mixture were subjected to mRNA enrichment protocol using the MicrobExpress kit (Ambion Applied Biosystems), which employs capture hybridization by magnetic separation to remove 16S and 23S rRNA. In a second step, antisense amino-allyl dUTP marked RNA (aRNA) was obtained by amplification with both the MessageAmp II-Bacteria and the Amino-Allyl MessageAmp II kits (Ambion). The entire mmoC (S81887), tceA (AF228507) and vcrA (AY322364) genes sequences associated to SP6 promoter sequence at their 3’ end were synthesized by Biomatik Corporation (USA) and cloned into the pGH vector. Antisense RNAs (aRNAs) were produced by in vitro transcription using the MEGAscript SP6 Kit (Ambion).

tag: origin

value: environmental sample


title: Sheep rumen content

description: Total RNA extracted from sheep rumen content farmed at INRA of Clermont-Ferrand-Theix (France)

source_name: antisense mRNA from rumen (6µg)

value: Sheep rumen extract


title: SalivaryGlands_Fed_6days_rep2

value: Male

value: Salivary Glands


title: Synthetic genes and sheep rumen content

description: Antisense RNAs (aRNAs) were produced by in vitro transcription from pGH vector containing the entire mmoC, tceA and vcrA genes sequences (synthesized by Biomatik Corporation (USA))

organism:
synthetic construct
uncultured organism

source_name: 10^11 copies of mmoC, vcrA and tceA aRNA mixed with antisense mRNA from rumen (6µg)

value: Synthetic genes


title: SalivaryGlands_Infected_6days_rep2

value: Yes


title: SalivaryGlands_Infected_6days_rep1


title: SalivaryGlands_Fed_6days_rep1


title: SalivaryGlands_Fed_2days_rep3


title: WTC-WTT:Est

source_name: low-iron

value: low-iron


title: SalivaryGlands_Fed_2days_rep2


title: Family1_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: SalivaryGlands_Fed_2days_rep1


title: Family1_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: Family1_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: Family1_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: WTC-WTF:Est

value: WT


title: WTC-WTH:Est

value: low-iron + 10 uM Hemin


title: HXT-WTT:Est

value: low-iron + 5 uM Transferrin

value: hapX mutant


title: SalivaryGlands_Infected_2days_rep3

value: A. marginale


title: RapCA Rep 4

city: Columbus

first: Maqsood

middle: A

last: Chotani

state: OH

address: 700 Children's Drive

department: Center for Cardiovascular and Pulmonary Research

institute: Nationwide Childrens Hospital

description: Biological replicate 4 of 4

hyb_protocol: Refer to Agilent miRNA hybridization protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C). Images were quantified using Agilent Feature Extraction Software (version 10.7)

data_processing: Data were processed using alogorithms specified by the Agilent Feature Extraction software (version 10.7). This data is stored in the FE “.txt” files. The intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process.

source_name: micro-vascular smooth muscle cells derived from Rap1a knockout murine model transduced with RapCA Shuttle vector

label_protocol: Refer to Agilent miRNA labeling protocol

growth_protocol: Microvascular smooth muscle (mVSM) cells were were grown in Ham's growth medium that contained a 50:50 DMEM/F-12 solution, 10% FBS, L-glutamine, and antibiotics/antimycotic (10% FBS Ham's medium).

extract_protocol: Cells were washed twice with PBS  and Total RNA was extracted using the Ambion mirVANA kit.

treatment_protocol: Cells were transduced with virus overnight in serum-free (SF)-Ham's medium at time of plating. The medium was replaced next day with 0.5% FBS Ham's medium following one wash in this medium, and cells were allowed to recover for 48 hours.

tag: condition/variation

value: mVSM-RapCA


title: HXH-HXT:Est


title: HXF-WTF:Est


title: HXH-WTH:Est


title: SalivaryGlands_Infected_2days_rep2


title: RapCA Rep 1

description: Biological replicate 1 of 4.


title: RapCA Rep 2

description: Biological replicate 2 of 4


title: Patient 3,  P53KD, rep3

city: Singapore

first: Tongming

last: Liu

address: 60 Biopolis street

department: Cancer stem group

country: Singapore

institute: Genome Institute of Singapore

description:
4609526052_A
Replicate 3 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized with a shift to the 75 percentile using GeneSpring GX 11.0. A T test 0.05 on the normalized intensity followed by a ratio change (2-fold) was used to generate the gene list.

source_name: Mesenchymal stem cells, p53 KD

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: MSCs were cultured in MSC medium.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyzer.

treatment_protocol: MSCs were infected with lentivirus for p53 knockdown and retrovirus for TERT overexpression, empty as control.

value: mesenchymal stem cells

value: p53 knockdown

tag: patient


title: Control Rep 4

description: Biological replicate 4 of 4

source_name: micro-vascular smooth muscle cells derived from Rap1a knockout murine model transduced with empty Shuttle vector

value: mVSM Rap1a -/-


title: SalivaryGlands_Unfed_0days_rep2

value: No

tag: infection


title: SalivaryGlands_Fed_9days_rep1

value: Male


title: Patient 3, P53KD+TERT, rep3

description:
4609526125_H
Replicate 3 of 3.

source_name: Mesenchymal stem cells, p53 KD + TERT

tag: cell type

value: p53 knockdown + TERT overexpression


title: Family1_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

tag: tissue

value: paternal blood


title: RapCA Rep 3

description: Biological replicate 3 of 4


title: SalivaryGlands_Unfed_0days_rep3

value: Salivary Glands


title: Control Rep 3

description: Biological replicate 3 of 4


title: Patient 2, P53KD+TERT, rep2

description:
4609526125_E
Replicate 2 of 3.


title: Patient 2, P53KD, rep2

description:
4609526125_F
Replicate 2 of 3.


title: Patient 3, Control, rep3

description:
4609526125_G
Replicate 3 of 3.

source_name: Mesenchymal stem cells, control

value: empty control


title: SalivaryGlands_Infected_2days_rep1

value: Yes


title: Patient 2, Control, rep2

description:
4609526125_D
Replicate 2 of 3.


title: IL-exp6_Dll4-Fc_2.1-2

source_name: IL-exp6_Dll4-Fc_2.1-2 sample

value: retina

source_name: IL-exp6 common reference

value: pooled of equal amount of RNA from this experiment


title: Control Rep 2

description: Biological replicate 2 of 4


title: SalivaryGlands_Unfed_0days_rep1


title: HXF-HXH:Est

source_name: low-iron + 10 uM Hemin

value: low-iron + 10 uM Hemin

value: low-iron + 100 uM FeCl3


title: Control Rep 1

description: Biological replicate 1 of 4.


title: Midgut_Fed_2days_rep3

value: Midgut


title: HXC-HXT:Est

value: hapX mutant

value: low-iron

source_name: low-iron + 5 uM Transferrin

value: low-iron + 5 uM Transferrin


title: Midgut_Fed_2days_rep1


title: HXC-WTC:Est

value: WT


title: SalivaryGlands_Infected_9days_rep2

value: A. marginale


title: HXC-HXH:Est


title: Midgut_Fed_2days_rep2


title: Midgut_Infected_2days_rep3


title: Midgut_Infected_2days_rep1


title: Midgut_Unfed_0days_rep3

value: No


title: Midgut_Infected_2days_rep2

value: Male


title: Patient 1, P53KD, rep1

description:
4609526125_C
Replicate 1 of 3.

value: mesenchymal stem cells

value: p53 knockdown


title: H3H-WTH:Est

value: hap3 mutant


title: Midgut_Unfed_0days_rep1


title: H3T-HXT:Est


title: HXC-HXF:Est

source_name: low-iron + 100 uM FeCl3


title: Array 38

city: Austin

first: Lauren

last: O'Connell

state: TX

address: 1 University Station-CO930

department: Section of Integrative Biology

institute: University of Texas at Austin

description: Subordinate male loop

hyb_protocol: Cy3- and Cy5-labeled samples were combined and mixed with yeast tRNA, polydA/dT, SSC, and SDS and heated to 100C for 2 minutes before being applied to microarray slides. Slides were cover slipped and incubated in custom hybridization chambers in a 65C water bath for 16 hours. Slides were then washed in a series of 3 solutions containing decreasing amounts of SSC and SDS before drying via centrifugation.

scan_protocol: Scanned using a GenePix 4000B array scanner and imaged using GenePix Pro 6.0.

data_processing: Scans were gridded and spots with diameter < 60 were removed from analysis. Intensities were normalized within each array using the LIMMA package for R by loess. A linear model was fit to each array using the lmFit function and significant differences between the two groups (vehicle and ER antagonist treated within either Dominant or Subordinate loops) were found using empirical Bayesian statistics via the function eBayes and corrected for multiple hypothesis testing using FDR. Individual arrays were analyzed by building a contrast matrix from the lmFit data and a Benjamini-Hochberg cut-off was applied to control for multiple hypothesis testing. Single-channel intensities were extracted from the normalized M-values using Microsoft Excel and sample M1 as a reference.

organism: Haplochromis burtoni

label_protocol:
Two rounds of amplification using MessageAmpII kit (Ambion)
500 ng of RNA were primed with 1 uL of 5 ug/ul oligodT and random hexamer solution at 70C for 10 minutes. RNA was reverse transcribed using SuperScriptII Reverse Transcriptase, amino allyl-dUTP/dNTP solution and DTT at 42C for 2 hours. Samples were treated with 1N NaOH and 0.5M EDTA at 65C for 15 minutes then neutralized with 1M HEPES. Samples were purified using the Qiagen MinElute kit and eluted with 0.1M Na bicarbonate. Samples were labeled by mixing 10 uL with Amersham CyDye Post-Labeling Reactive Dye dissolved in 1 uL DMSO in the dark for 1 hour then neutralized with 3M NaOAc and cleaned using the Qiagen MinElute Kit.

extract_protocol: RNA extracted using Trizol following manufacturer's instructions

value: preoptic area of brain

value: vehicle

value: ER antagonist


title: Midgut_Unfed_0days_rep2


title: H3H-HXH:Est


title: H3T-WTT:Est

value: Hap3 mutant


title: Array 42

description: Subordinate male loop


title: Array 36

description: Subordinate male loop


title: Patient 1, Control, rep1

description:
4609526125_A
Replicate 1 of 3.

value: empty control


title: Array 40

description: Subordinate male loop


title: Array 16

description: Subordinate male loop


title: H3H-H3T:Est

value: low-iron + 10 uM Hemin


title: Array 15

description: Subordinate male loop


title: Patient 1, P53KD+TERT, rep1

description:
4609526125_B
Replicate 1 of 3.

value: p53 knockdown + TERT overexpression


title: H3F-WTF:Est

value: low-iron + 100 uM FeCl3


title: Array 30

description: Subordinate male loop


title: Array 32

description: Subordinate male loop


title: Array 13

description: Subordinate male loop


title: H3F-H3T:Est


title: Array 11

description: Subordinate male loop


title: H3F-HXF:Est

value: hapX mutant


title: H3F-H3H:Est


title: H3C-H3T:Est

value: low-iron + 5 uM Transferrin

value: low-iron


title: H3C-HXC:Est


title: H3C-H3H:Est


title: Array 28

description: Subordinate male loop


title: H3C-WTC:Est

value: WT


title: Array 24

description: Subordinate male loop


title: Array 22

description: Subordinate male loop


title: Array 18

description: Subordinate male loop


title: Array 20

description: Subordinate male loop


title: Array 26

description: Subordinate male loop


title: H3C-H3F:Est


title: C1T-WTT:Est

value: cir1 mutant


title: MDSC_Syngenic_2

city: NANTES

first: Nahzli

last: DILEK

address: 30 Bd Jean-Monnet, CHU Hôtel-Dieu

institute: INSERM UMR643

description:
Syngeneic
antibodies details: Purified anti-MHC class II (OX6) and anti-CD3 (G4.18) were prepared in our laboratory from the corresponding hybridomas obtained from the European Cell Culture Collection (Salisbury, UK). Goat anti-mouse IgG Dynabeads were purchased from Invitrogen/Life Technologies, cat n 110.33. Anti-CD80 (3H5) and anti-CD86 (24F) mouse antibodies were prepared in our laboratory from hybridoma given by Dr. H. Yagita (Juntendo University School of Medicine, Tokyo, Japan). FITC-conjugated anti-mouse was purchased from Jackson ImmunoResearch Laboratories (West Grove, PA, USA), cat n 715-095-150. Anti-FITC Microbeads were from Miltenyi, cat n 130-048-701.

hyb_protocol: Array hybridization was performed for 16 h at 55°C. An additional 3400 control spots were present on the chip to cover various steps in the hybridization process.

scan_protocol: Chemiluminescence detection, image acquisition, and analysis were performed using the Applied Biosystems chemiluminescence detection kit (part no. 436875D), analyzer (part no. 4338036) and version 1.1 analyzer software (part no. 4336391) according to the manufacturer’s protocol.

data_processing: Microarray raw data were analyzed by the R language and environment for statistical computing and graphics. Genes were identified using the Panther Protein Classification System Probe ID database.

label: Digoxigenin-UTP

organism: Rattus norvegicus

source_name: MDSCs

label_protocol: The Applied Biosystems rat genome survey microarray (part no. 4337467) contained 26,857 60-mer oligonucleotide probes representing 27,088 individual rat genes. An additional 3400 control spots were present on the chip to cover various steps in the hybridization process.  Digoxigenin-UTP labeled cRNA was generated and amplified from 0.5 µg of total RNA from each sample using an Applied Biosystems NanoAmp chemiluminescent reverse transcriptase-in vitro transcription (RT-IVT) labeling kit (part no. 4365715).

growth_protocol: Rats were maintained in an SPF-free animal facility according to the institutional guidelines of the “Institut National de la Santé et de la Recherche Médicale” (INSERM).

extract_protocol: Peripheral blood leucocytes were isolated from heparinized blood by removing erythrocytes with hypotonic lysis solution. A depletion of MHC class II + and CD3+ cells was performed with specific mAbs; followed by anti-mouse IgG-coated Dynabeads (Life Technologies). MDSCs were identified by staining 30 min at 4°C with purified anti-rat CD80/86 (3H5/24F) mAbs and FITC-conjugated anti-mouse IgG secondary Ab (Jackson ImmunoResearch Laboratories). MDSCs were isolated using automated magnetic cell sorting (AutoMACS, Miltenyi) of cells based on their expression of CD80/86.  Total RNA from MDSCs was prepared using the TRIzol (Invitrogen Life Technologies) extraction method. Ten micrograms of total RNA was cleaned up using RNeasy columns (Qiagen). RNA quantity and quality were determined using a NanoDrop spectrophotometer and an Agilent 2100 bioanalyzer. A rRNA 28S/18S ratio of 1.0 ± 0.1 was considered as acceptable for RNA amplification.

treatment_protocol: Lewis 1W (LEW.1W, haplotype RT1u) and Lewis 1A (LEW.1A, haplotype RT1a) rats (Centre d’Elevage Janvier, Le Genest-Saint-Isle, France) share the same genetic background but are MHC I and II mismatched. Heterotopic transplantations of 8 to 12 weeks old LEW.1W kidneys on LEW.1A animals were carried out according to the technique described by Ono & Lindsey. For syngeneic transplantations LEW.1A kidneys on LEW.1A recipients were achieved. Live-sustaining allotransplantations were performed aseptically and a binephrectomy was performed 7 days after transplantation as previously described. Blood urea and creatinine and urine protein/creatinine ratios were measured throughout the posttransplant period. Blood urea < 8 mM and blood creatinine < 40 mM were considered as normal. Transplant tolerance induction was obtained by treating rats with anti-CD28 (JJ319) antibody.

value: myeloid-derived suppressor cells (MDSCs)

tag: transplantation

value: Syngeneic

tag: state

tag: day post transplantation


title: Array 43

description: Dominant male loop

tag: treatment


title: MDSC_Syngenic_1


title: LNP(Cy5)×1.2%NP S(Cy3)_Pooled Sample 2

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of Spleen Sample 2

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 9.5.3.1; normalization method: lowess and rank consistency

source_name: Treatment Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Animals were housed at the Animal Institution in Showa University, and maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights turned on at 8:00 AM) and had access to chow (CE-2, CLEA Japan) and tap water ad libitum.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: 1.2%NP diet

tag: group

value: Treatment

tag: strain

value: Spleen

source_name: Control Cy5

treatment_protocol: control LNP diet

value: Control


title: LNP(Cy3)×1.2%NP L(Cy5)_Pooled Sample 1

description: Dye-swap (Cy3/Cy5) of Liver Sample 1

source_name: Control Cy3

value: Liver

source_name: Treatment Cy5


title: C1T-HXT:Est


title: Array 41

description: Dominant male loop

value: preoptic area of brain

value: ER antagonist

value: vehicle


title: LNP(Cy5)×1.2%NP L(Cy3)_Pooled Sample 2

description: Dye-swap (Cy5/Cy3) of Liver Sample 2


title: C1T-H3T:Est

value: Hap3 mutant


title: LNP(Cy3)×1.2%NP S(Cy5)_Pooled Sample 1

description: Dye-swap (Cy3/Cy5) of Spleen Sample 1


title: C1H-H3H:Est

value: low-iron + 10 uM Hemin


title: C1H-WTH:Est


title: C1H-C1T:Est


title: MDSC_Tolerant_anti-CD28_2

description:
Tolerant state
antibodies details: Purified anti-MHC class II (OX6) and anti-CD3 (G4.18) were prepared in our laboratory from the corresponding hybridomas obtained from the European Cell Culture Collection (Salisbury, UK). Goat anti-mouse IgG Dynabeads were purchased from Invitrogen/Life Technologies, cat n 110.33. Anti-CD80 (3H5) and anti-CD86 (24F) mouse antibodies were prepared in our laboratory from hybridoma given by Dr. H. Yagita (Juntendo University School of Medicine, Tokyo, Japan). FITC-conjugated anti-mouse was purchased from Jackson ImmunoResearch Laboratories (West Grove, PA, USA), cat n 715-095-150. Anti-FITC Microbeads were from Miltenyi, cat n 130-048-701.

value: Allogeneic

value: Tolerant state


title: Array 39

description: Dominant male loop


title: MDSC_Tolerant_anti-CD28_1


title: C1H-HXH:Est

value: hapX mutant


title: C1F-HXF:Est

value: low-iron + 100 uM FeCl3


title: C1F-WTF:Est

value: WT


title: Array 12

description: Dominant male loop


title: Array 31

description: Dominant male loop


title: Array 14

description: Dominant male loop


title: Healthy bone marrow EPCs, IFNa treated, 231

city: Ann Arbor

first: Celine

middle: C

last: Berthier

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
BM_T_231
Gene expression data from healthy bone-marrow EPCs incubated with IFNa.

hyb_protocol: Standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual).

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: The data were analyzed using the GenePattern pipeline: the RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization. Healthy EPCs, lupus EPCs and healthy bone marrow EPCs were normalized separately.

source_name: Healthy bone-marrow EPCs incubated with IFNa

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

extract_protocol: Total RNA was isolated with Tri-pure (Roche), and further purified and concentrated using an Rneasy kit (Qiagen).

treatment_protocol: Cells were incubated in the presence or absence of IFNa for 6 hours prior to RNA harvesting.

value: bone marrow

value: CD133+ endothelial progenitor cells (EPCs)

tag: disease state

value: healthy

value: IFNa


title: Array 34

description: Dominant male loop


title: C1F-H3F:Est

value: cir1 mutant

value: hap3 mutant


title: Healthy bone marrow EPCs, IFNa treated, 120

description:
BM_T_120
Gene expression data from healthy bone-marrow EPCs incubated with IFNa.


title: Array 35

description: Dominant male loop


title: Healthy bone marrow EPCs, IFNa treated, 222

description:
BM_T_222
Gene expression data from healthy bone-marrow EPCs incubated with IFNa.


title: Array 27

description: Dominant male loop


title: Healthy bone marrow EPCs, IFNa treated, 228

description:
BM_T_228
Gene expression data from healthy bone-marrow EPCs incubated with IFNa.