title: Mo17xB73 13 DAP endosperm tissue biological replicate 2

description: No other relevant details


title: B73xMo17 13 DAP endosperm tissue biological replicate 1

status: Public on Sep 01 2007

type: RNA

city: Saint Paul

first: Nathan

middle: M

last: Springer

state: MN

address: 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

description: No other relevant details

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: MAS5.0 values are reported; the .cel file is also available

label: biotin

molecule: total RNA

organism: Zea mays

source_name: Zea mays 13 day after pollination endosperm tissue

label_protocol: Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).

growth_protocol: Endosperm tissues were isolated from kernels of inbreds Mo17 and B73, and hybrids Mo17xB73 and B73xMo17 for gene expression analysis.  Samples were collected during August 2005 from field-grown maize plants grown on the St. Paul campus Agricultural Experiment Station.  Inbred and hybrid crosses were performed at three different dates to produce biological replicates.  The crosses for all genotypes within a biological replicate were performed within 30 minutes of each other.  Six ears of each genotypes were harvested at 13 DAP.  Six endosperms were collected from each of the six ears and pooled for a total of 36 endosperms from each genotype by biological replicate combination.  All tissues were flash frozen in a dry-ice cooled ethanol bath, and subsequently stored at −80˚C.

extract_protocol: RNAs for 13 DAP endosperm tissues were isolated using the plant RNeasy kit, according to the manufacturer’s instructions (Qiagen Corp., Valencia, CA).  All purified RNA samples were quantified and qualified using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and agarose gel electrophoresis.

tag: Characteristics	Stage

value: 13 day after pollination endosperm; Genotype:B73xMo17


title: PBMCs__sys52B 050403

city: Dallas

first: Florence

last: Allantaz

state: TX

address: 3434 Live Oak Street

institute: Baylor Institute for Immunology Research

description: PBMCs from SoJIA patient.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Homo sapiens

source_name: PBMCs from SoJIA patient.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNeasy Mini

tag: Age

value: 14 yrs, when sample taken.

tag: Gender

value: F

tag: Race

value: White

tag: Illness

value: JIA Systemic Onset

tag: Symptoms

value: Fever arthritis

tag: Treatment


title: PBMCs__sys32A 111402

description: PBMCs from SoJIA patient.

value: 9 yrs, when sample taken.

value: Steroids PO


title: PBMCs__sys35A 091902

description: PBMCs from SoJIA patient.

value: 12 yrs, when sample taken.

value: Steroids PO, Methotrexate


title: PBMCs__sys33A 092902

description: PBMCs from SoJIA patient.

value: 17 yrs, when sample taken.

value: Hispanic

value: Steroids PO, Steroids IV, Methotrexate


title: NA_uc_24h_vs_NA_c_TN24h_1

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Nicotiana attenuata and Solanum nigrum were challenged with different insects: Manduca sexta and Tupiocoris notatus in different combinations Goals of the study are first to haracterize the transcriptional response of two native Solanaceous plants (Nicotiana attenuata and Solanum nigrum) to attack from two herbivorous pests common on Solanaceous crops (Manduca sexta and Tupiocoris notatus). And second to identify genes involved in herbivore vaccination phenomenon. After germination, inbred and genetically characterized lines of N. attenuata DI92 and S. nigrum Sn30 originally collected from southwestern Utah in 1988, and Jena Germany in 2000, respectively, were grown in a greenhouse. Eggs of Manduca sexta (abbreviated M. s.) came from the North Carolina State University - Entomology Insectary and were hatched under 37°C. Nymphs and adults of Tupiocoris notatus (abbreviated T. n.) came from laboratory colonies started in 2000 with individuals collected from our Utah field sites. Plant were challenged with these different insect and combinations of them. All plants for a given treatment were enclosed in glass-and-mesh insect cages to avoid cross-infection. After 24 h or 5 days the herbivores and their frass were removed, and the above ground biomass of each plant was flash-frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Three independent replicate cages (biological replicates) were used for each of the 7 treatments resulting in a total of 21 cages per species. RNA extraction was performed according to the protocol using Trizol. The RNA samples represent a pooled sample from 4 plants grown in a cage.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Nicotiana attenuata

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Sterile germination, grown for 38 days in green house (16h/8h light/darkness, 65% humidity, 26 °C) in peat-clay substrate

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: Challenged with 15 Tupiocoris notatus adults for 1d, 24h

tag: Nicotiana attenuata, Leaves, Biotic stress

treatment_protocol: None, 24 h


title: PBMCs__SYS33A 090905

description: PBMCs from SoJIA patient.

value: 19 yrs, when sample taken.


title: NA_uc_5d_vs_NA_seqc_MS1d_TN4d_1

treatment_protocol: Sequentially challenged with 15 Manduca sexta neonate larvae for 1d followd by 15 Tupiocoris notatus adults for 4 d, 5d

treatment_protocol: None, 5 days


title: Mo17 13 DAP endosperm tissue biological replicate 2

description: No other relevant details

tag: Stage

value: 13 day after pollination endosperm; Genotype:Mo17


title: NA_uc_24h_vs_NA_c_TN5d_1

treatment_protocol: Challenged with 15 Tupiocoris notatus adults for 5d, 5d


title: Mo17xB73 13 DAP endosperm tissue biological replicate 1

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:Mo17xB73


title: B73 13 DAP endosperm tissue biological replicate 2

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:B73


title: B73 13 DAP endosperm tissue biological replicate 1

description: No other relevant details


title: PBMCs__sys51B 012704

description: PBMCs from SoJIA patient.

value: 3 yrs, when sample taken.


title: B73xMo17 13 DAP endosperm tissue biological replicate 2

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:B73xMo17


title: ST_LD41_SD15_vs_ST_LD56_1_FD

description: Plants of Solanum tuberosum subsp. andigena, which tuberize only under SD conditions, were grown in growth chambers under non-inductive LD conditions and half of the plants were transferred to inductive SD conditions for 1 or 15 days, whilst the rest of the plants were kept as controls in LD. Transgenic potato plants with reduced phyB levels, which tuberize irrespective of photoperiod, were also grown in LD conditions. All the plants, irrespective of treatment, were harvested 14 hours after the beggining of the photoperiod (i.e. immediately before dusk for plants on LD, and 8 hours after dusk for the plants on SD). A similar experimental protocol was used with plants of N. tabacum cv Hicks that flower at the same time irrespective of photoperiod and the isogenic line N. tabacum cv Hicks carrying the Maryland Mammoth mutant allele, which flower only on SD (i.e. the plants were grown under LD for 55 or 41 days in LD and then transferred for 1 or 15 days to SD conditions, respectively, whilst control plants were grown 56 days in LD). Finally, Nicotiana silvestris plants that flower only on LD were grown in non-inductive SD and then half of the plants were transferred to inductive LD conditions for 1 or 15 days. In all cases we harvested only the leaves, the organ in which daylength perception takes place and photoperiodic responses are initiated. SD conditions in this experiments were 8 hours of light/ 16 hours of darkness, 160 uEinstein, 22 °C. LD conditions were 16 hours of light/ 8 hours of darkness, 80 uEinstein, 22 °C. RNA was extracted with TRIZOL.

organism: Solanum tuberosum subsp. andigenum

treatment_protocol: 56 days Long Days

tag: Solanum tuberosum subsp. andigena, Leaves, Development

growth_protocol: Long Days: 16 h L / 8 hs D, 80 uE, 22 °C; Short Days: 8 h L / 16 h D, 160 uE, 22 °C

treatment_protocol: 41 Long days and 15 Short days


title: NA_uc_24h_vs_NA_c_MS24h_1

treatment_protocol: Challenged with 15 Manduca sexta neonate larvae for 1d, 24h


title: PBMCs__sys31A 090802

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: F

value: Steroids PO, steroids IV


title: PBMCs__sys62B 033104

description: PBMCs from SoJIA patient.

value: JIA Systemic Onset

value: Fever arthritis

value: Steroids PO, Steroids IV


title: NS_LD55_SD1_vs_NS_LD56_3

organism: Nicotiana sylvestris

treatment_protocol: 56 Short days

tag: Nicotiana sylvestris, Leaves, Development

growth_protocol: Short Days: 8 h L / 16 h D, 160 uE, 22 °C; Long Days: 16 h L / 8 hs D, 80 uE, 22 °C

treatment_protocol: 55 Short days and 1 Long day


title: PBMCs__sys29A 081302

description: PBMCs from SoJIA patient.

value: 15 yrs, when sample taken.

value: AA


title: PBMCs__sys49B 062002

description: PBMCs from SoJIA patient.

value: 11 yrs, when sample taken.

value: White

value: Steroids PO, Methotrexate


title: PBMCs__sys47B 033104

description: PBMCs from SoJIA patient.

value: 10 yrs, when sample taken.

value: M

value: Hispanic


title: Mo17 13 DAP endosperm tissue biological replicate 1

description: No other relevant details

value: 13 day after pollination endosperm; Genotype:Mo17


title: PBMCs__sys44B 112102

description: PBMCs from SoJIA patient.

value: 13 yrs, when sample taken.


title: PBMCs__sys42B 111402

description: PBMCs from SoJIA patient.


title: PBMCs__sys28A 081302

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.

value: Arthritis

value: Steroids PO, Steroids IV, Methotrexate


title: PBMCs__sys40B 060202

description: PBMCs from SoJIA patient.

value: Infliximab


title: PBMCs__sys37B 110502

description: PBMCs from SoJIA patient.

value: 8 yrs, when sample taken.

value: JIA Systemic Onset

value: Steroids PO


title: NS_LD41_SD15_vs_NS_LD56_2

growth_protocol: Short Days: 8 h L / 16 h D, 160 uE, 22 °C

treatment_protocol: 41 Short days and 15 Long days


title: PBMCs__sys39B 111202

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: F

value: Fever arthritis

value: Steroids PO, Steroids IV


title: PBMCs__sys25A 092404

description: PBMCs from SoJIA patient.

value: 15 yrs, when sample taken.

value: White

value: Methotrexate


title: PBMCs__sys27A 111002

description: PBMCs from SoJIA patient.

value: M

value: AA


title: NS_LD55_SD1_vs_NS_LD56_1


title: NS_LD41_SD15_vs_NS_LD56_1


title: 2HA 10:4, biological rep 3

city: Canberra

first: Peta

last: Holmes

state: Australian Capital Territory

address: Building 46, Australian National University

department: Reseach School of Biological Sciences

country: Australia

institute: Genomic Interactions Group

description: Gene expression data from Medicago truncatula 2HA after 2 weeks 0f 10:4 treatment

hyb_protocol: Fifteen to 20 µg of each biotin-labeled fragmented cRNA sample was used to prepare 300 µL of hybridization mixture. Aliquots of each sample (100 µL) were hybridized for 16 hours at 45 degrees celcius onto Test3 arrays to check the quality of the samples prior to hybridization (200 µL) onto the Medicago GeneChip arrays

scan_protocol: GeneChips were scanned with the Agilent GeneArray Scanner (Affymetrix)

data_processing: To remove certain systematic biases from microarray, the raw Affymetrix data (.cel files) were normalized with the GCRMA (GC content – Robust Multi-Array Average) algorithm (ver. 2.2.0) including quantile normalization and variance stabilisation, using the affy package of the bioconductor software. The normalized average of the replicates was then log transformed in base 2 to reduce the proportional relationship between random error and signal intensity. Differentially expressed genes were identified by evaluating the log2 ratio between the two conditions

label: Biotin

organism: Medicago truncatula

source_name: Medicago truncatula 2HA leaf explants, 2 weeks on 10:4

label_protocol: Biotinylated cRNA was generated using the Enzo BioArray kit (Affymetrix), purified using RNeasy spin columns (Qiagen), according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Medicago truncatula cv Jemalong and a highly regenerable seed line 2HA (Nolan et al, Plant Cell Rep 8: 278–281), which was derived from cultivar Jemalong, were used for the plant growth explant tissue culture. The basal medium used for the culture was P4, which is based on Gamborg's B5 medium as described by Thomas et al (Plant Sci 69: 189–198). All cultures were grown in the dark.

extract_protocol: Total RNA was extracted and purified from plant tissues using the Qiagen RNeasy plant mini kit (Qiagen).

treatment_protocol: Leaf explants were plated onto P4 medium containing 10 µM NAA and 4 µM BAP (P4 10:4) for 2 weeks


title: NS_LD41_SD15_vs_NS_LD56_3


title: 2HA 10:4, biological rep 2


title: Jem 10:4, biological rep 2

description: Gene expression data from Medicago truncatula Jemalong after 2 weeks 0f 10:4 treatment

source_name: Medicago truncatula Jemmalong leaf explants, 2 weeks on 10:4

tag: Jemmalong


title: NS_LD55_SD1_vs_NS_LD56_2


title: Jem 10:4, biological rep 1


title: PBMCs__sys25A 110802

description: PBMCs from SoJIA patient.

value: 13 yrs, when sample taken.


title: 2HA 10:4, biological rep 1


title: NTmm_LD55_SD1_vs_NTmm_LD56_2

organism: Nicotiana tabacum

growth_protocol: Long Days: 16 h L / 8 hs D, 80 uE, 22 °C

treatment_protocol: 56 Long days

tag: Nicotiana tabacum, Leaves, Development

treatment_protocol: 55 Long days and 1 Short day


title: NTmm_LD55_SD1_vs_NTmm_LD56_3


title: Jem 10:4, biological rep 3


title: PBMCs__sys35B 091902

description: PBMCs from SoJIA patient.

value: 12 yrs, when sample taken.

value: Steroids PO, Methotrexate


title: PBMCs__sys23A 072302

description: PBMCs from SoJIA patient.

value: 7 yrs, when sample taken.


title: PBMCs__sys24A 072302

description: PBMCs from SoJIA patient.

value: Arthritis

value: Steroids PO, Steroids IV,  Infliximab


title: PBMCs__SYS33B 090905

description: PBMCs from SoJIA patient.

value: 19 yrs, when sample taken.

value: Hispanic

value: JIA Systemic Onset

value: Anakinra


title: PBMCs__sys33B 092902

description: PBMCs from SoJIA patient.

value: 17 yrs, when sample taken.

value: F


title: PBMCs__sys22A 052802

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: Steroids PO, steroids IV


title: NTmm_LD55_SD1_vs_NTmm_LD56_1


title: PBMCs__sys31B 090802

description: PBMCs from SoJIA patient.

value: White


title: NTmm_LD41_SD15_vs_NTmm_LD56_2


title: PBMCs__sys32B 111402

description: PBMCs from SoJIA patient.

value: 9 yrs, when sample taken.

value: Fever arthritis

value: Steroids PO


title: PBMCs__SYS21A 042104

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.

value: AA

value: Methotrexate


title: NTmm_LD41_SD15_vs_NTmm_LD56_3


title: PBMCs__sys29B 081302

description: PBMCs from SoJIA patient.

value: 15 yrs, when sample taken.

value: Steroids PO, Methotrexate


title: NT_LD55_SD1_vs_NT_LD56_3


title: PBMCs__sys28B 081302

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.

value: Arthritis

value: Steroids PO, Steroids IV, Methotrexate


title: NTmm_LD41_SD15_vs_NTmm_LD56_1


title: PBMCs__sys21A 111704

description: PBMCs from SoJIA patient.

value: JIA Systemic Onset


title: PBMCs__sys21A 111402

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.


title: PBMCs__sys27B 111002

description: PBMCs from SoJIA patient.

value: 8 yrs, when sample taken.

value: M


title: Different set of restriction enzymes for genome digestion.

type: genomic

city: Kitashirakawa, Sakyoku

first: Ikuko

last: Hara-Nishimura

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

country: Japan

institute: Kyoto University

description: The full-output file from Feature Extraction Software was attached as a Supplementary file.

hyb_protocol: Hybridization was performed with an Oligo aCGH/ChIP-on-Chip Hybridization Kit (Agilent Technology) according to the standard protocol, except that Cot-1 DNA was not added to the hybridization solution. After 24-h, the microarray was washed in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technology) for 5 min at room temperature, in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technology) for 1 min at 37 ˚C and in acetonitrile for 1 min at room temperature.

scan_protocol: Immediately after washing the microarray slide was scanned by a DNA microarray scanner (Agilent Technologies).

data_processing: The signals were quantified and normalized of signals were performed with Feature Extraction Software ver. 9.1 (Agilent Technologies) with default parameters.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Col-0 genomic DNA digested by RsaI and AluI

label_protocol: Genomic DNA (1 micro g) was used for labeling reaction with a Genomic DNA Labeling Kit (Agilent technology) according to direct labeling protocol.

extract_protocol: Genomic DNA was extracted with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Double-stranded DNA was quantified with a Quant-iT dsDNA Broad-Range Assay Kit (Invitrogen, Carlsbad, CA). Quality of genomic DNA prepared was checked by agarose gel electrophoresis.

tag: Arabidopsis thaliana Col-0.

source_name: Mixture of Col-0 genomic DNA separately digested by either RsaI/AluI or DraI


title: NT_LD41_SD15_vs_NT_LD56_3


title: PBMCs__sys20A 071802

description: PBMCs from SoJIA patient.

value: F

value: Steroids PO, Steroids IV, Methotrexate, Infliximab


title: Col-0 vs mag2-2

tag: Arabidopsis thaliana mutant mag2-2 reported in Li et al.,(2006) Plant Cell. 18, 3535-3547.


title: PBMCs__sys25B 110802

description: PBMCs from SoJIA patient.

value: 13 yrs, when sample taken.

value: White

value: methotrexate, Anakinra


title: NT_LD55_SD1_vs_NT_LD56_2


title: NT_LD55_SD1_vs_NT_LD56_1


title: PBMCs__SYS25A 050703

description: PBMCs from SoJIA patient.

value: 14 yrs, when sample taken.

value: Fever arthritis


title: PBMCs__sys25B 092404

description: PBMCs from SoJIA patient.


title: NT_LD41_SD15_vs_NT_LD56_2


title: PBMCs__sys19A 051602

description: PBMCs from SoJIA patient.

value: 3 yrs, when sample taken.


title: PBMCs__sys17A 080105

description: PBMCs from SoJIA patient.

value: 10 yrs, when sample taken.

value: Methotrexate, Infliximab


title: Col-0 vs Ler

source_name: Ler

tag: Arabidopsis thaliana Ler.


title: Col-0 self comparison experiment 3

description:
This experiment was performed to assess the reproducablity of the AtMap1 array.
The full-output file from Feature Extraction Software was attached as a Supplementary file.


title: PBMCs__sys16A 070202

description: PBMCs from SoJIA patient.

value: Hispanic


title: PBMCs__sys17A 050905

description: PBMCs from SoJIA patient.


title: PBMCs__SYS25B 050703

description: PBMCs from SoJIA patient.


title: NT_LD41_SD15_vs_NT_LD56_1


title: Col-0 self comparison experiment 1

description: This experiment was performed to assess the reproducablity of the AtMap1 array.

source_name: Col-0 genomic DNA


title: PyMT.5

city: Bethesda

first: Jeffrey

middle: E

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

hyb_protocol: Twenty micrograms of total RNA from each sample was was labeled and hybridized as described in Hegde P. et al. Biotechniques 2000;29(3):548-50, 52-4.

scan_protocol: The array slides were scanned with an Axon 4000 scanner (Axon Instruments, Foster City, CA) Images were quantified using GenePix software.

data_processing: For each spot the channel signal was calculated as mean foreground minus median background. Bad and/or low intensity spots were excluded. Log2 ratios on each array were normalized with LOWESS. Insightful S-Plus 6.0 (Insightful Corp., Seattle, WA) was used for the data processing.

organism: Mus musculus

source_name: Gland mammary normal

label_protocol: The tumor RNA was labeled by using Cyanine 5-dUTP (Cy5), and reference normal samples were labeled with Cyanine 3-dUTP (Cy3) as described in Hegde P. et al. Biotechniques 2000;29(3):548-50, 52-4.

extract_protocol: Total RNA obtained by a two-step extraction method using TRIZOL® Reagent (Invitrogen) and RNeasy Mini protocol for RNA cleanup by QIAGEN (Valencia, CA).

tag: Strain

value: FVB

tag: Model

value: wild-type

source_name: Gland mammary tumor

value: MMTV-PyMT


title: PyMT.3


title: PBMCs__sys15A 070202

description: PBMCs from SoJIA patient.

tag: Age

value: 2 yrs, when sample taken.

value: JIA Systemic Onset


title: ST_LB56_Ri_PHYB_vs_ST_LD56_3


title: PyMT.4


title: Col-0 self comparison experiment 2

description:
This experiment was performed to assess the reproducablity of the AtMap1 array.
The full-output file was attached as a Supplementary file.


title: PBMCs__sys23B 072302

description: PBMCs from SoJIA patient.

value: 7 yrs, when sample taken.

tag: Gender

value: M

value: Methotrexate


title: ras.4

value: MMTV-ras


title: PBMCs__sys24B 072302

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

tag: Race

value: White

value: Arthritis

value: Steroids PO, Steroids IV,  Infliximab


title: ST_LB56_Ri_PHYB_vs_ST_LD56_1


title: PBMCs__SYS15A 042705

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.

value: F

tag: Illness

value: Fever arthritis

value: Steroids PO, Steroids IV, Methotrexate, Infliximab


title: PBMCs__SYS21B 042104

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.

value: AA

tag: Symptoms

value: Steroids PO, Steroids IV, Methotrexate


title: PyMT.1

value: FVB

value: wild-type

value: MMTV-PyMT


title: ST_LB56_Ri_PHYB_vs_ST_LD56_2


title: ras.5


title: PBMCs__sys21B 111704

description: PBMCs from SoJIA patient.

value: JIA Systemic Onset

tag: Treatment

value: methotrexate, Anakinra


title: PBMCs__sys13A 090304

description: PBMCs from SoJIA patient.


title: ST_LD55_SD1_vs_ST_LD56_3


title: PyMT.2


title: PBMCs__sys14A 063002

description: PBMCs from SoJIA patient.

value: 13 yrs, when sample taken.

value: M

value: Steroids PO, steroids IV, methotrexate


title: PBMCs__sys21B 111402

description: PBMCs from SoJIA patient.


title: ST_LD41_SD15_vs_ST_LD56_3


title: PBMCs__sys12A 062702

description: PBMCs from SoJIA patient.

value: White

value: Methotrexate


title: PBMCs__sys22B 052802

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: Steroids PO, steroids IV


title: PBMCs__sys12A 071304

description: PBMCs from SoJIA patient.

value: F

value: Fever arthritis

value: Steroids PO, Methotrexate


title: ST_LD41_SD15_vs_ST_LD56_2


title: PBMCs__sys13A 063002

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.

value: AA

value: Arthritis


title: ST_LD55_SD1_vs_ST_LD56_1


title: ras.2

value: FVB

value: wild-type

value: MMTV-ras


title: ras.3


title: PBMCs__sys12A 022704

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.

value: JIA Systemic Onset


title: ST_LD41_SD15_vs_ST_LD56_1


title: ST_LD55_SD1_vs_ST_LD56_2


title: PBMCs__sys19B 051602

description: PBMCs from SoJIA patient.

value: 3 yrs, when sample taken.

value: Steroids PO, Steroids IV, Methotrexate, Infliximab


title: PBMCs__sys20B 071802

description: PBMCs from SoJIA patient.

value: 9 yrs, when sample taken.

value: White


title: PBMCs__sys17B 080105

description: PBMCs from SoJIA patient.

value: 10 yrs, when sample taken.

value: M

value: Anakinra


title: c.myc.4

value: MMTV-myc


title: ras.1


title: c.myc.3


title: PBMCs__sys16B 070202

description: PBMCs from SoJIA patient.

value: F

value: Hispanic

value: Fever arthritis


title: PBMCs__sys02A 092704

description: PBMCs from SoJIA patient.

value: 13 yrs, when sample taken.

value: Steroids PO, Methotrexate, Infliximab


title: PBMCs__sys17B 050905

description: PBMCs from SoJIA patient.

value: Arthritis


title: Sus_Mock_vs_nematode_48h_2

description: A pair of nearly isogenic tomato (Solanum lycopersicum) lines were used. These are: Motelle (Mi/Mi), root-knot nematode resistant and Moneymaker (mi/mi) root-knot nematode susceptible. A potato aphid (red biotype), imported from France, was used for infestation. An equal volume of sterile 1% carboxymethyl cellulose in water was added to the cleaned nematodes to keep them in suspension. The inoculum, consisting of 75-100 J2s, was dispensed in 10 µl aliquots using a repeat pipetter.  The inoculum was pipetted 2 mm beneath the root tips. Control seedlings were inoculated with 0.5% carboxymethyl cellulose.  After the desired incubation time (24 h or 36 h), seedlings were taken out of the boxes and a few set aside to check nematode infection rate. In our hand, this system results in 50% infection rate. The rest of the seedlings were placed on a water-saturated filter paper and the roots aligned.  About 1 cm of the infected root tip was excised with a blade and quickly frozen on a polycarbonate membrane-lined 50 mm diameter Petri dish floating on liquid nitrogen and stored at -80C. Plants were grown for 6 weeks in a growth chamber under 16 h light/8 h dark at 25C in UCMix/sand, irrigated with water or MiracleGroR solution, then moved to an insect growth room (25C) 4-6 days before aphid infestation. Individual tomato leaflets were infested with 30-40 mixed stages of the potato aphids using plastic leaf cages. Four leaflets and two plants of each genotype were infested. Two plants of each genotype were used as controls. After the desired infestation time (6, 12, 24 or 48 h), leaflets were excised from the plants with a blade and sprayed with 1% SDS to force aphids to remove their stylets from the leaf tissue.  Aphids were carefully removed from the leaflets and quickly frozen in liquid nitrogen. Control leaflets were excised and sprayed with 1% SDS before freezing. Samples were stored at -80C. RNA was isolated using the hot phenol method.

organism: Solanum lycopersicum

growth_protocol: Seeds were germinated on wet Whatman paper in the dark, at room temperature, 5-6 days then incubated at 23C, under light conditions, until the seedlings were ready to be inoculated (3-5 h)

treatment_protocol: Nematode infected, 36 h

tag: Solanum lycopersicum, Roots, Biotic stress

treatment_protocol: Mock infected, 36 h


title: Res_Mock_vs_nematode_24h_2

treatment_protocol: Nematode infected, 24 h

treatment_protocol: Mock infected, 24 h


title: PBMCs__sys02A 052802

description: PBMCs from SoJIA patient.

value: 11 yrs, when sample taken.


title: PBMCs__sys15B 070202

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.


title: PBMCs__sys06A 053002

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: Asian

value: JIA Systemic Onset


title: PBMCs__sys01A 080402

description: PBMCs from SoJIA patient.

value: 17 yrs, when sample taken.


title: c.myc.1

value: FVB

value: wild-type


title: Res_Mock_vs_nematode_48h_2


title: Sus_Mock_vs_nematode_24h_2


title: Sus_Mock_vs_nematode_48h_1


title: c.myc.2


title: PBMCs__SYS15B 042705

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.


title: neu.5


title: neu.3


title: neu.4


title: PBMCs__sys14B 063002

description: PBMCs from SoJIA patient.

value: M

value: White

value: Steroids PO, steroids IV, methotrexate


title: PBMCs__sys12B 062702

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.

value: F

value: Anakinra


title: PBMCs__SLE90A_112002

description: PBMCs from SLE patient.

source_name: PBMCs from SLE patient.

value: Hispanic

value: SLE

value: SLEDAI 4

value: Steroids PO, Steroids IV


title: PBMCs__sys13B 090304

description: PBMCs from SoJIA patient.

value: AA

value: Steroids PO


title: Res_Mock_vs_nematode_24h_1


title: PBMCs__sys13B 063002

description: PBMCs from SoJIA patient.

value: 2 yrs, when sample taken.

value: JIA Systemic Onset


title: Res_Mock_vs_nematode_48h_1


title: PBMCs__SLE91A_021604

description: PBMCs from SLE patient.

value: 10 yrs, when sample taken.

value: Asian

value: SLEDAI 12


title: PBMCs__SLE96A_021804

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.


title: neu.2

value: FVB

value: wild-type


title: c3tag.5

value: C3(1)/SV40 T/t-antigen


title: PBMCs__sys12B 071304

description: PBMCs from SoJIA patient.

value: 6 yrs, when sample taken.

value: F

value: White

value: Arthritis


title: neu.1


title: c3tag.4


title: PBMCs__SLE82A_032604

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: SLE

value: SLEDAI 8


title: Sus_Mock_vs_aphid_24h_2

growth_protocol: Growth chamber under 16 h light/8 h dark at 25C in UCMix/sand, irrigated with water or MiracleGro solution, then moved to insect growth room (25C) 4-6 days before infestation

treatment_protocol: Aphid infested, 24 h

tag: Solanum lycopersicum, Leaves, Biotic stress

treatment_protocol: Mock infested, 24 h


title: PBMCs__SLE83A 110102

description: PBMCs from SLE patient.

value: 8 yrs, when sample taken.

value: AA

value: SLEDAI 2

value: Steroids PO


title: Sus_Mock_vs_nematode_24h_1


title: PBMCs__sys12B 022704

description: PBMCs from SoJIA patient.

value: 4 yrs, when sample taken.

value: JIA Systemic Onset

value: Fever arthritis

value: Steroids PO, Methotrexate


title: Sus_Mock_vs_aphid_12h_2

treatment_protocol: Aphid infested, 12 h

treatment_protocol: Mock infested, 12 h


title: Sus_Mock_vs_aphid_48h_2

treatment_protocol: Aphid infested, 48 h

treatment_protocol: Mock infested, 48 h


title: PBMCs__SLE79_102402

description: PBMCs from SLE patient.

value: 10 yrs, when sample taken.

value: Hispanic


title: PBMCs__SLE85A_110602

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.

value: SLEDAI 12


title: PBMCs__SLE88_072402

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: F

value: White

value: SLEDAI 18

value: Steroids PO and IV, Cytoxan


title: Sus_Mock_vs_aphid_6h_2_FD

treatment_protocol: Aphid infested, 6 h

treatment_protocol: Mock infested, 6 h


title: c3tag.3

value: FVB

value: wild-type

value: C3(1)/SV40 T/t-antigen


title: PBMCs__sys06B 053002

description: PBMCs from SoJIA patient.

value: 5 yrs, when sample taken.

value: Asian

value: Arthritis

value: Steroids PO, Steroids IV, Methotrexate, Infliximab


title: PBMCs__sys02B 092704

description: PBMCs from SoJIA patient.

value: JIA Systemic Onset

value: Fever arthritis

value: methotrexate, Anakinra


title: PBMCs__sys02B 052802

description: PBMCs from SoJIA patient.

value: 11 yrs, when sample taken.


title: Sus_Mock_vs_aphid_6h_2


title: PBMCs__SLE74_091102

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: AA

value: SLE

value: SLEDAI 6

value: Steroids PO


title: PBMCs__sys01B 080402

description: PBMCs from SoJIA patient.

value: F

value: White


title: c3tag.1

value: FVB

value: wild-type


title: PBMCs__SLE75A_060203

description: PBMCs from SLE patient.

value: Hispanic


title: BRCA.5

value: Brca1 Co/Co;MMTV-cre;p53


title: Res_Mock_vs_aphid_48h_2


title: PBMCs__SLE96B_021804

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.

value: SLEDAI 4


title: BRCA.4


title: PBMCs__SLE65_12140

description: PBMCs from SLE patient.

value: 10 yrs, when sample taken.

value: SLEDAI 8

value: Steroids PO, Steroids IV, Cytoxan


title: PBMCs__SLE62A_030504

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: SLEDAI 2

value: Steroids PO, Steroids IV


title: c3tag.2

value: C3(1)/SV40 T/t-antigen


title: Res_Mock_vs_aphid_24h_2


title: PBMCs__SLE91B_021604

description: PBMCs from SLE patient.

value: Asian

value: SLE

value: SLEDAI 12


title: PBMCs__SLE90B_112202

description: PBMCs from SLE patient.

value: 11 yrs, when sample taken.

value: F


title: PBMCs__SLE88_072402B

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: White

value: SLEDAI 18

value: Steroids PO and IV, Cytoxan


title: PBMCs__SLE67_042803

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.

value: Imuran


title: BRCA.3

value: wild-type

value: Brca1 Co/Co;MMTV-cre;p53


title: Res_Mock_vs_aphid_6h_2


title: PBMCs__SLE61A 111601

description: PBMCs from SLE patient.

value: M

value: AA

value: SLEDAI 10

value: Steroids PO, Cellcept


title: BRCA.2


title: PBMCs__SLE60A_021604

description: PBMCs from SLE patient.

value: 12 yrs, when sample taken.

value: Hispanic

value: SLEDAI 4

value: Steroids PO, Steroids IV


title: PBMCs__SLE57_072402

description: PBMCs from SLE patient.

value: SLE


title: BRCA.1


title: Res_Mock_vs_aphid_6h_2_FD


title: PBMCs__SLE85B_110602

description: PBMCs from SLE patient.

value: F

value: SLEDAI 12


title: PBMCs__SLE56A 100402

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: SLEDAI 20


title: p53_EL.3


title: Res_Mock_vs_aphid_12h_2


title: p53_EL.4


title: PBMCs__SLE83B 110102

description: PBMCs from SLE patient.

value: 8 yrs, when sample taken.

value: SLEDAI 2

value: Steroids PO


title: p53_EL.2

value: wild-type


title: PBMCs__SLE82B_032604

description: PBMCs from SLE patient.

value: SLEDAI 8


title: PBMCs__SLE53_042803

description: PBMCs from SLE patient.


title: PBMCs__SLE51A_071702

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: SLEDAI 11


title: Sus_Mock_vs_aphid_24h_1


title: Sus_Mock_vs_aphid_48h_1


title: PBMCs__SLE50A_010803

description: PBMCs from SLE patient.

value: 15 yrs, when sample taken.

value: AA


title: Sus_Mock_vs_aphid_12h_1


title: Sus_Mock_vs_aphid_6h_1


title: p53_EL.1


title: PBMCs__SLE75_060203

description: PBMCs from SLE patient.

value: Hispanic

value: SLEDAI 6


title: p53_DM.4

value: Balb/c


title: p53_DM.5


title: PBMCs__SLE43A_012302

description: PBMCs from SLE patient.

value: SLE

value: Steroids PO, Cytoxan


title: Res_Mock_vs_aphid_24h_1


title: PBMCs__SLE79_102402B

description: PBMCs from SLE patient.

value: 10 yrs, when sample taken.

value: F


title: p53_DM.2


title: PBMCs__SLE36A 100501

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.

value: SLEDAI 20


title: PBMCs__SLE67_042803B

description: PBMCs from SLE patient.

value: White

value: SLEDAI 2

value: Imuran


title: Sus_Mock_vs_aphid_6h_1_FD


title: Res_Mock_vs_aphid_12h_1


title: PBMCs__SLE45_090902

description: PBMCs from SLE patient.

value: 9 yrs, when sample taken.

value: SLEDAI 16


title: Res_Mock_vs_aphid_48h_1


title: Res_Mock_vs_aphid_6h_1_FD


title: p53_DM.1

value: wild-type


title: PBMCs__SLE62B_030504

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: Steroids PO, Steroids IV


title: PBMCs__SLE27_020102

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: AA

value: SLEDAI 14

value: Steroids PO and Cytoxan


title: Res_Mock_vs_aphid_6h_1


title: PBMCs__SLE61B 111601

description: PBMCs from SLE patient.

value: M

value: SLE

value: SLEDAI 10

value: Steroids PO, Cellcept


title: PBMCs__SLE35_110701

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.

value: Hispanic

value: SLEDAI 8

value: Steroids PO and IV and Cellcept


title: PBMCs__SLE65_121402B

description: PBMCs from SLE patient.

value: 10 yrs, when sample taken.

value: F

value: Steroids PO, Steroids IV, Cytoxan


title: FVB.LT.4

source_name: Lung tissue tumor

label_protocol: The reference RNA was labeled by using Cyanine 5-dUTP (Cy5), and the tumor or normal samples were labeled with Cyanine 3-dUTP (Cy3) as described in Hegde P. et al. Biotechniques 2000;29(3):548-50, 52-4.

value: FVB

value: CC10/SV40 T/t-antigen

source_name: Stratagene Universal Reference RNA

tag: Stratagene Universal Reference RNA


title: PBMCs__SLE31A_110602

description: PBMCs from SLE patient.

value: 8 yrs, when sample taken.


title: FVB.LT.3


title: p53_DM.3

value: Balb/c

value: wild-type


title: PBMCs__SLE57_072402B

description: PBMCs from SLE patient.

value: 12 yrs, when sample taken.

value: AA

value: Steroids PO, Steroids IV


title: FVB.LT.2


title: PBMCs__SLE56B 100402

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: SLE

value: SLEDAI 20

value: Steroids PO and IV, Cytoxan


title: PBMCs__SLE17A_103101

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: M

value: Asian

value: SLEDAI 2

value: Steroids PO


title: FVB.LT.1

value: FVB


title: PBMCs__SLE53_042803B

description: PBMCs from SLE patient.

value: F

value: Hispanic


title: PBMCs__SLE20_060603

description: PBMCs from SLE patient.

value: SLEDAI 16

value: Steroids PO, Cellcept


title: FVB.LN.4

source_name: Lung tissue normal

value: wild-type


title: PBMCs__SLE21_030602

description: PBMCs from SLE patient.

value: 10 yrs, when sample taken.

value: SLEDAI 12


title: PBMCs__SLE74_091102B

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: AA

value: SLEDAI 6


title: Chicken liver, fat (FL) versus lean (LL) lines, 11 week of age, replicate 1

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

description: Liver from fat (FL) and lean (LL) chickens, 11 week of age, replicate 1

hyb_protocol: A cDNA spotted glass slide (Del-Mar 14K Chicken Integrated Systems microarray) was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in deionized water and dry spinning for 5 min at 1,000 x g. The labeled cDNA was dried down (Speed Vac) and reconstituted prior to hybridization in a 30 microliter volume of pre-warm DIG Easy Hyb solution (Roche Diagnostics; Indianapolis, IN). The two target samples (Alexa 555 and Alexa 647 labeled) were pooled and mixed with 2.5 microliter of 10 mg/ml Yeast tRNA, 2.5 microliter of 10 mg/ml salmon testes DNA (Sigma, Louis, MO) and 2.5 microliter of 1 microgram/microliter of pSport 6.1(Invitrogen) vector (PCR amplified product from “empty” pSport 6.1 vector sequence). The target mixture was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated mircoarray slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (approximately 16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, slides were sequentially washed with 1 x SSC, 0.2% SDS, and 0.5% DTT at 50 degrees C for 10 min, then 0.1 x SSC, 0.2% SDS, and 0.5% DTT for 5 min at room temperature, and finally 0.1 x SSC and 0.5% DTT for 1 min at room temperature, with nitrogen gas bubbled through each of the washes to prevent interference from ozone. The slides were subsequently rinsed in dH2O and dried by centrifugation. Slides were stored until scanning in individual 50 ml tubes covered in aluminum foil and filled with nitrogen gas.

scan_protocol: Each microarray slide was scanned using a GenePix 4000B microarray scanner (Molecular Devices; Sunnyvale, CA) set at 635 nm for Alexa647 and 532 nm for Alexa555 after adjustment of the PMT count ratio (635/532) to 1. Two high-resolution TIFF images (embedded in a single file) were generated for each slide.

data_processing: Image analysis was performed on high-resolution TIFF images using GenePix Pro 4.1 (Molecular Devices, Sunnyvale, CA). The results of image analysis [GenePix Report (GPR) files] were automatically merged with Excel files containing the clone identification number/plate address and gene name/function (from the highest BLAST score). Data in the VALUE column are based on the loess-normalized ratio of the loess-normalized log2 Alexa 555 and Alexa 647 values. The values are based on median intensity values (not background corrected) for Alexa 555 and Alexa 647.

label: Alexa Flour 555

organism: Gallus gallus

label_protocol: Twenty micrograms of total RNA were indirectly labeled using SuperScript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA). Briefly, the first strand cDNA synthesis was performed in a 30 microliter final volume containing 1x first-strand buffer, 5 micrograms of anchored oligo(dT)20, DTT, dNTP mix (including aminoallyl- and aminohexyl-modified nucleotides), 40 U of RNaseOUT and 800 U of SuperScript III reverse transcriptase with an incubation at 46 degrees Celsius for 3 hours. The original RNA was destroyed by NaOH hydrolysis and followed by neutralization with HCl. The cDNAs were purified using a low-elution volume spin cartridge (Invitrogen; Carlsbad, CA) and labeled with either Alexa Fluor 555 or Alexa Fluor 647 succinimidyl ester in the dark at room temperature for 2 hours. After purification of labeled cDNAs with a low-elution-volume spin cartridge, the efficiency of dye incorporation was determined using the Microarray Module on the NanoDrop ND-1000 spectrophotometer and the Base:Dye Ratio Calculator on the Invitrogen website.

growth_protocol: Standard broiler chicken growth protocol

extract_protocol: Total RNA was extracted using a RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA).

treatment_protocol: Divergently selected on abdominal fat weight (FL genotype) for seven generations.

tag: Liver FL cockerel, 11 week of age

label: Alexa Flour 647

label_protocol: Twenty micrograms of total RNA were indirectly labeled following the SuperScript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted using the RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE). The RNA integrity was examined using the RNA 6000 Nano Assay kit and Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Divergently selected on abdominal fat weight (LL genotype) for seven generations.

tag: Liver LL cockerel, 11 week of age


title: PBMCs__SLE50B_010803

description: PBMCs from SLE patient.

value: 15 yrs, when sample taken.

value: SLE


title: PBMCs__SLE114A

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: SLEDAI 14


title: PBMCs__SLE121A_022704

description: PBMCs from SLE patient.

value: 12 yrs, when sample taken.

value: SLEDAI 10


title: PBMCs__SLE60B_021604

description: PBMCs from SLE patient.

value: SLEDAI 4

value: Steroids PO, Steroids IV


title: PBMCs__SLE51B_071702

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: F

value: Hispanic

value: SLEDAI 11


title: Chicken liver, fat (FL) versus lean (LL) lines, 9 week of age, replicate 2

description: Liver from fat (FL) and lean (LL) chickens, 9 week of age, replicate 2

tag: Liver LL cockerel, 9 week of age

tag: Liver FL cockerel, 9 week of age


title: Chicken liver, fat (FL) versus lean (LL) lines, 11 week of age, replicate 2

description: Liver from fat (FL) and lean (LL) chickens, 11 week of age, replicate 2


title: PBMCs__SLE43B_102302

description: PBMCs from SLE patient.

value: Steroids PO, Cytoxan


title: PBMCs__SLE149A

description: PBMCs from SLE patient.

value: M

value: Other

value: SLEDAI 20


title: Chicken liver, fat (FL) versus lean (LL) lines, 11 week of age, replicate 4

description: Liver from fat (FL) and lean (LL) chickens, 11 week of age, replicate 4


title: FVB.LN.2

value: FVB

value: wild-type


title: PBMCs__SLE45_090902B

description: PBMCs from SLE patient.

value: 9 yrs, when sample taken.

value: AA

value: SLE

value: SLEDAI 16


title: PBMCs__SLE108A_061103

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: White

value: SLEDAI 10


title: Chicken liver, fat (FL) versus lean (LL) lines, 9 week of age, replicate 1

description: Liver from fat (FL) and lean (LL) chickens, 9 week of age, replicate 1


title: PBMCs__SLE113A

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: Asian

value: SLEDAI 24


title: FVB.MT.3

value: C3(1)/SV40 T/t-antigen


title: FVB.MT.4


title: FVB.LN.3


title: Chicken liver, fat (FL) versus lean (LL) lines, 11 week of age, replicate 3

description: Liver from fat (FL) and lean (LL) chickens, 11 week of age, replicate 3


title: Chicken liver, fat (FL) versus lean (LL) lines, 9 week of age, replicate 4

description: Liver from fat (FL) and lean (LL) chickens, 9 week of age, replicate 4


title: PBMCs__SLE36B 100501

description: PBMCs from SLE patient.

value: 16 yrs, when sample taken.

value: F

value: Hispanic


title: PBMCs__SLE35_110701B

description: PBMCs from SLE patient.

value: M

value: SLEDAI 8

value: Steroids PO and IV and Cellcept


title: PBMCs__SLE106_060203

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: SLEDAI 4

value: Steroids PO


title: FVB.MT.2

value: FVB


title: PBMCs__SLE31B_110602

description: PBMCs from SLE patient.

value: 8 yrs, when sample taken.

value: SLE


title: PBMCs__SLE27_020102B

description: PBMCs from SLE patient.

value: AA

value: SLEDAI 14

value: Steroids PO and Cytoxan


title: FVB.LN.1

value: wild-type


title: Chicken liver, fat (FL) versus lean (LL) lines, 7 week of age, replicate 2

description: Liver from fat (FL) and lean (LL) chickens, 7 week of age, replicate 2

tag: Liver LL cockerel, 7 week of age

tag: Liver FL cockerel, 7 week of age


title: PBMCs__SLE105_053003

description: PBMCs from SLE patient.

value: 12 yrs, when sample taken.

value: SLEDAI 16

value: Steroids PO, Cellcept


title: Chicken liver, fat (FL) versus lean (LL) lines, 7 week of age, replicate 4

description: Liver from fat (FL) and lean (LL) chickens, 7 week of age, replicate 4


title: FVB.MN.4

tag: Strain


title: FVB.MN.3

tag: Model


title: PBMCs__SLE21_030602B

description: PBMCs from SLE patient.

tag: Age

value: 10 yrs, when sample taken.

value: F

value: Hispanic

value: SLEDAI 12


title: PBMCs__SLE20_060603B

description: PBMCs from SLE patient.

tag: Gender


title: PBMCs__SLE100_050703

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

tag: Race

value: Steroids PO and IV


title: PBMCs__PPA1-4 020502A

description: PBMCs from PAPA patient.

source_name: PBMCs from PAPA patient.

value: 40 yrs, when sample taken.

value: M

value: White

tag: Illness

value: PAPA

value: Skin Involvement

value: Steroids PO


title: FVB.MN.2

value: FVB


title: PBMCs__SLE17B_103102

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: Asian

value: SLE

tag: Symptoms

value: SLEDAI 2


title: FVB.MN.1

value: wild-type


title: Chicken liver, fat (FL) versus lean (LL) lines, 5 week of age, replicate 4

description: Liver from fat (FL) and lean (LL) chickens, 5 week of age, replicate 4

tag: Liver LL cockerel, 5 week of age

tag: Liver FL cockerel, 5 week of age


title: Chicken liver, fat (FL) versus lean (LL) lines, 7 week of age, replicate 1

description: Liver from fat (FL) and lean (LL) chickens, 7 week of age, replicate 1


title: Chicken liver, fat (FL) versus lean (LL) lines, 7 week of age, replicate 3

description: Liver from fat (FL) and lean (LL) chickens, 7 week of age, replicate 3


title: Chicken liver, fat (FL) versus lean (LL) lines, 5 week of age, replicate 3

description: Liver from fat (FL) and lean (LL) chickens, 5 week of age, replicate 3


title: Chicken liver, fat (FL) versus lean (LL) lines, 9 week of age, replicate 3

description: Liver from fat (FL) and lean (LL) chickens, 9 week of age, replicate 3


title: PBMCs__SLE111_070303

description: PBMCs from SLE patient.

value: 15 yrs, when sample taken.

value: F

value: SLEDAI 18

tag: Treatment


title: C57.SVT.5

source_name: Seminal vesicle tumor

value: PB/SV40 T/t-antigen (TRAMP)

tag: Stratagene Universal Reference RNA


title: PBMCs__H46_111302

description: PBMCs from healthy patient.

source_name: PBMCs from healthy patient.

value: 5 yrs, when sample taken.

value: Healthy


title: PBMCs__H98A 010305

description: PBMCs from healthy patient.

value: 16 yrs, when sample taken.


title: FVB.MT.1

value: C3(1)/SV40 T/t-antigen


title: PBMCs__SLE114B

description: PBMCs from SLE patient.

value: AA

value: SLEDAI 14


title: C57.SVT.6


title: PBMCs__SLE121B_022704

description: PBMCs from SLE patient.

value: 12 yrs, when sample taken.

value: Hispanic

value: SLEDAI 10

value: Steroids PO


title: Chicken liver, fat (FL) versus lean (LL) lines, 3 week of age, replicate 2

description: Liver from fat (FL) and lean (LL) chickens, 3 week of age, replicate 2

tag: Liver LL cockerel, 3 week of age

tag: Liver FL cockerel, 3 week of age


title: C57.SVT.4


title: Chicken liver, fat (FL) versus lean (LL) lines, 3 week of age, replicate 4

description: Liver from fat (FL) and lean (LL) chickens, 3 week of age, replicate 4


title: Chicken liver, fat (FL) versus lean (LL) lines, 5 week of age, replicate 2

description: Liver from fat (FL) and lean (LL) chickens, 5 week of age, replicate 2


title: PBMCs__H42A 011705

description: PBMCs from healthy patient.

value: 9 yrs, when sample taken.

value: M


title: PBMCs__H45_092702

description: PBMCs from healthy patient.


title: C57.SVT.3


title: C57.SVT.2


title: PBMCs__H30_081402

description: PBMCs from healthy patient.

value: 10 yrs, when sample taken.


title: PBMCs__H36_082802A

description: PBMCs from healthy patient.

value: 7 yrs, when sample taken.

value: White


title: Chicken liver, fat (FL) versus lean (LL) lines, 5 week of age, replicate 1

description: Liver from fat (FL) and lean (LL) chickens, 5 week of age, replicate 1


title: PBMCs__SLE108B_061103

description: PBMCs from SLE patient.

value: 17 yrs, when sample taken.

value: F

value: SLE


title: C57.SVT.1

value: PB/SV40 T/t-antigen (TRAMP)


title: PBMCs__SLE149B

description: PBMCs from SLE patient.

value: 15 yrs, when sample taken.

value: Other

value: SLEDAI 20


title: PBMCs__SLE113B

description: PBMCs from SLE patient.

value: 13 yrs, when sample taken.

value: Asian

value: SLEDAI 24


title: PBMCs__SLE111B_070303

description: PBMCs from SLE patient.

value: Hispanic

value: SLEDAI 18


title: C57.SVN.4

source_name: Seminal vesicle normal

value: wild-type


title: PBMCs__SLE106_060203B

description: PBMCs from SLE patient.

value: 14 yrs, when sample taken.

value: AA

value: SLEDAI 4

value: Steroids PO


title: PBMCs__H28_Healthy_U133A

description: PBMCs from healthy patient.

value: 11 yrs, when sample taken.

value: Healthy


title: Chicken liver, fat (FL) versus lean (LL) lines, 3 week of age, replicate 3

description: Liver from fat (FL) and lean (LL) chickens, 3 week of age, replicate 3


title: Chicken liver, fat (FL) versus lean (LL) lines, 3 week of age, replicate 1

description: Liver from fat (FL) and lean (LL) chickens, 3 week of age, replicate 1


title: PBMCs__H37_Healthy_U133A

description: PBMCs from healthy patient.

value: 8 yrs, when sample taken.

value: F

value: White


title: Chicken liver, fat (FL) versus lean (LL) lines, 1 week of age, replicate 2

description: Liver from fat (FL) and lean (LL) chickens, 1 week of age, replicate 2

tag: Liver LL cockerel, 1 week of age

tag: Liver FL cockerel, 1 week of age


title: Chicken liver, fat (FL) versus lean (LL) lines, 1 week of age, replicate 4

description: Liver from fat (FL) and lean (LL) chickens, 1 week of age, replicate 4


title: PBMCs__SLE100_050703B

description: PBMCs from SLE patient.

value: SLE

value: Steroids PO and IV


title: C57.SVN.3


title: C57.SVN.1


title: PBMCs__H178_A

description: PBMCs from healthy patient.

value: 17 yrs, when sample taken.


title: PBMCs__PPA1-4 020502B

description: PBMCs from PAPA patient.

value: 40 yrs, when sample taken.

value: M

value: PAPA

value: Skin Involvement


title: Chicken liver, fat (FL) versus lean (LL) lines, 1 week of age, replicate 3

description: Liver from fat (FL) and lean (LL) chickens, 1 week of age, replicate 3


title: C57.SVN.2

value: wild-type


title: C57.PT.5

source_name: Gland prostate tumor

value: PB/SV40 T/t-antigen (TRAMP)


title: PBMCs__SLE105_053003B

description: PBMCs from SLE patient.

value: 12 yrs, when sample taken.

value: Hispanic

value: SLEDAI 16

value: Steroids PO, Cellcept


title: C57.PT.4


title: PBMCs__H98B 010305

description: PBMCs from healthy patient.

value: 16 yrs, when sample taken.

value: Healthy


title: PBMCs__H45_092702B

description: PBMCs from healthy patient.

value: F

value: AA


title: C57.PT.3


title: PBMCs__H166_A

description: PBMCs from healthy patient.

value: 14 yrs, when sample taken.


title: PBMCs__H176_Healthy_U133A

description: PBMCs from healthy patient.

value: 15 yrs, when sample taken.

value: White


title: PBMCs__H27_112202A

description: PBMCs from healthy patient.

value: 6 yrs, when sample taken.


title: PBMCs__H152_Healthy_U133A

description: PBMCs from healthy patient.


title: PBMCs__H46_111302B

description: PBMCs from healthy patient.

value: 5 yrs, when sample taken.


title: PBMCs__H42B 011705

description: PBMCs from healthy patient.

value: 9 yrs, when sample taken.

value: M


title: PBMCs__H150_Healthy_U133A

description: PBMCs from healthy patient.

value: 13 yrs, when sample taken.


title: C57.PT.2

value: PB/SV40 T/t-antigen (TRAMP)


title: C57.PT.1


title: PBMCs__H149A 011005

description: PBMCs from healthy patient.

value: 12 yrs, when sample taken.


title: PBMCs__H36_082802B

description: PBMCs from healthy patient.

value: 7 yrs, when sample taken.


title: PBMCs__H122_A

description: PBMCs from healthy patient.


title: C57.PN.4

source_name: Gland prostate normal

value: wild-type


title: PBMCs__H148A 011005

description: PBMCs from healthy patient.

value: 8 yrs, when sample taken.


title: PBMCs__H30_081402B

description: PBMCs from healthy patient.

value: 10 yrs, when sample taken.

value: Hispanic


title: C57.PN.3


title: C57.PN.2


title: PBMCs__H28_Healthy_U133B

description: PBMCs from healthy patient.

value: 11 yrs, when sample taken.

value: F

value: Healthy


title: C57.PN.1


title: PBMCs__H04_010902

description: PBMCs from healthy patient.


title: PBMCs__H27_112202B

description: PBMCs from healthy patient.


title: PBMCs__H37_Healthy_U133B

description: PBMCs from healthy patient.


title: PBMCs__H03A

description: PBMCs from healthy patient.

value: 14 yrs, when sample taken.


title: PBMCs__H176_Healthy_U133B

description: PBMCs from healthy patient.

value: 15 yrs, when sample taken.

value: White


title: PBMCs__H152_Healthy_U133B

description: PBMCs from healthy patient.


title: PBMCs__H178_B

description: PBMCs from healthy patient.

value: 17 yrs, when sample taken.


title: PBMCs__H150_Healthy_U133B

description: PBMCs from healthy patient.


title: PBMCs__H149B 011005

description: PBMCs from healthy patient.


title: PBMCs__H01A

description: PBMCs from healthy patient.


title: PBMCs__FRA1-8 022503A

description: PBMCs from PAPA patient.

value: 20 yrs, when sample taken.

value: PAPA

value: Enbrel, Celebrex


title: PBMCs__H166_B

description: PBMCs from healthy patient.


title: PBMCs__H148B 011005

description: PBMCs from healthy patient.


title: PBMCs__H122_B

description: PBMCs from healthy patient.


title: PBMCs__FRA1-4 112102A

description: PBMCs from PAPA patient.

value: 40 yrs, when sample taken.

value: M

value: Arthritis

value: Celebrex


title: PBMCs__FRA1-13 022503A

description: PBMCs from PAPA patient.

value: 68 yrs, when sample taken.


title: PBMCs__FRA1-10 022503A

description: PBMCs from PAPA patient.

value: Methotrexate, Streoids PO


title: PBMCs__FRA1-1 111302A

description: PBMCs from PAPA patient.

value: 13 yrs, when sample taken.

value: Skin Involvement

value: Remicade, Steroids IV, Norvasc, Methotrexate


title: PBMCs__H02_100202A

description: PBMCs from healthy patient.

value: F

value: Hispanic

value: Healthy


title: PBMCs__H03B

description: PBMCs from healthy patient.

value: 14 yrs, when sample taken.

value: White


title: PBMCs__H04_100902B

description: PBMCs from healthy patient.

value: 10 yrs, when sample taken.


title: PBMCs__H01B

description: PBMCs from healthy patient.

value: 8 yrs, when sample taken.


title: PBMCs__FRA1-4 112102B

description: PBMCs from PAPA patient.

value: PAPA


title: PBMCs__H02_100202B

description: PBMCs from healthy patient.


title: Susceptible Group, Ventral tegmental area, Biological Replicate 3

first: guanghua

last: xiao

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: University of Texas Southwestern Medical Center

description: Ventral tegmental area, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 16h at 55 degC

scan_protocol: l Using an Illumina scanner; Standard scan factor.

data_processing: The Raw data was exact using MS5, and Quantile-Quantile Normalized with Affy R package.

source_name: Mouse Ventral tegmental area

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 200ng of total RNA; IVT: 2h

extract_protocol: RNA was extracted with RNAeasy Microkit according to manufacturer protocols

tag: Midline, 1mm thick, 14 gauge punches, pooled together from four mice (4 total)


title: PBMCs__FRA1-8 022503B

description: PBMCs from PAPA patient.

value: 20 yrs, when sample taken.

value: Enbrel, Celebrex


title: PBMCs__FRA1-13 022503B

description: PBMCs from PAPA patient.


title: Non-defeated Control Group, Ventral tegmental area, Biological Replicate 3

description: Ventral tegmental area, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control


title: Non-defeated Control Group, Nucleus accumbens, Biological Replicate 3

description: Nucleus accumbens, male 10.5 week old c57bl/6J mouse, NON-DEFEATED control

source_name: Mouse Nucleus accumbens

tag: Bilateral, 1mm-thick, 15 gauge punches, pooled together from four mice (8 total)


title: Unsusceptible Group, Ventral tegmental area, Biological Replicate 3

description: Ventral tegmental area, male 10.5 week old c57bl/6J mouse, UNSUSCEPTIBLE group


title: Unsusceptible Group, Nucleus accumbens, Biological Replicate 3

description: Nucleus accumbens, male 10.5 week old c57bl/6J mouse, UNSUSCEPTIBLE group


title: PBMCs__FRA1-1 111302B

description: PBMCs from PAPA patient.

value: M


title: Unsusceptible Group, Nucleus accumbens, Biological Replicate 2


title: Susceptible Group, Ventral tegmental area, Biological Replicate 2


title: Susceptible Group, Nucleus accumbens, Biological Replicate 3

description: Nucleus accumbens, male 10.5 week old c57bl/6J mouse, SUSCEPTIBLE group


title: PBMCs__FRA1-10 022503B

description: PBMCs from PAPA patient.

value: 11 yrs, when sample taken.


title: Non-defeated Control Group, Nucleus accumbens, Biological Replicate 2


title: Unsusceptible Group, Ventral tegmental area, Biological Replicate 2


title: Unsusceptible Group, Nucleus accumbens, Biological Replicate 1


title: Non-defeated Control Group, Ventral tegmental area, Biological Replicate 1


title: Non-defeated Control Group, Ventral tegmental area, Biological Replicate 2


title: Susceptible Group, Nucleus accumbens, Biological Replicate 2


title: Unsusceptible Group, Ventral tegmental area, Biological Replicate 1


title: Susceptible Group, Ventral tegmental area, Biological Replicate 1


title: Non-defeated Control Group, Nucleus accumbens, Biological Replicate 1


title: 5uM thiuram 3rd

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

description: In order to rescue data that had a higher intensity than the scanning range, arrays were scanned twice with lower laser power, representing with “LOW” in the title line. Data from higher power scanning with flag value 0 were used for LOWESS normalization processing. Data from lower power scanning were used only for follow up.

hyb_protocol: Hybridized for 16-18 h at 65 C

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).

data_processing: GeneSpring ver 7.3.1 (Agilent Technologies Inc.)

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: 5uM thiuram treatment for 2 h, Cy5

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy5-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1. The exponential growing cells were exposed with 5 uM thiuram(final concentration) for 2 h.

extract_protocol: Hot-phenol& Oligotex-dT30 mRNA purification kit (TaKaRa, Otsu, Japan)

treatment_protocol: Stock solution of thiuram (Wako; 204-11371) was dissolved with 100% DMSO.

tag: strain S288C

source_name: control (without treatment for 2h), Cy3

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy3-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.

treatment_protocol: without treatment


title: 5uM thiuram 2nd


title: 5uM thiuram 1st


title: Cd 20uM 2nd

source_name: 20uM Cadmium chloride treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1. The exponential growing cells were exposed with 20uM Cd (final concentration) for 2 h.

treatment_protocol: Stock solution of cadmium chloride (Wako; 039-12342) was dissolved with sterilized water.


title: Rhesus-PMd-R-3

status: Public on Aug 31 2007

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description: Animal had been bred in group cages without any experimental treatments.

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: Data were analyzed using the RMA algorithm using the GeneSpring GX 7.3 software (Agilent Technologies).

organism: Macaca mulatta

source_name: PMd, right hemisphere

extract_protocol: The tissues were homogenized using a conventional rotor-stator homogenizer. Then total RNA was extracted from tissues using RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and was cleaned up using Qiagen RNeasy mini kit or Qiagen RNeasy MinElute kit (Qiagen).

treatment_protocol: Adequate measures were taken to minimize pain and discomfort, in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals (NIH publication no. 80-23). Monkeys were perfused with 500-1000 ml of ice-cold saline containing heparin sodium (1000 units/ml, Novo Heparin, Leo Pharmaceutical Products, Ballerup, Denmark) through the ascending aorta within 15 minutes after an overdose injection of pentobarbital sodium (50 mg/kg, i.p., Somnopentyl, Kyoritsu Shoji, Tokyo, Japan). The four neocortical areas (M1, PMd, PMv and A46) were determined from sulcal landmarks. We used the “forelimb region” of the M1 for the present analysis, which was located around the superior genu of the central sulcus. The PMd and PMv were taken from the caudal bank of upper and lower limbs of the arcuate sulcus and their convex regions rostral to the M1, respectively. A46 was taken from both the upper and lower bank of the principal sulcus. Each area from right and left hemisphere was dissected on crushed ice and was immediately frozen in liquid nitrogen.

value: female, Age; 2.7 years


title: Cd 20uM 1st


title: Rhesus-PMv-R-2

source_name: PMv, right hemisphere

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site

value: male, Age; 2.6 years


title: Cd 20uM 3rd


title: Rhesus-PMv-R-3


title: Rhesus-M1-R-1

source_name: M1, right hemisphere

value: male, Age; 2.7 years


title: Rhesus-PMd-R-1


title: Rhesus-PMd-L-1

source_name: PMd, left hemisphere


title: Rhesus-PMv-R-1


title: Rhesus-PMd-L-2


title: Rhesus-PMv-L-1

source_name: PMv, left hemisphere


title: Rhesus-A46-R-3

source_name: A46, right hemisphere


title: Rhesus-PMd-R-2


title: Rhesus-M1-R-3


title: Rhesus-M1-L-1

source_name: M1, left hemisphere


title: Rhesus-M1-L-2


title: Rhesus-PMd-L-3


title: Chicken liver, fat (FL) versus lean (LL) lines, 1 week of age, replicate 1

description: Liver from fat (FL) and lean (LL) chickens, 1 week of age, replicate 1


title: Rhesus-A46-L-2

source_name: A46, left hemisphere


title: Rhesus-M1-R-2


title: Rhesus-A46-R-2


title: Rhesus-M1-L-3


title: Rhesus-A46-L-3


title: Rhesus-PMv-L-3


title: Rhesus-PMv-L-2


title: Rhesus-A46-L-1


title: Rhesus-A46-R-1


title: sgkA OE - 0mM cis - biological replication 2 - technical replication2

city: Houston

first: Nancy

last: Van Driessche

address: One Baylor Plaza

institute: Baylor college of medicine

hyb_protocol: Labeled cDNA in PerfectHybTM Plus Hybridization buffer (SIGMA H-7033) was hybridized to the arrays after heat treatment (95°C, 2 min) using a GeneTAC hybridization station (Genomic Solutions) according to the manufacturer’s recommended protocol. Labeled cDNA was hybridized to the arrays using a GeneTAC automatic hybridization station (Genomic Solutions) for 2 hours at 65C.  Arrays were sequentially washed with 3 solutions, 2x SSC, 0.5% SDS; 0.5x SSC, 0.5% SDS; 0.1x SSC, for 30 sec at room temperature twice each.

scan_protocol: The arrays were scanned with a ScanArray5000 scanner (GSI Lumonics) according to the manufacturer’s recommended protocol.  PMT and Laser settings were not recorded.

data_processing: All images were processed with the Imagene software package.

organism: Dictyostelium discoideum

source_name: Total RNA from sgkA OE cells, treated with 0mM cisplatin labeled with Alexa647

label_protocol: Total RNA (10 µg) was mixed with 1 µg of labeled [dT(18)] primer in 13 µl of water, incubated at 70°C for 10 minutes and on ice for 2-5 minutes.  Reaction buffer (Gibco-BRL), 0.1M DTT, 0.5 mM of each dNTP and 200U Superscript II (Gibco-BRL) were added and the reaction was incubated at 42°C for 2 hours.  Experimental RNA samples were labeled with Cy5 primers and the reference RNA sample was labeled with Cy3.  Both of the primers were HPLC-purified by the manufacturer (Operon Technologies).  Reverse transcription reactions were terminated with 0.1M EDTA.  RNA was degraded by adding 0.3 N NaOH and incubating at 60°C for 20 minutes.  The reaction was neutralized with 0.4 M Tris.HCl pH7.6.  Labeled cDNA was purified by ethanol precipitation, resuspended in 10 µl of DDW and mixed with 130 µl of PerfectHybTM Plus Hybridization buffer (SIGMA H-7033).

growth_protocol: Cells were grown in shaking suspension in HL5 medium, with the appropriate supplements for auxotrophy or drug selection.

extract_protocol: 2x106 cells/ml cells (treated or untreated) were collected, resuspended in 1 ml TRIZOL reagent (Life Technologies) and total RNA was extracted according to the manufacturer’s protocol.  The RNA was resuspended in 20 mM MOPS (pH7.0) and its concentration was determined by spectrophotometry and verified by Northern blot analysis and staining with methylene blue, which also tested RNA integrity.

treatment_protocol: Exponentially growing cells (2x106 cells/ml) were divided into twelve 50 ml aliquots in 500 ml flasks. The cells were shaken for 30 min, 300 µM cisplatin was added to 6 cultures (PT buffer was added to the 6 controls), and the cells were shaken for 3 hr at 22C in the dark. Samples (1 ml) were drawn and assayed for viability. The remaining cells were washed with phosphate buffered saline (PBS) and resuspended in 1.0 ml TRIzol reagent (Life Technologies, Gaithersburg, MD) and RNA was extracted.

tag: sgkA OE

source_name: Total RNA from developed AX4 cells (0,3,6,12,17 and 24hours) labeled with Cyanine3

tag: strain


title: sgkA OE - 0mM cis - biological replication 2 - technical replication1


title: sgkA OE - 0mM cis - biological replication 1 - technical replication3


title: sgkA OE - 0mM cis - biological replication 1 - technical replication5


title: sgkA OE - 0mM cis - biological replication 1 - technical replication2


title: sgkA OE - 300mM cis - biological replication 1 - technical replication5

source_name: Total RNA from sgkA OE cells, treated with 300mM cisplatin labeled with Alexa647


title: sgkA OE - 300mM cis - biological replication 2 - technical replication3


title: sgkA OE - 300mM cis - biological replication 2 - technical replication4


title: sgkA OE - 300mM cis - biological replication 1 - technical replication2


title: sgkA OE - 0mM cis - biological replication 1 - technical replication4


title: sgkA OE - 0mM cis - biological replication 2 - technical replication5


title: sgkA OE - 300mM cis - biological replication 2 - technical replication5


title: sglA- - 0mM cis - biological replication 2 - technical replication4

source_name: Total RNA from sglA- cells, treated with 0mM cisplatin labeled with Alexa647

tag: sglA-


title: sglA- - 0mM cis - biological replication 1 - technical replication4


title: sglA- - 0mM cis - biological replication 1 - technical replication5


title: sglA- - 0mM cis - biological replication 2 - technical replication1


title: sglA- - 0mM cis - biological replication 2 - technical replication2


title: sgkA OE - 300mM cis - biological replication 2 - technical replication1


title: sgkA OE - 300mM cis - biological replication 2 - technical replication2


title: sgkA OE - 0mM cis - biological replication 2 - technical replication3


title: sglA- - 0mM cis - biological replication 2 - technical replication3


title: sgkA OE - 0mM cis - biological replication 1 - technical replication1


title: sglA- - 0mM cis - biological replication 2 - technical replication5


title: sgkA OE - 300mM cis - biological replication 1 - technical replication1


title: sgkA OE - 300mM cis - biological replication 1 - technical replication4


title: sglA- - 0mM cis - biological replication 1 - technical replication2


title: sgkA OE - 300mM cis - biological replication 1 - technical replication3


title: sglA- - 0mM cis - biological replication 1 - technical replication3


title: sglA- - 300mM cis - biological replication 2 - technical replication2

source_name: Total RNA from sglA- cells, treated with 300mM cisplatin labeled with Alexa647


title: Susceptible Group, Nucleus accumbens, Biological Replicate 1

source_name: Mouse Nucleus accumbens


title: sglA- - 300mM cis - biological replication 2 - technical replication1


title: sglA- - 300mM cis - biological replication 1 - technical replication5


title: sglA- - 300mM cis - biological replication 1 - technical replication4


title: sglA- - 300mM cis - biological replication 2 - technical replication4


title: AX4 - 0mM cis - biological replication 5 - technical replication5

source_name: Total RNA from AX4 cells, treated with 0mM cisplatin labeled with Alexa647


title: sglA- - 0mM cis - biological replication 1 - technical replication1


title: sglA- - 300mM cis - biological replication 2 - technical replication3


title: sglA- - 300mM cis - biological replication 2 - technical replication5


title: AX4 - 0mM cis - biological replication 6 - technical replication4


title: sglA- - 300mM cis - biological replication 1 - technical replication1


title: sglA- - 300mM cis - biological replication 1 - technical replication2


title: sglA- - 300mM cis - biological replication 1 - technical replication3


title: AX4 - 0mM cis - biological replication 6 - technical replication2


title: AX4 - 0mM cis - biological replication 6 - technical replication5


title: AX4 - 0mM cis - biological replication 6 - technical replication1


title: AX4 - 0mM cis - biological replication 4 - technical replication4


title: AX4 - 0mM cis - biological replication 5 - technical replication2


title: AX4 - 0mM cis - biological replication 4 - technical replication5


title: AX4 - 0mM cis - biological replication 6 - technical replication3


title: AX4 - 0mM cis - biological replication 5 - technical replication4


title: AX4 - 0mM cis - biological replication 4 - technical replication3


title: AX4 - 0mM cis - biological replication 5 - technical replication1


title: AX4 - 0mM cis - biological replication 3 - technical replication5


title: AX4 - 0mM cis - biological replication 5 - technical replication3


title: AX4 - 0mM cis - biological replication 4 - technical replication1


title: AX4 - 0mM cis - biological replication 3 - technical replication4


title: AX4 - 0mM cis - biological replication 3 - technical replication3


title: AX4 - 0mM cis - biological replication 4 - technical replication2


title: AX4 - 0mM cis - biological replication 2 - technical replication5


title: AX4 - 0mM cis - biological replication 3 - technical replication1


title: AX4 - 0mM cis - biological replication 2 - technical replication2


title: AX4 - 0mM cis - biological replication 1 - technical replication4


title: AX4 - 0mM cis - biological replication 2 - technical replication3


title: AX4 - 0mM cis - biological replication 3 - technical replication2


title: AX4 - 0mM cis - biological replication 1 - technical replication5


title: AX4 - 0mM cis - biological replication 2 - technical replication4


title: AX4 - 0mM cis - biological replication 1 - technical replication2


title: AX4 - 0mM cis - biological replication 2 - technical replication1


title: sgkA OE - 0mM cis - biological replication 2 - technical replication4


title: AX4 - 300mM cis - biological replication 6 - technical replication1

source_name: Total RNA from AX4 cells, treated with 300mM cisplatin labeled with Alexa647


title: AX4 - 300mM cis - biological replication 6 - technical replication2


title: AX4 - 300mM cis - biological replication 6 - technical replication3


title: AX4 - 300mM cis - biological replication 6 - technical replication4


title: AX4 - 300mM cis - biological replication 6 - technical replication5


title: AX4 - 300mM cis - biological replication 5 - technical replication1


title: AX4 - 0mM cis - biological replication 1 - technical replication3


title: AX4 - 300mM cis - biological replication 4 - technical replication3


title: AX4 - 0mM cis - biological replication 1 - technical replication1


title: AX4 - 300mM cis - biological replication 4 - technical replication5


title: AX4 - 300mM cis - biological replication 3 - technical replication5


title: AX4 - 300mM cis - biological replication 5 - technical replication4


title: AX4 - 300mM cis - biological replication 4 - technical replication1


title: AX4 - 300mM cis - biological replication 4 - technical replication4


title: AX4 - 300mM cis - biological replication 5 - technical replication5


title: AX4 - 300mM cis - biological replication 4 - technical replication2


title: AX4 - 300mM cis - biological replication 5 - technical replication3


title: AX4 - 300mM cis - biological replication 5 - technical replication2


title: AX4 - 300mM cis - biological replication 3 - technical replication4


title: AX4 - 300mM cis - biological replication 3 - technical replication1


title: AX4 - 300mM cis - biological replication 3 - technical replication2


title: AX4 - 300mM cis - biological replication 2 - technical replication5


title: AX4 - 300mM cis - biological replication 3 - technical replication3


title: AX4 - 300mM cis - biological replication 2 - technical replication2


title: Prologued aerobic glucose limited chemostat culture D=0.1/h - 2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade et al., 2004; Piper et al., 2002). Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008 Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138

data_processing: MAS5.0 calculated intensity with global array targetting at 150

label: Biotinylated dUTP - streptavidine Phycoerythrin (SAPE)

source_name: Prologued aerobic glucose limited chemostat culture 200 generations old

growth_protocol:
Media.
Synthetic medium containing mineral salts and vitamins was prepared and sterilized as described by Verduyn et al. (1992). For chemostat cultivation, the glucose concentration in reservoir media was 7·5 g l–1 (0·25 mol C l–1). This medium composition has previously been demonstrated to sustain glucose-limited cultivation of S. cerevisiae CEN.PK113-7D (Lange & Heijnen, 2001; Verduyn et al., 1992). For batch cultivation, the initial glucose concentration was 20 g l–1.
Chemostat cultivation.
Aerobic chemostat cultivation was performed at a dilution rate of 0·10 h–1 at 30 °C in 1·5 l laboratory fermenters (Applikon) at a stirrer speed of 800 r.p.m. The working volume of the cultures was kept at 1·0 l by a peristaltic effluent pump coupled to an electrical level sensor. This set-up ensured that under all growth conditions, biomass concentrations in samples taken directly from the culture differed by <1 % from those in samples taken from the effluent line . The exact working volume was measured after each experiment. The pH was kept at 5·0±0·1 by an ADI 1030 biocontroller (Applikon), via the automatic addition of 2 mol KOH l–1. The fermenter was flushed with air at a flow rate of 0·5 l min–1 using a Brooks 5876 mass-flow controller. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (model 34 100 3002; Ingold), and it remained above 60 % of air saturation. Chemostat cultures were routinely checked for potential bacterial and fungal infection by phase-contrast microscopy.
Verduyn, C., Postma, E., Scheffers, W. A. & van Dijken, J. P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts: a continuous study on regulation of respiration and alcoholic fermentation. Yeast 8, 501–517

extract_protocol: Cells were rapidly (within 3 s) transferred from the chemostat culture into liquid nitrogen to immediately quench the metabolism. The frozen cell suspension (about 40 g cell broth) was thawed gently on ice. After complete thawing, the cell suspension was centrifuged at 0 °C, 5000 g, for 5 min. Total RNA extraction from the pellets was performed using the hot-phenol method

treatment_protocol: Liquid nitrogen quenching

tag: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. Kötter, Frankfurt, Germany


title: Ethanol limited chemostat D=0.1/h -3

hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip® microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001–37008

source_name: ethanol limited aerobic chemostat culture

growth_protocol:
Strain and Growth Conditions—Wild-type S. cerevisiae strain CEN.PK113–7D (MATa) (1) was grown at 30 °C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in Ref. 2.  Cultures were fed with a defined mineral medium that limited growth by glucose, ethanol, acetate, or maltose with all other growth requirements in excess. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm, and the airflow was 0.5 liters_min-1. Dissolved oxygen tension was measured online with an Ingold model 34-100-3002 probe, and was between 60 and 75% of air saturation. The off-gas was cooled by a condenser connected to a cryostat set at 2 °C and analyzed as previously described (3). Steady-state samples were taken after 10–14 volume changes to avoid strain adaptation caused by long term cultivation (4).
Media—The defined mineral medium composition was based on that described by Verduyn et al. (5). The carbon source was 256 mmol
of carbon/liter.
1. Pronk, J. T., Wenzel, T. J., Luttik, M. A. H., Klaassen, C. C. M., Scheffers, W. A., and van Dijken, J. P. (1994) Microbiology 140, 601–610
2. van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959
3. van Maris, A. J. A., Luttik, M. A. H., Winkler, A. A., van Dijken, J. P., and Pronk, J. T. (2003) Appl. Environ. Microbiol. 69, 2094–2099
4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9721–9726
5- Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1992) Yeast 8, 501–517

treatment_protocol: liquid nitrogen quenching

tag: Prototrophic S. cerevisiae strain CEN.PK113–7D (MATa)


title: Ethanol limited chemostat D= 0.1 /h -2

scan_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip® microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001–37008

source_name: Ethanol limited aerobic chemostat culture


title: Maltose limited chemostat culture D= 0.1/h -2

hyb_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008

source_name: Aerobic maltose limited chemostat culture

growth_protocol:
Strain and Growth Conditions Wild-type S. cerevisiae strain CEN.PK113-7D (MATa) (1) was grown at 30 Â°C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in Ref. 2.  Cultures were fed with a defined mineral medium that limited growth by glucose, ethanol, acetate, or maltose with all other growth requirements in excess. The dilution rate was set at 0.10 h-1. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm, and the airflow was 0.5 liters_min-1. Dissolved oxygen tension was measured online with an Ingold model 34-100-3002 probe, and was between 60 and 75% of air saturation. The off-gas was cooled by a condenser connected to a cryostat set at 2 Â°C and analyzed as previously described (3). Steady-state samples were taken after 10-14 volume changes to avoid strain adaptation caused by long term cu
 ltivation (4).
	Media The defined mineral medium composition was based on that described by Verduyn et al. (5). The carbon source was 256 mmol
of carbon/liter.
	1. Pronk, J. T., Wenzel, T. J., Luttik, M. A. H., Klaassen, C. C. M., Scheffers, W. A., and van Dijken, J. P. (1994) Microbiology 140, 601-610
	2. van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959
	3. van Maris, A. J. A., Luttik, M. A. H., Winkler, A. A., van Dijken, J. P., and Pronk, J. T. (2003) Appl. Environ. Microbiol. 69, 2094-2099
	4. Ferea, T. L., Botstein, D., Brown, P. O., and Rosenzweig, R. F. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9721-9726
	5- Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1992) Yeast 8, 501-517

tag: Prototrophic S. cerevisiae strain CEN.PK113â€“7D (MATa)


title: Maltose limited chemostat culture  D=0.1/h -3

scan_protocol: Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays were performed as described previously (6) 6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008


title: Aerobic nitrogen limited chemostat culture with 79% CO2 D=0.1/h -1

hyb_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).

source_name: Steady state Aerobic nitrogen limited chemostat culture with 79% CO2

growth_protocol:
Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described by Verdyun (1992) with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
 For CO2-enriched aerobic cultivation, cultures were sparged with a defined gas mixture containing 79% CO2 and 21% O2 (HoekLoos, Schiedam, The Netherlands).

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D [18] was used for this study


title: Prolongued aerobic glucose limited chemostat culture D=0.1/h -3

scan_protocol: The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade et al., 2004; Piper et al., 2002). Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008 Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138

source_name: Prolongued aerobic glucose limited chemostat culture 200 generations old

tag: The haploid, prototrophic S. cerevisiae strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from Dr P. Kötter, Frankfurt


title: Aerobic nitrogen limited chemostat culture with 79% CO2 D=0.1/h -3

scan_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D was used for this study


title: Maltose limited chemostat culture D =0.1/h -1

source_name: Aerobic maltose limited chemostat

label_protocol:
Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays were performed as described previously (6)
6- Piper, M. D. W., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S.,Nielsen, J., and Pronk, J. T. (2002) J. Biol. Chem. 277, 37001-37008


title: Anaerobic glucose limited chemostat culture with 100% CO2 D=0.1/h -3

source_name: steady state Anaerobic glucose limited chemostat culture with 100% CO2

label_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).

growth_protocol:
Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described [20] with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
 For CO2-enriched anaerobic cultivation, the nitrogen sparging gas was replaced by pure (>99.99%) CO2 (HoekLoos, Schiedam, The Netherlands).


source_name: Steady state Anaerobic glucose limited chemostat culture with 100%CO2

extract_protocol: One hundred millilitres of culture was sampled directly from the fermentor into a beaker containing 200–300 ml of liquid nitrogen and then processed . Total RNA was extracted with phenol/chloroform. mRNA extraction, cDNA synthesis and labelling, as well as array hybridisation against Affymetrix YG-S98 GeneChips® was performed as described in the Affymetrix user’s manual. Data acquisition was performed using the software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0 (Affymetrix, Santa Clara, CA, USA).


title: Prologued aerobic glucose limited chemostat culture  D=0.1/h - 1

source_name: Prologued aerobic glucose limited chemostat culture  200 generation old

label_protocol:
The results for each growth condition were derived from three independently cultured replicates. Sampling of cells from chemostats, probe preparation, and hybridization to Affymetrix GeneChip microarrays, as well as data acquisition and analysis, were performed as previously described (Daran-Lapujade et al., 2004; Piper et al., 2002).
Piper, M. D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. & Pronk, J. T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277, 37001–37008
Daran-Lapujade, P., Jansen, M. L., Daran, J. M., Van Gulik, W., de Winde, J. H. & Pronk, J. T. (2004). Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae: a chemostat culture study. J Biol Chem 279, 9125–9138

tag: The haploid, prototrophic S. cerevisiae

tag: strain CEN.PK113-7D (MATa MAL2-8c SUC2) was obtained from

tag: Dr P. Ko¨tter, Frankfurt, Germany. Precultures were grown to stationary

tag: phase in shake-flask cultures of synthetic medium , adjusted to pH 6?0 and containing 2% (w/v) glucose.

tag: After adding sterile glycerol (30 %, v/v), 2 ml aliquots were stored

tag: in sterile vials at 280 uC. These frozen stock cultures were used to

tag: inoculate precultures for chemostat cultivation.


title: Aerobic glucose limited chemostat culture with 79% CO2 D=0.1/h -3

source_name: Steady state Aerobic glucose limited chemostat culture with 79% CO2

growth_protocol:
Cells were grown at 30 °C in laboratory fermenters (Applikon, Schiedam, The Netherlands) with a working volume of 1 l as described in . Cultures were fed with a defined synthetic medium that was designed to allow for steady-state growth limited by either carbon or nitrogen, with all other requirements in excess and at a constant residual concentration. The dilution rate was set to 0.10 h−1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2-M KOH with the use of an Applikon ADI 1030 Biocontroler. Stirrer speed was 800 rpm, and the gas flow was 0.5 l min−1.
Synthetic media were prepared as described [20] with the following modifications: for carbon-limited cultivation, the medium contained 5.0 g l−1 of (NH4)2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and either 7.5 g l−1 of glucose or 5.76 g l−1 of ethanol. For nitrogen-limited cultures, 1.0 g l−1 of (NH4)2SO4, 5,3 g l−1 of K2SO4, 3.0 g l−1 of KH2PO4, 0.5 g l−1 of MgSO4 · 7H2O, and the necessary glucose to keep the residual glucose concentration at 18 g l−1 (59 and 62.2 g l−1 for the CO2-untreated and -treated cultures, respectively). This was done to avoid differences in the degree of glucose repression.
 For CO2-enriched aerobic cultivation, cultures were sparged with a defined gas mixture containing 79% CO2 and 21% O2 (HoekLoos, Schiedam, The Netherlands).


title: Aerobic glucose limited chemostat culture with 79% CO2 D=0.1/h -1

source_name: Steady stateAerobic glucose limited chemostat culture with 79% CO2

tag: The prototrophic S. cerevisiae strain CEN.PK113-7D was used for this study.