title: Oregon 10

status: Public on Mar 26 2008

city: Columbia

first: Sean

middle: P

last: Place

state: SC

address: 715 Sumter St.

department: Biological Sciences

institute: University of South Carolina

hyb_protocol: Samples were brought to a final volume of 45 µl in 25 mM Hepes, 0.75 mg/ml tRNA (Sigma, St. Louis MO, USA), 3X SSC, and 0.2% SDS. Samples were boiled for 1 min, allowed to cool to room temperature, and then applied to microarray slides. Hybridizations were conducted overnight at 65°C in hybridization chambers (Genetix, Boston, MA, USA). After hybridization, slides were washed gently by immersion in 1X SSC and 0.1% SDS for 10 min at 45 °C with gentle agitation to remove unbound dye. Slides were then washed gently in 0.1X SSC for 10 min at RT, dipped 5X in 0.06X SSC wash solution, and dried by centrifugation at 600 RPM for 5 min.

scan_protocol: The slides were scanned on an AXON GenePix 4000B microarray scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA). Intensity data were extracted using GenePix Pro 4.0 software and the ratio of Cy5 to Cy3 fluorescence was quantified for each spot on the arrays.

data_processing: Spatial and intensity based trends in the data were removed by Lowess normalization using Acuity 4.0 software.

organism: Mytilus californianus

source_name: Ref RNA pool

label_protocol: Ten µg of total RNA was reverse transcribed (RT) to cDNA, using anchored oligo(dT15) primers and amino-allyl dUTP. The RNA template was removed from the RT reactions by incubating at 70°C for 15 min in 0.2 mM NaOH and 0.1 mM EDTA. Single stranded cDNA was EtOH precipitated at -20 °C for 1h, washed once with 70 % EtOH, and re-suspended in 10 µl sodium bicarbonate (pH 9.0). Each sample was labeled with cyanine monoreactive dye (GE Healthcare, Piscataway, NJ, USA), prepared in 100 µl of dimethylsulfoxide (DMSO). cDNA was incubated with 5 µl of dye for 1h at room temperature in the dark. The fluorescently labeled cDNAs were cleaned by passing over PCR purification columns (Qiagen, Valencia, CA, USA) and eluted in 33 µl of dH2O.

extract_protocol: Total RNA from approximately 100 mg of frozen tissue was extracted using TRIzol® (Invitrogen, Carlsbad, CA, USA) following the manufactures recommendations. Following isolation of total RNA, the RNA was further cleaned by resuspending the RNA in 0.1 ml of DEPC treated water and adding 0.3 ml of 6 M guanidine HCl and 0.2 ml of 100% EtOH. The entire volume was loaded onto a spin column (Ambion, Austin, TX, USA) and centrifuged for 1 min at 12,000 x g at 4°C. Flow-through was discarded, and filters were washed 2X with 0.2 ml 80% EtOH. RNA was eluted off of the filters 2X with 0.1 ml of DEPC treated water. RNA was precipitated by the addition of 0.1 vol of 3 M sodium acetate (pH 5.0) and 2.5 vol of 100% EtOH, mixed by inversion of tubes and placed at -80°C for 1h. After this period, tubes were centrifuged at 12,000 x g for 20 min at 4°C. Pellets were washed 2X with 80% EtOH and resuspended in 30 µl of DEPC treated water. Final RNA concentrations were determined using a ND-1000 UV/visible spectrometer (NanoDrop Technologies, Wilmington, DE, USA). Only RNA samples with a 260:280 ratio of ≥ 1.9 were used for this analysis.

tag: Total RNA pooled from gill tissue isolated from 10 lab acclimated mussels

source_name: Oregon gill sample 5 dye swap

tag: Field Acclimatized gill tissue. Collected at low tide from individuals with a minimum/ maximum shell length of 40 – 60 mm.


title: Day-3Gel-Exp6

status: Public on Mar 28 2008

type: RNA

city: Santiago

first: Dario

last: Sepulveda

state: RM

address: Beacuhef 861

department: Chemical Engineering and Biotechnology

country: Chile

institute: Universidad de Chile

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_3_BiolRep2

hyb_protocol: Agilent 60-mer oligo microarray processing protocol

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2565BA Agilent’s Feature Extraction software (G2567AA, version 7.2) was used to identify spot and feature outliers. Spot quality was assessed and, if not discarded, multiple spots of the same gene were averaged (geometric mean).

data_processing: SNNLERM-algorithm was used to calculate normalized signal intensity ratios and confidence levels

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cell, gelatin coating, day 3

label_protocol: Low RNA input Fluorescent linear amplification kit

growth_protocol: Standard growth protocol.

extract_protocol: Total Rna Isolation mini-kit from Agilent

treatment_protocol: medium used was ES-Diff (Same as ES-MEM but without sodium pyruvate and without LIF). Three conditions were used for cell differentiation: Embryoid Body (EB) formation, where the cells were cultured in non-adherent plastic dishes, Gelatin coated plates (GEL) where cells were cultured on plates coated with a solution at 0.1% gelatin and Matrigel coated plates (MAT) where the plates were treated with a 0.1% protein Matrigel

tag: differentiation on a gelatin coated plate

growth_protocol: cells were cultured on gelatin-coated flasks in ES-MEM medium (DMEM high glucose, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 mM 2-ME, 2 mM L-glutamine, 15% fetal bovine serum, penicillin/streptomycin 50 mg/ml each, and 1000 U LIF/ml). All  cell cultures were carried out in a humidified incubator at 37ºC with 5% CO2

tag: total RNA was pooled from R1 cells differentiating with embryoid body formation protocol. Samples of equal amounts of RNA from days 1 through 7 were mixed, and this was used as REFERENCE RNA.


title: British Columbia 2

country: USA

source_name: British Columbia gill sample 2


title: British Columbia 3

source_name: British Columbia gill sample 3


title: British Columbia 1

source_name: British Columbia gill sample 1


title: British Columbia 4

source_name: British Columbia gill sample 4


title: British Columbia 5

source_name: British Columbia gill sample 5


title: British Columbia 9

source_name: British Columbia gill sample 4 dye swap


title: British Columbia 7

source_name: British Columbia gill sample 2 dye swap


title: British Columbia 6

source_name: British Columbia gill sample 1 dye swap


title: British Columbia 10

source_name: British Columbia gill sample 5 dye swap


title: Oregon 9

source_name: Oregon gill sample 4 dye swap


title: British Columbia 8

source_name: British Columbia gill sample 3 dye swap


title: Day-5Gel-Exp1

description: R1_Embryonic_Stem_Cell_Gelatin_Coating_plate_Day_5

source_name: embryonic stem cell, gelatin coating, day 5


title: Oregon 8

source_name: Oregon gill sample 3 dye swap


title: Day-3Mat-Exp1

description: R1_Embryonic_Stem_Cell_Matrigel_Coating_plate_Day_3

source_name: embryonic stem cell, Matrigel coating, day 3

tag: differentiation on a Matrigel coated plate


title: Oregon 4

source_name: Oregon gill sample 4

source_name: Ref RNA pool


title: Oregon 7

source_name: Oregon gill sample 2 dye swap


title: Oregon 5

source_name: Oregon gill sample 5


title: Oregon 3

source_name: Oregon gill sample 3


title: Oregon 6

source_name: Oregon gill sample 1 dye swap


title: Oregon 2

source_name: Oregon gill sample 2


title: California 7

source_name: California gill sample 2 dye swap


title: California 3

source_name: California gill sample 3


title: Baja 10

extract_protocol: Total RNA from approximately 100 mg of frozen tissue was extracted using TRIzol® (Invitrogen, Carlsbad, CA, USA) following the manufactures recommendations. Following isolation of total RNA, the RNA was further cleaned by resuspending the RNA in 0.1 ml of DEPC treated water and adding 0.3 ml of 6 M guanidine HCl and 0.2 ml of 100% EtOH. The entire volume was loaded onto a spin column (Ambion, Austin, TX, USA) and centrifuged for 1 min at 12,000 x g at 4°C. Flow-through was discarded, and filters were washed 2X with 0.2 ml 80% EtOH. RNA was eluted off of the filters 2X with 0.1 ml of DEPC treated water. RNA was precipitated by the addition of 0.1 vol of 3 M sodium acetate (pH 5.0) and 2.5 vol of 100% EtOH, mixed by inversion of tubes and placed at -80°C for 1h. After this period, tubes were centrifuged at 12,000 x g for 20 min at 4°C. Pellets were washed 2X with 80% EtOH and resuspended in 30 µl of DEPC treated water. Final RNA concentrations were determined using a ND-1000 UV/visible spectrometer (NanoDrop Technologies, Wilmington, DE, USA). Only RNA samples with a 260:280 ratio of ≥ 1.9 were used for this analysis. Total RNA extracted the gill tissue of 10 individuals was pooled for use as a source of reference RNA.

source_name: Baja gill sample 5 dye swap


title: California 4

source_name: California gill sample 4


title: California 6

source_name: California gill sample 1 dye swap


title: Oregon 1

source_name: Oregon gill sample 1


title: California 5

source_name: California gill sample 5


title: California 10

source_name: California gill sample 5 dye swap


title: California 8

source_name: California gill sample 3 dye swap


title: California 1

source_name: California gill sample 1


title: Baja 9

source_name: Baja gill sample 4 dye swap


title: California 9

source_name: Ref RNA pool

source_name: California gill sample 4 dye swap


title: Lung 0.5DE/saline rep4

city: carrboro

first: Tina

last: Stevens

state: NC

address: 138 marlowe ct

institute: UNC

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse 430A gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: biotin

source_name: lung, 500 ug/m3 DE for 4hr/day for 5 days and saline for 3 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA from frozen lung tissue was isolated using Rneasy (Qiagen, Valencia,CA) following manufacture's protocol.

tag: Female BALB/c 6-8 weeks


title: Baja 8

source_name: Baja gill sample 3 Dye swap


title: Baja 7

source_name: Baja gill sample 2 dye swap


title: Lung 0.5DE/saline rep3


title: Lung 2.0DE/saline rep1

source_name: lung, 2000 ug/m3 DE for 4hr/day for 5 days and saline for 3 days


title: Baja 5

source_name: Baja gill sample 5

source_name: REF RNA pool

tag: Gill tissue of 10 individuals collected from Santa Barbara, CA were lab acclimated at 13°C for 3 weeks but otherwise untreated, and pooled for use as a source of reference RNA.


title: Baja 6

source_name: Baja gill sample 1 dye swap


title: Lung 2.0DE/saline rep3


title: Baja 4

source_name: Baja gill sample 4


title: Lung 2.0DE/saline rep4


title: Baja 3

source_name: Baja gill sample 3


title: Lung Air/saline rep4

source_name: lung, filtered air  for 4hr/day for 5 days and saline for 3 days


title: Lung 0.5DE/saline rep1


title: Lung 0.5DE/saline rep2


title: Lung Air/saline rep3


title: Baja 1

scan_protocol: The slides were scanned on an AXON GenePix 4000B microarray scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).  Intensity data were extracted using GenePix Pro 4.0 software and the ratio of Cy5 to Cy3 fluorescence was quantified for each spot on the arrays.

data_processing: spatial and intensity based trends in the data were removed by Lowess normalization using Acuity 4.0 software.

source_name: Baja gill sample 1

extract_protocol: Total RNA from approximately 100 mg of frozen tissue was extracted using TRIzol® (Invitrogen, Carlsbad, CA, USA) following the manufactures recommendations.  Following isolation of total RNA, the RNA was further cleaned by resuspending the RNA in 0.1 ml of DEPC treated water and adding 0.3 ml of 6 M guanidine HCl and 0.2 ml of 100% EtOH. The entire volume was loaded onto a spin column (Ambion, Austin, TX, USA) and centrifuged for 1 min at 12,000 x g at 4°C. Flow-through was discarded, and filters were washed 2X with 0.2 ml 80% EtOH. RNA was eluted off of the filters 2X with 0.1 ml of DEPC treated water. RNA was precipitated by the addition of 0.1 vol of 3 M sodium acetate (pH 5.0) and 2.5 vol of 100% EtOH, mixed by inversion of tubes and placed at -80°C for 1h. After this period, tubes were centrifuged at 12,000 x g for 20 min at 4°C. Pellets were washed 2X with 80% EtOH and resuspended in 30 µl of DEPC treated water. Final RNA concentrations were determined using a ND-1000 UV/visible spectrometer (NanoDrop Technologies, Wilmington, DE, USA). Only RNA samples with a 260:280 ratio of ≥ 1.9 were used for this analysis.

tag: Field collected gill tissue from mussels collected at low tide. minimum/ maximum shell length of 40 – 60 mm

source_name: REF pool RNA


title: Lung Air/saline rep2


title: Lung 2.0DE/saline rep2


title: Lung 2.0DE/OVA rep4

source_name: lung, 2000 ug/m3 DE for 4hr/day for 5 days and 100 ug OVA for 3 days


title: Lung 0.5DE/OVA rep4

source_name: lung, 500 ug/m3 DE for 4hr/day for 5 days and 100 ug OVA for 3 days


title: Lung 0.5DE/OVA rep3


title: Lung 2.0DE/OVA rep2


title: Lung 0.5DE/OVA rep2


title: Baja 2

source_name: Baja gill sample 2


title: Lung Air/saline rep1


title: Lung 2.0DE/OVA rep3


title: E3.5 embryo ratio to E2.5

status: Public on Mar 25 2008

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: mouse embryos at different stages to identify genes during the development of ICM, TE, and PrE

hyb_protocol: Labelled probes were hybridised according to Wigle et al. (2002).

scan_protocol: Slides were scanned with a Genepix Axon 4000 microarray scanner.

data_processing: Spot intensities were quantified and median back ground corrected with the supplied Genepix software and exported as tables. Duplicate samples were analyzed and probe spot intensities were averaged. Expression data was set as a log2 ratio of the genes expression relative to E2.5.

source_name: mRNA from mouse embryo E3.5

label_protocol: SMART (Clontech) reverse transcription and PCR were adapted for each developmental stage to amplify cDNAs. To generate probes for array hybridization, 1 microgram of cDNA was labeled by incorporation of either Cy5 or Cy3-dCTP during random hexamer-primed primer extension in the presence of Klenow DNA polymerase (Roche) according to Livesey et al. (2000)

growth_protocol: ICR embryos were collected by flushing the oviduct for stages 2.5, or the uterus for stages 3.5. Stages 4.5 and older were dissected from the uterus. None of the vaginal plug was considered as E0.5.

extract_protocol: Embryos from the different stages were pooled for mRNA extraction with the Micro-Fast Track isolation kit (Invitrogen, 45-0036). Three independent pools (for three independant experiments) were made for each stage, in average 106 embryos at E2.5, 61 at E3.5, 47 at E4.5, 28 at E4.8, 17 at E5.5 and 19 at E6.5.

treatment_protocol: The embryos were not chemically treated in any way

tag: ICR timed mated

source_name: mRNA from mouse embryo E2.5


title: E4.5 embryo ratio to E2.5

source_name: mRNA from mouse embryo E4.5


title: Lung 2.0DE/OVA rep1


title: Lung Air/OVA rep2

source_name: lung, filtered air for 4hr/day for 5 days and 100 ug OVA for 3 days


title: Lung Air/OVA rep1

source_name: lung, filtered air  for 4hr/day for 5 days and 100 ug OVA for 3 days


title: Lung Air/OVA rep4


title: E6.0 embryo ratio to E2.5

source_name: mRNA from mouse embryo E6.0


title: Lung 0.5DE/OVA rep1


title: E4.75 embryo ratio to E2.5

source_name: mRNA from mouse embryo E4.75


title: TG hippocampus 4/WT hippocampus 3 (LGTC)

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Hybridization in SSC/SDS buffer at 55C in GeneTac hybstation

scan_protocol: Agilent scanner

data_processing: Loess normalization (limma)

source_name: Hippocampus DLCK transgenic mice / Hippocampus WT mice

label_protocol: Amplification with Ambion's MessageAmp kit with aa-UTP incorporation and subsequent coupling to GE Healthcare succinimidyl ester-modifed Cy3 and Cy5 dyes

extract_protocol: Trizol

tag: Male C57/BL6j


title: TG hippocampus 2/WT hippocampus 1 (LGTC)


title: WT hippocampus 1/TG hippocampus 4 (LGTC)

source_name: Hippocampus WT mice / Hippocampus DLCK transgenic mice


title: WT hippocampus 6/TG hippocampus 1 (LGTC)


title: TG hippocampus 5/WT hippocampus 6 (Agilent)

hyb_protocol: Default Agilent hybridization protocol


title: TG hippocampus 4/WT hippocampus 3 (Agilent)


title: TG hippocampus 1/WT hippocampus 5 (LGTC)


title: WT hippocampus 6/TG hippocampus 1 (Agilent)


title: TG hippocampus 2/WT hippocampus 1 (Agilent)


title: WT hippocampus 5/TG hippocampus 3 (LGTC)


title: WT hippocampus 4/TG hippocampus 2 (LGTC)


title: TG hippocampus 3/WT hippocampus 4 (Agilent)


title: TG hippocampus 5/WT hippocampus 6 (LGTC)


title: WT hippocampus 5/TG hippocampus 3 (Agilent)


title: TG hippocampus 3/WT hippocampus 4 (LGTC)


title: WT hippocampus 4/TG hippocampus 2 (Agilent)


title: WT hippocampus 3/TG hippocampus 5 (Agilent)


title: TG hippocampus 1/WT hippocampus 5 (Agilent)


title: WT hippocampus 1/TG hippocampus 4 (Agilent)


title: MCF10_3

status: Public on Mar 24 2008

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: Human breast cell line MCF10, cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

hyb_protocol: Hybridization was performed in 4x standard saline citrate, 1x bovine serum albumin, 2 µg/ml DNAs, and 0.1% sodium dodecyl sulphate at 42°C for 15 hours.

scan_protocol: Slides were washed, dried and then scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) at wavelengths of 635 and 532 nm for Cy5 and Cy3 dyes, respectively.

data_processing: To obtain 10-m resolution images, which were quantified using the GenePix Pro 4.0 program (Axon Instruments Inc., Union City, CA).

organism: Homo sapiens

source_name: MCF10 CONFLUENT DYE-CY3

extract_protocol: Total RNA was isolated using Rneasy Midi Kit (Qiagen, Hilden, Germany) as indicated by the manufacturer

tag: MCF10 growths at confluent

source_name: MCF10 SPARSE DYE-CY5

tag: SPARSE MCF10 cells


title: MCF10_3R

label_protocol: Hybridization was performed in 4x standard saline citrate, 1x bovine serum albumin, 2 µg/ml DNAs, and 0.1% sodium dodecyl sulphate at 42°C for 15 hours.


title: MCF10_2R


title: MCF10_2

label_protocol: dye swap


title: Nitrosomonas europaea_exposure to 1 uM CdCl2_60min_biological rep3.

status: Public on Mar 22 2008

city: Corvallis

first: Sunhwa

last: Park

state: OR

address: 116 Gilmore

department: Biological & Ecological Eng.

institute: Oregon State University

description: the activity of nitrosomonas europaea was inhibited about more than 50% by 1 uM CdCl2.

hyb_protocol: 0.16 ug/ul of six cDNA samples (three controls and three treatments) were hybridized at 60 rpm for 16 h to zebrafish genome array.

scan_protocol: The arrays were scanned using Affymetrix GeneChip Scanner 3000 at 570 nm.

data_processing: The data was analyzed with single array analysis in GeneChip Operating Software (GCOS)

organism: Nitrosomonas europaea

source_name: N. europaea cultured in batch reactor with 50 mM HEPES buffer and 5 mM total ammonia source, exposure to 1 uM CdCl2, 60 min

label_protocol: The 3’termini of the cDNA fragmentation were labeled with 7.5 mM GeneChip DNA labeling reagent (Affymetrix).

growth_protocol: (NH4)2SO4 (5 mM) in 50 mM HEPES buffer, 700rpm, in gas-tight 1.67 L reactor vessels, injection of 1 uM CdCl2

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.

treatment_protocol: Injection of Injection of 1uM CdCl2, 60min

tag: N. europaea cells cultured in 25 mM (NH4)2SO4 (50 mM of total NH4+) were harvested in mid to late exponential phase. The cells (OD600=0.07) were washed twice with 40 mM NaHPO4 (pH 7.8) to remove residual ammonia and were resuspended in 1000 ml of 50 mM HEPES buffer. The cells (500 ml) were then placed in gas-tight 1.67 L reactor vessels (Wheaton Double-sidearm Cell stir). (NH4)2SO4 (5 mM) was injected in the reactor vessels and the cultures were stirred with a magnetic stirring bar. Once the cell reached pseudo-steady state in Batch-reactor, the 1 uM CdCl2 was injected into just treatment reactor.


title: N. europaea_cadium_control condition_60min_biological rep3.

description: showed 100 % activity of nitrosomonas europaea, control condition(no inhibition), Quasi-steady state

source_name: N. europaea cultured in Batch reactor with 50 mM HEPES buffer and 5 mM total ammonia source, 60 min

growth_protocol: (NH4)2SO4 (5 mM) in 50 mM HEPES buffer, 700rpm, in gas-tight 1.67 L reactor vessels, no injection of cadmium

treatment_protocol: No injection of cadmium, 60min


title: WT hippocampus 3/TG hippocampus 5 (LGTC)


title: Nitrosomonas europaea_exposure to 1 uM CdCl2_60min_biological rep1.

treatment_protocol: Injection of 1uM CdCl2, 60min


title: Nitrosomonas europaea_exposure to 1 uM CdCl2_60min_biological rep2.


title: VS94 SAPI 4h control

status: Public on Mar 21 2008

city: College Station

first: Tarun

last: Bansal

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University

description: RNA extracted from suspension cells of VS94 after growth in SAPI medium at 37C.

hyb_protocol: Following Affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (169 Format) with total 80ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, 7.8% DMSO and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: VS94 SAPI 4h control

label_protocol:
Following Affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: Overnight culture was used to inoculate 100 mL fresh SAPI medium and incubated at 37C for specified time. The cells were then collected. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)

tag: RNA extracted from VS94 after growth in SAPI medium at 37C


title: N. europaea_cadium_control condition_60min_biological rep2.


title: VS94 SAPI 3.5h control

source_name: VS94 SAPI 3.5h control


title: VS94 SAPI 3.5h 100uM AI-2

description: RNA extracted from suspension cells of VS94 after growth in SAPI medium at 37C in presence of AI-2.

source_name: VS94 SAPI 3.5h 100uM AI-2

tag: RNA extracted from VS94 after growth in SAPI medium at 37C in presence of AI-2


title: SG_w1118(3)_14APF_rep2

status: Public on Mar 20 2008

city: Fayetteville

first: Michael

last: Lehmann

state: AR

address: SCEN 601

institute: University of Arkansas

description: Salivary glands from w1118 animals heat shocked at 9.5 hours after puparium formation and dissected at 14 hours after puparium formation.

hyb_protocol: Hybridization was performed following the instructions provided in the Affymetrix Manual (Section 2), using a Fluidics Station 450 and the Midi_euk2 v3 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000 Scanner 7G and Genechip Operation Software (GCOS) v. 1.4.

data_processing: The data were processed and normalized using dChip 2006. The median intensity of the baseline assay used for normalization was 134.

organism: Drosophila melanogaster

source_name: Salivary glands from strain w1118, heat shocked, dissected at 14 hours after puparium formation

label_protocol: Biotin-labeled cRNA was produced using the One-Cycle Eukaryotic Target Labeling Assay recommended by Affymetrix. Labeling was carried out exactly as specified in the instructions manual, section 2.

growth_protocol: Animals were kept at 25 °C, except during heat shock period.

extract_protocol: Salivary glands were dissected on ice and directly transferred to TRIzol Reagent (Invitrogen, Carlsbad, California). To support lysis of the tissue, the mixture was subjected to vigorous vortexing. Total RNA was isolated according to the instructions of the manufacturer. As a last step of the extraction procedure, the RNA was purified using an RNeasy Minikit (Qiagen, Hilden, Germany).

treatment_protocol: Animals were subjected to a 30-min heat shock treatment at 37 °C at 9.5 hours after puparium formation. Salivary glands were dissected for RNA extraction at 14 hours after puparium formation.

tag: Salivary glands of strain w1118, heat shocked, dissected at 14 hours after puparium formation.


title: California 2

source_name: California gill sample 2

source_name: Ref RNA pool


title: MCF10_1R


title: MCF10_1

source_name: MCF10 CONFLUENT DYE-CY5

label_protocol: Direct hybridization

source_name: MCF10 SPARSE DYE-CY3


title: N. europaea_cadium_control condition_60min_biological rep1

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was then purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.


title: VS94 SAPI 4.5h 100uM AI-2

source_name: VS94 SAPI 4.5h 100uM AI-2


title: VS94 SAPI 4h 100uM AI-2

source_name: VS94 SAPI 4h 100uM AI-2


title: VS94 SAPI 5.5h 100uM AI-2

source_name: VS94 SAPI 5.5h 100uM AI-2


title: VS94 SAPI 5.5h control

source_name: VS94 SAPI 5.5h control


title: VS94 SAPI 4.5h control

source_name: VS94 SAPI 4.5h control


title: SG_w1118(3)_14APF_rep1

source_name: salivary glands of strain w1118, heat shocked, dissected at 14 hours after puparium formation


title: Male vs. Male rep 2

type: genomic

city: Cambridge

first: Erik

last: Dopman

state: MA

address: 16 Divinity Ave, Bio. Labs

department: Organismic and Evolutionary Biology

institute: Harvard University

description: Replicate 2 of 3

hyb_protocol: According to Pollack (2002)

scan_protocol: GenePix 4000B Scanner using GenePix Pro 6 using manufacturer's instructions

data_processing: sequential spatial and intensity normalization

molecule: genomic DNA

source_name: bdgp

label_protocol: Invitrogen BioPrime Plus Array CGH Labeling System

extract_protocol: QIAamp DNA Mini Kit; Qiagen

tag: male, whole fly

tag: Sequenced strain of D. melanogaster


title: Male vs. Female rep 2

description: Replicate 2 of 3

source_name: female

tag: female, whole fly

source_name: male


title: Male vs. Female rep 3

description: Replicate 3 of 3


title: Male vs. Male rep 1

description: Replicate 1 of 3


title: New York (USA) isofemale line ny211 rep 3

description: Replicate 3 of 4

tag: New York (USA) isofemale line


title: New York (USA) isofemale line ny211 rep 4

description: Replicate 4 of 4


title: Male vs. Female rep 1

description: Replicate 1 of 3


title: Male vs. Male rep 3

description: Replicate 3 of 3


title: The Netherlands isofemale line no1 rep 4

description: Replicate 4 of 4

tag: The Netherlands isofemale line


title: The Netherlands isofemale line no1 rep 3

description: Replicate 3 of 4


title: The Netherlands isofemale line no1 rep 2

description: Replicate 2 of 4


title: New York (USA) isofemale line ny211 rep 2

description: Replicate 2 of 4


title: Cameroon isofemale line md43 rep1

description: Replicate 1 of 4

tag: Cameroon isofemale line


title: Cameroon isofemale line md43 rep3

description: Replicate 3 of 4


title: New York (USA) isofemale line ny211 rep 1

description: Replicate 1 of 4


title: Cameroon isofemale line md43 rep4

description: Replicate 4 of 4


title: Cameroon isofemale line md43 rep2

description: Replicate 2 of 4


title: French Polynesia isofemale line fp8 rep4

description: Replicate 4 of 4

tag: French Polynesia isofemale line


title: Kenya isofemale line k121 rep4

description: Replicate 4 of 4

tag: Kenya isofemale line


title: Kenya isofemale line k121 rep2

description: Replicate 2 of 4


title: Kenya isofemale line k121 rep1

description: Replicate 1 of 4


title: French Polynesia isofemale line fp8 rep2

description: Replicate 2 of 4


title: Kenya isofemale line k121 rep3

description: Replicate 3 of 4


title: E5.5 embryo ratio to E2.5

source_name: mRNA from mouse embryo E5.5

source_name: mRNA from mouse embryo E2.5


title: The Netherlands isofemale line no1 rep 1

description: Replicate 1 of 4


title: Lung Air/OVA rep3

source_name: lung, filtered air for 4hr/day for 5 days and 100 ug OVA for 3 days

tag: Female BALB/c 6-8 weeks


title: 4-day-old,infected during 4 hours with INV+,biological rep4

city: Paris

first: Thierry

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

institute: Pasteur Institute

description: RNA from intestinal tissue of 4-day or 7-day mice infected or not with invasive or non-invasive  Shigella strains for 2 or 4 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MOE430A probe array cartridge. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After staining using PE-streptavidin, arrays were scanned at 488 nm using an Argon-ion laser

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

source_name: infected with invasive (INV+) mouse intestinal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, following by clean-up ising RNEasy Mini kit from Qiagen.

treatment_protocol: After 2 or 4 hours of intra-gastric infection with Shigella, a section of intestin was removed and extracted.

tag: BALB/c Mice

tag: Age

value: 4 day-old mice


title: 7-day-old, infected during 4 hours with INV+,biological rep1

value: 7 day-old mice


title: 7-day-old, infected during 4 hours with INV+,biological rep3


title: 4-day-old, infected during 4 hours with INV+,biological rep1


title: French Polynesia isofemale line fp8 rep3

description: Replicate 3 of 4


title: 4-day-old, infected during 4 hours with INV+,biological rep3


title: 7-day-old, infected during 4 hours with INV+,biological rep2


title: 7-day-old, infected during 4 hours with INV-,biological rep3

source_name: infected with non-invasive (INV-) mouse intestinal tissue


title: 7-day-old, infected during 4 hours with INV-,biological rep2


title: 4-day-old, infected during 4 hours with INV+,biological rep2


title: 4-day-old, infected during 4 hours with INV-,biological rep1


title: 4-day-old,infected during 4 hours with INV-,biological rep4


title: 7-day-old, infected during 2 hours with INV+,biological rep2


title: 7-day-old, infected during 4 hours with INV-,biological rep1


title: 4-day-old, infected during 4 hours with INV-,biological rep3


title: 7-day-old, infected during 2 hours with INV+,biological rep4


title: 4-day-old, infected during 4 hours with INV-,biological rep2


title: 4-day-old, infected during 2 hours with INV+,biological rep2


title: 7-day-old, infected during 2 hours with INV+,biological rep1


title: 4-day-old,infected during 2 hours with INV+,biological rep3


title: 7-day-old, infected during 2 hours with INV+,biological rep3


title: 7-day-old, infected during 2 hours with INV-,biological rep3


title: 4-day-old, infected during 2 hours with INV+,biological rep1


title: French Polynesia isofemale line fp8 rep1

description: Replicate 1 of 4


title: 7-day-old, infected during 2 hours with INV-,biological rep2


title: 4-day-old, infected during 2 hours with INV-,biological rep3


title: 4-day-old,infected during 2 hours with INV-,biological rep4


title: 4-day-old, infected during 2 hours with INV-,biological rep2


title: 4-day-old, infected during 2 hours with INV-,biological rep1


title: 4-day-old, biological rep4

source_name: non-infected mouse intestinal tissue


title: 7-day-old, biological rep1


title: 4-day-old, biological rep3


title: 7-day-old, infected during 2 hours with INV-,biological rep1


title: 7-day-old, biological rep7


title: 7-day-old, biological rep3


title: 7-day-old, biological rep2


title: 4-day-old, biological rep2


title: 7 days post SMV infection

status: Public on Mar 17 2008

city: London

first: Mohan

last: babu

address: 1391 Sandford

department: Virology

institute: AAFC

hyb_protocol: As per Moy et al (2004)

scan_protocol: As per Moy et al (2004)

data_processing: Processed using Gene Spring version 7.3. software

organism: Glycine max

source_name: 7 days post SMV infection

label_protocol: Indirect labelling Protocol from Amersham biosciences

growth_protocol: soybean leaves grown in greenhouse conditions at 80% RH with a day/night regime of 16 h light at 24 degree celcius followed by 8 h dark at 16 degree celcius

tag: Samples collected from 7 days post SMV infection

source_name: Mock inoculated samples from 7 days

tag: mock inoculated samples collected from 7 days.


title: 21 days post SMV infection

data_processing: Processed with Gene Spring version 7.3. software

source_name: 21 days post SMV infection

label_protocol: Indirect labelling protocol

growth_protocol: Plants were maintained in a greenhouse at 80% RH with a day/night regime of 16 h light at 24 degree Celcius followed by 8 h dark at 16 degree Celcius.

tag: 21 days post SMV infected soybean leaf tissues

source_name: 21 days old mokc inoculated samples

label_protocol: Indirect labelling protocol from Amersham Biosciences

tag: 21 days old mock inoculated soybean leaf tissues


title: germinated zoospore cysts, replicate 1

status: Public on Mar 15 2008

city: Riverside

first: Howard

middle: S

last: Judelson

state: CA

address: Boyce Hall

department: Plant Pathology

institute: University of California

description: Germinated cysts, with many germ tubes containing appressoria

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: MAS 5.0

label: Biotin

organism: Phytophthora infestans

source_name: germinated cysts and appressoria from P. infestans

label_protocol: standard Affymetrix procedures

growth_protocol: Sporangia were harvested from rye-sucrose agar plates (ca. 10 days old).  Sporangia were then rubbed off the plates using cold water and a bent glass rod.  Sporangial suspensions were purified from hyphae by passage through 50 micron nylon mesh, and then placed at 10C for 120-150 minutes.  Zoospores were then passed through 10 micron mesh to remove ungerminated sporangia, and vortexed for 60 sec. to induce encystment.  They were then incubated at 10°C in plastic plates overnight.  Tissues were then concentrated by gentle centrifugation.

extract_protocol:
RNA was extracted by grinding in liquid nitrogen followed by use of the RNAEasy
Plant Mini kit (Qiagen, Valencia, CA USA) according the manufacturer's instructions.

tag: Isolate 88069


title: 14 days post SMV infection

source_name: 14 days post SMV infection

tag: 14 days post SMV infection samples

source_name: 14 days Mock inoculated samples

tag: 14 days Mock inoculated samples from Amersham Biosciences


title: germinated cysts and appressoria, replicate 2

source_name: P. infestans germinated cysts with appressoria

growth_protocol: Sporangia were harvested from rye-sucrose agar plates (ca. 10 days old).  Sporangia were then rubbed off the plates using cold water and a bent glass rod.  Sporangial suspensions were purified from hyphae by passage through 50 micron nylon mesh, and then placed at 10C for 120-150 minutes.  Zoospores were then passed through 10 micron mesh to remove ungerminated sporangia, vortexed 60 sec to induce encystment, and then incubated at 10°C in plastic plates overnight.  The resulting germinated cysts were then concentrated by gentle centrifugation.


title: swimming zoospores, replicate 1

description: Swimming zoospores; may contain small amounts of ungerminated sporangia or germinated cysts (<5%)

source_name: P. infestans zoospores

growth_protocol: Sporangia were harvested from rye-sucrose agar plates (ca. 10 days old).  Sporangia were then rubbed off the plates using cold water and a bent glass rod.  Sporangial suspensions were purified from hyphae by passage through 50 micron nylon mesh, and then placed at 10C for 120-150 minutes.  Zoospores were then passed through 10 micron mesh to remove ungerminated sporangia, and then concentrated by gentle centrifugation.


title: 4-day-old, biological rep1


title: Resistant Isolate 5674, Experiment 3

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description: Each resistant isolate was compared to its susceptible parent, and the TAC1 knockout was compared to the susceptible parent (5457) of the resistant isolate, 5674.

hyb_protocol: The cRNA pellet was suspended in 10 μl of RNase-free water and 10 μg was fragmented by ion-mediated hydrolysis at 95°C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate.  The fragmented cRNA was hybridized for 16 h at 45°C to the C. albicans NimbleExpress GeneChip arrays.  Arrays were washed at 25°C with 6 × SSPE, 0.01% Tween 20 followed by a stringent wash at 50°C with 100 mM MES, 0.1 M NaCl, 0.01% Tween 20.  Hybridizations and washes employed the Affymetrix Fluidics Station 450 using their standard EukGE-WS2v5 protocol.  The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes) and the fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).

scan_protocol: The scanned images were analysed using software resident in GeneChip Operating System v2.0 (GCOS; Affymetrix).  Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (250).

data_processing: The signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM – MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes.

organism: Candida albicans

source_name: Candida albicans isolate 5674, mid-log phase

label_protocol: cRNA was synthesized and labelled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray HighYield RNA Transcript Labelling Kit (ENZO Diagnostics).  Double stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 μl of RNase-free water.  The cDNA was incubated as recommended with reaction buffer, biotin-labelled ribonucleotides, dithtiothreitol, RNase inhibitor mix and T7 RNA polymerase for 5 h at 37°C.  The labelled cRNA was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and ethanol precipitated at −20°C overnight.

extract_protocol: Hot Phenol Method

tag: Fluconazole resistant isolate 5674


title: swimming zoospores, replicate 2

source_name: motile zoospores from P. infestans


title: Susceptible Isolate 5457, Experiment 3

source_name: Candida albicans isolate 5457, mid-log phase

tag: Fluconazole susceptible isolate 5457


title: cleaving sporangia, replicate 1

description: Sporangia undergoing zoosporogenesis (cleaving sporangia) were obtained by placing a sporangial suspension at 10°C for 60 min; after this time signs of cleavage were visible in about 70% of sporangia, although only a small amount (<2%) had actually released zoospores.

source_name: 60 min cold-treated sporangia

growth_protocol: Sporangia were harvested from rye-sucrose agar plates (ca. 10 days old).  Sporangia were then rubbed off the plates using cold water and a bent glass rod.  Sporangial suspensions were purified from hyphae by passage through 50 micron nylon mesh, and then placed at 10C for 60 minutes.


title: TAC1 knockout strain SZY31, Experiment 1

source_name: Candida albicans strain SZY31, mid-log phase

tag: Strain with CaTAC1 knocked out in resistant 5674


title: TAC1 knockout strain SZY31, Experiment 3

tag: Strain with CaTAC1 knocked out in resistant isolate 5674


title: cleaving sporangia, replicate 2

source_name: sporangia chilled for 60 min


title: Ungerminated sporangia, replicate 1

description: sporangia were harvested rapidly to avoid inducing zoosporogenesis, and hence are assumed to represent "ungerminated sporangia"

data_processing: MAS5.0, per chip normalization

source_name: asexual sporangia, ungerminated

growth_protocol: Cultures were initiated on rye-sucrose media (1.5% agar) and incubated at 18C for about 8 days in the dark.  Plates were flooded with water, rubbed with a glass rod to release the sporangia, run through a 50 micron mesh to remove hyphal fragments, and the sporangia decanted into 50 ml plastic tubes.  Sporangia were then concentrated by gentle centrifugation using a swinging bucket rotor. Samples were then resuspended in a minimal volume of water.

extract_protocol: Samples were ground in liquid nitrogen, and then processed using the Qiagen Plant RNAeasy Mini kit.


title: Susceptible Isolate 5457, Experiment 2


title: Resistant Isolate 5674, Experiment 2


title: Resistant Isolate 5674, Experiment 1


title: Ungerminated sporangia, replicate 2


title: Susceptible Isolate 5457, Experiment 1

source_name: Candida albicans isolate 5457


title: TAC1 knockout strain SZY31, Experiment 2


title: Resistant Isolate Gu5, Experiment 1

source_name: Candida albicans isolate Gu5, mid-log phase

tag: Fluconazole resistant isolate Gu5


title: Susceptible Isolate C43, Experiment 2

source_name: Candida albicans isolate C43, mid-log phase

tag: Fluconazole susceptible isolate C43


title: Susceptible Isolate Gu2, Experiment 1

source_name: Candida albicans isolate Gu2, mid-log phase

tag: Fluconazole susceptible isolate Gu2


title: Nonsporulating hyphae, replicate 2

description: nonsporulating control

source_name: P. infestans nonsporulating hyphae, 3-4 day old

growth_protocol: Cultures were initiated from sporangial suspensions in clarified rye-sucrose media.  Cultures were incubated at 18C for 3-4 days and harvested before asexual sporulation occurred.  Cultures were harvested by gentle filtration on filter paper.


title: Susceptible Isolate C43, Experiment 3


title: Resistant Isolate Gu5, Experiment 3


title: Nonsporulating hyphae, replicate 1

description: nonsporulating control

source_name: nonsporulating hyphae, 3-4 day old


title: Susceptible Isolate Gu2, Experiment 2


title: Susceptible Isolate C43, Experiment 1


title: Resistant Isolate C56, Experiment 2

source_name: Candida albicans isolate C56, mid-log phase

tag: Fluconazole resistant isolate C56


title: Susceptible Isolate Gu2, Experiment 3


title: Resistant Isolate C56, Experiment 3


title: Resistant Isolate C56, Experiment 1


title: Susceptible Isolate 3, Experiment 1

source_name: Candida albicans isolate 3, mid-log phase

tag: Fluconazole susceptible isolate 3


title: Resistant Isolate Gu5, Experiment 2


title: Resistant Isolate 17, Experiment 3

source_name: Candida albicans isolate 17, mid-log phase

tag: Fluconazole resistant isolate 17


title: Susceptible Isolate 3, Experiment 3


title: Susceptible Isolate 3, Experiment 2


title: Human IgG IP

status: Public on Mar 14 2008

city: Bethesda

first: J Raphael

last: Gibbs

state: MD

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: RNA immunoprecipitated with a nonspecific IgG control antibody

hyb_protocol: Illumina Whole Genome Gene Expression Rev. D

scan_protocol: BeadStation

data_processing: Illumina BeadStudio Intensity value output unnormalized and background subtracted. Where the value is the is the average signal of four Human IgG IP replicates.

source_name: Human M17 Neuroblastoma Cells

growth_protocol: Cultured in DMEM with 10% FBS

extract_protocol: TRIZOL

tag: Immunoprecipitated RNA comparison


title: Resistant Isolate 17, Experiment 1


title: Human rhabdomyosarcoma cell line_A204_STY

first: Xueying

last: Mao

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary

description: SNP genotyping data (STY) from A204

hyb_protocol: Affymetrix 500K mapping assay protocol

scan_protocol: SNP arrays were scanned using Affymetrix GeneChip scanner 3000-7G

data_processing: Data Analysis workflow for GeneChip® Human Mapping 250K Arrays using GCOS and GTYPE

source_name: cell line

label_protocol: Affymetrix 500K mapping assay protocol

extract_protocol: Phenol-Chroloform extraction

tag: cell line was from human muscle


title: PbK-infected mouse brain, day 14 rep2

city: Sydney

first: Jenny

last: Miu

state: NSW

address: 92-94 Parramatta Rd

department: Department of Pathology

country: Australia

institute: University of Sydney

hyb_protocol: Following purification of the labelled probe (60ul), a 11.25ul hybridisation pre-blocker mix (consisting of tRNA (1.6mg/ml; Sigma), Cot-1 DNA (4mg/ml; Invitrogen), poly dA oligonucleotide (0.8mg/ml; Geneworks), 5x Denhart’s (1% (w/v) Ficoll 400, 1% (w/v) polyvinylpyrrolidon (PVP), 1% (w/v) bovine serum albumin (BSA)) containing filtered herring sperm DNA (5mg/ml; Invitrogen), was added and the mixture dried to ~12.6ul using a Speed Vac (Savant). To hydrolyse samples, 20x sodium chloride-sodium citrate (SSC) (5.4ul) and formamide (18ul; Invitrogen) were added, mixed well, and heated to 100oC for 3 min, before the addition of 10% (w/v) sodium dodecyl sulfate (SDS) (0.45ul), taking care to remove all bubbles. After applying the probe to 22.5K Compugen mouse oligonucleotide arrays (~22,500 genes; Ramaciotti Centre, UNSW), slides were coverslipped and placed into a humidified chamber and incubated at 42oC overnight for ~16 hours. After hybridisation, slides were immersed in a wash solution (0.5x SSC, 0.01% (w/v) SDS) to remove the coverslip and any remaining unincorporated probe. Arrays were washed by gently agitating slides in wash solutions at room temperature. Slides were washed in 3 wash solutions (0.5x SSC, 0.01% (w/v) SDS, 1 min; 0.5x SSC, 3 min; 0.06x SSC, 3 min) and then dried carefully by placing them into Falcon tubes containing Kimwipes and centrifuged at 800 rpm, 5 min. Slides were kept protected from light until scanned.

scan_protocol: Slides were scanned and spot intensities determined using an Axon scanner (GenePix 3.0; Molecular Devices). The dyes are stimulated with a laser to measure the fluorescence, at 635nm for red (Cy5) and at 532nm for green (Cy3). To generate an ideal pixel ratio of ~1.0, similar intensities of each dye are required, and this was obtained by using a photomultiplier tube (PMT) voltage of ~600 (range 500-600).

data_processing: Basic normalisation procedures were carried out in GenePix 3.0, including background subtraction and removal of poor quality spots. The generated GenePix Results (.gpr) files were then imported into Limma for loess normalisation (R, Bioconductor project).

source_name: PbK-infected mouse brain

label_protocol: RNA (75ug) was primed with oligo dTs (0.2mg/ml; Geneworks) and incubated at 70oC, 10 min. cDNA was generated in a 30ul reaction mixture containing 1x Superscript III buffer (Invitrogen), 6.7mM DTT (Invitrogen), 2mM dNTP (containing 25mM dATP, 25mM dCTP, 25mM dGTP, 15mM dTTP, 10mM daaUTP; Sigma) and Superscript III (13.3U/ul; Invitrogen), and incubated at 42oC, 2.5 hrs. Samples were then hydrolysed by the addition of NaOH (55.56mM) and EDTA (55.56mM), and incubated at 65oC, 15 min, before adding acetic acid (50mM). cDNA was purified using columns as described in an QIAquick Purification Kit (Qiagen). Briefly, cDNA was bound to columns and washed, but not eluted, allowing coupling of either Cy3 or Cy5 dye to each sample. Aliquots of Cy3 or Cy5 (Amersham) were resuspended in 120uL NaHCO3 (0.1M, pH 9.0), and 20uL applied directly to the centre of the column membrane. These were incubated in the dark, at room temperate for 1 hr. 80uL dH2O was then added to the column, which was centrifuged at 13,000 rpm, 60 sec, and the eluate containing the labelled cDNA collected in a fresh tube. Cy3 and Cy5 labelled samples chosen for comparison on each array were then combined into one reaction and purified using a QIAquick Purification Kit (Qiagen). Buffer PB (500ul) was first added to eluates labelled with Cy3, mixed well and applied to a new column, to allow binding to the membrane. Samples were centrifuged at 13,000 rpm, 60 sec and the eluate discarded. This was repeated for Cy5-labelled samples. Columns were washed well with Buffer PE (750ul, spin 13,000 rpm, 60 sec; x 2), before centrifuging the empty column to dry the membrane (spin 13,000 rpm, 60 sec). Samples containing both Cy3- and Cy5-labelled probes were then eluted with Buffer EB (30uL, spin 13,000 rpm, 60 sec; x 2).

extract_protocol: Individual brains extracted from mice were immediately placed into tubes containing TRIzol (1mL; Invitrogen) and Zirconia beads (100ul; Biospec Products Inc) and homogenised using a Fast Prep FP120 homogeniser (Q-Biogene). To extract RNA, chloroform (200uL) was added to the tubes and centrifuged at 14,000 rpm, 4oC, 15 min. The top layer containing RNA was removed and placed into a fresh tube containing isopropanol (500uL) and centrifuged at 14,000 rpm, 4oC, 10 min. After precipitating the RNA, the pellet was washed with 75% (v/v) cold ethanol (1ml), resuspended by vortex and centrifuged at 14,000 rpm, 4oC, 5 min. The pellet was then air-dried and resuspended in water (20uL), and the RNA stored at –80oC.

tag: Strain

tag: Gender

value: Female

tag: Age

value: 6-8 weeks

tag: Disease

value: P. berghei K173 (day 14)

source_name: Uninfected control mouse brain

value: Uninfected control


title: PbK-infected mouse brain, day 6 rep3

value: P. berghei K173 (day 6)

value: Uinfected control


title: PbK-infected mouse brain, day 6 rep5


title: PbK-infected mouse brain, day 14 rep3


title: PbK-infected mouse brain, day 14 rep5


title: KO Mouse DJ-1 IP

description: nonspecific RNA immunoprecipitated with the DJ-1 antibody from KO mouse brains

data_processing: Illumina BeadStudio Intensity value output unnormalized and background subtracted.

source_name: Mouse Whole Brain

label_protocol: Illumina Whole Genome Gene Expression Rev. D


title: PbK-infected mouse brain, day 14 rep1


title: PbK-infected mouse brain, day 6 rep4


title: Human DJ-1 IP

description: RNA immunoprecipitated with DJ-1 antibody

data_processing: Illumina BeadStudio Intensity value output unnormalized and background subtracted. Where the value is the is the average signal of six Human DJ-1 IP replicates.


title: PbA-infected mouse brain, day 6 rep3

source_name: PbA-infected mouse brain

value: P. berghei ANKA (day 6)


title: PbA-infected mouse brain, day 6 rep2

tag: Tissue

value: Brain


title: PbA-infected mouse brain, day 6 rep5

value: P. berghei ANKA  (day 6)


title: A23 vs A23 Replica 5

status: Public on Mar 13 2008

city: Los Angeles

first: Christopher

address: 23-151 CHS, 650 Charles E. Young Drive

department: Molecular and Medical Pharmacology

institute: UCLA

hyb_protocol: Standard Agilent Hybridization protocols for expression microarrays were followed, 17 hour hybridization time

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions.  Agilent Feature Extractor software was used to extract the data.

data_processing: Each value was divided by the control channel.

organism: Cricetulus griseus

source_name: Total RNA from cell line A23 labeled with cy5

label_protocol: 20 ug of total RNA was labeled using the Agilent Fluorescent Direct Labeling Protocol

growth_protocol: A23 cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks until 75% confluent.  Harvested by trypsinization, then pelleting.

extract_protocol: RNA isolation was done with Qiagen RNeasy Mini Kit per protocol recommended by the manufacturer.

tag: hamster fibroblast cell line

source_name: Total RNA from cell line A23 labeled with cy3


title: PbK-infected mouse brain, day 6 rep2


title: WT Mouse DJ-1 IP

description: nonspecific RNA immunoprecipitated with the DJ-1 antibody from WT mouse brains

data_processing: Illumina BeadStudio Intensity value output unnormalized and background subtracted. Where the value is the is the average signal of three WT Mouse DJ-1 IP replicates.


title: Resistant Isolate 17, Experiment 2


title: PbK-infected mouse brain, day 14 rep4


title: PbK-infected mouse brain, day 6 rep1

value: P. berghei K173  (day 6)


title: Human rhabdomyosarcoma cell line_A204_NSP

description: SNP genotyping data (NSP) from A204


title: A23 vs A23 Replica 4


title: PbA-infected mouse brain, day 6 rep1


title: Human ovarian carcinoma cell line_CH1_STY

description: SNP genotyping data (STY) from CH1

tag: cell line was from female patient


title: Human leiomyosarcoma cell line_SKUT1B_STY

description: SNP genotyping data (STY) from SKUT1B

tag: cell line was from mesodermal tumor (mixed), grade II


title: Human breast carcinoma cell line_CAL51_STY

description: SNP genotyping data (STY) from CAL51


title: Human leiomyosarcoma cell line_SKUT1B_NSP

description: SNP genotyping data (NSP) from SKUT1B

tag: cell line was from mesodermal tumor (mixed), grade III


title: A23 vs A23 Replica 3


title: A23 vs A23 Replica 2


title: Human breast carcinoma cell line_CAL51_NSP

description: SNP genotyping data (NSP) from CAL51


title: Human ovarian carcinoma cell line_CH1_NSP

description: SNP genotyping data (NSP) from CH1


title: Hamster Liver vs Mouse Liver

description: Biological Replica 1, log10 ratios are cy5/cy3

data_processing: The expression data was normalized using GeneSpring (Agilent Technologies).  Each value was divided by the control channel and each chip normalized to the 50th percentile for the measurements taken from that chip.

source_name: Total RNA from Chinese hamster whole liver

growth_protocol: RH and A23 cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks until 75% confluent.  Harvested by trypsinization, then pelleting.

tag: whole liver RNA

source_name: Total RNA from mouse whole liver


title: Mouse Liver vs Hamster Liver

description: Biological Replica 2 (dye swap), log10 ratios are cy5/cy3

source_name: Total RNA from hamster whole liver


title: Hamster Brain vs Mouse Brain

source_name: Total RNA from Chinese hamster whole brain

tag: whole brain RNA

source_name: Total RNA from mouse whole brain


title: T31 Cell Line 99 Replica 2

organism:
Cricetulus griseus
Mus musculus

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 99 labeled with cy5

tag: Fragments of mouse strain 129aa fused with hamster cell line A23


title: Mouse Brain vs Hamster Brain

source_name: Total RNA from hamster whole brain


title: T31 Cell Line 94 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 94 labeled with cy5


title: T31 Cell Line 98 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 98 labeled with cy5


title: T31 Cell Line 100 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 100 labeled with cy5


title: T31 Cell Line 95 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 95 labeled with cy5


title: T31 Cell Line 91 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 91 labeled with cy5


title: T31 Cell Line 92 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 92 labeled with cy5


title: T31 Cell Line 84 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 84 labeled with cy5


title: A23 vs A23 Replica 1


title: T31 Cell Line 83 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 83 labeled with cy5


title: PbA-infected mouse brain, day 6 rep4

source_name: PbA-infected mouse brain

value: P. bergehi ANKA (day 6)

source_name: Uninfected control mouse brain


title: T31 Cell Line 89 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 89 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: T31 Cell Line 93 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 93 labeled with cy5


title: T31 Cell Line 81 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 81 labeled with cy5


title: T31 Cell Line 97 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 97 labeled with cy5


title: T31 Cell Line 76 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 76 labeled with cy5


title: T31 Cell Line 90 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 90 labeled with cy5


title: T31 Cell Line 85 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 85 labeled with cy5


title: T31 Cell Line 88 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 88 labeled with cy5


title: T31 Cell Line 86 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 86 labeled with cy5


title: T31 Cell Line 96 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 96 labeled with cy5


title: T31 Cell Line 82 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 82 labeled with cy5


title: T31 Cell Line 77 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 77 labeled with cy5


title: T31 Cell Line 73 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 73 labeled with cy5


title: T31 Cell Line 80 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 80 labeled with cy5


title: T31 Cell Line 87 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 87 labeled with cy5


title: T31 Cell Line 78 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 78 labeled with cy5


title: T31 Cell Line 74 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 74 labeled with cy5


title: T31 Cell Line 75 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 75 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: T31 Cell Line 79 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 79 labeled with cy5


title: T31 Cell Line 72 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 72 labeled with cy5


title: T31 Cell Line 69 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 69 labeled with cy5


title: T31 Cell Line 70 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 70 labeled with cy5


title: T31 Cell Line 71 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 71 labeled with cy5


title: T31 Cell Line 68 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 68 labeled with cy5


title: T31 Cell Line 66 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 66 labeled with cy5


title: T31 Cell Line 62 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 62 labeled with cy5


title: T31 Cell Line 64 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 64 labeled with cy5


title: T31 Cell Line 54 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 54 labeled with cy5


title: T31 Cell Line 65 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 65 labeled with cy5


title: T31 Cell Line 60 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 60 labeled with cy5


title: T31 Cell Line 51 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 51 labeled with cy5


title: T31 Cell Line 58 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 58 labeled with cy5


title: T31 Cell Line 50 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 50 labeled with cy5


title: T31 Cell Line 49 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 49 labeled with cy5


title: T31 Cell Line 57 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 57 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: T31 Cell Line 56 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 56 labeled with cy5


title: T31 Cell Line 52 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 52 labeled with cy5


title: T31 Cell Line 53 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 53 labeled with cy5


title: T31 Cell Line 59 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 59 labeled with cy5


title: T31 Cell Line 63 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 63 labeled with cy5


title: T31 Cell Line 45 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 45 labeled with cy5


title: T31 Cell Line 61 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 61 labeled with cy5


title: T31 Cell Line 44 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 44 labeled with cy5


title: T31 Cell Line 48 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 48 labeled with cy5


title: T31 Cell Line 55 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 55 labeled with cy5


title: T31 Cell Line 46 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 46 labeled with cy5


title: T31 Cell Line 47 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 47 labeled with cy5


title: T31 Cell Line 41 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 41 labeled with cy5


title: T31 Cell Line 37 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 37 labeled with cy5


title: T31 Cell Line 43 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 43 labeled with cy5


title: T31 Cell Line 39 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 39 labeled with cy5


title: T31 Cell Line 40 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 40 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: T31 Cell Line 38 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 38 labeled with cy5


title: T31 Cell Line 36 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 36 labeled with cy5


title: T31 Cell Line 42 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 42 labeled with cy5


title: T31 Cell Line 34 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 34 labeled with cy5


title: T31 Cell Line 30 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 30 labeled with cy5


title: T31 Cell Line 29 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 29 labeled with cy5


title: T31 Cell Line 32 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 32 labeled with cy5


title: T31 Cell Line 31 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 31 labeled with cy5


title: T31 Cell Line 33 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 33 labeled with cy5


title: T31 Cell Line 35 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 35 labeled with cy5


title: T31 Cell Line 23 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 23 labeled with cy5


title: T31 Cell Line 15 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 15 labeled with cy5


title: T31 Cell Line 14 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 14 labeled with cy5


title: T31 Cell Line 21 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 21 labeled with cy5


title: T31 Cell Line 24 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 24 labeled with cy5


title: T31 Cell Line 27 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 27 labeled with cy5


title: T31 Cell Line 16 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 16 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: T31 Cell Line 22 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 22 labeled with cy5


title: T31 Cell Line 25 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 25 labeled with cy5


title: T31 Cell Line 13 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 13 labeled with cy5


title: T31 Cell Line 17 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 17 labeled with cy5


title: T31 Cell Line 26 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 26 labeled with cy5


title: T31 Cell Line 18 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 18 labeled with cy5


title: T31 Cell Line 12 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 12 labeled with cy5


title: T31 Cell Line 19 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 19 labeled with cy5


title: T31 Cell Line 20 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 20 labeled with cy5


title: T31 Cell Line 28 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 28 labeled with cy5


title: T31 Cell Line 11 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 11 labeled with cy5


title: Control experiment to determine DNA copy number of the A23 cell line relative to hamster

description: control experiment to determine the copy number of the A23 cell line relative to hamster

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

data_processing: sliding window average of 10 probes

source_name: A23 Hamster Cell Line

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions.  Genomic DNA was fragmented using restriction exzymes.  Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy5/cy3 labeled dUTP.

growth_protocol: A23 cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks until 75% confluent.  Harvested by trypsinization, then pelleting.  Chinese hamster kidney was harvested.

extract_protocol: DNA was extracted using the Qiagen Dneasy Tissue kit according to the manufacturer's instructions

tag: Hamster fibroblast cell line

source_name: Chinese Hamster Kidney Genomic DNA

tag: genomic DNA from hamster kidney


title: DNA from T31 Cell Line 100

data_processing: The CGH data were normalized as follows. First, the data for each array were subtracted by its own individual mode (a CGH value corresponding to the primary peak). This gave the primary mode for each array a log10(RH/A23) copy number ratio of zero. In the next step, the CGH data was pooled over all arrays and the primary and second modes estimated by modeling the data as a mixture of two Gaussian distributions 4. Because extra copy regions in the autosomes represent three copies (one mouse and two hamster copies) compared to two (two hamster copies), the data for the autosomes was multiplied by a common scaling factor of (log10[3/2])/(secondary mode CGH value - primary mode CGH value). Consequently, the normalized CGH data for the autosomes had a primary mode at log10(2 copies/2 copies) = 0 and a secondary mode at log10(3 copies/2 copies) = 0.176. Since extra copy regions on the X chromosome represent two copies (one mouse plus one hamster) compared to one (one hamster copy), the data for the X chromosome was multiplied by log10(2/1)/(secondary mode CGH value - primary mode CGH value), giving a secondary mode at log10(2 copies/1 copy) = 0.301.

source_name: DNA from T31 Cell Line 100

tag: Radiation Hybrid Cell Line


title: DNA from T31 Cell Line 99

source_name: DNA from T31 Cell Line 99


title: T31 Cell Line 5 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 5 labeled with cy5


title: T31 Cell Line 10 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 10 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: T31 Cell Line 8 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 8 labeled with cy5


title: T31 Cell Line 3 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 3 labeled with cy5


title: T31 Cell Line 100 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 100


title: DNA from T31 Cell Line 98

source_name: DNA from T31 Cell Line 98


title: T31 Cell Line 1 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 1 labeled with cy5


title: T31 Cell Line 98 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 98


title: DNA from T31 Cell Line 97

source_name: DNA from T31 Cell Line 97


title: T31 Cell Line 4 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 4 labeled with cy5


title: DNA from T31 Cell Line 95

source_name: DNA from T31 Cell Line 95


title: T31 Cell Line 2 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 2 labeled with cy5


title: T31 Cell Line 9 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 9 labeled with cy5


title: T31 Cell Line 99 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 99


title: T31 Cell Line 7 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 7 labeled with cy5


title: DNA from T31 Cell Line 96

source_name: DNA from T31 Cell Line 96

source_name: A23 Hamster Cell Line


title: T31 Cell Line 6 Replica 2

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 6 labeled with cy5

source_name: Total RNA from cell line A23 labeled with cy3


title: DNA from T31 Cell Line 94

source_name: DNA from T31 Cell Line 94


title: DNA from T31 Cell Line 90

source_name: DNA from T31 Cell Line 90


title: DNA from T31 Cell Line 93

source_name: DNA from T31 Cell Line 93


title: DNA from T31 Cell Line 91

source_name: DNA from T31 Cell Line 91


title: DNA from T31 Cell Line 85

source_name: DNA from T31 Cell Line 85


title: DNA from T31 Cell Line 89

source_name: DNA from T31 Cell Line 89


title: DNA from T31 Cell Line 87

source_name: DNA from T31 Cell Line 87


title: T31 Cell Line 97 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 97


title: DNA from T31 Cell Line 92

source_name: DNA from T31 Cell Line 92


title: DNA from T31 Cell Line 88

source_name: DNA from T31 Cell Line 88


title: DNA from T31 Cell Line 86

source_name: DNA from T31 Cell Line 86


title: DNA from T31 Cell Line 84

source_name: DNA from T31 Cell Line 84


title: T31 Cell Line 91 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 91


title: DNA from T31 Cell Line 83

source_name: DNA from T31 Cell Line 83

source_name: A23 Hamster Cell Line


title: T31 Cell Line 93 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 93


title: DNA from T31 Cell Line 82

source_name: DNA from T31 Cell Line 82


title: DNA from T31 Cell Line 80

source_name: DNA from T31 Cell Line 80


title: T31 Cell Line 95 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 95


title: T31 Cell Line 96 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 96


title: DNA from T31 Cell Line 79

source_name: DNA from T31 Cell Line 79


title: T31 Cell Line 92 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 92


title: T31 Cell Line 94 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 94


title: T31 Cell Line 87 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 87


title: DNA from T31 Cell Line 77

source_name: DNA from T31 Cell Line 77


title: T31 Cell Line 86 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 86


title: T31 Cell Line 84 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 84


title: DNA from T31 Cell Line 78

source_name: DNA from T31 Cell Line 78


title: T31 Cell Line 89 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 89


title: T31 Cell Line 82 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 82


title: DNA from T31 Cell Line 75

source_name: DNA from T31 Cell Line 75

source_name: A23 Hamster Cell Line


title: T31 Cell Line 88 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 88


title: DNA from T31 Cell Line 73

source_name: DNA from T31 Cell Line 73


title: DNA from T31 Cell Line 76

source_name: DNA from T31 Cell Line 76


title: T31 Cell Line 83 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 83


title: T31 Cell Line 90 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 90


title: DNA from T31 Cell Line 72

source_name: DNA from T31 Cell Line 72


title: T31 Cell Line 81 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 81


title: DNA from T31 Cell Line 71

source_name: DNA from T31 Cell Line 71


title: T31 Cell Line 85 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 85


title: T31 Cell Line 80 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 80


title: DNA from T31 Cell Line 70

source_name: DNA from T31 Cell Line 70


title: T31 Cell Line 79 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 79


title: T31 Cell Line 77 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 77


title: DNA from T31 Cell Line 69

source_name: DNA from T31 Cell Line 69


title: DNA from T31 Cell Line 68

source_name: DNA from T31 Cell Line 68


title: T31 Cell Line 78 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 78


title: DNA from T31 Cell Line 66

source_name: DNA from T31 Cell Line 66

source_name: A23 Hamster Cell Line


title: DNA from T31 Cell Line 62

source_name: DNA from T31 Cell Line 62


title: DNA from T31 Cell Line 65

source_name: DNA from T31 Cell Line 65


title: DNA from T31 Cell Line 64

source_name: DNA from T31 Cell Line 64


title: T31 Cell Line 74 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 74


title: T31 Cell Line 71 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 71


title: T31 Cell Line 69 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 69


title: T31 Cell Line 73 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 73


title: T31 Cell Line 72 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 72


title: T31 Cell Line 70 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 70


title: T31 Cell Line 75 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 75


title: T31 Cell Line 76 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 76


title: T31 Cell Line 68 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 68


title: T31 Cell Line 66 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 66


title: DNA from T31 Cell Line 59

source_name: DNA from T31 Cell Line 59


title: T31 Cell Line 65 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 65


title: DNA from T31 Cell Line 81

source_name: DNA from T31 Cell Line 81

source_name: A23 Hamster Cell Line


title: DNA from T31 Cell Line 60

source_name: DNA from T31 Cell Line 60


title: DNA from T31 Cell Line 63

source_name: DNA from T31 Cell Line 63


title: DNA from T31 Cell Line 58

source_name: DNA from T31 Cell Line 58


title: DNA from T31 Cell Line 55

source_name: DNA from T31 Cell Line 55


title: DNA from T31 Cell Line 54

source_name: DNA from T31 Cell Line 54


title: DNA from T31 Cell Line 57

source_name: DNA from T31 Cell Line 57


title: DNA from T31 Cell Line 56

source_name: DNA from T31 Cell Line 56


title: DNA from T31 Cell Line 61

source_name: DNA from T31 Cell Line 61


title: DNA from T31 Cell Line 74

source_name: DNA from T31 Cell Line 74


title: T31 Cell Line 60 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 60


title: T31 Cell Line 63 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 63


title: DNA from T31 Cell Line 53

source_name: DNA from T31 Cell Line 53


title: DNA from T31 Cell Line 52

source_name: DNA from T31 Cell Line 52


title: T31 Cell Line 58 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 58


title: T31 Cell Line 64 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 64


title: T31 Cell Line 62 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 62


title: DNA from T31 Cell Line 50

source_name: DNA from T31 Cell Line 50

source_name: A23 Hamster Cell Line


title: T31 Cell Line 61 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 61


title: T31 Cell Line 56 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 56


title: T31 Cell Line 57 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 57


title: DNA from T31 Cell Line 49

source_name: DNA from T31 Cell Line 49


title: DNA from T31 Cell Line 51

source_name: DNA from T31 Cell Line 51


title: T31 Cell Line 55 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 55


title: DNA from T31 Cell Line 44

source_name: DNA from T31 Cell Line 44


title: DNA from T31 Cell Line 46

source_name: DNA from T31 Cell Line 46


title: T31 Cell Line 54 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 54


title: DNA from T31 Cell Line 43

source_name: DNA from T31 Cell Line 43


title: T31 Cell Line 53 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 53


title: T31 Cell Line 51 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 51


title: T31 Cell Line 52 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 52


title: T31 Cell Line 59 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 59


title: DNA from T31 Cell Line 48

source_name: DNA from T31 Cell Line 48


title: DNA from T31 Cell Line 47

source_name: DNA from T31 Cell Line 47

source_name: A23 Hamster Cell Line


title: DNA from T31 Cell Line 41

source_name: DNA from T31 Cell Line 41


title: DNA from T31 Cell Line 39

source_name: DNA from T31 Cell Line 39


title: T31 Cell Line 49 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 49


title: T31 Cell Line 50 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 50


title: DNA from T31 Cell Line 45

source_name: DNA from T31 Cell Line 45


title: T31 Cell Line 47 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 47


title: T31 Cell Line 46 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 46


title: DNA from T31 Cell Line 42

source_name: DNA from T31 Cell Line 42


title: DNA from T31 Cell Line 38

source_name: DNA from T31 Cell Line 38


title: T31 Cell Line 44 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 44


title: DNA from T31 Cell Line 40

source_name: DNA from T31 Cell Line 40


title: T31 Cell Line 45 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 45


title: DNA from T31 Cell Line 37

source_name: DNA from T31 Cell Line 37


title: T31 Cell Line 48 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 48


title: DNA from T31 Cell Line 34

source_name: DNA from T31 Cell Line 34


title: DNA from T31 Cell Line 36

source_name: DNA from T31 Cell Line 36

source_name: A23 Hamster Cell Line


title: T31 Cell Line 43 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 43


title: T31 Cell Line 42 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 42


title: T31 Cell Line 41 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 41


title: DNA from T31 Cell Line 35

source_name: DNA from T31 Cell Line 35


title: T31 Cell Line 37 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 37


title: DNA from T31 Cell Line 31

source_name: DNA from T31 Cell Line 31


title: DNA from T31 Cell Line 29

source_name: DNA from T31 Cell Line 29


title: T31 Cell Line 36 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 36


title: T31 Cell Line 38 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 38


title: DNA from T31 Cell Line 27

source_name: DNA from T31 Cell Line 27


title: DNA from T31 Cell Line 30

source_name: DNA from T31 Cell Line 30


title: DNA from T31 Cell Line 28

source_name: DNA from T31 Cell Line 28


title: DNA from T31 Cell Line 26

source_name: DNA from T31 Cell Line 26


title: T31 Cell Line 35 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 35


title: DNA from T31 Cell Line 21

source_name: DNA from T31 Cell Line 21


title: DNA from T31 Cell Line 25

source_name: DNA from T31 Cell Line 25

source_name: A23 Hamster Cell Line


title: DNA from T31 Cell Line 23

source_name: DNA from T31 Cell Line 23


title: DNA from T31 Cell Line 24

source_name: DNA from T31 Cell Line 24


title: DNA from T31 Cell Line 32

source_name: DNA from T31 Cell Line 32


title: DNA from T31 Cell Line 22

source_name: DNA from T31 Cell Line 22


title: T31 Cell Line 31 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 31


title: DNA from T31 Cell Line 20

source_name: DNA from T31 Cell Line 20


title: T31 Cell Line 40 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 40


title: T31 Cell Line 30 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 30


title: DNA from T31 Cell Line 33

source_name: DNA from T31 Cell Line 33


title: T31 Cell Line 33 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 33


title: T31 Cell Line 27 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 27


title: T31 Cell Line 32 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 32


title: DNA from T31 Cell Line 19

source_name: DNA from T31 Cell Line 19


title: T31 Cell Line 24 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 24


title: DNA from T31 Cell Line 17

source_name: DNA from T31 Cell Line 17


title: DNA from T31 Cell Line 16

source_name: DNA from T31 Cell Line 16

source_name: A23 Hamster Cell Line


title: DNA from T31 Cell Line 18

source_name: DNA from T31 Cell Line 18


title: T31 Cell Line 34 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 34


title: T31 Cell Line 23 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 23


title: DNA from T31 Cell Line 12

source_name: DNA from T31 Cell Line 12


title: DNA from T31 Cell Line 15

source_name: DNA from T31 Cell Line 15


title: DNA from T31 Cell Line 14

source_name: DNA from T31 Cell Line 14


title: DNA from T31 Cell Line 11

source_name: DNA from T31 Cell Line 11


title: DNA from T31 Cell Line 13

source_name: DNA from T31 Cell Line 13


title: T31 Cell Line 39 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 39


title: T31 Cell Line 22 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 22


title: T31 Cell Line 28 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 28


title: T31 Cell Line 20 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 20


title: T31 Cell Line 18 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 18


title: DNA from T31 Cell Line 10

source_name: DNA from T31 Cell Line 10


title: T31 Cell Line 16 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 16


title: T31 Cell Line 14 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 14


title: DNA from T31 Cell Line 6

source_name: DNA from T31 Cell Line 6

source_name: A23 Hamster Cell Line


title: T31 Cell Line 15 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 15


title: DNA from T31 Cell Line 7

source_name: DNA from T31 Cell Line 7


title: T31 Cell Line 19 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 19


title: DNA from T31 Cell Line 9

source_name: DNA from T31 Cell Line 9


title: DNA from T31 Cell Line 5

source_name: DNA from T31 Cell Line 5


title: T31 Cell Line 12 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 12


title: T31 Cell Line 13 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 13


title: DNA from T31 Cell Line 3

source_name: DNA from T31 Cell Line 3


title: DNA from T31 Cell Line 8

source_name: DNA from T31 Cell Line 8


title: T31 Cell Line 11 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 11


title: DNA from T31 Cell Line 2

source_name: DNA from T31 Cell Line 2


title: DNA from T31 Cell Line 1

source_name: DNA from T31 Cell Line 1


title: T31 Cell Line 10 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 10


title: T31 Cell Line 17 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 17


title: T31 Cell Line 26 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 26


title: DNA from T31 Cell Line 4

source_name: DNA from T31 Cell Line 4

source_name: A23 Hamster Cell Line


title: T31 Cell Line 7 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 7


title: T31 Cell Line 21 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 21


title: T31 Cell Line 6 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 6


title: T31 Cell Line 29 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 29


title: A23 (transfected with Pcdh7, cy5) / A23 (tranfected with empty vector, cy3), biological replica 1

description: biological replicate 1 of 2

source_name: Total RNA from A23 tranfected with Pcdh7 labeled with cy5

label_protocol: RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to manufacturer's instructions.  This kit generated labeled cRNA targets.

growth_protocol: A23 and HEK cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks

treatment_protocol: Cells were transfected with Pcdh7 subcloned into the pCMV-sport6 vector (Invitrogen) using Effectene (Qiagen) according to manufacturer's instructions.  Parallel transfections of the empty vector alone were also performed.  The cells were harvested 48 hours after transfection.

tag: A23 lung fibroblast derived cell line

source_name: total RNA from HEK transfected with empty vector labeled with cy3


title: A23 (transfected with Pcdh7, cy5) / A23 (tranfected with empty vector, cy3), biological replica 2

description: biological replicate 2 of 2

source_name: total RNA from A23 transfected with empty vector labeled with cy3


title: T31 Cell Line 8 Replica 1

source_name: Total RNA from cell line A23 labeled with cy5

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 8


title: T31 Cell Line 4 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 4


title: T31 Cell Line 1 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 1


title: 96h ActA timepoint

status: Public on Mar 12 2008

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: 96h timepoint in an Activin A-driven differentiation timecourse experiment

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 17h at 55 degrees Celsius

scan_protocol: Using an Illumina scanner; gain factor: 2

data_processing: In BeadStudio 1.5, biological replicates were grouped, background subtracted and normalised using the "rank invariant" algorithm. Value = "25" denotes expression below ca. 50% of the detection threshold.

source_name: human embryonic stem cells

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 400ng of total RNA; IVT: 7h

growth_protocol: N2B27 medium contained DMEM/F12 (Hyclone), N2 and B27 supplements (Invitrogen), 0.5% BSA (fraction V, Invitrogen), non-essential amino acids, glutamine, pen/strep (Invitrogen), 0.1 mM ß-mercaptoethanol, and 100 ng/ml Activin A (R&D).

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion following the manufacturer's instructions

treatment_protocol: hES cells grown in N2B27-based chemically defined medium were treated for 96h with recombinant Activin A in the absense of FGF2

tag: line H1


title: HEK (transfected with Pcdh7, cy5) / HEK (tranfected with empty vector, cy3), biological replica 2

description: biological replicate 2 of 2

source_name: Total RNA from HEK tranfected with Pcdh7 labeled with cy5

tag: HEK 293 cell line, human epithelial kidney


description: H1 hES cells grown in MEF-conditioned medium in the context of a medium comparison.

data_processing: In BeadStudio 1.5, data were background subtracted and normalised using the "cubic spline" algorithm. Value = "30" denotes expression below ca. 50% of the detection threshold.

growth_protocol: On Matrigel-coated dishes, cells were grown in MEF-conditioned medium prepared using CF1 mouse inactivated fibroblasts and following a standard protocol. Cells were harvested four days after passaging.


title: 36h ActA timepoint

description: 36h timepoint in an Activin A-driven differentiation timecourse experiment

treatment_protocol: hES cells grown in N2B27-based chemically defined medium were treated for 36h with recombinant Activin A in the absense of FGF2


title: 24h ActA timepoint

description: 24h timepoint in an Activin A-driven differentiation timecourse experiment

treatment_protocol: hES cells grown in N2B27-based chemically defined medium were treated for 24h with recombinant Activin A in the absense of FGF2


title: 12h ActA timepoint

description: 12h timepoint in an Activin A-driven differentiation timecourse experiment

treatment_protocol: hES cells grown in N2B27-based chemically defined medium were treated for 12h with recombinant Activin A in the absense of FGF2


title: H1 hES cells grown in N2B27 medium

description: H1 hES cells grown in N2B27-based medium in the context of a medium comparison.

growth_protocol: On Matrigel-coated dishes, cells were grown in N2B27 medium that contained DMEM/F12 (Hyclone), N2 and B27 supplements (Invitrogen), 0.5% BSA (fraction V, Invitrogen), non-essential amino acids, glutamine, pen/strep (Invitrogen), 0.1 mM ß-mercaptoethanol, and 20 ng/ml FGF2 (Peprotech). Cells were adapted to growth in N2B27, replated, and harvested four days after passaging.


title: T31 Cell Line 2 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 2


title: T31 Cell Line 5 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 5


title: T31 Cell Line 3 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 3


title: 48h ActA timepoint

description: 48h timepoint in an Activin A-driven differentiation timecourse experiment

treatment_protocol: hES cells grown in N2B27-based chemically defined medium were treated for 48h with recombinant Activin A in the absense of FGF2


title: 72h ActA timepoint

description: 72h timepoint in an Activin A-driven differentiation timecourse experiment

treatment_protocol: hES cells grown in N2B27-based chemically defined medium were treated for 72h with recombinant Activin A in the absense of FGF2


title: 0h Activin A control

description: Non-stimulated control (0h timepoint) in an Activin A-driven differentiation timecourse experiment

growth_protocol: N2B27 medium contained DMEM/F12 (Hyclone), N2 and B27 supplements (Invitrogen), 0.5% BSA (fraction V, Invitrogen), non-essential amino acids, glutamine, pen/strep (Invitrogen), 0.1 mM ß-mercaptoethanol, and 20 ng/ml FGF2 (Peprotech).

treatment_protocol: hES cells grown in N2B27-based chemically defined medium.


title: T31 Cell Line 25 Replica 1

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 25


title: hES cells in N2B27 - non-stimulated control for BMP4-stimulated sample

description: Non-stimulated control in a short-term BMP4 stimulation experiment

data_processing: In BeadStudio 1.5, biological replicates were grouped, background subtracted and normalised using the "cubic spline" algorithm. Value = "20" denotes expression below ca. 50% of the detection threshold.

treatment_protocol: Cells were adapted to N2B27-based chemically defined medium, replated, and harvested three days after passaging.


title: Drosophila CL8 sample 4

city: Columbus

first: Amanda

last: Simcox

state: OH

address: 484 W. 12th Avenue

department: Molecular Genetics

institute: The Ohio State University

description: Affymetrix standard reagents and protocols were used for labeling, hybridizing and scanning.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: R and bioconductor were used to preprocess and analyze the data

source_name: Drosophila cell culture

label_protocol: Affymetrix standard protocol

extract_protocol: Qiagen RNeasy

tag: Cell line, Drosophila


title: HEK (transfected with Pcdh7, cy5) / HEK (tranfected with empty vector, cy3), biological replica 1

description: biological replicate 1 of 2


title: hES cells in N2B27 - 2h stimulated with Activin A

description: Activin A-treated sample in a short-term Activin A stimulation experiment

data_processing: In BeadStudio 1.5, data were background subtracted and normalised using the "cubic spline" algorithm. Value = "20" denotes expression below ca. 50% of the detection threshold.

growth_protocol: N2B27 medium contained DMEM/F12 (Hyclone), N2 and B27 supplements (Invitrogen), 0.5% BSA (fraction V, Invitrogen), non-essential amino acids, glutamine, pen/strep (Invitrogen), 0.1 mM ß-mercaptoethanol, and 20 ng/ml FGF2 (Peprotech). Activin A (Peprotech) was used at 100 ng/ml.

treatment_protocol: Cells were adapted to N2B27-based chemically defined medium, replated, and, three days after passaging, stimulated with Activin A for 2h.


title: H1 hES cells in N2B27 - non-stimulated control for Activin A-stimulated sample

description: Non-stimulated control in a short-term Activin A stimulation experiment


title: H9 hES cells grown in MEF-CM, then for 1 day in UM, then for 4h in UM_GTA

description: This is one of two treatment samples from a re-stimulation experiment using MEF-conditioned medium or unconditioned medium plus Activin A, TGFß1, and Gremlin.

data_processing: In BeadStudio 1.5, biological replicates were grouped, background subtracted and normalised using the "cubic spline" algorithm. Value = "25" denotes expression below ca. 50% of the detection threshold.

treatment_protocol: H9 cells were grown for 3 days in MEF-conditioned medium, then starved for 1 day in unconditioned medium plus 10 ng/ml FGF2, then re-stimulated with unconditioned medium plus Activin A, TGFß1, and Gremlin for 4h.

tag: line H9


title: Drosophila CL8 sample 3


title: Drosophila CL8 sample 2