title: adrenal gland high stress 8054

city: Dummerstorf

first: Eduard

last: Murani

address: Wilhelm-Stahl-Allee 2

department: Molecular Biology

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: EU SABRE Wp8 project

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Affymetrix Expression Console v1.1.1 using MAS5.0

organism: Sus scrofa domesticus

source_name: porcine adrenal gland, high aggressiveness mixing treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA

tag: stress level

value: high


title: Blast-infected SHZ-2, 24 hours, replicate2

status: Public on May 31 2011

type: RNA

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replicate 2 of 3, Blast-infected SHZ-2 after 24 hours.

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: Blast-infected SHZ, 24hours

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Autoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 0 hour

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: TRIzol
manual: Invitrogen

treatment_protocol:
Treatment method: spray inoculation
Growth environment: greenhouse
Growth stage:  21-day-old plant
Light condition: Continuous dark
Temperature: 25℃
Humidity: 100%
Fungus inoculation: Magnaporthe oryzae, strain PO6-6
Fungus inoculation: spraying water suspended of 7 ×10e5 spores/ml
Fungus inoculation: 24hours

tag: strain

tag: cultivar

value: indica

tag: tissue

value: whole plant

tag: plant height

value: 5 cm above ground

source_name: Mock inoculation SHZ, 24hours

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of InternationAu Rice Research Institute, Philippines. Auutoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 0 hour

treatment_protocol:
Treatment method: spray inoculation
Growth environment: greenhouse
Growth stage:  21-day-old plant
Light condition: Continuous dark
Temperature: 25℃
Humidity: 100%
Mock inoculation: sterile distilled water
Mock inoculation: spraying water
Mock inoculation: 24hours


title: adrenal gland high stress 8027

description: EU SABRE Wp8 project

label: biotin

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


title: Blast-infected SHZ-2, 24 hours, replicate3

description: Biological replicate 3 of 3, Blast-infected SHZ-2 after 24 hours.


title: pre-treatment tumor biopsy HSP_247

city: Barcelona

first: MIGUEL ANGEL

last: PAVON

state: Barcelona

address: Sant Antoni Maria Claret, 167

department: INSTITUT INVESTIGACIÓ BIOMÉDICA SANT PAU

country: Spain

institute: HOSPITAL DE LA SANTA CREU I SANT PAU

description:
Gene expression data from a pre-treatment tumor biopsy
Patients included in our microarray study (n=63) were treated from 1999 to 2007 at Hospital de la Santa Creu i Sant Pau (HSCSP). All had a pathologically confirmed, untreated, locally advanced (stage III, IVA & IVB) HNSCC. Patients defined as not operable at diagnosis were treated with concomitant CRT (stage IVB), whereas operable patients (stage III or IVA) were treated with IC followed by CRT/RT or surgery.  Induction Chemotherapy consisted on the administration of cisplatin at a dose of 100 mg/m2 on day 1, and 5-FU at a dose of 1,000 mg/m2/day by continuous intravenous infusion on days 2 to 6 every 3 weeks, per three courses.   After IC, patients whose tumour showed a complete response or a partial response above 50% received radiotherapy (IC+RT) or chemo radiotherapy (IC+CRT). Patients with stable or progressive disease after IC were treated with surgery (IC+SURGERY). Radiotherapy, at a total dose of 70 Gy, was administered to the primary tumor and clinically positive nodes, in 35 fractions of 2 Gy each, over a 7-week period. Nodal areas not clinically involved by tumor received a total dose of 50 Gy. Concomitant chemo radiotherapy (cCRT) consisted in RT at the same doses plus 3 cycles of cisplatin at a dose of 100mg/m2 on day 1 every 3 weeks.
Probe microarray washing and staining was performed in a Fluidics Station 450 applying the midi_euk2v3_450 protocol.

hyb_protocol: Ten micrograms of biotinylated cRNA, previously fragmented, were hybridized to the Affymetrix HG-U133A 2.0 microarray at 45ºC for 16 hours in the Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned using a Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA, USA).The acquisition of microarray images was performed using GCOS software

data_processing: All the microarrays “.CEL” files included in the study were pre-processed applying the Robust Multi-array Average (RMA) algorithm (Irizarry, Hobbs et al. 2003) implemented in the Bioconductor statistical affy package  (http://www.bioconductor.org).

organism: Homo sapiens

source_name: pre-treatment tumor biopsy

label_protocol: cDNA and cRNA synthesis were performed using 2μg of total RNA from each biopsy as starting material and the GeneChip One-Cycle Target Labelling and Control Reagents Kit, following the instructions described in the Affymetrix user’s manual (Affymetrix, Santa Clara, CA, USA). After “in vitro” transcription, we obtained biotinylated cRNA. cRNA quality was checked using the Agilent 2100 Bioanalyzer.

extract_protocol: The study was performed using 63 fresh pre-treatment primary tumor biopsies and five normal mucosa samples obtained from HNSCC patients. A sample aliquot was used for pathological diagnosis of the malignancy and another aliquot was immersed in RNAlater (Applied Biosystems Incorp, Foster City, CA), frozen in cold isopentane and kept in liquid nitrogen until RNA processing. Total RNA was extracted with Trizol (Invitrogen Ltd, Paisley, UK) and the phenol-chloroform method as previously described (Pavon, Parreno et al. 2008). Samples were, then, cleaned-up using RNeasy® Spin columns (Qiagen Incorp, Valencia, CA). Total RNA was quantified spectrophotometrically. The Agilent 2100 Bioanalyzer and the RNA Nano 6000 kit (Agilent Technologies, Santa Clara, USA) were used to determine the integrity of total RNA samples. Only samples with an RNA integrity number (RIN) higher than seven were included.

tag: sex

value: male

tag: tumor size (t)

tag: node involvement (n)

value: POSITIVE

tag: distant metastasis (m)

value: NEGATIVE

tag: patient treatment plan

value: IC+SURGERY

value: HNSCC tumor


title: EC1118 Reference sample point 0_2

city: LOGROÑO

first: Vanessa

last: Penacho

state: LA RIOJA

address: c/ Madre de Dios, 51

department: Oenology & Viticulture

institute: ICVV/CSIC

hyb_protocol: 15 μg of cRNA were fragmented and hybridized to the Affymetrix GeneChip® Yeast Genome 2.0. Array in GeneChip® Hybridization Oven 640 for 16 h at 45°C. Hybridized microarrays were washed and stained with a streptavidin-phycoerythrin conjugate (SAPE) in a GeneChip® Fluidics Station 450.

scan_protocol: Hybridized cRNA was finally identified by the fluorescence signal in a GeneChip® 3000 scanner.

data_processing: The .CEL files generated from the scanning were converted to gene expression signals using the RMA software (Irizarry et al., 2003).

label: Biotin

organism: Saccharomyces cerevisiae

label_protocol: Double stranded cDNA was synthesized from 5 μg of total RNA using Onecycle cDNA Synthesis Kit (Affymetrix). After cDNA purification using the GeneChip Sample Cleanup Module (Affymetrix), this DNA was used as template for the in vitro transcription using the 3' IVT Express Labeling Kit (Affymetrix) to obtain the biotin labelled cRNA. Its size profile is evaluated with Bioanalyzer 6000.

growth_protocol: Growth under individual unstressed conditions, in YPD medium at 28 ºC until mid-exponential growth phase (OD =1.0 at 600 nm).

extract_protocol: RNA was extracted from yeast cells exactly as previously described in Chomczynski and Sacchi (1987). Total RNA was then purified using the RNeasy Mini Kit-RNA Cleanup (Qiagen) according to the manufacturer's instructions. Concentration of total RNA was measured at 260 nm in a ND-1000 Spectrophotometer (Nanodrop, Thermo Fisher Scientific Inc.) and sample quality was checked using RNA Nano Labchips in a Bioanalyzer 6000 (Agilent Technologies).

value: EC1118 (Lallemand Inc.)

tag: sampling

value: exponential-growth phase as external reference

tag: sampling point

tag: biological replicate


title: adrenal gland high stress 5053

description: EU SABRE Wp8 project


title: Blast-infected TXZ-13, 48 hours, replicate2

description: Biological replicate 2 of 3, Blast-infected TXZ-13 after 48 hours.

source_name: Blast-infected TXZ, 48hours

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Autoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 24 hours

source_name: Mock inoculation TXZ, 48hours

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (W:21.59cm ×D:11.43cm × H:8.89cm)
Growth media: Soil collected fielf of InternationAu Rice Research Institute, Philippines. Auutoclaved prior to use
No of seedlings per pot : 15
Light condition: Natural conditions
Temperature: 28±3℃
Growth time (before treatment): 21 days after sowing
Growth time (after treatment): 24 hours


title: Blast-infected SHZ-2, 24 hours, replicate1

description: Biological replicate 1 of 3, Blast-infected SHZ-2 after 24 hours.


title: Blast-infected TXZ-13, 48 hours, replicate3

description: Biological replicate 3 of 3, Blast-infected TXZ-13 after 48 hours.


title: Day10_uninfected_rep3 _Dchip

city: South Bend

first: Kasturi

last: Haldar

email: khaldar@nd.edu, ptamez@nd.edu

state: IN

address: 107 Galvin Life Sciences

department: Biology

country: USA

institute: University of Notre Dame

description: Gene expression data from differentiating hematopoietic stem cells that are mitotic

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with 2 programs, GenePattern and Dchip. For GenePattern, Data were normalized with RMA using the “ExpressionFileCreator” module and filtered using the default settings of “PreprocessDataset” module. Dchip data were normalized using model-based expression and default settings.

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 10, uninfected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: Human primary erythroblasts were generated by culturing CD34 early hematopoietic progenitors initially isolated from growth factor-mobilized peripheral blood (purchased from ALL Cells, Inc.) using an Isolex 300i cell selection device. The culture contained 15% fetal bovine serum, 15% human serum, Isocove’s modified Dulbecco’s medium (IMDM), 10 ng/ml interleukin-3, 2 units/ml EPO, and 50 ng/ml SCF. During the  initial 8 days of culture, cells were fed on days 3 and 6 by adding equal volumes of fresh culture media supplemented with growth factors. However, no new interleukin-3 was added after the initial addition on day 0, and the amount of SCF added to the fresh media was gradually decreased at each feeding (day 3, 25 ng/ml; day 6, 10 ng/ml; day 8, 2 ng/ml). The amount of EPO added was 2 units/ml during each feeding. On day 8 of culture, cells were further purified by flow cytometry sorting for GlyA/CD71 or CD71 cells using a MoFlo high speed flow cytometer.  The purity of the population isolated by this method was 98–99%. Sorted cells were cultured in the same media as before with EPO and SCF, except the concentration of SCF was reduced to 2 ng/ml. Cells were fed one more time on day 10 of culture by adding equal volumes of fresh media with only EPO (2 units/ml) during this final feeding.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified over Qiagen columns (Rneasy) according to manufacturer's recommendations

treatment_protocol: Plasmodium falciparum 3D7 was synchronized by successive rounds of Percoll and sorbitol. Late stage schizonts were used to initiate infection of 2x10^6 erythroblasts at a multiplicity of infection =5. Erythroblasts were infected on day 10 (polychromatic stage) and day 14 (orthochromatic) of culture. Cells were resuspended at 1x10^6/ml in Iscove’s Modified Dulbecco’s Medium supplemented with 30% human serum and 2 units/ml EPO and incubated in 5% CO2-humidified chamber at 37ºC. Cells were harvested after 24 hr for RNA isolation.

tag: cell type

value: growth factor-mobilized CD34+ hematopoietic stem cells

tag: developmental stage

value: differentiated to day 10 (polychromatophilic stage)


title: pre-treatment tumor biopsy HSP_253

value: female


title: EC1118 Reference sample point 0_3


title: Blast-infected SHZ-2, 48 hours, replicate1

description: Biological replicate 1 of 3, Blast-infected SHZ-2 after 48 hours.

source_name: Blast-infected SHZ, 48hours

source_name: Mock inoculation SHZ, 48hours


title: pre-treatment tumor biopsy HSP_273


title: Day10_uninfected_rep1 _Dchip


title: Day10_uninfected_rep2 _Dchip


title: EC1118 Reference sample point 0_1


title: Blast-infected TXZ-13, 48 hours, replicate1

description: Biological replicate 1 of 3, Blast-infected TXZ-13 after 48 hours.


title: adrenal gland high stress 4066

description: EU SABRE Wp8 project


title: pre-treatment tumor biopsy HSP_246

value: IC+RT


title: Blast-infected TXZ-13, 24 hours, replicate3

description: Biological replicate 3 of 3, Blast-infected TXZ-13 after 24 hours.

source_name: Blast-infected TXZ, 24hours

source_name: Mock inoculation TXZ, 24hours


title: pre-treatment tumor biopsy HSP_242


title: adrenal gland high stress 4034

description: EU SABRE Wp8 project


title: Blast-infected TXZ-13, 24 hours, replicate2

description: Biological replicate 2 of 3, Blast-infected TXZ-13 after 24 hours.


title: pre-treatment tumor biopsy HSP_233

value: CRT


title: adrenal gland high stress 5020

description: EU SABRE Wp8 project


title: adrenal gland low stress 8039

description: EU SABRE Wp8 project

source_name: porcine adrenal gland, low aggressiveness mixing treatment

value: low


title: pre-treatment tumor biopsy HSP_241


title: pre-treatment tumor biopsy HSP_227

value: IC+CRT


title: non-meristematic tissues, biological rep1

city: Melbourne

first: farzad

last: haerizadeh

state: VIC.

address: University of Melbourne

department: land & food

country: Australia

institute: Melbourne University

description: Gene expression data from embryos in slow phase of cellularisation.

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

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

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

organism: Glycine max

source_name: non-meristematic tissues

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

growth_protocol: 28 degree centigrade, natural day light (long days)  in potting mix (soil:perlite:sand) grow for 10 days without fertilizer

extract_protocol: QIAGEN Total RNA extraction kit

treatment_protocol: Fresh root tips were dissected under microscope and were frozen immediately in liquid nitrogen, also the rest of the nonmeroistematic parts for non meristem samples were snap frozen.

value: non-meristematic tissues (leaf)

tag: genotype

value: Bragg

tag: age

value: 10 days old


title: pre-treatment tumor biopsy HSP_226


title: pre-treatment tumor biopsy HSP_245

value: male


title: adrenal gland low stress 5075

description: EU SABRE Wp8 project

tag: stress level


title: Day14_uninfected_rep5_GenePattern

description: Gene expression data from differentiating hematopoietic stem cells that are preparing to extrude the nucleus

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 14, uninfected

value: differentiated to day 14 (orthochromatic stage)


title: non-meristematic tissues, biological rep2


title: adrenal gland high stress 3059

description: EU SABRE Wp8 project

value: high


title: Day14_infected_rep3_GenePattern

description: Gene expression data from differentiating hematopoietic stem cells that are preparing to extrude the nucleus and infected

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 14, infected with Plasmodium falciparum for 24 h


title: Day14_uninfected_rep3_GenePattern


title: adrenal gland high stress 3067

description: EU SABRE Wp8 project


title: Day14_uninfected_rep4_GenePattern


title: Day14_infected_rep2_GenePattern


title: pre-treatment tumor biopsy HSP_225

value: POSITIVE

value: NEGATIVE


title: RAM, biological rep3

source_name: 0.5 mm root tip

value: root apical meristem (RAM)


title: Day14_infected_rep1_GenePattern


title: Blast-infected TXZ-13, 24 hours, replicate1

description: Biological replicate 1 of 3, Blast-infected TXZ-13 after 24 hours.

tag: strain

value: indica

value: whole plant

value: 5 cm above ground


title: RAM, biological rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: Day14_uninfected_rep2_GenePattern

value: growth factor-mobilized CD34+ hematopoietic stem cells


title: pre-treatment tumor biopsy HSP_221

value: IC+SURGERY

value: HNSCC tumor


title: adrenal gland low stress 4049

description: EU SABRE Wp8 project

value: low


title: adrenal gland low stress 4016

description: EU SABRE Wp8 project


title: pre-treatment tumor biopsy HSP_217


title: Day14_uninfected_rep1_GenePattern


title: adrenal gland low stress 8005

description: EU SABRE Wp8 project


title: pre-treatment tumor biopsy HSP_215

value: IC+RT


title: Day10_infected_rep3_GenePattern

description: Gene expression data from differentiating hematopoietic stem cells that are mitotic and infected

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 10, infected with Plasmodium falciparum for 24 h

value: differentiated to day 10 (polychromatophilic stage)


title: pre-treatment tumor biopsy HSP_216


title: adrenal gland low stress 3035

description: EU SABRE Wp8 project


title: RAM, biological rep1

value: Bragg


title: pre-treatment tumor biopsy HSP_207

value: IC+CRT


title: Day10_infected_rep1_GenePattern


title: Day10_infected_rep2_GenePattern


title: pre-treatment tumor biopsy HSP_210

value: male


title: Day10_uninfected_rep5_GenePattern


title: Day10_uninfected_rep2_GenePattern


title: Day10_uninfected_rep3_GenePattern


title: Day10_uninfected_rep4_GenePattern


title: pre-treatment tumor biopsy HSP_202

value: female


title: Huh7 EZH2 ChIP-chip Replicate 2 Slide 2

type: genomic

city: Shatin

first: Richard

middle: KW

last: CHOY

address: 1/F, Block E, Prince of Wales Hospital

department: Obstetrics & Gynaecology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Huh7 Replicate 2 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Huh7 cells input

label_protocol: DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.

growth_protocol: The 2 HCC cell lines were maintained in DMEM supplemented with 10% FBS.

extract_protocol: ChIP assays were performed as described previously (Lee et al. Nat Protoc 2006;1:729-748). IP and input DNA were then purified with standard phenol/chloroform method.

treatment_protocol: No treatment was performed. EZH2 target genes in normal condition were identified.

tag: cell line

source_name: Huh7 cells immunoprecipitated


title: pre-treatment tumor biopsy HPS_200

tag: tissue


title: pre-treatment tumor biopsy HSP_214


title: adrenal gland low stress 3022

description: EU SABRE Wp8 project


title: PLC5 EZH2 ChIP-chip Replicate 2 Slide 2

description: PLC5 Replicate 2 of 2

source_name: PLC5 cells input

source_name: PLC5 cells immuoprecipitated


title: PLC5 EZH2 ChIP-chip Replicate 2 Slide 1

description: PLC5 Replicate 2 of 2


title: Huh7 EZH2 ChIP-chip Replicate 2 Slide 1

description: Huh7 Replicate 2 of 2


title: Day10_uninfected_rep1_GenePattern


title: adrenal gland low stress 5041

description: EU SABRE Wp8 project


title: PLC5 EZH2 ChIP-chip Replicate 1 Slide 2

description: PLC5 Replicate 1 of 2


title: PLC5 EZH2 ChIP-chip Replicate 1 Slide 1

description: PLC5 Replicate 1 of 2


title: Patient 452 treated 4h

status: Public on May 30 2011

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: Gene expression data from whole PB samples from CLL patient collected at the indicated time point after the first infusion of SPC2996

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133Plus_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (G7 update).

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: Patient 452 treated 4h

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: Whole PB samples were collected at the designated time points and stored at -80°C for up to 3 years in the PAXgene blood stabilizing system. After thawing, RNA was extracted employing the QIAGEN PAXgene extraction kit and repurified using the Rneasy MinElute Cleanup kit (QIAGEN).

tag: tumor type

value: chronic lymphocytic leukemia

tag: tissue type

value: whole peripheral blood

tag: therapeutic agent

tag: dose group

value: 6mg per kg

tag: time point

value: 4h post tx


title: Patient 452 treated 24h

source_name: Patient 452 treated 24h

value: 24h post tx


title: Huh7 EZH2 ChIP-chip Replicate 1 Slide 2

description: Huh7 Replicate 1 of 2


title: Patient 451 control

description: Gene expression data from whole PB samples from CLL patient collected before the first infusion of SPC2996

source_name: Patient 451 control

value: pre-tx


title: Patient 450 treated 4h

source_name: Patient 450 treated 4h

value: 4mg per kg


title: Huh7 EZH2 ChIP-chip Replicate 1 Slide 1

description: Huh7 Replicate 1 of 2


title: Patient 452 control

source_name: Patient 452 control


title: Patient 451 treated 24h

source_name: Patient 451 treated 24h


title: Patient 450 treated 4 weeks

source_name: Patient 450 treated 4 weeks

value: 4weeks post tx


title: Patient 449 treated 4 weeks

source_name: Patient 449 treated 4 weeks


title: Patient 450 treated 24h

source_name: Patient 450 treated 24h


title: Patient 449 treated 4h

source_name: Patient 449 treated 4h


title: Patient 448 treated 24h

source_name: Patient 448 treated 24h


title: Patient 448 treated 4h

source_name: Patient 448 treated 4h


title: Patient 448 control

source_name: Patient 448 control


title: Patient 452 treated 4 weeks

source_name: Patient 452 treated 4 weeks


title: Patient 451 treated 4 weeks

source_name: Patient 451 treated 4 weeks


title: Patient 449 control

source_name: Patient 449 control


title: Patient 451 treated 4h

source_name: Patient 451 treated 4h


title: Patient 443 treated 24h

source_name: Patient 443 treated 24h


title: Patient 449 treated 24h

source_name: Patient 449 treated 24h


title: Day14_uninfected_rep1 _Dchip

source_name: CD34+-derived Hematopoietic stem cells in vitro differentiated to day 14, uninfected

value: growth factor-mobilized CD34+ hematopoietic stem cells

value: differentiated to day 14 (orthochromatic stage)


title: Patient 444 treated 24h

source_name: Patient 444 treated 24h


title: Patient 450 control

source_name: Patient 450 control


title: Patient 443 treated 4 weeks

source_name: Patient 443 treated 4 weeks


title: Patient 444 control

source_name: Patient 444 control


title: Patient 441 treated 24h

source_name: Patient 441 treated 24h


title: Patient 441 control

source_name: Patient 441 control


title: Patient 443 control

source_name: Patient 443 control


title: Patient 428 treated 4 weeks

source_name: Patient 428 treated 4 weeks


title: Patient 427 treated 4 weeks

source_name: Patient 427 treated 4 weeks

value: 2mg per kg


title: Patient 428 treated 4h

source_name: Patient 428 treated 4h


title: Patient 428 control

source_name: Patient 428 control


title: Patient 427 control

source_name: Patient 427 control


title: Patient 425 treated 4 weeks

source_name: Patient 425 treated 4 weeks


title: Patient 424 treated 24h

source_name: Patient 424 treated 24h


title: Patient 425 treated 24h

source_name: Patient 425 treated 24h


title: Patient 424 control

source_name: Patient 424 control


title: Patient 422 treated 24h

source_name: Patient 422 treated 24h

value: 1mg per kg


title: Patient 404 treated 4h

source_name: Patient 404 treated 4h


title: Patient 422 treated 4 weeks

source_name: Patient 422 treated 4 weeks


title: Patient 404 treated 24h

source_name: Patient 404 treated 24h


title: Patient 422 control

source_name: Patient 422 control


title: Patient 425 control

source_name: Patient 425 control


title: Patient 402 treated 24h

source_name: Patient 402 treated 24h

value: 0.2mg per kg


title: Patient 411 treated 24h

source_name: Patient 411 treated 24h


title: Patient 403 treated 4 weeks

source_name: Patient 403 treated 4 weeks


title: Patient 403 treated 24h

source_name: Patient 403 treated 24h


title: Patient 428 treated 24h

source_name: Patient 428 treated 24h


title: Patient 404 control

source_name: Patient 404 control


title: Patient 402 treated 4 weeks

source_name: Patient 402 treated 4 weeks


title: Patient 401 control

source_name: Patient 401 control


title: Patient 427 treated 24h

source_name: Patient 427 treated 24h


title: Patient 411 treated 4 weeks

source_name: Patient 411 treated 4 weeks


title: Patient 401 treated 24h

source_name: Patient 401 treated 24h


title: Patient 424 treated 4 weeks

source_name: Patient 424 treated 4 weeks


title: Patient 411 control

source_name: Patient 411 control


title: Patient 402 control

source_name: Patient 402 control


title: sample 104

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: buccal swab sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged using iScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip to chip variation. Finally, average beta is recalculated from normalized intensities: methylated intensity / (methylated + unmethylated intensities).  Data row was removed if >50% of the data points at that site were deemed bad during the QC process.

label: Cy3 and Cy5

source_name: Buccal Swabs

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Isohelix Buccal DNA Isolation Kits (Cell Projects) and purified and concentrated using DNA Clean & Concentrator (Zymo Research) according to manufacturer's instruction.

tag: gender

value: Male

tag: maternal stress infancy

tag: maternal stress preschool

tag: paternal stress infancy

tag: paternal stress preschool

value: 15 years old

value: bucca

value: epithelial cell


title: sample 108

description: buccal swab sample

tag: cell type


title: sample 109

description: buccal swab sample

value: Female


title: sample 105

description: buccal swab sample


title: sample 102

description: buccal swab sample


title: sample 101

description: buccal swab sample


title: sample 096

description: buccal swab sample


title: sample 103

description: buccal swab sample


title: sample 097

description: buccal swab sample


title: sample 088

description: buccal swab sample


title: sample 089

description: buccal swab sample


title: sample 106 (reps a,b)

description:
technical replicates
sample 106a
sample 106b


title: sample 090

description: buccal swab sample


title: sample 085

description: buccal swab sample


title: sample 099 (reps a,b,c)

description:
technical replicates
sample 099a
sample 099b
sample 099c


title: sample 091

description: buccal swab sample


title: sample 092

description: buccal swab sample


title: sample 093

description: buccal swab sample


title: sample 095

description: buccal swab sample


title: sample 084

description: buccal swab sample


title: sample 086

description: buccal swab sample


title: sample 082

description: buccal swab sample


title: sample 081

description: buccal swab sample


title: sample 080

description: buccal swab sample


title: sample 077

description: buccal swab sample


title: sample 083

description: buccal swab sample


title: sample 098

description: buccal swab sample


title: sample 107

description: buccal swab sample


title: sample 078

description: buccal swab sample


title: sample 087

description: buccal swab sample


title: sample 100

description: buccal swab sample


title: sample 073

description: buccal swab sample


title: sample 075

description: buccal swab sample


title: sample 064

description: buccal swab sample


title: sample 068

description: buccal swab sample


title: sample 079

description: buccal swab sample


title: sample 060

description: buccal swab sample


title: sample 071

description: buccal swab sample


title: sample 061

description: buccal swab sample


title: sample 076

description: buccal swab sample


title: sample 069

description: buccal swab sample


title: sample 067

description: buccal swab sample


title: sample 065

description: buccal swab sample


title: sample 059

description: buccal swab sample


title: sample 063

description: buccal swab sample


title: sample 072

description: buccal swab sample


title: sample 058

description: buccal swab sample


title: sample 070

description: buccal swab sample


title: sample 056

description: buccal swab sample


title: sample 066

description: buccal swab sample


title: sample 054

description: buccal swab sample


title: sample 062

description: buccal swab sample


title: sample 052

description: buccal swab sample


title: sample 055

description: buccal swab sample


title: Patient 403 control

source_name: Patient 403 control

value: chronic lymphocytic leukemia

value: whole peripheral blood


title: sample 053

description: buccal swab sample


title: sample 057

description: buccal swab sample


title: sample 051

description: buccal swab sample


title: sample 049

description: buccal swab sample


title: sample 039

description: buccal swab sample


title: sample 040

description: buccal swab sample


title: sample 050

description: buccal swab sample


title: sample 036

description: buccal swab sample


title: sample 041

description: buccal swab sample


title: sample 045

description: buccal swab sample


title: sample 047

description: buccal swab sample


title: sample 044

description: buccal swab sample


title: sample 032

description: buccal swab sample


title: sample 033

description: buccal swab sample


title: sample 048

description: buccal swab sample


title: sample 031

description: buccal swab sample


title: sample 042

description: buccal swab sample


title: sample 037

description: buccal swab sample


title: sample 026

description: buccal swab sample


title: sample 046

description: buccal swab sample


title: sample 025

description: buccal swab sample


title: sample 027

description: buccal swab sample


title: sample 030

description: buccal swab sample


title: sample 023

description: buccal swab sample


title: sample 043

description: buccal swab sample


title: sample 024

description: buccal swab sample


title: sample 038

description: buccal swab sample


title: sample 034

description: buccal swab sample


title: sample 035

description: buccal swab sample


title: sample 029

description: buccal swab sample


title: sample 028

description: buccal swab sample


title: sample 022

description: buccal swab sample


title: sample 094

description: buccal swab sample


title: sample 020

description: buccal swab sample


title: Microdissection IPMC3

city: Sendai

first: Shin

last: Hamada

state: Miyagi

address: 1-1 Seiryo-machi, Aobaku

department: Division of Gastroenterology

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Labeled RNA was diluted by hybridization buffer and hybridized with array slide for 20 hours.

scan_protocol: Hybridized array slides were scanned by Agilent Microarray Scanner (Agilent Technologies), and fluorescent signal of each spot was corrected using Agilent Feature Extraction v.9.1.3.1 (Agilent Technologies).

data_processing: Fluorescent signal of each spot was corrected using Agilent Feature Extraction v.9.1.3.1 (Agilent Technologies).  The background signal was subtracted from each spot’s signal.

label: cyanine 3

source_name: IPMC

label_protocol: One hundred ng of total RNA from each sample was labeled by cyanine 3-cytidine bisphosphate using miRNA Complete Labeling Reagent and Hyb kit (Agilent Technologies)

extract_protocol: Total cellular RNA was extracted from microdissected sample or pancreatic cancer cell line using the mirVana™ miRNA Isolation Kit (Applied Biosystems, Foster City, CA).

value: IPMC

tag: sample type

value: surgically resected sample


title: sample 016

description: buccal swab sample

tag: age


title: Microdissection IPMC5


title: Microdissection IPMC1


title: sample 021

description: buccal swab sample


title: sample 017

description: buccal swab sample


title: Microdissection IPMC2


title: Microdissection IPMC6


title: Microdissection IPMA6

source_name: IPMA

value: IPMA


title: sample 019

description: buccal swab sample


title: Microdissection IPMC4


title: sample 018

description: buccal swab sample


title: Microdissection IPMA2


title: Microdissection IPMA3


title: Microdissection IPMA4


title: Microdissection IPMA5


title: sample 015

description: buccal swab sample


title: sample 012

description: buccal swab sample


title: sample 010

description: buccal swab sample


title: sample 014

description: buccal swab sample


title: sample 011

description: buccal swab sample


title: sample 008

description: buccal swab sample


title: Microdissection IDA4

source_name: IDA

value: IDA


title: sample 009

description: buccal swab sample


title: Microdissection IPMA1


title: sample 013

description: buccal swab sample


title: sample 007

description: buccal swab sample


title: Cultured cell PANC1

source_name: Cultured cell

value: human pancreatic cancer cell line


title: Microdissection IDA5


title: Microdissection IDA3


title: Microdissection IDA1


title: Cultured cell KLM1


title: Cultured cell MIAPACA2


title: sample 074

description: buccal swab sample


title: sample 002

description: buccal swab sample


title: Microdissection IDA2


title: sample 003

description: buccal swab sample


title: Cultured cell BXPC3


title: sample 005

description: buccal swab sample


title: sample 006 (reps a,b)

description:
technical replicates
sample 006a
sample 006b


title: sample 004

description: buccal swab sample


title: E2+MPA 6h treated 3

city: Torino

first: Daniela

last: Cimino

state: Torino

address: Via Nizza 52

department: Oncological Science

country: Italy

institute: Molecular Biotechnology Center

description: biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the rank invariant method with the BeadStudio software v3.4.0 (Illumina).

source_name: Normal human breast epithelial cell

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: HBE cells were maintained in HAM’s medium containing NaHCO3 (0.24%), penicillin-streptomycin (1%), cortisol (5 ng/ml), T3 (6.5 ng/ml), choleratoxin (10 ng/ml), transferrin (5 mg/ml), insulin (0.016 U/ml) and EGF (10 ng/ml) and 5% human serum (HS).

extract_protocol: RNA was extracted with Trizol reagent, in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: After seeding, cells were starved for twenty four hours in serum free and phenol red free medium. Then cells were treated with estradiol (10-8 M) or with progesterone (10-7 M) and  MPA (10-7 M) in combination with estradiol (10-8 M). Control cells were treated with ethanol as vehicle (1:1000). The treatment was carried out in a phenol red free medium containing 5% charcoal-stripped HS for a period of six hours.

value: cell cultures from normal breast specimens obtained from women undergoing surgery for reduction mammoplasty

value: 15-25 years

tag: treatment group

value: E2+MPA 6h treated


title: E2+MPA 6h treated 1

description: biological replicate 1


title: E2+MPA 6h treated 2

description: biological replicate 2


title: sample 001

description: buccal swab sample


title: Secondary MMTV-Neu Tumor WT573

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

description: Gene expression data from secondary MMTV-Neu tumor generated with a single TIC

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data were normalised using quantile normalization with BeadStudio

organism: Mus musculus

source_name: Mouse Mammary Tumor

label_protocol: standard Illumina protocol

extract_protocol: Total RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: FvB

tag: size

value: Mammary Tumor less than 1.0 cm diameter

value: Secondary MMTV-Neu Mammary Tumor


title: Secondary MMTV-Neu Tumor WT592

tag: tissue


title: Secondary MMTV-Neu Tumor WT596


title: Secondary MMTV-Neu Tumor WT614


title: Secondary MMTV-Neu Tumor WT620


title: Secondary MMTV-Neu Tumor WT583


title: Secondary MMTV-Neu Tumor WT641


title: Cultured cell ASPC1

tag: cell line


title: Secondary MMTV-Neu Tumor WT593


title: sip53mut.exp3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

description: MDA-MB-231 siRNA for mutant-p53, biological replicate C

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: standard Affymetrix protocol

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction) using the R/Bioconductor package affy.

label_protocol: Affymetrix GeneChip IVT Labeling Kit, according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

tag: transfectant

value: siRNA for p53


title: Secondary MMTV-Neu Tumor WT636

description: Gene expression data from secondary MMTV-Neu tumor generated with lin- cells


title: Secondary MMTV-Neu Tumor WT575


title: sip53mut.exp2

description: MDA-MB-231 siRNA for mutant-p53, biological replicate B


title: E2+P4 6h treated 2

description: biological replicate 2

value: E2+P4 6h treated


title: Raji_mi-Ctrl_4

city: Nantes

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

description:
Raji_Mi_CTRL_24h_4_56779_2
Each sample represents one channel of a dual-channel array.

hyb_protocol: The labeled cRNA samples were fragmented in fragmentation buffer at 60°C for 30 min before the microarray hybridization. Samples were hybridized to a whole human genome 4x44K Agilent microarrays during 14 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters.

data_processing: Data extraction of median feature intensity without background subtraction was peformed with Feature Extraction software v9.1.3.1 (Agilent Technologies). In order to remove systemic signal intensity bias between each array, median feature intensity were normalized with the function lowess (Locally weighted scatterplot smoothing) method, and then spots with half of the samples exhibiting signal less than the mean of all median signals were removed.

source_name: Raji cells transfected with control mimic at 24 hours

label_protocol: Cyanine-3 (Cy3) and cyanine-5 (Cy-5) labeled cRNA was prepared from 100ng using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer’s protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Raji cells were cultured in 6-well plates in RPMI 1640 medium supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), sodium pyruvate (1 mM), and 10% heat-inactivated fetal calf serum (FCS) (Gibco, Cergy-Pontoise, France) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: 24 hours after transfection, cells were centrifuged and lysed with 1mL TRIzol (Invitrogen, Cergy Pontoise, France). RNA extraction was performed following manufacturer’s recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Raji cells (1×10^6 cells/well in 6-well plates) were electroporated on an Amaxa Nucleofector using the Amaxa kit V (Lonza, Cologne, Germany) following manufacturer’s recommendations with 1.5µg of meridian Mimic for miR-142-3p or control (Dharmacon-ThermoFisher, Lafayette, CO).

value: Raji

value: human Burkitt's lymphoma

value: male

tag: treatment

value: expression of control mimic

tag: treatment duration

value: 24 hrs


title: sip53mut.exp1

description: MDA-MB-231 siRNA for mutant-p53, biological replicate A


title: E2 6h treated 3

description: biological replicate 3

value: E2 6h treated


title: siCtrl.exp3

description: MDA-MB-231 siRNA-Control, biological replicate C

value: siRNA for LacZ


title: E2+P4 6h treated 1

description: biological replicate 1


title: E2 6h treated 2

description: biological replicate 2


title: Secondary MMTV-Neu Tumor WT562


title: Raji_mi-Ctrl_2

description:
Raji_Mi_CTRL_24h_2_56779_1
Each sample represents one channel of a dual-channel array.


title: siCtrl.exp2

description: MDA-MB-231 siRNA-Control, biological replicate B


title: Raji_mi-142-3p_1

description:
Raji_Mi_3p_24h_1_56779_3
Each sample represents one channel of a dual-channel array.

source_name: Raji cells transfected with miR-142-3p mimic at 24 hours

value: expression of miR-142-3p mimic


title: Raji_mi-Ctrl_3

description:
Raji_Mi_CTRL_24h_3_56779_4
Each sample represents one channel of a dual-channel array.


title: Primary MMTV-Neu Tumor N147

description: Gene expression data from primary MMTV-Neu tumor

value: Primary MMTV-Neu Mammary Tumor


title: siCtrl.exp1

description: MDA-MB-231 siRNA-Control, biological replicate A


title: Raji_mi-142-3p_3

description:
Raji_Mi_3p_24h_3_56779_4
Each sample represents one channel of a dual-channel array.


title: E2 6h treated 1

description: biological replicate 1

value: cell cultures from normal breast specimens obtained from women undergoing surgery for reduction mammoplasty


title: E2+P4 6h treated 3

description: biological replicate 3

value: 15-25 years


title: Primary MMTV-Neu Tumor N182


title: siPin1.exp3

description: MDA-MB-231 siRNA for Pin1, biological replicate C

value: siRNA for Pin1


title: control untreated 3

description: biological replicate 3

value: control untreated


title: siPin1.exp2

description: MDA-MB-231 siRNA for Pin1, biological replicate B


title: Raji_mi-Ctrl_1

description:
Raji_Mi_CTRL_24h_1_56779_3
Each sample represents one channel of a dual-channel array.


title: Raji_mi-142-3p_4

description:
Raji_Mi_3p_24h_4_56779_2
Each sample represents one channel of a dual-channel array.


title: Raji_mi-142-3p_2

description:
Raji_Mi_3p_24h_2_56779_1
Each sample represents one channel of a dual-channel array.


title: Primary MMTV-Neu Tumor N133

value: FvB

value: Mammary Tumor less than 1.0 cm diameter


title: control untreated 2

description: biological replicate 2


title: Primary MMTV-Neu Tumor N86


title: RAW264.7 infected with CEP 1

status: Public on May 29 2011

city: Cambridge

first: Kenneth

last: Hu

state: MA

address: 31 Ames Street

institute: Massachusetts Institute of Technology

description: Gene expression data from CEP infected RAW264.7 macrophage cell line at MOI 7 for 18 hrs replicate 1

hyb_protocol: Affymetrix standard protocol

scan_protocol: Scanned using Affymetrix Genechip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.

source_name: RAW264.7 infected with CEP replicate 1 at MOI7 for 18hrs

growth_protocol: Cell lines were grown in T75 to 80% confluency

treatment_protocol: cells were infected with parasite strains at the indicated Multiplicity of Infection(MOI) for 18 hours before RNA harvesting

value: RAW264.7 Macrophage cell

value: grown to 80% confluency in T75

tag: infection

value: CEP


title: J774 mock infected 2

description: Gene expression data from uninfected J774 macrophage cell line for 18 hrs replicate 2

source_name: J774 uninfected replicate 2 for 18hrs

value: J774 Macrophage cell

value: uninfected


title: RAW264.7 infected with Me49 2

description: Gene expression data from Me49 infected RAW264.7 macrophage cell line at MOI 7 for 18 hrs replicate 2

source_name: RAW264.7 infected with Me49 replicate 2 at MOI7 for 18hrs


title: J774 mock infected 1

description: Gene expression data from uninfected J774 macrophage cell line for 18 hrs replicate 1

source_name: J774 uninfected replicate 1 for 18hrs


title: J774 infected with CEP 1

description: Gene expression data from CEP infected J774 macrophage cell line at MOI 7 for 18 hrs replicate 1

source_name: J774 infected with CEP replicate 1 at MOI7 for 18hrs


title: RAW264.7 infected with CEP 2

description: Gene expression data from CEP infected RAW264.7 macrophage cell line at MOI 7 for 18 hrs replicate 2

source_name: RAW264.7 infected with CEP replicate 2 at MOI7 for 18hrs


title: J774 infected with CEP 2

description: Gene expression data from CEP infected J774 macrophage cell line at MOI 7 for 18 hrs replicate 2

source_name: J774 infected with CEP replicate 2 at MOI7 for 18hrs


title: RAW264.7 infected with Me49 1

description: Gene expression data from Me49 infected RAW264.7 macrophage cell line at MOI 7 for 18 hrs replicate 1

source_name: RAW264.7 infected with Me49 replicate 1 at MOI7 for 18hrs


title: siPin1.exp1

description: MDA-MB-231 siRNA for Pin1, biological replicate A


title: DC2.4 infected with Me49 1

description: Gene expression data from Me49 infected DC2.4 Dendritic cell line at MOI 7 for 18 hrs replicate 1

source_name: DC2.4 infected with Me49 replicate 1 at MOI7 for 18hrs

value: DC2.4 Dendritic Cell


title: RAW264.7 mock infected 2

description: Gene expression data from uninfected RAW264.7 macrophage cell line for 18 hrs replicate 2

source_name: RAW264.7 uninfected replicate 2 for 18hrs


title: DC2.4 infected with Me49 2

description: Gene expression data from Me49 infected DC2.4 Dendritic cell line at MOI 7 for 18 hrs replicate 2

source_name: DC2.4 infected with Me49 replicate 2 at MOI7 for 18hrs


title: RAW264.7 mock infected 1

description: Gene expression data from uninfected RAW264.7 macrophage cell line for 18 hrs replicate 1

source_name: RAW264.7 uninfected replicate 1  for 18hrs


title: BALB BMDM infected with RH 1

description: Gene expression data from BALB/c Bone Marrow Derived Macrophages infected with RH  replicate 1

hyb_protocol: standard Affymetrix protocol

source_name: BALB BMDM infected with RH for 18hrs 1

growth_protocol: BMDM's were plated at 3x10^6 cells per well in 6 well plates.

treatment_protocol: BMDM's were infected with parasite strains for 18 hours before RNA harvesting

value: Bone Marrow-Derived Macrophages

tag: genetic background

value: BALB/c

value: 6-7 days incubated after harvesting

value: RH


title: J774 infected with Me49 1

description: Gene expression data from Me49 infected J774 macrophage cell line at MOI 7 for 18 hrs replicate 1

source_name: J774 infected with Me49 replicate 1 at MOI7 for 18hrs


title: DC2.4 mock infected 2

description: Gene expression data from uninfected DC2.4 Dendritic cell line for 18 hrs replicate 2

source_name: DC2.4 uninfected replicate 2 for 18hrs


title: BALB BMDM infected with RH ΔROP16 2

description: Gene expression data from BALB/c Bone Marrow Derived Macrophages infected with RH ΔROP16 replicate 2

source_name: BALB BMDM infected with RH ΔROP16 for 18hrs 2

value: RH ΔROP16


title: BW25113 bdcA (yjgI) mutant

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of E. coli K-12 yjgI mutant after 15 hours of growth in LB with glasswool at 37ºC

hyb_protocol: Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, 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.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system.

data_processing: GenomeChipOperating Software (GCOS) software with MAS 5.0 Expression Analysis Default Setting.

organism: Escherichia coli

label_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: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

treatment_protocol: LB 15 h 37C glasswool biofilm cells

value: BW25113 bdcA (yjgI) mutant


title: J774 infected with Me49 2

description: Gene expression data from Me49 infected J774 macrophage cell line at MOI 7 for 18 hrs replicate 2

source_name: J774 infected with Me49 replicate 2 at MOI7 for 18hrs


title: DC2.4 infected with CEP 2

description: Gene expression data from CEP infected DC2.4 Dendritic cell line at MOI 7 for 18 hrs replicate 2

source_name: DC2.4 infected with CEP replicate 2 at MOI7 for 18hrs


title: DC2.4 infected with CEP 1

description: Gene expression data from CEP infected DC2.4 Dendritic cell line at MOI 7 for 18 hrs replicate 1

source_name: DC2.4 infected with CEP replicate 1 at MOI7 for 18hrs


title: BALB BMDM infected with RH 2

description: Gene expression data from BALB/c Bone Marrow Derived Macrophages infected with RH replicate 2

source_name: BALB BMDM infected with RH for 18hrs 2


title: PS-134-D2

status: Public on May 28 2011

city: Ames

first: Chris

last: Tuggle

address: Kildee Hall 2255

institute: Iowa State University

hyb_protocol: Following fragmentation, 6.5 microg of cRNA were hybridized for 16 hr at 45C on GeneChipÂ® Porcine Genome Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were extracted by Affy (R package) using default settings and global scaling by quantile normalization method.

organism: Sus scrofa

source_name: Persistent shedding pig at day 2 of post inoculation

label_protocol: Biotinylated cRNA were prepared by the GeneChipÂ® One-Cycle target labeling kit according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: The piglets were raised in climate-controlled, fully enclosed isolation facilities at the USDA-ARS-National Animal Disease Center (NADC) in Ames, IA.  The pigs tested fecal negative for Salmonella three times before challenge with Salmonella.

extract_protocol: Total RNA was prepared from 4.5-9.0 ml of solution from the PAXgene Blood RNA tubes using the PAXgene Blood RNA kit (Qiagen, Cat. no. 762164). The DNA was removed by in-solution DNase I digestion and RNeasy mini elute kit cleanup as recommended by QIAGEN.

treatment_protocol: The pigs were intranasal challenge with 109 colony forming units (cfu) of nalidixic acid resistant ST c4232 at 7 weeks of age. Fecal and blood samples were collected from each animal at 0, 2, 7, 14, and 20 dpi.

tag: animal#

tag: shedding type

value: persistent shedding (PS) pig

value: Salmonella enterica serovar Typhimurium (ST)

tag: time (days post-infection)

value: peripheral blood


title: BALB BMDM mock infection 2

description: Gene expression data from uninfected BALB/c Bone Marrow Derived Macrophages replicate 2

source_name: Uninfected BALB BMDM 2


title: PS-134-D0

source_name: Persistent shedding pig at day 0 of post inoculation


title: PS-118-D0


title: PS-115-D0


title: PS-105-D0


title: PS-142-D0


title: BALB BMDM mock infection 1

description: Gene expression data from uninfected BALB/c Bone Marrow Derived Macrophages replicate 1

source_name: Uninfected BALB BMDM 1


title: PS-108-D0


title: DC2.4 mock infected 1

description: Gene expression data from uninfected DC2.4 Dendritic cell line for 18 hrs replicate 1

source_name: DC2.4 uninfected replicate 1 for 18hrs


title: PS-115-D2


title: BW25113 WT

description: RNA extracted from biofilm cells of E. coli K-12 wild type after 15 hours of growth in LB with glasswool at 37ºC

source_name: biofilm cells from E. coli K-12 wild type


title: LS-143-D2

source_name: Low shedding pig at day 2 of post inoculation

value: low shedding (LS) pig


title: PS-105-D2


title: LS-140-D0

source_name: Low shedding pig at day 0 of post inoculation


title: LS-140-D2


title: Primary MMTV-Neu Tumor N135

description: Gene expression data from primary MMTV-Neu tumor

source_name: Mouse Mammary Tumor

value: FvB

value: Mammary Tumor less than 1.0 cm diameter

value: Primary MMTV-Neu Mammary Tumor


title: BALB BMDM infected with RH ΔROP16 1

description: Gene expression data from BALB/c Bone Marrow Derived Macrophages infected with RH ΔROP16 replicate 1

source_name: BALB BMDM infected with RH ΔROP16 for 18hrs 1


title: MMTV-Neu N222+229 Tumor, CD24- fraction

description: Gene expression data from Non-tumor initiating fraction of the tumor

hyb_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek software and absolute expression values were obtained

growth_protocol: Five independent primary mammary tumors from MMTV-Neu model (N250, N261, N283, N222, N229) were harvested and tumor cells were dissociated mechanically into single cell suspension.

extract_protocol: Total RNA was purified from the 8 samples using PicoPure RNA Isolation Kit (Arcturus)

treatment_protocol: Cells from each tumor (with the exception of N222 and N229, which were combined in a 1:1 ratio to obtain enough cells for the experiment) were FACS sorted into TIC and non-TIC/CD24- fraction.

value: primary mammary tumor

tag: genotype

value: MMTV-Neu

tag: tumor size

value: less than 1.0 cm diameter


title: control untreated 1

description: biological replicate 1

source_name: Normal human breast epithelial cell

tag: cell type

value: cell cultures from normal breast specimens obtained from women undergoing surgery for reduction mammoplasty

value: 15-25 years

value: control untreated


title: PS-142-D2


title: MMTV-Neu N283 Tumor, CD24- fraction

scan_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

source_name: Non-tumor initiating fraction of the tumor


title: LS-101-D2


title: MMTV-Neu N222+229 Tumor, TIC fraction

description: Gene expression data from fraction of the tumor with highly purified Tumor Initiating Cells

source_name: Fraction of the tumor with highly purified Tumor Initiating Cells

label_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: MMTV-Neu N260 Tumor, CD24- fraction


title: LS-101-D0


title: MMTV-Neu N260 Tumor, TIC fraction


title: LS-106-D2


title: 10h_bio02_tech03

status: Public on May 27 2011

city: Oak Ridge

first: Babu

last: Raman

state: TN

address: One Bethel Valley Road

institute: Oak Ridge National Laboratory

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454094

scan_protocol: Microarray slides were scanned in ScanArray Express scanner (Perkin Elmer, Waltham, MA) and signals were quantified in ImaGene version 6.0 (BioDiscovery Inc., El Segundo, CA).

data_processing: Statistical data analysis was conducted using JMP Genomics software (SAS Institute Inc., Cary, NC). The array signal intensities were background-corrected, log2-transformed and data for duplicated probes on the arrays were averaged and normalized using the Data-Standardize method. Low-quality array data were discarded based on scatter plots, correlation coefficients, principal component analysis and other quality control criteria. One-way ANOVA analysis was conducted with the 6hr samples as the control at a False Discovery Rate of 2% (P-value < 0.01) to identify differentially expressed genes of statistical significance. ANOVA analysis data are linked as a supplementary file on the Series record.

organism: Acetivibrio thermocellus ATCC 27405

source_name: Avicel batch fermentation

label_protocol: The 6hr time-point total RNA sample was used as the reference and all other time-point samples (8, 10, 12, 14, 16hr) were compared to the reference in cDNA/cDNA arrays. For each time-point comparison, equal amount of the extracted total RNA samples was labeled with Cy3-dUTP/Cy5-dUTP fluorescent dyes (GE Healthcare, Piscataway, NJ), mixed and hybridized onto custom oligo-arrays in dye swap experiments as described earlier [Chhabra SR, J Bacteriol., 2006 188(5); PMID 16484192].

growth_protocol: Batch fermentations of C. thermocellum ATCC 27405 wild-type strain were conducted in 3L BioStat B jacketed glass fermentors (Sartorius Stedim Biotech, Bohemia, NY) using a 2L working volume of MTC medium (mineral salt medium containing 1g/L yeast extract; [16]) at 58C and 300rpm, with pH controlled at 7.0 using 3N NaOH. Fermentors with medium containing only the carbon substrate, 5g/L crystalline cellulose (Avicel® PH105, FMC Biopolymer, Philadelphia, PA), were sparged with ultra-high purity nitrogen and vigorously agitated overnight, followed by addition of the remaining medium components and sparged for an additional 2-3hrs with nitrogen gas. A 10% v/v inoculum of overnight (16-20hrs) 5g/L Avicel® bottle cultures was used to inoculate the fermentors and the gas inlet/exhaust lines were clamped post inoculation.

extract_protocol: Fermentation samples for RNA isolation were harvested by spinning down ~30mL culture in 50mL Oak Ridge tubes at 8000 rpm and 4C for 10-15mins and the supernatant was discarded. The solid pellet fraction containing cells and any residual Avicel® was resuspended in 1mL of TRIzol (Invitrogen, Carlsbad, CA), flash frozen in liquid nitrogen and stored at -80C until further use. Total RNA was extracted from the cell pellets as follows. Briefly, the frozen cell solution in TRIzol was thawed on ice and the cell solution (~1mL) was added to a 2mL tube containing 1mL of 0.1mm glass beads (BioSpec Products, Bartlesville, OK) ashed at 250C overnight. Cells were lysed by rapid agitation of the tubes at 6500rpm for 1min in three 20s-On/20s-Off cycles using the Precellys® bead beater (Bertin Technologies, France). Subsequently, the cell lysate (~0.8mL) in TRIzol was phase separated by addition of 200uL chloroform and the RNA was precipitated by addition of 500uL 100% isopropanol. The precipitated RNA pellet was washed with 1mL of 75% ethanol and resuspended in 100uL of RNase-free water. Any contaminating DNA was digested by in-solution DNase-I (Qiagen, Valencia, CA) treatment and the RNA sample was cleaned using the RNeasy mini kit (Qiagen, Valencia, CA) as per manufacturer’s instructions.

tag: phase

tag: biorep

tag: techrep


title: 06h_bio01_tech18

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454093

hyb_protocol: For each time-point comparison, equal amount of the extracted total RNA samples was labeled with Cy3-dUTP/Cy5-dUTP fluorescent dyes (GE Healthcare, Piscataway, NJ), mixed and hybridized onto custom oligo-arrays in dye swap experiments as described earlier [Chhabra SR, J Bacteriol., 2006 188(5); PMID 16484192].


title: 06h_bio01_tech10

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454109


title: 14h_bio02_tech03

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454110


title: MMTV-Neu N251 Tumor, TIC fraction

tag: strain


title: 08h_bio01_tech01

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454104


title: LS-143-D0

tag: tissue


title: 12h_bio02_tech04

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452876


title: 06h_bio02_tech12

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454111


title: PS-108-D2


title: 08h_bio02_tech03

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454106


title: 06h_bio01_tech06

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454105


title: 06h_bio02_tech08

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454107


title: 10h_bio01_tech01

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454092


title: PS-118-D2


title: 14h_bio02_tech04

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454111


title: 06h_bio01_tech01

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452871


title: 06h_bio02_tech11

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454110


title: 16h_bio01_tech01

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452883


title: 16h_bio02_tech03

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452885


title: 06h_bio02_tech16

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452886


title: 06h_bio02_tech03

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452875


title: 12h_bio01_tech02

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452872


title: 14h_bio01_tech01

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13454108


title: MMTV-Neu N283 Tumor, TIC fraction

description: Gene expression data from fraction of the tumor with highly purified Tumor Initiating Cells


title: LS-106-D0


title: 14h_bio01_tech02

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454109


title: 06h_bio01_tech09

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454108


title: 08h_bio02_tech04

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454107


title: 16h_bio02_tech04

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452886


title: 06h_bio01_tech17

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454092


title: 08h_bio01_tech02

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454105


title: 12h_bio02_tech03

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452875


title: 06h_bio02_tech07

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454106


title: 10h_bio02_tech04

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13453965


title: MMTV-Neu N251 Tumor, CD24- fraction

description: Gene expression data from Non-tumor initiating fraction of the tumor


title: 06h_bio01_tech02

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452872


title: 06h_bio01_tech05

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454104


title: 06h_bio02_tech19

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454094


title: 12h_bio01_tech01

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452871


title: 10h_bio01_tech02

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13454093


title: 16h_bio01_tech02

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452884


title: 06h_bio01_tech13

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452883


title: 06h_bio02_tech04

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452876


title: 06h_bio02_tech15

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy3_13452885


title: SL29-S27-1

city: Stanford

first: Yi-Ching

last: Ong

state: CA

address: 299 W. Campus Dr.

department: Microbiology & Immunology

institute: Stanford University

description: Gene expression data from SL-29s infected with indicated T. gondii strain, 24 hpi

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridizedl on GeneChip Chicken Genome Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

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

data_processing: The data were normalized using Robust Multichip Average normalization and analyzed using MeV v. 4.6.1 from the TM4 software suite.

organism: Gallus gallus

source_name: SL-29 chicken embryonic fibroblasts infected with Toxoplasma gondii of indicated strain, 24 hpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for one-cycle amplification from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 3, Affymetrix).

growth_protocol: SL-29 (ATCC CRL-1590) chicken embryonic fibroblast cells were grown to confluence in Dulbecco’s modified Eagle’s medium (30-2002; ATCC, Manassas, VA) supplemented with 5% FCS (Hyclone, Logan, UT) and 5% tryptose phosphate broth (Sigma, St. Louis, MO).  Passage #<10 for all experiments performed.

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

treatment_protocol: SL-29 cells were infected with Toxoplasma gondii tachyzoites (prepared by syringe-lysis from infected HFFs and extensive washing in PBS) of the indicated strain at multiplicity of infection ~3; 24 hours post-infection, the supernatant was removed and cells were lysed in Trizol for RNA extraction.

tag: cell line

value: SL-29 (chicken embryonic fibroblasts)

tag: parasite strain

tag: time point

value: 24hr post-infection


title: SL29-CL29-1


title: CEF_RH_1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Chicken Genome Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

source_name: SL-29 chicken embryonic fibroblasts infected with Toxoplasma gondii of indicated strain, 5 hpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug starting total RNA (3' IVT Express Kit, Affymetrix).

growth_protocol: Primary chicken embryonic fibroblasts (CEFs) were derived from specific pathogen-free fertilized eggs purchased from Charles River (Wilmington, MA).  Fibroblasts were prepared from 12-day old embryos and maintained in complete DMEM, comprised of Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% heat-inactivated fetal calf serum (FCS; Hyclone, Logan, UT), 2 mM L-glutamine, 100 U/mL penicillin and 100 μg ml−1 streptomycin.   For CEF maintenance, complete DMEM was additionally supplemented with 1% heat-inactivated chicken serum (Invitrogen, Carlsbad, CA), and 1 mM sodium pyruvate (Invitrogen, Carlsbad, CA).

treatment_protocol: SL-29 cells were infected with Toxoplasma gondii tachyzoites (prepared by syringe-lysis from infected HFFs and extensive washing in PBS) of the indicated strain at multiplicity of infection ~3; 5 hours post-infection, the supernatant was removed and cells were lysed in Trizol for RNA extraction.

value: RH

value: 5hr post-infection


title: SL29-STD10-1


title: SL29-S2T-1


title: SL29-STG4-1


title: CEF_ROP16KO_1


title: T(Diff) cells -1

city: Chapel Hill

first: Gary

last: Johnson

state: NC

address: 120 Mason Farm Drive,4009 Genetic Medicine Building,CB#7365

department: Pharmacology

institute: UNC-Chapel Hill

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent Scanner

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken using Genespring software.

source_name: reference: TS(WT) cells

extract_protocol: total RNA

value: trophoblast stem (TS) cells

tag: protocol

value: wild-type control (TS^WT)

source_name: test: T(Diff) cells-1

extract_protocol: Qiagen Rneasy Kit

value: differentiated for 4 days (T^Diff)


title: SL29-S23-1


title: SL29-C96H6-1


title: T(Diff) cells -2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

source_name: test: T(Diff) cells-2


title: SL29-STF3-1


title: SL29-S30-1


title: SL29-STC8-1


title: 06h_bio01_tech14

description:
Microarrays containing 2980 unique and 10 group 70-mer oligonucleotide probes representing ~97% of the 3163 Open Reading Frames (ORFs) in the 2003 draft assembly of C. thermocellum ATCC 27405 were constructed as described earlier [Brown SD et al., Appl Biochem Biotechnol 2007 137-140(1-12); PMID: 18478424]. The probe sequences were later compared to the completed genome sequence using reciprocal BLAST analysis and assigned new ORF numbers. Based on the comparison, 79 probes which did not have any BLAST hits and 108 probes that only had partial hits to annotated ORFs in the closed genome were either excluded or marked-up during downstream data analysis.
Cy5_13452884


title: SL29-C96B4-1


title: SL29-C96C12-1


title: SL29-STD3-1


title: TS(Ki4) cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: test: TS(Ki4) cells

value: inactive MAP3K4 (TS^KI4)


title: T(Inv) cells -2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

source_name: test: T(Inv) cells-2

value: differentiated for 4-days and isolated following invasion through Matrigel (T^Inv)


title: T(Inv) cells -3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: test: T(Inv) cells-3


title: SL29-STC7-1


title: TS(Ki4) cells -1 Repl1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: test: TS(Ki4) cells-1 Repl1


title: TS(Ki4) cells -2 Repl1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

source_name: test: TS(Ki4) cells-2 Repl1