title: POAG 6

status: Public on Aug 31 2013

type: RNA

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cellular Biology and Anatomy

country: USA

institute: Augusta University

description: case

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software limma in Bioconductor was used to perform the quantile normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: trabecular meshwork

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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

tag: disease state

value: Primary Open-Angle Glaucoma

tag: collection

value: surgery

tag: postmortem delay (hr)

tag: tissue

value: trabecular meshwork


title: POAG 10

description: case


title: POAG 13

description: case


title: POAG 15

description: case


title: Control 12

description: control

value: Control

value: Donated eye


title: POAG 5

description: case


title: Control 16

description: control


title: POAG 17

description: case


title: POAG 7

description: case


title: Control 17

description: control


title: Control 19

description: control


title: Control 10

description: control


title: Control 18

description: control


title: POAG 16

description: case


title: POAG 8

description: case


title: POAG 9

description: case


title: POAG 12

description: case


title: POAG 14

description: case


title: Control 14

description: control


title: Control 8

description: control


title: Control 15

description: control


title: Control 13

description: control


title: Control 4

description: control


title: Control 11

description: control


title: Control 9

description: control


title: Control 7

description: control


title: POAG 11

description: case


title: Control 6

description: control


title: Control 5

description: control


title: Control 1

description: control


title: POAG 3

description: case


title: Control 3

description: control


title: POAG 1

description: case


title: POAG 4

description: case


title: Control 2

description: control


title: SLEC-Ba20-Liver-02

city: Oklahoma City

first: florea

last: lupu

address: 825 NE 13th Street

institute: Oklahoma Medical Research Foundation

description: Gene expression data from E.coli challenged baboon liver

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized using Model 640 hybridization oven for 16 hr at 45C on GeneChip Human Genome Array U133A 2.0. GeneChips were washed and stained in the Affymetrix GeneChip® 450 fluidics station.

scan_protocol: GeneChips were scanned using GeneChip® 3000 7G scanner with autoloader (0.51 micron resolution)

data_processing: RMA

label: Biotin

organism: Papio cynocephalus

source_name: E.coli challenged animal's liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Live E. coli organisms (serotype B7-086a:K61; American Type Culture Collection, Rockville, MD), stored in the lyophilized state at 4°C after growth in tryptic soybean agar, were reconstituted and used. To eliminate differences due to E. coli strain variations, all animals were infused with E. coli from this single isolate.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, RNA was further purified with the Qiagen DNeasyTissue kit (Qiagen, Valencia, CA) and the contaminant genomic DNA was removed with a Qiagen on-column DNase digestion kit. RNA concentrations are determined on a scanning UV/VIS spectrophotometer Nanodrop ND-1000 Spectrophotometer. RNA Quality Assessment by using Agilent 2100 Bioanalyzer Capillary Gel Electrophoresis System.

treatment_protocol: Papio cyanocephalus baboons were held for 30 days at the OUHSC animal facility. Only healthy tuberculosis free animals with hemoglobin greater than 10 g/dL and white blood cell (WBC) count less than 12,000 were included in the study. Animals were infused with 1x109 live E. coli (LD50 dose) as described before. The time point at which the infusion was started is further indicated as T0, a time point of n hours thereafter referred to as T+n hours. Compstatin was administered as a 10-mg/kg iv. bolus followed by 60μg/kg/min continuous infusion. Three experimental E. coli groups were studied: (i) E. coli challenge only (n=4); (ii) E. coli plus compstatin treatment from T0 to T+8 (n=4; prevention regimen); (iii) E. coli plus compstatin from T+5 to T+11 (n=4; rescue regimen). The control group comprising three animals received saline infusion only.

value: Liver

tag: stress

value: E.coli (serotype B7-086a:K61) challenge

tag: agent

value: untreated

tag: sepsis stage


title: SLEC-CST5-Ba100-Liver-03

description: Gene expression data from second stage compstatin treated E.coli challenged baboon liver

source_name: second stage compstatin treated animal's liver

value: compstatin

value: second stage

tag: protocol

value: rescue regimen


title: SLEC-CST5-Ba94-Liver-01


title: SLEC-CST5-Ba95-Liver-02


title: POAG 2

description: case


title: SLEC-CST0-Ba90-Liver-01

description: Gene expression data from early stage compstatin treated E.coli challenged baboon liver

source_name: early stage compstatin treated animal's liver

value: early stage

value: prevention regimen


title: SLEC-CST0-Ba93-Liver-03


title: SLEC-Ba92-Liver-03


title: SLEC-CST0-Ba91-Liver-02


title: Ctl-Ba12-Liver-02

description: Gene expression data from healthy baboon liver

source_name: liver from healthy animal

value: control


title: SLEC-CST5-Ba100-Lung-03

description: Gene expression data from second stage compstatin treated E.coli challenged baboon lung

source_name: second stage compstatin treated animal's lung

value: Lung


title: SLEC-Ba92-Lung-03

description: Gene expression data from E.coli challenged baboon lung

source_name: E.coli challenged animal's Lung


title: Ctl-Ba6-Liver-01


title: SLEC-CST0-Ba91-Lung-02

description: Gene expression data from early stage compstatin treated E.coli challenged baboon lung

source_name: early stage compstatin treated animal's lung


title: SLEC-CST0-Ba93-Lung-03


title: SLEC-CST0-Ba90-Lung-01


title: Ctl-Ba21-Lung-03

description: Gene expression data from healthy baboon lung

source_name: Lung from healthy animal


title: SLEC-Ba20-Lung-02


title: SLEC-Ba11-Liver-01


title: SLEC-CST5-Ba94-Lung-01


title: Ctl-Ba12-Lung-02


title: SLEC-CST5-Ba95-Lung-02


title: Ctl-Ba6-Lung-01


title: SLEC-Ba11-Lung-01


title: sid2-1_1day15%PEG_rep1

city: Helsinki

first: Jing

last: Li

address: Viikinkaari 5D

department: Department of Bioscience

country: Finland

institute: University of Helsinki

description:
Biological replicate 1 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array5.gpr

hyb_protocol: For each array, 800ng of each 3 labelled aRNA samples were mixed in 1.5ml nuclease-free microfuge tube with 10x Agilent Blocking agent, 25xAgilent Fragmentation buffer and incubated at 60°C for exactly 30 minutes. A 55µl 2xAgilent GEx Hybridization Buffer HI-RPM was added to stop the fragmentation. After pipetting to mix and centrifuging, a 100µl of the fragmentation mixture was hybridized to Agilent Arabidopsis (V4) Gene Expression Microarray for 17 hours at 65°C. After hybridiztion, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried the slide by spinning it for 1 minute in a slide centrifuge.

scan_protocol: After washing, the slides were scanned with GenePix 4200 AL scanner (Axon Instruments, Union City, CA, USA) at 635, 532 and 488 nm.

data_processing: The gpr files were produced by GenePixPro 5.0 (Axon Instruments) and imported into R 2.14 and the analysis was done with BioConductor using Limma package (http://www.springerlink.com/content/g26110k024423738/). Analyzed spots were background normalized using norm-exp model from Limma package and then different measurement groups were quantile normalized.

organism: Arabidopsis thaliana

source_name: sid2-1 single mutant, 15%PEG, 1day, replicate 1

label_protocol: Dye coupling reaction was performed after aRNA was synthesized, Cy3 or Hyper5 (GE Healthcare) or ARES Labeling Kit with Alexa Fluor 488 (Invitrogen) was used to label 5µg of amino allyl-modified aRNA, followed by purification of dye labelled aRNA with Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

growth_protocol: Arabidopsis thaliana seeds were firstly put on ½ MS (Duchefa) plates and kept in +4°C for 3 or 4 days and then put the plates into in vitro room for germination. After 7 days, we transferred the green seedlings to the pots filled with mixture of peat and vermiculite (2:1) in the growth room at 22°C with 70/90% relative humidity. The light intensity is 120µmol m-2sec-1 and with a 12/12h light /dark cycle. The plants were growing for 3 or 4 weeks.

extract_protocol: RNA was extracted with RNeasy® plant mini kit (Qiagen) following the manufacturer's recommendations.RNA was quantified by a NanoDrop-1000 spectrophotometer and the RNA integrity was analyzed by Agilent 2100 Bioanalyzer and the RNA was not degraded. After DNase digestion, RNA was purified by RNeasy® MinElute cleanup Kit (Qiagen).

treatment_protocol: Three weeks old plants in the soil were watered by 15% PEG6000, then collected samples at one day time point. The plants watered with water were used as control.

tag: background cultivar

value: Columbia

tag: developmental stage

value: Three weeks old plants

value: Leaves


title: wrky54wrky70_1day15%PEG_rep1

description:
Biological replicate 1 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array8.gpr

label: Alexa Fluor 488

source_name: wrky54wrky70 double mutant, 15%PEG, 1day, replicate 1


title: sid2-1_1day15%PEG_rep3

description:
Biological replicate 3 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array4.gpr

source_name: sid2-1 single mutant, 15%PEG, 1day, replicate 3


title: sid2-1_1day15%PEG_rep2

description:
Biological replicate 2 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array8.gpr

source_name: sid2-1 single mutant, 15%PEG, 1day, replicate 2


title: Col-WT_1day15%PEG_rep3

description:
Biological replicate 3 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array7.gpr

source_name: wild type plant, 15%PEG, 1day, replicate 3


title: wrky54wrky70_1day15%PEG_rep3

description:
Biological replicate 3 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array1.gpr

source_name: wrky54wrky70 double mutant, 15%PEG, 1day, replicate 3


title: wrky54wrky70sid2-1_1day15%PEG_rep3

description:
Biological replicate 3 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array8.gpr

source_name: wrky54wrky70sid2-1 triple mutant, 15%PEG, 1day, replicate 3


title: wrky54wrky70sid2-1_control_rep1

description:
Biological replicate 1 of 3, untreated,harvested after watering with water
array1.gpr

source_name: wrky54wrky70sid2-1 triple mutant, control, replicate 1


title: wrky54wrky70sid2-1_1day15%PEG_rep2

description:
Biological replicate 2 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array2.gpr

source_name: wrky54wrky70sid2-1 triple mutant, 15%PEG, 1day, replicate 2


title: wrky54wrky70sid2-1_control_rep3

description:
Biological replicate 3 of 3, untreated,harvested after watering with water
array5.gpr

source_name: wrky54wrky70sid2-1 triple mutant, control, replicate 3


title: wrky54wrky70sid2-1_control_rep2

description:
Biological replicate 2 of 3, untreated,harvested after watering with water
array2.gpr

source_name: wrky54wrky70sid2-1 triple mutant, control, replicate 2


title: sid2-1_control_rep3

description:
Biological replicate 3 of 3, untreated,harvested after watering with water
array7.gpr

source_name: sid2-1 single mutant, control, replicate 3


title: wrky54wrky70sid2-1_1day15%PEG_rep1

description:
Biological replicate 1 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array4.gpr

source_name: wrky54wrky70sid2-1 triple mutant, 15%PEG, 1day, replicate 1


title: wrky54wrky70_1day15%PEG_rep2

description:
Biological replicate 2 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array4.gpr

source_name: wrky54wrky70 double mutant, 15%PEG, 1day, replicate 2


title: Col-WT_1day15%PEG_rep1

description:
Biological replicate 1 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array3.gpr

source_name: wild type plant, 15%PEG, 1day, replicate 1


title: sid2-1_control_rep2

description:
Biological replicate 2 of 3, untreated,harvested after watering with water
array6.gpr

source_name: sid2-1 single mutant, control, replicate 2


title: wrky54wrky70_control_rep2

source_name: wrky54wrky70 double mutant, control, replicate 2


title: Col-WT_control_rep2

source_name: wild type plant, control, replicate 2


title: Col-WT_1day15%PEG_rep2

description:
Biological replicate 2 of 3, harvested after 1 day treatment by watering with 15% PEG6000
array6.gpr

source_name: wild type plant, 15%PEG, 1day, replicate 2


title: Col-WT_control_rep1

source_name: wild type plant, control, replicate 1


title: Hep_3D [X5701375050_K]

city: Ilmenau

first: Uta

last: Fernekorn

department: Nano-Biosystem Technology

country: Germany

institute: Ilmenau Technical University

description: total RNA electrophoretically detected by RNA Integrity Number (RIN method)

scan_protocol: Illumina BeadArray Reader with BeadScan 3.6.17 Scanning software

data_processing: The data were normalized using log 2 variance stabilization, a method described by W. Huber et al. in Bioinformatics 18 Suppl.1:96-S104. (2002).Distribution of p- values of the bead signals and false discovery rates were calculated using the R- package fdr-tool [R Foundation for Statistical Computing, Vienna, Austria].  A linear model was applied with the cell type and culture conditions were regarded as co- variants. Altogether, probes giving a false positive rate of 0.1% were selected and further processed via hierarchical clustering.

source_name: Hepatocyte

label_protocol: RNA extracts were labeled with Biotin and after hybridized on a Sentrix® BeadChip  (Illumina: human HT12v4) detected via Cy3-Streptavidin

growth_protocol: Hepatocytes were cultivated for five days under 2D and 3D statical and perfused conditions. 3D cultivation was performed in a structured, microporous scaffold. Cultivation was started with 0.25 x106 in 2D and with 1x 106 vital cells for the 3D experiments. The day of seeding was defined as d0.

extract_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion, Applied Biosystems)

tag: group

tag: cell type

value: hepatocarcinoma cell

tag: cell line


title: wrky54wrky70_control_rep3

source_name: wrky54wrky70 double mutant, control, replicate 3


title: Col-WT_control_rep3

source_name: wild type plant, control, replicate 3


title: Hep_3DBR [X5701375049_E]


title: Hep_3D [X5701375050_J]


title: sid2-1_control_rep1

description:
Biological replicate 1 of 3, untreated,harvested after watering with water
array3.gpr

source_name: sid2-1 single mutant, control, replicate 1


title: Hep_2D [X5701375050_I]


title: Hep_2D [X5701375050_E]


title: wrky54wrky70_control_rep1

source_name: wrky54wrky70 double mutant, control, replicate 1


title: Hep_3DBR [X5701375049_D]


title: L. lactis 712d

city: Tsukuba

first: Miho

last: Kobayashi

address: 2 Ikenodai

department: Animal Products Research

country: Japan

institute: National Institute of Livestock and Grassland Science

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Lactococcus cremoris

source_name: pAG6-cured variant of NIAI712

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA from the cells was prepared by using an RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol. The RNA concentrations and the quality of RNA preparations were checked by determining the absorbance ratios at wavelengths of 260 and 280 nm.

tag: genotype

value: an 8.7 kb plasmid cured variant

tag: phenotype

value: slow milk coaguration phenotype


title: Lactococcus lactis NIAI712

source_name: Lactococcus lactis NIAI712 wild-type

value: wild type

value: normal


title: Hep_3D [X5701375049_C]


title: Hep_2D [X5701375050_H]


title: UMA07121

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: Human breast tissue sample gene expression analyzed on agilent catalog 4X44k v1 human array

hyb_protocol: Agilent standard protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

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

source_name: Human Reference B

label_protocol: Agilent protocol

extract_protocol: Qiagen RNEasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty Tissue

label_protocol: Agilent standard protocol

extract_protocol: Qiagen Rneasy Mini

tag: age

value: 34 years old

tag: status

value: premenopausal

value: normal breast tissue


title: UMA07167

value: 70 years old

value: postmenopausal


title: UMA07122

value: 19 years old


title: UMA07115_rep1

value: 39 years old


title: UMA07098

value: 14 years old


title: UMA07116

value: 33 years old


title: UMA07117

value: 49 years old

value: unknown menopausal status


title: UMA07115


title: UMA07096


title: UMA07093_rep1

value: 27 years old


title: UMA07097

value: 22 years old


title: UMA07118

value: 18 years old


title: UMA07099

value: 36 years old


title: UMA07093


title: UMA07079_rep1

value: 23 years old


title: UMA07084

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 17 years old


title: UMA07084_rep1

value: premenopausal


title: UMA07079

value: normal breast tissue


title: UMA07056

value: 50 years old

value: perimenopausal


title: UMA07057

value: 29 years old


title: UMA07078

value: 34 years old


title: UMA07096_rep1


title: UMA07054


title: UMA07053


title: UMA07052

value: 30 years old


title: SUMOchip_IGGrechip_FLAG-SUMO_WT_EMB_rep2

type: genomic

city: Berkeley

first: Barbara

last: Meyer

state: CA

address: 16 Barker Hall

department: Molecular and Cellular Biology

institute: University of California Berkeley

hyb_protocol: Hybridization protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

scan_protocol: Sample scan protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: ChIP input DNA from wild type XX embryo expressing FLAG-tagged SUMO

label_protocol: 3 µg of amplified ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Worms grown on HB101 E. coli

extract_protocol: Embryo extracts were prepared as described previously (Jans et al. 2009) except FLAG-tagged SDC-2 (TY2095) ChIP extracts were pre-cleared with protein G sepharose. Briefly, embryos collected by bleaching were crosslinked in 2% formaldehyde in M9 for 30 min at 20oC and quenched with 100 mM Tris-HCl (pH 7.5). Samples were then washed twice with M9, once with Homogenization Buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF) and frozen in liquid nitrogen. 10mM N-Ethylmaleimide (NEM) was added to the Homogenization Buffer used to make extracts for sequential ChIP. Samples were sonicated to a range of 200 bp – 1 kb using a Heat System XL2020 Sonicator with a Misonix 419 tip for 10x30 sec at 10%, then centrifuged at 5,000 x g for 20 minutes at 4°C.  The supernatant was again sonicated for 10x30 sec at 10% and spun at 20,000 x g for 20 minutes at 4°C. The resulting supernatant was pre-cleared with protein A sepharose for 30 min and frozen in liquid nitrogen.  Immunoprecipitations were performed with the appropriate antibody (as displayed in the beginning of each sample name) and were washed and processed as described in Pferdehirt et al.

treatment_protocol: Briefly, gravid hermaphrodites were bleached and embryos crosslinked with 2% formaldehyde in M9 at room temperature for 30 minutes.  Crosslinking was quenched with 100mM Tris-HCl (pH 7.5).  Embryos were resuspended and frozen in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF).  Samples were sheared with a sonicator.

tag: strain

source_name: FLAG (SUMO) ChIP, IGG reChIP DNA from XX embryos expressing FLAG-tagged SUMO

growth_protocol: Worms grown on NG agar with HT115 bacteria expressing smo-1 RNAi

value: Wild type XX embryo expressing FLAG-tagged SUMO


title: UMA07049


title: SUMOchip_IGGrechip_FLAG-SUMO_WT_EMB_rep1

value: wild type XX embryo expressing FLAG-tagged SUMO


title: IGG_control_smo1RNAi_EMB_rep2

source_name: ChIP input DNA from smo-1(RNAi) XX embryo

value: smo-1(RNAi) XX embryo

source_name: IGG control ChIP DNA from smo-1(RNAi) XX embryo


title: SDC-2_smo1RNAi_EMB_rep2

value: smo-1(RNAi) XX embryos expressing FLAG-tagged SDC-2 (y74)

source_name: SDC-2 ChIP DNA from smo-1(RNAi) XX embryos expressing FLAG-tagged SDC-2


title: SDC-3_smo1RNAi_EMB_rep2

source_name: SDC-3 ChIP DNA from smo-1(RNAi) XX embryo


title: DPY-28_smo1RNAi_EMB_rep1

source_name: DPY-28 ChIP DNA from smo-1(RNAi) XX embryo


title: SUMOchip_DPY27rechip_FLAG-SUMO_WT_EMB_rep1

source_name: FLAG (SUMO) ChIP, DPY-27 reChIP DNA from XX embryos expressing FLAG-tagged SUMO


title: DPY-28_smo1RNAi_EMB_rep2


title: DPY-30_smo1RNAi_EMB_rep2

source_name: DPY-30 ChIP DNA from smo-1(RNAi) XX embryo


title: SUMOchip_FLAG-SUMO_WT_EMB_rep1

source_name: FLAG (SUMO) ChIP DNA from XX embryos expressing FLAG-tagged SUMO


title: UMA07050

value: 39 years old


title: IGG_control_smo1RNAi_EMB_rep1


title: DPY-26_smo1RNAi_EMB_rep2

source_name: DPY-26 ChIP DNA from smo-1(RNAi) XX embryo


title: DPY-26_smo1RNAi_EMB_rep1


title: SUMOchip_DPY27rechip_FLAG-SUMO_WT_EMB_rep2


title: DPY-28_WT_EMB_rep2

source_name: ChIP input DNA from wild type N2 XX embryo

value: wild type N2 XX embryo

source_name: DPY-28 ChIP DNA from wild type N2 XX embryo


title: DPY-27chip_FLAG-SUMO_WT_EMB

source_name: DPY-27 ChIP DNA from XX embryos expressing FLAG-tagged SUMO


title: SDC-2_WT_EMB_rep2

source_name: ChIP input DNA from wild type XX embryos expressing FLAG-tagged SDC-2

value: wild type XX embryos expressing FLAG-tagged SDC-2 (y74)

source_name: SDC-2 ChIP DNA from wild type XX embryos expressing FLAG-tagged SDC-2


title: UMA07046

source_name: Human Reference B

source_name: Reduction Mammoplasty Tissue

value: 33 years old

value: postmenopausal


title: UMA07047

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 17 years old


title: UMA07048

value: 55 years old

value: normal breast tissue


title: SUMOchip_FLAG-SUMO_WT_EMB_rep2

source_name: ChIP input DNA from wild type XX embryo expressing FLAG-tagged SUMO


title: UMA07045

value: 43 years old


title: SDC-3_smo1RNAi_EMB_rep1

source_name: ChIP input DNA from smo-1(RNAi) XX embryo


title: SDC-2_WT_EMB_rep1


title: DPY-27_smo1RNAi_EMB_rep1

source_name: DPY-27 ChIP DNA from smo-1(RNAi) XX embryo


title: DPY-28_WT_EMB_rep1


title: UMA07044

value: 20 years old

value: premenopausal


title: UMA07039

value: 56 years old


title: UMA07036

value: 50 years old

value: perimenopausal


title: UMA07042


title: UMA07032


title: UMA07034

value: 34 years old


title: UMA07041

value: 51 years old


title: DPY-30_smo1RNAi_EMB_rep1

value: smo-1(RNAi) XX embryo


title: UMA07031

value: 45 years old


title: UMA07037


title: UMA07043


title: SDC-3_WT_EMB_rep1

growth_protocol: Worms grown on NG agar with HT115 bacteria expressing empty vector (L4440) control RNAi

value: wild type N2 XX embryo

source_name: SDC-3 ChIP DNA from wild type N2 XX embryo


title: SDC-2_smo1RNAi_EMB_rep1

value: smo-1(RNAi) XX embryos expressing FLAG-tagged SDC-2 (y74)

source_name: SDC-2 ChIP DNA from smo-1(RNAi) XX embryos expressing FLAG-tagged SDC-2


title: UMA07029

value: 42 years old


title: UMA07029_rep1

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: UMA07025

value: 32 years old


title: UMA07030

value: 49 years old

value: postmenopausal


title: UMA07022

value: 36 years old

value: unknown menopausal status

value: normal breast tissue


title: UMA07023

value: 31 years old

value: premenopausal


title: UMA07028_rep1

value: 39 years old


title: UMA07020

value: 59 years old


title: CRC-136

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

institute: Kyushu university

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Fluorescence intensities were determined with an Agilent DNA Microarray Scanner.

data_processing: Expression levels were quantified by G2567AA Feature Extraction Software Version A.7.5.1 (Agilent Technologies), which used the  LOWESS (locally weighted linear regression curve fit) normalization method. Further analyses were performed using GeneSpring version 7.3.

source_name: colorectal cancer

label_protocol: Cyanine (Cy)-labeled cRNA was prepared using T7 linear amplification as described in the Agilent Low RNA Input Fluorescent Linear Amplification Kit Manual (Agilent Technologies).

extract_protocol: Total RNA was extracted with QIAGEN RNeasy minElute Spin Column (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection

value: microdissected colorectal cancer cells

tag: sample type

value: tumor

tag: sample identifier

tag: gender

value: F

tag: tumor-nodes-metastasis (tnm) classification - t

tag: tumor-nodes-metastasis (tnm) classification - n

tag: tumor-nodes-metastasis (tnm) classification - m

tag: fstage

tag: tnm (stage)

tag: dukes

value: A

tag: his type

value: wel

tag: depth

value: pSM


title: CRC-138

tag: cell type

value: B

value: mod

value: pSS


title: UMA07038

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 40 years old

value: postmenopausal

tag: tissue


title: CRC-140

value: M


title: CRC-139

value: D


title: UMA07018

tag: reference

value: 29 years old

value: premenopausal

value: normal breast tissue


title: DPY-30_WT_EMB_rep1

value: wild type N2 XX embryo

source_name: DPY-30 ChIP DNA from wild type N2 XX embryo


title: UMA07019

tag: age

value: 36 years old


title: UMA07021

tag: status


title: UMA07027

value: 54 years old


title: CRC-137

value: microdissected colorectal cancer cells

value: tumor

value: por

value: pA


title: CRC-135

value: mod

value: pSE


title: CRC-134

value: F

value: C

value: pSS


title: DPY-30_WT_EMB_rep2

tag: strain


title: UMA07015

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 19 years old


title: UMA07016

value: 15 years old


title: CRC-133

tag: sample type

value: M

value: B

value: wel


title: UMA07013

value: 43 years old

value: unknown menopausal status

value: normal breast tissue


title: UMA07012_rep1

value: 32 years old

value: perimenopausal


title: UMA07010

value: 53 years old

value: postmenopausal


title: UMA07012


title: UMA07011

value: 54 years old


title: UMA07009


title: UMA07017

value: premenopausal


title: U2932_24h_R406_A

city: Boston

first: Stefano

last: Monti

state: MA

address: 72 East Concord st. E-613B

department: Medicine

institute: Boston University

description:
73_U2932_24h_R406_A
Lymphoma cell line U2932 treated with R406 at 24h (replicate A).

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix).

data_processing: The raw CEL files were converted into probeset-specific expression values using the RMA summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004).

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: Five lymphoma cell lines, DHL4, DHL6, LY7, HBL1, and U2932, were propagated in their appropriate growth media under standard conditions.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols.

treatment_protocol: Each lymphoma cell line was profiled in triplicate at baseline (0h) and at two time points (6h, 24h) after treatment with R406. At 6 and 24 hours, cell lines were also profiled with vehicle alone (DMSO) to account for cell growth conditions.

tag: cell line

value: diffuse large B-cell lymphoma (DLBCL) cells

tag: treatment

tag: time

tag: replicate

value: A


title: U2932_24h_R406_C

description:
75_U2932_24h_R406_C
Lymphoma cell line U2932 treated with R406 at 24h (replicate C).

value: C


title: U2932_24h_DMSO_A

description:
70_U2932_24h_DMSO_A
Lymphoma cell line U2932 treated with DMSO at 24h (replicate A).

value: DMSO


title: U2932_24h_DMSO_B

description:
71_U2932_24h_DMSO_B
Lymphoma cell line U2932 treated with DMSO at 24h (replicate B).


title: Wildtype H9 hESC derived CM 1

city: La Jolla

first: Fei

last: Yi

address: 10010 North Torrey Pines Road

institute: Salk Institute

description: Gene expression data

hyb_protocol: After hybridization cocktails preparation, the Affymetrix GeneChip Primeview Gene Expression Arrays were hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The statistical analysis of the data was performed using GenePattern platform from Broad Institute. Briefly, raw CEL files were imported into GenePattern platform and normalized using RMA algorithm. The Hierarchical Clustering analysis was performed using the HierarchicalClustering module of the software. The dendrograms and the heat map of the clustered gene expression data were visualized by the HierarchicalClusteringViewer module.

source_name: Human CM

label_protocol: The Affymetrix GeneChip microarrays was performed by the Functional Genomics Core Facility at The Salk Institute for Biological Studies following the manufacturer’s protocol (Affymetrix, Santa Clara, CA). Briefly, 100 ng of total RNA of each sample were processed using Affymetrix GeneChip 3’ IVT Expression Kit following the manufacturer’s protocol. For each sample, 12.5 μg fragmented and labeled aRNA were hybridized to the Affymetrix PrimeView Human Gene Expression Arrays.

growth_protocol: H9 cells were cultured in mTeSR. H9-NSCs were cultured in NSC maintainance medium. H9-CMs were cultured in RPMI/B27 medium.

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Qiagen).

treatment_protocol: H9 cells were collected at passage 38. H9-NSCs were collected at passage 2. H9-CMs were collected on day25 of differentiation.

tag: genotype

value: WT / WT


title: Wildtype H9 hESC derived CM 2

description: Gene expression data


title: Wildtype H9 hESC derived CM 3

description: Gene expression data


title: U2932_24h_R406_B

description:
74_U2932_24h_R406_B
Lymphoma cell line U2932 treated with R406 at 24h (replicate B).


title: U2932_24h_DMSO_C

description:
72_U2932_24h_DMSO_C
Lymphoma cell line U2932 treated with DMSO at 24h (replicate C).


title: UMA07006

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 44 years old


title: UMA07004

value: 50 years old


title: UMA07008

value: 51 years old


title: DPY-26_WT_EMB_rep2

value: wild type N2 XX embryo

source_name: DPY-26 ChIP DNA from wild type N2 XX embryo


title: UMA07005

value: normal breast tissue


title: DPY-27_WT_EMB_rep1

source_name: DPY-27 ChIP DNA from wild type N2 XX embryo


title: UMA07002

value: 35 years old


title: UMA07003

value: 46 years old

value: unknown menopausal status


title: UMA07007


title: U2932_6h_R406_B

description:
68_U2932_6h_R406_B
Lymphoma cell line U2932 treated with R406 at 6h (replicate B).

value: B


title: U2932_6h_R406_A

description:
67_U2932_6h_R406_A
Lymphoma cell line U2932 treated with R406 at 6h (replicate A).


title: Wildtype H9 hESC derived NSC 3

description: Gene expression data

source_name: Human NSC


title: Wildtype H9 hESC derived NSC 1

description: Gene expression data


title: SDC-3_WT_EMB_rep2

source_name: ChIP input DNA from wild type N2 XX embryo


title: U2932_6h_DMSO_C

description:
66_U2932_6h_DMSO_C
Lymphoma cell line U2932 treated with DMSO at 6h (replicate C).


title: U2932_0_DMSO_B

description:
62_U2932_0_DMSO_B
Lymphoma cell line U2932 treated with DMSO at 0h (replicate B).


title: HBL-1_24h_R406_B

description:
59_HBL1_24h_R406_B
Lymphoma cell line HBL1 treated with R406 at 24h (replicate B).


title: HBL-1_24h_DMSO_A

description:
55_HBL1_24h_DMSO_A
Lymphoma cell line HBL1 treated with DMSO at 24h (replicate A).

source_name: HBL1, DMSO, 24h


title: U2932_0_DMSO_C

description:
63_U2932_0_DMSO_C
Lymphoma cell line U2932 treated with DMSO at 0h (replicate C).


title: HBL-1_24h_DMSO_C

description:
57_HBL1_24h_DMSO_C
Lymphoma cell line HBL1 treated with DMSO at 24h (replicate C).


title: HBL-1_24h_DMSO_B

description:
56_HBL1_24h_DMSO_B
Lymphoma cell line HBL1 treated with DMSO at 24h (replicate B).


title: U2932_6h_R406_C

description:
69_U2932_6h_R406_C
Lymphoma cell line U2932 treated with R406 at 6h (replicate C).


title: DPY-27_WT_EMB_rep2


title: HBL-1_24h_R406_C

description:
60_HBL1_24h_R406_C
Lymphoma cell line HBL1 treated with R406 at 24h (replicate C).


title: U2932_0_DMSO_A

description:
61_U2932_0_DMSO_A
Lymphoma cell line U2932 treated with DMSO at 0h (replicate A).


title: U2932_6h_DMSO_A

description:
64_U2932_6h_DMSO_A
Lymphoma cell line U2932 treated with DMSO at 6h (replicate A).


title: Wildtype H9 hESC derived NSC 2

description: Gene expression data


title: Wildtype H9 hESC 2

description: Gene expression data

source_name: Human hESC


title: HBL-1_24h_R406_A

description:
58_HBL1_24h_R406_A
Lymphoma cell line HBL1 treated with R406 at 24h (replicate A).


title: U2932_6h_DMSO_B

description:
65_U2932_6h_DMSO_B
Lymphoma cell line U2932 treated with DMSO at 6h (replicate B).


title: HBL-1_6h_R406_C

description:
54_HBL1_6h_R406_C
Lymphoma cell line HBL1 treated with R406 at 6h (replicate C).


title: Wildtype H9 hESC 3

description: Gene expression data


title: HBL-1_6h_R406_B

description:
53_HBL1_6h_R406_B
Lymphoma cell line HBL1 treated with R406 at 6h (replicate B).


title: UMA07036_244k

description: Human breast tissue sample gene expression analyzed on agilent catalog 4X44k v1 human array

value: perimenopausal


title: Wildtype H9 hESC 1

description: Gene expression data


title: UMA07028_244k

value: 39 years old

value: premenopausal


title: SpleenTreg_FoxP3EGFP_rep2

city: Frederick

first: Charles

middle: Andrew

last: Stewart

state: MD

address: 1050 Boyles Street

department: Center For Cancer Research

institute: National Cancer Institute

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent-014868 Whole Mouse Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs in a rotating incubator, washed at 37° C for 1 min, and stained with Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Data were analyzed by NIAArrayTools (Sharov et al. 2005, Bioinformatics, 21(10): 2548-9), quartile normalization and log10 transformation.

organism: Mus musculus

source_name: Spleen Treg, FoxP3-EGFP mouse

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Biotin-labelled cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: MC38 colon carcinoma were implanted sub-cutaneously in syngeneic VERT-X or FoxP3-EGFP reporter mice and allowed to form established tumors. Spleens were taken from tumor-free mice. At 2 weeks, established tumors were pooled, digested, and single cells were stained with antibodies against cell surface markers to identify Treg cells.

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacturer's instructions. RNA was purified using RNeasy Min-elute (Qiagen) RNA isolation kit. Total RNA samples were quantitated by UV spectrophotometry (OD260/280). Quality of the total RNA was assessed by using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Treg were sorted using a BD Aria II flow sorter directly into RNA-lysis buffer (RLT, Qiagen) using the phenotype FSC/SSC/CD45+/CD11blow/CD3+CD4+ to identify CD4 T cells, followed by EGFP to identify FoxP3+ Treg from FoxP3-EGFP reporter mice, and CD25+CD120b+/low to identify Treg from VERT-X (IL-10EGFP reporter) mice.

tag: strain/background

value: FoxP3-EGFP C57BL/6

value: spleen

value: total Treg


title: SpleenTreg_FoxP3EGFP_rep3


title: HBL-1_6h_R406_A

description:
52_HBL1_6h_R406_A
Lymphoma cell line HBL1 treated with R406 at 6h (replicate A).

value: diffuse large B-cell lymphoma (DLBCL) cells

value: A


title: MC38TumorTreg_FoxP3EGFP_rep3

source_name: MC38 tumor Treg, FoxP3-EGFP mouse

value: MC38 tumor


title: HBL-1_6h_DMSO_B

description:
50_HBL1_6h_DMSO_B
Lymphoma cell line HBL1 treated with DMSO at 6h (replicate B).

source_name: HBL1, DMSO, 6h

value: DMSO


title: SpleenTreg_FoxP3EGFP_rep1


title: DPY-26_WT_EMB_rep1


title: HBL-1_6h_DMSO_A

description:
49_HBL1_6h_DMSO_A
Lymphoma cell line HBL1 treated with DMSO at 6h (replicate A).


title: HBL-1_6h_DMSO_C

description:
51_HBL1_6h_DMSO_C
Lymphoma cell line HBL1 treated with DMSO at 6h (replicate C).

value: C


title: MC38TumorTreg_FoxP3EGFP_rep2


title: MC38TumorTreg_VERTX_IL10pos_rep3

source_name: IL10 positive MC38 tumor Treg, VERT-X mouse

value: VERT-X C57BL/6

value: IL10+ Treg


title: UMA07014

source_name: Human Reference B

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty Tissue

value: 29 years old

value: normal breast tissue


title: LY7_24h_R406_B

description:
44_LY7_24h_R406_B
Lymphoma cell line LY7 treated with R406 at 24h (replicate B).

value: B


title: LY7_24h_DMSO_B

description:
41_LY7_24h_DMSO_B
Lymphoma cell line LY7 treated with DMSO at 24h (replicate B).

source_name: LY7, DMSO, 24h


title: LY7_24h_DMSO_A

description:
40_LY7_24h_DMSO_A
Lymphoma cell line LY7 treated with DMSO at 24h (replicate A).


title: LY7_6h_R406_B

description:
38_LY7_6h_R406_B
Lymphoma cell line LY7 treated with R406 at 6h (replicate B).


title: MC38TumorTreg_VERTX_IL10pos_rep2


title: MC38TumorTreg_FoxP3EGFP_rep1


title: HBL-1_0_DMSO_C

description:
48_HBL1_0_DMSO_C
Lymphoma cell line HBL1 treated with DMSO at 0h (replicate C).

source_name: HBL1, DMSO, 0h


title: LY7_6h_DMSO_C

description:
36_LY7_6h_DMSO_C
Lymphoma cell line LY7 treated with DMSO at 6h (replicate C).

source_name: LY7, DMSO, 6h


title: LY7_24h_DMSO_C

description:
42_LY7_24h_DMSO_C
Lymphoma cell line LY7 treated with DMSO at 24h (replicate C).


title: LY7_24h_R406_C

description:
45_LY7_24h_R406_C
Lymphoma cell line LY7 treated with R406 at 24h (replicate C).


title: HBL-1_0_DMSO_A

description:
46_HBL1_0_DMSO_A
Lymphoma cell line HBL1 treated with DMSO at 0h (replicate A).


title: HBL-1_0_DMSO_B

description:
47_HBL1_0_DMSO_B
Lymphoma cell line HBL1 treated with DMSO at 0h (replicate B).


title: LY7_24h_R406_A

description:
43_LY7_24h_R406_A
Lymphoma cell line LY7 treated with R406 at 24h (replicate A).


title: LY7_6h_R406_C

description:
39_LY7_6h_R406_C
Lymphoma cell line LY7 treated with R406 at 6h (replicate C).


title: LY7_6h_R406_A

description:
37_LY7_6h_R406_A
Lymphoma cell line LY7 treated with R406 at 6h (replicate A).


title: Paraquat_1

city: Leuven

last: De Coninck

address: Kasteelpark Arenberg 20

country: Belgium

institute: KU Leuven

description: paraquat treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)

hyb_protocol: A mixture of fragmented biotinylated DNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip® Arabidopsis Tiling 1.0R Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix)

data_processing:
Background correction, log2 transformation and interslide normalization were performed with the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. Since the tiling arrays were based on the A. thaliana genome sequence of the 2007’s version of the TAIR database, the corresponding TAIR7 genome annotation was used for the analysis of the tiling array data. All steps of our strategy are illustrated in Figure S1. In a first step the average log2 intensities of biological replicates were calculated and a threshold value of 8.8 was chosen to identify transcriptionally active probes. This threshold was determined by comparing the log2 intensity distribution of genomic regions with known expression status (expressed and not expressed). Probes with log2 intensities below the threshold that were surrounded by transcriptionally active probes were considered active and vice versa to remove the effect of probes with poor hybridization properties. Secondly, groups of 4-13 successive transcriptionally active probes were combined into short transcriptionally active regions (TARs). Selection of even smaller regions would lead to a high number of false positives and to the identification of very small genes that are difficult to amplify in later stage, while all active regions of 14-15 successive probes were already annotated (TAIR7), supporting our choice of size limits. In a third step, TARs were withheld if the number of transcriptionally active probes was smaller in the control than in the PQ treatment and if the average log2 intensity of all probes in the smallest of the two regions was at least 1.4 higher in the PQ treatment than in the control. Both rules were based on the tiling array results for genomic regions that were known to be induced upon PQ treatment. The former rule was added because of the frequent occurrence of probes having zero intensity in one of the four hybridizations. In small regions these zero values can have substantial influence on the average log2 intensity leading to false positive calls. The threshold for upregulation by PQ was refined by comparing qRT-PCR and tiling array results for 30 selected TARs. All upregulations of 1.4 or more (corresponding to 2.6 fold or more) in the tiling arrays could be confirmed by qRT-PCR supporting our choice of threshold (data not shown). Finally, each selected region was compared to the A. thaliana TAIR7 genome annotation and only regions that were located in intergenic regions, introns or pseudogenes were withheld.
Results file (*signal.txt) descriptions:  first column = position on chromosome (Name: chromosome ID); second column = log transformed, normalized and background corrected intensity.

source_name: A. thaliana leaves (4 weeks old, sprayed with 25 µM paraquat)

label_protocol: Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Seeds of Arabidopsis thaliana wild-type ecotype Columbia-0 (Col-0) were obtained from the European A. thaliana stock Centre (NASC; http://nasc.nott.ac.uk/home.html). They were sown on ‘Zaai- en Stekgrond’ (DCM, Sint-Katelijne-Waver, Belgium) and grown in a growth chamber with 21°C temperature, 75% humidity and a 12h day-light cycle with a light intensity of approximately 120 μmol m-2s-1.

extract_protocol: After 48h treatment, RNA from A. thaliana leaves was isolated by the guanidinium isothiocyanate method (TRIzol reagent; Invitrogen, Carlsbad, USA) followed by purification using the RNeasy Mini Kit (Qiagen, Valencia, USA). First, approximately 100 mg plant material was crushed in liquid nitrogen, 1 ml of TRIzol reagent was added and samples were mixed and incubated for 5 min at room temperature. Following centrifugation (20,000 x g, 10 min, 4°C) the supernatant was transferred to a fresh tube and 200 µl of chloroform was added. The thoroughly mixed samples were incubated for 2 min at room temperature and the upper aqueous phase was transferred to a fresh tube after centrifugation (20,000 x g, 15 min, 4°C). An equal volume of 70% ethanol was added after which the samples were thoroughly shaken and applied onto a Qiagen column. The procedure was continued according to the manufacturer’s instructions. To selectively use mRNA for the tiling array analysis, RNA is converted into cDNA via an oligodT primer and reverse transcriptase. This cDNA was then used as a template for generation of cRNA.

treatment_protocol: Rosette leaves from soil-grown four-week old A. thaliana plants were sprayed with paraquat (25 µM methylviologendichlorodehydrate 98%, Sigma-Aldrich, St. Louis, MO, US) to obtain an equal and proportional distribution. Control plants were mock treated by spraying with H2O. The treated plants were kept at 100% relative humidity for 48h.

value: 4 weeks old

value: leaves

value: paraquat


title: Gene expression in reeS mutant biol rpt 3

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

hyb_protocol: Microarrays were pre-hybridised in a solution of 25 % formamide, 5X SSC, 0.1 % SDS and 10 mg/ml of herring sperm DNA at 42˚C for 45 mins.  Labelled cDNA was hybridised to the prehybridised microarrays according to the instructions provided with the Geneisphere 3DNA 900MPX kit

scan_protocol: The dried microarrays were scanned using a GMS418 microarray scanner (Affymetrix), scans were aquired using GMS scanner software (V.1.51.0.42) (Affymetrix) and quantified using Imagene version 5.1 (BioDiscovery).

data_processing: Quantified ImaGene files from four independant microarray experiments were analysed using the LIMMA software package for R.  Each microarray experiment was performed using an independant biological replicate, thus providing four independant biological replicates with two dye-swaps.  Spot intensities were firstly normalised per print tip group before being normalised between arrays using a Lowess algorithm.  Spot intensities were then log2 transformed and expression values calculated as the ratio of log2 intensity of reeS mutant/wild-type.

organism: Clostridium perfringens str. 13

source_name: reeS mutant during exponential growth

label_protocol: cDNA synthesis and labelling with Cy3 or Cy5 using 4 μg of total RNA was performed according to the Genisphere 3DNA 900MPX kit (Genisphere) according to the manufacturer's instructions.

growth_protocol: Bacterial strains were cultured for 4 hrs at 37˚C in sterile TPYG broth (5 % [w/v] tryptone, 0.5 % [w/v] proteose peptone, 0.3 % [w/v] yeast extract and 0.1 % [w/v] sodium thioglycolate, supplimented with sterile glucose to a final concentration of 0.38 % [v/v] after autoclaving) under anaerobic conditions.

extract_protocol: Cells were harvested from 15 ml aliquots of bacterial culture by centrifugation at 5800 x g for 10 mins.  Cell pellets were treated with lysozyme (10 mg/ml) for 15 mins prior to RNA extraction using TriZol (Invitrogen) according to the manufacturer's instructions.  Repeated rounds to DNase I digestion and Trizol extraction were performed until  DNA contaminiation was removed.

treatment_protocol: Gene expression was compared between a reeS mutant of C. perfringens strain 13 and wild-type

tag: genotype/variation

value: reeS mutant

source_name: wild-type strain 13 during exponential growth

value: wild-type


title: Gene expression in reeS mutant biol rpt 4


title: H2O_1

source_name: A. thaliana leaves (4 weeks old)

value: H2O (control)


title: Gene expression in reeS mutant biol rpt 2


title: LY7_6h_DMSO_A

description:
34_LY7_6h_DMSO_A
Lymphoma cell line LY7 treated with DMSO at 6h (replicate A).

value: diffuse large B-cell lymphoma (DLBCL) cells


title: H2O_4


title: Gene expression in reeS mutant biol rpt 1


title: LY7_6h_DMSO_B

description:
35_LY7_6h_DMSO_B
Lymphoma cell line LY7 treated with DMSO at 6h (replicate B).


title: LY7_0_DMSO_A

description:
31_LY7_0_DMSO_A
Lymphoma cell line LY7 treated with DMSO at 0h (replicate A).

source_name: LY7, DMSO, 0h

value: A


title: milk fat globule, goat 10, 18h PI

city: Jouy en josas

first: Pauline

middle: Marie

last: Brenaut

address: Domaine de Vilvert

country: France

institute: INRA

description:
Gene expression in MFG 18h after S.aureus injection in the mammary gland
MilkFatGlobule_10S_T3

hyb_protocol: 300 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 25X fragmentation buffer following the manufacturers instructions. Fragmented and labelled cRNA samples were diluted in 2X GEx Hybridisation Buffer Hi-RPM and hybridised on the 15K ovine microarray for 17 hours at 60°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 019921_D_F_20110821) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Capra hircus

source_name: milk fat globule, goat 10, 18h PI

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from120 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with Agilent bioanalyzer 2100.

extract_protocol: Total RNA was extracted using  method with Phenol/chloroform with (Trizol, Invitrogen). Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.One hundred and twenty ng of RNA were converted to labelled cRNA with Cy3 using Agilent procedure.

treatment_protocol: Injection of S. aureus DV137 (10^3 CFU/mL) in the left udder of goats, sampling of milk every 6hrs after injection

tag: animal

tag: time (hrs)

value: milk fat globule

tag: infection

value: S. aureus


title: LY7_0_DMSO_B

description:
32_LY7_0_DMSO_B
Lymphoma cell line LY7 treated with DMSO at 0h (replicate B).

tag: cell type

value: DMSO


title: MC38TumorTreg_VERTX_IL10pos_rep1

value: VERT-X C57BL/6

tag: tissue

value: MC38 tumor


title: milk fat globule, goat 10, 24h PI

description:
Gene expression in MFG 24h after S.aureus injection in the mammary gland
MilkFatGlobule_10S_T4

source_name: milk fat globule, goat 10, 24h PI


title: MC38TumorTreg_VERTX_IL10neg_rep3

source_name: IL10 negative MC38 tumor Treg, VERT-X mouse

value: IL10- Treg


title: DHL6_24h_DMSO_C

description:
27_DHL6_24h_DMSO_C
Lymphoma cell line DHL6 treated with DMSO at 24h (replicate C).

source_name: DHL6, DMSO, 24h

value: C


title: MC38TumorTreg_VERTX_IL10neg_rep1


title: milk fat globule, goat 10, 12h PI

description:
Gene expression in MFG 12h after S.aureus injection in the mammary gland
MilkFatGlobule_10S_T2

source_name: milk fat globule, goat 10, 12h PI


title: DHL6_24h_R406_C

description:
30_DHL6_24h_R406_C
Lymphoma cell line DHL6 treated with R406 at 24h (replicate C).


title: LY7_0_DMSO_C

description:
33_LY7_0_DMSO_C
Lymphoma cell line LY7 treated with DMSO at 0h (replicate C).


title: DHL6_24h_R406_A

description:
28_DHL6_24h_R406_A
Lymphoma cell line DHL6 treated with R406 at 24h (replicate A).


title: milk fat globule, goat 9, 24h PI

description:
Gene expression in MFG 24h after S.aureus injection in the mammary gland
MilkFatGlobule_9S_T4

source_name: milk fat globule, goat 9, 24h PI


title: DHL6_24h_DMSO_A

description:
25_DHL6_24h_DMSO_A
Lymphoma cell line DHL6 treated with DMSO at 24h (replicate A).


title: milk fat globule, goat 10, non-infected

description:
Gene expression in MFG before S.aureus injection in the mammary gland
MilkFatGlobule_10S_T0

source_name: milk fat globule, goat 10, non-infected

value: non-infected


title: milk fat globule, goat 9, 12h PI

description:
Gene expression in MFG 12h after S.aureus injection in the mammary gland
MilkFatGlobule_9S_T2

source_name: milk fat globule, goat 9, 12h PI


title: milk fat globule, goat 9, 18h PI

description:
Gene expression in MFG 18h after S.aureus injection in the mammary gland
MilkFatGlobule_9S_T3

source_name: milk fat globule, goat 9, 18h PI


title: xyang01_si_Med23_oligoB_rep2

city: Shanghai

first: Xu

last: Yang

address: 320 Yueyang Road

country: China

institute: Insititute of biochemistry and cell biology

description: Gene expression data from si-Med23 A549 RNAi oligoB

hyb_protocol: The Affymetrix GeneChip arrays were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix GeneChip arrays were scanned using the Affymetrix GeneArray scanner.

data_processing: The microarray data were normalized using the Robust Multichip Average (RMA) method. We discarded probe sets that did not have signals above background in more than 75% of the arrays for all samples using the Affymetrix MAS5 present/absent calls.

source_name: A549 cells with RNAi oligo against Med23, oligoB

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

growth_protocol: A549 cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% FBS, and were maintained inside the incubator with 5% CO2.

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

treatment_protocol: No treatment prior to experiment was applied.

value: lung cancer cell


title: xyang01_si_Med23_oligoC_rep3

description: Gene expression data from si-Med23 A549 RNAi oligoC

source_name: A549 cells with RNAi oligo against Med23, oligoC


title: DHL6_24h_R406_B

description:
29_DHL6_24h_R406_B
Lymphoma cell line DHL6 treated with R406 at 24h (replicate B).

value: B


title: DHL6_24h_DMSO_B

description:
26_DHL6_24h_DMSO_B
Lymphoma cell line DHL6 treated with DMSO at 24h (replicate B).


title: MC38TumorTreg_VERTX_IL10neg_rep2


title: DHL6_6h_DMSO_C

description:
21_DHL6_6h_DMSO_C
Lymphoma cell line DHL6 treated with DMSO at 6h (replicate C).

source_name: DHL6, DMSO, 6h


title: xyang01_si_Elk1_oligoC_rep3

description: Gene expression data from si-Elk1 A549 RNAi oligoC

source_name: A549 cells with RNAi oligo against Elk1, oligoC


title: xyang01_si_Ctrl_rep3

description: Gene expression data from control A549 rep3

source_name: A549 cells with control oligo, rep3


title: DHL6_6h_R406_C

description:
24_DHL6_6h_R406_C
Lymphoma cell line DHL6 treated with R406 at 6h (replicate C).


title: DHL6_6h_R406_A

description:
22_DHL6_6h_R406_A
Lymphoma cell line DHL6 treated with R406 at 6h (replicate A).


title: DHL6_6h_R406_B

description:
23_DHL6_6h_R406_B
Lymphoma cell line DHL6 treated with R406 at 6h (replicate B).


title: milk fat globule, goat 9, non-infected

description:
Gene expression in MFG before S.aureus injection in the mammary gland
MilkFatGlobule_9S_T0

source_name: milk fat globule, goat 9, non-infected


title: xyang01_si_Elk1_oligoB_rep2

description: Gene expression data from si-Elk1 A549 RNAi oligoB

source_name: A549 cells with RNAi oligo against Elk1, oligoB


title: xyang01_si_Elk1_oligoA_rep1

description: Gene expression data from si-Elk1 A549 RNAi oligoA

source_name: A549 cells with RNAi oligo against Elk1, oligoA


title: DHL6_6h_DMSO_B

description:
20_DHL6_6h_DMSO_B
Lymphoma cell line DHL6 treated with DMSO at 6h (replicate B).


title: milk fat globule, goat 7, 24h PI

description:
Gene expression in MFG 24h after S.aureus injection in the mammary gland
MilkFatGlobule_7S_T4

source_name: milk fat globule, goat 7, 24h PI


title: xyang01_si_Ctrl_rep2

description: Gene expression data from control A549 rep2

source_name: A549 cells with control oligo, rep2


title: milk fat globule, goat 4, 12h PI

description:
Gene expression in MFG 12h after S.aureus injection in the mammary gland
MilkFatGlobule_4S_T2

source_name: milk fat globule, goat 4, 12h PI


title: xyang01_si_Med23_oligoA_rep1

description: Gene expression data from si-Med23 A549 RNAi oligoA

source_name: A549 cells with RNAi oligo against Med23, oligoA


title: milk fat globule, goat 7, non-infected

description:
Gene expression in MFG before S.aureus injection in the mammary gland
MilkFatGlobule_7S_T0

source_name: milk fat globule, goat 7, non-infected


title: milk fat globule, goat 7, 12h PI

description:
Gene expression in MFG 12h after S.aureus injection in the mammary gland
MilkFatGlobule_7S_T2

source_name: milk fat globule, goat 7, 12h PI


title: milk fat globule, goat 7, 18h PI

description:
Gene expression in MFG 18h after S.aureus injection in the mammary gland
MilkFatGlobule_7S_T3

source_name: milk fat globule, goat 7, 18h PI


title: milk fat globule, goat 4, 18h PI

description:
Gene expression in MFG 18h after S.aureus injection in the mammary gland
MilkFatGlobule_4S_T3

source_name: milk fat globule, goat 4, 18h PI


title: DHL6_0_DMSO_B

description:
17_DHL6_0_DMSO_B
Lymphoma cell line DHL6 treated with DMSO at 0h (replicate B).

source_name: DHL6, DMSO, 0h


title: DHL4_24h_R406_C

description:
15_DHL4_24h_R406_C
Lymphoma cell line DHL4 treated with R406 at 24h (replicate C).


title: DHL6_6h_DMSO_A

description:
19_DHL6_6h_DMSO_A
Lymphoma cell line DHL6 treated with DMSO at 6h (replicate A).


title: DHL6_0_DMSO_A

description:
16_DHL6_0_DMSO_A
Lymphoma cell line DHL6 treated with DMSO at 0h (replicate A).


title: DHL4_24h_R406_B

description:
14_DHL4_24h_R406_B
Lymphoma cell line DHL4 treated with R406 at 24h (replicate B).


title: DHL4_24h_R406_A

description:
13_DHL4_24h_R406_A
Lymphoma cell line DHL4 treated with R406 at 24h (replicate A).


title: DHL4_24h_DMSO_C

description:
12_DHL4_24h_DMSO_C
Lymphoma cell line DHL4 treated with DMSO at 24h (replicate C).

source_name: DHL4, DMSO, 24h


title: xyang01_si_Ctrl_rep1

description: Gene expression data from control A549 rep1

source_name: A549 cells with control oligo, rep1


title: DHL6_0_DMSO_C

description:
18_DHL6_0_DMSO_C
Lymphoma cell line DHL6 treated with DMSO at 0h (replicate C).


title: milk fat globule, goat 3, 18h PI

description:
Gene expression in MFG 18h after S.aureus injection in the mammary gland
MilkFatGlobule_3S_T3

source_name: milk fat globule, goat 3, 18h PI


title: milk fat globule, goat 3, 24h PI

description:
Gene expression in MFG 24h after S.aureus injection in the mammary gland
MilkFatGlobule_3S_T4

source_name: milk fat globule, goat 3, 24h PI


title: DHL4_24h_DMSO_B

description:
11_DHL4_24h_DMSO_B
Lymphoma cell line DHL4 treated with DMSO at 24h (replicate B).


title: DHL4_24h_DMSO_A

description:
10_DHL4_24h_DMSO_A
Lymphoma cell line DHL4 treated with DMSO at 24h (replicate A).


title: milk fat globule, goat 3, 12h PI

description:
Gene expression in MFG 12h after S.aureus injection in the mammary gland
MilkFatGlobule_3S_T2

source_name: milk fat globule, goat 3, 12h PI


title: milk fat globule, goat 4, 24h PI

description:
Gene expression in MFG 24h after S.aureus injection in the mammary gland
MilkFatGlobule_4S_T4

source_name: milk fat globule, goat 4, 24h PI


title: milk fat globule, goat 4, non-infected

description:
Gene expression in MFG before S.aureus injection in the mammary gland
MilkFatGlobule_4S_T0

source_name: milk fat globule, goat 4, non-infected


title: DHL4_6h_R406_C

description:
9_DHL4_6h_R406_C
Lymphoma cell line DHL4 treated with R406 at 6h (replicate C).


title: DHL4_6h_R406_B

description:
8_DHL4_6h_R406_B
Lymphoma cell line DHL4 treated with R406 at 6h (replicate B).


title: milk fat globule, goat 3, non-infected

description:
Gene expression in MFG before S.aureus injection in the mammary gland
MilkFatGlobule_3S_T0

source_name: milk fat globule, goat 3, non-infected


title: UMA07014_rep1

description: Human breast tissue sample gene expression analyzed on agilent catalog 4X44k v1 human array

source_name: Human Reference B

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty Tissue

value: 29 years old

value: premenopausal

value: normal breast tissue


title: UMA07013_rep1

tag: age

value: 43 years old

value: unknown menopausal status


title: UMA07039_rep1_244K

value: 56 years old

tag: status

value: postmenopausal


title: DHL4_6h_DMSO_C

description:
6_DHL4_6h_DMSO_C
Lymphoma cell line DHL4 treated with DMSO at 6h (replicate C).

source_name: DHL4, DMSO, 6h

value: diffuse large B-cell lymphoma (DLBCL) cells


title: sdc2_embryo_rep2

description: sdc-2(y93,RNAi) mixed stage embryos

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip C. ElegansGenome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: Arrays were normalized by RMA (Robust Multichip Average) using Affymetrix Expression Console software (Irizarry et al. 2003). Data were analyzed by ArrayStar. Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. 2003. Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4: 249-264.

source_name: embryos from XX sdc-2(y93) worms grown on bacteria expressing sdc-2 RNAi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: All worms for embryo microarray expression experiments were first grown to high density on NG agar plates with concentrated HB101 at 20°C.  For empty vector control, synchronous L1 larvae were spotted onto RNAi plates (NG agar with 100ug/ml Carb and 1mM IPTG) with concentrated HT115 bacteria carrying an empty RNAi vector (L4440).  Worms were grown for ~96 hours at 20°C before collecting embryos by bleaching.  For smo-1 RNA and sdc-2 RNAii, synchronous L1 larvae were first grown on HB101 for 24 hours to reach the L2/L3 stage and then transferred to RNAi plates spotted with concentrated HT115 bacteria carrying an Ahringer feeding library bacteria plasmid expressing double stranded RNA to smo-1 (Kamath et al. 2003). Worms were grown for 72 hours at 20°C on RNAi before harvesting embryos by bleaching.

extract_protocol: Gravid adults were bleached and 100 µl aliquots of embryos were snap frozen in liquid nitrogen and stored at -80C. An aliquot was thawed at 65C for 10 minutes, resuspended in 1ml Trizol (Invitrogen, Carlsbad, CA), vortexed vigorously to resuspend, and incubated for 20 minutes at room temperature. The sample was then centrifuged for 15 minutes at 12,000xg at 4C. The aqueous phase was transferred to a new tube and 100 µl of BCP (1-bromo-3-chloropropane) (MRC, Cincinnati, OH) was added, the sample was mixed by vortexing, incubated for 15 minutes at room temperature, and centrifuged for 10 minutes at 12,000xg at 4C. The aqueous phase was transferred to a new tube and nucleic acid was precipitated by addition of 500 µl of isopropanol. The sample was incubated for 10 minutes at room temperature, centrifuged at 12,000xg for 8 minutes, washed in 70% ethanol and air dried for 5 minutes. Nucleic acid was resuspended in 100 µl nuclease-free water and RNA quantified with a UV spectrophotometer. One hundred micrograms of RNA was then treated with 3 µl RQ1-DNAse (Promega, Madison, WI) and RNA isolated with the RNAeasy kit as per the manufacturer's protocol (Qiagen, Valencia, CA). RNA was again quantified with a UV spectrophotometer and cDNA was prepared from 5 µg RNA using the Protoscript Kit (NEB, Ipswich, MA) and diluted 1:15 in water.

tag: developmental stage

value: mixed stage embryos

tag: grown on bacteria expressing

value: sdc-2 RNAi


title: DHL4_6h_DMSO_B

description:
5_DHL4_6h_DMSO_B
Lymphoma cell line DHL4 treated with DMSO at 6h (replicate B).

tag: cell line

value: DMSO


title: DHL4_6h_R406_A

description:
7_DHL4_6h_R406_A
Lymphoma cell line DHL4 treated with R406 at 6h (replicate A).

tag: treatment

value: A


title: C3

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: 9–12 weeks old male C57BL/6 mice were purchased from Charles River.

extract_protocol: After 28 days, kidneys were collected and total RNA was obtained using the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion).

treatment_protocol: Mice underwent anesthesia by intraperitoneal injection of pentobarbital (50 mg/kg body weight) and were subjected to Unilateral Ureteral Obstruction (UUO). After standard laparotomy, the left proximal ureter was exposed and ligated with 4-0 silk at two points. The sham operation consisted of a similar identification of the left ureter without ligation.

tag: group

value: non-treated

tag: strain

tag: gender

value: male

value: 9–12 weeks old


title: C1


title: S1

value: treated


title: DHL4_6h_DMSO_A

description:
4_DHL4_6h_DMSO_A
Lymphoma cell line DHL4 treated with DMSO at 6h (replicate A).

tag: time

tag: replicate


title: C2


title: sdc2_embryo_rep1

description: sdc-2(y93,RNAi) mixed stage embryos

tag: genotype/variation


title: smo1_embryo_rep3

description: smo-1(RNAi) mixed stage embryos

source_name: embryos from XX N2 worms grown on bacteria expressing smo-1 RNAi

value: Wild type (N2)

value: smo-1 RNAi


title: smo1_embryo_rep2

description: smo-1(RNAi) mixed stage embryos


title: DHL4_0_DMSO_B

description:
2_DHL4_0_DMSO_B
Lymphoma cell line DHL4 treated with DMSO at 0h (replicate B).

source_name: DHL4, DMSO, 0h

value: B


title: sdc2_embryo_rep3

description: sdc-2(y93,RNAi) mixed stage embryos


title: WT_embryo_rep1

description: Wild type (N2) mixed stage embryos

source_name: embryos from XX N2 worms grown on bacteria expressing empty vector (L4440) RNAi

value: empty vector (L4440) RNAi


title: WT_embryo_rep3

description: Wild type (N2) mixed stage embryos


title: WT_embryo_rep2

description: Wild type (N2) mixed stage embryos


title: UMA07016_rep1

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 15 years old

value: premenopausal

value: normal breast tissue


title: smo1_embryo_rep1

description: smo-1(RNAi) mixed stage embryos


title: S3


title: S4


title: DHL4_0_DMSO_C

description:
3_DHL4_0_DMSO_C
Lymphoma cell line DHL4 treated with DMSO at 0h (replicate C).

value: diffuse large B-cell lymphoma (DLBCL) cells

value: C


title: DHL4_0_DMSO_A

description:
1_DHL4_0_DMSO_A
Lymphoma cell line DHL4 treated with DMSO at 0h (replicate A).


title: C4


title: sm_osmotic_stress_rep2

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

description: This sample is of S. mutans UA159 cultured firstly cultured in the normal condition, and then submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl).It is the second of three hyperosmotic stimuli strain biological replicates used in this experiment, each from separate cultures.

data_processing: The raw data (.pair file) was subjected to RMA algorithm normalization and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Streptococcus mutans UA159

source_name: 0.4M NaCl hyperosmotic stimuli 15 minutes

growth_protocol:
For the control group, the S.mutans UA159 strains were cultured in brain heart infusion broth (BHI; Difco, Sparks, MD) at 37℃ in a 5% CO2 atmosphere to mid-logarithmic phase.
For the hyperosmotic stimuli group, the S.mutans UA159 strains were cultured in brain heart infusion broth (BHI; Difco, Sparks, MD) at 37℃ in a 5% CO2 atmosphere to mid-logarithmic phase. Then the strains  were submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl).

extract_protocol: Total RNA was extracted using the RNAProtect Bacteria Reagent (Qiagen) and RNeasy Mini kits (Qiagen). Rnase-Free DNase Set (Qiagen) was used to remove genome DNA. A Nanodrop ND 1000 spectrophotometer (Thermo Scientific) was used to confirm total RNA concentrations, while an Agilent 2100 Bioanalyser (Agilent Technologies, CA, USA) was used to evaluate the RNA quality. The isolated RNA was stored at -80℃ until use.

tag: genotype

value: Wild type

tag: phenotype

value: normal

tag: accession


title: sm_osmotic_stress_rep3

description: This sample is of S. mutans UA159 cultured firstly cultured in the normal condition, and then submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl).It is the third of three hyperosmotic stimuli strain biological replicates used in this experiment, each from separate cultures.


title: sm_osmotic_stress_rep1

description: This sample is of S. mutans UA159 cultured firstly cultured in the normal condition, and then submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl).It is the first of three hyperosmotic stimuli strain biological replicates used in this experiment, each from separate cultures.


title: SGLT1 mTECs [5357957041_E]

city: Heidelberg

first: Benedikt

last: Brors

address: Im Neuenheimer Feld 280

institute: DKFZ

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957041_E

hyb_protocol: TechNote (Pinto et al., 2009); http://www.miltenyibiotec.com/download/poster_en/1617/_MACS_SuperAmp_Technology.pdf

scan_protocol: Scanned on Illumina BeadStation

data_processing: Raw Illumina data from bead arrays have been processed with Bead Studio or Genome Studio. Bead-level data were averaged using default settings and written in tabular format. Further processing was done in R version 14.1 (http://www.r-project.org). Probe-level data were normalized using quantile normalization from the limma package (v 3.10.1) and log2-transformed. Log ratios were calculated between different conditions and genes sorted according to these log2-ratios. Values from replicates were averaged prior to calculating log2-ratios.

source_name: Human mTECs

label_protocol: Biotinylated cDNA was prepared with the μMACS™ SuperAmp™ protocol for Illumina arrays

extract_protocol: Total RNA was isolated using μMACS™ SuperAmp™ protocol (Miltenyi Biotec)

tag: cell type

value: Human mTECs

tag: cell fraction

value: SGLT1 mTECs

tag: antigen status


title: CEACAM5 mTECs [4127199069_C]

description:
Human-6 v2 Expression BeadChip (Illumina)
4127199069_C

value: CEACAM5 mTECs


title: SGLT1 mTECs [5357957041_C]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957041_C


title: CEACAM5 mTECs [4127199069_A]

description:
Human-6 v2 Expression BeadChip (Illumina)
4127199069_A


title: CEACAM5 mTECs [4127199069_B]

description:
Human-6 v2 Expression BeadChip (Illumina)
4127199069_B


title: SGLT1 mTECs [5357957041_F]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957041_F


title: CEACAM5 mTECs [4127199069_D]

description:
Human-6 v2 Expression BeadChip (Illumina)
4127199069_D


title: SGLT1 mTECs [5357957013_F]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957013_F


title: sm_normal_cultured_strains_rep3

description: This sample is of S. mutans UA159 cultured in the normal condition. It is the third of three normally cultured biological replicates used in this experiment, each from separate cultures.

source_name: normal cultured strains


title: SGLT1 mTECs [5357957041_A]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957041_A


title: CD630_WT-cy3_sigD3-cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Biological replicate 2 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: strain C630E grown 6h in BHI (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E was grown for 6 hours in BHI medium.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen)

value: C630E Mullany

value: wild type

source_name: sigD mutant grown 6h in TY

value: sigD mutant


title: CEACAM5 mTECs [4127199069_F]

description:
Human-6 v2 Expression BeadChip (Illumina)
4127199069_F


title: CD630_WT-cy3_sigD5-cy5

description: Biological replicate 3 of 4.


title: SGLT1 mTECs [5357957041_D]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957041_D


title: SGLT1 mTECs [5357957013_E]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957013_E


title: CD630_WT-cy5_sigD6-cy3

description: Biological replicate 4 of 4.


title: SGLT1 mTECs [5357957013_D]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957013_D


title: CEACAM5 mTECs [4127199069_E]

description:
Human-6 v2 Expression BeadChip (Illumina)
4127199069_E


title: MUC1 mTECs [4139659055_D]

description:
Human-6 v2 Expression BeadChip (Illumina)
4139659055_D

value: MUC1 mTECs


title: MUC1 mTECs [4139659055_F]

description:
Human-6 v2 Expression BeadChip (Illumina)
4139659055_F


title: SGLT1 mTECs [5357957041_B]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957041_B


title: CD630_WT-cy3_sigD1-cy5

description: Biological replicate 1 of 4.


title: MUC1 mTECs [4139659055_C]

description:
Human-6 v2 Expression BeadChip (Illumina)
4139659055_C


title: sm_normal_cultured_strains_rep2

description: This sample is of S. mutans UA159 cultured in the normal condition. It is the second of three normally cultured biological replicates used in this experiment, each from separate cultures.


title: MUC1 mTECs [4139659055_E]

description:
Human-6 v2 Expression BeadChip (Illumina)
4139659055_E


title: SGLT1 mTECs [5357957013_C]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957013_C


title: MUC1 mTECs [4078729149_F]

description:
Human-6 v2 Expression BeadChip (Illumina)
4078729149_F


title: sm_normal_cultured_strains_rep1

description: This sample is of S. mutans UA159 cultured in the normal condition. It is the first of three normally cultured biological replicates used in this experiment, each from separate cultures.


title: SGLT1 mTECs [5357957013_B]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957013_B


title: TM0259_miRNA

status: Public on Aug 30 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient TM0259

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55?C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 10.7.3.1 software (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as 'absent' (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37?C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

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

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: vh status [igvh mutational status (fais et al. j clin invest, 1998)

value: mut


title: TG0139_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient TG0139

value: unmut


title: SL0083_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SL0083


title: SG0114_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SG0114


title: RS0325_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RS0325


title: SA0093_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SA0093


title: MUC1 mTECs [4078729149_E]

description:
Human-6 v2 Expression BeadChip (Illumina)
4078729149_E


title: SGLT1 mTECs [5357957013_A]

description:
Human-6 v3 Expression BeadChip (Illumina)
5357957013_A


title: Wt Fructose x Wt Xylose 6h Replicate 1

city: Ribeirão Preto

first: Ana

middle: Cristina

last: Colabardini

state: São Paulo

address: Av do Café s/n Cidade Universitária

department: Ciências Farmacêuticas

country: Brazil

institute: FCFRP-USP

description: Biological replicate 1 of 2

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans FGSC A4

source_name: total RNA from Wt grown 16h; labeled with Cyanine-3

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: A. nidulans wild type strain was grown on minimal medium with fructose 1% and then transfered to xylose 1% during 6, 12 and 24hours

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

tag: growth condition

value: Wt grown on fructose 1% along 16h

source_name: total RNA from Wt grown 16h on Fructose 1% and transfered to Xylose 1% during 6h ; labeled with Cyanine-5


title: MUC1 mTECs [4078729149_C]

description:
Human-6 v2 Expression BeadChip (Illumina)
4078729149_C


title: PV0322_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PV0322


title: Wt Fructose x Wt Xylose 24h Replicate 2

description: Biological replicate 2 of 2

source_name: total RNA from Wt grown 16h on Fructose 1% and transfered to Xylose 1% during 24h ; labeled with Cyanine-5


title: Wt Fructose x Wt Xylose 6h Replicate 2

description: Biological replicate 2 of 2

value: Wt grown 16h on Fructose 1% and transfered to Xylose 1% during 6h


title: RD0296_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RD0296


title: PG0028_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PG0028


title: Wt Fructose x Wt Xylose 12h Replicate 2

description: Biological replicate 2 of 2

source_name: total RNA from Wt grown 16h on Fructose 1% and transfered to Xylose 1% during 12h ; labeled with Cyanine-5


title: MUC1 mTECs [4078729149_D]

description:
Human-6 v2 Expression BeadChip (Illumina)
4078729149_D


title: PA0351_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PA0351


title: NM0156_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient NM0156


title: PF0177_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PF0177


title: NG0068_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient NG0068


title: Wt Fructose x Wt Xylose 24h Replicate 1

description: Biological replicate 1 of 2

value: Wt grown 16h on Fructose 1% and transfered to Xylose 1% during 24h


title: Wt Fructose x Wt Xylose 12h Replicate 1

description: Biological replicate 1 of 2

value: Wt grown 16h on Fructose 1% and transfered to Xylose 1% during 12h


title: MO0174_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MO0174


title: Female Ctr [spleen]

city: Noda

first: Masakazu

last: Umezawa

state: Chiba

address: 2641 Yamazaki

department: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

hyb_protocol: Cy3-labelled RNA was hybridized to a SurePrint G3 Mouse GE 8x60K microarray according to the protocol of Takara Bio, Inc. (Shiga, Japan).

scan_protocol: The microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and scanned by a DNA microarray Scanner G2565CA (Agilent Technologies).

data_processing: Scanner output images were normalized and digitalized by Agilent Feature Extraction software  (in Feb. 2012) according to the Minimum Information About a Microarray Experiment (MIAME) guidelines (Brazma et al., 2001) and a pre-processing method for Agilent data (Zahurak et al., 2007).

source_name: offspring mouse of control

label_protocol: After purification of RNA by ethanol precipitation and RNeasy Micro Kit (Qiagen, Hilden, Germany), the integrity of extracted RNA was evaluated with capillary electrophoresis using a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). Total RNAs were pooled for each group. Each of the pooled RNA samples was labeled by Cy3.

growth_protocol: ICR mice were purchased from SLC Inc. (Hamamatsu, Shizuoka, Japan) and were housed under controlled temperature (23 ± 1 °C) and humidity (55% ± 5%), with a 12-hr dark/light cycle and ad libitum access to food and water. All animals were treated and handled in accordance with national guidelines for the care and use of laboratory animals and with the approval of institutional animal care and use committee.

extract_protocol: Spleen tissues for gene expression analysis were homogenized in Isogen (Nippon Gene Co., Ltd., Tokyo, Japan). Total RNA was isolated according to the manufacturer's protocol and suspended in RNase-free water.

treatment_protocol: Pregnant ICR mice were treated twice, on gestational days (GD) 5 and 9, with CB-NP (95 microg/kg/time) via intranasal instillation. Control animals were treated with distilled water (1 mL/kg body weight) weight each time.

value: ICR

value: female

tag: age

value: 5d-old (offspring mouse of control)

tag: tissue

value: spleen


title: Female CB-NP [spleen]

source_name: offspring mouse treated with CB-NP

value: 5d-old (offspring mouse of CB-NP_treated)


title: Male CB-NP [spleen]

value: male


title: Male Ctr [spleen]


title: MC0055_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MC0055


title: MA0151_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MA0151


title: LF0102_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient LF0102


title: LV0118_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient LV0118


title: IL0066_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient IL0066


title: GR0092_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GR0092


title: HG0135_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient HG0135


title: GG0027_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GG0027


title: CT0356_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CT0356


title: FM0309_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FM0309


title: GD0262_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GD0262


title: GD0158_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GD0158


title: FS0155_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FS0155


title: FR0283_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient FR0283


title: CM0289_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CM0289


title: GD0051_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient GD0051


title: CD0310_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CD0310


title: BP0326_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BP0326


title: AM0220_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AM0220


title: CM0246_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CM0246


title: BV0229_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient BV0229


title: CM0057_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CM0057


title: CA0101_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient CA0101


title: AR0242_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AR0242


title: AM0067_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AM0067


title: VS0140_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VS0140


title: WB0269_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient WB0269


title: VP0089_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VP0089


title: VR0031_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VR0031


title: VD0354_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VD0354


title: VC0315_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VC0315


title: VC0142_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VC0142


title: AM0034_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient AM0034


title: VB0013_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient VB0013


title: UL0266_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient UL0266


title: RC0116_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RC0116


title: SF0098_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SF0098


title: SR0112_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SR0112


title: SG0168_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SG0168


title: SS0299_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SS0299


title: RG0077_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RG0077


title: TL0397_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient TL0397


title: RA0211_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RA0211


title: PV0286_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PV0286


title: PS0212_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PS0212


title: PM0340_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PM0340


title: RB0040_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RB0040


title: RA0288_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RA0288


title: RR0157_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RR0157


title: SA0021_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SA0021


title: SA0205_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SA0205


title: SA0219_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient SA0219


title: RS0260_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient RS0260


title: PM0117_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PM0117


title: PG0327_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PG0327


title: PL0022_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PL0022


title: PD0164_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PD0164


title: Topotecan24hr_washout

city: Carrboro

first: Chandri

last: Yandava

address: 101 Renee Lynne Court

department: Carolina Institute for Developmental Disabilities

institute: University of North Carolina at Chapel Hill

description:
MoGene-2_1-st
Gene Expression data for dose response to Topotecan  treatment of  mouse cultured cortical neurons

hyb_protocol: Arrays for experiments (1) and (3) were washed and stained using the Affymetrix Gene Fluidics station 450. Hybridization was performed at 48˚C for 17 hours. Arrays for other experiments were run using the Affymetrix GeneTitan system. Steps subsequent to hybridization were performed with the Beckman Coulter FXP Target Express Robot. Hybridization was performed at 45˚C for 16 hours with the Affymetrix GeneTitan instrument, controlled using AGCC software.

scan_protocol: GeneTitan arrays were scanned using the Affymetrix GeneTitan instrument, controlled by AGCC software. Individual arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G Plus with autoloader.

data_processing: Arrays were normalized and expression values determined using Affymetrix Expression Console. Linear RMA normalization was used for all experiments.

source_name: cultured cortical neurons

label_protocol: RNA was labeled using the Affymetrix/Ambion WT Expression kit, combined with Affymetrix GeneChip WT terminal labeling kit.

growth_protocol: Mouse cortical neurons were cultured from E13-15 mouse embryos for 7 days in vitro.

extract_protocol: Total RNA was extracted from mouse cortical neurons using Trizol reagent.

treatment_protocol: After 7 days in vitro, mouse cortical neurons were treated with drug or vehicle. After 24 or 72 hrs drug treatement, total RNA was prepared.

tag: treatment

value: cultured cortical neurons


title: Topotecan24hr


title: Topotecan_1µM_vehicle_5


title: Topotecan_1µM_vehicle_4


title: Topotecan_1µM_vehicle_6


title: PA0146_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PA0146


title: PA0271_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PA0271


title: PA0234_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PA0234


title: PA0145_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient PA0145


title: OM0201_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient OM0201


title: OV0127_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient OV0127


title: OI0282_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient OI0282


title: NS0060_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient NS0060


title: NB0333_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient NB0333


title: MS0321_miRNA

description: MicroRNA profiling data from Chronic Lymphocytic Leukemia patient MS0321