title: sgs1△ tangeretin, repeat 1

description:
S4_H010
Sgs1-TAN

source_name: sgs1△, tangeretin treated

value: trp d.o medium with 30 μM tangeretin

value: Cells were grown in trp d.o medium 4h at 30˚C with 30 μM tangeretin. Tangeretin was dissolved in DMSO; final DMSO concentration in medium was 0.2% v/v.


title: sgs1△ tangeretin, repeat 2

status: Public on Mar 16 2013

type: RNA

city: Taipei

first: SHIN YEN

last: CHONG

address: No. 1, Sec. 4, Roosevelt Road,

department: Institute of Food Science and Technology

country: Taiwan

institute: National Taiwan University

description:
S4_H011
Sgs1-TAN

hyb_protocol: The hybridization protocol was provided by the Phalanx Biotech Group (see http://www.onearray.com/ for protocols).

scan_protocol: The scan protocol was provided by the Phalanx Biotech Group (see http://www.onearray.com/ for protocols), and .gpr files were provided.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. Data were analyzed and calibrated by Rosetta Resolver software. The normalized intensity is the mean of the normalized data after median normalization.

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: The label protocol was provided by the Phalanx Biotech Group (see http://www.onearray.com/ for protocols).

extract_protocol: Total RNA were extracted following the hot-phenol process (Collart and Oliviero, 2001) and converted into cDNA.

tag: strain

tag: genotype/variation

value: sgs1 deletion (MATα his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 trp1∆::HPH sgs1∆::kanMX4 pRS414-GAL1-HO-TRP1)

tag: treatment

tag: treatment duration

value: 4 hrs

tag: treatment protocol


title: sgs1△ control, repeat 2

description:
S3_H008
Sgs1

source_name: sgs1△, control

value: trp d.o medium

value: Cells were grown in trp d.o medium 4h at 30˚C with 0.2% v/v DMSO.


title: sgs1△ tangeretin, repeat 3

description:
S4_H012
Sgs1-TAN


title: ngp

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label: biotin

organism: Homo sapiens

source_name: ngp

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol

tag: cell type

value: Neuroblastoma cell

tag: cell line

value: ngp


title: WT tangeretin, repeat 3

description:
S2_H006
WT-TAN

source_name: WT, tangeretin treated

value: wild type (MATα his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 trp1∆::HPH pRS414-GAL1-HO-TRP1)


title: sgs1△ control, repeat 1

description:
S3_H007
Sgs1


title: sjnb12


title: shep21n


title: WT tangeretin, repeat 2

description:
S2_H005
WT-TAN


title: WT tangeretin, repeat 1

description:
S2_H004
WT-TAN


title: WT control, repeat 2

description:
S1_H002
WT

source_name: WT, control


title: nmb

source_name: nmb

value: nmb


title: gimen

source_name: gimen

value: gimen


title: WT control, repeat 3

description:
S1_H003
WT


title: sknas

source_name: sknas

value: sknas


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 60 minutes, replicate 3

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

country: USA

institute: University of Florida

hyb_protocol: The slides were hybridized to a mixture containing equal amounts of test and reference cDNA for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems), and then washed.

scan_protocol: Hybridized slides were scanned using a GenePix scanner (Axon Instruments, Inc., Union City, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website. Single-channel images of the slides were loaded into Spotfinder and overlaid. A spot grid was created according to PFGRC specifications and manually adjusted to fit all spots. The Microarray Data Analysis System (MIDAS) software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting. MIDAS also utilized In-Slide Replicate Analysis to average the intensities of the spots that were replicated on the microarray slide. Spots that were missing or labeled as bad during the upstream processes in 50% of the slides were cut off in the output files, which also did not include control spots printed on the slides. Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P value of 0.001.

organism: Enterococcus faecalis OG1RF

source_name: 80μg/mL cephalothin, 60 minute exposure RNA

label_protocol: Once RNA was purified as described above, cDNA was generated from 2ug RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Invitrogen, Gaithersburg, MD) to increase cDNA yields. Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: Cells were grown in FMC medium supplemented with 10mM gluocse to OD600 of 0.3 at 37°C.

extract_protocol: RNA was isolated from homogenized E. faecalis cells grown in BHI medium to OD600 of 0.3 with or without exposure to antibiotics by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at -20°C overnight. RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes. RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 mL samples were run on an agarose gel to verify RNA integrity. The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier. Final RNA concentrations were determined in triplicate.

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 80μg/mL cephalothin for 60 minutes.

tag: genotype

value: wild-type

tag: growth phase

value: cephalothin

value: 60 minutes

source_name: Wild-type mid-log RNA

growth_protocol: Cells were grown in Brain-Heart medium to OD600 of 0.5 at 37°C.

extract_protocol: RNA was isolated from homogenized E. faecalis cells grown in BHI medium to OD600 of 0.5 without exposure to antibiotics by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at -20°C overnight. RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes. RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 mL samples were run on an agarose gel to verify RNA integrity. The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier. Final RNA concentrations were determined in triplicate.

tag: sample type

value: reference


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 60 minutes, replicate 4


title: WT control, repeat 1

description:
S1_H001
WT


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 60 minutes, replicate 2


title: strain D2 LPS stimulations at 6 hours, repeat 2

status: Public on Mar 17 2013

city: Tel-Aviv

first: Irit

last: Gat Viks

address: Department of Cell Research and Immunology

department: Cell Research and Immunology

country: Israel

institute: Tel-Aviv University

hyb_protocol: Standard Affymetrix protocols for mouse ht arrays

data_processing: RMA algorithm was applied using the ExpressionFileCreator procedure (version 11) in the GenePattern software (http://genepattern.broadinstitute.org/gp).

label: Biotin

organism: Mus musculus

source_name: D2 LPS stimulations at 6 hrs

growth_protocol: mouse primary BMDCs (Gat-Viks et al. 2012)

extract_protocol: miRNEASY (QIAGEN) as recommended by manufactor

tag: age

value: 12 weeks

value: primary bone marrow dendritic cell


title: Huh7_5-FU

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology and Nephrology

country: Japan

institute: Graduate School of Medicine, Chiba University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human GE 4x44K v2 (catalog # G4845A)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Huh7 EpCAM- cells, 5-FU treated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One Color Spike Mix Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Mini kit (Qiagen, Valencia, CA, USA) following the manufacturer's recommendations.

treatment_protocol: Huh1 cells and Huh7 cells were treated with disulfiram (0.1μM) or 5-FU (1μM) for 48 hours. Fluorescence-activated cell sorting was used to isolate EpCAM-negative HCC cells.

value: Huh7 EpCAM- cells


title: Huh1_DSF

source_name: Huh1 EpCAM- cells, DSF treated

value: Huh1 EpCAM- cells

value: DSF


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 30 minutes, replicate 4

source_name: 80μg/mL cephalothin, 30 minute exposure RNA

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 80μg/mL cephalothin for 30 minutes.

value: 30 minutes


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 60 minutes, replicate 1


title: Huh7_control

source_name: Huh7 EpCAM- cells, control

value: Control


title: Huh7_DSF

source_name: Huh7 EpCAM- cells, DSF treated


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 30 minutes, replicate 2


title: sknfi

source_name: sknfi

value: Neuroblastoma cell

value: sknfi


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 30 minutes, replicate 1


title: Huh1_5-FU

source_name: Huh1 EpCAM- cells, 5-FU treated


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 60 minutes, replicate 3

source_name: 80μg/mL bacitracin, 60 minute exposure RNA

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 80μg/mL bacitracin for 60 minutes.

value: bacitracin


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 60 minutes, replicate 2


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 60 minutes, replicate 1


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 30 minutes, replicate 4

source_name: 80μg/mL bacitracin, 30 minute exposure RNA

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 80μg/mL bacitracin for 30 minutes.


title: E. faecalis OG1RF exposed to 80μg/mL cephalothin for 30 minutes, replicate 3


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 30 minutes, replicate 3


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 60 minutes, replicate 4


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 30 minutes, replicate 1


title: HT-29, stimulated with NaB, replicate #3

city: Dhaka

first: Protim

last: Sarker

address: Mohakhali

country: Bangladesh

institute: icddr,b

description:
PS08_NaB
Gene expression data from HT-29 cells stimulated with 2 mM NaB.

hyb_protocol: Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Expression Console (v 1.1) using the following methods. Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: HT-29 cells stimulated with 2 mM NaB

label_protocol: Total RNA was converted to sense strand cRNA using the Ambion WT expression kit. For fragmentation and labeling, the GeneChip WT Target Labeling kit was used.

growth_protocol: HT-29 (ATCC, HTB-38) was grown up to 80-90% confluence in culture medium (RPMI-1640 supplemented with 10% fetal calf serum, 25 mM HEPES, 2 mM L-glutamine amd penicillin-streptomycin [Invitrogen]) in 6-well tissue culture plates (Corning) at 37C in 5% CO2.

extract_protocol: Extraction of RNA from cells was performed utilizing the RNeasy RNA purification kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Culture media was discarded, cells were rinsed with PBS and stimulated with 2 mM NaB (Sigma) alone or in combination with 125/150 ug/ml ciprofloxacin (Sigma) in culture medium in the absence of fetal calf serum and penicillin-streptomycin for 24 hours at 37C in 5% CO2. Cells incubated with only culture medium served as an unstimulated control.

value: colonic epithelial cell line

value: NaB


title: Huh1_control

source_name: Huh1 EpCAM- cells, control


title: HT-29, stimulated with NaB and ciprofloxacin, replicate #3

description:
PS09_NaB_Cip150
Gene expression data from HT-29 cells stimulated with 2 mM NaB and 150 ug/ml ciprofloxacin.

value: NaB and ciprofloxacin


title: E. faecalis OG1RF exposed to 80μg/mL bacitracin for 30 minutes, replicate 2

value: wild-type


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 30 minutes, replicate 3

source_name: 20μg/mL ampicillin, 30 minute exposure RNA

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 20μg/mL ampicillin for 30 minutes.

value: ampicillin


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 60 minutes, replicate 4

source_name: 20μg/mL ampicillin, 60 minute exposure RNA

treatment_protocol: Upon reaching OD600 = 0.3, cells were treated with 20μg/mL ampicillin for 60 minutes.

value: 60 minutes


title: HT-29, unstimulated, replicate #3

description:
PS07_uns
Gene expression data from HT-29 cells stimulated only with culture media.

value: media control


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 60 minutes, replicate 3

value: reference


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 30 minutes, replicate 4


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 30 minutes, replicate 2


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 60 minutes, replicate 2


title: SI_NET

type: genomic

city: Rochester

first: Ganesh

last: Boora

state: MN

address: 200 First Street

institute: Mayo Clinic

description: Tumor/Normal

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent SureTag kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (11.0.1.1) and used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: SI-NET

label_protocol: 500 ng of Tumor DNA was labeled with Cy5 and 500ng of normal sample DNA was labeled in Cy3

extract_protocol: DNA was extracted by spin column protocol (Qiagen – Dneasy kit)

treatment_protocol: Tissue stored at -80°C which were snap frozen in liquid nitrogen at the time of surgery.

tag: tissue type

value: small intestine neuroendocrine tumor

source_name: benign small bowel

value: matched normal sample


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 30 minutes, replicate 1

source_name: Wild-type mid-log RNA


title: HT-29, stimulated with NaB and ciprofloxacin, replicate #2

description:
PS06_NaB_Cip150
Gene expression data from HT-29 cells stimulated with 2 mM NaB and 150 ug/ml ciprofloxacin.


title: HT-29, stimulated with NaB, replicate #2

description:
PS05_NaB
Gene expression data from HT-29 cells stimulated with 2 mM NaB.


title: E. faecalis OG1RF control, replicate 4

source_name: Control OD600 = 0.3 RNA


title: E. faecalis OG1RF control, replicate 3


title: E. faecalis OG1RF exposed to 20μg/mL ampicillin for 60 minutes, replicate 1


title: HT-29, unstimulated, replicate #2

description:
PS04_uns
Gene expression data from HT-29 cells stimulated only with culture media.


title: E. faecalis OG1RF control, replicate 1


title: E. faecalis OG1RF control, replicate 2


title: HT-29, stimulated with NaB, replicate #1

description:
PS02_NaB
Gene expression data from HT-29 cells stimulated with 2 mM NaB.


title: HT-29, stimulated with NaB and ciprofloxacin, replicate #1

description:
PS03_NaB_Cip125
Gene expression data from HT-29 cells stimulated with 2 mM NaB and 125 ug/ml ciprofloxacin.


title: 30 min AuCN 500 µM single

status: Public on Mar 15 2013

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

country: Germany

hyb_protocol: Hybridisation was done by the service providers ImaGenes GmbH (Berlin) or IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service providers ImaGenes GmbH (Berlin) or IMGM Laboratories GmbH (Martinsried)

data_processing: First, all spots not related to CH34 were removed (e.g. bright and dark corners, bringing it down from 15743 to 15206 spots). Secondly, some oligonucleotides were spotted more than one time (up to four times). In these cases, a mean signal was calculated and assigned to the oligo. 9,735 probes of the 15,207 remains. Normalized signal intensity: The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength. Its deviation was half of the sum of both intensity deviations and the distance (D) value the distance between spot and background pixel intensities divided by the sum of the deviations

organism: Cupriavidus metallidurans CH34

source_name: cells of C. metallidurans

label_protocol: Labeling was done by the service providers ImaGenes GmbH (Berlin) or IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans cultures were grown in Mineral salts medium + 0.2 % Na-gluconate to a cell turbidity of 100 Klett, metal species added, incubated for 10-30 min, then harvest cells by centrifugation for 1' in 2.0 ml Tubes.

extract_protocol: RNeasy Mini Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: time

value: 30 min

value: AuCN 500 uM


title: Midgut (G) biological replicate 2

city: Pretoria

first: Christian

last: Stutzer

state: Gauteng

address: Lynnwood road

department: Biochemistry

country: South Africa

institute: University of Pretoria

description:
G2
Biological replicate 2 of 2. Midgut, harvested after 20 days post infestation.
2009-09-23_252449710002_G2.gpr

hyb_protocol: Hybridization was performed at 65oC for 17 hours. Prior to scanning, each slide was washed, rinsed and dried in Stabilization and Drying Solution (Agilent Technologies, USA). Following a drying step, slides were scanned with the GenePixTM 4000B microarray laser scanner (Molecular devices Inc., USA).Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on a 4000B microarray laser scanner (Molecular devices Inc., USA) Images were quantified using GenepixPro feature extraction software (v6.0, Axon Molecular Devices, USA).

data_processing: Images were quantified using GenepixPro feature extraction software (v6.0, Axon Molecular Devices, USA).  Normalization within slides was performed using the Limma package in R (http://CRAN.R-project.org), employing the locally weighted scatterplot smoothing (LOWESS) technique, followed by Gquantile normalization between slides. The Limma package also used to calculate the fold change between each group pair-wise comparison, to identify significantly differentially expressed transcripts with p-values adjusted for multiple comparisons false discovery rates.

organism: Rhipicephalus microplus

source_name: Midgut

label_protocol: 3 µg of high quality DNaseI-treated total RNA was used for cDNA synthesis using 500 U SuperscriptTM III (InvitrogenTM life technologies, USA), a poly-dT primer (250 pmol), random nanomers (775 pmol) and 5 mM each dATP, dTTP, dGTP, with 5 mM aminoallyl dUTP for Cyanine 3-dCTP/Cyanine 5-dCTP dye coupling.  DNA was primed at 70°C for 10 min, then reversed transcribed at 42°C for 16 h.

growth_protocol: R. microplus (Mozambique strain) larvae, hatched at 25oC (75-85% humidity), were allowed to feed on Holstein-Friesian cattle.

extract_protocol: Total RNA was isolated according to manufacturer’s guidelines for TRI REAGENT

tag: gender

value: Female

value: day 20

value: Mozambique

tag: developmental stage

value: adult

tag: tissue

value: Midgut

source_name: [reference] pooled life stages day 4, 5, 7, 13 and 15 and tissues at day 20

tag: reference composition

value: mixed for life stages, female for adult tissues

value: female


title: Salivary gland (SG) biological replicate 2, technical repeat

description:
SG2R
Technical replicate of biological replicate 2. Salivary glands, harvested after 20 days post infestation.
2009-09-23_252449710002_SG2R.gpr

source_name: Salivary glands

tag: strain

value: Salivary glands

value: life stages day 4, 5, 7, 13 and 15 and tissues at day 20


title: Midgut (G) biological replicate 1

description:
G1
Biological replicate 1 of 2. Midgut, harvested after 20 days post infestation.
2009-09-23_252449710002_G1.gpr


title: Midgut (G) biological replicate 2, technical repeat

description:
G2R
Technical replicate of biological replicate 2. Midgut, harvested after 20 days post infestation.
2009-09-23_252449710002_G2R.gpr


title: 30 min KCN 500µM single

value: KCN 500uM


title: Midgut (G) biological replicate 1, technical repeat

description:
G1R
Technical replicate of biological replicate 1. Midgut, harvested after 20 days post infestation.
2009-09-23_252449710002_G1R.gpr


title: amc106

value: Neuroblastoma cell


title: sknsh

source_name: sknsh

value: sknsh


title: HT-29, unstimulated, replicate #1

description:
PS01_uns
Gene expression data from HT-29 cells stimulated only with culture media.

value: colonic epithelial cell line

value: media control


title: Salivary gland (SG) biological replicate 1, technical repeat

description:
SG1R
Technical replicate of biological replicate 1. Salivary glands, harvested after 20 days post infestation.
2009-09-23_252449710002_SG1R.gpr


title: Ovary (O) biological replicate 1

description:
O1
Biological replicate 1 of 2. Ovaries, harvested after 20 days post infestation.
2009-09-29_252449710001_O1.gpr

source_name: Ovaries

value: Ovaries


title: 10 min AuCl4 50 µM single

value: 10 min

value: AuCl4 50 uM


title: Salivary gland (SG) biological replicate 2

description:
SG2
Biological replicate 2 of 2. Salivary glands, harvested after 20 days post infestation.
2009-09-23_252449710002_SG2.gpr

value: Female


title: Ovary (O) biological replicate 2, technical repeat

description:
O2R
Technical replicate of biological replicate 2. Ovaries, harvested after 20 days post infestation.
2009-09-29_252449710001_O2R.gpr

value: day 20


title: Salivary gland (SG) biological replicate 1

description:
SG1
Biological replicate 1 of 2. Salivary glands, harvested after 20 days post infestation.
2009-09-23_252449710002_SG1.gpr

value: Mozambique


title: 30 min KCN 5 mM, 3 replicates - rep1

value: 30 min

value: KCN 5 mM


title: 30 min AuCN 5 mM, 3 replicates - rep3

value: AuCN 5 mM


title: 30 min KCN 5 mM, 3 replicates - rep2


title: Ovary (O) biological replicate 2

description:
O2
Biological replicate 2 of 2. Ovaries, harvested after 20 days post infestation.
2009-09-29_252449710001_O2.gpr

value: adult

value: mixed for life stages, female for adult tissues

value: female


title: 30 min AuCN 5 mM, 3 replicates - rep2


title: 30 min KCN 5 mM, 3 replicates - rep3


title: 10 min KCN 50 µM, 3 replicates - rep2

value: KCN 50 uM


title: 10 min KCN 50 µM, 3 replicates - rep1


title: 10 min AuCN 50 µM, 3 replicates - rep3

value: AuCN 50 uM


title: Against CDK8 and CDK19 rep1

city: San Diego

first: Taiki

last: Tsutsui

state: California

address: 9500 Gilman Dr

department: CMM

institute: UCSD

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.

source_name: Against CDK8 and CDK19 double transfected cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.

extract_protocol: RNA was prepared using RNeazy column (QIAGEN).

treatment_protocol: We transfect two siRNA against CDK8 and CDK19 at a same time using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 10nM each. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr

value: HeLa s3


title: SC2

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression in subcutaneous adipocytes

hyb_protocol: The RNA was subjected to Affymetrix Human Genes ST 1.0 gene chip assay

scan_protocol: CEL files were generated from the Affymetrix GeneChip Scanner 3000 7G using Expression Console v1.1.1 (Affymetrix)

data_processing:
CEL files were subjected to RMA normalization using Affymetrix CDF probeset definitions with genespring v 7.
Relative gene expression levels were calculated based on the ratio of each sample’s RMA signal intensity (2**RMA) to that of the median for each probeset across the six samples.

source_name: Subcutaneous adipocyte harvested from subject with terminal illness or injury and no metabolic or atherosclerotic disease

label_protocol: Purified RNAs were analyzed for concentration and integrity using the Agilent Bioanalyzer  RNA 6000 Pico Kit (Agilent Technologies Inc., Santa Clara, CA) and then labeled as appropriate for hybridization to Human Genes ST 1.0 GeneChip (Affymetrix Inc., Santa Clara, CA) using the Affymetrix WT labeling kit

growth_protocol: Adipose tissue was digested with collagenase, and digests were filtered, centrifuged, and treated with erythrocyte lysis buffer.  Cells were plated in Dulbecco's modified Eagle's medium-Ham's F-12 with 7.5% FBS and antibiotics.  After 18 hours cells were detached and replated until the cultures were essentially pure adipocyte populations.

extract_protocol: RNA was extracted from preadipocytes cells with RNeasy lipid mini kits (Qiagen)

treatment_protocol: Preadipocytes were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum, and expanded. After two passages, cells were plated onto 10 cm dishes and allowed to differentiated in adipogenic differentiation medium (Cell Signal) for 7 days

value: Subcutaneous adipocyte


title: 10 min Au-thiosulfate 500 µM, 3 replicates - rep3

value: Au-thiosulfate 500 uM


title: 10 min AuCN 50 µM, 3 replicates - rep1


title: 30 min AuCN 5 mM, 3 replicates - rep1


title: SC1


title: PV2

description: Gene expression in perivascular adipocytes overlying the left coronary artery

source_name: Perivascular adipocyte harvested from the left coronary artery of subject with terminal illness or injury and no metabolic or atherosclerotic disease

value: Perivascular adipocyte


title: SC3


title: human islets, ID79

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

description: Gene expression data from human pancreatic islets

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized onto the GeneChip® Human Gene 1.0 ST whole transcript based assay overnight in the GeneChip® Hybridization oven 6400 using standard procedures. The arrays were washed and stained in a GeneChip® Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing:
The array data was summarized and normalized with Robust Multi-array Analysis (RMA) method using the software 'Expression Console' (Affymetrix). Sample data tables contains unique 18808 ID_REFs which corresponds to probes that map uniquely to one gene, with a unique mapping position in the human genome (hg19, b37).
R version 2.14.1 (2011-12-22) Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Portuguese_Portugal.1252
LC_CTYPE=Portuguese_Portugal.1252
[3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Portugal.1252
attached base packages: [1] stats, graphics, grDevices utils, datasets, methods, base
other attached packages: [1] affy_1.32.1, Biobase_2.14.0
loaded via a namespace (and not attached):
[1] affyio_1.22.0, BiocInstaller_1.2.1, preprocessCore_1.16.0
[4] tools_2.14.1 zlibbioc_1.0.1

source_name: Islets from non-diabetic donor

label_protocol: Briefly, 100-200 ng total RNA was processed as indicated by GeneChip® Expression 3’-Amplification Reagents Onecycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) was used to produce double-stranded cDNA. This was used as a template to generate biotintargeted cRNA following the manufacturer’s specifications.

extract_protocol: Total RNA was isolated with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 bioanalyzer (Bio-Rad, Hercules, CA, USA) and a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to RNA preparation.

tag: cadaver donor id

tag: donor group

value: non-diabetic donors

value: male

tag: bmi

value: pancreatic islets


title: 10 min AuCN 50 µM, 3 replicates - rep2

value: 10 min

tag: treatment


title: human islets, ID76


title: PV1


title: human islets, ID80

source_name: Islets from GADA positive donor

value: GADA positive


title: human islets, ID77


title: human islets, ID78


title: 10 min Au-malate 500µM, 3 replicates - rep2

value: Au-malate 500uM


title: PV3


title: human islets, ID73


title: human islets, ID72


title: human islets, ID71


title: 10 min Au-malate 500µM, 3 replicates - rep1


title: 10 min Au-thiosulfate 500 µM, 3 replicates - rep2


title: 10 min Au-thiosulfate 500 µM, 3 replicates - rep1


title: 10 min Au-malate 500µM, 3 replicates - rep3


title: 10 min without treatment, 3 replicates - rep1

value: untreated


title: NMFH2

city: Tainan

first: Chien-Feng

last: Li

address: 901 Chunghwa Road

department: Pathology/Medical Research

institute: Chi-Mei Medical Center

hyb_protocol: The samples were rehydrated in Roche NimbleGen Hybridization Buffer (Roche NimbleGen Inc.), denatured at 95oC for 5 min, and then cooled to 42oC. Hybridizations were carried out for 18 hr (16~20 hr) at 42oC in the NimbleGen Service Laboratory.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for NimbleGen Human CGH 3x720K Whole-Genome Tiling v3.0 Array data extraction. Data were extracted from scanned images using NimbleScan 2.3 extraction software (Roche NimbleGen, Inc.).

source_name: Myxofibrosarcoma cell line (NMFH2)

label_protocol: DNA samples were labeled using Roche Nimblegen's standard protocol. Total genomic DNA from each tumor were directly labeled by random primer extension labeling (Cy3) without an intervening whole-genome amplification step. The reference DNA samples were labeled with Cy5.

extract_protocol: Based on H&E sections, regions suitable for DNA extraction were dissected from 12 fresh specimens after trimming necrotic and fibrous areas to assure higher than 80% of tumor content. For each case, 1 μg of total genomic DNA at a concentration of 500 ng/μl was extracted from fresh tissue by using "recoverall DNA Purification Kits" (Ambion, Austin, TX) for hybridization against oligonucleotide microarrays. To ensure DNA integrity, each sample should have an A260/280 ratio of 1.7 to 2.0 and no sign of degradation, as evaluated by gel electrophoresis.

tag: cell type

value: myxofibrosarcoma cells

source_name: Lymphocytes from gender-matched donor 08

value: lymphocytes from gender-matched donor


title: 10 min without treatment, 3 replicates - rep2


title: Monocyte NS 6h 2

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: Monocytes unstimulated (6 hours)

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours..

scan_protocol: he arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing:
Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered for probes with signals below background and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, principal component analysis (PCA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Genes were considered to be differentially expressed when the false discovery rae [23] was below 1% and absolute fold change (FC) was above 2.0 in at least one of the 18 pair combinations.
the "processed signal" from feature extractor was used, with no further background correction
the normalization was done with the "quantile" algorithm as mentioned
the dataset was filtered to remove controls, spot below BG, spot not found (Agilent FLAG), and saturated spots (Agilent FLAG). For each probe, the probe ws removed if the FLAG was set TRUE in > 75% of the samples
the dataset was then summarized for replicated (identical) probes (to keep only one)

source_name: Monocytes unstimulated (6 hours)

label_protocol: In brief, 250 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: Leukopacks from normal blood donor buffy coats were provided from the Etablissement Français du Sang (Marseille, France). Peripheral blood mononuclear cells were isolated from blood samples after deposition over a Ficoll density cushion. They were then subjected to CD14+ magnetic cell sorting using a monocyte isolation kit (Miltenyi Biotec, Paris, France). This procedure resulted in more than 95% monocyte purity, as assessed by flow cytometry. CD14+ cells (10e6 cells per assay) were differentiated into macrophages. In brief, they were incubated in RPMI 1640 containing 20 mM HEPES, 10% human serum AB+, 2 mM L-glutamine, 100 IU/ml penicillin and 100 µg/ml streptomycin (Life Technologies, Saint Aubin, France) for 3 days, and fetal calf serum was substituted by human serum for 4 supplementary days. More than 95% of the cells were macrophages, as assessed by CD68 expression and CD14 down-modulation.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.

treatment_protocol: Monocytes and monocyte-derived macrophages were stimulated with 20 ng/ml recombinant human IFN-gamma (PeproTech, Neuilly-sur-Seine, France) or IL-4 (AbCys, Paris, France) for 6 or 18 hours.

tag: stimulation

value: NO

value: NS

value: Monocyte

tag: ifng


title: 10 min without treatment, 3 replicates - rep3


title: human islets, ID70


title: Monocyte IL4 6h 3

description: Monocytes stimulated with IL-4 for 6 hours

value: YES


title: Monocyte IFNG 6h 3

description: Monocytes stimulated with IFN-gamma for 6 hours

value: IFNg


title: Monocyte NS 6h 3

description: Monocytes unstimulated (6 hours)


title: Monocyte IL4 6h 2

source_name: Monocytes stimulated with IL-4 for 6 hours


title: BMP - rep 3

city: Reading

first: Phil

middle: G

last: Knight

address: Hopkins Building, Whiteknights

country: United Kingdom

institute: University of Reading

hyb_protocol: Standard Affymetrix workflow by accredited service provider

data_processing:
Raw hybridization data were stored as .cel files and loaded into Genespring GX software for probe summarization (robust multi-array averaging, RMA algorithm), filtering and statistical analysis using the GeneSpring ‘biological significance’ workflow utility for a gene-level experiment.
Affymetrix Expression Console rma.chp files were provided since submitter doesn't have access to Genespring GX software (licence expired since analysis was done).

organism: Bos taurus

source_name: adult bovine ovarian theca cels in primary culture

growth_protocol: Bovine ovarian theca interna cells (TC) were isolated from adult bovine ovaries obtained from the slaughterhouse

extract_protocol: Total RNA was isolated using the Ribopure RNA isolation kit (Ambion) according to the manufacturer’s instructions

treatment_protocol: Cells were were plated out in in 24-well plates (0.5 x106 viable cells/ml/well) and cultured for 6 days under defined serum-free conditions with treatments present on days 3-6 inclusive. TC were treated for 4 days with BMP6 (10 ng/ml) under both basal and LH-stimulated conditions (± 160 pg LH/ml).

tag: protocol

value: BMP

value: bovine theca cells


title: Monocyte NS 6h 1

description: Monocytes unstimulated (6 hours)


title: Monocyte IFNG 6h 2

source_name: Monocytes stimulated with IFN-gamma for 6 hours


title: human islets, ID67

value: female


title: BMP - rep 4

scan_protocol: Standard Affymetrix workflow by accredited service provider


title: LH - rep 3

label_protocol: Standard Affymetrix workflow by accredited service provider

value: LH


title: LH + BMP - rep 4

value: LH + BMP


title: Monocyte NS 18h 3

description: Monocytes unstimulated (18 hours)

source_name: Monocytes unstimulated (18 hours)


title: LH + BMP - rep 3


title: LH - rep 4


title: Monocyte IL4 6h 1


title: LH + BMP - rep 2


title: control -rep 4

value: control


title: Monocyte IFNG 6h 1


title: control -rep 3


title: Monocyte NS 18h 2

description: Monocytes unstimulated (18 hours)


title: LH - rep 2


title: Monocyte NS 18h 1

description: Monocytes unstimulated (18 hours)


title: HBM_infected_4h_rep3

city: Beijing

first: Feng

last: Xue

state: Beijing

address: No. 95, Yong'an Road

department: Department of Microbiology and Parasitology

country: China

institute: Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University

hyb_protocol: The labeled samples were hybridized to the OneArrayTM whole genome microarray with Phalanx hybridization buffer using cover slides. After overnight hybridization at 50°C, non-specific binding targets were washed away using 3 different washing steps.

scan_protocol: The slides were dried using centrifugation and scanned using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA, USA). The Cy5 fluorescent intensities of each spot were analyzed using GenePix Pro 6.0 software (Molecular Devices). The signal intensity of each spot was corrected by subtracting background signals in the immediate surroundings. Spots which flag <0 and SNR <3, and the control probes were filtered out.

data_processing: Spots that passed the above-mentioned criteria were normalized using quantile normalization according to the manufacturer’s recommendation and tested for differential expression. The differential expressed genes were further analyzed using Agilent GeneSpring GX software (version 10.0). Considering that primary cells were a mixture of several related cell types with limited purity, regulated genes with more than 3 folds (P<0.05) of up-regulation or down-regulation were defined as significantly regulated genes.

label_protocol: For each sample, about 10 μg of total RNA was mixed with 600 ng of random hexamer primers (TaKaRa, Otsu, Japan) and denaturalized at 65℃ for 5 min. Then the first strand cDNA was synthesized using 2 μl (400 U) SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) according to the protocol recommended by the manufacturer. The double strand cDNA (ds cDNA) sample was then synthesized using 2nd Strand Synthesis section of M-MLV RTase cDNA Synthesis Kit (TaKaRa, Otsu, Japan) according to the manufacturers’ instructions. Following RNase H (Invitrogen, Carlsbad, CA) and RNase A (Ambion, Texas) digestion for 1 h, ds cDNA sample was purified using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany) according to QIAquick Spin handbook. The double-stranded cDNA templates were labeled using Amersham Mono-functional Cy5 CyDye.

growth_protocol: Murine peritoneal macrophages (MPMs) were isolated from male BALB/c mice (6 to 8 weeks old) by washing the peritoneal cavities with cold RPMI 1640 medium. Macrophages were seeded in 75cm2 tissue culture flasks (Corning. Inc., Big Flats, NY) and the cell numbers were counted in a haemocytometer. The cells were cultured in RPMI 1640 medium (supplemented with 10% heat-inactivated fetal bovine serum, 100 μg/ml of penicillin, and 100 μg/ml of streptomycin) for 2 h at 37°C under a humidified atmosphere containing 5% CO2. After the pre-incubation, non-adherent cells were removed gently by washing with PBS (0.01M, pH 7.4), and the purity of the remaining macrophages was tested by Wright’s staining. Human peripheral blood monocytes (HBMs) were isolated from 6 healthy donors using standard Ficoll-Hypaque gradient centrifugation as previously described. The monocytes were seeded and counted according to the above-mentioned protocol of MPM, then pre-incubated overnight at 37°C under a humidified atmosphere containing 5% CO2. After the pre-incubation, the monocytes was thoroughly washed with autocleaved PBS to remove non-adherent cells, and then continuously incubated for 5 days in a medium containing 500 U/ml of granulocyte-macrophage colony stimulating factor (GM-CSF; eBioscience, CA, USA) to differentiate the cells into macrophages.

extract_protocol: At sample harvesting, MPM and HBM cell cultures were washed 3 times using autocleaved PBS to remove leptospiral cells. The total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA), then purified using RNeasy Mini Kit (QIAGEN, Hilden, Germany) with on-column DNase digestion (QIAGEN, Hilden, Germany) according to the RNeasy Mini handbook. RNA quantity and integrity was determined using RNA 6000 Nano Laboratory-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The MPM and HBM cell cultures were washed 3 times with autocleaved PBS, renewed with new medium without antibiotics, and further cultured for 12 h before infection. Leptospiral cells were harvested by centrifugation at 8,000 g for 10 min at 20℃, and then washed twice with PBS. The bacterial pellets were re-suspended in 37℃ RPMI 1640 medium to final concentration of 108 per ml. Then 10 ml of leptospiral suspension (10^9) were added into 10^7 cells (bacteria: cell = 100:1) and incubated at 37°C under a humidified atmosphere containing 5% CO2. Cell samples were collected at 3 intervals (1, 2 and 4 hours) respectively in the cell infection models, and 3 biological replicates were designed for each sample. Previous cytokine mRNA kinetic expression research showed that most of the cytokine transcripts can be detected as early as 1h after infection in animal infection model, which indicated that the rapid gene regulation of innate immune response can be detected within 4-hour window period in this study. The MPM and HBM cell cultures not infected by L. interrogans were used as negative controls.

value: Human peripheral blood monocytes (HBM)

tag: infected with

value: pathogenic Leptospira

tag: time point

value: 4h after infection


title: BMP - rep 2


title: Monocyte IL4 18h 3

description: Monocytes stimulated with IL-4 for 18 hours


title: control -rep 2


title: LH + BMP - rep 1


title: Monocyte IL4 18h 2

source_name: Monocytes stimulated with IL-4 for 18 hours


title: LH - rep 1


title: control -rep 1


title: BMP - rep 1


title: GFP ASO_24h

city: Tokyo

first: Tetsuro

last: Hirose

address: 2-4-7 Aomi, Koutou

department: Biomedical Research Institute

institute: AIST

description: Gene expression after 24hr treatment with GFP ASO

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°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 nitrogen gas blow.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HeLa treated with GFP ASO for 24 hours

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

growth_protocol: HeLa cells were cultured in DMEM medium containing 10% FBS.

extract_protocol: total RNAs were extracted using RNAeazy kit (Qiagen).

treatment_protocol: 1x106 cells were nucleofected with 400 pmol GFP ASO or NEAT1#12 ASO as described in Sasaki et al., PNAS 2009, and incubated for 6~24 hours.

value: GFP ASO

tag: cell line

value: HeLa cells


title: HBM_infected_2h_rep1

value: 2h after infection


title: HBM_infected_2h_rep3


title: NEAT1#12ASO_24h

description: Gene expression after 24hr treatment with NEAT1#12 ASO

source_name: HeLa treated with NEAT1#12 ASO for 24 hours

tag: time

value: NEAT1#12 ASO


title: GFP ASO_12h

description: Gene expression after 12hr treatment with GFP ASO

source_name: HeLa treated with GFP ASO for 12 hours


title: HBM_infected_4h_rep1


title: HBM_infected_2h_rep2


title: NEAT1#12ASO_6h

description: Gene expression after 6hr treatment with NEAT1#12 ASO

source_name: HeLa treated with NEAT1#12 ASO for 6 hours

value: 6 h


title: Monocyte IL4 18h 1

value: Monocyte


title: GFP ASO_6h

description: Gene expression after 6hr treatment with GFP ASO

source_name: HeLa treated with GFP ASO for 6 hours


title: HBM_infected_4h_rep2


title: NEAT1#12ASO_12h

description: Gene expression after 12hr treatment with NEAT1#12 ASO

source_name: HeLa treated with NEAT1#12 ASO for 12 hours


title: HBM_infected_1h_rep3

value: 1h after infection


title: Monocyte IFNG 18h 2

description: Monocytes stimulated with IFN-gamma for 18 hours

value: YES

value: IFNg


title: Monocyte IFNG 18h 3

source_name: Monocytes stimulated with IFN-gamma for 18 hours


title: DMSO treated ST88-14 Cell Replicate 2

city: Detroit

first: Michael

middle: A

last: Tainsky

state: MI

address: 110 E Warren  Room 311

department: Center for Molecular Medicine and Genetics

institute: Wayne State University

description: comparison 2

hyb_protocol: standard hybridization methods described by the manufacturer

scan_protocol: Agilent Technologies Scanner G2505B US45102939

data_processing: Images were quantified using Agilent Feature Extraction Software. Microarray data was normalized within arrays using loess normalization followed by normalizing between arrays using quantile normalization as implemented in the Bioconductor library limma.

source_name: Malignant Peripheral Nerve Sheath Tumor

label_protocol: Labeled targets were synthesized from the purified RNA using linear amplification and indirect labeling by incorporation of aminoallyl-labeled nucleotide with the TargetAmp 1-round aminoallyl-aRNA amplification kit 101 (Epicentre Technologies), which was subsequently modified by the covalent addition of Alexa dye (Epicentre Technologies).

growth_protocol: Human MPNST ST88-14(Nf1-/-) cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 5% fetal bovine serum (Hyclone Laboratories).

extract_protocol: Total RNA was extracted from the cells using RNeasy mini Kit (#74106, Qiagen) with genomic DNA removal by RNase-Free DNase Set (#79254, Qiagen).  RNA integrity was determined by an Agilent Bioanalyzer 2100.

treatment_protocol: 10 μM U0126 (CalBiochem) or 10 μl DMSO was applied to the ST88-14(Nf1-/-) pre-seeded in 10 cm plate for 18h before harvest for mRNA.

value: DMSO

source_name: Universal Human Reference RNA

value: mixture of 10 human cell lines


title: Monocyte IFNG 18h 1


title: DMSO treated ST88-14 Cell Replicate 3

description: comparison 2


title: Macrophage NS 18h 3

description: Monocytes-Derived Macrophages unstimulated (18 hours)

value: NO

value: NS

value: Monocytes-Derived Macrophages


title: 10 min KCN 50 µM, 3 replicates - rep3

source_name: cells of C. metallidurans

value: 10 min

value: KCN 50 uM


title: HBM_infected_1h_rep2

value: Human peripheral blood monocytes (HBM)

value: pathogenic Leptospira


title: HBM_infected_1h_rep1


title: DMSO treated ST88-14 Cell Replicate 1

description: comparison 2


title: Macrophage NS 18h 2

source_name: Monocytes-Derived Macrophages unstimulated (18 hours)


title: U0126 treated ST88-14 Cell Replicate 2

description: comparison 2


title: HBM_uninfected_control_rep1

value: none (uninfected control)


title: HBM_uninfected_control_rep2


title: scrambled control siRNA treated ST88-14 Cell Replicate 3

description: comparison 3

treatment_protocol: Human NRas siRNA, control siRNA and siRNA Transfection Reagent (Santa Cruz Biotechnology) were used according to the manufacturer’s instructions.  ST88-14 cells were plated at 1.5X105 cells per 10 cm plate 24 hours prior to transfection.  4 μl of siRNA (~30nM) and 4 μl of siRNA transfection reagent, each diluted in 400μl of Optimem (Invitrogen), were combined and after a 30 minute incubation added to the 3.2 ml of Optimem in each plate.  Same amount of scrambled control siRNA was used as control.  Following a 6 h incubation of cells with transfection solution, medium was replaced by growth medium.  Cells were harvested 48 to 72 h later.

value: scrambled control


title: Ovary (O) biological replicate 1, technical repeat

description:
O1R
Technical replicate of biological replicate 1. Ovaries, harvested after 20 days post infestation.
2009-09-29_252449710001_O1R.gpr

source_name: Ovaries

tag: gender

value: Female

tag: age

value: day 20

value: Mozambique

value: adult

value: Ovaries

source_name: [reference] pooled life stages day 4, 5, 7, 13 and 15 and tissues at day 20

value: mixed for life stages, female for adult tissues

value: female


title: Macrophage IL4 18h 3

description: Monocytes-Derived Macrophages stimulated with IL-4 for 18 hours

value: YES


title: 12h after CT285 infection. Gills. 02

city: Burjassot

first: Agnès

last: Callol Junyer

address: Dr. Moliner, 50

department: Microbiology & Ecology

country: Spain

institute: University of Valencia

description: Gene expression at 12h after 1h of bath infection with vibrio vulnificus rtx double mutant (CT285)

hyb_protocol: 1.65 μg of cRNA-labbled of each sample was used for the hybridization to custom european eel array during 17h at 65ºC following the instructions of Agilent’s GE Hybridization Kit.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. Txt files generated were imported into the Gene GeneSpring software GX 12.5.

data_processing: Percentile shift normalization was made to adjust all spot intensities in an array. This normalization takes each column in an experiment independently, and computes the median expression values for this array, across all spots. It then subtracts this value from the expression value of each entity (Bolstad et al, 2003). After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected genes that have outlier samples, and filter out genes that have a low variation in expression values across all samples.

organism: Anguilla anguilla

source_name: In vivo CT285 infection. Gills at 12h after 1h of bath infection

label_protocol: RNA samples were labelled with a single dye, Cy3. Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling were performed according to agilent Quick Amp Labelling kit instructions.

growth_protocol: Eels were reared in the fish facilities of University of Valencia under controlled conditions and feeded daily. Before the experiment, fishes were acclimated for 24h in the experimental tanks containing dechlorinated fresh water with 1.5% NaCl, with continuous aeration.

extract_protocol: Gills were shredded with a Polytron homogenizer and used for total RNA extraction. RNA was purified by adding 1ml of TRI Reagent (Sigma-Aldrich) and processed following the manufacturer’s instructions. Possible contaminating DNA in RNA solutions were eliminated using RNeasy MinElute Cleanup kit (Qiagen) with a DNase I (Qiagen) digestion at room temperature for 15 min according to manufacturer’s protocol.

treatment_protocol: Individuals were infected during 1h by bath immersion with either; Vibrio vulnificus Biotype 2 serovar E (R99 or wild type) or CT285 (ΔrtxA13) at the LD50 determined for R99. After infection, fish were transferred into new tanks, containing clean water and kept under constant conditions until sampling (0h,3h, 12h).

tag: tissue

value: Gills

tag: weight


title: 12h after CT285 infection. Gills. 01


title: HBM_uninfected_control_rep3


title: 3h after CT285 infection. Gills. 03

description: Gene expression at 3h after 1h of bath infection with vibrio vulnificus rtx double mutant (CT285)

source_name: In vivo CT285 infection. Gills at 03h after 1h of bath infection


title: Macrophage IFNG 18h 3

description: Monocytes-Derived Macrophages stimulated with IFN-gamma for 18 hours

value: IFNg


title: 12h after CT285 infection. Gills. 03


title: U0126 treated ST88-14 Cell Replicate 3

description: comparison 2

value: mixture of 10 human cell lines


title: TAC at ZT15, biological rep3

city: Guelph

first: Elena

last: Tsimakouridze

address: 50 Stone Rd E

country: Canada

institute: University of Guelph

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

data_processing: The data were analyzed with GeneSpring GX Software v. 11.5 using default Affymetrix settings and DeltaGene.

source_name: TAC mouse heart ZT15

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

growth_protocol: The mice had either TAC or SHAM surgeries, then lived for 8 weeks after surgery (either SHAM or Transverse Aortic Constricton). After 8 weeks, the TAC and SHAM mice were sacrificed over 24 hrs at six timepoints.

extract_protocol: Total RNA was extracted using the Trizol method according to the manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid Nitrogen.

value: left ventricle of heart

tag: disease state

value: cardiovascular disease (TAC)

value: 15 hr


title: Macrophage NS 18h 1

value: NO

value: NS

value: Monocytes-Derived Macrophages


title: TAC at ZT19, biological rep3

source_name: TAC mouse heart ZT19

value: 19 hr


title: TAC at ZT11 ,biological rep3

source_name: TAC mouse heart ZT11

value: 11 hr


title: Macrophage IL4 18h 2

source_name: Monocytes-Derived Macrophages stimulated with IL-4 for 18 hours


title: 3h after CT285 infection. Gills. 02


title: TAC at ZT23, biological rep3

source_name: TAC mouse heart ZT23

value: 23 hr


title: 3h after CT285 infection. Gills. 01


title: Macrophage IFNG 18h 2

source_name: Monocytes-Derived Macrophages stimulated with IFN-gamma for 18 hours


title: daf-16, Fast , rep 3

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from 4 day adult

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with PLIER algorithm using GeneSpring GX 11.0.2.

organism: Caenorhabditis elegans

source_name: daf-16, Fast

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (two-Cycle Target Labeling Assays) from 100 ng total RNA.

growth_protocol: Worms were fed til day 2 of adult.

extract_protocol: Total RNAs were prepared by using Trizol (Invitrogen).

treatment_protocol: Worms were subject to Fed or Fasted conditions for indicated time and total RNA was extracted.

tag: strain background

tag: genotype/variation

value: daf-16 mutants

value: Fast


title: daf-16, Fast , rep 1

description: Gene expression data from 4 day adult


title: 0h after CT285 infection. Gills. 03

description: Gene expression after 1h of bath infection with vibrio vulnificus rtx double mutant (CT285)

source_name: In vivo CT285 infection. Gills at 00h after 1h of bath infection


title: TAC at ZT19, biological rep2


title: TAC at ZT15, biological rep2


title: daf-16, Fed , rep 3

description: Gene expression data from 4 day adult

source_name: daf-16, Fed

value: Fed


title: daf-16, Fast , rep 2

description: Gene expression data from 4 day adult


title: daf-16, Fed , rep 2

description: Gene expression data from 4 day adult


title: daf-16, Fed , rep 1

description: Gene expression data from 4 day adult


title: 0h after CT285 infection. Gills. 02


title: jun-1, Fast , rep 3

description: Gene expression data from 4 day adult

source_name: jun-1, Fast

value: jun-1 mutant


title: Macrophage IL4 18h 1

value: YES


title: jun-1, Fast , rep 2

description: Gene expression data from 4 day adult


title: 12h after R99 infection. Gills. 03

description: Gene expression at 12h after 1h of bath infection with vibrio vulnificus wild type (R99)

source_name: In vivo R99 infection. Gills at 12h after 1h of bath infection

value: Gills


title: TAC at ZT07, biological rep2

source_name: TAC mouse heart ZT07

value: 7 hr


title: jun-1, Fast , rep 1

description: Gene expression data from 4 day adult


title: TAC at ZT19, biological rep1


title: TAC at ZT03, biological rep2

source_name: TAC mouse heart ZT03

value: 3 hr


title: 3h after R99 infection. Gills. 01

description: Gene expression at 3h after 1h of bath infection with vibrio vulnificus wild type (R99)

source_name: In vivo R99 infection. Gills at 03h after 1h of bath infection


title: TAC at ZT11, biological rep2

value: left ventricle of heart


title: TAC at ZT03, biological rep1

value: cardiovascular disease (TAC)


title: TAC at ZT23, biological rep2


title: TAC at ZT15, biological rep1

value: 15 hr


title: TAC at ZT11, biological rep1


title: Neonate, nonylphenol 60 ug/L, replicate C

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by Quantile normalization and baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA with Benjamini-Hochberg multiple-tests correction to test for significant differential expression of microarray targets.

organism: Daphnia magna

source_name: Whole daphnia

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All experiments were performed using a well-characterized single clone of Daphnia magna (Clone F), maintained indefinitely as pure parthenogenetic cultures. Individual or bulk cultures of 10 animals/L were maintained in ASTM hard synthetic water. Individual or bulk cultures were fed daily with Chorella vulgaris Beijerinck (5x105 cells/mL, respectively, corresponding to 1.8 mg C/mL; [24]). C. vulgaris was grown axenically in Jaworski/Euglena gracilis 1: 1 medium (CCAP, 1989). The culture medium was changed every day, and neonates were removed within 24 h. Photoperiod was set to 14h light: 10h dark cycle and temperature at 20 ± 1oC.

extract_protocol: Qiagen Rneasy

treatment_protocol: Groups of twenty juveniles < 24 h old were exposed to selected exposure levels in 0.5 L of ASTM hard water with food present (5x105 cells/mL of C. vulgaris) during 3 consecutive days. Contaminants were dosed using acetone as a carrier (0.1 ml/L). Treatments were quadruplicated. At the end of exposure the 20 juveniles of each treatment per replicate were collected, pooled in an eppendorf, flash- frozen in liquid N2 and preserved at -80 oC until RNA extraction.For adult reproductive tests, exposures started with 8-9 day old gravid females, which were exposed during three consecutive broods to the studied chemicals (10-14 days). Just after releasing their fourth clutch into the brood pouch, eggs were gently flushed from the brood pouch and females were immediately flash- frozen in liquid N2 and preserved at 80oC until RNA extraction.

tag: Stage

value: juvenile

value: nonylphenol 60 ug/L


title: jun-1, Fed , rep 3

description: Gene expression data from 4 day adult

source_name: jun-1, Fed

tag: treatment


title: TAC at ZT07, biological rep1


title: 0h after R99 infection. Gills. 03

description: Gene expression after 1h of bath infection with vibrio vulnificus wild type (R99)

source_name: In vivo R99 infection. Gills at 00h after 1h of bath infection


title: 12h after R99 infection. Gills. 02


title: jun-1, Fed , rep 1

description: Gene expression data from 4 day adult


title: TAC at ZT07, biological rep3


title: Neonate, nonylphenol 60 ug/L, replicate D


title: 0h after CT285 infection. Gills. 01


title: 3h after R99 infection. Gills. 03


title: jun-1, Fed , rep 2

description: Gene expression data from 4 day adult


title: TAC at ZT23, biological rep1


title: 3h after R99 infection. Gills. 02


title: kgb-1, Fast , rep 3

description: Gene expression data from 4 day adult

source_name: kgb-1, Fast

value: kgb-1 mutant


title: Neonate, nonylphenol 60 ug/L, replicate A


title: 12h after R99 infection. Gills. 01


title: U0126 treated ST88-14 Cell Replicate 1

description: comparison 2

source_name: Malignant Peripheral Nerve Sheath Tumor

source_name: Universal Human Reference RNA

value: mixture of 10 human cell lines


title: Neonate, nonylphenol 60 ug/L, replicate B


title: Neonate, nonylphenol 20 ug/L, replicate D

value: nonylphenol 20 ug/L


title: kgb-1, Fast , rep 2

description: Gene expression data from 4 day adult


title: Macrophage IFNG 18h 1

value: IFNg

tag: cell type

value: Monocytes-Derived Macrophages


title: 0h after R99 infection. Gills. 02


title: SHAM at ZT19, biological rep3

source_name: SH mouse heart ZT19

value: normal

value: 19 hr


title: 0h after R99 infection. Gills. 01


title: Handling Control. Gills. 02

description: Gene expression for control individuals after handling, 1h at infection tanks with fresh water

source_name: Gills Handling control


title: kgb-1, Fed , rep 3

description: Gene expression data from 4 day adult

source_name: kgb-1, Fed

value: Fed


title: Neonate, fluoxetine 40 ug/L, replicate D

value: fluoxetine 40 ug/L


title: Neonate, nonylphenol 20 ug/L, replicate C


title: Control. Gills. 03

description: Gene expression for control individuals

source_name: Gills Control

value: Gills


title: Neonate, fluoxetine 40 ug/L, replicate C


title: Neonate, nonylphenol 20 ug/L, replicate A


title: SHAM at ZT07, biological rep3

source_name: SH mouse heart ZT07

value: 7 hr


title: N2, Fast , rep 3

description: Gene expression data from 4 day adult

source_name: N2, Fast

value: wild type

value: Fast


title: Handling Control. Gills. 01


title: SHAM at ZT03, biological rep3

source_name: SH mouse heart ZT03

value: left ventricle of heart

value: 3 hr


title: SHAM at ZT23, biological rep3

source_name: SH mouse heart ZT23

value: 23 hr


title: Control. Gills. 02

description: Gene expression for control individuals


title: kgb-1, Fed , rep 1

description: Gene expression data from 4 day adult


title: TAC at ZT03, biological rep3

value: cardiovascular disease (TAC)


title: Handling Control. Gills. 03


title: N2, Fast , rep 2

description: Gene expression data from 4 day adult


title: Control. Gills. 01

description: Gene expression for control individuals


title: Neonate, fluoxetine 40 ug/L, replicate B

value: juvenile


title: kgb-1, Fed , rep 2

description: Gene expression data from 4 day adult

value: kgb-1 mutant


title: kgb-1, Fast , rep 1

description: Gene expression data from 4 day adult


title: SHAM at ZT11, biological rep3

source_name: SH mouse heart ZT11

value: 11 hr


title: N2, Fed , rep 3

description: Gene expression data from 4 day adult

source_name: N2, Fed


title: Neonate, fluoxetine 40 ug/L, replicate A


title: SHAM at ZT15, biological rep3

source_name: SH mouse heart ZT15

value: 15 hr


title: N2, Fast , rep 1

description: Gene expression data from 4 day adult


title: N2, Fed , rep 2

description: Gene expression data from 4 day adult


title: Neonate, fluovoxamine 10 ug/L, replicate D

source_name: Whole daphnia

value: fluovoxamine 10 ug/L


title: SHAM at ZT15, biological rep2

value: normal


title: N2, Fed , rep 1

description: Gene expression data from 4 day adult


title: SHAM at ZT07, biological rep2


title: SHAM at ZT11, biological rep2


title: N2, Fast 48 h, rep 2

description: Gene expression data from 4 day adult

source_name: N2, Fast 48 h

value: Fast 48 h


title: Neonate, nonylphenol 20 ug/L, replicate B

value: nonylphenol 20 ug/L


title: Neonate, fluovoxamine 10 ug/L, replicate B


title: Neonate, fluovoxamine 10 ug/L, replicate C


title: SHAM at ZT03, biological rep2


title: SHAM at ZT23, biological rep2


title: H9 EB 0mM EtOH B

city: Los Angeles

first: Yong

last: Kim

state: CA

address: 10833 Le Conte Ave

institute: UCLA

description: H9 EB 0mM EtOH B

hyb_protocol: Standard protocol by UCLA genomic core

scan_protocol: Standard protocol by UCLA genomic core

data_processing: Robust Multi-array Average (RMA) was used as normalization algorithm in the Bioconductor package .

source_name: hESCs, EBs, no EtOH

label_protocol: Random C3 and C5 by UCLA genomic core

growth_protocol: Standard hESC protocol with mTeSR

extract_protocol: Strandard RNA isolation using Rneasy mini kit from Qiagen

treatment_protocol: 20mM ethanol for 24 hours

tag: agent

value: no EtOH


title: H9 EB 20mM EtOH A

description: H9 EB 20mM EtOH A

source_name: hESCs, EBs 20 mM EtOH

value: 20 mM EtOH


title: Neonate, fluovoxamine 10 ug/L, replicate A


title: H9 EB 20mM EtOH B

description: H9 EB 20mM EtOH B


title: H9 EB 0mM EtOH A

description: H9 EB 0mM EtOH A


title: H9 Undiff 20mM EtOH B

description: H9 Undiff 20mM EtOH B

source_name: hESCs, undiff, 20 mM EtOH


title: SHAM at ZT19, biological rep2

value: 19 hr


title: N2, Fast 48 h, rep 1

description: Gene expression data from 4 day adult

value: wild type


title: SHAM at ZT19, biological rep1


title: H9 Undiff 20mM EtOH A

description: H9 Undiff 20mM EtOH A


title: N2, Fast 24 h, rep 2

description: Gene expression data from 3 day adult

source_name: N2, Fast 24 h

value: Fast 24 h


title: Adult, nonylphenol 60 ug/L, replicate H

value: adult

value: nonylphenol 60 ug/L


title: N2, Fast 36 h, rep 1

description: Gene expression data from 3 day adult

source_name: N2, Fast 36 h

value: Fast 36 h


title: Neonate, acetone, replicate A

value: acetone


title: Neonate, acetone, replicate D

value: juvenile


title: N2, Fast 36 h, rep 2

description: Gene expression data from 3 day adult


title: SHAM at ZT11, biological rep1

value: left ventricle of heart


title: H9 Undiff 0mM EtOH A

description: H9 Undiff 0mM EtOH A

source_name: hESCs, undiff, no EtOH


title: SHAM at ZT15, biological rep1


title: genomic DNA of F2 AR, biological rep3

city: La Jolla

first: zhi

last: zhang

address: 10901 North Torrey Pines Rd.

department: Development and Ageing

institute: Sanford-Burnham Medical Research Institute

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 F2 flies
Drosophila_F2_AR_3

hyb_protocol: Following fragmentation, 10 ug of labeled genomic DNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000 7G.

data_processing:
All statistical analysis code was written in R language. The required coordinate file for SFP analysis of Drosophila Genome 2.0 was obtained from Bioconductor. Briefly, the raw .CEL files from scanned arrays were read into R as the log-transferred intensity of 25mer perfect match (PM) probes after background correction and quantile normalization to ensure that all arrays have the same overall distribution. All 12 arrays were evaluated with >99% present call using MAS5 algorithm assuming high quality of hybridization.
Matrices contain log-transformed intensity of perfect match (PM) probes

organism: Drosophila melanogaster

source_name: Drosophila genomic DNA of F2 derived from yw and WE70 with abnormal heart phenotype (high arrhythmicity).

label_protocol: 50 μl fragmented genomic DNA was used in the labeling reaction with 22.5 U terminal deoxynucleotidyl transferase (rTDT) (Promega) and 1 μL (1 mM) Biotin N6-ddATP (Enzo) under the following temperature cycle: 37°C for 90 min, 99°C for 15 min and 12°C for 5 min. Gel-shift assays were performed to confirm labeling efficiency. Subsequently, the labeled products were hybridized to Affymetrix Chips (Drosophila Genome 2.0) using standard Affymetrix protocols at the Salk Institute’s Genomic Facility Center.

growth_protocol: ~15 female flies at 1 week old age are collected at room temperature (RT) on normal food source according to the different genotype.

extract_protocol: For each biological replicate genomic DNA was generated from 15 parental or selected F2 flies using DNA Easy prep kit (Qiagen).  To avoid RNA contamination, genomic DNA was treated with 1.5μl RNAse at 37°C for 30 min.  Linear amplification of genomic DNA was performed using the REPLI-g midi kit to a concentration of ~ 1μg/μl.  Five μg of amplified genomic DNA was fragmented with 1 U RQ1 DNase (Promega) for 2 min at room temperature (18–22°C) in standard buffer followed by incubation with 2ul EDTA at 65°C  for 10 min, and digestion was confirmed on 3% agarose gels by the existence of sheared products with ~50–100 bp length.

treatment_protocol: 1-week old female flies were anaesthetized with five minutes of FlyNap before semi-dissection. Whole body tissue are stored at -80c after semi-dissection.

tag: genotype

value: F2 derived from yw and WE70

value: 1 week old female


title: genomic DNA of F2 AR, biological rep2

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 F2 flies
Drosophila_F2_AR_2


title: Neonate, acetone, replicate C


title: H9 Undiff 0mM EtOH B

description: H9 Undiff 0mM EtOH B


title: SHAM at ZT03, biological rep1

value: 3 hr


title: N2, Fast 24 h, rep 1

description: Gene expression data from 3 day adult


title: Neonate, acetone, replicate B


title: Adult, nonylphenol 60 ug/L, replicate F


title: N2, Fast 18 h, rep 2

description: Gene expression data from 2 day adult

source_name: N2, Fast 18 h

value: Fast 18 h


title: genomic DNA of F2 SD, biological rep3

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 F2 flies
Drosophila_F2_SD_3

source_name: Drosophila genomic DNA of F2 derived from yw and WE70 with abnormal heart phenotype (narrow heart tube).


title: genomic DNA of F2 AR, biological rep1

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 F2 flies
Drosophila_F2_AR_1


title: SHAM at ZT23, biological rep1

value: normal

value: 23 hr


title: genomic DNA of F2 SD, biological rep2

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 F2 flies
Drosophila_F2_SD_2


title: SHAM at ZT07, biological rep1

source_name: SH mouse heart ZT07

value: 7 hr


title: Adult, nonylphenol 60 ug/L, replicate A


title: Adult, nonylphenol 60 ug/L, replicate C


title: N2, Fast 18 h, rep 1

description: Gene expression data from 2 day adult


title: genomic DNA of F2 SD, biological rep1

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 F2 flies
Drosophila_F2_SD_1


title: genomic DNA of WE70, biological rep3

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 WE70 flies
Drosophila_WE70_3

source_name: Drosophila genomic DNA of WE70 (highly inbred line).

value: WE70 (highly inbred line)


title: Adult, nonylphenol 20 ug/L, replicate G

value: nonylphenol 20 ug/L


title: genomic DNA of WE70, biological rep2

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 WE70 flies
Drosophila_WE70_2


title: Adult, nonylphenol 20 ug/L, replicate E


title: Adult, nonylphenol 20 ug/L, replicate C


title: genomic DNA of WE70, biological rep1

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 WE70 flies
Drosophila_WE70_1


title: N2, Fast 12 h, rep 1

description: Gene expression data from 2 day adult

source_name: N2, Fast 12 h

value: wild type

value: Fast 12 h


title: N2, Fast 9 h, rep 2

description: Gene expression data from 2 day adult

source_name: N2, Fast 9 h

value: Fast 9 h


title: Adult, fluoxetine 40 ug/L, replicate F

value: adult

value: fluoxetine 40 ug/L


title: N2, Fast 12 h, rep 2

description: Gene expression data from 2 day adult


title: Adult, fluoxetine 40 ug/L, replicate G


title: genomic DNA of yw, biological rep2

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 yw flies
Drosophila_YW_2

source_name: Drosophila genomic DNA of yw (wild type).

value: yellow white


title: N2, Fast 3 h, rep 1

description: Gene expression data from 2 day adult

source_name: N2, Fast 3 h

value: Fast 3 h


title: Adult, nonylphenol 20 ug/L, replicate B

source_name: Whole daphnia


title: N2, Fed 48 h, rep 2

description: Gene expression data from 4 day adult

source_name: N2, Fed 48 h

value: Fed 48 h


title: Adult, fluoxetine 40 ug/L, replicate C


title: wild-type

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: liver

label_protocol: Biotinylated cRNA was generated from five micrograms of total RNA according to the Affymetrix Eukaryote One-cycle Target labeling assay (Affymetrix Gene Expression Technical Manual, 2006)

growth_protocol: Livers were isolated from E14.5 mouse embyos

extract_protocol: RNA was isolated using the Trizol method as per the manufacturer's recommended protocol (Invitrogen, Carlsbad, CA).

value: liver

tag: developmental stage

value: E14.5 embryos

tag: strain

value: wild-type


title: 5min HCMV

first: ANYOU

last: WANG

address: Gonda BLDG

department: Human Genetics

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized following affy protocol

scan_protocol: GeneChips were scanned in stanford affy central

data_processing: The data were analyzed with R.2.10

source_name: cell

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

growth_protocol: human foreskin fibroblasts were grownconfluence of ~80% when infected with HCMV Towne strain

extract_protocol: RNA was purified using the RNeasy RNA purification kit (QIAGEN Inc. Valencia, CA) followed by DNase treatment to eliminate all traces of DNA, according to the manufacturer's recommendation

treatment_protocol: The MOI 10 was used to infect cells for RNA extraction

value: foreskin fibroblasts

tag: time of hcmv infection

value: 5 minutes


title: N2, Fast 9 h, rep 1

description: Gene expression data from 2 day adult


title: genomic DNA of yw, biological rep1

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 yw flies
Drosophila_YW_1

value: 1 week old female


title: genomic DNA of yw, biological rep3

description:
Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 yw flies
Drosophila_YW_3


title: Prox1-conditional KO

value: Prox1 f/f;Foxa3Cre


title: N2, Fast 3 h, rep 2

description: Gene expression data from 2 day adult


title: N2, Fast 6 h, rep 1

description: Gene expression data from 2 day adult

source_name: N2, Fast 6 h

value: Fast 6 h


title: Adult, fluoxetine 40 ug/L, replicate B


title: scrambled control siRNA treated ST88-14 Cell Replicate 2

description: comparison 3

source_name: Malignant Peripheral Nerve Sheath Tumor

tag: cell line

tag: protocol

value: scrambled control

source_name: Universal Human Reference RNA

value: mixture of 10 human cell lines


title: Adult, fluovoxamine 10 ug/L, replicate E

value: fluovoxamine 10 ug/L


title: N2, Fast 6 h, rep 2

description: Gene expression data from 2 day adult

value: wild type


title: N2, Fed 24 h, rep 2

description: Gene expression data from 3 day adult

source_name: N2, Fed 24 h

value: Fed 24 h


title: siNRAS treated ST88-14 Cell Replicate 2

description: comparison 3

value: siNRAS


title: Adult, fluovoxamine 10 ug/L, replicate H

value: adult


title: N2, Fed 48 h, rep 1

description: Gene expression data from 4 day adult


title: MPM_infected_4h_rep3

value: BALB/c

tag: gender

value: male

value: 6-8 wks

value: Murine peritoneal macrophages (MPM)

tag: infected with

value: pathogenic Leptospira

tag: time point

value: 4h after infection


title: scrambled control siRNA treated ST88-14 Cell Replicate 1

description: comparison 3

tag: tissue


title: siNRAS treated ST88-14 Cell Replicate 3

description: comparison 3


title: N2, Fed 0 h, rep 2

description: Gene expression data from 2 day adult

source_name: N2, Fed 0 h

value: Fed 0 h


title: MPM_infected_4h_rep2

tag: age


title: 25min HCMV

value: foreskin fibroblasts

value: 25 minutes


title: siNRAS treated ST88-14 Cell Replicate 1

description: comparison 3


title: scrambled control treated Replicate 3

description: comparison 4

source_name: sporadic Malignant Peripheral Nerve Sheath Tumor

growth_protocol: STS26T(Nf1+/+) cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 5% fetal bovine serum (Hyclone Laboratories).

treatment_protocol: Human Nf1 siRNA, control siRNA and siRNA Transfection Reagent (Santa Cruz Biotechnology) were used according to the manufacturer’s instructions.  STS26T(Nf1+/+) cells were plated at 1.5X105 cells per 10 cm plate 24 hours prior to transfection.  4 μl of siRNA (~30nM) and 4 μl of siRNA transfection reagent, each diluted in 400μl of Optimem (Invitrogen), were combined and after a 30 minute incubation added to the 3.2 ml of Optimem in each plate.  Same amount of scrambled control siRNA was used as control.  Following a 6 h incubation of cells with transfection solution, medium was replaced by growth medium.  Cells were harvested 48 to 72 h later.


title: Adult, fluovoxamine 10 ug/L, replicate B


title: N2, Fed 24 h, rep 1

description: Gene expression data from 3 day adult

tag: strain background


title: MPM_infected_4h_rep1


title: Donor 112-Neg versus Donor 112-Pos

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Paired RNA samples from p24+ (latently infected) and p24- (uninfected) cells from 4 donors (4 biological replicas) were labeled using a two-color design with dye-swap control. Thus, paired RNA samples from p24+ cells and p24- cells of two donors were labeled with Cy3 and Cy5, respectively; whereas, paired RNA samples from p24+ cells and p24- cells of the other two donors were labeled with Cy5 and Cy3, respectively. Fragmentation was carried out by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility by incubating at 60 degrees Celsius for 30 minutes and stopped by adding equal volume of 2x hybridization buffer (Agilent Technologies). Fragmented targets were added on 4 Whole Human Genome Microarray 44K (Agilent Technologies). The microarrays were assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60 degrees Celsius for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility with the Agilent G2505B microarray scanner under default settings recommended by Agilent Technologies for gene expression microarrays with 100% PMT and 10 micrometer resolutions. Data was extracted using Feature Extraction Software version 10.5.1.1 (Agilent Technologies).

data_processing: Within-array dye effects were corrected by the 'loess' normalization method, while the ”scale” method was applied to standardize the log2 fold change distributions across the arrays, by using the median-absolute-value as scale estimator. . No background subtraction was performed prior to normalization. Positive and negative microarray control features were not used to compute the 'loess' smoothing and were not considered in subsequent analyses. Data pre-processing was performed using the R/Bioconductor package 'limma'.

source_name: CD4+ cells from healthy donor: 112 ; HIV infection status: NEGATIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. cRNA was labeled with Cy5, purified using RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 mircrogram of Cy5-labeled sample was mixed with control targets (G4112F, Agilent Technologies).

extract_protocol: Cells were washed with PBS, fixed in 1% paraformaldehyde (PFA, Sigma-Aldrich) in PBS at 4°C for 20 minutes, permeabilized with 0.1% saponin (Sigma-Aldrich) for 5 minutes at 4°C, stained for the detection of intracellular HIV-1 p24gag with FITC-labeled KC57 antibody (Beckman Coulter) for 20 minutes on ice, and finally washed twice with ice-cold PBS. Latently infected (HIV-1 p24+) and uninfected cells (HIV-1 p24-) from the same culture were then sorted by Flow Cytometry with a DAKO-Cytomation MoFlo High Speed cell sorter. Total RNA was isolated from sorted cells using the RNeasy FFPE Kit (Qiagen) following manufacturer’s protocol with a few modifications. The treatment with xylene and the subsequent ethanol precipitation step were omitted. The incubation steps at 55°C, and at 80°C were shortened (12 minutes instead of 15) to reduce RNA degradation. RNA was eluted from the column with RNase-free water, quantified by NanoDrop, and stored at -80°C. RNA quality was confirmed by UV spectrophotometry and by analysis with an Agilent 2100 Bioanalyzer.

treatment_protocol: Anonymized cells were obtained from an HIV-1 negative, healthy volunteer. CD4+ T cells latently infected with HIV-1 were generated as previously described (Marini et al., 2008). Briefly, PBMCs were isolated from peripheral blood of healthy volunteers by Ficoll-Paque PLUS (GE Healthcare). Total CD4+ T cells were enriched by negative selection (CD4+ T Cell Isolation Kit from Miltenyi Biotec), and activated in plates coated with anti-CD3 (eBioscience) and anti-CD28 (Beckman Coulter) in the presence of 50 U/ml IL-2 (Roche Biochemicals). Activated cells were infected 3 days post-activation with 5,000 50% tissue culture infective dose (TCID50) per 1,000,000 cells of gradient-purified HIV-1IIIB (Advanced Biotechnologies Inc.) for 2 h at 37°C. Finally, cells were plated at 0.5x1,000,000 cells/ml in fresh RPMI 1640 supplemented with 1% penicillin/streptomycin, 1% glutamine, 1% nonessential amino acids, 1% sodium pyruvate, 50 uMolar 2-mercaptoethanol (all from Invitrogen), 50 ug/ml gentamicin (Sigma), 10% human AB serum (Cellgro), 50 U/ml IL-2, and cultured until 10-15% cells were infected, followed by intracellular FACS on HIV-1 p24gag.. Cells were then allowed to rest for a week in the presence of 1 ng/ml IL-7 (R&D Systems).

value: CD4+ lymphocytes purified from PBMCs

tag: hiv-1 infection status

value: negative

tag: healthy donor

source_name: Resting primary CD4+ T cells generated in vitro from healthy donor: 112 ; HIV infection status: POSITIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. cRNA was labeled with Cy3, purified using RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 mircrogram of Cy3-labeled sample was mixed with control targets (G4112F, Agilent Technologies).

treatment_protocol: Anonymized cells were obtained from an HIV-1 negative, healthy volunteer. CD4+ T cells latently infected with HIV-1 were generated as previously described (Marini et al., 2008). Briefly, PBMCs were isolated from peripheral blood of healthy volunteers by Ficoll-Paque PLUS (GE Healthcare). Total CD4+ T cells were enriched by negative selection (CD4+ T Cell Isolation Kit from Miltenyi Biotec), and activated in plates coated with anti-CD3 (eBioscience) and anti-CD28 (Beckman Coulter) in the presence of 50 U/ml IL-2 (Roche Biochemicals). Activated cells were infected 3 days post-activation with 5,000 50% tissue culture infective dose (TCID50) per 1,000,000 cells of gradient-purified HIV-1IIIB (Advanced Biotechnologies Inc.) for 2 h at 37°C. Finally, cells were plated at 0.5x1,000,000 cells/ml in fresh RPMI 1640 supplemented with 1% penicillin/streptomycin, 1% glutamine, 1% nonessential amino acids, 1% sodium pyruvate, 50 uMolar 2-mercaptoethanol (all from Invitrogen), 50 ug/ml gentamicin (Sigma), 10% human AB serum (Cellgro), 50 U/ml IL-2, and cultured until 10-15% cells were infected, followed by intracellular FACS on HIV-1 p24gag. Cells were then allowed to rest for a week in the presence of 1 ng/ml IL-7 (R&D Systems).

value: positive


title: MPM_infected_2h_rep3

value: 2h after infection


title: scrambled control treated Replicate 2

description: comparison 4

value: scrambled control

value: mixture of 10 human cell lines


title: MPM_infected_2h_rep1


title: Donor 111-Pos versus Donor 111-Neg

data_processing: Within-array dye effects were corrected by the 'loess' normalization method, while the ”scale” method was applied to standardize the log2 fold change distributions across the arrays, by using the median-absolute-value as scale estimator. No background subtraction was performed prior to normalization. Positive and negative microarray control features were not used to compute the 'loess' smoothing and were not considered in subsequent analyses. Data pre-processing was performed using the R/Bioconductor package 'limma'.

source_name: Resting primary CD4+ T cells generated in vitro from healthy donor: 111 ; HIV infection status: POSITIVE

label_protocol: Total RNA (0.4 microgram) was reverse transcribed into first- and second strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. cRNA was labeled with Cy5, purified using RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.85 microgram of Cy5-labeled sample was mixed with control targets (G4112F, Agilent Technologies). For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

treatment_protocol: Anonymized cells were obtained from an HIV-1 negative, healthy volunteer. CD4+ T cells latently infected with HIV-1 were generated as previously described (Marini et al., 2008). Briefly, PBMCs were isolated from peripheral blood of healthy volunteers by Ficoll-Paque PLUS (GE Healthcare). Total CD4+ T cells were enriched by negative selection (CD4+ T Cell Isolation Kit from Miltenyi Biotec), and activated in plates coated with anti-CD3 (eBioscience) and anti-CD28 (Beckman Coulter) in the presence of 50 U/ml IL-2 (Roche Biochemicals). Activated cells were infected 3 days post-activation with 5×1,000 50% tissue culture infective dose (TCID50) per 1,000,000 cells of gradient-purified HIV-1IIIB (Advanced Biotechnologies Inc.) for 2 h at 37°C. Finally, cells were plated at 0.5,000,000 cells/ml in fresh RPMI 1640 supplemented with 1% penicillin/streptomycin, 1% glutamine, 1% nonessential amino acids, 1% sodium pyruvate, 50 uMolar 2-mercaptoethanol (all from Invitrogen), 50 ug/ml gentamicin (Sigma), 10% human AB serum (Cellgro), 50 U/ml IL-2, and cultured until 10-15% cells were infected, followed by intracellular FACS on HIV-1 p24gag. Cells were then allowed to rest for a week in the presence of 1 ng/ml IL-7 (R&D Systems).

source_name: CD4+ cells from healthy donor: 111 ; HIV infection status: NEGATIVE


title: Adult, acetone, replicate F

tag: Stage

tag: treatment

value: acetone


title: Adult, acetone, replicate E

value: adult


title: N2, Fed 0 h, rep 1

description: Gene expression data from 2 day adult

tag: genotype/variation

value: wild type


title: Adult, acetone, replicate G


title: siNF1 treated STS26T Replicate 3

description: comparison 4


title: MPM_infected_1h_rep3

value: BALB/c

value: male

tag: cell type

value: 1h after infection


title: MPM_infected_1h_rep2

value: 6-8 wks

value: Murine peritoneal macrophages (MPM)

value: pathogenic Leptospira


title: Adult, fluovoxamine 10 ug/L, replicate A

value: fluovoxamine 10 ug/L


title: siNF1 treated STS26T Replicate 1

description: comparison 4


title: scrambled control treated Replicate 1

description: comparison 4


title: siNF1 treated STS26T Replicate 2

description: comparison 4


title: MPM_uninfected_control_rep3

value: none (uninfected control)


title: MPM_infected_1h_rep1


title: ST88-14 Cell Replicate 3

description: Comparison 1

growth_protocol: Human MPNST ST88-14(Nf1-/-) cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 5% fetal bovine serum (Hyclone Laboratories). Normal human Schwann cell lines were cultured in DMEM supplemented with 10% FBS, 2 μM forskolin, and 10nM heregulin.

treatment_protocol: normal culture