title: ulcerative colitis colon mucosa Kelle35

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa Kelle35

value: Colon mucosa


title: Crohn's disease colon mucosa Kelle31

status: Public on Jun 01 2013

type: genomic

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description: Crohn's disease colon mucosa sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing: GenomeStudio software version 2010.3.0.30128

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: colon mucosa Kelle31

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from colon mucosa samples using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol following bead beating and Qiagen TissueLyser treatment. All samples were quality tested with PicoGreen prior to proceeding with the microarrays.

tag: gender

value: Female

tag: age (y)

tag: tissue

tag: disease state

value: Crohn's disease


title: cell line control8

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

molecule: total RNA

source_name: human pancreatic cancer

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: cell line: Cells were grown in RPM I 1640 supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C. Tumor(mouse): Each mouse was inoculated with Panc1 cells (5×106 cells/animal) subcutaneously on the flank regions of the mouse.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: cell line: Panc1 cells were treated with 10 mM metformin or without metformin for 72 h. Tumor: The metformin-treated group was injected 5 times a week intraperitoneally (i.p.) at 1 mg/body or 2 mg/body per day for 5 weeks.

tag: pancreatic cancer

value: cell line

tag: agent

value: control


title: Crohn's disease colon mucosa Kelle30

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle30


title: cell line control7


title: Crohn's disease colon mucosa Kelle29

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle29


title: As Replicate3 96 Hour Female

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: Biological replicate 3 of 3: chloroaniline-treated at 96 Hr

hyb_protocol: Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_16.5K_oligo_COMP_v3Apx zebrafish oligo probes.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized. Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Female zebrafish liver tissue

label_protocol: For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were maintained at room temperature (26°C + 1°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Female zebrafish were exposed to 15ppm (~ 192 µM) arsenic [As(V)] for 8, 24, 48, and 96 hours at room temperature.

value: female

tag: sample type

value: Arsenic-treated liver tissue

value: liver

tag: treatment

value: Arsenic

tag: time

source_name: Male and female zebrafish liver tissue

value: male and female

value: untreated


title: cell line metformin6

value: metformin


title: cell line control6


title: Crohn's disease colon mucosa Kelle28

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle28


title: cell line metformin5


title: Crohn's disease colon mucosa Kelle26

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle26


title: As Replicate1 48 Hour Female

description: Biological replicate 1 of 3: chloroaniline-treated at 48 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: As Replicate2 96 Hour Female

description: Biological replicate 2 of 3: chloroaniline-treated at 96 Hr


title: Liver biopsy sample obtained from a patient with biliary atresia_B1

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45˚C on the GeneChip® Human Gene 1.0 ST Array (Affymetrix, CA). Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Expression data (Affymetrix .CEL format) imported to GeneSpring software:
1. Normalized all data using RMA (Robust Muti-array Average) methods.
2. Performed baseline transformation to median of 7 normal control samples.
There was no other option to specifically normalize data across all samples.

label: Biotin

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA).

extract_protocol:
Wedge liver biopsy samples were obtained from infants with biliary atresia during intraoperative cholangiogram. Wedge or needle liver biopsy samples from other causes of intrahepatic cholestasis were obtained during diagnostic procedures. Liver biopsy samples from deceased-donor children were obtained during procedure to confirm the eligibiity of the patients as a donor.
Biopsy samples were snap frozen in liquid nitrogen, and stored at -80˚C by the time of RNA isolation.
Total RNA was isolated from liver biopsy samples using RNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).

tag: condition

value: Biliary Atresia

tag: age of biopsy

value: 66 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B4

value: 55 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B3

value: 33 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B2

value: 76 days


title: cell line control5


title: As Replicate2 48 Hour Female

description: Biological replicate 2 of 3: chloroaniline-treated at 48 Hr


title: As Replicate3 48 Hour Female

description: Biological replicate 3 of 3: chloroaniline-treated at 48 Hr


title: As Replicate1 96 Hour Female

description: Biological replicate 1 of 3: chloroaniline-treated at 96 Hr


title: cell line metformin4


title: Crohn's disease colon mucosa Kelle24

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle24

value: Male

value: Colon mucosa


title: Crohn's disease colon mucosa Kelle22

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle22

value: Crohn's disease


title: cell line control4

value: cell line

value: control


title: As Replicate2 24 Hour Female

description: Biological replicate 2 of 3: chloroaniline-treated at 24 Hr

value: female

value: Arsenic-treated liver tissue


title: rec114-8D, 4h in SPM

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

description: WCE 4h meiosis.CEL

hyb_protocol: Hybridization to Affymetrix S. cerevisiae Tiling  1.0R Arrays was carried out at 42C for 16 hours. The following washing and staining steps were done with an Affymetrix 450 station. All reagents used are described in the Affymetrix ChIP Assay Protocol.

scan_protocol: Each array was scanned by Genechip Scanner 3000 (Affymetrix, CA) at default settings for this type of array.

data_processing:
Primary data analysis was performed with GeneChip Operating Software (GCOS, Affymetrix). Resulting Cel files were analyzed by the Tiling Analysis Software (TAS, v 1.1.02, Affymetrix, two sample comparison analysis (IP versus WCE), without normalization and results in linear scale were exported as  RPT text file) in the format specified by Affymetrix.
GSM* txt files are in tab separated format provided by Affymetrix Tiling Analysis Software. The first column represents the chromosomal position, the second column "fold enrichment" over the control experiment (WCE, 4 hours, if not specified otherwise). The columns are separated by 25 headers specifying the identity of the chromosome; sequence #8-#23 contain chromosome1 to chromosome16, sequence #24 mitochondrial DNA, sequence #25 the yeast 2mikron plasmid.

GSE43384_230811 Spo11 rad50S -FA t6 all profiles bw500 decile normalized.xls
Content: K-smoothed profiles (bandwidth 500, genome wide) corresponding to the three ChIPchip datasets on meiotic DSB formation (Spo11-ChIPs) in Excel format (Excel 2004 preferred).

GSE43384_130411 Rec114 t4 all profiles bw1000 decile normalized.xls
Content: K-smoothed profiles (bandwidth 1000, genome wide) corresponding to the three ChIPchip datasets on meiotic protein-DNA association (Rec114-ChIPs) in Excel format (Excel 2004 preferred).

organism: Saccharomyces cerevisiae

source_name: Rec114 ChIP with anti-Rec114 antibody in rec114-8D mutanty

label_protocol: Two rounds of amplification, DNA fragmentation, and end-labeling, were performed according to the Affymetrix ChIP protocol.

growth_protocol: Meiotic cultures of diploid S. cerevisiae SK1 strain were set up as follows: A saturated YPD culture was used to inoculate 300 ml liquid SPS medium (.5% yeast extract, 1% Bacto peptone, 1% potassium acetate, .17% Yeast nitrgen base w/o aa, 0.05 M potassium biphtalate, pH 5.5) 1:400 and grown in a 3-liter baffled flask at 200 rpm at 30°C for 14 hrs. Cells were harvested, washed once, resuspended at an OD660 of  1.1 in sporulation medium (1% potassium acetate pH 7.0, supplemented with amino acids and  .001% PPG) and shaken at 200 rpm at 30°C for the appropriate time.

extract_protocol: Except for the samples labelled "-FA", where formaldehyde was omitted, cells were fixed in 1% formaldehyde for 30min. 1X10^9 cells were crushed by glassbeads using a MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka). Chromosomal DNA was sheared to an average size of 500-1000bp by sonication. Chromatin IP was performed as described in Katou et al. (Methods Enzym., 409,389-410, 2006).

tag: strain

tag: genotype

tag: bait protein

tag: antibody

value: rabbit, anti-Rec114, affinity purified

tag: meiotic timepoint

value: 4 hours

source_name: WCE 4h meiosis


title: rec114-8A, 4h in SPM

description: WCE 4h meiosis.CEL

source_name: Rec114 ChIP with anti-Rec114 antibody in rec114-8A mutant


title: normal colon mucosa Kelle21

description: Normal colon mucosa sample

source_name: colon mucosa Kelle21

value: normal


title: cell line control2


title: cell line metformin2

value: metformin


title: cell line control3


title: cell line metformin3


title: As Replicate1 24 Hour Female

description: Biological replicate 1 of 3: chloroaniline-treated at 24 Hr

value: liver

value: Arsenic

value: male and female

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: As Replicate3 24 Hour Female

description: Biological replicate 3 of 3: chloroaniline-treated at 24 Hr


title: Liver biopsy sample obtained from a patient with biliary atresia_B5

value: Biliary Atresia

value: 65 days


title: cell line metformin1


title: cell line control1


title: normal colon mucosa Kelle19

description: Normal colon mucosa sample

source_name: colon mucosa Kelle19

value: Male

value: Colon mucosa


title: NP Replicate3 96 Hour Female

treatment_protocol: Female zebrafish were exposed to 7 mg/L nitrophenol for 8, 24, 48, and 96 hours at room temperature.

value: Nitrophenol-treated liver tissue

value: Nitrophenol


title: normal colon mucosa Kelle17

description: Normal colon mucosa sample

source_name: colon mucosa Kelle17

value: Female


title: As Replicate3 8 Hour Female

description: Biological replicate 3 of 3: chloroaniline-treated at 8 Hr

value: female

value: Arsenic-treated liver tissue


title: As Replicate1 8 Hour Female

description: Biological replicate 1 of 3: chloroaniline-treated at 8 Hr


title: NP Replicate2 96 Hour Female


title: normal colon mucosa Kelle20

description: Normal colon mucosa sample

source_name: colon mucosa Kelle20


title: normal colon mucosa Kelle18

description: Normal colon mucosa sample

source_name: colon mucosa Kelle18


title: DSBs in rec114-8D, rad50S, 6h in meiosis

description: WCE 4h meiosis.CEL

source_name: Spo11-myc ChIP with anti-myc antibody in rec114-8D, rad0S mutant

value: JCY1662:Mata/alpha, Spo11-myc18::TRP1/Spo11-myc18::TRP1, rad50S::URA3/rad50S::URA3, REC114-8D::hphMX4/REC114-8D::hphMX6

value: mouse, anti-myc 9E10

value: 6 hours


title: Rec114, 4h in SPM

description: WCE 4h meiosis.CEL

source_name: Rec114 ChIP with anti-Rec114 antibody in WT

value: rabbit, anti-Rec114, affinity purified

value: 4 hours


title: DSBs in rec114-8A, rad50S, 6h in meiosis

description: WCE 4h meiosis.CEL

source_name: Spo11-myc ChIP with anti-myc antibody in rec114-8A, rad0S mutant

value: JCY1658:Mata/alpha, Spo11-myc18::TRP1/Spo11-myc18::TRP1, rad50S::URA3/rad50S::URA3, REC114-8A::hphMX4/REC114-8A::hphMX5


title: DSBs in rad50S, 6h in meiosis

description: WCE 4h meiosis.CEL

data_processing:
Primary data analysis was performed with GeneChip Operating Software (GCOS, Affymetrix). Resulting Cel files were analyzed by the Tiling Analysis Software (TAS, v 1.1.02, Affymetrix, two sample comparison analysis (IP versus WCE), without normalization and results in linear scale were exported as  RPT text file) in the format specified by Affymetrix.
GSM*txt files are in tab separated format provided by Affymetrix Tiling Analysis Software. The first column represents the chromosomal position, the second column "fold enrichment" over the control experiment (WCE, 4 hours, if not specified otherwise). The columns are separated by 25 headers specifying the identity of the chromosome; sequence #8-#23 contain chromosome1 to chromosome16, sequence #24 mitochondrial DNA, sequence #25 the yeast 2mikron plasmid.

GSE43384_230811 Spo11 rad50S -FA t6 all profiles bw500 decile normalized.xls
Content: K-smoothed profiles (bandwidth 500, genome wide) corresponding to the three ChIPchip datasets on meiotic DSB formation (Spo11-ChIPs) in Excel format (Excel 2004 preferred).

GSE43384_130411 Rec114 t4 all profiles bw1000 decile normalized.xls
Content: K-smoothed profiles (bandwidth 1000, genome wide) corresponding to the three ChIPchip datasets on meiotic protein-DNA association (Rec114-ChIPs) in Excel format (Excel 2004 preferred).

source_name: Spo11-myc ChIP with anti-myc antibody in rad0S mutant

value: JCY1667:Mata/alpha, Spo11-myc18::TRP1/Spo11-myc18::TRP1, rad50S::URA3/rad50S::URA3, REC114::hphMX4/REC114::hphMX4


title: normal colon mucosa Kelle15

description: Normal colon mucosa sample

source_name: colon mucosa Kelle15

value: normal


title: Crohn's disease colon mucosa Kelle32

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle32

value: Crohn's disease


title: NP Replicate1 96 Hour Female

source_name: Female zebrafish liver tissue

value: liver

source_name: Male and female zebrafish liver tissue

value: male and female

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: As Replicate2 8 Hour Female

description: Biological replicate 2 of 3: chloroaniline-treated at 8 Hr

value: Arsenic


title: NP Replicate1 48 Hour Female

value: Nitrophenol-treated liver tissue

value: Nitrophenol


title: NP Replicate3 24 Hour Female

value: female


title: Embryoid bodies from BJ-iPS29

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

description: Gene expression data from embryoid bodies differentiated by the withdrawal of bFGF from the ES culture media and allowed to aggregate in a petri dish0.02% DMSO for 12 h

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

label: biotin

source_name: Embryoid bodies from BJ-iPS29

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: Cells were grown for 30 days on petri dishes using knockout DMEM media supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Sigma).

extract_protocol: total RNA from was isolated using 5 Prime RNA isolation kit

treatment_protocol: total RNA was isolated from embryoid bodies differentiated by the withdrawal of bFGF from the ES culture media and allowed to aggregate in a petri dish

tag: cell type

value: Embryoid bodies from human induced pluripotent stem cells

tag: cell line


title: primary foreskin fibroblasts (FS fibroblasts)

description: Gene expression data from human primary foreskin fibroblasts

growth_protocol: Cells were grown using  DMEM medium supplemented with 10% FBS,

treatment_protocol: total RNA was isolated from  primary human foreskin fibroblasts

value: primary human foreskin fibroblasts

value: FS-fibroblats


title: normal colon mucosa Kelle16

description: Normal colon mucosa sample

source_name: colon mucosa Kelle16

tag: gender

value: Female

tag: age (y)

value: Colon mucosa


title: normal colon mucosa Kelle14

description: Normal colon mucosa sample

source_name: colon mucosa Kelle14

value: Male

tag: tissue

tag: disease state


title: Teratoma from FS-iPS1

description: gene expression data from teratomas formed 30 days after the injection of undifferentiated human induced pluripotent stem cells into the idney capsule of NOD-SCID mice

source_name: Teratoma from FS-iPS1

growth_protocol: Cells were grown on mouse embryonic fibroblasts (MEFs) using knockout DMEM medium supplemented with 15 % FBS (Hyclone), 5%KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Sigma) and 8 ng/ml FGF2 (R&D systems)].  Cultures were passaged every 3 to 7 days.

treatment_protocol: total RNA was isolated from teratomas formed 30 days after the injection of undifferentiated human induced pluripotent stem cells into the kidney capsule of NOD-SCID mice

value: Teratoma from human induced pluripotent stem cells


title: NP Replicate1 24 Hour Female


title: NP Replicate2 24 Hour Female


title: Teratoma from BJ-iPS28

source_name: Teratoma from BJ-iPS28


title: NP Replicate3 48 Hour Female


title: CD31pos-CD45neg-PFV, biological rep 3

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

description: Gene expression data from hematopoietic embryoid bodies after 10 days in hem conditions, sorted on CD31 positive and CD45 negative markers

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and baseline transformation to the median of all samples using GeneSpring 6.0 software.

source_name: human pluripotent stem cells (hPSCs)

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

value: Hematopoietic embryoid bodies after 10 days in hem conditions, CD31 positive CD45 negative


title: CD31pos-CD45neg-PFV, biological rep 2

label_protocol: In accordance with manufacturer's protocols


title: normal colon mucosa Kelle13

description: Normal colon mucosa sample

source_name: colon mucosa Kelle13

value: normal


title: Teratoma from BJ-iPS29

source_name: Teratoma from BJ-iPS29


title: PAD4-/- LSK

city: Bunkyo-ku

first: Katsuhiko

last: Nakashima

state: Tokyo

address: 7-3-1 Hongo

department: Faculty of Medicine

institute: The University of Tokyo

description: gene expression in PAD4-deficient LSK cells

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software v9.5 using default parameters (protocol GE1-v5_95_Feb07). The dataset was normalized using the 75 percentile median shift method.

organism: Mus musculus

source_name: PAD4-deficient LSK cells

label_protocol: 300 ng of total RNA was amplified and labeled using the One-Color Agilent Quick Amp Labeling kit

growth_protocol: LSK cells were collected from mouse bone marrow cells stained with lineage marker, anti-Sca-1, and anti-c-kit antibodies using FACS.

extract_protocol: Total RNA was isolated with Trizol reagent.

value: LSK cells in bone marrow


title: NP Replicate2 8 Hour Female

value: liver

value: male and female


title: Crohn's disease colon mucosa Kelle25

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle25

value: Crohn's disease


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF126

city: Boston

first: Alexey

last: Fedulov

state: MA

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

description: Maternal status: asthma

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: RMA normalization with background adjustment

source_name: splenic CD11c+ dendritic cells

label_protocol: Standard Affymetrix procedure

growth_protocol: Maternal sensitization is achieved by initial i.p. injections of 5 μg OVA with 1 mg alum in 0.1 ml PBS into mice at 3 and 7 days of age. After weaning, female mice are exposed to aerosols of allergen (3% (w/v) OVA (grade V, Sigma-Aldrich) in PBS, pH 7.4) for 10 min on 3 consecutive days at 4, 8, and 12 wk of age, and then mated with normal male mice. The aerosol exposure is performed within individual compartments of a mouse pie chamber (Braintree Scientific, Braintree, MA) using a Pari IS2 nebulizer (Sun Medical Supply, Kansas City, KS) connected to air compressor (PulmoAID; DeVilbiss, Somerset, PA). These female mice were shown to consistently have strong allergic airway inflammation and evidence of Th2 polarization.

extract_protocol: Dendritic cells were isolated from splenocyte suspension using magnetic cell separation (Miltenyi). Genomic DNA was isolated using Qiagen procedure.

treatment_protocol: Neonate mice were either naïve, or sensitized with a single i.p. injection of 5 ug of OVA with 1 mg alum in 0.1 PBS at day 3.

value: splenic CD11c+ dendritic cells

value: allergen-sensitized

tag: maternal status

value: asthma


title: WT LSK

description: gene expression in wild-type LSK cells

source_name: wild-type LSK cells


title: NP Replicate3 8 Hour Female

value: female

tag: sample type

value: Nitrophenol-treated liver tissue

value: Nitrophenol

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF125

description: Maternal status: asthma

tag: treatment


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF127

description: Maternal status: asthma


title: TAL/ADH co-expressing strain 70 mM furfural Run 2

city: Kobe

first: Akihiko

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

institute: Kobe University

description: TAL-ADH 70 mM Run 2

hyb_protocol: 1.65 ug 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 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Yeast Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Region 61x21.6 mm, Scan resolution 5um, R PMT is set to 100% and G PMT is set to 100%, XRD=0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 Apr08) and Grid: 015072_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MT8-1X/TAL-ADH, 70 mM (2)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the One-Color Low-input QuickAmp Labeling 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, and its quality checked by Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was obtained by following the protocol provided for the Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA, USA). RNA concentration and quality were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.

value: TAL-ADH co-expresssing strain

tag: agent

value: furfural


title: normal colon mucosa Kelle10

description: Normal colon mucosa sample

source_name: colon mucosa Kelle10

value: Male

value: Colon mucosa


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF124

description: Maternal status: asthma


title: TAL/ADH co-expressing strain 70 mM furfural Run 1

description: TAL-ADH 70 mM Run 1

source_name: MT8-1X/TAL-ADH, 70 mM (1)


title: CD31pos-CD45neg-PFV, biological rep 1

value: Hematopoietic embryoid bodies after 10 days in hem conditions, CD31 positive CD45 negative


title: Day 10 hematopoietic EB cells, bilogical rep 3

description: Gene expression data from hematopoietic embryoid bodies after 10 days in hem conditions

value: Hematopoietic embryoid bodies after 10 days in hem conditions


title: TAL/ADH co-expressing strain 0 mM furfural Run 2

description: TAL-ADH 0 mM Run 2

source_name: MT8-1X/TAL-ADH, 0 mM (2)

value: control


title: NP Replicate2 48 Hour Female

source_name: Female zebrafish liver tissue

value: liver

tag: time

source_name: Male and female zebrafish liver tissue

value: male and female


title: NP Replicate1 8 Hour Female


title: TAL/ADH co-expressing strain 0 mM furfural Run 1

description: TAL-ADH 0 mM Run 1

source_name: MT8-1X/TAL-ADH, 0 mM (1)


title: NP Replicate3 96 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 96 Hr

source_name: Male zebrafish liver tissue

treatment_protocol: Male zebrafish were exposed to 7 mg/L nitrophenol for 8, 24, 48, and 96 hours at room temperature.

value: male


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF123

description: Maternal status: asthma

value: splenic CD11c+ dendritic cells

value: allergen-sensitized


title: NP Replicate2 96 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 96 Hr


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF120

description: Maternal status: normal control

value: normal control


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF121

description: Maternal status: normal control


title: Day 10 hematopoietic EB cells, bilogical rep 1


title: Undifferentiated H9 cells, biological rep 2

description: Gene expression data from undifferentiated human H9 stem cells

value: Undifferentiated human H9 embryonic stem cells


title: Day 10 hematopoietic EB cells, bilogical rep 2


title: TAL-expressing strain 70 mM furfural Run 1

description: TAL expressing 70 mM Run 1

value: TAL expressing strain


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF119

description: Maternal status: normal control


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF118

description: Maternal status: normal control


title: TAL-expressing strain 70 mM furfural Run 2

description: TAL expressing 70 mM Run 2


title: Undifferentiated H9 cells, biological rep 1


title: NP Replicate2 48 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 48 Hr

value: Nitrophenol-treated liver tissue

value: Nitrophenol

value: untreated


title: NP Replicate1 96 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 96 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: TAL-expressing 0 mM furfural Run 2

description: TAL expressing 0 mM Run 2


title: NP Replicate2 24 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 24 Hr


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF90

description: Maternal status: asthma

value: asthma


title: NP Replicate3 48 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 48 Hr


title: Animal TRPC-8 - TreatmentC

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain ventral tegmental area (VTA)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with RMA

organism: Rattus norvegicus

source_name: age-matched control (water)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 2-cycle protocol from 25 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA was extracted using Trizol followed by Qiagen RNeasy mini kit.

value: ventral tegmental area (VTA)


title: NP Replicate1 48 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 48 Hr


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF91

description: Maternal status: asthma


title: NP Replicate3 24 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 24 Hr


title: Animal TRPC-7 - TreatmentC


title: control strain 70 mM furfural Run 2

description: Control 70 mM Run 2

value: Control

value: furfural


title: TAL-expressing strain 0 mM furfural Run 1

description: TAL expressing 0 mM Run 1

value: control


title: Animal TRP-8 - TreatmentE

source_name: ethanol treatment


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF89

description: Maternal status: asthma


title: control strain 70 mM furfural Run 1

description: Control 70 mM Run 1


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF87

description: Maternal status: normal control


title: control strain 0 mM furfural Run 2

description: Control 0 mM Run 2


title: Allergen Sensitized pup of Asthmatic Mother Dendritic Cell RNA AF88

description: Maternal status: asthma


title: NP Replicate1 24 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 24 Hr

value: liver


title: Animal TRPC-6 - TreatmentC


title: NP Replicate3 8 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 8 Hr

value: male and female


title: NP Replicate2 8 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 8 Hr

value: male


title: Animal TRP-6 - TreatmentE


title: Animal TRP-7 - TreatmentE


title: Animal TRP-5 - TreatmentE


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF86

description: Maternal status: normal control

value: splenic CD11c+ dendritic cells


title: Animal TRPC-5 - TreatmentC


title: control strain 0 mM furfural Run 1

description: Control 0 mM Run 1


title: CA Replicate3 96 Hour Female

treatment_protocol: Female zebrafish were exposed to 30 µg/L chloroaniline for 8, 24, 48, and 96 hours at room temperature.

value: female

value: Chloroaniline-treated liver tissue

value: Chloroaniline


title: DC DUAL 4h replicate 4

city: Oxford

first: Oliver

last: Brain

state: Oxfordshire

address: Headley Way

department: TGU

country: United Kingdom

institute: Nuffield Dept of Medicine

description: Gene expression in human MDDCs following stimulation for 24 h with NOD2 and / or TLR2 ligands

hyb_protocol: The labelled purified product was then fragmented and hybridised at 55C for 20hours.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).

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

source_name: Monocyte-derived dendritic cells

label_protocol: 100ng of Total RNA was dephosphorylated using a Calf Intestine Alkaline Phosphatase and incubated at 37C for 30minutes. The samples were then denatured with 100% DMSO at 100C for 5minutes. Cy3 labelled pCp were ligated onto the RNA using a T4 RNA Ligase and incubated at 16C for 2hours. The labelled RNA was purified using Micro Bio-Spin 6 columns as according to manufacturers guidelines

extract_protocol: Total RNA extracted using Qiagen miRNeasy kit following manufacturers instructions.

treatment_protocol: Five million DCʼs were left unstimulated, or stimulated with 1 μg/ml Muramyl Dipeptide (MDP, Invivogen), or 1 μg/ml Pam3CSK4 (Invivogen), or both, for 24 hours at 37°C, 5% CO2, in 5 ml R10.

tag: age

value: day 5

tag: stimulation conditions

value: Muramyl dipeptide plus Pam3CSK4

tag: treatment time

value: 4 hr


title: DC MDP 24h replicate 4

value: Muramyl dipeptide

value: 24 hr


title: DC DUAL 24h replicate 4


title: NP Replicate1 8 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 8 Hr

value: Nitrophenol-treated liver tissue

value: Nitrophenol

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: CA Replicate2 96 Hour Female


title: Naive pup of Asthmatic Mother Dendritic Cell RNA AF83

description: Maternal status: asthma

value: allergen-naïve

value: asthma


title: Animal TRPC-4 - TreatmentC

value: ventral tegmental area (VTA)


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF85

description: Maternal status: normal control

value: allergen-sensitized

value: normal control


title: Allergen Sensitized pup of Control Mother Dendritic Cell RNA AF84

description: Maternal status: normal control

value: splenic CD11c+ dendritic cells


title: DC PAM 4h replicate 4


title: Naive pup of Asthmatic Mother Dendritic Cell RNA AF81

description: Maternal status: asthma


title: CA Replicate1 96 Hour Female

value: female

value: Chloroaniline-treated liver tissue

value: liver

value: male and female


title: Animal TRPC-3 - TreatmentC


title: Animal TRP-4 - TreatmentE


title: Naive pup of Asthmatic Mother Dendritic Cell RNA AF80

description: Maternal status: asthma


title: Naive pup of Asthmatic Mother Dendritic Cell RNA AF82

description: Maternal status: asthma


title: DC MDP 4h replicate 4

value: day 5

value: 4 hr


title: DC DUAL 24h replicate 3

value: Muramyl dipeptide plus Pam3CSK4

value: 24 hr


title: CA Replicate2 48 Hour Female

value: Chloroaniline


title: DC PAM 24h replicate 3


title: DC MDP 24h replicate 3

value: Muramyl dipeptide


title: DC DUAL 4h replicate 3


title: Animal TRPC-2 - TreatmentC


title: DC PAM 4h replicate 3


title: CA Replicate3 48 Hour Female

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Naive pup of Control Mother Dendritic Cell RNA AF79

description: Maternal status: normal control

value: allergen-naïve


title: Animal TRPC-1 - TreatmentC

value: ventral tegmental area (VTA)


title: Naive pup of Control Mother Dendritic Cell RNA AF76

description: Maternal status: normal control


title: CA Replicate3 24 Hour Female


title: Animal TRP-1 - TreatmentE


title: DC MDP 4h replicate 3


title: Animal TRP-2 - TreatmentE


title: SPIO-LPS_3

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Primary mouse bone marrow macrophage cells pretreated with SPIO for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep3

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

source_name: primary mouse bone marrow macrophage cells exposed to SPIO-LPS

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Primary bone marrow cells were isolated from 4-6 week old C57/BL6 mice following euthanasia by CO2 asphyxiation.    Cells were flushed from isolated femurs and cultured at a concentration of 6x106 cells in 100 cm2 dishes with 10 mL RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 20% conditioned medium obtained from L929 cell cultures. Every two days nonadherent cells were washed off and fresh medium was added.  Conditioned medium was obtained from L929 cells cultured in RPMI supplemented with L-glutamine, Pen-Strep, 10% FBS.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: For cell treatments, 1.5x106 adherent cells were re-plated in 6-well plates in RPMI 1640 supplemented with L-glutamine, Pen-Strep and 10% FBS.  Just prior to exposure, the nanoparticles were sonicated (Fisher Scientific, Model 100) in FBS and brought up with media to the required concentration and volume. Media without ENPs was used as a control.  After 24hrs of ENP exposure, media was aspirated, cells were washed, and 2ml fresh media with or without 10ng/ml LPS (Escherichia coli O111:B4, LIST Biological Laboratories Inc.) was added.

tag: background strain

value: bone marrow macrophage cells

value: SPIO-LPS


title: SPIO-LPS_2

description: Primary mouse bone marrow macrophage cells pretreated with SPIO for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep2


title: SPIO-LPS_1

description: Primary mouse bone marrow macrophage cells pretreated with SPIO for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep1


title: CA Replicate1 24 Hour Female


title: DC DUAL 24h replicate 2


title: CA Replicate2 8 Hour Female


title: CA Replicate3 8 Hour Female


title: SPIO_3

description: Primary mouse bone marrow macrophage cells pretreated with SPIO for 24 hr, then exposed to control media for 4 hr, biological rep3

source_name: primary mouse bone marrow macrophage cells exposed to SPIO

value: SPIO


title: CA Replicate1 8 Hour Female

value: female


title: BN6 PBMCs, BN3 plasma

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: AlloBN3s OnBN6c C119

hyb_protocol: The Affymetrix GeneChip rat genome RD230 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (v.6.5 (6.11.0321)) to determine signal log ratios.  Each sample was independently analyzed (1 array for each time point/condition for 24 arrays; +9 arrays for BN allogenaic challenges).  This time series data was analysis by S.T.E.M. - Short Time-series Expression Miner.

source_name: Brown Norway PBMCs stimulated with Brown Norway 3 plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Fresh PBMCs of healthy Brown Norway (BN) rats (~180 days old males, to avoid variation introduced by estrous or pubertal status) were isolated by density gradient centrifugation.

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 20% autologous BN (self-baseline control), allogeneic BN (healthy-unrelated control), DRlyp/lyp, or DR+/+ plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: strain

value: Brown Norway (BN)

value: male

value: ~180 days

tag: responder cells

value: Brown Norway PBMCs

tag: stimulated with

value: 20% allogeneic BN (healthy-unrelated control)


title: BN2 PBMCs, BN6 plasma

description: AlloBN6s OnBN2c C130

source_name: Brown Norway PBMCs stimulated with Brown Norway 6 plasma


title: BN1 PBMCs, BN6 plasma

description: AlloBN6s OnBN1c C129


title: SPIO_2

description: Primary mouse bone marrow macrophage cells pretreated with SPIO for 24 hr, then exposed to control media for 4 hr, biological rep2


title: BN1 PBMCs, BN4 plasma

description: AlloBN4s OnBN1c C120

source_name: Brown Norway PBMCs stimulated with Brown Norway 4 plasma


title: Control Replicate3 96 Hour Female

description: Biological replicate 3 of 3: control at 96 Hr

value: Untreated liver tissue

value: liver

value: Untreated

value: Singapore wild-type

value: male and female


title: DC MDP 24h replicate 2

value: day 5

value: Muramyl dipeptide

value: 24 hr


title: DC DUAL 4h replicate 2

value: Muramyl dipeptide plus Pam3CSK4

value: 4 hr


title: DC PAM 24h replicate 2


title: Control Replicate2 96 Hour Female

description: Biological replicate 2 of 3: control at 96 Hr

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: SPIO_1

description: Primary mouse bone marrow macrophage cells pretreated with SPIO for 24 hr, then exposed to control media for 4 hr, biological rep1

value: bone marrow macrophage cells

value: SPIO


title: Control Replicate1 96 Hour Female

description: Biological replicate 1 of 3: control at 96 Hr

value: female


title: DC PAM 4h replicate 2


title: Silica-LPS_2

description: Primary mouse bone marrow macrophage cells pretreated with silica for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep2

source_name: primary mouse bone marrow macrophage cells exposed to silica-LPS

value: Silica-LPS


title: BN6 PBMCs, BN2 plasma

description: AlloBN2s OnBN6c C90

source_name: Brown Norway PBMCs stimulated with Brown Norway 2 plasma

value: Brown Norway (BN)

value: male

value: ~180 days

value: Brown Norway PBMCs

value: 20% allogeneic BN (healthy-unrelated control)


title: DC DUAL 24h replicate 1


title: BN6 PBMCs, BN1 plasma

description: AlloBN1s OnBN6c C85

source_name: Brown Norway PBMCs stimulated with Brown Norway 1 plasma


title: BN2 PBMCs, BN1 plasma

description: AlloBN1s OnBN2c C81


title: Control Replicate3 48 Hour Female

description: Biological replicate 3 of 3: control at 48 Hr

value: Untreated liver tissue

value: liver

value: Untreated

value: Singapore wild-type

value: male and female


title: BN1 PBMCs, BN2 plasma

description: AlloBN2s OnBN1c C86


title: Silica-LPS_3

description: Primary mouse bone marrow macrophage cells pretreated with silica for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep3


title: Control Replicate1 48 Hour Female

description: Biological replicate 1 of 3: control at 48 Hr


title: DC MDP 4h replicate 2

value: day 5

value: Muramyl dipeptide

value: 4 hr


title: DC PAM 24h replicate 1

value: 24 hr


title: Control Replicate2 48 Hour Female

description: Biological replicate 2 of 3: control at 48 Hr

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: BN2 PBMCs, DR60 plasma

description: DR60 OnBN2c C65

source_name: Brown Norway PBMCs stimulated with DR+/+ day 60 plasma

value: DR+/+ day 60 plasma


title: Silica_2

description: Primary mouse bone marrow macrophage cells pretreated with silica for 24 hr, then exposed to control media for 4 hr, biological rep2

source_name: primary mouse bone marrow macrophage cells exposed to silica

value: bone marrow macrophage cells

value: Silica


title: BN6 PBMCs, DR60 plasma

description: DR60 OnBN6c C68

value: Brown Norway (BN)

value: male

value: ~180 days


title: Silica_3

description: Primary mouse bone marrow macrophage cells pretreated with silica for 24 hr, then exposed to control media for 4 hr, biological rep3


title: Control Replicate2 24 Hour Female

description: Biological replicate 2 of 3: control at 24 Hr

source_name: Female zebrafish liver tissue

value: female

value: Untreated liver tissue


title: Silica_1

description: Primary mouse bone marrow macrophage cells pretreated with silica for 24 hr, then exposed to control media for 4 hr, biological rep1


title: Silica-LPS_1

description: Primary mouse bone marrow macrophage cells pretreated with silica for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep1

value: Silica-LPS


title: BN1 PBMCs, DR60 plasma

description: DR60 OnBN1c C64

value: Brown Norway PBMCs


title: BN6 PBMCs, DR50 plasma

description: DR50 OnBN6c C63

source_name: Brown Norway PBMCs stimulated with DR+/+ day 50 plasma

value: DR+/+ day 50 plasma


title: LPS_3

description: Primary mouse bone marrow macrophage cells pretreated with control media for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep3

source_name: primary mouse bone marrow macrophage cells exposed to LPS

value: LPS


title: BN2 PBMCs, DR50 plasma

description: DR50 OnBN2c C60


title: Control Replicate3 24 Hour Female

description: Biological replicate 3 of 3: control at 24 Hr

value: liver

value: Untreated

value: Singapore wild-type

source_name: Male and female zebrafish liver tissue

value: male and female


title: DC DUAL 4h replicate 1

description: Gene expression in human MDDCs following stimulation for 24 h with NOD2 and / or TLR2 ligands

value: day 5

value: Muramyl dipeptide plus Pam3CSK4

value: 4 hr


title: DC PAM 4h replicate 1


title: DC MDP 24h replicate 1

value: Muramyl dipeptide

value: 24 hr


title: DC MDP 4h replicate 1


title: Control Replicate1 24 Hour Female

description: Biological replicate 1 of 3: control at 24 Hr

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Control Replicate2 8 Hour Female

description: Biological replicate 2 of 3: control at 8 Hr

value: female


title: Control Replicate3 8 Hour Female

description: Biological replicate 3 of 3: control at 8 Hr

value: Untreated liver tissue


title: DC US 24h replicate 4

value: Unstimulated


title: DC US 4h replicate 4


title: DC US 24h replicate 3


title: LPS_2

description: Primary mouse bone marrow macrophage cells pretreated with control media for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep2

value: bone marrow macrophage cells


title: LPS_1

description: Primary mouse bone marrow macrophage cells pretreated with control media for 24 hr, then exposed to lipopolysaccharide (LPS) for 4 hr, biological rep1


title: BN6 PBMCs, DR40 plasma

description: DR40 OnBN6c C58

source_name: Brown Norway PBMCs stimulated with DR+/+ day 40 plasma

value: Brown Norway (BN)

value: male

value: ~180 days

value: Brown Norway PBMCs

value: DR+/+ day 40 plasma


title: CON_3

description: Primary mouse bone marrow macrophage cells exposed to media (control, CON), biological rep3

source_name: primary mouse bone marrow macrophage cells exposed to control media (CON)

value: control


title: BN2 PBMCs, DR40 plasma

description: DR40 OnBN2c C55


title: Control Replicate1 8 Hour Female

description: Biological replicate 1 of 3: control at 8 Hr

value: liver

value: Untreated

value: Singapore wild-type

value: male and female


title: BN1 PBMCs, DR40 plasma

description: DR40 OnBN1c C54


title: BN1 PBMCs, DR50 plasma

description: DR50 OnBN1c C59

value: DR+/+ day 50 plasma


title: DC US 4h replicate 3

source_name: Monocyte-derived dendritic cells

value: day 5

value: 4 hr


title: CON_2

description: Primary mouse bone marrow macrophage cells exposed to media (control, CON), biological rep2


title: CON_1

description: Primary mouse bone marrow macrophage cells exposed to media (control, CON), biological rep1


title: CA Replicate3 96 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 96 Hr

source_name: Male zebrafish liver tissue

treatment_protocol: Male zebrafish were exposed to 30 µg/L chloroaniline for 8, 24, 48, and 96 hours at room temperature.

value: Chloroaniline-treated liver tissue

value: Chloroaniline

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: BN6 PBMCs, DR30 plasma

description: DR30 OnBN6c C53

source_name: Brown Norway PBMCs stimulated with DR+/+ day 30 plasma

value: Brown Norway (BN)

value: DR+/+ day 30 plasma


title: CA Replicate2 96 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 96 Hr

value: male


title: BN2 PBMCs, DR30 plasma

description: DR30 OnBN2c C50

value: ~180 days

value: Brown Norway PBMCs


title: SW480 cells induced wirh doxycycline for 48 hours (expressing KIAA1199) rep3

city: Zurich

first: Michal

middle: J

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

description: human cell line

hyb_protocol: 45C for 16 hours in a Affymetrix hybridization station.  Then washings were performed in the Affymetrix Fluidics Station 450 (protocol FS450_0001 and reagents from Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: Cell intenstities (.CEL files) were processed in R using ENSG-level Brainarray chip description file. RMA was used to estimate gene-level signal based on probe intensities.

source_name: colorectum

label_protocol: Whole Transcript Sense Target Labeling kit of Affymetrix

growth_protocol: standard growth for human colon cancer cell lines (RPMI 1649 medium, supplemented with 10%Tet-system-approved fetal calf serum, 100 IU penicillin, 100 ug/ml streptomycin, 7 ug/ml blasticidin S, and 0.4 mg/ml G418)

extract_protocol: Qiagen RNeasy

treatment_protocol: exposed to doxycycline (50 ng/ml) for 48 hours

tag: induction

value: induced with doxycycline

tag: cell type

tag: cell line

value: colon cancer cell line.


title: DC US 24h replicate 2

value: Unstimulated

value: 24 hr


title: SW480 cells uninduced rep3

description: human cell line

value: non induced


title: DC US 4h replicate 2


title: CA Replicate1 96 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 96 Hr

tag: gender

tag: tissue

value: liver

value: male and female


title: DC US 24h replicate 1

value: day 5


title: DC US 4h replicate 1

value: 4 hr


title: CA Replicate2 48 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 48 Hr

value: Chloroaniline-treated liver tissue

value: Chloroaniline


title: CA Replicate3 48 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 48 Hr

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: SW480 cells induced wirh doxycycline for 48 hours (expressing KIAA1199) rep2

description: human cell line


title: BN6 PBMCs, DP60 plasma

description: DP60 OnBN6c C48

source_name: Brown Norway PBMCs stimulated with DRlyp/lyp day 60 plasma

value: Brown Norway (BN)

value: DRlyp/lyp day 60 plasma


title: BN2 PBMCs, DP60 plasma

description: DP60 OnBN2c C44

value: male

value: ~180 days


title: CA Replicate1 48 Hour Female

description: Biological replicate 1 of 3: chloroaniline-treated at 48 Hr

value: female


title: CA Replicate3 24 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 24 Hr


title: CA Replicate1 48 Hour Male


title: SW480 cells uninduced rep2

description: human cell line

value: colon cancer cell line.


title: CA Replicate2 24 Hour Female

description: Biological replicate 2 of 3: chloroaniline-treated at 24 Hr


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown aerobically, replicate 3

city: SA

first: David

last: Kolodrubetz

address: 7703 Floyd Curl Dr

department: Microbiology and Immunology

institute: UTHSCSA

description:
AAM155 +O2, Replicate3
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown aerobically. It is the third of four mutant strain biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: Robust Multi-Array Analysis (RMA; Irizarry et al. Biostatistics 4:249) in the NimbleScan Software Package (v2.6, Roche NimbleGen, Madison, WI) was first used to do background corrections of raw expression data (.pair files) from individual sample sets. Then, RMA was used to do quantile normalization (Bolstad et al. Bioinformatics 19:185) across the eight sample sets (anaerobically grown) being compared and to do median polishing to reduce the contribution of outlier probes to the single expression value derived from multiple probes for a given gene in a sample set. Similarly, RMA was used to do quantile normalization (Bolstad et al. Bioinformatics 19:185) across the eight sample sets (aerobically grown) being compared and to do median polishing to reduce the contribution of outlier probes to the single expression value derived from multiple probes for a given gene in a sample set.

organism: Aggregatibacter actinomycetemcomitans

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

growth_protocol: A. actinomycetemcomitans strains JP2 and AAM155 were grown in TSBYE (3% tryptic soy broth plus 0.6% yeast extract) either anaerobically (5% CO2, 10% H2, 85% N2) to mid-log phase (OD600nm = 0.35 ) in a Coy chamber (Coy Laboratory Products, Ann Arbor, MI) at 37°C with shaking or aerobically (5% CO2, 95% air) to mid-log phase (OD600nm = 0.35 ) in a water-jacketed CO2 incubator (Forma Scientific) at 37°C with shaking.

extract_protocol: RNA was isolated from mid-log phase A. actinomycetemcomitans cells using RNAprotect® Bacterial Reagent (Qiagen, Inc., Valencia, CA) and the RNeasy® Mini Kit (Qiagen). The manufacturer's instructions were followed with the following notes: 2.5 ml of cells were lysed with 10 mg/ml lysozyme (Sigma, St. Louis, MO) for 15 min. The RNase-free DNase Set (Qiagen) was used for DNase treatment at twice the manufacturer's recommended concentration. RNA quality and concentration were determined by analysis with an Agilent 2100 Bioanalyzer at Roche-NimbleGen.

tag: genotype

value: Mlc deletion

tag: growth condition

value: aerobic

tag: leukotoxin level

value: low


title: CA Replicate2 24 Hour Male

tag: sample type

value: liver

tag: treatment


title: SW480 cells induced wirh doxycycline for 48 hours (expressing KIAA1199) rep1

description: human cell line

value: induced with doxycycline


title: BN1 PBMCs, DR30 plasma

description: DR30 OnBN1c C49

tag: age

value: Brown Norway PBMCs

value: DR+/+ day 30 plasma


title: BN6 PBMCs, DP50 plasma

description: DP50 OnBN6c C42

source_name: Brown Norway PBMCs stimulated with DRlyp/lyp day 50 plasma

value: DRlyp/lyp day 50 plasma


title: SW480 cells uninduced rep1

description: human cell line

value: non induced


title: CA Replicate1 24 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 24 Hr

value: Chloroaniline-treated liver tissue

value: Chloroaniline

tag: time

value: male and female

value: untreated


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 7

description: Biological replicate 7 of 7: estradiol-treated at 50 µg/L for 96 Hr

hyb_protocol: Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_23K_oligo_COMP_v4Apx zebrafish oligo probes.

treatment_protocol: Male zebrafish were exposed to 0.5, 5, 50 µg/L estradiol for 24 and 96 hours at room temperature.

value: male

value: Estradiol-treated liver tissue

value: Estradiol-Treated at 50 ug/L

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown aerobically, replicate 4

description:
AAM155 +O2, Replicate4
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown aerobically. It is the fourth of four mutant strain biological replicates used in this experiment, each from separate cultures.

value: Mlc deletion


title: Naive pup of Control Mother Dendritic Cell RNA AF77

description: Maternal status: normal control

source_name: splenic CD11c+ dendritic cells

value: splenic CD11c+ dendritic cells

value: allergen-naïve

tag: maternal status

value: normal control


title: BN1 PBMCs, DP50 plasma

description: DP50 OnBN1c C37

value: Brown Norway (BN)

value: ~180 days


title: CA Replicate3 8 Hour Male

description: Biological replicate 3 of 3: chloroaniline-treated at 8 Hr

value: liver


title: BN1 PBMCs, DP60 plasma

description: DP60 OnBN1c C43

value: Brown Norway PBMCs

value: DRlyp/lyp day 60 plasma


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown aerobically, replicate 1

description:
AAM155 +O2, Replicate1
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown aerobically. It is the first of four mutant strain biological replicates used in this experiment, each from separate cultures.

value: aerobic

value: low


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 6

description: Biological replicate 6 of 7: estradiol-treated at 50 µg/L for 97 Hr

value: male and female


title: DC PAM 24h replicate 4

description: Gene expression in human MDDCs following stimulation for 24 h with NOD2 and / or TLR2 ligands

value: day 5

tag: stimulation conditions

tag: treatment time

value: 24 hr


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown aerobically, replicate 2

description:
AAM155 +O2, Replicate2
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown aerobically. It is the second of four mutant strain biological replicates used in this experiment, each from separate cultures.

tag: strain


title: A. actinomycetemcomitans wild type strain JP2, grown aerobically, replicate 4

description:
JP2 +O2, Replicate4
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown aerobically. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures.

value: wild type

value: high


title: BN2 PBMCs, DP50 plasma

description: DP50 OnBN2c C38

value: male

tag: responder cells

tag: stimulated with

value: DRlyp/lyp day 50 plasma


title: CA Replicate1 8 Hour Male

description: Biological replicate 1 of 3: chloroaniline-treated at 8 Hr

value: Chloroaniline-treated liver tissue

value: Chloroaniline

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: A. actinomycetemcomitans wild type strain JP2, grown aerobically, replicate 1

description:
JP2 +O2, Replicate1
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown aerobically. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures.


title: A. actinomycetemcomitans wild type strain JP2, grown aerobically, replicate 2

description:
JP2 +O2, Replicate2
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown aerobically. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures.


title: A. actinomycetemcomitans wild type strain JP2, grown aerobically, replicate 3

description:
JP2 +O2, Replicate3
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown aerobically. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures.


title: CA Replicate2 8 Hour Male

description: Biological replicate 2 of 3: chloroaniline-treated at 8 Hr


title: BN6 PBMCs, DP40 plasma

description: DP40 OnBN6c C36

source_name: Brown Norway PBMCs stimulated with DRlyp/lyp day 40 plasma

value: Brown Norway (BN)

value: ~180 days

value: DRlyp/lyp day 40 plasma


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown anaerobically, replicate 4

description:
AAM155 -O2, Replicate4
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown anaerobically. It is the fourth of four mutant strain biological replicates used in this experiment, each from separate cultures.

value: Mlc deletion

value: anaerobic


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 5

description: Biological replicate 5 of 7: estradiol-treated at 50 µg/L for 97 Hr

value: Estradiol-treated liver tissue

value: liver

value: Estradiol-Treated at 50 ug/L


title: Control Replicate3 96 Hour Male

description: Biological replicate 3 of 3: control at 96 Hr

value: Untreated liver tissue

value: Untreated

value: Singapore wild-type

value: male and female


title: BN1 PBMCs, DP40 plasma

description: DP40 OnBN1c C31

value: male

value: Brown Norway PBMCs


title: BN6 PBMCs, BN4 plasma

description: AlloBN4s OnBN6c C123

source_name: Brown Norway PBMCs stimulated with Brown Norway 4 plasma

value: 20% allogeneic BN (healthy-unrelated control)


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 3

description: Biological replicate 3 of 7: estradiol-treated at 50 µg/L for 97 Hr

value: untreated


title: BN2 PBMCs, DP40 plasma

description: DP40 OnBN2c C32


title: Control Replicate2 96 Hour Male

description: Biological replicate 2 of 3: control at 96 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 4

description: Biological replicate 4 of 7: estradiol-treated at 50 µg/L for 97 Hr


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown anaerobically, replicate 3

description:
AAM155 -O2, Replicate3
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown anaerobically. It is the third of four mutant strain biological replicates used in this experiment, each from separate cultures.

value: low


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 1

description: Biological replicate 1 of 7: estradiol-treated at 50 µg/L for 97 Hr


title: BN1 PBMCs, DP30 plasma

description: DP30 OnBN1c C25

source_name: Brown Norway PBMCs stimulated with DRlyp/lyp day 30 plasma

value: Brown Norway (BN)

value: ~180 days

value: DRlyp/lyp day 30 plasma


title: BN6 PBMCs, DP30 plasma

description: DP30 OnBN6c C30


title: Estradiol-Treated at 50 µg/L for 24 Hour, Replicate 6

description: Biological replicate 6 of 6: estradiol-treated at 50 µg/L for 24 Hr


title: Estradiol-Treated at 50 µg/L for 24 Hour, Replicate 5

description: Biological replicate 5 of 6: estradiol-treated at 50 µg/L for 24 Hr


title: BN2 PBMCs, DP30 plasma

description: DP30 OnBN2c C26


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown anaerobically, replicate 2

description:
AAM155 -O2, Replicate2
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown anaerobically. It is the second of four mutant strain biological replicates used in this experiment, each from separate cultures.

value: Mlc deletion

value: anaerobic


title: Control Replicate1 96 Hour Male

description: Biological replicate 1 of 3: control at 96 Hr

value: liver


title: A. actinomycetemcomitans Mlc mutant strain AAM155, grown anaerobically, replicate 1

description:
AAM155 -O2, Replicate1
Formerly Actinobacillus actinomycetemcomitans.
This sample is of A. actinomycetemcomitans strain AAM155, an isogenic deletion mutant in which the gene for Mlc has been replaced by a spectinomycin resistance gene cassette, grown anaerobically. It is the first of four mutant strain biological replicates used in this experiment, each from separate cultures.


title: Control Replicate1 48 Hour Male

description: Biological replicate 1 of 3: control at 48 Hr


title: Control Replicate2 48 Hour Male

description: Biological replicate 2 of 3: control at 48 Hr


title: Ovariant tissue harvest at Day 7, Patient 4

city: Woluwé-St-Lambert

first: Jérôme

last: Ambroise

address: 30, Chapelle-aux-Champs (box B1.30.24)

department: Institut de Recherche Expérimentale et Clinique (IREC)

country: Belgium

institute: Université catholique de Louvain

description: Gene expression data of ovarian tissue for patient 4 at Day 7 after xenografting

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

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

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

source_name: Ovarian biopsies from patient

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

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

treatment_protocol: Ovarian biopsies measuring 8 by 4 mm were obtained from patients . One fragment was frozen-thawed, thawed and immediately processed for RNA extraction. The second fragment was grafted in nude mice for 7 days.

value: adult

value: avascular ovarian cortex

tag: sample group

value: Ovariant tissue grafted in nude mice for 7 days


title: A. actinomycetemcomitans wild type strain JP2, grown anaerobically, replicate 4

description:
JP2 -O2, Replicate4
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown anaerobically. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures.

value: wild type

value: high


title: A. actinomycetemcomitans wild type strain JP2, grown anaerobically, replicate 3

description:
JP2 -O2, Replicate3
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown anaerobically. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures.


title: Control Replicate3 48 Hour Male

description: Biological replicate 3 of 3: control at 48 Hr

value: male

value: Untreated liver tissue

value: Untreated

value: Singapore wild-type

value: male and female


title: Estradiol-Treated at 50 µg/L for 24 Hour, Replicate 4

description: Biological replicate 4 of 6: estradiol-treated at 50 µg/L for 24 Hr

value: Estradiol-treated liver tissue

value: Estradiol-Treated at 50 ug/L

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: A. actinomycetemcomitans wild type strain JP2, grown anaerobically, replicate 2

description:
JP2 -O2, Replicate2
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown anaerobically. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures.


title: Estradiol-Treated at 50 µg/L for 96 Hour, Replicate 2

description: Biological replicate 2 of 7: estradiol-treated at 50 µg/L for 97 Hr


title: Control Replicate2 24 Hour Male

description: Biological replicate 2 of 3: control at 24 Hr


title: Estradiol-Treated at 50 µg/L for 24 Hour, Replicate 3

description: Biological replicate 3 of 6: estradiol-treated at 50 µg/L for 24 Hr


title: Ovariant tissue harvest at Day 7, Patient 3

description: Gene expression data of ovarian tissue for patient 3 at Day 7 after xenografting


title: Control Replicate1 24 Hour Male

description: Biological replicate 1 of 3: control at 24 Hr


title: A. actinomycetemcomitans wild type strain JP2, grown anaerobically, replicate 1

description:
JP2 -O2, Replicate1
Formerly Actinobacillus actinomycetemcomitans.
This sample is of wild-type A. actinomycetemcomitans strain JP2 grown anaerobically. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures.


title: Control Replicate3 8 Hour Male

description: Biological replicate 3 of 3: control at 8 Hr


title: Ovariant tissue harvest at Day 0, Patient 3

description: Gene expression data of ovarian tissue for patient 3 frozen-thawed, thawed and immediately processed

value: Ovariant tissue harvest at Day 0


title: Ovariant tissue harvest at Day 7, Patient 2

description: Gene expression data of ovarian tissue for patient 2 at Day 7 after xenografting


title: Estradiol-Treated at 50 µg/L for 24 Hour, Replicate 1

description: Biological replicate 1 of 6: estradiol-treated at 50 µg/L for 24 Hr


title: Estradiol-Treated at 50 µg/L for 24 Hour, Replicate 2

description: Biological replicate 2 of 6: estradiol-treated at 50 µg/L for 24 Hr


title: Ovariant tissue harvest at Day 0, Patient 4

description: Gene expression data of ovarian tissue for patient 4 frozen-thawed, thawed and immediately processed


title: Control Replicate2 8 Hour Male

description: Biological replicate 2 of 3: control at 8 Hr


title: Estradiol-Treated at 5 µg/L for 96 Hour, Replicate 4

description: Biological replicate 4 of 6: estradiol-treated at 5 µg/L for 96 Hr

value: Estradiol-Treated at 5 ug/L


title: microglia_rep3

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

description: in vitro P1 microglial culture, DIV10, replicate 3

hyb_protocol: The labeled RNA was hybridized to Agilent human miRNA microarrays for 20 hours at 55°C with rotation.

scan_protocol: The arrays were scanned with an Agilent microarray scanner with high dynamic range settings as specified by the manufacturer.

data_processing: Agilent Feature Extraction Software was used to extract the data

source_name: microglia

label_protocol: Each sample was prepared according to the Agilent’s miRNA Microarray System protocol. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH, Otelfingen, Switzerland), denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH, Otelfingen, Switzerland).

growth_protocol: Dissociated neuronal and glial cultures for the microarray analyses were prepared from cortexes of postnatal day 1 (P1) rats. To obtain neuronal cultures, cells were grown in Neurobasal media with cytosine arabinoside (Ara-C) in order to eliminate glial cells. To obtain astroglial cultures dissociated cells were grown in MEM complemented with horse serum and after 10 days cultures were shaken on a rotary shaker at 300 rpm overnight in order to eliminate oligodendroglial, microglial and neuronal cells. Microglial cultures were prepared by collecting the supernatant 7 DIV of the original cortical cultures. When mixed cortical cultures reach confluence, microglial cells float in the media, being unable to attach to uncoated surface covered with astrocytes. To prepare oligodendroglial cultures, we collected the supernatant from mixed cultures 10 DIV, washed the culture with fresh medium and shake it for 30 – 60 min, afterwards the supernatant was plated on poly-l-lysin coated plates.

extract_protocol: Total RNA used for the qPCR analyses was isolated using mirVana Ambion® kit.

tag: cell type

value: microglia


title: microglia_rep2

description: in vitro P1 microglial culture, DIV10, replicate 2


title: Control Replicate3 24 Hour Male

description: Biological replicate 3 of 3: control at 24 Hr

hyb_protocol: Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_16.5K_oligo_COMP_v3Apx zebrafish oligo probes.

data_processing: The data were global median normalized. Normalized ratio of means defined by CH1/CH2

tag: gender

value: liver


title: microglia_rep1

description: in vitro P1 microglial culture, DIV10, replicate 1


title: Estradiol-Treated at 5 µg/L for 96 Hour, Replicate 1

description: Biological replicate 1 of 6: estradiol-treated at 5 µg/L for 96 Hr

tag: tissue


title: Estradiol-Treated at 5 µg/L for 96 Hour, Replicate 3

description: Biological replicate 3 of 6: estradiol-treated at 5 µg/L for 96 Hr


title: Estradiol-Treated at 5 µg/L for 96 Hour, Replicate 2

description: Biological replicate 2 of 6: estradiol-treated at 5 µg/L for 96 Hr


title: oligodendrocytes_rep2

description: in vitro P1 oligodendroglial culture, DIV10, replicate 2

source_name: oligodendrocytes

value: oligodendrocytes


title: Ovariant tissue harvest at Day 0, Patient 1

description: Gene expression data of ovarian tissue for patient 1 frozen-thawed, thawed and immediately processed

value: adult

value: avascular ovarian cortex


title: Control Replicate1 8 Hour Male

description: Biological replicate 1 of 3: control at 8 Hr


title: oligodendrocytes_rep1

description: in vitro P1 oligodendroglial culture, DIV10, replicate 1


title: Ovariant tissue harvest at Day 7, Patient 1

description: Gene expression data of ovarian tissue for patient 1 at Day 7 after xenografting

value: Ovariant tissue grafted in nude mice for 7 days


title: oligodendrocytes_rep3

description: in vitro P1 oligodendroglial culture, DIV10, replicate 3


title: astrocytes_rep4

description: in vitro P1 astroglial culture, DIV10, replicate 4

source_name: astrocytes

value: astrocytes


title: Ovariant tissue harvest at Day 0, Patient 2

description: Gene expression data of ovarian tissue for patient 2 frozen-thawed, thawed and immediately processed


title: Estradiol-Treated at 5 µg/L for 24 Hour, Replicate 5

description: Biological replicate 5 of 6: estradiol-treated at 5 µg/L for 24 Hr

value: male

source_name: Male and female zebrafish liver tissue


title: astrocytes_rep3

description: in vitro P1 astroglial culture, DIV10, replicate 3


title: F2365_O1-001

city: West Lafayette

first: Haley

last: Oliver

address: 745 agriculture mall dr

description: For 'F2365 O1-002 rna 1.gpr' and 'F2365 O1-002 rna 3.gpr', mutant is labeled with Cy5 and wildtype with Cy3.  For 'F2365 O1-002 rna 2 .gpr' the dyes are reversed.

hyb_protocol: Briefly, microarray slides were blocked in a prehybridization buffer supplemented with bovine serum albumen (BSA) (Sigma-Aldrich), washed with deionized water then isopropyl alcohol. Dried Cy3- and Cy5-labeled cDNA was hydrated with hybridization buffer containing 0.6 mg/ml sheared salmon sperm DNA (Invitrogen), denatured twice at 95ºC for 5 minutes and briefly centrifuged. cDNA was hybridized to the microarray at 42ºC for 16 hours. Following hybridization, slides were washed according to the PFGRC/JCVI M008 protocol and dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.) using the following general scanning parameters: pixel size=10, focus position=20, lines to average=1, laser power=100%. The auto-PMT function was used to scan the slides with an acceptable PMT range of 400-900. Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis. The PFGRC/JCVI L. monocytogenes microarray contained multiple probes for certain loci that lacked a 70mer consensus sequence for a given locus among the four strains represented on the microarray. In instances where multiple probes were present for a single locus, the probe that best matched the sequence for a given strain used in the present study was selected as the representative probe for subsequent analyses for that strain. BLASTN was used to calculate the hybridization index (HI), the percent identity between each probe and each strain; BLASTN results were parsed to compare percent identity between each strain and the probes. EGD-e locus names were used to describe the corresponding open reading frames (ORFs) in the lineage I, IIIA, and IIIB strains as these genomes have not yet been annotated; EGD-e locus names were also used in lieu of 10403S locus names to facilitate comparisons among all strains in this study. Genes unique to F2365, F6852 and H7858 (i.e. genes with no EGD-e homologue) maintained their locus names. Genes with higher transcript levels in a wildtype strain compared to its isogenic ΔsigB mutant (fold change > 1.5) and adjusted p-values < 0.05 were considered positively differentially expressed, and thus σB-dependent.

label: Cy3, Cy5

organism: Listeria monocytogenes

label_protocol: The Pathogen Functional Genomics Resource Center/J. Craig Venter Institute (PFGRC/JCVI) L. monocytogenes microarray version 2 was used to identify mRNA transcript level differences between wildtype strains and their respective ∆sigB mutants. The PFGRC/JCVI microbial RNA aminoallyl labeling for microarray standard operating procedure M007 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to reverse transcribe and label the total RNA. Spectrophotometry was used to quantify cDNA and total picomoles of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ) incorporation. Cy3- and Cy5-labeled cDNA was combined and thoroughly dehydrated prior to hybridization. PFGRC/JCVI standard operating procedure M008 (publicly available at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html) was used to hybridize the Cy-dye labeled cDNA to the microarray.

growth_protocol: Bacteria were initially grown in 5 ml of BHI broth at 37°C with shaking (230 rpm) for 15 h. A 1% inoculum was transferred to 5 ml of prewarmed BHI broth and grown to an OD600 of ∼0.4. After growth to an OD600 of ∼0.4, a ∼1% (vol/vol) inoculum was transferred to 50 ml of prewarmed (37°C) BHI broth in a 300-ml nephelo flask (Bellco, Vineland, NJ) to obtain a calculated OD600 of 0.004 (the volume transferred was adjusted based on the actual OD600 of the starting inoculum). Following the second passage, cells were collected at stationary phase (defined as growth to an OD600 of 1.0, followed by incubation for an additional 3 h).

extract_protocol: RNAProtect bacterial reagent (Qiagen, Valencia, CA) was added to the cultures according to manufacturer’s instructions to stabilize the mRNA; pellets were stored at -80°C prior to RNA isolation. RNA was isolated as previously described. Briefly, bacterial cells were lysed enzymatically with lysozyme (Fisher Scientific, Pittsburg, PA), and mechanically, using 6 sonication bursts (Misonix, Farmingdale, NY) at 18W on ice for 30 seconds. Total RNA was isolated and purified using the RNeasy Midi kit (Qiagen) according to the manufacturer’s protocol. RNA was eluted from the column using RNase-free water. Total RNA was incubated with RNasin (Promega, Madison, WI) to inhibit RNases, and RQ1 DNase (Promega) to remove DNA contamination. After phenol:chloroform extraction, UV spectrophotometry (Nanodrop, Wilmington, DE) was used to quantify and assess purity of the RNA. RNA integrity was assessed by agarose gel electrophoresis. Purified RNA was stored in RNase-free water at -80°C prior to reverse transcription.

treatment_protocol: No treatment differences between wildtype and mutant.

tag: genotype/variation

value: wildtype

label: Cy5, Cy3

value: ΔsigB


title: leaves_earthworms_ggt_biological rep2

city: Créteil

first: Ruben

last: Puga-Freitas

address: 61 Avenue du Général de Gaulle

country: France

institute: Université Paris-Est Créteil

description: Gene expression data from plants inoculated with the the earthworm A. caliginosa and thepathogenic fungus G. graminis

hyb_protocol: Fragmented cRNA was hybridized on Affymetrix GeneChip Wheat Genome array for 16 h at 45°C along with internal hybridization controls. Washing and staining procedures were performed in an Affymetrix Fluidics Station 450.

data_processing: Probe-level expression data (CEL files) were produced using GeneChip® Operation Software (GCOS) version 1.4 and data were normalized using the MAS5 algorithm. Quality-control and statistical analyses (background adjustment, normalization, and probe-level summarization of data) used the GC-Robust Multi-Array average algorithm (GC-RMA) from the GeneSpring GX11 Software.

organism: Triticum aestivum

source_name: Wheat leaves, plants inoculated with earthworms and G. graminis

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

growth_protocol: In a greenhouse experiment, plants were grown in a sandy soil during 52 days. There was 4 levels of treatment (plants only (C), inoculated with Ggt (GGT), inoculated with earthworms (E) or inoculated with earthworms and Ggt (E_GGT)), with 3 plants per treatments.

extract_protocol: RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, France) with an on-column DNase digestion using DNase I (Qiagen, France) according to the manufacturer's instructions.

treatment_protocol: Plants were inoculated or not with Gaeumannomyces graminis var tritici. In treatments with earthworms, two weeks after Ggt inoculation living earthworms were added to the devoted microcosms

value: leaves


title: Estradiol-Treated at 5 µg/L for 24 Hour, Replicate 4

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

institute: National University of Singapore

description: Biological replicate 4 of 6: estradiol-treated at 5 µg/L for 24 Hr

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

label_protocol: For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

value: Estradiol-treated liver tissue

value: male and female


title: astrocytes_rep2

description: in vitro P1 astroglial culture, DIV10, replicate 2


title: leaves_earthworms_ggt_biological rep3

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


title: leaves_earthworms_ggt_biological rep1


title: astrocytes_rep1

description: in vitro P1 astroglial culture, DIV10, replicate 1


title: Estradiol-Treated at 5 µg/L for 24 Hour, Replicate 6

description: Biological replicate 6 of 6: estradiol-treated at 5 µg/L for 24 Hr

value: untreated


title: leaves_ggt_biological rep3

description: Gene expression data from plants inoculated with the pathogenic fungus G. graminis

source_name: Wheat leaves, plants inoculated with G. graminis


title: Estradiol-Treated at 5 µg/L for 24 Hour, Replicate 3

description: Biological replicate 3 of 6: estradiol-treated at 5 µg/L for 24 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Estradiol-Treated at 0.5 µg/L for 96 Hour, Replicate 6

description: Biological replicate 6 of 6: estradiol-treated at 0.5 µg/L for 96 Hr

value: Estradiol-Treated at 0.5 ug/L


title: neurons_rep3

description: in vitro P1 neuronal culture, DIV10, replicate 3

source_name: neurons

value: neurons


title: leaves_earthworms_biological rep2

description: Gene expression data from plants inoculated with soil macroorganism A. caliginosa

source_name: Wheat leaves, plants inoculated with earthworms


title: Estradiol-Treated at 5 µg/L for 24 Hour, Replicate 1

description: Biological replicate 1 of 6: estradiol-treated at 5 µg/L for 24 Hr

source_name: Male zebrafish liver tissue

value: Estradiol-Treated at 5 ug/L


title: leaves_earthworms_biological rep1


title: neurons_rep2

description: in vitro P1 neuronal culture, DIV10, replicate 2


title: neurons_rep1

description: in vitro P1 neuronal culture, DIV10, replicate 1


title: Estradiol-Treated at 0.5 µg/L for 96 Hour, Replicate 5

description: Biological replicate 5 of 6: estradiol-treated at 0.5 µg/L for 96 Hr

value: liver


title: Estradiol-Treated at 0.5 µg/L for 96 Hour, Replicate 4

description: Biological replicate 4 of 6: estradiol-treated at 0.5 µg/L for 96 Hr


title: Estradiol-Treated at 5 µg/L for 24 Hour, Replicate 2

description: Biological replicate 2 of 6: estradiol-treated at 5 µg/L for 24 Hr


title: leaves_ggt_biological rep1


title: Estradiol-Treated at 0.5 µg/L for 96 Hour, Replicate 2

description: Biological replicate 2 of 6: estradiol-treated at 0.5 µg/L for 96 Hr


title: Estradiol-Treated at 0.5 µg/L for 96 Hour, Replicate 3

description: Biological replicate 3 of 6: estradiol-treated at 0.5 µg/L for 96 Hr


title: leaves_control_biological rep2

description: Gene expression data from control plants

source_name: Wheat leaves, control plants


title: MGK119-1

city: Mississauga

first: Claude

last: Lachance

address: 1329 Meyerside Drive

institute: Bio-Rad

description: Spleen S. suis SC84 6h Rep 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were first raw-filtered in order to identify and remove probesets that were not detected and then normalised using robust spline normalization with FlexArray v1.6

source_name: C57BL/6 TLR2-KO spleen infected with Chinese strain (SC84) of Streptococcus suis

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

growth_protocol: Bacterial culture was prepared by transferring 10 μl of 1/1,000 dilutions of 8-h cultures into 30 ml of THB, which was incubated for 16 h at 37°C without agitation. Stationary-phase bacteria were washed twice in PBS (pH 7.3). The bacterial pellet was then resuspended and adjusted to a concentration of 5 × 10^8 c.f.u. ml-1.

extract_protocol: RNA was homogenized from RNAlater-stabilized spleen tissus, extracted and DNAse I treated using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice (C57BL/6 and C57BL/6 TLR2-KO) were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain SC84.

value: C57BL/6 TLR2-KO

value: Spleen

value: Female


title: MGK120-1

description: Spleen S. suis SC84 6h Rep 3


title: Estradiol-Treated at 0.5 µg/L for 96 Hour, Replicate 1

description: Biological replicate 1 of 6: estradiol-treated at 0.5 µg/L for 96 Hr


title: CD44KO white adipose tissue_HFD_rep4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
251486837666_1_3
RNA samples from CD44KO mice fed with a HFD.

hyb_protocol: For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: CD44KO mice fed with a HFD for 21 weeks

label_protocol: Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer's protocol.

extract_protocol: Qiagen RNeasy mini kit.

treatment_protocol: Liver and white adipose tissue (WAT) from WT and CD44KO mice fed with a high-fat diet (HFD; 35% fat) for 21 weeks.

tag: strain/background

value: CD44 knockout

value: 7 months

value: white adipose tissue (WAT)

value: 35% fat diet (high fat)

tag: treatment duration

value: 21 weeks


title: CD44KO white adipose tissue_HFD_rep5

description:
251486837664_1_4
RNA samples from CD44KO mice fed with a HFD.

value: male


title: Estradiol-Treated at 0.5 µg/L for 24 Hour, Replicate 6

description: Biological replicate 6 of 6: estradiol-treated at 0.5 µg/L for 24 Hr

tag: sample type

value: Estradiol-treated liver tissue


title: CD44KO white adipose tissue_HFD_rep1

description:
251486837666_1_2
RNA samples from CD44KO mice fed with a HFD.

tag: treatment


title: Wildtype white adipose tissue_HFD_rep5

description:
251486837665_1_2
RNA samples from WT mice fed with a HFD.

source_name: WT mice fed with a HFD for 21 weeks

value: wildtype

tag: age


title: Estradiol-Treated at 0.5 µg/L for 24 Hour, Replicate 4

description: Biological replicate 4 of 6: estradiol-treated at 0.5 µg/L for 24 Hr

tag: time

value: male and female

value: untreated


title: MGK083-1

description: Spleen S. suis SC84 6h Rep 4

source_name: C57BL/6 spleen infected with Chinese strain (SC84) of Streptococcus suis


title: Estradiol-Treated at 0.5 µg/L for 24 Hour, Replicate 3

description: Biological replicate 3 of 6: estradiol-treated at 0.5 µg/L for 24 Hr

value: Estradiol-Treated at 0.5 ug/L

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: MGK122-1

description: Spleen S. suis SC84 6h Rep 4


title: Estradiol-Treated at 0.5 µg/L for 24 Hour, Replicate 5

description: Biological replicate 5 of 6: estradiol-treated at 0.5 µg/L for 24 Hr


title: CD44KO white adipose tissue_HFD_rep2

description:
251486837664_1_3
RNA samples from CD44KO mice fed with a HFD.


title: Estradiol-Treated at 0.5 µg/L for 24 Hour, Replicate 2

description: Biological replicate 2 of 6: estradiol-treated at 0.5 µg/L for 24 Hr


title: CD44KO white adipose tissue_HFD_rep3

description:
251486837665_1_3
RNA samples from CD44KO mice fed with a HFD.


title: MGK094-1

description: Spleen S. suis SC84 6h Rep 1


title: Untreated Control Replicate 7 of 96h

description: Biological replicate 7 of 7: control at 96 Hr

value: Untreated liver tissue


title: MGK081-1

description: Spleen S. suis SC84 6h Rep 2


title: MGK080-1

description: Spleen S. suis SC84 6h Rep 1


title: Estradiol-Treated at 0.5 µg/L for 24 Hour, Replicate 1

description: Biological replicate 1 of 6: estradiol-treated at 0.5 µg/L for 24 Hr

value: liver


title: MGK082-1

description: Spleen S. suis SC84 6h Rep 3


title: Wildtype white adipose tissue_HFD_rep3

description:
251486837665_1_4
RNA samples from WT mice fed with a HFD.


title: leaves_control_biological rep1

value: leaves


title: CD44KO liver_HFD_rep4

description:
251486837667_1_4
RNA samples from CD44KO mice fed with a HFD.


title: Wildtype white adipose tissue_HFD_rep4

description:
251486837664_1_2
RNA samples from WT mice fed with a HFD.


title: Wildtype white adipose tissue_HFD_rep2

description:
251486837665_1_1
RNA samples from WT mice fed with a HFD.


title: MGK118-1

description: Spleen S. suis P1/7 6h Rep 3

source_name: C57BL/6 TLR2-KO spleen infected with European strain (P1/7) of Streptococcus suis

treatment_protocol: Mice (C57BL/6 and C57BL/6 TLR2-KO) were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain P1/7.

value: C57BL/6 TLR2-KO

value: Spleen


title: Untreated Control Replicate 6 of 96h

description: Biological replicate 6 of 7: control at 96 Hr


title: CD44KO liver_HFD_rep5

description:
251486837668_1_4
RNA samples from CD44KO mice fed with a HFD.

value: CD44 knockout


title: Wildtype white adipose tissue_HFD_rep1

description:
251486837664_1_1
RNA samples from WT mice fed with a HFD.

value: 7 months