title: control 3 day 0

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: no disease D0

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1,65µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44k using Agilent's recommended hybridization chamber.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9,1 was used to read out and process the microarray image files. The software determines feature intensities including background subtraction.

data_processing: the signal intensities from single experiment raw data lists are normalized by dividing the intensities values by their median

source_name: cells before osteoblastic differentiation from healthy donor

label_protocol: 1µg of total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit/Low RNA Input Linear Amp Kit (Agilent Technologies) following manufacturer's protocol.

growth_protocol: Mononuclear cells from human bone marrow were separate were separate by Ficoll and cultivated in medium alphaMEM with 10% of FCS and induced to differentiate in osteoblastic lineage during 21 days

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer Platform (Agilent Technologies)

treatment_protocol: Bone marrow mesenchymal stromal cells induced to differentiate in osteoblastic lineage during 21 days

value: bone marrow mesenchymal stem cells (BM-MSC)

tag: disease status

value: no disease


title: control 3 day 21

status: Public on Jan 10 2015

type: RNA

description: no disease D21

molecule: total RNA

organism: Homo sapiens

source_name: cells after osteoblastic differentiation from healthy donor

tag: cell type


title: control 6 day 0

description: no disease D0


title: pmf 1 day 21

description: primary myelofibrosis D21

source_name: cells after osteoblastic differentiation from patient with primary myelofibrosis

value: primary myelofibrosis


title: 4flc/svp.LD._Leaf.r2

status: Public on Jan 11 2015

city: Cologne

first: Julieta

last: Mateos

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: Biotinylated cRNA samples were mixed in 250 μL of Hybridization Mix (Affymetrix; 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix; 900454). Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.

data_processing: The raw data (CEL files) were subjected to RMA.

label: biotin

organism: Arabidopsis thaliana

source_name: flc-/svp- 2 weeks Short Days + 2 Long days-ZT8-Leaf

label_protocol: Total RNA samples (150 ng) were reverse transcribed into double-stranded cDNA and then in vitro transcribed in the presence of biotin-labeled nucleotides using the GeneChip 3′ IVT Express kit (Affymetrix; 901229) including poly(A) controls as recommended by the manufacturer. The quality and quantity of the biotinylated cRNA were determined using NanoDrop ND 1000 and Bioanalyzer 2100. Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35 min. at 94°C in fragmentation buffer (Affymetrix).

growth_protocol: Plants were grown on soil in short days at 22°C.

extract_protocol: RNA was extracted using the RNA Plant Mini kit, QIAGEN  from leaves and apices.

treatment_protocol: Plants were collected either after two weeks growing in short days or transfered to two days to long days. All genotypes were collected at ZT8.

tag: developmental stage

value: 2 weeks old short days

tag: treatment

value: additional 2 long days

tag: tissue

value: Leaf

tag: cultivar

value: Columbia


title: pmf 2 day 0

description: primary myelofibrosis D0

source_name: cells before osteoblastic differentiation from patient with primary myelofibrosis


title: pmf 4 day 21

description: primary myelofibrosis D21


title: pmf 1 day 0

description: primary myelofibrosis D0


title: control 5 day 21

description: no disease D21


title: control 4 day 21

description: no disease D21


title: pmf 4 day 0

description: primary myelofibrosis D0


title: control 1 day 0

description: no disease D0


title: control 4 day 0

description: no disease D0


title: control 6 day 21

description: no disease D21


title: control 2 day 0

description: no disease D0


title: pmf 3 day 0

description: primary myelofibrosis D0


title: pmf 2 day 21

description: primary myelofibrosis D21


title: control 2 day 21

description: no disease D21


title: 3flc/SVP._SD._Leaf.r3

source_name: flc-/SVP+ 2 weeks Short Days - ZT8-Leaf

value: additional 2 short days


title: pmf 1

description: primary myelofibrosis

data_processing: standard Agilent Feature Extraction normalization

source_name: bone marrow mesenchymal stromal cell from patient with primary myelofibrosis

growth_protocol: Mononuclear cells from human bone marrow were separate were separate by Ficoll and cultivated in medium alphaMEM with 10% of FCS

treatment_protocol: After adhesion cells were amplified during 3 passages in alphaMEM with 10% of FCS. Between each passage cells were trypsinated

tag: disease state

value: bone marrow mesenchymal stromal cell


title: pmf 3

description: primary myelofibrosis


title: H295R_GRα, RU486 treated, biological rep C

city: Sydney

first: Roderick

last: Clifton-Bligh

state: NSW

address: Westbourne St St Leonards

department: Cancer Genetics

country: Australia

institute: Kolling Institute of Medical Research, University of Sydney

hyb_protocol: Following fragmentation, cDNA was hybridized to the probe array for 17 hr at 45C. Immediately following hybridization, the array underwent an automated washing and staining protocol (FS450_007) using the GeneChip Wash and Stain Kit on the Fluidics Station 450.

scan_protocol: The probe array was scanned with the GeneChip Scanner 3000 7G to produce CEL data files.

data_processing: Raw intensities from each microarray were background corrected, normalized and summarized using the robust multiarray averaging (RMA) algorithm implemented in the Bioconductor software package aroma.affymetrix. Differential expression was assessed using linear modeling and empirical Bayes moderated t-statistics (Limma). An additive AMOVA model was fitted for each probeset with drug treatment and cell type as the two explanatory factors.  Probes were selected as being differentially expressed when the false discovery rate adjusted P value was <0.05.

source_name: H295R_GRα cells, RU486 100 nM treated for 6 h

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using random hexamers according to the Affymetrix protocol

growth_protocol: H295R cells (ATCC, #CRL-2128) were grown in DMEM/F12 supplemented with 1% ITS+ Premix, 5% fetal calf serum, 100 IU/mL penicillin,  100 µg/mL streptomycin, 75 µg/mL Zeocin in a 5% CO2 humidified incubator at 37oC

extract_protocol: Cells were rinsed with filtered PBS then extracted with Tri-Reagent according to manufacturer's instructions.

treatment_protocol: Once 70% confluent, cells were serum-starved for 24 hours then triplicate samples were treated for 6 hours with dexamethasone 100 nM, RU486 100 nM or solvent vehicle (ethanol) control.

tag: atcc catalog number

tag: cell line

tag: stable over-expression status

value: stably overexpressing pcDNA4_GRα, non inducible


title: control 1 day 21

description: no disease D21


title: control 5 day 0

description: no disease D0


title: pmf 2

description: primary myelofibrosis


title: pmf 6

description: primary myelofibrosis


title: H295R_GRα, RU486 treated, biological rep A

description: There are no processed data for this sample as the raw data did not pass quality control measures.


title: pmf 3 day 21

description: primary myelofibrosis D21


title: pmf 4

description: primary myelofibrosis


title: pmf 5

description: primary myelofibrosis


title: H295R_GRα, RU486 treated, biological rep B


title: control 5

description: no disease

source_name: bone marrow mesenchymal stromal cell from healthy donor


title: H295R_GRα, dexamethasone treated, biological rep C

source_name: H295R_GRα cells, dexamethasone 100 nM treated for 6 h

value: Dexamethasone 100 nM, 6 h


title: H295R_GRα, vehicle treated, biological rep A

source_name: H295R_GRα cells, vehicle (ethanol) treated for 6 h

value: Vehicle (ethanol) control, 6 h


title: control 1

description: no disease


title: H295R_GRα, dexamethasone treated, biological rep B


title: control 3

description: no disease


title: H295R_GRα, dexamethasone treated, biological rep A


title: Peripheral rep3

city: Chiba

first: Yukie

last: Yoshii

address: Anagawa 4-9-1, Inage

country: Japan

institute: National Institute of Radiological Sciences

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp 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.

growth_protocol: Cells were incubated in a humidified atmosphere of 5% CO2 in air at 37°C. DMEM medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum and antibiotics was used for growth medium. Exponentially growing cells were used for the experiments. Cells were trypsinized, and the number of viable cells was counted by the trypan blue dye-exclusion method.

extract_protocol: Total RNAs were extracted from samples with a PureLink RNA Mini Kit (Life Technologies).

treatment_protocol: HT-29 cells suspended in phosphate-buffered saline (PBS) (at 1 x 10^7) were subcutaneously injected into the flank of the BALB/c nude mouse. Central and peropheral regions were obtained from the xenograft tumors.

tag: tissue type

value: Xenograft tumor


title: H295R_Control, dexamethasone treated, biological rep C

source_name: H295R_Control (empty vector) cells, dexamethasone 100 nM treated for 6 h

value: stably overexpressing pcDNA4_empty vector, non inducible


title: control 2

description: no disease


title: Peripheral rep2

source_name: Peripheral rep2


title: H295R_Control, dexamethasone treated, biological rep B


title: H295R_Control, RU486 treated, biological rep C

source_name: H295R_Control (empty vector) cells, RU486 100 nM treated for 6 h


title: Aorta_DHA7_CK_C61cy5_K93cy3

city: Saint-Genès-Champanelle

first: Cécile

last: Gladine

address: Centra INRA de Clermont-Ferrand/Theix

department: Human Nutrition

institute: INRA

description: Whole aorta (from aortic root to iliac separation) was used for the RNA extraction

hyb_protocol: The fluorescently labelled cRNAs were hybridized using the Agilent gene expression hybridization kit (5188-5242, Agilent technologies, Wilmington, DE, USA). Briefly, 825 ng cyanine 3-labelled, linearly amplified cRNA were mixed with 825 ng cyanine 5-labelled, linearly amplified cRNA. The mix was loaded onto the Agilent's Mouse GE 4x44K v2 Microarrays (Agilent Microarray Design ID 026655) following a reference design. Hybridization proceeded in a hybridization oven set to 65°C for 17 h. Then, the slides were washed in solutions I, II and III (Agilent technologies, Wilmington, DE, USA) and air-dried.

scan_protocol: Slides were scanned immediately after washing using the Agilent Microarray Scanner (G2505 B, Agilent technologies, Wilmington, DE, USA) and spot identification and quantification were performed using Agilent Feature Extraction Software 10.7 (Agilent technologies, Wilmington, DE, USA).

data_processing: probe replicates were averaged. Therefore, each probe ID is unique

organism: Mus musculus

source_name: DHA (C)

label_protocol: Extracted RNA was then amplified and labeled using the Agilent Low Input QuickAmp labeling kit (5190-2306, Agilent technologies, Wilmington, DE, USA) according to the manufacturer’s instructions. Purity and fluorescent intensity of the amplified and labeled cRNA was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA): all samples had a yield of 825 ng cRNA and a specific activity of 8.0 pmol Cy3 or Cy5 per mg cRNA.

extract_protocol: The entire aorta (i.e. thoracic and abdominal sections) was used for RNA extraction. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Purity and yield of RNA was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Aorta were collected after 20 weeks of dietary intervention and immediatly frozen into liquid nitrogen

tag: gender

value: male

tag: genotype

value: LDLR-/-

value: aorta

tag: age

value: 28 weeks

tag: strain

source_name: Control (K)


title: H295R_Control, vehicle treated, biological rep A

source_name: H295R_Control (empty vector) cells, vehicle (ethanol) treated for 6 h


title: control 6

description: no disease

value: no disease


title: H295R_Control, RU486 treated, biological rep B


title: control 4

description: no disease


title: H295R_Control, vehicle treated, biological rep C


title: H295R_GRα, vehicle treated, biological rep C


title: Aorta_DHA5_CK_C22cy3_K93cy5


title: Aorta_DHA8_CK_C86cy5_K25cy3


title: H295R_Control, dexamethasone treated, biological rep A


title: Aorta_DHA4_CK_C129cy3_K111cy5


title: H295R_Control, vehicle treated, biological rep B


title: Aorta_DHA3_CK_C124cy5_K89cy3


title: Aorta_DHA6_CK_C29cy5_K109cy3


title: H295R_GRα, vehicle treated, biological rep B


title: H295R_Control, RU486 treated, biological rep A


title: Peripheral rep1

source_name: Peripheral rep1


title: PA14 wild-type LB OD600=1.5, 30 min 80 mM H2O2

status: Public on Jan 09 2015

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

description: Gene expression data for PA14 wild-type with H2O2.

hyb_protocol: Following affymetrix protocol.  Prepared hybridization cocktail for Single Probe Array (100 midi Format) with total 130 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA.  After loading of hybridization cocktail in Affymetrix P. aeruginosa Genome Array, the hybridization was performed at 50°C, with 60 rpm for 16 hours.  After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

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

data_processing: Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS).

organism: Pseudomonas aeruginosa

source_name: PA14 wild-type with H2O2

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

growth_protocol: Strains were grown in LB at 37°C with shaking at 250 rpm.  16 h overnight cultures were diluted at 1:100 into fresh LB, grown to OD600=1.5, and exposed to 80 mM H2O2 for 30 min at 37°C without shaking (for +H2O2 samples).

extract_protocol: Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104).

treatment_protocol: Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice.

value: wild type


title: PA14 lasR rhlR LB OD600=1.5, 30 min 80 mM H2O2

description: Gene expression data for PA14 lasR rhlR with H2O2.

source_name: PA14 lasR rhlR with H2O2

value: lasR rhlR


title: Central_rep2


title: Aorta_DHA2_CK_C108cy5_K25cy3


title: Central_rep1


title: Central_rep3


title: PA14 wild-type LB OD600=1.5

description: Gene expression data for PA14 wild-type without H2O2.

source_name: PA14 wild-type without H2O2


title: PA14 lasR rhlR LB OD600=1.5

description: Gene expression data for PA14 lasR rhlR without H2O2.

source_name: PA14 lasR rhlR without H2O2


title: DBA/2J d3 10^4 HK213 #3 [set 2]

city: St Louis

first: Adrianus

middle: Cornelis Maria

last: Boon

state: Missouri

address: 660 Euclid Avenue

department: Department of Medicine

institute: Washington University School of Medicine

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
DBA_H5N1day3_3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: details unavailable

label_protocol: Standard Illumina label protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The extracted RNA was subjected to a RNA clean-up protocol (Qiagen) according to manufacturer's instructions.

treatment_protocol: Inoculated with 10000 Egg infectious units of A/Hong Kong/213/2003 H5N1 influenza A virus for 72 hours. Uninfected control animals were included.

value: female

value: 6-8 weeks

tag: infected with

value: Highly Pathogenic H5N1 influenza A virus infected

value: whole lung homogenate


title: 129/SvImJ  d3 10^4 HK213 #2 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
129SV_H5N1day3_2


title: C57BL/6J d3 10^4 HK213 #3 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
C57_H5N1day3_3


title: SM/J d3 10^4 HK213 #3 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
SMJ_H5N1day3_3

value: SM/J


title: C57BL/6J d3 10^4 HK213 #2 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
C57_H5N1day3_2


title: 129/SvImJ  d3 10^4 HK213 #3 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
129SV_H5N1day3_3


title: DBA/2J d3 10^4 HK213 #1 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
DBA_H5N1day3_1


title: SM/J d3 10^4 HK213 #1 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
SMJ_H5N1day3_1


title: DBA/2J d3 10^4 HK213 #2 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
DBA_H5N1day3_2


title: Aorta_DHA1_CK_C106cy3_K25cy5


title: Balb/cJ d3 10^4 HK213 #3 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
BalbCJ_H5N1day3_3

source_name: Balb/cJ d3 10^4 HK213

value: Balb/cJ


title: 129/SvImJ d3 10^4 HK213 #1 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
129SV_H5N1day3_1


title: Balb/cJ d3 10^4 HK213 #2 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
BalbCJ_H5N1day3_2


title: A/J d3 10^4 HK213 #3 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
AJ_H5N1day3_3

value: A/J


title: SM/J uninfected #2 [set 2]

description:
Gene expression data from lungs of unfected mice
SMJ_day0_2

source_name: SM/J uninfected

value: none (uninfected)


title: C57BL/6J d3 10^4 HK213 #1 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
C57_H5N1day3_1


title: SM/J uninfected #3 [set 2]

description:
Gene expression data from lungs of unfected mice
SMJ_day0_3


title: Balb/cJ d3 10^4 HK213 #1 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
BalbCJ_H5N1day3_1


title: SM/J d3 10^4 HK213 #2 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
SMJ_H5N1day3_2


title: SM/J uninfected #1 [set 2]

description:
Gene expression data from lungs of unfected mice
SMJ_day0_1


title: DBA/2J uninfected #2 [set 2]

description:
Gene expression data from lungs of unfected mice
DBA_day0_2

source_name: DBA/2J uninfected


title: A/J d3 10^4 HK213 #1 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
AJ_H5N1day3_1


title: 129/SvImJ uninfected #3 [set 2]

description:
Gene expression data from lungs of unfected mice
129SV_day0_3

source_name: 129/SvImJ uninfected


title: A/J d3 10^4 HK213 #2 [set 2]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
AJ_H5N1day3_2


title: C57BL/6J uninfected #1 [set 2]

description:
Gene expression data from lungs of unfected mice
C57_day0_1

source_name: C57BL/6J uninfected


title: C57BL/6J uninfected #3 [set 2]

description:
Gene expression data from lungs of unfected mice
C57_day0_3


title: A/J uninfected #1 [set 2]

description:
Gene expression data from lungs of unfected mice
AJ_day0_1

source_name: A/J uninfected


title: 129/SvImJ uninfected #1 [set 2]

description:
Gene expression data from lungs of unfected mice
129SV_day0_1


title: C57BL/6J uninfected #2 [set 2]

description:
Gene expression data from lungs of unfected mice
C57_day0_2


title: A/J uninfected #2  [set 2]

description:
Gene expression data from lungs of unfected mice
AJ_day0_2


title: A/J uninfected #3 [set 2]

description:
Gene expression data from lungs of unfected mice
AJ_day0_3


title: SM/J uninfected #1 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185027_JB_258_A

treatment_protocol: Inoculated with 10000 Egg infectious units of A/Hong Kong/213/2003 H5N1 influenza A virus for 72 hours

value: none (uninfected contol)


title: SM/J uninfected #2 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185027_JB_259_B


title: 129/SvImJ uninfected #2 [set 2]

description:
Gene expression data from lungs of unfected mice
129SV_day0_2


title: Balb/cJ uninfected #1 [set 2]

description:
Gene expression data from lungs of unfected mice
BalbCJ_day0_1

source_name: Balb/cJ uninfected


title: Balb/cJ uninfected #3 [set 2]

description:
Gene expression data from lungs of unfected mice
BalbCJ_day0_3


title: SM/J d7 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185030_JB_269_F

value: Highly Pathogenic H5N1 influenza A virus


title: DBA/2J uninfected #1 [set 2]

description:
Gene expression data from lungs of unfected mice
DBA_day0_1


title: SM/J uninfected #3 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185027_JB_260_C


title: Balb/cJ uninfected #2 [set 2]

description:
Gene expression data from lungs of unfected mice
BalbCJ_day0_2


title: SM/J d7 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185030_JB_268_E


title: SM/J d1 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185027_JB_263_F


title: SM/J d7 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185030_JB_266_C


title: SM/J d7 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185030_JB_267_D


title: SM/J d1 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185030_JB_265_B


title: DBA/2J uninfected #8 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185029_JB_37_C


title: SM/J d1 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185030_JB_264_A


title: DBA/2J uninfected #10 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185029_JB_39_B


title: SM/J d1 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185027_JB_262_E


title: DBA/2J d7 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185021_JB_41_F


title: SM/J uninfected #4 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185027_JB_261_D


title: DBA/2J d7 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185029_JB_43_F


title: DBA/2J uninfected #9 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185029_JB_38_A


title: DBA/2J d7 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185029_JB_42_E


title: C57BL/6 uninfected #11 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185016_JB_50_D

source_name: C57BL/6 uninfected


title: C57BL/6 d7 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185021_JB_231_A


title: LG/J-5R-2

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

description: Tissue lysate containing RNA and microRNA

hyb_protocol: The quantification of mRNAs using the Affymetrix QuantiGene 2.0 Plex Assay kit.  An appropriate volume of working bead mix was prepared scaled for 96-well plate format: 18.5 uL nuclease-free water, 33.3 uL lysis mixture, 2 uL blocking reagent, 0.2 uL proteinase K, 1 uL capture beads and 5 uL probe set.  The working bead mix was vortexed for 10 sec and 60 uL of it was dispensed into each well of the hybridization plate followed by addition of 40 uL of tissue homogenate to each well.  The plate was sealed using a pressure seal and placed on an inverted plate lid placed onto the VorTemp 56 shaking incubator and incubated for 18-22 h at 54oC at 600 rpm.  Post-incubation, the contents of the hybridization plate were transferred to a magnetic separation plate after centrifugation at 240X g for 60 sec and mixing the contents a few times with a pipette.  The magnetic separation plate was inserted into the hand-held magnetic plate washer and washed the plate three times using 100 uL of wash buffer per well.  Then 100 uL of pre-amplifier working reagent (36 uL of 2.0 pre-amplifier in 12 mL of amplifier diluent) was dispensed into each well of the magnetic separation plate, sealed and incubated at 50C for 1 h while shaking at 600 rpm.  After incubation, the plate was washed as above and 100 uL of amplifier working reagent per well and again incubated at 50C for 60 min at 600 rpm.  Then the plate was washed again and 100 uL of label probe working reagent was added to each well and the sealed plate was placed into VorTemp and incubated at 50C for 60 min at 600 shaking rpm.  After 60 min, the washing procedure was repeated as above, 100 uL of SAPE working reagent  was pipetted into each well.  The plate was foiled, removed from plate washer and placed on a shaking platform at room temperature with shaking at 800 rpm for 60 sec followed by shaking at 600 rpm for 30 min.  The plate was washed with 130 uL of SAPE wash buffer in each assay well, sealed the plate, removed from plate washer, wrapped in aluminum foil and allowed to shake at 800 rpm for 3 min at room temperature.

scan_protocol: Finally, the plate was read on Luminex set for specified bead regions with the following parameters: 100 uL sample size, 5,000–25,000 DD gate, 45 sec time out and 100 bead events per bead region.

data_processing: The average signal values were noted and subtracted from the background signal and finally normalized with a housekeeping gene by dividing the average signal value of the target gene with the average signal value of the reference gene.

label: Streptavidin phycoerythrin

source_name: Right knee joint

growth_protocol: Knee joint sections were taken from mice which underwent full-thicknees articular cartilage repair at 8 weeks old. They were raised on normal diet and standard procedures.

treatment_protocol: Samples were from mice with different genetic background with varying degree of healing capacity.

value: LG/J (Large/Jackson)

tag: phenotype

value: Healer

tag: sample type

tag: mouse#

tag: knee (side)

value: Right

tag: technical replicate


title: DBA/2J d1 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185021_JB_36_B

tag: tissue


title: LG/J-5L-1

source_name: Left knee joint

value: Left


title: DBA/2J d1 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185021_JB_33_E


title: LG/J-5L-2


title: C57BL/6 d7 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185016_JB_53_B


title: Balb/c uninfected #1 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185018_JB_270_A

source_name: Balb/c uninfected

value: Balb/c


title: C57BL/6 uninfected #9 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185016_JB_48_C


title: C57BL/6 d1 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185028_JB_46_E


title: DBA/2J d7 10^4 HK213 #5 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185029_JB_44_D


title: C57BL/6 d7 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185028_JB_52_A


title: C57BL/6 d1 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185016_JB_47_F


title: Balb/c uninfected #3 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185018_JB_272_C


title: Balb/c uninfected #2 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185018_JB_271_B


title: C57BL/6 d7 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185016_JB_51_A


title: Balb/c uninfected #4 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185018_JB_273_D


title: C57BL/6 uninfected #10 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185016_JB_49_E


title: DBA/2J d1 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185021_JB_34_D


title: DBA/2J d1 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185021_JB_35_C


title: LG/J-4L-2

description: Tissue lysate containing RNA and microRNA


title: Balb/c d7 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185025_JB_281_F


title: LG/J-4L-1


title: C57BL/6 d1 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185028_JB_45_C


title: LG/J-5R-1


title: Balb/c d7 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185025_JB_280_E


title: Balb/c d7 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185025_JB_278_C


title: Balb/c d7 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185025_JB_279_D


title: Balb/c d1 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185025_JB_277_B


title: LG/J-4R-2


title: LG/J-4R-1


title: LG/J-3R-2


title: LG/J-2L-1


title: LG/J-3L-1


title: LG/J-3R-1


title: LG/J-2L-2


title: LG/J-2R-2


title: LG/J-2R-1


title: LG/J-3L-2


title: LG/J-1L-2


title: Balb/c d1 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185018_JB_274_E


title: A/J uninfected #4 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185003_JB_285_D


title: Balb/c d1 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185025_JB_276_A


title: A/J uninfected #2  [set 1]

description:
Gene expression data from lungs of unfected mice
4117185003_JB_283_B


title: LG/J-1R-1


title: A/J d7 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185017_JB_293_F


title: A/J d7 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185017_JB_292_E


title: A/J d7 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185017_JB_290_C


title: LG/J-1L-1


title: Balb/c d1 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185018_JB_275_F


title: HuH7.rep2

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Labelled cDNA was purified with RNeasy MinElute Cleanup Kit Cat.# 74204 (Izasa/Qiagen). Labeled cDNA was hybridized to SurePrint G3 Human GE 8x60 Agilent® Microarray chip (ID: G4858A-028004).using Gene Expression Hybridization Kit Cat. # 5188-5242).

scan_protocol: Microarray Scanner Agilent G2505X class C

data_processing: The data were normalized with Bioconductor software using quantiles.

label_protocol: For future sample normalization, RNA was treated with One-Color RNA Spike-In Kit cat. # 5188-5282 (Agilent). 200ng of RNA were used for cDNA preparation with Low Input Quick Amp Labeling Kit, one-color Cat. # 5190-2305, Agilent®. Sample labelling with dye3 (cy3) fluorofor was made with previous cited kit. Labelled cDNA was purified with RNeasy MinElute Cleanup Kit Cat.# 74204 (Izasa/Qiagen).

growth_protocol: HuH7 cells were incubated at 37 degress in 5% CO2 environment with DMEM media plus antibiotics and 10% FCS

extract_protocol: RNA was isolated with TRIZOL (SIGMA)

treatment_protocol: HuH7 cells were treated with 10000 units/ml of IFN a2 and RNA was isolated 3 days post-treatment

tag: cell type

value: Human liver (hepato cellular carcinoma) cells

tag: treated with

value: none (control)

tag: time point

value: 3 days post-treatment


title: A/J uninfected #3 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185003_JB_284_C

value: female

value: 6-8 weeks


title: HuH7·IFN.rep3

tag: cell line

value: 10000 units/ml of IFN


title: A/J d1 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185017_JB_289_B

value: whole lung homogenate


title: A/J d7 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185017_JB_291_D


title: A/J d1 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185003_JB_287_F


title: A/J uninfected #1 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185003_JB_282_A


title: HuH7·IFN.rep2


title: HuH7·IFN.rep1


title: A/J d1 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185017_JB_288_A


title: HuH7.rep3


title: SM/J-5L-2

description: Tissue lysate containing RNA and microRNA

value: SM/J (Small/Jackson)

value: Non-healer


title: SM/J-5R-2


title: LG/J-1R-2


title: SM/J-5L-1


title: SM/J-5R-1


title: SM/J-4R-2


title: SM/J-4R-1


title: SM/J-3L-2


title: SM/J-4L-1


title: SM/J-4L-2


title: A/J d1 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185003_JB_286_E

value: A/J


title: SM/J-3L-1


title: 129/SvImJ uninfected #4 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185020_JB_297_C

value: none (uninfected contol)


title: 129/SvImJ uninfected #1 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185020_JB_294_F


title: 129/SvImJ d7 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185019_JB_303_C

value: Highly Pathogenic H5N1 influenza A virus


title: 129/SvImJ uninfected #3 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185020_JB_296_D


title: 129/SvImJ d1 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185020_JB_298_B


title: 129/SvImJ uninfected #2 [set 1]

description:
Gene expression data from lungs of unfected mice
4117185020_JB_295_E


title: SM/J-3R-1


title: 129/SvImJ d1 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185019_JB_301_E


title: 129/SvImJ d7 10^4 HK213 #1 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185019_JB_302_D


title: 129/SvImJ d1 10^4 HK213 #2 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185020_JB_299_A


title: 129/SvImJ d7 10^4 HK213 #4 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185019_JB_305_A


title: 129/SvImJ d1 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185019_JB_300_F


title: SM/J-2R-2


title: SM/J-1R-2


title: SM/J-1R-1


title: SM/J-2R-1


title: HuH7.rep1


title: SM/J-3R-2


title: SM/J-1L-2


title: SM/J-1L-1


title: S12ΔtrgI_30_b

city: Leiden

first: Johannes

middle: H.

last: de Winde

address: Rapenburg 70

country: Netherlands

institute: Universiteit Leiden

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 30 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

hyb_protocol: Hybridisation was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara, California, USA).

scan_protocol: Scanning of the microarrays was carried out by ServiceXS (Leiden, The Netherlands) on a high resolution Gene Chip Scanner 3000 7G system with autoloader (Affymetrix) using standard default analysis settings (filter: 570 nm; pixel size: 2,5 μm).

data_processing: Microarray data were imported into the GeneSpring GX 7.3.1 software package (Agilent Technologies, Santa Clara, California, USA) using the GC RMA algorithm. Normalisation: signals below 0.01 were taken as 0.01; per chip: normalise to 50th percentile; per gene: normalise to median. After normalisation of the data, probesets representing control genes were removed, as well as absolute non-changing loci (between 0.667- and 1.334-fold change). The resulting set of 6164 differentially expressed loci was used for further investigation. The overall transcriptional activity change during toluene exposure was quantified by calculating the total number of differentially expressed genes for each time point after toluene addition, using the transcript levels at t = 0 as reference. Overrepresentation of specific groups of genes among the total response-groups was determined using the hyper-geometric test in the R statistical program environment. For example: if a group of genes selected for upregulation following toluene exposure, the chance that an x-number of genes of COG group A are in that group of upregulated genes is being assessed. Or, in other words, it can be assessed what the chance is that this group of upregulated genes contains 50% COG group A while all genes contains 30% COG group A.

organism: Pseudomonas putida S12

source_name: whole cells, 5 toluene, timepoint 30 min

label_protocol: Random priming, cDNA synthesis, purification and labelling were performed according to the microarray manufacturer’s instructions (Affymetrix, Santa Clara, California, USA).

growth_protocol: Cells were batch cultured in Luria broth. At an optical density at 600 nm of 0.5-0.6 (early exponential phase cultures), sampling was started.

extract_protocol: 1-ml culture samples were quenched in 1 ml ice-cold methanol, centrifuged and 1 ml RNAlater (Ambion, Foster City, California, USA) was applied to prevent RNA degradation. Pellets were flash frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using the RNeasy Mini Purification Kit (Qiagen, Hilden, Germany). mRNA was isolated using the MICROBExpress Bacterial mRNA Purification Kit (Ambion).

treatment_protocol: At time point 0, the first sample was drawn. Immediately thereafter, 5 mM toluene was added and sampling was continued at time point 1 minute, then 2, 5, 10, and 30 minutes.

tag: toluene concentration (mm)

tag: time point of sampling (minutes)


title: KYSE30-OE-Epist-R3

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7

data_processing: The microarray data were quantile normalized using the R limma package. The fold change and two-tailed Student’s t test were applied for statistical analysis of differentially expressed genes. Heatmap and Scatterplot were drawn with the functions in R

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

growth_protocol: KYSE30 cells were maintained in RPMI 1640 (Life Technology) supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000.

treatment_protocol: The Epist sequence was cloned into the lentivector pCDH-MSCV-MCS-EF1-GFP+Puro cDNA Cloning and Expression Vector (SBI CD713B-1). 293T cells were cultured in T-175 flasks at 40%~50% confluence before transfection. Transfection was performed using Lipofectamine 2000 (Life Technologies). For each flask, 20.25 μg of lentivectors, 13.2 μg of pMDL-g/p, 5.1 μg of RSV-REV and 7.125 μg of VSVG were added to 4 ml OptiMEM (Life Technologies). 100 μl of Lipofectamine 2000 was diluted in 4 ml OptiMEM and it was added to the plasmid mixture after 5 min. The complete mixture was incubated at room temperature for 20 min before being added to cells. After 6 h, the medium was changed to 30 ml DMEM + 20% FBS. The medium was collected at 48 h and 72 h and centrifuged at 3,000 rpm at 4 °C for 10 min to pellet the cell debris. The supernatant was filtered through a 0.45 μm low protein binding membrane. The virus was ultracentrifuged at 20000 g for 2 h at 4°C and then resuspended overnight at 4°C in PBS. Aliquots were stored at -80°C.

value: Esophageal Squamous Cell Carcinoma

tag: treatment

value: Epist overexpression


title: KYSE30-OE-Epist-R1


title: KYSE30-OE-control-R3

value: control


title: KYSE30-OE-Epist-R2


title: 129/SvImJ d7 10^4 HK213 #3 [set 1]

description:
Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice
4117185019_JB_304_B

tag: gender


title: S12ΔtrgI_30_a

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 30 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12ΔtrgI_10_b

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 10 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

source_name: whole cells, 5 toluene, timepoint 10 min


title: S12ΔtrgI_5_a

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 5 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

source_name: whole cells, 5 toluene, timepoint 5 min


title: KYSE30-OE-control-R1


title: S12ΔtrgI_10_a

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 10 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: Basal,shROR2 Sample 1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The BCM GARP Core performed hybridizations of the labeled product to Agilent Sure Print 3 Mouse GE 8x60K microarrays.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner.

data_processing: Arrays were processed using bioconductor (quantile normalized).

source_name: Basal

label_protocol: RNA was subsequently amplified from biological triplicates using NuGEN Ovation Pico WTA V2 kit (cat# 3302-12) and Cy3-labeled using the Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.5.

growth_protocol: Primary mammary epithelial cells were isolated as previously described (Shore et al. 2012, PMID: 22911650).  The resultant epithelial organoid preparation was subjected to 0.25% trypsin at 37oC for 5 min, washed, and filtered through a 0.4um cell strainer to obtain single mammary epithelial cells.  Single cells were washed 2 times with 1x PBS prior to lentiviral transduction, RNA isolation, or FACS staining.

extract_protocol: RNA from sorted shLUC and shRor2 samples was isolated using the Arcturus PicoPure Kit (KIT0204) from Applied Biosystems. The BCM Genomic and RNA Profiling Core (GARP) performed sample quality checks using the Nanodrop ND-1000 and Agilent Bioanalyzer Nano chip.

treatment_protocol: Single mammary epithelial cells were seeded at a density of 500,000 to 1,000,000 cells in a 24-well low attachment plate and infected at a MOI-30 with designated lentiviruses in 800ul of growth media.  Cells were infected overnight for approximately 16 hrs.  The following day, aggregated cells were washed three times with PBS and resuspended in a 1:1 ratio of growth factor reduced matrigel:HBSS at 100,000 cells per 10ul injection volume.

value: basal

tag: outgrowth


title: KYSE30-OE-control-R2


title: S12ΔtrgI_5_b

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 5 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

tag: strain


title: 14% Stretch 3

city: Seattle

first: Vishal

last: Nigam

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: Seattle Childrens Research Institute

hyb_protocol: Following fragmentation cDNA was hybridized to Affymetrix Human Gene 1.0 gene chips for 16 h at 45 degrees in Affymetrix oven

scan_protocol: Scanned on Affymetrix 7G scanner

data_processing:
The exon expression data were analyzed using Genespring GX 12.5.  Summarization was performed using the RMA16 algorithm and baseline transformed to the median of all samples.
# Technology : Affymetrix.ExonExprChip.HuGene-1_0-st-v1_na31_hg19_2010-09-03

source_name: AVICs, 14% Stretch

label_protocol: 3 IVT Express Kit was used

growth_protocol: Human aortic valve interstitial cells (AVICs) were cultured from failed organ donors under an IRB exempt protocol using methods previously described (Jianb  et al Ann Thorac Surg 2003, Osaman L et al Circulation 2006, and Nigam et al J Heart Valve Disease 2010).

extract_protocol: RNAeasy columns (Qiagen) were used to isolate RNA

treatment_protocol: AVICs were cultured on collagen 1 coated Bioflex plates (Flexcell International) and exposed to 14% cyclic stretch at 1 hz or static conditions for 24h.

value: aortic valve interstitial cells


title: S12ΔtrgI_2_b

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 2 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

source_name: whole cells, 5 toluene, timepoint 2 min


title: Basal,shROR2 Sample 3


title: Basal,shROR2 Sample 2


title: 14% Stretch 1


title: Basal,shLUC Sample 2

value: shLUC


title: S12ΔtrgI_2_a

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 2 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: 14% Stretch 2


title: Static 2

source_name: AVICs, Static


title: Basal,shLUC Sample 1


title: Basal,shLUC Sample 3


title: Static 3


title: Static 1


title: S12ΔtrgI_1_a

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 1 minute_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

source_name: whole cells, 5 toluene, timepoint 1 min


title: S12ΔtrgI_0_b

description:
Pseudomonas putida S12ΔtrgI_0 mM toluene_timepoint 0 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.

source_name: whole cells, 0 toluene, timepoint 0


title: S12ΔtrgI_1_b

description:
Pseudomonas putida S12ΔtrgI_5 mM toluene_timepoint 1 minute_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: Luminal,shROR2 Sample 2

source_name: Luminal

value: luminal


title: Luminal,shROR2 Sample 1


title: Luminal,shLUC Sample 2


title: S12_30_b

description:
Pseudomonas putida S12_5 mM toluene_timepoint 30 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12_30_a

description:
Pseudomonas putida S12_5 mM toluene_timepoint 30 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12ΔtrgI_0_a

description:
Pseudomonas putida S12ΔtrgI_0 mM toluene_timepoint 0 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: Luminal,shLUC Sample 1


title: Luminal,shLUC Sample 3


title: S12_10_b

description:
Pseudomonas putida S12_5 mM toluene_timepoint 10 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: LSK/Flt3+

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy array were used

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package (v.1.23) was used for RMA normalization and raw data processing using default settings for background correction and normalization. All analyses were performed using R software.

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the PerfectPure RNA extraction kit from 5 Prime

tag: strain background

tag: genotype/variation

value: wild type

value: bone marrow cells

tag: cell fraction


title: S12_5_a

description:
Pseudomonas putida S12_5 mM toluene_timepoint 5 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12_10_a

description:
Pseudomonas putida S12_5 mM toluene_timepoint 10 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12_5_b

description:
Pseudomonas putida S12_5 mM toluene_timepoint 5 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12_2_b

description:
Pseudomonas putida S12_5 mM toluene_timepoint 2 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: Hdac3 null LSK/Flt3- Sample 2

source_name: Hdac3 null LSK/Flt3-

value: Hdac3 null LSK/Flt3-


title: Hdac3 null LSK/Flt3- Sample 1


title: BW25113 ΔmqsRA HEPES-glu 30 min 4.5% deoxycholate

description: Gene expression data for BW25113 ΔmqsRA with deoxycholate stress.

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

organism: Escherichia coli BW25113

source_name: BW25113 ΔmqsRA with deoxycholate stress

growth_protocol: Strains were grown in LB at 37°C with shaking at 250 rpm.  16 h overnight cultures were diluted to OD600 = 0.05 in HEPES-glucose (0.4%), grown to OD600 ~ 0.6, and exposed to 4.5% deoxycholate for 30 min.

value: ΔmqsRA


title: S12_2_a

description:
Pseudomonas putida S12_5 mM toluene_timepoint 2 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: LSK/Flt3-


title: S12_1_b

description:
Pseudomonas putida S12_5 mM toluene_timepoint 1 minute_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: BW25113 HEPES-glu 30 min 4.5% deoxycholate

description: Gene expression data for BW25113 with deoxycholate stress.

source_name: BW25113 with deoxycholate stress

value: WT


title: S12_1_a

description:
Pseudomonas putida S12_5 mM toluene_timepoint 1 minute_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: S12_0_b

description:
Pseudomonas putida S12_0 mM toluene_timepoint 0 minutes_b
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: Prefrontal Cortex 21 input, methyl-depleted

type: genomic

city: Baltimore

first: Jerry

last: Guintivano

state: MD

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

description: DNA methylation data from human brain

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software and the charm bioconductor package v1.0.1 using a) quantile and b) subset-quantile normalization. Percent methylation calculated.

molecule: genomic DNA

source_name: Input fraction from PFC21

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

growth_protocol: genomic DNA was isolated from frozen tissue, i.e not grown in culture

extract_protocol: DNA was extracted from tissues using the MasterPure DNA Purification kit (Epicentre Biotechnologies) and 10 µg of DNA were sheared using a Hydroshear device (Digilab, Holliston, MA) into 1.6 kb-3 kb fragments. Sheared DNA was then divided into two fractions. One fraction was digested overnight at 37°C with the methyl-sensitive enzyme McrBC (NEB, Ipswich, MA). Following digestion, cut and uncut fractions from the same sample were electrophoresed in adjacent wells of a 1% agarose gel. Areas corresponding to the 1.6 kb-3 kb regions were excised and purified using Qiagen Spin Gel Purification columns (Qiagen, Germantown, MD). The gel-purified DNA was quantified on a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Rockford, IL) and 30 ng of DNA from each fraction was amplified using a GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO). The amplified DNA was then isolated with a Qiagen PCR Purification column, then quantified on NanoDrop.

treatment_protocol: no treatment

tag: sample type

value: Input fraction

value: prefrontal cortex

source_name: Methyl-depleted fraction from PFC21

value: Methyl-depleted fraction


title: Whole Hippocampus TBI+E33 drug rep1

status: Public on Jan 08 2015

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: miRNA expression of whole hippocampus 24hr post-injury

hyb_protocol: Labeled target was applied to Agilent miRNA 8x15K arrays (Design ID# 019159) and hybridized overnight.

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

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: Whole hippocampus, fluid percussion injury, E33 drug treatment, rep1

label_protocol: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Rats were subjected to experimental severe fluid percussion brain injury (with and without drug treatments), sham injury or were sacrificed with no treatment (naïve) and brains were removed 24 hours later, stored in RNA later and total RNA isolated at GenUs Biosystems. Drug treatments

value: Sprague-Dawley

value: hippocampus


title: Whole Hippocampus TBI+E33 drug rep2

source_name: Whole hippocampus, fluid percussion injury, E33 drug treatment, rep2


title: S12_0_a

description:
Pseudomonas putida S12_0 mM toluene_timepoint 0 minutes_a
0 toluene was present at timepoint 0. Immediately after that, 5 mM toluene was added and sampling was continued starting at timepoint 1 minute.


title: Prefrontal Cortex 19 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC19

source_name: Methyl-depleted fraction from PFC19


title: Whole Hippocampus TBI+JM6 drug rep2

source_name: Whole hippocampus, fluid percussion injury, JM6 drug treatment, rep2


title: Whole Hippocampus TBI+JM6 drug rep1

source_name: Whole hippocampus, fluid percussion injury, JM6 drug treatment, rep1


title: Whole Hippocampus Traumatic Brain Injury rep2

source_name: Whole hippocampus, fluid percussion injury, rep2


title: Whole Hippocampus TBI+PMI drug rep3

source_name: Whole hippocampus, fluid percussion injury, PMI drug treatment, rep3


title: Prefrontal Cortex 20 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC20

source_name: Methyl-depleted fraction from PFC20


title: Prefrontal Cortex 18 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC18

source_name: Methyl-depleted fraction from PFC18


title: Whole Hippocampus TBI+PMI drug rep2

source_name: Whole hippocampus, fluid percussion injury, PMI drug treatment, rep2


title: Whole Hippocampus TBI+PMI drug rep1

source_name: Whole hippocampus, fluid percussion injury, PMI drug treatment, rep1


title: Whole Hippocampus Naïve rep3

source_name: Whole hippocampus, no treatment, rep3


title: Whole Hippocampus Sham rep2

source_name: Whole hippocampus, Sham injury, rep2


title: Whole Hippocampus Traumatic Brain Injury rep1

source_name: Whole hippocampus, fluid percussion injury, rep1


title: Whole Hippocampus Traumatic Brain Injury rep3

source_name: Whole hippocampus, fluid percussion injury, rep3


title: Whole Hippocampus Sham rep1

source_name: Whole hippocampus, Sham injury, rep1


title: Prefrontal Cortex 15 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC15

source_name: Methyl-depleted fraction from PFC15


title: Whole Hippocampus Naïve rep2

source_name: Whole hippocampus, no treatment, rep2


title: Whole Hippocampus TBI+JM6 drug rep3

source_name: Whole hippocampus, fluid percussion injury, JM6 drug treatment, rep3


title: Prefrontal Cortex 13 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC13

source_name: Methyl-depleted fraction from PFC13


title: Prefrontal Cortex 12 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC12

source_name: Methyl-depleted fraction from PFC12


title: Prefrontal Cortex 22 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC22

source_name: Methyl-depleted fraction from PFC22


title: Normal myometrium [NL033]

city: New York

first: Douglas

last: Levine

state: NY

address: 1275 York Ave.

department: Surgery

institute: MSKCC

description: Gene expression data

hyb_protocol: All hybridizations were carried out at 45°C for 16–17 h.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 2500

data_processing: Microarray Analysis 5.0 software (Affymetrix) was used to normalize data to a target intensity of 500.

source_name: Normal myometrium

label_protocol: Beginning with total RNA the poly(A) RNA pool was specifically converted to cDNA and then amplified and labeled with biotin.

extract_protocol: Ambion mirVana miRNA Isolation Kit (Life Technologies, Grand Island, NY)

value: Female


title: Normal myometrium [NL031]

description: Gene expression data


title: Whole Hippocampus Naïve rep1

source_name: Whole hippocampus, no treatment, rep1


title: Normal myometrium [NL036]

description: Gene expression data


title: Prefrontal Cortex 11 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC11

source_name: Methyl-depleted fraction from PFC11


title: Normal myometrium [NL029]

description: Gene expression data


title: Normal myometrium [NL027]

description: Gene expression data


title: Normal myometrium [NL028]

description: Gene expression data


title: Prefrontal Cortex 16 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC16

source_name: Methyl-depleted fraction from PFC16


title: Normal myometrium [NL025]

description: Gene expression data


title: Normal myometrium [NL026]

description: Gene expression data


title: Normal myometrium [NL022]

description: Gene expression data


title: Normal myometrium [NL024]

description: Gene expression data


title: Prefrontal Cortex 8 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC8

extract_protocol: DNA was extracted from tissues using the MasterPure DNA Purification kit (Epicentre Biotechnologies) and 10 µg of DNA were sheared using a Hydroshear device (Digilab, Holliston, MA) into 1.6 kb-3 kb fragments.  Sheared DNA was then divided into two fractions.  One fraction was digested overnight at 37°C with the methyl-sensitive enzyme McrBC (NEB, Ipswich, MA).  Following digestion, cut and uncut fractions from the same sample were electrophoresed in adjacent wells of a 1% agarose gel.  Areas corresponding to the 1.6 kb-3 kb regions were excised and purified using Qiagen Spin Gel Purification columns (Qiagen, Germantown, MD).  The gel-purified DNA was quantified on a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Rockford, IL)  and 30 ng of DNA from each fraction was amplified using a GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO).  The amplified DNA was then isolated with a Qiagen PCR Purification column, then quantified on NanoDrop.

source_name: Methyl-depleted fraction from PFC8


title: Normal myometrium [NL023]

description: Gene expression data


title: Normal myometrium [NL035]

description: Gene expression data


title: Normal myometrium [NL021]

description: Gene expression data


title: Normal myometrium [NL019]

description: Gene expression data


title: Prefrontal Cortex 9 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC9

source_name: Methyl-depleted fraction from PFC9


title: Prefrontal Cortex 5 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC5

source_name: Methyl-depleted fraction from PFC5


title: Prefrontal Cortex 7 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC7

source_name: Methyl-depleted fraction from PFC7


title: Normal myometrium [NL012]

description: Gene expression data


title: Normal myometrium [NL013]

description: Gene expression data


title: Normal myometrium [NL015]

description: Gene expression data


title: Normal myometrium [NL030]

description: Gene expression data


title: Normal myometrium [NL011]

description: Gene expression data


title: Normal myometrium [NL018]

description: Gene expression data


title: Normal myometrium [NL006]

description: Gene expression data


title: Normal myometrium [NL009]

description: Gene expression data


title: Normal myometrium [NL007]

description: Gene expression data


title: Normal myometrium [NL005]

description: Gene expression data


title: Normal myometrium [NL010]

description: Gene expression data


title: Normal myometrium [NL003]

description: Gene expression data


title: Leiomyosarcoma [X76]

description: Gene expression data

source_name: Tumor


title: Prefrontal Cortex 6 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC6

source_name: Methyl-depleted fraction from PFC6


title: Prefrontal Cortex 14 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC14

source_name: Methyl-depleted fraction from PFC14


title: Normal myometrium [NL001]

description: Gene expression data

source_name: Normal myometrium


title: Prefrontal Cortex 4 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC4

source_name: Methyl-depleted fraction from PFC4


title: Normal myometrium [NL004]

description: Gene expression data


title: Normal myometrium [NL002]

description: Gene expression data


title: Leiomyosarcoma [X75]

description: Gene expression data


title: Prefrontal Cortex 10 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC10

source_name: Methyl-depleted fraction from PFC10


title: Prefrontal Cortex 17 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC17

source_name: Methyl-depleted fraction from PFC17


title: Leiomyosarcoma [X74]

description: Gene expression data


title: Leiomyosarcoma [X72]

description: Gene expression data


title: Prefrontal Cortex 1 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC1

source_name: Methyl-depleted fraction from PFC1


title: Prefrontal Cortex 2 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC2

source_name: Methyl-depleted fraction from PFC2


title: Leiomyosarcoma [X40]

description: Gene expression data


title: Leiomyosarcoma [TB6424]

description: Gene expression data


title: Leiomyosarcoma [X36]

description: Gene expression data


title: Leiomyosarcoma [JB1075]

description: Gene expression data


title: Leiomyosarcoma [JB2883]

description: Gene expression data


title: Leiomyosarcoma [JB804]

description: Gene expression data


title: Leiomyosarcoma [TB120946]

description: Gene expression data


title: Leiomyosarcoma [JB1541]

description: Gene expression data


title: Leiomyosarcoma [TB9004]

description: Gene expression data


title: Leiomyosarcoma [JB109]

description: Gene expression data


title: Fibroid [FBR036]

description: Gene expression data

source_name: Fibroid


title: Leiomyosarcoma [TB117247]

description: Gene expression data

source_name: Tumor


title: Leiomyosarcoma [X32]

description: Gene expression data


title: Leiomyosarcoma [JB2486]

description: Gene expression data


title: Leiomyosarcoma [JB1583]

description: Gene expression data


title: Leiomyosarcoma [JB72]

description: Gene expression data


title: Leiomyosarcoma [JB2124]

description: Gene expression data


title: Leiomyosarcoma [X71]

description: Gene expression data


title: Prefrontal Cortex 3 input, methyl-depleted

description: DNA methylation data from human brain

source_name: Input fraction from PFC3

source_name: Methyl-depleted fraction from PFC3


title: Fibroid [FBR031]

description: Gene expression data


title: Leiomyosarcoma [TB14004]

description: Gene expression data


title: Fibroid [FBR030]

description: Gene expression data


title: Leiomyosarcoma [JB2692]

description: Gene expression data


title: Leiomyosarcoma [X73]

description: Gene expression data


title: Fibroid [FBR034]

description: Gene expression data


title: Fibroid [FBR027]

description: Gene expression data


title: Fibroid [FBR028]

description: Gene expression data


title: Fibroid [FBR020]

description: Gene expression data


title: Fibroid [FBR021]

description: Gene expression data


title: Fibroid [FBR022]

description: Gene expression data


title: Fibroid [FBR013]

description: Gene expression data


title: Fibroid [FBR009]

description: Gene expression data


title: Fibroid [FBR025]

description: Gene expression data


title: Fibroid [FBR006]

description: Gene expression data


title: M93

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description: total RNA from relapsed glioma 2

hyb_protocol: Hybridization was performed according to Affymetrix protocol

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

data_processing: The data were analyzed with R package affy and rma normalized.

source_name: relapsed glioma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: The mutant EGFR driven glioma cells were subcutaneouly implanted to the flanks of Nu/Nu mice under normal animal housing condition.

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

treatment_protocol: The tumor bearimg mice were treated with or without doxcycline (2g/L in drinking water). The tumors were collected when they reached 2cm3

value: relapsed glioma


title: Fibroid [FBR019]

description: Gene expression data


title: Fibroid [FBR007]

description: Gene expression data


title: M92

description: total RNA from relapsed glioma 1


title: Fibroid [FBR005]

description: Gene expression data


title: Fibroid [FBR010]

description: Gene expression data


title: Fibroid [FBR008]

description: Gene expression data


title: Fibroid [FBR024]

description: Gene expression data


title: M96

description: total RNA from relapsed glioma 3


title: Fibroid [FBR011]

description: Gene expression data


title: M102L

description: total RNA from control glioma 2

source_name: control glioma

value: control glioma


title: Fibroid [FBR002]

description: Gene expression data


title: Fibroid [FBR015]

description: Gene expression data


title: Fibroid [FBR001]

description: Gene expression data


title: M100R

description: total RNA from control glioma 1


title: Fibroid [FBR016]

description: Gene expression data


title: Interscapular brown adipose tissue in mice fed High-fat diet 24 weeks rep2

city: Daegu

first: Sanggyu

last: Lee

address: 1370 Sankyuk-dong, Bukgu

country: South Korea

institute: Kyungpook National University

description:
replicate 2
B24H2

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). The data were normalised using quantile normalisation with beadarray in R

source_name: Interscapular brown adipose_High-fat diet_24 wks

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

growth_protocol: All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-76 semi-purified diet or AIN-76 semi-purified diet with 39.2 kcal% fat (American Institute of Nutrition, 1977) consisting of 20% fat and 1% cholesterol.

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

treatment_protocol: C57BL/6J mice were fed a high-fat diet (HFD) or normal diet (ND) and sacrificed at 5 time-points (2, 4, 8, 20 and 24 weeks) over 24 weeks.

tag: age

value: 7 weeks

tag: diet

value: High-fat diet

value: 24 weeks

value: Interscapular brown adipose tissue


title: Leiomyosarcoma [X34]

description: Gene expression data


title: Interscapular brown adipose tissue in mice fed Normal diet 20 weeks rep2

description:
replicate 2
B20N2

source_name: Interscapular brown adipose_Normal diet_20 wks

value: Normal diet

value: 20 weeks

tag: tissue


title: Interscapular brown adipose tissue in mice fed High-fat diet 20 weeks rep3

description:
replicate 3
B20H3

source_name: Interscapular brown adipose_High-fat diet_20 wks


title: Interscapular brown adipose tissue in mice fed Normal diet 24 weeks rep1

description:
replicate 1
B24N1

source_name: Interscapular brown adipose_Normal diet_24 wks


title: M95R

description: total RNA from control glioma 4

tag: cell type


title: Interscapular brown adipose tissue in mice fed Normal diet 8 weeks rep3

description:
replicate 3
B8N3

source_name: Interscapular brown adipose_Normal diet_8 wks

value: 8 weeks


title: Interscapular brown adipose tissue in mice fed High-fat diet 24 weeks rep3

description:
replicate 3
B24H3


title: Interscapular brown adipose tissue in mice fed High-fat diet 24 weeks rep1

description:
replicate 1
B24H1


title: Interscapular brown adipose tissue in mice fed Normal diet 24 weeks rep3

description:
replicate 3
B24N3


title: Interscapular brown adipose tissue in mice fed Normal diet 8 weeks rep2

description:
replicate 2
B8N2


title: Interscapular brown adipose tissue in mice fed High-fat diet 8 weeks rep2

description:
replicate 2
B8H2

source_name: Interscapular brown adipose_High-fat diet_8 wks


title: Interscapular brown adipose tissue in mice fed Normal diet 20 weeks rep3

description:
replicate 3
B20N3


title: Interscapular brown adipose tissue in mice fed High-fat diet 20 weeks rep2

description:
replicate 2
B20H2


title: Interscapular brown adipose tissue in mice fed High-fat diet 20 weeks rep1

description:
replicate 1
B20H1


title: Interscapular brown adipose tissue in mice fed Normal diet 8 weeks rep1

description:
replicate 1
B8N1


title: Interscapular brown adipose tissue in mice fed High-fat diet 4 weeks rep1

description:
replicate 1
B4H1

source_name: Interscapular brown adipose_High-fat diet_4 wks

value: 4 weeks


title: Interscapular brown adipose tissue in mice fed High-fat diet 8 weeks rep1

description:
replicate 1
B8H1


title: Interscapular brown adipose tissue in mice fed Normal diet 24 weeks rep2

description:
replicate 2
B24N2


title: Interscapular brown adipose tissue in mice fed High-fat diet 8 weeks rep3

description:
replicate 3
B8H3


title: Interscapular brown adipose tissue in mice fed Normal diet 4 weeks rep3

description:
replicate 3
B4N3

source_name: Interscapular brown adipose_Normal diet_4 wks


title: Interscapular brown adipose tissue in mice fed High-fat diet 2 weeks rep1

description:
replicate 1
B2H1

source_name: Interscapular brown adipose_High-fat diet_2 wks

value: 2 weeks


title: Interscapular brown adipose tissue in mice fed High-fat diet 2 weeks rep3

description:
replicate 3
B2H3


title: Interscapular brown adipose tissue in mice fed Normal diet 20 weeks rep1

description:
replicate 1
B20N1


title: Interscapular brown adipose tissue in mice fed High-fat diet 4 weeks rep2

description:
replicate 2
B4H2


title: ctrl_T0_D2

city: Bodø

first: Corinna

last: Lau

address: Prinsensgate 164

department: Research Department

country: Norway

institute: Nordland Hospital Bodø

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit (Affymetrix P/N 900720): 17±1 hours, 45oC, 60 rpm in hybridization oven; washing and staining on Fluidics Station 450 using protocol FS450_0007

scan_protocol: GeneChip® Scanner 3000 7G; GeneChip® Operating Software (GCOS).

data_processing: Robust Multichip Analysis by Partek® Genomics Suite software™ (transcripts with log2(signal value)<4 were excluded from the list)

source_name: healthy donor 1, PBS, 0 min, day 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA using Affymetrix® GeneChip® Whole Transcript (WT) Sense Target Labelling Assay (Manual: P/N701880 Rev.4)

extract_protocol: total RNA was isolated from whole blood using Applied Biosystems ABI PRISM™ 6100 Nucleic Acid PrepStation and AB6100 total RNA chemistry; RNA integrity with average RIN of 8.8 was verified by 2100 Bioanalyzer (Agilent).

treatment_protocol: fresh venous blood supplied with anticoagulant (50 µg/mL lepirudin) was incubated at 37oC for 120 min or 0 min (T0) with PBS, inflammatory activator (Escherichia coli strain LE392) or activator and various inhibitors or inhibitor controls prior to addition of 10 mM EDTA, lysis in Applied Biosystems AB6100 total RNA chemistry lysis buffer and storage at -80oC until RNA extraction

value: fresh venous blood anticoagulated with 50 µg/mL thrombin-inhibitor lepirudin

tag: genotype

value: healthy donor 1

value: sufficent

tag: activator

tag: inhibitor


title: Interscapular brown adipose tissue in mice fed High-fat diet 4 weeks rep3

description:
replicate 3
B4H3

tag: time point


title: Interscapular brown adipose tissue in mice fed Normal diet 4 weeks rep2

description:
replicate 2
B4N2


title: ctrl2_T0_D2

source_name: healthy donor 2, PBS, 0 min, day 2

value: healthy donor 2


title: Interscapular brown adipose tissue in mice fed High-fat diet 2 weeks rep2

description:
replicate 2
B2H2


title: Interscapular brown adipose tissue in mice fed Normal diet 2 weeks rep1

description:
replicate 1
B2N1

source_name: Interscapular brown adipose_Normal diet_2 wks


title: Interscapular brown adipose tissue in mice fed Normal diet 0 weeks rep1

description:
replicate 1
B0N1

source_name: Interscapular brown adipose_Normal diet_0 wks

value: 0 weeks


title: C5D_T0_D2

source_name: C5 deficient, PBS, 0 min, day 2

value: C5 deficient patient with two aberrant C5 mRNA products  with deletions of exon 27 and exons 26 and 27, respectively

value: deficient


title: C5DR_inhibitor ctrl_D2

source_name: C5 deficient, C5-reconstituted, E.coli, inhibitor controls, 120min, day 2

value: C5 reconstituted

value: 5 x E06/mL E. coli

value: inhibitor controls


title: C5DR_C5aR antagonist_D1_No2

source_name: C5 deficient, C5-reconstituted, E.coli, C5aR-inhibition, 120min, day 1, replicate 2

value: 1 x E06/mL E. coli

value: C5a receptor antagonist


title: C5DR_C5aR antagonist_D2

source_name: C5 deficient, C5-reconstituted, E.coli, C5aR-inhibition, 120min, day 2


title: C5DR_inhibitor ctrl_D1_No2

source_name: C5 deficient, C5-reconstituted, E.coli, inhibitor controls, 120min, day 1, replicate 2


title: C5DR_inhibitor ctrl_D1

source_name: C5 deficient, C5-reconstituted, E.coli, inhibitor controls, 120min, day 1, replicate 1


title: Interscapular brown adipose tissue in mice fed Normal diet 0 weeks rep2

description:
replicate 2
B0N2

value: 7 weeks

value: Normal diet

value: Interscapular brown adipose tissue


title: C5DR_anti-CD14+Compstatin_D2

source_name: C5 deficient, C5-reconstituted, E.coli, combined inhibition, 120min, day 2

value: anti-CD14 and Compstatin


title: C5DR_C5aR antagonist_D1

source_name: C5 deficient, C5-reconstituted, E.coli, C5aR-inhibition, 120min, day 1, replicate 1


title: Interscapular brown adipose tissue in mice fed Normal diet 2 weeks rep2

description:
replicate 2
B2N2

value: 2 weeks


title: Interscapular brown adipose tissue in mice fed Normal diet 2 weeks rep3

description:
replicate 3
B2N3


title: Interscapular brown adipose tissue in mice fed Normal diet 0 weeks rep3

description:
replicate 3
B0N3


title: Fibroid [FBR033]

description: Gene expression data

source_name: Fibroid

value: Female


title: C5DR_anti-CD14_D1

source_name: C5 deficient, C5-reconstituted, E.coli, CD14-inhibition, 120min, day 1, replicate 1

value: fresh venous blood anticoagulated with 50 µg/mL thrombin-inhibitor lepirudin


title: C5DR_anti-CD14_D1_No2

source_name: C5 deficient, C5-reconstituted, E.coli, CD14-inhibition, 120min, day 1, replicate 2


title: C5DR_anti-CD14+Compstatin_D1_No2

source_name: C5 deficient, C5-reconstituted, E.coli, combined inhibition, 120min, day 1, replicate 2


title: Interscapular brown adipose tissue in mice fed Normal diet 4 weeks rep1

description:
replicate 1
B4N1

source_name: Interscapular brown adipose_Normal diet_4 wks

value: 4 weeks


title: C5DR_anti-CD14_D2

source_name: C5 deficient, C5-reconstituted, E.coli, CD14-inhibition, 120min, day 2


title: C5DR_anti-CD14+Compstatin_D1

source_name: C5 deficient, C5-reconstituted, E.coli, combined inhibition, 120min, day1, replicate 1


title: C5DR_Compstatin_D2

source_name: C5 deficient, C5-reconstituted, E.coli, C3-inhibition, 120min, day 2

value: Compstatin


title: C5DR_E.coli_D2

source_name: C5 deficient, C5-reconstituted, E.coli, 120min, day 2


title: C5D_anti-CD14_D2

source_name: C5 deficient, E.coli, CD 14-inhibition, 120min, day 2


title: C5DR_PBS_D1

source_name: C5 deficient, C5-reconstituted, PBS, 120min, day 1, replicate 1


title: C5D_E.coli_D1_No2

source_name: C5 deficient, E.coli, 120min, day 1, replicate 2


title: C5D_PBS_D2

source_name: C5 deficient, PBS, 120min, day 2


title: C5DR_PBS_D2

source_name: C5 deficient, C5-reconstituted, PBS, 120min, day 2


title: C5DR_PBS_D1_No2

source_name: C5 deficient, C5-reconstituted, PBS, 120min, day 1, replicate 2


title: C5D_anti-CD14+Compstatin_D2

source_name: C5 deficient, E.coli, combined inhibition, 120min, day 2


title: C5D_anti-CD14_D1_No2

source_name: C5 deficient, E.coli, CD 14-inhibition, 120min, day 1, replicate 2


title: C5DR_Compstatin_D1_No2

source_name: C5 deficient, C5-reconstituted, E.coli, C3-inhibition, 120min, day 1, replicate 2


title: C5D_E.coli_D1

source_name: C5 deficient, E.coli, 120min, day 1, replicate 1


title: C5D_anti-CD14+Compstatin_D1_No2

source_name: C5 deficient, E.coli, combined inhibition, 120min, day 1, replicate 2


title: C5D_inhibitor ctrl_D1_No2

source_name: C5 deficient, E.coli, inhibitor controls, 120min, day 1, replicate 2


title: C5D_anti-CD14_D1

source_name: C5 deficient, E.coli, CD 14-inhibition, 120min, day 1, replicate 1


title: C5DR_E.coli_D1

source_name: C5 deficient, C5-reconstituted, E.coli, 120min, day 1, replicate 1


title: C5D_inhibitor ctrl_D2

source_name: C5 deficient, E.coli, inhibitor controls, 120min, day 2


title: C5D_E.coli_D2

source_name: C5 deficient, E.coli, 120min, day 2


title: C5D_anti-CD14+Compstatin_D1

source_name: C5 deficient, E.coli, combined inhibition, 120min, day 1, replicate 1


title: C5D_C5aR antagonist_D1

source_name: C5 deficient, E.coli, C5aR-inhibition, 120min, day 1, replicate 1


title: C5DR_E.coli_D1_No2

source_name: C5 deficient, C5-reconstituted, E.coli, 120min, day 1, replicate 2


title: C5D_Compstatin_D1

source_name: C5 deficient, E.coli, C3-inhibition, 120min, day 1, replicate 1


title: C5D_C5aR antagonist_D1_No2

source_name: C5 deficient, E.coli, C5aR-inhibition, 120min, day 1, replicate 2


title: C5D_Compstatin_D1_No2

source_name: C5 deficient, E.coli, C3-inhibition, 120min, day 1, replicate 2


title: C5D_C5aR antagonist_D2

source_name: C5 deficient, E.coli, C5aR-inhibition, 120min, day 2


title: C5D_inhibitor ctrl_D1

source_name: C5 deficient, E.coli, inhibitor controls, 120min, day 1, replicate 1


title: C5DR_Compstatin_D1

source_name: C5 deficient, C5-reconstituted, E.coli, C3-inhibition, 120min, day 1, replicate 1


title: C5D_Compstatin_D2

source_name: C5 deficient, E.coli, C3-inhibition, 120min, day 2


title: ctrl2_inhibitor ctrl_D1

source_name: healthy donor 2, E.coli, inhibitor controls, 120min, day 1

value: healthy donor 2

value: sufficent


title: C5D_PBS_D1_No2

source_name: C5 deficient, PBS, 120min, day 1, replicate 2

value: C5 deficient patient with two aberrant C5 mRNA products  with deletions of exon 27 and exons 26 and 27, respectively

value: deficient


title: C5D_PBS_D1

source_name: C5 deficient, PBS, 120min, day 1, replicate 1


title: ctrl_inhibitor ctrl_D2

source_name: healthy donor 1, E.coli, inhibitor controls, 120min, day 2

value: healthy donor 1

value: 5 x E06/mL E. coli


title: ctrl_anti-CD14_D1

source_name: healthy donor 1, E.coli, CD 14-inhibition, 120min, day 1

value: 1 x E06/mL E. coli


title: ctrl_inhibitor ctrl_D1

source_name: healthy donor 1, E.coli, inhibitor controls, 120min, day 1

value: inhibitor controls


title: ctrl_anti-CD14_D2

source_name: healthy donor 1, E.coli, CD 14-inhibition, 120min, day 2


title: ctrl2_anti-CD14_D2

source_name: healthy donor 2, E.coli, CD14-inhibition, 120min, day 2


title: ctrl2_C5aR antagonist_D1

source_name: healthy donor 2, E.coli, C5aR-inhibition, 120min, day 1

value: C5a receptor antagonist


title: ctrl2_anti-CD14+Compstatin_D2

source_name: healthy donor 2, E.coli, combined inhibition, 120min, day 2


title: ctrl2_inhibitor ctrl_D2

source_name: healthy donor 2, E.coli, inhibitor controls, 120min, day 2


title: ctrl_anti-CD14+Compstatin_D1

source_name: healthy donor 1, E.coli, combined inhibition, 120min, day 1


title: ctrl_anti-CD14+Compstatin_D2

source_name: healthy donor 1, E.coli, combined inhibition, 120min, day 2


title: ctrl2_C5aR antagonist_D2

source_name: healthy donor 2, E.coli, C5aR-inhibition, 120min, day 2


title: ctrl2_E.coli_D2

source_name: healthy donor 2, E.coli, 120min, day 2


title: ctrl_C5aR antagonist_D1

source_name: healthy donor 1, E.coli, C5aR-inhibition, 120min, day 1


title: ctrl2_anti-CD14_D1

source_name: healthy donor 2, E.coli, CD14-inhibition, 120min, day 1


title: ctrl2_anti-CD14+Compstatin_D1

source_name: healthy donor 2, E.coli, combined inhibition, 120min, day 1


title: ctrl_E.coli_D1

source_name: healthy donor 1, E.coli, 120min, day 1


title: ctrl_Compstatin_D1

source_name: healthy donor 1, E.coli, C3-inhibition, 120min, day 1


title: ctrl_Compstatin_D2

source_name: healthy donor 1, E.coli, C3-inhibition, 120min, day 2


title: ctrl2_Compstatin_D2

source_name: healthy donor 2, E.coli, C3-inhibition, 120min, day 2


title: ctrl2_Compstatin_D1

source_name: healthy donor 2, E.coli, C3-inhibition, 120min, day 1


title: ctrl_PBS_D2

source_name: healthy donor 1, PBS, 120min, day 2


title: ctrl_E.coli_D2

source_name: healthy donor 1, E.coli, 120min, day 2


title: ctrl_C5aR antagonist_D2

source_name: healthy donor 1, E.coli, C5aR-inhibition, 120min, day 2


title: ctrl2_E.coli_D1

source_name: healthy donor 2, E.coli, 120min, day 1


title: ctrl2_PBS_D2

source_name: healthy donor 2, PBS, 120min, day 2


title: ctrl2_PBS_D1

source_name: healthy donor 2, PBS, 120min, day 1


title: ctrl_PBS_D1

source_name: healthy donor 1, PBS, 120min, day 1


title: 1465_liver

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: liver

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 16 week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

value: liver

value: female

value: 16 weeks


title: 1458_liver

value: male

value: A/J


title: 1473_liver

value: NZB/BlNJ


title: 1495_liver


title: 1468_liver

value: SM/J


title: 1501_liver

value: AKR/J


title: 1463_liver


title: 1481_liver


title: 1464_liver


title: 1484_liver


title: 1483_liver


title: 1488_liver


title: 1444_liver

value: I/LnJ


title: 1470_liver


title: 1445_liver


title: 1455_liver


title: 1453_liver


title: 1498_liver


title: 1499_liver


title: 1438_liver


title: 1489_liver


title: 1437_liver


title: 1469_liver


title: 1494_liver


title: 1496_liver


title: 1462_liver


title: 1485_liver


title: 1459_liver


title: 1448_liver


title: 1474_liver


title: 1433_liver

value: MA/MyJ


title: 1426_liver


title: 1428_liver

value: SJL/J


title: 1423_liver


title: 1427_liver


title: 1365_liver


title: 1356_liver


title: 1283_liver

value: NZW/LacJ


title: 1343_liver

value: CE/J


title: 1347_liver


title: 1314_liver


title: 1302_liver


title: 1341_liver


title: 1364_liver


title: 1261_liver


title: 1313_liver

value: KK/HlJ


title: 1301_liver


title: 1324_liver


title: 1355_liver


title: 1267_liver

value: LP/J


title: 1265_liver


title: 1320_liver


title: 1351_liver


title: 1360_liver


title: 1422_liver


title: 1270_liver


title: 1271_liver


title: 1321_liver


title: 1284_liver


title: 1264_liver


title: 1257_liver


title: 1247_liver


title: 1255_liver


title: 1259_liver


title: 1233_liver


title: 1243_liver


title: 1237_liver


title: 1234_liver


title: 1193_liver


title: 1203_liver


title: 1162_liver


title: 1188_liver


title: 1161_liver


title: 1187_liver


title: 1198_liver


title: 1156_liver


title: 1218_liver


title: 1201_liver


title: 1204_liver


title: 1159_liver


title: 1181_liver


title: 1185_liver


title: 1152_liver


title: 1211_liver


title: 1210_liver


title: 1182_liver


title: 1189_liver


title: 1230_liver


title: 1217_liver


title: 1168_liver


title: 1149_liver


title: 1140_liver


title: 1143_liver


title: 1147_liver


title: 1146_liver


title: 1127_liver


title: 1151_liver


title: 1134_liver


title: 1121_liver


title: 1083_liver


title: 1071_liver


title: 1068_liver


title: 1062_liver


title: 1090_liver


title: 1046_liver


title: 1047_liver


title: 1026_liver


title: 1110_liver


title: 1095_liver


title: 1109_liver


title: 1070_liver


title: 1080_liver


title: 1076_liver


title: 1064_liver


title: 1060_liver


title: 1059_liver


title: 1031_liver


title: 1027_liver


title: 1093_liver


title: 999_liver


title: 1011_liver


title: 1055_liver


title: 1017_liver


title: 1022_liver


title: 1020_liver


title: 993_liver


title: 973_liver


title: 969_liver


title: 957_liver


title: 960_liver


title: 936_liver


title: 927_liver


title: 983_liver


title: 977_liver


title: 905_liver


title: 997_liver


title: 963_liver


title: 930_liver


title: 897_liver


title: 986_liver

value: NOD/ShiLtJ


title: 895_liver


title: 898_liver


title: 891_liver


title: 985_liver


title: 889_liver


title: 894_liver


title: 903_liver


title: 886_liver


title: 890_liver


title: 883_liver


title: 879_liver


title: 881_liver


title: 884_liver


title: 873_liver


title: 887_liver


title: 872_liver


title: 868_liver


title: 880_liver


title: 857_liver


title: 863_liver


title: 865_liver


title: 867_liver


title: 862_liver


title: 861_liver


title: 869_liver


title: 837_liver


title: 885_liver


title: 808_liver

value: BTBR T<+> tf/J


title: 799_liver

value: liver


title: 847_liver


title: 831_liver


title: 811_liver


title: 874_liver

value: female


title: 800_liver

value: 16 weeks


title: 763_liver

value: male


title: 787_liver


title: 792_liver


title: 795_liver


title: 791_liver


title: 762_liver


title: 767_liver


title: 766_liver


title: 738_liver


title: 764_liver


title: 743_liver


title: 786_liver


title: 735_liver


title: 765_liver


title: 744_liver


title: 733_liver


title: 736_liver


title: 728_liver


title: 732_liver


title: 727_liver


title: 705_liver


title: 706_liver


title: 699_liver


title: 700_liver


title: 697_liver


title: 696_liver


title: 695_liver


title: 707_liver


title: 691_liver

value: CBA/J


title: 690_liver


title: 671_liver


title: 688_liver


title: 649_liver

value: FVB/NJ


title: 668_liver


title: 644_liver


title: 698_liver


title: 631_liver


title: 669_liver


title: 642_liver


title: 687_liver


title: 641_liver


title: 651_liver


title: 592_liver

value: BALB/cJ


title: 640_liver


title: 606_liver


title: 582_liver


title: 577_liver


title: 608_liver


title: 599_liver


title: 581_liver


title: 591_liver


title: 579_liver


title: 659_liver


title: 600_liver


title: 665_liver


title: 584_liver


title: 572_liver


title: 557_liver


title: 570_liver


title: 561_liver


title: 576_liver


title: 547_liver


title: 573_liver


title: 538_liver


title: 540_liver


title: 562_liver


title: 546_liver


title: 534_liver


title: 536_liver


title: 521_liver


title: 501_liver


title: 516_liver


title: 522_liver


title: 525_liver


title: 537_liver


title: 513_liver