title: A5_thymus_4months, biological rep1

description: mouse ID: A5


title: 5124_Tumor

status: Public on Nov 01 2015

type: genomic

city: Austin

first: Grace

last: Chappell

state: TX

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

country: USA

institute: ToxStrategies, Inc.

description: biological replicate 24 of 26

hyb_protocol: Equal amounts (minimum 3500 ng) of Cy3-labeled reference DNA  and Cy5-labeled sample DNA were hybridized on the same array (Agilent 4x44K CGH microarray),  hybridized and washed according to the manufacturer's (Agilent) protocol.

scan_protocol: The signals from both Cy3 and Cy5 on the hybridized array were detected by laser scanner (Agilent G2565 Series scanner Model C).

data_processing: The images were converted to digital data by Agilent Feature Extraction Software (v 8.5.1.1).  Samples underwent background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Mus musculus

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl12

label_protocol: Genomic DNA (minimum 500ng) from samples (reference and samples) were digested by restrict enzymes (Alu I and Rsa I). The fragmented DNA was labeled with either Cy3-dUTP or Cy5-dUTP, amplified with Exo(-) Klenow,  and purified.

extract_protocol: Total DNA was extracted using a Qiagen DNEasy kit according to the manufacturer's instructions

treatment_protocol: At 2 weeks of age, mice were injected i.p. with DEN (1mg/kg) in sterile saline (15 µl/g). At 8 weeks of age (6 weeks after a single injection of DEN or vehicle as detailed above), and were injected i.p. twice weekly with CCl4 (0.2ml/kg) diluted in olive oil vehicle for 14 additional weeks.  Mice were maintained on animal chow with free access to food/water for the duration of the study. Vehicle-control mice were injected with sterile saline and olive oil vehicles in place of DEN and CCl4, respectively. Liver tumors were separated at the time of sacrifice, and both tumor and non-tumor tissues were flash frozen in liquid nitrogen

tag: tissue

value: liver tumor

tag: strain

tag: Sex

value: male

source_name: pooled DNA from normal liver from vehicle-control mice

value: liver


title: A11_thymus_18months, biological rep2

type: RNA

city: Huddinge

first: Maria

last: Eriksson

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: mouse ID: A11

hyb_protocol: A total of 5.5 μg of labeled and fragmented single-stranded cDNA was hybridized to the arrays and incubated in a 45º C oven for 16-18 hours, 60 rpm rotation (Affymetrix Gene Chip Hybridization Oven 640). Arrays were washed and stained using the FS450_0001 fluidic script (Affymetrix Gene Chip Fluidics Station 450)

scan_protocol: Scanning was performed by Affymetrix Gene Chip scanner 3000 7G.

data_processing:
The core meta probe set and control probes were analyzed in Partek Genomic Suite v.6.6 (Partek Inc., St. Louis, MO, USA). RMA background correction algorithm was selected and adjusted for GC content (GC-RMA). For the normalization of probe signals a quantile normalization and median polish probe set summarization was used and converted to log2 scale.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

label: biotin

molecule: total RNA

source_name: wild-type, thymus, 18 months

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mice were housed in the experimental animal facility with a 12-hour light/dark cycle, a temperature of 20-22°C and 50-75% air humidity (Karolinska Hospital, Huddinge, Sweden). They were supplied with R36 pellets (Lactamin, Sweden) and drinking water ad libitum and aged up to desired age.

extract_protocol: Mice were euthanized by cervical dislocation.Tissues were dissected and immediately transferred to liquid N2 to be stored at -80° C prior to homogenization and RNA extraction. Total RNA was extracted with Trizol  and  purified using an RNeasy cleanup kit. The RNA integrity was assessed by the Agilent 2100 Bioanalyzer. The RNA quality criteria for proceeding with exon arrays were a 18S/28S ratio above 1.5 and an RNA integrity number (RIN-value) ≥ 8.0. For array hybridization and Whole Transcript Sense Target Labeling Synthesis, 200 ng of RNA was processed using the Gene Chip WT cDNA Synthesis Kit, (Affymetrix)

treatment_protocol: No treatments

value: thymus

tag: age (months)

tag: gender

tag: genotype

value: wild-type


title: 5120_NT

description: biological replicate 20 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl9

value: liver non-tumor


title: SHSY5Y cells_Gelsemium 2c_rep4

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 5.1).

scan_protocol: Each microarray was scanned using an Axon GenePix 4400 A at 532 nm and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction.

organism: Homo sapiens

source_name: SHSY5Y cells_Gelsemium 2c

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 5.1).

growth_protocol: Neuroblastoma cells adherent onto Petri dishes at standard density were collected  after mild treatment with Trypsin-PBS solution (5 mg/L).

extract_protocol: Total RNA was extracted from 3.5 x 106  cells with Qiagen RNAeasy Mini Kit (Qiagen S.p.A., Milan, Italy) following the manufacturer’s instructions (Animal cells Spin protocol), including genomic DNA elimination step in column.  The qualitative parameters A260/A280>1.8, A260/A230>1.7; RNA integrity number>7 were evaluated.

tag: cell line

value: SHSY5Y (ATCC N. CRL-2266)

tag: cell type

value: neuroblastoma


title: 5114_NT

description: biological replicate 14 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl6


title: 5115_Tumor

description: biological replicate 15 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl8


title: SHSY5Y cells_Gelsemium 3c_rep2

source_name: SHSY5Y cells_Gelsemium 3c


title: 5116_Nt

description: biological replicate 16 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl8


title: SHSY5Y cells_Gelsemium 2c_rep3


title: 5113_NT

description: biological replicate 13 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl5


title: 5114_Tumor

description: biological replicate 14 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl7


title: SHSY5Y cells_Gelsemium 2c_rep1


title: A31_skeletal.muscle_28months, biological rep5

description: mouse ID: A31

source_name: wild-type, thigh skeletal muscle, 28 months

value: skeletal muscle


title: SHSY5Y cells_Gelsemium 3c_rep3


title: SHSY5Y cells_Gelsemium 3c_rep1


title: 5113_Tumor

description: biological replicate 13 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl6


title: 5115_NT

description: biological replicate 15 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl7


title: P150KD_morula_embryos_rep4

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description:
Gene expression in  morula P150KD embryo
P150KD4_morula

hyb_protocol: 1.65 ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized at 65°C for 17 hours according to manufacture's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images of microarray slides were processed using Feature Extraction software 10.5.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 (Agilent Technologies) and normalized by default setting.

source_name: Morula P150siRNA-injected, embryo, replicate4

label_protocol: 5.0 ug of amplified RNA was labelled with Cyanine-3 (Cy3) dye (GE Healthcare) for 90 minutes at RT. Labelled RNAs were purified with RNeasy MinElute kit (Qiagen) and checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: In vitro fertilized (IVF)  embryos injected control siRNA or P150 siRNA were cultured in potassium modified simplex optimization medium (KSOM) at 37.5 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) from 10 morula embryos and subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies).

treatment_protocol: Morula embryos at E3.0 were subjected to microarray gene analyses.

tag: developmental stage

value: morula

tag: injection

value: P150 siRNA

value: embryo at E3.0


title: 5116_Tumor

description: biological replicate 16 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl9


title: SHSY5Y cells_Gelsemium 3c_rep4


title: SHSY5Y cells_Gelsemium 2c_rep2


title: A10_skeletal.muscle_18months, biological rep5

description: mouse ID: A10

source_name: wild-type, thigh skeletal muscle, 18 months


title: A13_skeletal.muscle_18months, biological rep3

description: mouse ID: A13


title: A29_skeletal.muscle_28months, biological rep3

description: mouse ID: A29


title: 5112_Tumor

description: biological replicate 12 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl5


title: SHSY5Y cells_Gelsemium 4c_rep4

source_name: SHSY5Y cells_Gelsemium 4c


title: A27_skeletal.muscle_28months, biological rep1

description: mouse ID: A27


title: A15_skeletal.muscle_18months, biological rep4

description: mouse ID: A15


title: P150KD_morula_embryos_rep5

description:
Gene expression in  morula P150KD embryo
P150KD5_morula

source_name: Morula P150siRNA-injected, embryo, replicate5


title: A11_skeletal.muscle_18months, biological rep1

description: mouse ID: A11


title: A28_skeletal.muscle_28months, biological rep2

description: mouse ID: A28


title: A12_skeletal.muscle_18months, biological rep2

description: mouse ID: A12


title: A30_skeletal.muscle_28months, biological rep4

description: mouse ID: A30


title: 6JA4_skeletal.muscle_4months, biological rep5

description: mouse ID: 6JA4

source_name: wild-type, thigh skeletal muscle, 4 months


title: 5112_NT

description: biological replicate 12 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl12

source_name: pooled DNA from normal liver from vehicle-control mice


title: P150KD_morula_embryos_rep1

description:
Gene expression in  morula P150KD embryo
P150KD1_morula

source_name: Morula P150siRNA-injected, embryo, replicate1


title: 5109_Tumor

description: biological replicate 9 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl9


title: 6JA3_skeletal.muscle_4months, biological rep3

description: mouse ID: 6JA3


title: 5111_NT

description: biological replicate 11 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl11


title: A31_bone_28months, biological rep5

description: mouse ID: A31

source_name: wild-type, tibia  bone, 28 months

value: tibia bone


title: 6JA1_skeletal.muscle_4months, biological rep2

description: mouse ID: 6JA1


title: siControl_morula_embryos_rep2

description:
Gene expression in  morula control embryo
Con2_morula

source_name: Morula siControl-injected, embryo, replicate2

value: Control siRNA


title: Unaffected liver mouse 6602

city: Boston

first: Lee

middle: Alan

last: Albacker

state: MA

address: 200 Longwood Ave

department: Department of Systems Biology

institute: Harvard Medical School

hyb_protocol: Arrays were hybridized in hybridization buffer (Agilent) in a hybridization oven and sequentially washed.

scan_protocol: Images were scanned with a Agilent Technologies Scanner G2505C US22502664

data_processing: Agilent feature extraction (v 10.5.1.1) was used for background subtraction and linear normalization

source_name: unaffected liver tissue

label_protocol: 3 ug of genomic DNA was labeled using Agilent labeling kits

extract_protocol: Genomic DNA using Machery-Nagel DNA extraction kit occording to manufacturers instructions, subsequent steps performed at BioMicroCenter MIT

value: unaffected liver tissue

tag: age

value: 13.2 months

tag: tumor grade

value: not applicable

value: female

source_name: control liver


title: P150KD_morula_embryos_rep2

description:
Gene expression in  morula P150KD embryo
P150KD2_morula

source_name: Morula P150siRNA-injected, embryo, replicate2


title: 5110_Tumor

description: biological replicate 10 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl10

value: liver tumor

value: male


title: A8_skeletal.muscle_4months, biological rep1

description: mouse ID: A8


title: siControl_morula_embryos_rep1

description:
Gene expression in  morula control embryo
Con1_morula

source_name: Morula siControl-injected, embryo, replicate1


title: Unaffected liver mouse 6642

value: 12.3 months

value: liver


title: siControl_morula_embryos_rep3

description:
Gene expression in  morula control embryo
Con3_morula

source_name: Morula siControl-injected, embryo, replicate3


title: Hepatocellular carcinoma mouse 6642

source_name: tumor tissue

value: liver tumor tissue

value: Hepatocellular Carcinoma


title: WILD TYPE B25

city: Berlin

first: Susann

last: Förster

address: R. Rössle Str 10

country: Germany

institute: MDC

description: Gene expression in WT mouse 4

hyb_protocol: probes were then hybridized at 37°C for 17 hrs at 10 rpm in the array.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 6x80k arrays

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Agilent.SingleColor.28005 microarray, Software GeneSpring 12.6, normalized signal intensities (Threshold: 1.0, Logbase: 2, Normalization: Shift to 75 percentile, Baseline Transformation: median of all samples)

source_name: stomach of  old WT mouse

label_protocol: 0.3ug of RNA were used for cDNA synthesis, that was performed using oligo dT's. cDNA was then labeled with Cy3.

growth_protocol: Animals were bred and kept according to institutional guidelines

extract_protocol: Total RNA was extracted using the a universal RNA extraction kit from ROBOKLON, according to the manufacturers protocol. Obtained RNA was treated with DNase I.

treatment_protocol: Animals were sacrificed at birth by decapitation

value: WT

value: stomach


title: Hepatocellular carcinoma mouse 6565

value: 14.7 months


title: A30_bone_28months, biological rep4

description: mouse ID: A30

value: wild-type


title: 5110_NT

description: biological replicate 10 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl10

value: liver non-tumor


title: Unaffected liver mouse 6487

value: 12.8 months


title: WILD TYPE 162

description: Gene expression in WT mouse 3


title: Hepatocellular carcinoma mouse 6602


title: 5111_Tumor

description: biological replicate 11 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl11


title: WILD TYPE 158

description: Gene expression in WT mouse 2


title: 5108_Tumor

description: biological replicate 8 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl8


title: A29_bone_28months, biological rep3

description: mouse ID: A29

value: tibia bone


title: P150KD_morula_embryos_rep3

description:
Gene expression in  morula P150KD embryo
P150KD3_morula

source_name: Morula P150siRNA-injected, embryo, replicate3

value: morula

value: P150 siRNA

value: embryo at E3.0


title: A28_bone_28months, biological rep2

description: mouse ID: A28


title: Unaffected liver mouse 6565

value: unaffected liver tissue

value: not applicable

value: female


title: 5107_Tumor

description: biological replicate 7 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl7

value: liver tumor

value: male

source_name: pooled DNA from normal liver from vehicle-control mice


title: Hepatocellular carcinoma mouse 6487

value: liver tumor tissue

value: liver


title: 5108_NT

description: biological replicate 8 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl8


title: 5107_NT

description: biological replicate 7 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl7


title: 6JA2_skeletal.muscle_4months, biological rep4

description: mouse ID: 6JA2

source_name: wild-type, thigh skeletal muscle, 4 months

value: skeletal muscle


title: C_EBP KO 92

description: Gene expression in CEBP beta KO mouse 5

source_name: stomach of  old C/EBP beta KO mouse

value: C/EBPbeta KO

value: stomach


title: 5109_NT

description: biological replicate 9 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl9


title: Hepatocellular carcinoma 2 mouse 6240

value: 16.2 months

value: Hepatocellular Carcinoma

source_name: control liver


title: Unaffected liver mouse 6240

source_name: unaffected liver tissue


title: 5106_Tumor

description: biological replicate 6 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl6


title: WILD TYPE 149

description: Gene expression in WT mouse 1

value: WT


title: 5106_NT

description: biological replicate 6 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl6

value: liver non-tumor


title: C_EBP KO 155

description: Gene expression in CEBP beta KO mouse 2


title: 5104_Tumor

description: biological replicate 4 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl4


title: C_EBP KO 228

description: Gene expression in CEBP beta KO mouse 3


title: A11_bone_18months, biological rep2

description: mouse ID: A11

source_name: wild-type, tibia  bone, 18 months

value: tibia bone

value: wild-type


title: A10_bone_18months, biological rep1

description: mouse ID: A10


title: C_EBP KO 152

description: Gene expression in CEBP beta KO mouse 1


title: 5105_NT

description: biological replicate 5 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl5


title: A14_bone_18months, biological rep4

description: mouse ID: A14


title: A13_bone_18months, biological rep3

description: mouse ID: A13


title: A20_bone_4months, biological rep5

description: mouse ID: A20

source_name: wild-type, tibia  bone, 4 months


title: A27_bone_28months, biological rep1

description: mouse ID: A27

source_name: wild-type, tibia  bone, 28 months


title: 5105_Tumor

description: biological replicate 5 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl5


title: A.E7-stim for 6hr-U74B2v

city: Seoul

first: Kyungho

last: Choi

address: 103 Daehak-ro, Jongno-gu

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University College of Medicine

description: cRNAs from AE.7 cells stimulated for 6hrs were hybridized on mouse genome U74B(version2) chip.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U74 A then on B and last on C Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: The data were analyzed with Microarray Suite version 4.0 (MAS 4.0) using Affymetrix default analysis settings and global scaling as normalization method. The target intensity of each array was arbitrarily set to 150.

source_name: A.E7 T cells stimulated for 6hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were stimulated with whole pigeon cytochrome c protein in the presence of irradiated (3000 R) B10.A splenocytes as a source of APC. After 48 h, the cells were expanded in IL-2 (10U/ml) containing complete medium and rested for at least 2 weeks before restimulation or experimental use.

extract_protocol: Total RNA was extracted using RNeasy kit(Qiagen) according to the manufacturer's instructions.

treatment_protocol: 5x10^6 cells were added to each well of the 6-well plate pre-coated with anti-TCR antbody. After 0, 2, 4 and 6hrs at 37C, 5% CO2, cells were harvested by scraping and frozen at -70C until RNA extraction. For the maintenance phase sample, cells were stimulated for 16hrs, washed three times, and incubated in fresh complete media at 37C, 5% CO2 without further stimulation for 5days before cell harvest and RNA extraction.

value: T cell clone

value: murine B10.A origin

tag: treatment

value: anti-TCR antibody

tag: time point


title: A.E7-stim for 5day-U74B2v

description: cRNAs from AE.7 cells stimulated for 16hrs and rested for 5days were hybridized on mouse genome U74B(version2) chip.

source_name: A.E7 T cells stimulated for 16hrs and rested for 5days

value: 5 days


title: A.E7-stim for 2hr-U74B2v

description: cRNAs from AE.7 cells stimulated for 2hrs were hybridized on mouse genome U74B(version2) chip.

source_name: A.E7 T cells stimulated for 2hrs


title: Hepatocellular carcinoma 4 mouse 6240

source_name: tumor tissue

value: female


title: Hepatocellular adenoma mouse 6199

value: 12 months

value: Hepatocellular Adenoma

value: male


title: Unaffected liver mouse 5901

value: unaffected liver tissue

value: not applicable

value: liver


title: A.E7-stim for 4hr-U74B2v

description: cRNAs from AE.7 cells stimulated for 4hrs were hybridized on mouse genome U74B(version2) chip.

source_name: A.E7 T cells stimulated for 4hrs


title: 5104_NT

description: biological replicate 4 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl4

source_name: pooled DNA from normal liver from vehicle-control mice


title: Unaffected liver mouse 6199

source_name: control liver


title: Hepatocellular adenoma mouse 5901

value: liver tumor tissue


title: A.E7-stim for 0hr-U74B2v

description: cRNAs from AE.7 cells unstimulated were hybridized on mouse genome U74B(version2) chip.

source_name: A.E7 T cells unstimulated


title: C_EBP KO 40

description: Gene expression in CEBP beta KO mouse 4

source_name: stomach of  old C/EBP beta KO mouse

value: C/EBPbeta KO

value: stomach


title: A15_bone_18months, biological rep5

description: mouse ID: A15


title: A19_bone_4months, biological rep4

description: mouse ID: A19


title: Unaffected liver mouse 5884

source_name: unaffected liver tissue

value: 14.2 months


title: A18_bone_4months, biological rep3

description: mouse ID: A18

value: tibia bone


title: A.E7-stim for 0hr-U74C2v

description: cRNAs from AE.7 cells unstimulated were hybridized on mouse genome U74C(version2) chip.


title: A17_bone_4months, biological rep2

description: mouse ID: A17

value: wild-type


title: A.E7-stim for 6hr-U74C2v

description: cRNAs from AE.7 cells stimulated for 6hrs were hybridized on mouse genome U74C(version2) chip.

value: T cell clone


title: A.E7-stim for 5day-U74C2v

description: cRNAs from AE.7 cells stimulated for 16hrs and rested for 5days were hybridized on mouse genome U74C(version2) chip.

value: murine B10.A origin


title: A16_bone_4months, biological rep1

description: mouse ID: A16


title: A.E7-stim for 6hr-U74A2v

description: cRNAs from AE.7 cells stimulated for 6hrs were hybridized on mouse genome U74A(version2) chip.

value: anti-TCR antibody


title: Unaffected liver mouse 2430

value: 16.9 months


title: Hepatocellular adenoma mouse 5884

value: female


title: Tango_ChIPSeq_1 and 2

status: Public on Oct 30 2015

type: SRA

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

library_source: genomic

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: antibody name

value: Tango

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: Yki_ChIPSeq_1 and 2

value: Yki

tag: strain


title: Bcd_INPUT_1


title: A.E7-stim for 4hr-U74C2v

description: cRNAs from AE.7 cells stimulated for 4hrs were hybridized on mouse genome U74C(version2) chip.

tag: tissue


title: Bcd_ChIPSeq_1 and 2

value: Bcd


title: A.E7-stim for 4hr-U74A2v

description: cRNAs from AE.7 cells stimulated for 4hrs were hybridized on mouse genome U74A(version2) chip.


title: Hepatocellular adenoma mouse 2430

value: Hepatocellular Adenoma

tag: Sex

value: male


title: Hnf4_INPUT_1


title: A.E7-stim for 2hr-U74A2v

description: cRNAs from AE.7 cells stimulated for 2hrs were hybridized on mouse genome U74A(version2) chip.


title: Hnf4_ChIPSeq_1 and 2


title: A.E7-stim for 5day-U74A2v

description: cRNAs from AE.7 cells stimulated for 16hrs and rested for 5days were hybridized on mouse genome U74A(version2) chip.

value: 5 days


title: A.E7-stim for 0hr-U74A2v

description: cRNAs from AE.7 cells unstimulated were hybridized on mouse genome U74A(version2) chip.


title: CG WT 200 mM NaCl vs 200 GABA Replicate 3

status: Public on Oct 22 2015

city: Bielefeld

first: João

middle: M. P.

last: Jorge

address: Universitätsstraße 25

institute: University of Bielefeld

description: technical replicate 3 of 3

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was done with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were up- or downregulated in WT with 200 mM GABA in both replicates were taken into account for further analysis (p-value < 0.05, mRNA value > 2).

organism: Corynebacterium glutamicum

source_name: growth of C. glutamicum supplemented with 200 mM NaCl

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: LB seed culture was inoculated from an agar plate and grown overnight. The cells were harvested by centrifugation (4000 x g, 10 min) and washed once with CGXII medium lacking the carbon source. Finally, 50 mL of CGXII medium containing 4% of glucose, the necessary supplements, and either 200 mM NaCl or 200 mM GABA was inoculated to an OD600 of 1.0. Cells were grown until mid-exponential phase (OD between 15 and 26) and were spilled in two falcons (half filled with ice) and centrifuged (4000 x g, 10 minutes, 4ºC). Supernatant was discarded and cells were kept at -80ºC.

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: 200 mM NaCl or 200 mM GABA were added to CGXII medium  from the beginning of the growth

source_name: growth of C. glutamicum supplemented with 200 mM GABA


title: CG WT 200 mM NaCl vs 200 GABA Replicate 1

description: technical replicate 1 of 3


title: A.E7-stim for 2hr-U74C2v

description: cRNAs from AE.7 cells stimulated for 2hrs were hybridized on mouse genome U74C(version2) chip.


title: BRCAX, cancer, V_RR-1455, set 2

status: Public on Oct 21 2015

city: Salt Lake City

first: Andrea

last: Bild

state: UT

address: 112 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

hyb_protocol: Manufacturer instructions were followed.

scan_protocol: Axon GenePix Scanner (GenePix 4000B).

data_processing:
Raw CEL files were normalized using a pre-release version of the Single-Channel Array Normalization (SCAN) method. We then filtered probes using the PLANdbAffy database; probes that PLANdbAffy did not classify as green or that mapped to a single nucleotide variant were excluded. The remaining probes were summarized into gene-level values using a 10% trimmed mean based on gene/probe mappings in PLANdbAffy (using Entrez Gene identifiers as a key); genes that contained fewer than five probes were discarded. Gene-level values were then adjusted for batch with the ComBat software using cohort and processing facility to define the batches. Finally, genes whose expression was correlated with clinical or health-survey variables were excluded.

For our normalization process, we used the "full" set of probes.
The .pgf and .mps files were not usedduring the normalization process, but they do indicate which genes (Entrez IDs) and probes were used.
Probe group file: HuEx-1_0-st-v2.hg18.custom.pgf
Meta-probeset file: HuEx-1_0-st-v2.hg18.custom.mps

source_name: PBMCs, family history, developed cancer, no BRCA1/2 mutation

label_protocol: Affymetrix Exon module kit.

growth_protocol: Not applicable.

extract_protocol: RNA was extracted using the RiboPure RNA Isolation Kit.

treatment_protocol: Not applicable.

value: peripheral blood mononuclear cells

value: yes

tag: cohort

value: Ontario

value: no


title: BRCAX, cancer, Z_RR-778, set 2


title: BRCA1/2, no cancer, RR-3275, set 2

source_name: PBMCs, family history, did not develop cancer, BRCA1/2 mutation


title: BRCA1/2, cancer, RR-3299, set 2

source_name: PBMCs, family history, developed cancer, BRCA1/2 mutation


title: BRCA1/2, no cancer, Q_RR-3283, set 2


title: BRCAX, cancer, X_RR-1083, set 2


title: BRCA1/2, no cancer, T_RR-3292, set 2


title: BRCAX, cancer, W_RR-922, set 2


title: BRCAX, cancer, Y_RR-841, set 2


title: BRCAX, cancer, U_RR-2236, set 2


title: No family history, no cancer, RR-3281, set 2

source_name: PBMCs, no family history, did not develop cancer, no BRCA1/2 mutation


title: BRCA1/2, no cancer, O_RR-3285, set 2


title: BRCA1/2, no cancer, N_RR-3294, set 2


title: BRCA1/2, no cancer, RR-3289, set 2


title: No family history, no cancer, AS_RR-3277, set 2


title: BRCA1/2, no cancer, K_RR-3290, set 2


title: BRCA1/2, no cancer, P_RR-3274, set 2


title: BRCA1/2, cancer, B_RR-1519, set 2


title: BRCA1/2, cancer, RR-3287, set 2


title: BRCA1/2, cancer, J_RR-1226, set 2


title: BRCA1/2, cancer, D_RR-3301, set 2


title: No family history, no cancer, AR_RR-3278, set 2


title: No family history, no cancer, AP_RR-3280, set 2


title: No family history, no cancer, AO_RR-3288, set 2


title: BRCA1/2, no cancer, L_RR-3286, set 2


title: BRCAX, no cancer, AN_RR-3297, set 2

source_name: PBMCs, family history, did not develop cancer, no BRCA1/2 mutation


title: BRCA1/2, cancer, A_RR96-12, set 2


title: BRCA1/2, cancer, C_RR-3293, set 2


title: BRCAX, no cancer, AJ_RR-3296, set 2


title: BRCA1/2, cancer, E_RR-2070, set 2


title: Sporadic cancer, J07, set 2

source_name: PBMCs, no family history, developed cancer, no BRCA1/2 mutation

value: Utah


title: BRCAX, no cancer, AE_RR-3300, set 2


title: BRCA1/2, cancer, K03, set 2


title: BRCA1/2, no cancer, K05, set 2


title: Sporadic cancer, J05, set 2


title: BRCAX, cancer, K02, set 2


title: Sporadic cancer, J08, set 2


title: Sporadic cancer, J03, set 2


title: BRCAX, no cancer, AG_RR-3298, set 2


title: No family history, no cancer, J12, set 2


title: Sporadic cancer, J06, set 2


title: BRCAX, no cancer, AH_RR-3295, set 2


title: BRCAX, no cancer, AI_RR-3291, set 2


title: BRCAX, cancer, K04, set 2


title: BRCAX, no cancer, AM_RR-1949, set 2


title: BRCA1/2, cancer, K01, set 2


title: No family history, no cancer, J02, set 2


title: BRCAX, no cancer, AF_RR-3276, set 2


title: BRCAX, cancer, AA_RR-849, set 2


title: No family history, no cancer, J11, set 2


title: BRCAX, no cancer, I11, set 2


title: No family history, no cancer, J09, set 2


title: No family history, no cancer, J10, set 2


title: Sporadic cancer, I13, set 2


title: BRCA1/2, no cancer, I12, set 2


title: No family history, no cancer, J01, set 2


title: BRCA1/2, no cancer, I10, set 2


title: BRCA1/2, no cancer, I09, set 2


title: BRCAX, no cancer, I05, set 2


title: BRCA1/2, no cancer, I08, set 2


title: Sporadic cancer, I02, set 2


title: Sporadic cancer, I04, set 2


title: BRCAX, cancer, H08, set 2


title: BRCAX, cancer, H12, set 2


title: Sporadic cancer, J04, set 2


title: BRCA1/2, cancer, G11, set 2


title: BRCAX, no cancer, H03, set 2


title: BRCAX, cancer, H09, set 2


title: BRCAX, no cancer, I06, set 2


title: BRCAX, no cancer, H06, set 2


title: Sporadic cancer, I03, set 2


title: BRCAX, no cancer, H04, set 2


title: Sporadic cancer, I01, set 2


title: BRCAX, cancer, G06, set 2


title: BRCAX, no cancer, H02, set 2


title: BRCA1/2, cancer, G10, set 2


title: BRCA1/2, no cancer, G07, set 2


title: BRCA1/2, cancer, G12, set 2


title: BRCAX, no cancer, I07, set 2


title: BRCAX, cancer, H07, set 2


title: BRCA1/2, no cancer, G09, set 2


title: BRCAX, cancer, H10, set 2


title: BRCAX, cancer, H11, set 2


title: BRCAX, no cancer, H01, set 2


title: BRCAX, cancer, G04, set 2


title: BRCAX, cancer, G05, set 2


title: BRCA1/2, no cancer, G08, set 2


title: BRCAX, no cancer, G03, set 2


title: BRCAX, no cancer, G02, set 2


title: BRCAX, no cancer, G01, set 2


title: No family history, no cancer, F12, set 2


title: No family history, no cancer, F11, set 2


title: Sporadic cancer, F02, set 2


title: BRCA1/2, no cancer, E05, set 2


title: BRCA1/2, cancer, E01, set 2


title: Sporadic cancer, F04, set 2


title: BRCA1/2, no cancer, E02, set 2


title: BRCAX, no cancer, E11, set 2


title: BRCA1/2, cancer, E10, set 2


title: Sporadic cancer, F03, set 2


title: BRCA1/2, cancer, E07, set 2


title: Sporadic cancer, F06, set 2


title: BRCAX, no cancer, E08, set 2


title: No family history, no cancer, F09, set 2


title: Sporadic cancer, F05, set 2


title: No family history, no cancer, F10, set 2


title: BRCA1/2, cancer, E09, set 2


title: Sporadic cancer, F01, set 2


title: BRCAX, cancer, E12, set 2


title: No family history, no cancer, F07, set 2


title: BRCA1/2, no cancer, E03, set 2


title: BRCAX, no cancer, D10, set 2


title: BRCAX, no cancer, D12, set 2


title: BRCAX, no cancer, D11, set 2


title: BRCA1/2, no cancer, E04, set 2


title: BRCAX, no cancer, D09, set 2


title: BRCA1/2, cancer, E06, set 2


title: BRCAX, cancer, D06, set 2


title: BRCA1/2, cancer, C10, set 2


title: BRCA1/2, cancer, C02, set 2


title: BRCAX, cancer, D04, set 2


title: BRCA1/2, no cancer, C07, set 2


title: BRCAX, cancer, D05, set 2


title: BRCAX, cancer, D01, set 2


title: BRCA1/2, no cancer, C06, set 2


title: BRCA1/2, cancer, C12, set 2


title: BRCA1/2, cancer, C03, set 2


title: BRCA1/2, no cancer, C09, set 2


title: BRCAX, cancer, D02, set 2


title: No family history, no cancer, B12, set 2


title: BRCA1/2, no cancer, C08, set 2


title: BRCAX, no cancer, B08, set 2


title: BRCAX, no cancer, B11, set 2


title: BRCAX, cancer, D03, set 2


title: BRCAX, cancer, B07, set 2


title: BRCA1/2, cancer, C01, set 2


title: BRCA1/2, no cancer, C04, set 2


title: BRCAX, no cancer, D07, set 2


title: BRCAX, no cancer, B10, set 2


title: BRCAX, cancer, B06, set 2


title: BRCA1/2, no cancer, C11, set 2


title: BRCAX, cancer, B05, set 2


title: BRCAX, no cancer, B09, set 2


title: BRCAX, no cancer, D08, set 2


title: BRCAX, cancer, B04, set 2


title: BRCAX, cancer, B03, set 2


title: BRCAX, no cancer, B02, set 2


title: No family history, no cancer, A10, set 2


title: BRCAX, no cancer, B01, set 2


title: No family history, no cancer, A01, set 2


title: No family history, no cancer, A07, set 2


title: Sporadic cancer, A02, set 2


title: No family history, no cancer, A08, set 2


title: Sporadic cancer, A06, set 2


title: BRCAX, cancer, U2017, set 1


title: BRCAX, cancer, V432, set 1


title: BRCAX, cancer, Y546, set 1


title: Sporadic cancer, A03, set 2


title: Sporadic cancer, A05, set 2


title: BRCAX, cancer, X524, set 1


title: BRCAX, cancer, W433, set 1


title: BRCA1/2, no cancer, Z3225, set 1


title: No family history, no cancer, A11, set 2


title: BRCAX, cancer, Q1080, set 1


title: BRCAX, cancer, S1133, set 1


title: Sporadic cancer, A04, set 2


title: BRCAX, cancer, P1075, set 1


title: BRCAX, cancer, T1463, set 1


title: BRCAX, cancer, R1104, set 1


title: BRCA1/2, cancer, C05, set 2


title: No family history, no cancer, A09, set 2


title: BRCA1/2, cancer, M1263, set 1


title: Sporadic cancer, J787, set 1


title: Sporadic cancer, H663, set 1


title: Sporadic cancer, E519, set 1


title: BRCA1/2, cancer, K1162, set 1


title: BRCAX, no cancer, AN757, set 1


title: Sporadic cancer, G660, set 1


title: BRCA1/2, no cancer, AC3228, set 1


title: BRCA1/2, no cancer, AD3231, set 1


title: BRCA1/2, cancer, L1176, set 1


title: Sporadic cancer, F548, set 1


title: Sporadic cancer, D480, set 1


title: Sporadic cancer, C474, set 1


title: No family history, no cancer, A12, set 2


title: BRCA1/2, no cancer, K05, set 1


title: BRCAX, no cancer, AL3236, set 1


title: BRCAX, no cancer, AH3232, set 1


title: BRCAX, cancer, K04, set 1


title: BRCAX, no cancer, AJ3234, set 1


title: BRCAX, no cancer, AM3237, set 1


title: BRCA1/2, no cancer, AA3226, set 1


title: BRCAX, no cancer, AI3233, set 1


title: BRCAX, no cancer, AK3235, set 1


title: BRCAX, no cancer, AF3229, set 1


title: BRCA1/2, no cancer, AB3227, set 1


title: BRCAX, no cancer, AE1543, set 1


title: Sporadic cancer, I782, set 1


title: BRCAX, no cancer, AG3230, set 1


title: BRCA1/2, cancer, K03, set 1


title: BRCAX, cancer, K02, set 1


title: BRCA1/2, cancer, K01, set 1


title: Sporadic cancer, J07, set 1


title: No family history, no cancer, J11, set 1


title: No family history, no cancer, J10, set 1


title: Sporadic cancer, J08, set 1


title: No family history, no cancer, J09, set 1


title: No family history, no cancer, J12, set 1


title: Sporadic cancer, J04, set 1


title: Sporadic cancer, J06, set 1


title: Sporadic cancer, I13, set 1


title: BRCAX, no cancer, I11, set 1


title: BRCA1/2, no cancer, I08, set 1


title: Sporadic cancer, I04, set 1


title: BRCAX, cancer, H12, set 1


title: BRCAX, no cancer, I06, set 1


title: Sporadic cancer, I01, set 1


title: BRCAX, cancer, H10, set 1


title: BRCA1/2, no cancer, I09, set 1


title: BRCA1/2, no cancer, I12, set 1


title: BRCAX, no cancer, I07, set 1


title: Sporadic cancer, I02, set 1


title: BRCA1/2, no cancer, I10, set 1


title: Sporadic cancer, J05, set 1


title: No family history, no cancer, J01, set 1


title: Sporadic cancer, I03, set 1


title: BRCAX, no cancer, I05, set 1


title: No family history, no cancer, J02, set 1


title: BRCAX, cancer, H09, set 1


title: Sporadic cancer, J03, set 1


title: BRCAX, cancer, H11, set 1


title: BRCAX, cancer, H08, set 1


title: BRCAX, no cancer, H03, set 1


title: BRCAX, no cancer, H06, set 1


title: BRCAX, no cancer, H02, set 1


title: BRCAX, cancer, H07, set 1


title: BRCAX, no cancer, H01, set 1


title: BRCA1/2, cancer, G11, set 1


title: BRCAX, no cancer, H04, set 1


title: BRCA1/2, no cancer, G09, set 1


title: BRCA1/2, cancer, G12, set 1


title: BRCA1/2, cancer, G10, set 1


title: BRCA1/2, no cancer, G07, set 1


title: BRCA1/2, no cancer, G08, set 1


title: BRCAX, cancer, G05, set 1


title: No family history, no cancer, F10, set 1


title: BRCAX, no cancer, G02, set 1


title: BRCAX, cancer, G06, set 1


title: BRCAX, no cancer, G03, set 1


title: No family history, no cancer, F07, set 1


title: BRCAX, cancer, G04, set 1


title: Sporadic cancer, F06, set 1


title: No family history, no cancer, F09, set 1


title: Sporadic cancer, F05, set 1


title: Sporadic cancer, F04, set 1


title: Sporadic cancer, F03, set 1


title: Sporadic cancer, F02, set 1


title: Sporadic cancer, F01, set 1


title: BRCAX, no cancer, G01, set 1


title: No family history, no cancer, F12, set 1


title: No family history, no cancer, F11, set 1


title: BRCAX, no cancer, E11, set 1


title: BRCA1/2, cancer, E09, set 1


title: BRCA1/2, cancer, E01, set 1


title: BRCA1/2, cancer, E10, set 1


title: BRCA1/2, no cancer, E05, set 1


title: BRCAX, cancer, E12, set 1


title: BRCA1/2, cancer, E07, set 1


title: BRCA1/2, cancer, E06, set 1


title: BRCA1/2, no cancer, E04, set 1


title: BRCA1/2, no cancer, E02, set 1


title: BRCAX, no cancer, E08, set 1


title: BRCA1/2, no cancer, E03, set 1


title: BRCAX, no cancer, D12, set 1


title: BRCAX, no cancer, D10, set 1


title: BRCAX, no cancer, D11, set 1


title: BRCAX, cancer, D03, set 1


title: BRCAX, no cancer, D07, set 1


title: BRCAX, no cancer, D09, set 1


title: BRCAX, no cancer, D08, set 1


title: BRCAX, cancer, D05, set 1


title: BRCAX, cancer, D06, set 1


title: BRCAX, cancer, D02, set 1


title: BRCA1/2, cancer, C12, set 1


title: BRCAX, cancer, D01, set 1


title: BRCA1/2, no cancer, C11, set 1


title: BRCAX, cancer, D04, set 1


title: BRCA1/2, no cancer, C08, set 1


title: BRCA1/2, no cancer, C09, set 1


title: BRCA1/2, no cancer, C07, set 1


title: BRCA1/2, no cancer, C06, set 1


title: BRCAX, no cancer, B11, set 1


title: BRCA1/2, no cancer, C04, set 1


title: BRCA1/2, cancer, C01, set 1


title: BRCA1/2, cancer, C03, set 1


title: BRCA1/2, cancer, C05, set 1


title: BRCAX, no cancer, B08, set 1


title: BRCA1/2, cancer, C02, set 1


title: No family history, no cancer, B12, set 1


title: BRCAX, no cancer, B09, set 1


title: BRCAX, cancer, B07, set 1


title: BRCAX, cancer, B06, set 1


title: BRCAX, cancer, B05, set 1


title: BRCAX, no cancer, B10, set 1


title: BRCAX, no cancer, B01, set 1


title: BRCAX, cancer, B04, set 1


title: BRCA1/2, cancer, C10, set 1


title: BRCAX, no cancer, B02, set 1


title: No family history, no cancer, A08, set 1


title: Sporadic cancer, A04, set 1


title: N43s_6_sequence_aligned.fastq

status: Public on Jul 31 2015

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

library_source: transcriptomic

data_processing:
Basecalling was done using Illumina CASAVA v1.4
Sequences were adaptor trimmed and aligned to hg18 genome using Novoalign V2.0.
Known piRNA sequences were downloaded from a publically available piRNA database (RNAdb: http://research.imb.uq.edu.au/rnadb/). The hg18 genome loci that matched perfectly to the piRNA sequences were identified and piRNA expression levels were counted using R scripts.
Genome_build: hg18
Supplementary_files_format_and_content: text format containing expression counts

source_name: Nomral renal tissue

extract_protocol:
Total RNA was isolated using the Recover All Total Nucleic Acid Isolation Kit (Ambion, Austin, TX, USA), following the manufacturers' protocols.
Libraries were prepared according to Illumina's instructions

tag: Stage

value: Normal


title: Sporadic cancer, A02, set 1


title: No family history, no cancer, A10, set 1


title: BRCAX, cancer, B03, set 1


title: No family history, no cancer, A11, set 1


title: No family history, no cancer, A12, set 1


title: No family history, no cancer, A07, set 1


title: Sporadic cancer, A03, set 1


title: No family history, no cancer, A09, set 1


title: M13_s_4_sequence_aligned.fastq

source_name: Renal carcinoma tissue

value: Metastatic


title: Sporadic cancer, A05, set 1


title: Sporadic cancer, A06, set 1


title: Wound_rep2

status: Public on Sep 30 2015

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

description: RNA extracted from the wound crust 28 days post infection from diabetic mouse 2.

hyb_protocol: For each Pseudomonas genome array (#900339, Affymetrix), labeled fragmented cDNA (3.5 ug from wound 1 and 2.5 ug from wound 2) was hybridized to the arrays at 50oC for 16 h with constant rotational mixing at 60 rpm. Washing and staining of the arrays were performed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 7G. Affymetrix GCOS v1.4 was used to generate CEL and CHP files.

data_processing: Affymetrix CEL files were imported into FlexArray v1.6.1 for QC and data analysis. The RMA algorithm was applied to the arrays, which included background correction, quantile normalization, and median polishing. A signal intensity (SI) filter was applied to the normalized data to select transcripts with SI> 26 in both arrays. For transcripts meeting this SI requirement in both arrays, the average SI was calculated and used to conservatively identify the most abundant transcripts in mouse wound crusts. The top 5% (285) of transcripts represented on the arrays were selected for a gene list for further analysis.

label: Biotin

organism: Pseudomonas aeruginosa PAO1

source_name: Wound crust from diabetic mouse 2, 28 days post infection

label_protocol: The RNA was reverse transcribed at 42° C overnight using 1 µl random primers, 1 µl Superase-In, 6 µl 5x first strand buffer, 3 µl 0.1 M DTT, 0.6 µl 100mM dNTPs, and 3 µl Superscript II. After synthesis, the remaining RNA was hydrolyzed by the addition of 0.5 M EDTA and 1 N sodium hydroxide. The cDNA samples were neutralized with 1 N HCl and 1 M sodium acetate. The reactions were then cleaned on MinElute columns according to the manufacturer's instructions. The resulting cDNA was fragmented with 0.6 Units DNase I per microgram cDNA for 10 minutes at 37° C. The enzyme was inactivated by heating to 98° C for 10 minutes.

growth_protocol: Pseudomonas aeruginosa PAO1 was grown overnight in LB medium at 37°C on a shaker and then diluted 1:1000 in sterile phosphate buffer solution to produce inocula for biofilm growth. For biofilm growth, polycarbonate membrane filters were cut using a 6 mm biopsy punch and sterilized with exposure to UVC light for 5 minutes on each side. The filters were inoculated with 2 μl of PAO1 and incubated at 37°C for 72 h, with transfer to fresh LB agar plates at 24 and 48 h prior to application to the wound. The mouse model was developed to study chronic wounds infected with P. aeruginosa biofilms in diabetic (db/db) mice and has been described in detail (Zhao et al., 2010, 2012). Briefly, six millimeter punch biopsy wounds were created on the dorsal surface of diabetic (db/db) mice, subsequently infected with P. aeruginosa (PAO1) biofilms two days post-wounding, and covered with semi-occlusive dressings for two weeks.

extract_protocol: RNA was extracted using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA). RNA quality was verified on a Bioanalyzer 2100 Nanochip (Agilent, Santa Clara, CA). Total RNA was quantified on the NanoDrop 1000 (NanoDrop Technologies, Wilmington, DE). P. aeruginosa-specific rRNA from within the total RNA was analyzed by RT-qPCR of the 16S rRNA.

treatment_protocol: Wound crusts from wounds infected with PAO1 from two mice were surgically excised at 28 d and the duplicate specimens were processed independently. Each wound crust was collected and stored in 1 ml of RNALater at -20oC.

tag: strain/background

value: wound crust

value: 28 days post infection


title: Wound_rep1

description: RNA extracted from the wound crust 28 days post infection from diabetic mouse 1.

source_name: Wound crust from diabetic mouse 1, 28 days post infection


title: N27_s_5_sequence_aligned.fastq


title: No family history, no cancer, A01, set 1

tag: cell type


title: MS patient 7 (after treatment)

status: Public on May 02 2015

city: Piscataway

first: Konstantin

last: Balashov

state: NJ

address: 683 Hoes Lane

department: Neurology

institute: Rutgers-RWJMS

description: Gene expression data from Plasmacytoid dendritic cells (pDCs) of MS patients after IFN-beta treatment

hyb_protocol: Hybridization, staining and washing of all arrays were prerormed in the Affymetrix hybridization oven and Fluidics module as per the manufacturer's protocols

scan_protocol: GeneChips were scanned using a Affymetrix GeneArray Scanner 3000.

data_processing: All arrays referred to in this study were assessed for array performance prior to data analysisusing Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter. The data were analyzed with GeneSpring software (Agilent Technologies).  RMA summarization, quantile normalization, and median of all samples baseline transformation parameters were chosen in expression data transformation step.

source_name: Plasmacytoid dendritic cells (pDCs) of MS patient after IFN-beta treatement

label_protocol: Fifty nanograms of total RNA from each sample was amplified to cDNA, fragmentated and biotinylated using the Nugen kits WT Ovation Pico.

growth_protocol: Peripheral blood mononuclear cells (PBMC) were separated from blood samples by Ficoll density gradient. Separation of pDCs was done by immunomagnetic sorting using BDCA-4 cell isolation kit. Separated pDCs were immediately resuspended in RNA cell protect reagent solution (Qiagen) to protect RNA from degradation and were stored at -80oC.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Further purified with Qiagen RNAeasy columns with DNase treatment.

treatment_protocol: We studied cells from 18-50 year old healthy donors (HD), patients with relapsing-remitting MS (RR MS) diagnosed according to the 2010 McDonald criteria. Each healthy subject had one blood draw. Each MS patient had two blood draws: before and three months after treatment with IFN-beta.

tag: disease state

value: MS

tag: individual

value: patient 7

value: Plasmacytoid dendritic cells (pDCs)

value: Female

tag: agent

value: IFN-beta


title: MS patient 8 (after treatment)

value: patient 8

value: Male

tag: age


title: MS patient 8 (before treatment)

description: Gene expression data from Plasmacytoid dendritic cells (pDCs) of MS patients before IFN-beta treatment

source_name: Plasmacytoid dendritic cells (pDCs) of MS patient before IFN-beta treatement

value: untreated


title: Healthy donor 6

description: Gene expression data from Plasmacytoid dendritic cells (pDCs) of healthy donors

value: control

value: Healthy donor 6


title: Healthy donor 8

source_name: Plasmacytoid dendritic cells (pDCs) of healthy donor

value: Healthy donor 8


title: MS patient 2 (before treatment)

value: patient 2


title: MS patient 9 (after treatment)

value: patient 9


title: MS patient 3 (before treatment)

value: patient 3


title: MS patient 5 (after treatment)

value: patient 5


title: MS patient 1 (after treatment)

value: patient 1


title: Healthy donor 3

value: Healthy donor 3


title: MS patient 6 (before treatment)

value: MS

value: patient 6


title: MS patient 4 (after treatment)

value: patient 4

value: Plasmacytoid dendritic cells (pDCs)


title: MS patient 9 (before treatment)

value: Female


title: MS patient 5 (before treatment)


title: Healthy donor 2

value: Healthy donor 2


title: Healthy donor 4

value: Healthy donor 4


title: MS patient 3 (after treatment)

value: Male

value: IFN-beta


title: MS patient 2 (after treatment)


title: MS patient 6 (after treatment)


title: Healthy donor 5

value: control

value: Healthy donor 5

value: untreated


title: MS patient 7 (before treatment)

value: patient 7


title: MS patient 1 (before treatment)


title: MS patient 4 (before treatment)


title: Healthy donor 1

value: Healthy donor 1


title: Healthy donor 7

value: Healthy donor 7


title: 142_V1C_Chd8

status: Public on Jan 21 2015

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

description: anonymized aligned ChIP-Seq reads were provided as raw data

data_processing:
Bowtie (v0.12.9)
zcat /sequencers/sequencerO/runs/131021_SN7001144_0397_AH7LYYADXX/Data/Intensities/BaseCalls/Unaligned/Project_Jc798/Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.fastq.gz | bowtie -B 1 -p 8 --chunkmbs 256 -m 1 -x 1000 /home/jc798/GENOME/contam/contam - --al=131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.contam   --un=131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.unaligned 131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.multi ; bowtie -B 1 -p 8 --chunkmbs 256 -m 1 -x 1000 /home/jl56/GENOME/hg19/dna/hg19_nh 131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.unaligned 131021_SN7001144_0397_AH7LYYADXX_Sample_JCOT_146_004/JCOT_146_004_TGACCA_L001_R1_010.bowtie
Custom perl script
Cotney et al, Cell 2013.
RSEQTools (0.6.0)
cat Sample_JCOT_166_141_DFC_Chd8.bowtie | bowtie2mrf genomic > ../mrf/Sample_JCOT_166_141_DFC_Chd8.mrf
RSEQTools (0.6.0) and wigToBigWig
cat Sample_JCOT_148_hNSC_H3K27ac_1.mrf | mrf2wig Sample_JCOT_148_hNSC_H3K27ac_1; cat Sample_JCOT_148_hNSC_H3K27ac_1_chr*.wig | grep -v track > Sample_JCOT_148_hNSC_H3K27ac_1.wig; rm Sample_JCOT_148_hNSC_H3K27ac_1_chr*.wig; wigToBigWig -clip Sample_JCOT_148_hNSC_H3K27ac_1.wig /home/jl56/GENOME/hg19/dna/hg19_nh.chrom.sizes Sample_JCOT_148_hNSC_H3K27ac_1.bw
Tophat (v2.0.9)
tophat -p 8 -G /data/ss64/ajw54/Tophat/transcriptome_data/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf  -o 4_Sample_JCOT_214_004_ --no-novel-juncs --no-novel-indels --read-mismatches 1 --read-gap-length 0 --read-edit-dist 1 --read-realign-edit-dist 0 --b2-N 1 -g 1 -m 0 -M --library-type=fr-firststrand /data/ss64/ajw54/Tophat/transcriptome_data/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome ../Sample_JCOT_214_004_R1.fastq.gz ../Sample_JCOT_214_004_R2.fastq.gz
Htseq (v0.5.4)
samtools view ../4_Sample_JCOT_214_004_/accepted_hits.sorted.bam | htseq-count -q -s reverse - /data/ss64/ajw54/Tophat/transcriptome_data/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf > 4_Sample_JCOT_214_004_counts.txt
Genome_build: hg19 for human samples
Genome_build: mm9 for mouse samples
Genome_build: UCSC KnownGene annotation (05/13/2013)
Supplementary_files_format_and_content: bam (anonymized aligned read cooridinates)
Supplementary_files_format_and_content: bed (peak calls in UCSC bed format)
Supplementary_files_format_and_content: bigWig (signal tracks)
Supplementary_files_format_and_content: counts.txt (abundance measurements per gene reported by HTSeq)

source_name: Human P5 Primary Visual Cortex

growth_protocol:
RNA-Seq: H9 derived human neural stem cells (hNSCs) were purchased from Life Science Technology (cat no. N7800100).  Cells were maintained in KnockOu™DMEM/F12 medium (12660-012, Life Science Technology) supplemented with StemPro® supplement (A1050801, Life Science), 20ng/ml basic FGF recombinant protein (GF003, EMD Millipore Corporation), and 20ng/ml EGF recombinant protein (GF144, EMD Millipore Corporation). These cells were cultured as a attached monolayer in tissue culture flasks precoated with the BD Metrigel  ™ hESC-qualified Matrix (354277, BD) in a 37C incubator with 5% CO2.
ChIP-seq: H9 derived human neural stem cells (hNSCs) were purchased from Life Science Technology (cat no. N7800100).  Cells were maintained in KnockOu™DMEM/F12 medium (12660-012, Life Science Technology) supplemented with StemPro® supplement (A1050801, Life Science), 20ng/ml basic FGF recombinant protein (GF003, EMD Millipore Corporation), and 20ng/ml EGF recombinant protein (GF144, EMD Millipore Corporation). These cells were cultured as a attached monolayer in tissue culture flasks precoated with the BD Metrigel  ™ hESC-qualified Matrix (354277, BD) in a 37oC incubator with 5% CO2.  Human brain tissue was excised from frozen brain slabs with a rotary cutting instrument. Mouse embryonic tissue was dissected from E17.5 mouse embryos harvested from timed pregnant mothers.

extract_protocol:
RNA-seq: Total RNA was extracted using the miRNeasy Micro Kit (217084, Qiagen), as described in the manufacturer’s instructions. The step of DNase I digestion was included to avoid potential DNA contamination.
Standard Illumina Multiplexed Paired-End Library Prep performed by the Yale Center for Genome Analysis (YCGA).
ChIP-seq: Nuclei were extracted in six pellet volumes of lysis buffer I (50 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubating on ice for 15 minutes.  Tissue was homogenized with a dounce homogenizer and nuclei were harvested by centrifugation at 2000g for 10 minutes at 4°C.  Nuclei were resuspended in five pellet volumes of nuclear lysis buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and incubated on ice for 20 minutes.  300 mL nuclear lysates in 1.5 mL tubes were sonicated using a Misonix S4000 with 431A cup horn (10 second pulses, 10 second rest, 20 minutes total, 2°C maintained by circulating chiller).  Following sonication insoluble material was pelleted by centrifugation at 16000g for 10 minutes at 4°C.  A small sample of soluble crosslinked chromatin was purified, checked for correct sonication size range and DNA concentration was measured.  100 ug of chromatin was diluted to 450 mL with dilution buffer (16.7 mM Tris pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, 1x Roche Complete Protease inhibitor, 5 mM sodium butyrate) and added to 50 uL of Protein G Dynabeads (Invitrogen) prebound with 10 mg of CHD8 antibody.  Samples were incubated overnight at 4°C with rotation.  Beads were precipitated on magnet stand and washed five times with 1 mL of wash buffer (100 mM Tris pH8.0, 500 mM LiCl, 1% NP-40, 1% deoxycholic acid, 1x Roche Complete protease inhibitor, 5mM sodium butyrate) and once with TE.  Immunoprecipiated chromatin was eluted from beads with 50 mL of elution buffer (TE + 1% SDS) at 65°C for 10 minutes.  Crosslinks were reversed overnight at 65°C.  Chromatin was treated with RNAseA and proteinase K then purified with Qiagen PCR cleanup kit.  Concentration of eluted chromatin was measured with PicoGreen (Invitrogen).

treatment_protocol:
RNA-seq: All shRNAs were transfected using Amaxa Nucleofector (Laza) according to the manufacturer’s instructions. The following shRNAs were used: shCHD8 #C (CloneID: V2LHS_201084, Thermo), mature antisense sequence TAAAGACTCCAATGAGCAG); shCHD8#G (Clone ID: V3LHS_311510, Thermo), mature antisense sequence ACTGTTGAATCATCTGCCT). After transfection, cells were grown for 48 hours in KnockOut™ DMEM/F-12 medium.  Cells were then trypsinized by Accutase (Life Science Technology) and sorted on FCS Aria II machine.  Both western blotting and RT-qPCR were used to determine the downregulation of CHD8 expression.
ChIP-seq: Human brain tissue or mouse cortex tissue were briefly homogenized and crosslinked with 1% formaldehyde at room temperature with rotation for 15 minutes.  Crosslinking was quenched with 150 mM glycine. hNSC cells were crosslinked on culture plates, quenched with glycine,  scraped off plates, and transferred to 15 mL conical tubes. Cultured cells or tissue were harvested by centrifugation at 1500g for 5 min at 4C.   Pelleted tissue was washed twice with cold PBS, flash frozen and stored at -80°C.

tag: developmental stage

value: Primary Visual Cortex

tag: chip antibody

value: CHD8 N terminus

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: 142_Striatum_Chd8

source_name: Human P5 Striatum

value: Striatum


title: 142_DFC_Chd8

source_name: Human P5 Dorsolateral Frontal Cortex

value: Dorsolateral Frontal Cortex


title: 536_043 PTU mouse

status: Public on Apr 28 2015

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: liver

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

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

value: liver

value: Negative

tag: ptu

value: Positive


title: 141_CBC_Chd8

source_name: Human P5 Cerebellum

value: Cerebellum


title: 141_DFC_Chd8


title: 141_Striatum_Chd8


title: 536_031 T3 stimulated mouse


title: 536_030 T3 stimulated mouse


title: Cell line drug naive_OPM-2

status: Public on Apr 19 2015

city: Aalborg

first: Steffen

middle: Falgreen

last: Larsen

address: Sdr Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

description: Gene expression data from cell lines before they are treated with chemotherapy

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip HG-U133 Plus 2.0 array using GeneChip Hybridization Oven 640 according to the manufacturer’s protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: Data were analyzed using R version 3.0.1  and several R and Bioconductor packages. The .CEL-files were pre-processed using the Robust Multichip Average procedure (RMA) as implemented in the just.rma function from the Bioconductor package affy. All RMA-normalised arrays passed the statistical quality control provided by the function arrayQualityMetrics in the R-package arrayQualityMetrics.

source_name: malignant human B-cell cell line

label_protocol: Biotinylated cRNA were prepared using the GeneChip Expression 3’ amplification One-cycle Target Labeling (Affymetrix) from 5 ug total RNA

growth_protocol: Cell lines were cultured under standard conditions at 37°C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was isolated using a modified protocol of Trizol Reagent and Qiagen RNeasy. Shortly Trizol was added to cell pellets and incubated for 5 minutes at RT, 200µl chloroform was added and 2 minutes incubation at RT, the mixture was centrifuges at 12,000 g for 10 minutes at 4°C. The aqurous phase transfered to a new tube and 100 % ethanol added in 1.25X the volume. Mix well and transfer to mirVana columns and follow the manufacturers instruction from this point.

treatment_protocol: 5*10^6 cells in the exponential phase were harvested for total RNA isolation.

tag: cell line

tag: disease

value: Multiple myeloma

tag: growth medium

value: RPMI+10% FBS

tag: cyclophosphamide auc

tag: cyclophosphamide

value: Sensitive

tag: doxorubicin auc

value: Intermediate

tag: vincristine auc

tag: vincristine


title: Cell line drug naive_MM1S


title: 142_CBC_Chd8

tag: tissue


title: Cell line drug naive_MOLP-8

value: RPMI+20% FBS

value: Resistant


title: Cell line drug naive_AMO-1

value: Plasmacytoma


title: 141_V1C_Chd8


title: 534_083 PTU mouse


title: Cell line drug naive_LP-1

value: IMDM+10% FBS


title: 537_029 T3 stimulated mouse


title: Cell line drug naive_DB

value: DB

value: Diffuse large B-cell lymphoma

value: RPMI+20 % FBS


title: 537_022 PTU mouse


title: Cell line drug naive_KMS-11


title: Cell line drug naive_RPMI-8226


title: GD 9 Embryos Treated with 400 mg/kg Hydroxyurea [SG11514161_252800514757_S001_GE1_1105_Oct12_1_1]

status: Public on Jan 15 2015

city: Montreal

first: Nazem

last: El Husseini

state: QC

address: 3655 Promenade Sir William Osler

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

description: Gene expression following 3 h of exposure to hydroxyurea.

hyb_protocol: After 17 h of hybridization at 65 degrees Celsius, the microarray slides were washed as per the recommendations for the Agilent hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (SureScan G2600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software Version 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12). Normalized by shift to 75.0 percentile.

source_name: GD 9 embryos treated with 400 mg/kg hydroxyurea

label_protocol: For each sample, 600 ng of Cy3-labeled cDNA was used for the single-color microarray.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Mississauga, ON, Canada). The RNA concentration and purity of each sample were assessed by spectrophotometry using a NanoDrop1000 spectrophotometer (Fisher Scientific) and Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: Gestational day 9 embryos were treated with saline or 400 mg/kg hydroxyurea. The embryos were incubated for 3 hours, then dams were euthanized and embryos explanted.

tag: strain/background

value: whole embryo

value: gestational day 9 (GD 9)

tag: treatment

value: 400 mg/kg hydroxyurea


title: Cell line drug naive_KMM-1


title: GD 9 Embryos Treated with Saline [SG11514161_252800514757_S001_GE1_1105_Oct12_2_3]

description: Gene expression following 3 h of exposure to saline.

source_name: GD 9 embryos treated with saline

tag: age

value: saline


title: Tumor 15

status: Public on Nov 01 2013

first: Atsushi

last: Terunuma

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

institute: National Cancer Institute

hyb_protocol: ssDNA was hybridized onto Gene Chip Human Gene 1.0 ST Arrays according to Affymetrix standard protocols (Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip ® Scanner Scanner 3000 as instructed by the manufacture.

data_processing: Expression values were generated by RMA within Affymetrix Expression Console software.

source_name: Human Breast Tumor

label_protocol: 250 ng of RNA was synthesized to cDNA using the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript Expression arrays (Life technologies, Grand Island, NY).  Fragmentation and labeling of the cDNA was carried-out using the GeneChip WT Terminal Labeling Kit (Affymetrix) according to standard protocols.

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen, Carlsbad, CA) as directed by the manufacturer. The quantity and quality of RNA was assessed with a Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: race

value: African-American

tag: tissue type

value: Tumor

tag: estrogen receptor status

value: Positive

tag: triple negative tumor

value: No

tag: Stage

value: IIA

tag: tumor grade

tag: node status

tag: survival (months)

tag: survival event

value: Dead

tag: death due to cancer

value: Yes

tag: neoadjuvant therapy

tag: hormone-therapy

tag: chemotherapy

tag: tumor or normal lhc


title: GD 9 Embryos Treated with 400 mg/kg Hydroxyurea [SG11514161_252800514734_S001_GE1_1105_Oct12_2_4]

tag: strain/background

tag: tissue


title: Tumor 22

tag: age

value: Alive


title: GD 9 Embryos Treated with 400 mg/kg Hydroxyurea [SG11514161_252800514734_S001_GE1_1105_Oct12_1_1]

tag: treatment


title: Placenta_Control_C5

status: Public on Feb 01 2013

city: Shanghai

first: qian

middle: Yu

last: Xiang

state: 上海市

address: Yixuanyuan road NO.138

country: China

institute: Fudan University

description: The sample is from normal pregnancies by caesarean section

hyb_protocol: All samples were hybridized in NimbleGen Hybridization System following their standard operating protocol. See www.nimblegen.com.

scan_protocol: The processed slides were scanned with the Axon GenePix 4000B microarray scanner according to the standard operating protocal.See www.nimblegen.com.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5), and Robust multi-array average (RMA) method was used to offer quantile normalization and background correction.

source_name: normal term placentas

label_protocol: The samples were labeled using a NimbleGen One-Color DNA Labeling Kit following their standard operating protocol.See www.nimblegen.com.

extract_protocol: Total RNAs were extracted from placentas using the mirVana™ miRNA Isolation Kit (Ambion) according to manufacturer’s instruction, including a DNase digestion step.

treatment_protocol: All clinical placentas from normal and pathological pregnancies were collected immediately after the caesarean section. Two ~ 1 cm3 fragments were dissected from the placenta, after removal of maternal blood by vigorous washing in phosphate buffered saline (PBS). The tissues were maintained in RNAlater

tag: phenotype

value: normal


title: Cell line drug naive_OCI-Ly7

tag: cell line

tag: disease

tag: growth medium

value: RPMI+10 % FBS

tag: cyclophosphamide auc

tag: cyclophosphamide

value: Intermediate

tag: doxorubicin auc

value: Resistant

tag: vincristine auc

tag: vincristine


title: Placenta_PE_P2

description: The sample is from preeclamptic pregnancies by caesarean section

source_name: preeclamptic term placentas

value: preeclampsia


title: Placenta_Control_C6


title: Cell line drug naive_KMS-12-BM

value: Multiple myeloma

value: RPMI+20% FBS


title: Expression profile of P. aeruginosa isolate BBa grown on Nematode Growth Medium (NGM) (replicate B)

status: Public on Dec 31 2011

city: Sydney

first: Jim

last: Manos

state: NSW

address: Camperdown

country: Australia

institute: University of Sydney

description: Microarrays were performed in biological duplicate for each sample in each condition tested (same isolate; with different culture, RNA extraction, and microarray) to assess biological variability at the culture level. Substitution of different biological (culture) replicates had little or no effect on the prediction of differentially expressed genes.

hyb_protocol: The overall quality of fragmented DNA was assessed using a Bioanalyser 2100 (Agilent GmbH, Germany) and hybridized to the P. aeruginosa PAO1 GeneChip microarray as suggested by the manufacturer (Affymetrix). A ‘test3’ array (Affymetrix-100 housekeeping genes) was used to determine cDNA suitability for the full array on the Affymetrix PAO1 GeneChip® (Affymetrix). Hybridizations were conducted at 50oC and 60 rpm for 16h, followed by washing of the chip.

scan_protocol: Scanning of the chip was conducted on an Affymetrix GeneChip Scanner 3000 at 532nm for excitation/570nm for emission. CEL and CHP files were generated using the scanner program GCOS (Affymetrix).

data_processing: Microarray data were analysed using BIOCONDUCTOR. The robust multi-array average (RMA) method was used for data normalization, incorporating probe level background-correction, quantile normalization, and linear extraction of a final expression measure for each gene per array. The empirical Bayes method was used to determine differential gene expression. The false discovery rate method was controlled to reduce false positives and a positive B-statistic (B>0) was used as a guide for statistically significant differential expression.

organism: Pseudomonas aeruginosa

source_name: Gram negative bacterium

label_protocol: Fragments 3’-end-labeled using GeneChip® DNA Labelling Reagent (Affymetrix).

growth_protocol: 100ul of an overnight LB culture of BBa was spread onto NGM and incubated for 72hrs at 25 degrees Celsius to mimic the growth conditions seen in a C. elegans slow killing model

extract_protocol: Cells were harvested at 72 h by scraping the lawn of bacteria from the NGM plate using a sterile cell scraper, followed by washing in ice-cold 1× PBS to increase cell yield and remove debris. Briefly, suspensions (~10 ml) were transferred to a 50 ml Falcon tube and washed 5× or until the pellet was cleared of non-cellular debris with an equal amount of 1× PBS by pelleting (5 min/5000 x g/4°C), and re-suspension in fresh ice-cold 1× PBS. All steps were performed on ice or at 4oC to avoid cell and RNA degradation. Cells were extracted for RNA as per the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix Inc. USA), using the Rneasy® Mini spin column (Qiagen). RNA quality and the presence of residual DNA were checked by formaldehyde agarose gel electrophoresis. cDNA was synthesized, fragmented and labelled as per the technical manual, and cDNA was purified using the MinEluteTM PCR Purification kit (Qiagen) and fragmented with DNase I (GE Healthcare Bio-Sciences, Australia).

tag: growth phase

value: stationary growth on NGM

tag: strain

value: BBa

tag: isolate

value: cystic fibrosis isolate from sputum sample


title: GD 9 Embryos Treated with Saline [SG11514161_252800514757_S001_GE1_1105_Oct12_1_2]

value: whole embryo

value: gestational day 9 (GD 9)

value: saline


title: Expression profile of P. aeruginosa isolate CJ-2009a grown on Nematode Growth Medium (NGM) (replicate B)

growth_protocol: 100ul of an overnight LB culture of CJ-2009a was spread onto NGM and incubated for 72hrs at 25 degrees Celsius to mimic the growth conditions seen in a C. elegans slow killing model


title: Expression profile of P. aeruginosa isolate CJ-1d grown on Nematode Growth Medium (NGM) (replicate B)

growth_protocol: 100ul of an overnight LB culture of CJ-1d was spread onto NGM and incubated for 72hrs at 25 degrees Celsius to mimic the growth conditions seen in a C. elegans slow killing model


title: Expression profile of P. aeruginosa isolate BB2009a grown on Nematode Growth Medium (NGM) (replicate A)

growth_protocol: 100ul of an overnight LB culture of BB2009a was spread onto NGM and incubated for 72hrs at 25 degrees Celsius to mimic the growth conditions seen in a C. elegans slow killing model


title: Placenta_PE_P3


title: Expression profile of P. aeruginosa isolate BBa grown on Nematode Growth Medium (NGM) (replicate A)


title: Expression profile of P. aeruginosa isolate BB2009a grown on Nematode Growth Medium (NGM) (replicate B)


title: Expression profile of P. aeruginosa isolate CJ-2009a grown on Nematode Growth Medium (NGM) (replicate A)


title: Placenta_PE_P1


title: GD 9 Embryos Treated with Saline [SG11514161_252800514734_S001_GE1_1105_Oct12_2_3]


title: Expression profile of P. aeruginosa isolate CJ-1d grown on Nematode Growth Medium (NGM) (replicate A)


title: Placenta_PE_P6


title: Placenta_Control_C2


title: Placenta_Control_C1


title: Placenta_PE_P4


title: GD 9 Embryos Treated with Saline [SG11514161_252800514734_S001_GE1_1105_Oct12_1_3]


title: Placenta_Control_C4


title: Placenta_Control_C3


title: HDF_10

status: Public on Jul 01 2013

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: Human dermal fibroblast line 10

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Human dermal fibroblast line 10

label_protocol: Manufature's protocol

growth_protocol: DMEM containing 10% fetal bovine serum (by day 7) or Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF (from day 8 to 28) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human somatic cells were transduced with OCT3/4, SOX2, KLF4 and c-MYC using retrovirus. From day 7 to 28, we collected TRA-1-60 positive cells as nascent reprogrammed cells.

tag: cell type

value: Human dermal fibroblasts


title: Placenta_Control_C7


title: GD 9 Embryos Treated with 400 mg/kg Hydroxyurea [SG11514161_252800514757_S001_GE1_1105_Oct12_2_4]

tag: strain/background

value: 400 mg/kg hydroxyurea


title: P. aeruginosa intermittent infection isolate 5Mel replicate 2

status: Public on Jul 16 2011

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
5Mel ASM GI

hyb_protocol: Hybridisation solution conatining labelled cDNA covered the entire slide so that all spots were interrogated at once.

scan_protocol: The slides were dried and then scanned using an Axon 5000B scanner. Images were captured using the GenePix program and individual Cy5 images were stored as tif files.  These files were then used for any subsequent Bioinformatics analysis.

data_processing: The raw data were re-scaled to account for differences in individual hybridisation intensities. Background corrected data were imported into Partek© software, version 6.4 2010 (Partek Inc.), and quantile normalisation (Bolstad et al, 2003) was carried out. Genes that were differentially expressed were determined by an ANOVA model with a p-value cut-off of 0.05. We have normalized across the groups that we are comparing only, i.e. All Mel data sets have been normalised against each other and all AES data sets have been normalised against each other. We have not normalised Mel against AES at this point because we are not comparing them in this way, only within groups.

source_name: same CF patient lung sputum at 5 yrs

label_protocol: cDNA was fragmented using DNaseI and quality-checked using a Bioanalyser (Agilent, Germany). Chosen samples were KreaTech labelled (Agilent) and the hybridized to the Combimatrix® PANarray at the Australian Genome Research Facility (AGRF Ltd, Melbourne) using Cy5 dye.

growth_protocol: 10 ml of ASMDM in McCartney bottles was inoculated with 50μl of a 1:100 dilution of an overnight culture just under the surface of the media, incubated with a loose lid to permit gas exchange at 37 °C and harvested at 72h

extract_protocol: Bacteria and associated biofilm material were removed from the thick surface growth and deep projections. Cells were washed in ice-cold 1xPBS and RNA extracted as per the Qiagen RNeasy protocol (Qiagen Corp).

tag: infrequent clonal strain code

value: 5Mel, isogenic with 1Mel


title: P. aeruginosa intermittent infection isolate 5Mel replicate 1

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
5Mel ASM T


title: normal rep 1

status: Public on Jun 24 2011

city: Shenyang

first: Tao

last: Meng

state: Liaoning

address: 155 North Nanjing Street

department: Department of Obstetrics

institute: The First Affiliated Hospital of China Medical University

description: replicate 1

data_processing: The data were normalised using quantile normalisation with Illumina Beadstudio.

source_name: normal

tag: ethnic group

value: Chinese

tag: age

value: 28 years

tag: tissue

value: normal placentas


title: normal rep 4

description: replicate 4

value: 32 years


title: preeclampsia rep 4

description: replicate 4

source_name: preeclampsia

value: placentas from preeclamptic pregnancies


title: preeclampsia rep 6

description: replicate 6

value: 31 years


title: normal rep 5

description: replicate 5


title: preeclampsia rep 5

description: replicate 5

value: 20 years


title: P. aeruginosa chronic infection isolate AES-1M replicate 1

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
AES-1M ASM Q

source_name: same CF patient lung sputum at 11.7 yrs

tag: australian epidemic strain-1 code

value: AES-1M, isogenic with AES-1R


title: P. aeruginosa chronic infection isolate AES-1M replicate 2

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
AES-1M ASM P

growth_protocol: 10 ml of ASMDM in McCartney bottles was inoculated with 50μl of a 1:100 diluteion of an overnight culture just under the surface of the media, incubated with a loose lid to permit gas exchange at 37 °C and harvested at 72h


title: P. aeruginosa early infection isolate AES-1R replicate 2

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
AES-1R ASM C

source_name: CF patient lung sputum at 14 months


title: P. aeruginosa early infection isolate AES-1R replicate 1

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
AES-1R ASM 1


title: normal rep 2

description: replicate 2

value: 27 years


title: P. aeruginosa early infection isolate 1Mel replicate 2

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
1Mel ASM 69

source_name: CF patient lung sputum at 7 months


title: P. aeruginosa early infection isolate 1Mel replicate 1

description:
cDNA synthesized from total RNA was fragmented with DNaseI, KreaTech labelled and spotted on 10251 spots for array.
1Mel ASM 4


title: preeclampsia rep 1

description: replicate 1

value: 24 years


title: preeclampsia rep 3

description: replicate 3

value: 30 years


title: normal rep 6

description: replicate 6

value: 29 years


title: human.placenta.668

status: Public on Dec 10 2010

city: Raleigh

first: Shengdar

last: Tsai

state: NC

address: 4700 Hillsborough St.

institute: North Carolina State University

hyb_protocol: Hybridization for Illumina Human6-v2 BeadArrays was performed according to manufacturer’s instructions.  Labeled cRNA was hybridized to BeadArrays at 58°C for 18 hr.  Washing, blocking, and streptavadin-Cy3 staining was performed out following manufacturer’s protocol.

scan_protocol: BeadChips were scanned on the BeadArray Reader and scanned images were analyzed using BeadStudio software.

data_processing: Transcript data was log2 transformed, and quantile normalized.

source_name: human placenta

label_protocol: Labeling for Illumina Human6-v2 BeadArrays was performed according to manufacturer’s instructions.  Briefly, the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Foster City, CA) was used for a first and second strand reverse transcription step from 500 ng of total RNA.  This was followed by an overnight in vitro transcription reaction that incorporates biotin-labeled nucleotides.  1.5 ug of biotin-labeled cRNA was mixed with an Illumina-supplied hybridization buffer containing several control oligonucleotides.

extract_protocol: Total RNA was isolated from term human placenta using the Totally RNA kit (Ambion) following the manufacturer’s instructions with slight modifications.  Briefly, homogenized tissue chilled in liquid nitrogen was lysed in 10 volumes of denaturation solution (200 mg tissue, 2 ml denaturation solution).  The lysed sample was pre-cleared of bulk genomic DNA and cellular debris by spinning at 4,000 x g for 5 minutes. The supernatant was sequentially extracted with equal volumes phenol:chloroform, and acid phenol:chloroform (pH 4.5) using phase divider gels (Sigma), then precipitated with an equal volume of 100% isopropanol.  The pellet was washed twice with 70% ethanol and resuspended in elution buffer (1 mM Tris-Cl). Total RNA was treated with Turbo DNA-free to remove traces of genomic DNA contamination (Ambion).  RNA integrity was assessed using a Bioanalyzer (Agilent Biotechnologies) and only samples with a RIN > 7 were used.

value: placenta

tag: gender

value: M

tag: classification

value: Control

tag: gestational age

tag: induction of labor

value: spontaneous

tag: batch

value: A


title: human.placenta.624


title: normal rep 3

description: replicate 3

value: Chinese


title: preeclampsia rep 2

description: replicate 2

value: 23 years


title: human.placenta.777

value: F


title: human.placenta.626

value: B


title: human.placenta.625


title: LP-1

status: Public on Apr 30 2011

first: Martin

last: Boegsted

address: Sdr. Skovvej 15

institute: Aalborg Hospital, Aarhus University Hospital

description: Gene expression data from the multiple myeloma cell line LP-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 -18 hr at 45˚ C on GeneChip HG U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: .CEL files were background corrected and normalized by the just.rma function in the Bioconductor package affy

source_name: Multiple myeloma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, P/N 702232 Rev. 2, Affymetrix).

growth_protocol: The cell lines were subcultured 2 times per week. Subcultured 24 hours before harvest for RNA extraction.

extract_protocol: Total RNA was extracted using Invitrogen TRIzol Reagent combined with Qiagen RNeasy Mini kit. RNA quality was assessed using the Bioanalyser

treatment_protocol: Untreated. The density of the culture was determined and 5 million cells were harvested and stored in 1 ml Trizol until RNA extraction.

tag: cell line

tag: culturing medium

value: IMDM, 10% FBS


title: OPM-2

description: Gene expression data from the multiple myeloma cell line OPM-2


title: MOLP-8

description: Gene expression data from the multiple myeloma cell line MOLP-8


title: AMO-1

description: Gene expression data from the plasmacytoma cell line AMO-1

source_name: Plasmacytoma cell line


title: human.placenta.784


title: human.placenta.701

value: induced


title: human.placenta.657


title: human.placenta.695

value: preeclamptic


title: OCI-Ly7

description: Gene expression data from the diffuse large B-cell lymphoma cell line cell line OCI-Ly7

source_name: Diffuse large B-cell lymphoma cell line


title: human.placenta.748


title: MM1S

description: Gene expression data from the multiple myeloma cell line MM1S


title: DB

description: Gene expression data from the diffuse large B-cell lymphoma cell line cell line DB

value: DB


title: human.placenta.705


title: human.placenta.779


title: KMS-11

description: Gene expression data from the multiple myeloma cell line KMS-11


title: RPMI-8226

description: Gene expression data from the multiple myeloma cell line RPMI-8226


title: human.placenta.623


title: KMM-1

description: Gene expression data from the multiple myeloma cell line KMM-1


title: KMS-12-BM

description: Gene expression data from the multiple myeloma cell line KMS-12-BM


title: human.placenta.801


title: human.placenta.617


title: human.placenta.756


title: human.placenta.005


title: human.placenta.751


title: human.placenta.031


title: human.placenta.024


title: human.placenta.693


title: human.placenta.749


title: human.placenta.774


title: human.placenta.047


title: human.placenta.787


title: human.placenta.020


title: human.placenta.798


title: human.placenta.763


title: human.placenta.045


title: human.placenta.682


title: human.placenta.776


title: human.placenta.662


title: human.placenta.010


title: human.placenta.014


title: human.placenta.744


title: human.placenta.687


title: human.placenta.652


title: human.placenta.015


title: human.placenta.674


title: human.placenta.743


title: human.placenta.726


title: human.placenta.746


title: human.placenta.775


title: human.placenta.036


title: human.placenta.041


title: human.placenta.009


title: human.placenta.032


title: human.placenta.646


title: human.placenta.730


title: human.placenta.021


title: human.placenta.017


title: human.placenta.037


title: human.placenta.703


title: human.placenta.758


title: human.placenta.012


title: human.placenta.013


title: human.placenta.761


title: human.placenta.710


title: human.placenta.006


title: human.placenta.008


title: PGRN_A

status: Public on Nov 27 2010

city: Lund

first: Björn

last: Nilsson

address: BMC

department: Hematology and Transfusion Medicine

institute: Lund University

description: Gene expression data from fibrobast activated with Granulin

hyb_protocol: Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained  and washed according to the Affymetrix protocol.

scan_protocol: Affymetrix GCS 3000 7G scanner using Affymetrix standard protocol

data_processing: Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0)

source_name: fibroblast

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

growth_protocol: Normal human mamary fibroblasts were cultured with DMEM medium containing 10% calf serum and 10% fetal bovine serum

extract_protocol: Total RNA was extracted from fibroblasts using RNA extraction kits according to the manufacturer’s instructions (Qiagen)

treatment_protocol: Cells were cultured for 6 days in presence of 1ug/ml recombinant human granulin protein or PBS control

tag: clinical status

value: Normal mamary human

value: mammary fibroblast

tag: treatment

value: granulin


title: PGRN_C


title: Stationary phase gene expression profile of P. aeruginosa PA14 grown in Luria Broth (replicateB)

status: Public on May 31 2010

description: Microarrays were performed in biological duplicate for each sample in each condition tested (same isolate; with different culture, RNA extraction, and microarray) to assess biological variability at the culture level. Substitution of different biological (culture) replicates had little or no effect on the prediction of differentially expressed genes.

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: 2ml of LB was inoculated with a plate culture and incubated for the required time at 37oC with shaking (220rpm). A negative control containing no bacterial inoculum was included to detect media contamination.

extract_protocol: Cells were harvested at mid-stationary phase by addition of two volumes of BacterialProtect reagent (Qiagen) and centirfugation as per the Qiagen manual. The pelleted cells were extracted for RNA  as per the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix Inc. USA). All steps were performed on ice or at 4oC to avoid cell and RNA degradation. RNA quality and the presence of residual DNA were checked by formaldehyde agarose gel electrophoresis. cDNA was synthesized, fragmented and labelled as per the technical manual, and cDNA was purified using the MinEluteTM PCR Purification kit (Qiagen) and fragmented with DNase I (GE Healthcare Bio-Sciences, Australia).

treatment_protocol: Several colonies of pure culture from blood agar were inoculated  in Luria broth (LB) and cells were grown to mid stationary phase (~10h) for RNA extraction.

tag: growth phase/media

value: stationary phase grown in Luria broth

tag: strain

tag: isolate

value: clincal burns wound isolate


title: Stationary phase gene expression profile of P. aeruginosa PA14 grown in Luria broth(replicateA)

value: clinical burns wound isolate


title: Gene expression profile of P. aeruginosa PA14 grown to early log phase in ASMDM (replicateA)

hyb_protocol: Hybridizations were conducted at 50oC and 60 rpm for 16h, followed by chip washing.

scan_protocol: Affymetrix GeneChip Scanner 3000 at 532nm for excitation/570nm for emission.

label_protocol: Fragments were 3’-end-labeled using GeneChip® DNA Labelling Reagent (Affymetrix).

growth_protocol: Ten ml of ASMDM in McCartney bottles was inoculated under the surface with a starting culture of OD600 0.003 McFarland 0.5 Standard (bioMerieux SA, Marcy I’Etoile, France). Cultures were incubated with shaking at 37oC, with uninoculated medium used as a blank. Cell density was monitored using optical density at OD600. Cells were harvested during exponential growth at an OD600 = 0.2±0.02.

extract_protocol: Cells were pelleted (5 min, 5000 x g, 4°C), resuspended in 1× PBS, and treated with RNAprotect™ (Qiagen). Total RNA was isolated using the RNeasy Mini Purification kit (Qiagen) and RNA concentration determined at A260/280nm. RNA quality and the presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (2). cDNA was synthesized, fragmented and labelled as per the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix Inc. USA). cDNA was purified using the MinEluteTM PCR Purification kit (Qiagen), fragmented with DNase I (GE Healthcare Bio-Sciences). The overall quality of fragmented DNA was assessed using a Bioanalyser 2100 (Agilent).

value: early log phase in ASMDM


title: Stationary phase gene expression profile of P. aeruginosa PA14 grown in ASMDM (replicateB)

growth_protocol: Ten ml ASMDM in McCartney bottles was inoculated with 50 μl of the diluted culture just under the surface of the media. Bottles were incubated statically with a loose lid to permit gas exchange at 37°C, and checked for growth every 24 h. A negative control containing no bacterial inoculum was included to detect media contamination.

extract_protocol: Cells were harvested at 72 h by removal of biofilm material from the thick surface growth and the deep anaerobic projections, followed by washing in ice-cold 1× PBS to increase cell yield and remove debris. Briefly, suspensions (~10 ml) were transferred to a 50 ml Falcon tube and washed 5× or until the pellet was cleared of non-cellular debris with an equal amount of 1× PBS by pelleting (5 min/5000 x g/4°C), and re-suspension in fresh ice-cold 1× PBS. All steps were performed on ice or at 4oC to avoid cell and RNA degradation. Cells were extracted for RNA  as per the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix Inc. USA), and the Rneasy® Midi spin column with a larger membrane and therefore a greater surface area, was used to increase RNA yield. RNA quality and the presence of residual DNA were checked by formaldehyde agarose gel electrophoresis. cDNA was synthesized, fragmented and labelled as per the technical manual, and cDNA was purified using the MinEluteTM PCR Purification kit (Qiagen) and fragmented with DNase I (GE Healthcare Bio-Sciences, Australia).

treatment_protocol: An overnight culture of P. aeruginosa UCBPP-PA14 was diluted in 1× Phosphate Buffered Saline (PBS) to an optical density equivalent to a MacFarland 0.5 Standard (bioMerieux), corresponding to ca. 1×108 CFU/ml.

value: stationary phase grown in ASMDM


title: Gene expression profile of P. aeruginosa PA14 grown to early log phase in ASMDM (replicateB)