title: Laminin alpha5-deficient mouse embryonic intestine_replicate L7

status: Public on Jun 30 2012

type: RNA

city: Illkirch

first: Bernard

last: Jost

address: 1, rue  Laurent Fries

country: France

institute: IGBMC

hyb_protocol: 1. The Cy3. and Cy5-labeled reverse transcription reactions were mixed together, and purified and concentrated using the Microcon YM-30 filter (Millipore; Molsheim, France) 2. Cy3. and Cy5-labeled and purified probes were resuspended in 40µl of hybridization solution (50 % formamide, 4X SSC, 0.6 % SDS, 5X Denhardt solution, 0.25 mg/ml of mouse Cot-1 DNA, 1mg/ml salmon sperm DNA and 1mg/ml poly(dA). 3. Before hybridization, this probe solution was incubated for at least 45 min at 46C after a 2 min denaturation at 95C (pre-annealing). 4. The slides were immersed in a prehybridization solution (50 % formamide, 4X SSC, 0.1 % SDS, 0.1 % BSA fraction V) for 30 min at 46C before probe hybridization in a humid chamber overnight at 46C. 5. Prior scanning, three posthybridization washes were performed (first in 2X SSC, 0.2 % SDS for 5 min at 65C; second in 2X SSC for 3 min at room temperature and finally in 0.2X SSC for 3 min at room temperature).

scan_protocol: Arrays were scanned using a ScanArray 4000 (Perkin Elmer, Courtaboeuf, France)

data_processing:
1. Raw numerical data were extracted from Cy3 and Cy5 images using Imagene 4.0 (BioDiscovery, El Segundo, CA, USA). Mean values of the fluorescent signal obtained for each spot and each channel were used for data analysis.
2. Intra-slide normalization was performed using a method based on invariant rank genes and LOWESS fitting using the Elea software (Tseng et al. 2001; http://www-microarrays.u-strasbg.fr/Elea/index.html).
3. The normalized log2 ratio (experiment/reference) was calculated for each slide.
4. The resultant log2 ratios were averaged from dye-swap duplicates.

molecule: total RNA

organism: Mus musculus

source_name: Laminin alpha5-deficient Mouse Embryonic Intestine

label_protocol:
1. The microarray experiments were performed in quadruple with independently prepared RNA from mutant and wild-type embryonic intestines derived from 4 different litters.
2. For each RNA sample, a dye-swap labeling and hybridization was performed using a common reference RNA sample corresponding to 15.5-day embryonic intestines of C57B1/6J mice.
3. Cy3. and Cy5. labeled cDNA probes were prepared by reverse transcription of 10 µg total RNA for 2 h at 42° C [400U SuperScript II from Gibco-BRL (Invitrogen Cell Culture, France), 1X reverse transcription buffer, 0.5mM DTT, 2µg anchored oligodT: T20VVN, 500µM dATP, 500µM dCTP, 500µM dGTP, 100µM dTTP and 0.1mM Cy3. or Cy5-dUTP in a 30µl reaction]
4. The reverse transcription was stopped by a 5 min heating at 70C and RNA was degraded by RNAse A (4µg) for 45 min at 37° C. For quality control, a small fraction of the probes was tested by agarose gel electrophoresis.

extract_protocol:
1. Total RNA was extracted using the Tri Reagent (Molecular Research Center Inc., Euromedex, France) according to the recommendations of the supplier.
2. Total RNA was subjected to a further purification by an additional phenol/chloroform 5/1 (V/V) extraction.
3. RNA concentration was determined by optical density at 260 nm. The integrity and purity of each RNA sample was checked by microcapillary electrophoresis using the Agilent 2100 Bioanalyser (Agilent Technologies, Massy, France).

treatment_protocol: Laminin alpha5-deficient mouse embryos at embryonic day 15.5 were removed by caesarean section from day 13.5 to 15.5 of gestation. Segments of intestines were taken and immediately stored in RNA Later (Ambion, Courtaboeuf, France).

tag: strain

tag: genotype/variation

value: Laminin alpha5-deficient

tag: age

tag: tissue

value: embryonic Intestine

source_name: common reference RNA sample corresponding to embryonic intestine


title: Laminin alpha5-deficient mouse embryonic intestine_replicate L8


title: Wild-type mouse embryonic intestine_replicate L4

source_name: wild-type mouse embryonic intestine

value: wild-type


title: Laminin alpha5-deficient mouse embryonic intestine_replicate L6


title: Wild-type mouse embryonic intestine_replicate L3


title: Laminin alpha5-deficient mouse embryonic intestine_replicate L5


title: Wild-type mouse embryonic intestine_replicate L2


title: Wild-type mouse embryonic intestine_replicate L1


title: E10_vehicle control pool vs SPPARgM-L70 (10000 nM) #2

city: Rahway

first: Yejun

last: Tan

state: NJ

address: 126 E. Lincoln Ave, POBox 2000

department: Molecular Profiling

country: USA

institute: Merck & Co.

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: E10_vehicle control pool

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: cell type

value: 3T3-L1 Adipocytes


title: E10_vehicle control pool vs PPARg full 4 (10000 nM) #1

source_name: PPARg full 4 (10000 nM) #1


title: E10_vehicle control pool vs LXR agonist 1 (10000 nM) #1

source_name: LXR agonist 1 (10000 nM) #1


title: E10_vehicle control pool vs LXR agonist 1 (10000 nM) #2

source_name: LXR agonist 1 (10000 nM) #2


title: E10_vehicle control pool vs PPARa agonist 1 (10000 nM) #1

source_name: PPARa agonist 1 (10000 nM) #1


title: E10_vehicle control pool vs PPARa agonist 1 (10000 nM) #2

source_name: PPARa agonist 1 (10000 nM) #2


title: E10_vehicle control pool vs PPARg full 4 (10000 nM) #2

source_name: PPARg full 4 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L70 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L69 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L68 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L66 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L68 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L67 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L66 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L69 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L67 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L65 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L65 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L63 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L64 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L3 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L62 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L62 (10000 nM) #2


title: E10_vehicle control pool vs SPPARgM-L64 (10000 nM) #2


title: E10_vehicle control pool vs rosiglitazone (10000 nM) #2

source_name: rosiglitazone (10000 nM) #2


title: E10_vehicle control pool vs rosiglitazone (10000 nM) #1

source_name: rosiglitazone (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L3 (10000 nM) #1


title: E10_vehicle control pool vs SPPARgM-L63 (10000 nM) #2


title: E9_vehicle control pool vs PPARg full 3 (10000 nM) #2

source_name: E9_vehicle control pool

source_name: PPARg full 3 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L61 (10000 nM) #2


title: E10_vehicle control pool vs vehicle control #2

source_name: vehicle control #2


title: E10_vehicle control pool vs vehicle control #3

source_name: vehicle control #3


title: E9_vehicle control pool vs PPARg full 3 (10000 nM) #1

source_name: PPARg full 3 (10000 nM) #1


title: E10_vehicle control pool vs vehicle control #1

source_name: vehicle control #1


title: E9_vehicle control pool vs SPPARgM-L60 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L58 (10000 nM) #1


title: E9_vehicle control pool vs SPPARgM-L60 (10000 nM) #1


title: E9_vehicle control pool vs SPPARgM-L56 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L59 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L58 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L57 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L56 (10000 nM) #1


title: E9_vehicle control pool vs SPPARgM-L59 (10000 nM) #1


title: E9_vehicle control pool vs SPPARgM-L61 (10000 nM) #1


title: E9_vehicle control pool vs COOH (645 nM) #1


title: E9_vehicle control pool vs SPPARgM-L55 (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L57 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L44 (3000 nM) #2

source_name: E8_vehicle control pool


title: E9_vehicle control pool vs rosiglitazone (10000 nM) #2


title: E9_vehicle control pool vs SPPARgM-L3 (10000 nM) #1


title: E9_vehicle control pool vs rosiglitazone (10000 nM) #1


title: E9_vehicle control pool vs SPPARgM-L3 (10000 nM) #2


title: E9_vehicle control pool vs vehicle control #2


title: E9_vehicle control pool vs SPPARgM-L55 (10000 nM) #1


title: E9_vehicle control pool vs vehicle control #3


title: E8_vehicle control pool vs SPPARgM-L45 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L45 (3000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L44 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L14 (10000 nM) #2


title: E9_vehicle control pool vs vehicle control #1


title: E8_vehicle control pool vs SPPARgM-L45 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L45 (3000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L44 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L44 (3000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L14 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L48 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L54 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L52 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L53 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L47 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L51 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L53 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L46 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L49 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L48 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L50 (10000 nM) #2


title: E8_vehicle control pool vs rosiglitazone (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L3 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L52 (10000 nM) #2


title: E8_vehicle control pool vs vehicle control #2


title: E8_vehicle control pool vs SPPARgM-L50 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L3 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L51 (10000 nM) #2


title: E8_vehicle control pool vs SPPARgM-L47 (10000 nM) #1


title: E8_vehicle control pool vs vehicle control #3


title: E8_vehicle control pool vs SPPARgM-L46 (10000 nM) #1


title: E8_vehicle control pool vs SPPARgM-L49 (10000 nM) #1


title: E8_vehicle control pool vs rosiglitazone (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L45 (1000 nM) #2

source_name: E7_vehicle control pool


title: E7_vehicle control pool vs SPPARgM-L44 (1000 nM) #2


title: E8_vehicle control pool vs vehicle control #1


title: E7_vehicle control pool vs SPPARgM-L45 (1000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L38 (1000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L39 (1000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L44 (1000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L43 (1000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L35 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L39 (1000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L44 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L43 (1000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L44 (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L43 (10000 nM) #2


title: E7_vehicle control pool vs PPARg full 2 (10000 nM) #2

source_name: PPARg full 2 (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L32 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L38 (1000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L30 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L32 (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L30 (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L45 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L41 (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L45 (10000 nM) #2


title: E7_vehicle control pool vs SPPARgM-L42 (10000 nM) #2


title: E7_vehicle control pool vs PPARg full 2 (10000 nM) #1

source_name: PPARg full 2 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L43 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L42 (10000 nM) #1


title: TDLU7

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description:
US10283824_252800412043
Biological replicate 7 of 8 lobules

hyb_protocol: According to the instructions of Agilent Gene Expression Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

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

organism: Homo sapiens

label_protocol: 100 ng of total RNA each sample was amplified and labeled using Agilent LowInput Quick Amp Labeling Kit according to the manufacturer’s protocol.

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the supplier’s instructions.

treatment_protocol: 8 breast duct samples and 8 lobule samples were obtained from premenopausal patients undergoing surgical treatment for their nipple discharge at the Guangdong Women and Children Hospital.Immediately after collection, all samples were rapidly preserved in RNAlater reagent, and a portion of each tissue sample was used for pathological examination.

value: Normal breast lobule tissue


title: E7_vehicle control pool vs SPPARgM-L41 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L40 (10000 nM) #1


title: Duct8

description:
US10283824_252800412042
Biological replicate 8 of 8 ducts

value: Normal breast duct tissue


title: Duct7

description:
US10283824_252800412042
Biological replicate 7 of 8 ducts


title: TDLU6

description:
US10283824_252800412043
Biological replicate 6 of 8 lobules


title: TDLU8

description:
US10283824_252800412043
Biological replicate 8 of 8 lobules


title: TDLU2

description:
US10283824_252800412043
Biological replicate 2 of 8 lobules


title: TDLU4

description:
US10283824_252800412043
Biological replicate 4 of 8 lobules


title: TDLU5

description:
US10283824_252800412043
Biological replicate 5 of 8 lobules


title: E7_vehicle control pool vs SPPARgM-L40 (10000 nM) #2


title: TDLU3

description:
US10283824_252800412043
Biological replicate 3 of 8 lobules


title: Duct6

description:
US10283824_252800412042
Biological replicate 6 of 8 ducts


title: TDLU1

description:
US10283824_252800412043
Biological replicate 1 of 8 lobules


title: E7_vehicle control pool vs SPPARgM-L39 (10000 nM) #2


title: Duct2

description:
US10283824_252800412039
Biological replicate 2 of 8 ducts


title: Duct3

description:
US10283824_252800412039
Biological replicate 3 of 8 ducts


title: E7_vehicle control pool vs SPPARgM-L38 (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L38 (10000 nM) #2


title: Duct5

description:
US10283824_252800412042
Biological replicate 5 of 8 ducts


title: E7_vehicle control pool vs rosiglitazone (10000 nM) #1


title: E7_vehicle control pool vs SPPARgM-L39 (10000 nM) #1


title: Duct4

description:
US10283824_252800412039
Biological replicate 4 of 8 ducts


title: Duct1

description:
US10283824_252800412039
Biological replicate 1 of 8 ducts


title: fetal B cells 38-40

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description:
IV121306_02x
Gene expression data from FEB sample

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a HP G2500A or Affymetrix 7G (x)

data_processing: The data were analyzed using the MAS5.0 algorithm and Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: pool of CD10+CD19+ cord blood B cells from donor 38-40

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Established cell lines were grown under standard conditions.

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

treatment_protocol: Cells were left untreated.

value: cord blood

value: fetal


title: fetal B cells 30-37

description:
sb112406_03x
Gene expression data from FEB sample

source_name: pool of CD10+CD19+ cord blood B cells from donor 30-37


title: E7_vehicle control pool vs SPPARgM-L3 (10000 nM) #2

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand


title: fetal B cells 25-29

description:
sb112406_01x
Gene expression data from FEB sample

source_name: pool of CD10+CD19+ cord blood B cells from donor 25-29


title: E7_vehicle control pool vs rosiglitazone (10000 nM) #2


title: E7_vehicle control pool vs vehicle control #3


title: E7_vehicle control pool vs SPPARgM-L3 (10000 nM) #1


title: fetal B cells 60

description:
sb021702_02
Gene expression data from FEB sample

source_name: CD10+CD19+ cord blood B cells from donor 60


title: E7_vehicle control pool vs vehicle control #2


title: E7_vehicle control pool vs vehicle control #1


title: fetal B cells 46

description:
sb021602_15
Gene expression data from FEB sample

source_name: CD10+CD19+ cord blood B cells from donor 46


title: E6_vehicle control pool vs SPPARgM-L36 (10000 nM) #1

source_name: E6_vehicle control pool


title: fetal B cells 42

description:
sb021602_14
Gene expression data from FEB sample

source_name: CD10+CD19+ cord blood B cells from donor 42


title: fetal B cells 59

description:
sb021702_01
Gene expression data from FEB sample

source_name: CD10+CD19+ cord blood B cells from donor 59


title: fetal B cells 48

description:
sb021602_16
Gene expression data from FEB sample

source_name: CD10+CD19+ cord blood B cells from donor 48


title: E6_vehicle control pool vs SPPARgM-L37 (10000 nM) #1


title: E6_vehicle control pool vs SPPARgM-L37 (10000 nM) #2


title: fetal B cells 41

description:
sb021602_13
Gene expression data from FEB sample

source_name: CD10+CD19+ cord blood B cells from donor 41


title: E6_vehicle control pool vs SPPARgM-L36 (10000 nM) #2


title: cell line NALM6

description:
IV070203_03
Gene expression data from cell line

source_name: cell line NALM-6

value: cell line


title: E6_vehicle control pool vs SPPARgM-L35 (10000 nM) #1


title: cALL patient 56

description:
sb021802_12
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 56

value: bone marrow

value: pediatric


title: E6_vehicle control pool vs SPPARgM-L34 (10000 nM) #1


title: cell line 697

description:
IV070203_02
Gene expression data from cell line

source_name: cell line 697


title: cell line CALL2

description:
IV070203_01
Gene expression data from cell line

source_name: cell line MHH-CALL2


title: cALL patient 54

description:
sb021802_10
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 54


title: cALL patient 55

description:
sb021802_11
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 55


title: E6_vehicle control pool vs SPPARgM-L33 (10000 nM) #2


title: E6_vehicle control pool vs SPPARgM-L31 (10000 nM) #1


title: E6_vehicle control pool vs SPPARgM-L35 (10000 nM) #2


title: E6_vehicle control pool vs SPPARgM-L32 (10000 nM) #2


title: cALL patient 53

description:
sb021802_09
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 53


title: E6_vehicle control pool vs SPPARgM-L33 (10000 nM) #1


title: cALL patient 52

description:
sb021802_08
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 52


title: E6_vehicle control pool vs SPPARgM-L31 (10000 nM) #2


title: E6_vehicle control pool vs SPPARgM-L34 (10000 nM) #2


title: E6_vehicle control pool vs SPPARgM-L32 (10000 nM) #1


title: cALL patient 57

description:
sb021802_13
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 57


title: E6_vehicle control pool vs SPPARgM-L3 (10000 nM) #2

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand


title: cALL patient 49

description:
sb021802_05
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 49


title: cALL patient 51

description:
sb021802_07
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 51


title: E6_vehicle control pool vs SPPARgM-L12 (10000 nM) #2


title: E6_vehicle control pool vs SPPARgM-L12 (10000 nM) #1


title: E6_vehicle control pool vs SPPARgM-L3 (10000 nM) #1


title: cALL patient 50

description:
sb021802_06
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 50


title: E6_vehicle control pool vs SPPARgM-L9 (10000 nM) #1

source_name: E6_vehicle control pool


title: cALL patient 48

description:
sb021802_04
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 48


title: cALL patient 47

description:
sb021802_03
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 47


title: E6_vehicle control pool vs COOH (10000 nM) #1


title: cALL patient 46

description:
sb021802_02
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 46


title: cALL patient 43

description:
sb021702_08
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 43


title: E6_vehicle control pool vs COOH (10000 nM) #2


title: cALL patient 45

description:
sb021802_01
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 45


title: cALL patient 42

description:
sb021702_07
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 42


title: cALL patient 40

description:
sb021702_05
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 40


title: E6_vehicle control pool vs SPPARgM-L9 (10000 nM) #2


title: cALL patient 38

description:
sb021702_03
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 38


title: cALL patient 41

description:
sb021702_06
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 41


title: cALL patient 34

description:
sb021602_08
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 34


title: cALL patient 39

description:
sb021702_04
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 39


title: cALL patient 36

description:
sb021602_09
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 36


title: E6_vehicle control pool vs vehicle control #3

source_name: vehicle control #3


title: E6_vehicle control pool vs rosiglitazone (10000 nM) #1

source_name: rosiglitazone (10000 nM) #1


title: E6_vehicle control pool vs vehicle control #1

source_name: vehicle control #1


title: E5_vehicle control pool vs SPPARgM-L19 (10000 nM) #1

source_name: E5_vehicle control pool


title: cALL patient 25

description:
sb021602_01
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 25


title: cALL patient 37

description:
sb021602_10
Gene expression data from cALL sample

source_name: peripheral blood from cALL patient 37

value: peripheral blood


title: E5_vehicle control pool vs SPPARgM-L25 (1000 nM) #2

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand


title: cALL patient 33

description:
sb021602_07
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 33


title: E6_vehicle control pool vs vehicle control #2

source_name: E6_vehicle control pool

source_name: vehicle control #2


title: E5_vehicle control pool vs SPPARgM-L25 (1000 nM) #1


title: cALL patient 31

description:
sb021602_05
Gene expression data from cALL sample

source_name: bone marrow from cALL patient 31


title: E5_vehicle control pool vs SPPARgM-L29 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L30 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L19 (10000 nM) #2


title: Lung_15mg silica_16 wk post-exposure_rep8

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description:
T16_L_S(15)_8
15mg/m³ silica_ 16 week post-exposure_rat 8
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc (San Diego, CA,), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc,) for 20 hrs at 580C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc,). This was followed by a non-stringent washing to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconducter using the 'lumi' and 'limma' packages. The 'lumi' Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packagees/2.2/ bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes genes undetected and resulting in a subset of genes detected on the array. A linear model analysis using 'limma' package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes.  Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

label: Biotin, Cy3-streptavidin

organism: Rattus norvegicus

source_name: 15mg/m³ silica_16 week post-exposure

label_protocol: Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72 ± 50 F), and humidity (50 ± 20%) with free access to food and water.

extract_protocol: Total RNA was isolated from the lung samples using RNeasy Fibrous Tissue Mini Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.

treatment_protocol: Rats were exposed to air (control) or crystalline silica by inhalation (15 mg/m³ , 6 hours/day, 5 days). Rats were sacrificed at 1, 2, 4, 8 and 16 weeks following the last silica exposure.

value: CDF Fisher 344

tag: gender

value: male

value: approximately 3 month old

value: lung


title: E5_vehicle control pool vs SPPARgM-L28 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L30 (10000 nM) #2


title: E5_vehicle control pool vs SPPARgM-L27 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L28 (10000 nM) #2


title: E5_vehicle control pool vs SPPARgM-L26 (10000 nM) #2


title: E5_vehicle control pool vs SPPARgM-L27 (10000 nM) #2


title: E5_vehicle control pool vs SPPARgM-L26 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L29 (10000 nM) #2


title: Lung_15mg silica_4 wk post-exposure_rep7

description:
T4_L_S(15)_7
15mg/m³ silica_ 4 week post-exposure_rat 39
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_4 week post-exposure


title: Lung_15mg silica_8 wk post-exposure_rep4

description:
T8_L_S(15)_4
15mg/m³ silica_ 8 week post-exposure_rat 20
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_8 week post-exposure


title: Lung_15mg silica_8 wk post-exposure_rep3

description:
T8_L_S(15)_3
15mg/m³ silica_ 8 week post-exposure_rat 19
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_1 wk post-exposure_rep7

description:
T1_L_S(15)_7
15mg/m³ silica_ 1 week post-exposure_rat 71
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_1 week post-exposure


title: Lung_15mg silica_16 wk post-exposure_rep3

description:
T16_L_S(15)_3
15mg/m³ silica_ 16 week post-exposure_rat 3
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E5_vehicle control pool vs SPPARgM-L25 (10000 nM) #2


title: E5_vehicle control pool vs SPPARgM-L12 (10000 nM) #2


title: Lung_15mg silica_2 wk post-exposure_rep5

description:
T2_L_S(15)_5
15mg/m³ silica_ 2 week post-exposure_rat 53
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_2 week post-exposure


title: E5_vehicle control pool vs SPPARgM-L25 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L12 (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L9 (10000 nM) #2


title: E5_vehicle control pool vs COOH (10000 nM) #2


title: E5_vehicle control pool vs COOH (10000 nM) #1


title: E5_vehicle control pool vs SPPARgM-L9 (10000 nM) #1


title: Lung_15mg silica_2 wk post-exposure_rep4

description:
T2_L_S(15)_4
15mg/m³ silica_ 2 week post-exposure_rat 52
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_0mg silica_8 wk post-exposure_rep1

description:
T8_L_S(0)_1
air (control)_ 8 week post-exposure_rat 25
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_8 week post-exposure


title: Lung_15mg silica_1 wk post-exposure_rep6

description:
T1_L_S(15)_6
15mg/m³ silica_ 1 week post-exposure_rat 70
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E5_vehicle control pool vs rosiglitazone (10000 nM) #1


title: Lung_15mg silica_4 wk post-exposure_rep6

description:
T4_L_S(15)_6
15mg/m³ silica_ 4 week post-exposure_rat 38
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_4 wk post-exposure_rep2

description:
T4_L_S(15)_2
15mg/m³ silica_  4 week post-exposure_rat 34
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E5_vehicle control pool vs vehicle control #5

source_name: vehicle control #5


title: Lung_15mg silica_1 wk post-exposure_rep2

description:
T1_L_S(15)_2
15mg/m³ silica_ 1 week post-exposure_rat 66
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E5_vehicle control pool vs vehicle control #6

source_name: vehicle control #6


title: E5_vehicle control pool vs rosiglitazone (10000 nM) #2

source_name: rosiglitazone (10000 nM) #2


title: E5_vehicle control pool vs vehicle control #4

source_name: vehicle control #4


title: Lung_0mg silica_2 wk post-exposure_rep4

description:
T2_L_S(0)_4
air (control)_ 2 week post-exposure_rat 60
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_2 week post-exposure


title: Lung_15mg silica_2 wk post-exposure_rep2

description:
T2_L_S(15)_2
15mg/m³ silica_  2 week post-exposure_rat 50
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_0mg silica_16 wk post-exposure_rep3

description:
T16_L_S(0)_3
air (control)_ 16 week post-exposure_rat 11
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_16 week post-exposure


title: Lung_15mg silica_8 wk post-exposure_rep6

description:
T8_L_S(15)_6
15mg/m³ silica_ 8 week post-exposure_rat 22
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_16 wk post-exposure_rep7

description:
T16_L_S(15)_7
15mg/m³ silica_ 16 week post-exposure_rat 7
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_0mg silica_2 wk post-exposure_rep1

description:
T2_L_S(0)_1
air (control)_ 2 week post-exposure_rat 57
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E6_vehicle control pool vs rosiglitazone (10000 nM) #2

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand


title: E4_vehicle control pool vs PPARa agonist 1 (10000 nM) #2

source_name: E4_vehicle control pool

source_name: PPARa agonist 1 (10000 nM) #2


title: Lung_0mg silica_8 wk post-exposure_rep2

description:
T8_L_S(0)_2
air (control)_ 8 week post-exposure_rat 26
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_0mg silica_1 wk post-exposure_rep1

description:
T1_L_S(0)_1
air (control)_ 1 week post-exposure_rat 73
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_1 week post-exposure


title: E5_vehicle control pool vs vehicle control #2

source_name: E5_vehicle control pool

source_name: vehicle control #2


title: Lung_15mg silica_2 wk post-exposure_rep1

description:
T2_L_S(15)_1
15mg/m³ silica_ 2 week post-exposure_rat 49
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L23 (10000 nM) #2


title: E4_vehicle control pool vs SPPARgM-L24 (10000 nM) #2


title: Lung_15mg silica_16 wk post-exposure_rep1

description:
T16_L_S(15)_1
15mg/m³ silica_  16 week post-exposure_rat 1
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_16 week post-exposure


title: Lung_15mg silica_4 wk post-exposure_rep1

description:
T4_L_S(15)_1
15mg/m³ silica_ 4 week post-exposure_rat 33
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_4 week post-exposure


title: Lung_15mg silica_ 1 wk post-exposure_rep1

description:
T1_L_S(15)_1
15mg/m³ silica_ 1 week post-exposure_rat 65
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_0mg silica_1 wk post-exposure_rep2

description:
T1_L_S(0)_2
air (control)_ 1 week post-exposure_rat 74
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L22 (10000 nM) #2


title: Lung_0mg silica_4 wk post-exposure_rep1

description:
T4_L_S(0)_1
air (control)_ 4 week post-exposure_rat 41
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_4 week post-exposure


title: E5_vehicle control pool vs vehicle control #3

source_name: vehicle control #3


title: E5_vehicle control pool vs vehicle control #1

source_name: vehicle control #1


title: Lung_0mg silica_16 wk post-exposure_rep2

description:
T16_L_S(0)_2
air (control)_ 16 week post-exposure_rat 10
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_0mg silica_4 wk post-exposure_rep2

description:
T4_L_S(0)_2
air (control)_ 4 week post-exposure_rat 42
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L21 (10000 nM) #1


title: E4_vehicle control pool vs SPPARgM-L6 (10000 nM) #2


title: E4_vehicle control pool vs PPARa agonist 1 (10000 nM) #1

source_name: PPARa agonist 1 (10000 nM) #1


title: E4_vehicle control pool vs SPPARgM-L21 (10000 nM) #2


title: E4_vehicle control pool vs SPPARgM-L5 (10000 nM) #1


title: E4_vehicle control pool vs SPPARgM-L5 (10000 nM) #2


title: E4_vehicle control pool vs SPPARgM-L24 (10000 nM) #1


title: Lung_15mg silica_8 wk post-exposure_rep1

description:
T8_L_S(15)_1
15mg/m³ silica_ 8 week post-exposure_rat 17
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_8 week post-exposure


title: Lung_15mg silica_8 wk post-exposure_rep5

description:
T8_L_S(15)_5
15mg/m³ silica_ 8 week post-exposure_rat 21
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_1 wk post-exposure_rep8

description:
T1_L_S(15)_8
15mg/m³ silica_  1 week post-exposure_rat  72
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_1 week post-exposure


title: E4_vehicle control pool vs SPPARgM-L22 (10000 nM) #1


title: E4_vehicle control pool vs SPPARgM-L6 (10000 nM) #1


title: E4_vehicle control pool vs SPPARgM-L23 (10000 nM) #1


title: Lung_15mg silica_16 wk post-exposure_rep4

description:
T16_L_S(15)_4
15mg/m³ silica_  16 week post-exposure_rat  4
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L3 (10000 nM) #2


title: Lung_15mg silica_4 wk post-exposure_rep5

description:
T4_L_S(15)_5
15mg/m³ silica_  4 week post-exposure_rat  37
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_2 wk post-exposure_rep8

description:
T2_L_S(15)_8
15mg/m³ silica_  2 week post-exposure_rat 56
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_2 week post-exposure


title: E4_vehicle control pool vs SPPARgM-L3 (600 nM) #3

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand

source_name: SPPARgM-L3 (600 nM) #3


title: Lung_15mg silica_8 wk post-exposure_rep7

description:
T8_L_S(15)_7
15mg/m³ silica_  8 week post-exposure_rat 23
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L3 (600 nM) #1

source_name: SPPARgM-L3 (600 nM) #1


title: Lung_15mg silica_1 wk post-exposure_rep4

description:
T1_L_S(15)_4
15mg/m³ silica_  1 week post-exposure_rat  68
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L3 (10000 nM) #3


title: Lung_0mg silica_8 wk post-exposure_rep4

description:
T8_L_S(0)_4
air (control)_ 8 week post-exposure_rat 28
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_8 week post-exposure


title: Lung_15mg silica_8 wk post-exposure_rep8

description:
T8_L_S(15)_8
15mg/m³ silica_  8 week post-exposure_rat 24
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs rosiglitazone (10000 nM) #2

source_name: E4_vehicle control pool

source_name: rosiglitazone (10000 nM) #2


title: Lung_15mg silica_16 wk post-exposure_rep5

description:
T16_L_S(15)_5
15mg/m³ silica_  16 week post-exposure_rat 5
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs SPPARgM-L3 (600 nM) #2

source_name: SPPARgM-L3 (600 nM) #2


title: Lung_0mg silica_2 wk post-exposure_rep3

description:
T2_L_S(0)_3
air (control)_ 2 week post-exposure_rat 59
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_2 week post-exposure


title: E4_vehicle control pool vs rosiglitazone (10000 nM) #3

source_name: rosiglitazone (10000 nM) #3


title: Lung_0mg silica_4 wk post-exposure_rep3

description:
T4_L_S(0)_3
air (control)_ 4 week post-exposure_rat 43
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_4 wk post-exposure_rep4

description:
T4_L_S(15)_4
15mg/m³ silica_  4 week post-exposure_rat 36
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E4_vehicle control pool vs vehicle control #2

source_name: vehicle control #2


title: E4_vehicle control pool vs rosiglitazone (600 nM) #1

source_name: rosiglitazone (600 nM) #1


title: Lung_0mg silica_1 wk post-exposure_rep4

description:
T1_L_S(0)_4
air (control)_ 1 week post-exposure_rat 76
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_1 week post-exposure


title: E4_vehicle control pool vs rosiglitazone (10000 nM) #1

source_name: rosiglitazone (10000 nM) #1


title: E4_vehicle control pool vs rosiglitazone (600 nM) #3

source_name: rosiglitazone (600 nM) #3


title: Lung_15mg silica_2 wk post-exposure_rep6

description:
T2_L_S(15)_6
15mg/m³ silica_  2 week post-exposure_rat  54
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_2 wk post-exposure_rep3

description:
T2_L_S(15)_3
15mg/m³ silica_  2 week post-exposure_rat  51
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_4 wk post-exposure_rep8

description:
T4_L_S(15)_8
15mg/m³ silica_  4 week post-exposure_rat 40
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_4 week post-exposure


title: E4_vehicle control pool vs rosiglitazone (600 nM) #2

source_name: rosiglitazone (600 nM) #2


title: E3_vehicle control pool vs SPPARgM-L20 (1075 nM) #2

source_name: E3_vehicle control pool


title: E4_vehicle control pool vs SPPARgM-L3 (10000 nM) #1


title: E4_vehicle control pool vs vehicle control #1

source_name: vehicle control #1


title: E3_vehicle control pool vs SPPARgM-L20 (1075 nM) #3


title: E3_vehicle control pool vs SPPARgM-L20 (1075 nM) #1


title: Lung_15mg silica_16 wk post-exposure_rep2

description:
T16_L_S(15)_2
15mg/m³ silica_  16 week post-exposure_rat 2
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_16 week post-exposure


title: Lung_15mg Silica_1 wk post-exposure_rep5

description:
T1_L_S(15)_5
15mg/m³ silica_ 1 week post-exposure_rat 69
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_1 week post-exposure


title: E3_vehicle control pool vs SPPARgM-L6 (1100 nM) #3

source_name: SPPARgM-L6 (1100 nM) #3


title: E3_vehicle control pool vs SPPARgM-L6 (1100 nM) #2

source_name: SPPARgM-L6 (1100 nM) #2


title: Lung_0mg silica_16 wk post-exposure_rep1

description:
T16_L_S(0)_1
air (control)_ 16 week post-exposure_rat 9
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_16 week post-exposure


title: E3_vehicle control pool vs SPPARgM-L6 (1100 nM) #1

source_name: SPPARgM-L6 (1100 nM) #1


title: Lung_15mg silica_1 wk post-exposure_rep3

description:
T1_L_S(15)_3
15mg/m³ silica_  1 week post-exposure_rat 67
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_2 wk post-exposure_rep7

description:
T2_L_S(15)_7
15mg/m³ silica_  2 week post-exposure_rat 55
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_2 week post-exposure


title: Lung_0mg silica_4 wk post-exposure_rep4

description:
T4_L_S(0)_4
air (control)_ 4 week post-exposure_rat 44
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_4 week post-exposure


title: E3_vehicle control pool vs SPPARgM-L19 (16032 nM) #2

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand


title: Lung_0mg silica_1 wk post-exposure_rep3

description:
T1_L_S(0)_3
air (control)_ 1 week post-exposure_rat 75
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: Lung_15mg silica_4 wk post-exposure_rep3

description:
T4_L_S(15)_3
15mg/m³ silica_ 4 week post-exposure_rat 35
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E3_vehicle control pool vs SPPARgM-L19 (16032 nM) #1


title: Lung_0mg silica_2 wk post-exposure_rep2

description:
T2_L_S(0)_2
air (control)_ 2 week post-exposure_rat 58
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_2 week post-exposure


title: E3_vehicle control pool vs SPPARgM-L9 (6324 nM) #2

source_name: SPPARgM-L9 (6324 nM) #2


title: Lung_0mg silica_8 wk post-exposure_rep3

description:
T8_L_S(0)_3
air (control)_ 8 week post-exposure_rat 27
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_8 week post-exposure


title: E3_vehicle control pool vs SPPARgM-L9 (6324 nM) #3

source_name: SPPARgM-L9 (6324 nM) #3


title: Lung_15mg silica_16 wk post-exposure_rep6

description:
T16_L_S(15)_6
15mg/m³ silica_ 16 week post-exposure_rat 6
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.


title: E3_vehicle control pool vs SPPARgM-L19 (16032 nM) #3


title: Lung_0mg silica_0 week post-exposure_rep8

description:
T0_L_S(0)_8
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc. (San Diego, CA,), each labeled cRNA sample was hybridized to the RatRef-12 v1.0 expression beadchip (Illumina, Inc.) for 20 hrs at 58C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules, and stained with Cy3-streptavidin conjugate (Illumina, Inc,). This was followed by a non-stringent washing to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform following the protocol provided by the manufacturer (Illumina, Inc., San Diego, CA).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconductor using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packages/2.2/bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes undetected genes, resulting in a subset of genes detected on the array. A linear model analysis using the 'limma' package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes. Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

label: Biotin

source_name: 0mg/m3 silica, 0 week post-exposure, rat 140 lung

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72± 50 F), and humidity (50 ± 20%) with free access to food and water.

extract_protocol: Total RNA was isolated from the lung samples using the RNeasy Fibrous Tissue Mini kit (Qiagen Inc, Valencia, CA) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase following the recommendations of the supplier.

treatment_protocol: Rats were exposed to air (control) or crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Rats were sacrificed at 16-hours following the last silica exposure.

value: 3 months

tag: treatment

value: air

tag: post-exposure time

value: 0 weeks

tag: sample type

value: control

tag: rat identifier


title: Lung_15mg silica_0 week post-exposure_rep8

description:
T0_L_S(15)_8
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 88 lung

value: 15mg/m3 crystalline silica


title: Lung_15mg silica_8 wk post-exposure_rep2

description:
T8_L_S(15)_2
15mg/m³ silica_ 8 week post-exposure_rat 18
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m³ silica_8 week post-exposure


title: Lung_0mg silica_0 week post-exposure_rep10

description:
T0_L_S(0)_10
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 106 lung


title: E3_vehicle control pool vs SPPARgM-L18 (126 nM) #3

source_name: E3_vehicle control pool

value: 3T3-L1 Adipocytes

source_name: SPPARgM-L18 (126 nM) #3


title: E3_vehicle control pool vs SPPARgM-L18 (126 nM) #1

source_name: SPPARgM-L18 (126 nM) #1


title: E3_vehicle control pool vs SPPARgM-L17 (285 nM) #2

source_name: SPPARgM-L17 (285 nM) #2


title: E3_vehicle control pool vs SPPARgM-L9 (6324 nM) #1

source_name: SPPARgM-L9 (6324 nM) #1


title: E3_vehicle control pool vs SPPARgM-L18 (126 nM) #2

source_name: SPPARgM-L18 (126 nM) #2


title: E3_vehicle control pool vs SPPARgM-L17 (285 nM) #3

source_name: SPPARgM-L17 (285 nM) #3


title: E3_vehicle control pool vs SPPARgM-L16 (221 nM) #3

source_name: SPPARgM-L16 (221 nM) #3


title: E3_vehicle control pool vs SPPARgM-L17 (285 nM) #1

source_name: SPPARgM-L17 (285 nM) #1


title: Lung_0mg silica_0 week post-exposure_rep9

description:
T0_L_S(0)_9
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 105 lung


title: Lung_0mg silica_0 week post-exposure_rep7

description:
T0_L_S(0)_7
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 139 lung


title: Lung_0mg silica_0 week post-exposure_rep2

description:
T0_L_S(0)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 90 lung


title: E3_vehicle control pool vs SPPARgM-L16 (221 nM) #2

source_name: SPPARgM-L16 (221 nM) #2


title: Lung_15mg silica_0 week post-exposure_rep2

description:
T0_L_S(15)_2
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 82 lung


title: Lung_15mg silica_0 week post-exposure_rep6

description:
T0_L_S(15)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 86 lung


title: Lung_0mg silica_0 week post-exposure_rep1

description:
T0_L_S(0)_1
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 89 lung


title: Lung_15mg silica_0 week post-exposure_rep1

description:
T0_L_S(15)_1
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 81 lung


title: E3_vehicle control pool vs SPPARgM-L15 (158 nM) #1

description: 3T3-L1 Adipocytes: Vehicle control pool vs. PPARg Ligand

source_name: E3_vehicle control pool

source_name: SPPARgM-L15 (158 nM) #1


title: E3_vehicle control pool vs SPPARgM-L16 (221 nM) #1

source_name: SPPARgM-L16 (221 nM) #1


title: Lung_0mg silica_0 week post-exposure_rep12

description:
T0_L_S(0)_12
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 108 lung


title: E3_vehicle control pool vs SPPARgM-L15 (158 nM) #3

source_name: SPPARgM-L15 (158 nM) #3


title: Lung_0mg silica_0 week post-exposure_rep6

description:
T0_L_S(0)_6
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 138 lung


title: E3_vehicle control pool vs SPPARgM-L15 (158 nM) #2

source_name: SPPARgM-L15 (158 nM) #2


title: Lung_15mg silica_0 week post-exposure_rep7

description:
T0_L_S(15)_7
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 87 lung


title: Lung_15mg silica_0 week post-exposure_rep4

description:
T0_L_S(15)_4
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 84 lung


title: E3_vehicle control pool vs SPPARgM-L14 (200 nM) #3

source_name: SPPARgM-L14 (200 nM) #3


title: E3_vehicle control pool vs SPPARgM-L14 (200 nM) #2

source_name: SPPARgM-L14 (200 nM) #2


title: Lung_0mg silica_0 week post-exposure_rep3

description:
T0_L_S(0)_3
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 91 lung


title: E3_vehicle control pool vs PPARa agonist 1 (10000 nM) #3

source_name: PPARa agonist 1 (10000 nM) #3


title: E3_vehicle control pool vs SPPARgM-L14 (200 nM) #1

source_name: SPPARgM-L14 (200 nM) #1


title: E3_vehicle control pool vs PPARa agonist 1 (10000 nM) #2

source_name: PPARa agonist 1 (10000 nM) #2


title: Lung_0mg silica_0 week post-exposure_rep5

description:
T0_L_S(0)_5
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 137 lung


title: E3_vehicle control pool vs SPPARgM-L5 (1800 nM) #3

source_name: SPPARgM-L5 (1800 nM) #3


title: Lung_0mg silica_0 week post-exposure_rep11

description:
T0_L_S(0)_11
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 107 lung


title: Lung_15mg silica_0 week post-exposure_rep5

description:
T0_L_S(15)_5
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 85 lung


title: Lung_15mg silica_0 week post-exposure_rep3

description:
T0_L_S(15)_3
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 15mg/m3 silica, 0 week post-exposure, rat 83 lung


title: E3_vehicle control pool vs PPARa agonist 1 (10000 nM) #1

source_name: E3_vehicle control pool

source_name: PPARa agonist 1 (10000 nM) #1


title: Lung_0mg silica_16 wk post-exposure_rep4

description:
T16_L_S(0)_4
air (control)_ 16 week post-exposure_rat 12
The labeling and hybridization of microarrays were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m³ silica_16 week post-exposure


title: E3_vehicle control pool vs SPPARgM-L5 (1800 nM) #2

source_name: SPPARgM-L5 (1800 nM) #2


title: Lung_0mg silica_0 week post-exposure_rep4

description:
T0_L_S(0)_4
The labeling and hybridization of the microarrays were performed at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

source_name: 0mg/m3 silica, 0 week post-exposure, rat 92 lung


title: E3_vehicle control pool vs SPPARgM-L3 (600 nM) #2

source_name: SPPARgM-L3 (600 nM) #2


title: E3_vehicle control pool vs SPPARgM-L5 (1800 nM) #1

source_name: SPPARgM-L5 (1800 nM) #1


title: RES-enriched Grape extract group, 12 months, patient number 28

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

hyb_protocol: Following fragmentation, 18 cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA), using CEL files obtained from Affymetrix Expression Console (version 1.1.2).

source_name: Isolated PBMCs from diabetic male patient_RES-enriched Grape extract_12 months

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 4 μg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Male patients' heparinised blood was processed within two hours after extraction and used to isolate PBMCs. Isolation was carried out under sterile conditions to avoid the activation of monocytes. Blood was diluted 1:1 with RPMI 1640 cell culture medium and processed by density gradient centrifugation with Histopaque-1077 (Sigma Aldrich) according to the manufacturer instructions. After washing the cells (x2) with phosphate buffer solution (PBS), the PBMCs were lysed using RLT Buffer (Qiagen) and stored at –80C for RNA extraction.

extract_protocol: Total RNA was isolated using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water, aliquoted and stored at –80C.

treatment_protocol: PBMCs were isolated at day 0, day 180 (6months) and day 365 (12 months) from the following groups:i) placebo (control), n=6 arrays (6 diabetic males); ii) grape extract, n=6 arrays (6 diabetic males); iii) resveratrol-enriched grape extract, n=6 arrays (6 diabetic males)

tag: dietary group

value: resveratrol-enriched grape extract (C)

tag: time point

value: 12 months

value: Isolated peripheral blood mononuclear cells (PBMCs)


title: RES-enriched Grape extract group, 12 months, patient number 41


title: RES-enriched Grape extract group, 12 months, patient number 22


title: E3_vehicle control pool vs COOH (3870 nM) #3


title: RES-enriched Grape extract group, 12 months, patient number 51


title: RES-enriched Grape extract group, 12 months, patient number 62


title: E3_vehicle control pool vs SPPARgM-L3 (600 nM) #3

source_name: SPPARgM-L3 (600 nM) #3


title: RES-enriched Grape extract group, 12 months, patient number 13


title: RES-enriched Grape extract group, 6 months, patient number 62

source_name: Isolated PBMCs from diabetic male patient_RES-enriched Grape extract_6 months

value: 6 months


title: E3_vehicle control pool vs rosiglitazone (600 nM) #2

source_name: rosiglitazone (600 nM) #2


title: E3_vehicle control pool vs COOH (3870 nM) #1


title: E3_vehicle control pool vs SPPARgM-L3 (600 nM) #1

source_name: SPPARgM-L3 (600 nM) #1


title: E3_vehicle control pool vs vehicle control #3

source_name: vehicle control #3


title: E3_vehicle control pool vs COOH (3870 nM) #2


title: E3_vehicle control pool vs vehicle control #4

source_name: vehicle control #4


title: E3_vehicle control pool vs rosiglitazone (600 nM) #1

source_name: rosiglitazone (600 nM) #1


title: E3_vehicle control pool vs rosiglitazone (600 nM) #3

source_name: rosiglitazone (600 nM) #3


title: RES-enriched Grape extract group, 6 months, patient number 41


title: RES-enriched Grape extract group, Time 0 (basal), patient number 62

source_name: Isolated PBMCs from diabetic male patient_RES-enriched Grape extract_basal expression level

value: day 0 (basal)


title: E3_vehicle control pool vs vehicle control #2

source_name: E3_vehicle control pool

source_name: vehicle control #2


title: E2_vehicle control pool vs LXR agonist 1 (3000 nM) #3

source_name: E2_vehicle control pool

source_name: LXR agonist 1 (3000 nM) #3


title: RES-enriched Grape extract group, 6 months, patient number 51


title: RES-enriched Grape extract group, 6 months, patient number 22


title: E2_vehicle control pool vs LXR agonist 1 (3000 nM) #1

source_name: LXR agonist 1 (3000 nM) #1


title: E3_vehicle control pool vs vehicle control #1

source_name: vehicle control #1


title: RES-enriched Grape extract group, 6 months, patient number 13


title: RES-enriched Grape extract group, 6 months, patient number 28


title: E2_vehicle control pool vs SPPARgM-L13 (300 nM) #2

source_name: SPPARgM-L13 (300 nM) #2


title: RES-enriched Grape extract group, Time 0 (basal), patient number 13


title: RES-enriched Grape extract group, Time 0 (basal), patient number 22


title: E2_vehicle control pool vs SPPARgM-L12 (1400 nM) #3


title: E2_vehicle control pool vs LXR agonist 1 (3000 nM) #2

source_name: LXR agonist 1 (3000 nM) #2


title: RES-enriched Grape extract group, Time 0 (basal), patient number 51


title: RES-enriched Grape extract group, Time 0 (basal), patient number 41


title: RES-enriched Grape extract group, Time 0 (basal), patient number 28


title: E2_vehicle control pool vs SPPARgM-L13 (300 nM) #3

source_name: SPPARgM-L13 (300 nM) #3


title: Grape extract group, 12 months, patient number 56

source_name: Isolated PBMCs from diabetic male patient_Grape extract group_12 months

value: grape extract (B)


title: Grape extract group, 12 months, patient number 32


title: E2_vehicle control pool vs SPPARgM-L12 (1400 nM) #1


title: Grape extract group, 12 months, patient number 15


title: E2_vehicle control pool vs SPPARgM-L13 (300 nM) #1

source_name: SPPARgM-L13 (300 nM) #1


title: E2_vehicle control pool vs SPPARgM-L12 (1400 nM) #2


title: E2_vehicle control pool vs SPPARgM-L11 (100 nM) #1

source_name: SPPARgM-L11 (100 nM) #1


title: E2_vehicle control pool vs SPPARgM-L11 (100 nM) #3

source_name: SPPARgM-L11 (100 nM) #3


title: Grape extract group, 6 months, patient number 56

source_name: Isolated PBMCs from diabetic male patient_Grape extract group_6 months


title: Grape extract group, 12 months, patient number 11


title: Grape extract group, 12 months, patient number 29


title: E2_vehicle control pool vs SPPARgM-L11 (100 nM) #2

source_name: SPPARgM-L11 (100 nM) #2


title: E2_vehicle control pool vs SPPARgM-L6 (1100 nM) #2

source_name: SPPARgM-L6 (1100 nM) #2


title: Grape extract group, 6 months, patient number 32


title: Grape extract group, 6 months, patient number 14


title: Grape extract group, Time 0 (basal), patient number 56

source_name: Isolated PBMCs from diabetic male patient_Grape extract group_basal expression level


title: E2_vehicle control pool vs SPPARgM-L10 (10000 nM) #1


title: E2_vehicle control pool vs SPPARgM-L10 (10000 nM) #3


title: Grape extract group, 6 months, patient number 11


title: Grape extract group, 6 months, patient number 29


title: E2_vehicle control pool vs SPPARgM-L6 (1100 nM) #3

source_name: SPPARgM-L6 (1100 nM) #3


title: Grape extract group, 6 months, patient number 15


title: E2_vehicle control pool vs SPPARgM-L10 (10000 nM) #2


title: E2_vehicle control pool vs SPPARgM-L9 (6300 nM) #3

source_name: SPPARgM-L9 (6300 nM) #3


title: E2_vehicle control pool vs SPPARgM-L6 (1100 nM) #1

source_name: E2_vehicle control pool

source_name: SPPARgM-L6 (1100 nM) #1


title: Grape extract group, Time 0 (basal), patient number 32


title: Grape extract group, Time 0 (basal), patient number 14


title: E2_vehicle control pool vs SPPARgM-L9 (6300 nM) #2

source_name: SPPARgM-L9 (6300 nM) #2


title: E2_vehicle control pool vs SPPARgM-L8 (1500 nM) #3

source_name: SPPARgM-L8 (1500 nM) #3


title: Grape extract group, Time 0 (basal), patient number 11


title: E2_vehicle control pool vs SPPARgM-L7 (3000 nM) #3

source_name: SPPARgM-L7 (3000 nM) #3


title: E2_vehicle control pool vs SPPARgM-L8 (1500 nM) #1

source_name: SPPARgM-L8 (1500 nM) #1


title: Grape extract group, Time 0 (basal), patient number 15


title: E2_vehicle control pool vs SPPARgM-L7 (3000 nM) #2

source_name: SPPARgM-L7 (3000 nM) #2


title: Placebo group, 12 months, patient number 34

source_name: Isolated PBMCs from diabetic male patient_Placebo_12 months

value: placebo (A)


title: Placebo group, 12 months, patient number 46


title: E2_vehicle control pool vs SPPARgM-L9 (6300 nM) #1

source_name: SPPARgM-L9 (6300 nM) #1


title: E2_vehicle control pool vs SPPARgM-L8 (1500 nM) #2

source_name: SPPARgM-L8 (1500 nM) #2


title: E2_vehicle control pool vs SPPARgM-L7 (3000 nM) #1

source_name: SPPARgM-L7 (3000 nM) #1


title: Control 2

city: Santiago de Compostela

first: Miguel

last: Abal

state: A Coruña

address: Trav Choupana s/n

department: Medical Oncology

institute: University Clinical Hospital

description: Gene expression of non-specific immunoisolated cells

hyb_protocol: Labeled cDNA was mixed with the Agilent hybridization master mix, incubated at 95ºC for 3 minutes. Afterwards, samples were dispensed onto 4x44K microarrays. For detailed methods see Agilent G4112-90000 protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities. The following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot).  Normalization was done with the quantile method implemented in the Limma Bioconductor  package.

source_name: Peripheral Blood, control 2

label_protocol: 1.65 µg of cDNA was ULS-Cy3 labeled following manufacturer instructions. Samples were incubated at 85ºC for 30 minutes. After removing non-reacted ULS, labeling degrees were evaluated as recommended. For detailed methods see Agilent G4112-90000 protocol.

extract_protocol: Circulating Tumor Cells (CTC) were immunoisolated from 7.5ml of peripheral blood from six metastatic colorectal patients. Blood was also obtained from three healthy donors. After immunoisolation, RNA was purified with the Qiamp Viral Mini kit (Qiagen) and globally amplified with a whole transcriptome amplification system (WTA2, Sigma-Aldrich). Final cDNA was purified by using the Qiaquick system (Qiagen).

value: Peripheral blood

value: non-specific immunoisolated cells


title: Patient 4

description: Gene expression of immunoisolated CTC

source_name: Peripheral Blood, patient 4

value: circulating tumor cells


title: Patient 5

description: Gene expression of immunoisolated CTC

source_name: Peripheral Blood, patient 5


title: Grape extract group, Time 0 (basal), patient number 29

source_name: Isolated PBMCs from diabetic male patient_Grape extract group_basal expression level

value: male


title: E2_vehicle control pool vs PPARa agonist 1 (10000 nM) #3

source_name: PPARa agonist 1 (10000 nM) #3


title: Placebo group, 12 months, patient number 33


title: Placebo group, 12 months, patient number 19


title: E2_vehicle control pool vs PPARa agonist 1 (10000 nM) #2

source_name: PPARa agonist 1 (10000 nM) #2


title: Patient 3

description: Gene expression of immunoisolated CTC

source_name: Peripheral Blood, patient 3


title: E2_vehicle control pool vs PPARa agonist 1 (10000 nM) #1

source_name: E2_vehicle control pool

source_name: PPARa agonist 1 (10000 nM) #1


title: Patient 2

description: Gene expression of immunoisolated CTC

source_name: Peripheral Blood, patient 2


title: Placebo group, 12 months, patient number 47


title: Patient 6

description: Gene expression of immunoisolated CTC

source_name: Peripheral Blood, patient 6


title: Control 1

source_name: Peripheral Blood, control 1


title: E2_vehicle control pool vs SPPARgM-L5 (1800 nM) #2

source_name: SPPARgM-L5 (1800 nM) #2


title: Patient 1

description: Gene expression of immunoisolated CTC

source_name: Peripheral Blood, patient 1


title: Placebo group, 6 months, patient number 52

source_name: Isolated PBMCs from diabetic male patient_Placebo_6 months


title: Placebo group, 6 months, patient number 46


title: Placebo group, 6 months, patient number 47


title: Grape extract group, 12 months, patient number 14

source_name: Isolated PBMCs from diabetic male patient_Grape extract group_12 months


title: E2_vehicle control pool vs SPPARgM-L5 (1800 nM) #1

source_name: SPPARgM-L5 (1800 nM) #1


title: E2_vehicle control pool vs SPPARgM-L3 (600 nM) #3

source_name: SPPARgM-L3 (600 nM) #3


title: Placebo group, 6 months, patient number 34


title: Placebo group, 6 months, patient number 19


title: Placebo group, 6 months, patient number 33


title: E2_vehicle control pool vs rosiglitazone (600 nM) #3

source_name: rosiglitazone (600 nM) #3


title: E2_vehicle control pool vs SPPARgM-L3 (600 nM) #2

source_name: SPPARgM-L3 (600 nM) #2


title: E2_vehicle control pool vs SPPARgM-L3 (600 nM) #1

source_name: SPPARgM-L3 (600 nM) #1


title: Placebo group, 12 months, patient number 52

source_name: Isolated PBMCs from diabetic male patient_Placebo_12 months


title: Placebo group, Time 0 (basal), patient number 52

source_name: Isolated PBMCs from diabetic male patient_Placebo_basal expression level


title: Placebo group, Time 0 (basal), patient number 47


title: E2_vehicle control pool vs rosiglitazone (600 nM) #2

source_name: rosiglitazone (600 nM) #2


title: FDu 2/11M

type: genomic

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were processed by the Affymetrix Power Tools (apt-probeset-genotype) using the BRLMM-P model, using manufacturer's default recommended parameters except for forcing all genders to female, due to complications for SNPs on the X chromosome.
Genomic DNA SNP comparison between artificially selected high lines (BEH, DAHi, DUH, MUH, EDH, RAHi, Du6/G154 and Du6i/G80) and unselected control lines.

molecule: genomic DNA

source_name: FztDU

label_protocol: standard protocol as per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tails using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: phenotype

tag: genetic background

value: FztDU

tag: line

value: tail

tag: weight


title: Control 3

source_name: Peripheral Blood, control 3


title: FDu 1/15F

value: female


title: Du6i 59M

value: high body weight


title: FDu 3/26M

value: control


title: FDu 5/35F


title: E2_vehicle control pool vs rosiglitazone (600 nM) #1

source_name: E2_vehicle control pool

value: 3T3-L1 Adipocytes

source_name: rosiglitazone (600 nM) #1


title: FDu 1/11M


title: FDu 2/36F


title: E2_vehicle control pool vs vehicle control #5

source_name: vehicle control #5


title: Du6i 47M


title: Placebo group, Time 0 (basal), patient number 46


title: Placebo group, Time 0 (basal), patient number 33


title: E2_vehicle control pool vs SPPARgM-L5 (1800 nM) #3

source_name: SPPARgM-L5 (1800 nM) #3


title: FDu 5/38M


title: FDu 4/23M


title: E2_vehicle control pool vs vehicle control #4

source_name: vehicle control #4


title: FDu 4/34F


title: E2_vehicle control pool vs vehicle control #3

source_name: vehicle control #3


title: Du6i 52F


title: Placebo group, Time 0 (basal), patient number 19


title: FDu 3/16F


title: E2_vehicle control pool vs vehicle control #2

source_name: vehicle control #2


title: Du6i 20M


title: DU6 32F


title: Placebo group, Time 0 (basal), patient number 34


title: E2_vehicle control pool vs vehicle control #1

source_name: vehicle control #1


title: Du6i 01F


title: Du6i 64F


title: E1_vehicle control pool vs SPPARgM-L1 (54 nM) #3

source_name: E1_vehicle control pool

source_name: SPPARgM-L1 (54 nM) #3


title: E1_vehicle control pool vs SPPARgM-L1 (54 nM) #2

source_name: SPPARgM-L1 (54 nM) #2


title: E1_vehicle control pool vs SPPARgM-L1 (54 nM) #1

source_name: SPPARgM-L1 (54 nM) #1


title: E1_vehicle control pool vs SPPARgM-L2 (300 nM) #3

source_name: SPPARgM-L2 (300 nM) #3


title: E1_vehicle control pool vs SPPARgM-L2 (300 nM) #2

source_name: SPPARgM-L2 (300 nM) #2


title: E1_vehicle control pool vs SPPARgM-L2 (300 nM) #1

source_name: SPPARgM-L2 (300 nM) #1


title: DU6 20M


title: DU6 51F


title: DU6 44F


title: E1_vehicle control pool vs SPPARgM-L3 (540 nM) #3

source_name: SPPARgM-L3 (540 nM) #3


title: E1_vehicle control pool vs SPPARgM-L3 (540 nM) #2

source_name: SPPARgM-L3 (540 nM) #2


title: DU6 12M


title: RAHi

source_name: RAHi

value: mixed

value: RAHi


title: E1_vehicle control pool vs SPPARgM-L3 (540 nM) #1

source_name: SPPARgM-L3 (540 nM) #1


title: EDL

source_name: PLIi

value: PLIi


title: EDH

source_name: PHIi

value: PHIi


title: ROH

source_name: ROHi

value: ROHi


title: ROL

source_name: ROLi

value: ROLi


title: E1_vehicle control pool vs SPPARgM-L4 (120 nM) #1

source_name: SPPARgM-L4 (120 nM) #1


title: DUH

source_name: DUHi

value: DUHi


title: Patient CLL22 Time point TP3 sample B

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Patient CLL22 Time point TP3 sample B

label_protocol: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns

extract_protocol: Genomic DNA was obtained from frozen tumors using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.

tag: pathology

value: CLL

tag: Stage

value: Progressive disease

tag: primary therapy

value: Pentostatin, cyclophosphamide and rituximab (PCR)

tag: secondary therapy

tag: tertiary therapy

value: Rituxan/Solu-Medrol

value: Peripheral blood

source_name: Female reference DNA sample

value: reference DNA


title: E1_vehicle control pool vs SPPARgM-L4 (120 nM) #3

source_name: E1_vehicle control pool

tag: cell type

source_name: SPPARgM-L4 (120 nM) #3


title: MUL

source_name: MULi

tag: gender

value: male

value: MULi

tag: tissue

value: tail

tag: age


title: DAHi 02

source_name: DAHi

value: high body weight

value: DAHi


title: MUH

source_name: MUHi

value: control

value: mixed

value: MUHi


title: Patient CLL22 Time point TP3 sample A

source_name: Patient CLL22 Time point TP3 sample A

tag: sample type


title: Patient CLL20 Time point TP1

source_name: Patient CLL20 Time point TP1

value: Diagnosis or near diagnosis


title: Patient CLL20 Time point TP3

source_name: Patient CLL20 Time point TP3


title: CD1


title: DU6 19M

value: FztDU


title: E1_vehicle control pool vs PPARg full 1 (6 nM) #2

value: 3T3-L1 Adipocytes

source_name: PPARg full 1 (6 nM) #2


title: Patient CLL21 Time point TP1

source_name: Patient CLL21 Time point TP1

value: CLL


title: Patient CLL19 Time point TP3

source_name: Patient CLL19 Time point TP3

value: Progressive disease


title: BEH

source_name: BEHi

value: BEHi


title: E1_vehicle control pool vs COOH (3870 nM) #3


title: BEL

source_name: BELi

value: BELi


title: Patient CLL22 Time point TP2

source_name: Patient CLL22 Time point TP2

value: Peripheral blood


title: E1_vehicle control pool vs PPARg full 1 (6 nM) #1

source_name: PPARg full 1 (6 nM) #1


title: E1_vehicle control pool vs SPPARgM-L4 (120 nM) #2

source_name: SPPARgM-L4 (120 nM) #2


title: Patient CLL21 Time point TP3

source_name: Patient CLL21 Time point TP3

value: Pentostatin, cyclophosphamide and rituximab (PCR)

source_name: Female reference DNA sample

value: reference DNA


title: DAHi 01

value: male


title: Patient CLL18 Time point TP2

source_name: Patient CLL18 Time point TP2


title: Patient CLL18 Time point TP1

source_name: Patient CLL18 Time point TP1


title: E1_vehicle control pool vs TZDfa (27 nM) #2

source_name: E1_vehicle control pool

source_name: TZDfa (27 nM) #2


title: E1_vehicle control pool vs rosiglitazone (540 nM) #3

source_name: rosiglitazone (540 nM) #3


title: Patient CLL19 Time point TP2

source_name: Patient CLL19 Time point TP2


title: E1_vehicle control pool vs COOH (3870 nM) #2


title: E1_vehicle control pool vs rosiglitazone (540 nM) #1

source_name: rosiglitazone (540 nM) #1


title: E1_vehicle control pool vs rosiglitazone (540 nM) #2

source_name: rosiglitazone (540 nM) #2


title: Patient CLL17 Time point TP2

source_name: Patient CLL17 Time point TP2


title: E1_vehicle control pool vs TZDfa (27 nM) #3

source_name: TZDfa (27 nM) #3


title: Patient CLL17 Time point TP3

source_name: Patient CLL17 Time point TP3


title: Patient CLL16 Time point TP3

source_name: Patient CLL16 Time point TP3


title: Rsp 50ng - 45%

city: Madison

first: Safak

last: Yilmaz

state: Wisconsin

address: 2 University Houses

institute: UW-Madison

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 45% formamide.  Total RNA in hybridization buffer is 50 ng.

hyb_protocol: 5 ng or 50ng of labeled target was hybridized with the microarray in 10 microliters of custom hybridization buffer (1M Na+, 20 mM Tris [pH=7.2], 0.02% SDS, and variable amounts of formamide) using a Nimblegen mixer matching the arrays used (see www.nimblegen.com).

scan_protocol: Scanning was performed with an Axon 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).  The wavelength and PMT gain were set at 532 nm and 430, respectively.  Two lines were averaged.  Fluorescence data was saved in TIFF files and processed using Nimblescan software (see www.nimblegen.com).

data_processing: Raw data (.pair files) was analyzed using Matlab (The MathWorks, Natick, MA).  For each probe, the average intensity of three replicates were calculated after the elimination of outliers based on a standard deviation test. The average of control (Nonsense) probes was subtracted from all averages to obtain background-corrected results.

organism: Cereibacter sphaeroides 2.4.1

source_name: Rhodobacter sphaeroides 2.4.1 wild-type

label_protocol:
Cloning protocol: For each organism, 16S rRNA gene was amplified with 27f and 1492r primers and cloned using TOPO10 cloning kit (Invitrogen, Carlsbad, CA).   The clones were sequenced to find operons that matched the GenBank sequences in accession codes used during probe design.  One matching clone for each organism was subsequently re-amplified with 27f and 1492r primers and purified using a QIAquick spin column (Qiagen, City, State) for the next step.
Cloned and purified 16S rRNA genes were Cy3-labeled using random prime amplification with Klenow fragment and a decalabel DNA labeling kit (Fermentas, St Leon-Rot, Germany).  A previously published protocol was followed (Loy, A. et al. 2011. PCR mutation detection protocols. Methods in Molecular Biolology. Vol. 688, pp. 187-206).

growth_protocol:
E. coli was grown to mid-log phase (O.D.600nm 0.3-0.4) in Lennox LB broth (Becton Dickinson, Franklin Lakes, NJ) at 37°C.
R. sphaeroides was phototrophically grown to mid-log phase (100-150 kletts) in Sistrom's minimal medium (Sistrom, W. 1960. Journal of General Microbiology. 22:778-785) amended with 33.9 mM succinate .

extract_protocol: Genomic DNA was extracted using Ultra Clean Soil DNA (MoBio Laboratories, Solana Beach, CA).

tag: genotype

value: Wild Type

value: normal

tag: accession

tag: hybridization buffer (formamide content)

value: 45% formamide

tag: hybridization buffer (total rna)

value: 50 ng


title: E1_vehicle control pool vs TZDfa (27 nM) #1

source_name: TZDfa (27 nM) #1


title: E1_vehicle control pool vs vehicle control #3

source_name: vehicle control #3


title: Rsp 50ng - 32.5%

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 32.5% formamide.  Total RNA in hybridization buffer is 50 ng.

tag: phenotype

value: 32.5% formamide


title: Patient CLL16 Time point TP2

source_name: Patient CLL16 Time point TP2


title: E1_vehicle control pool vs vehicle control #2

source_name: vehicle control #2


title: Rsp 50ng - 25%

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 25% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 25% formamide


title: E1_vehicle control pool vs PPARg full 1 (6 nM) #3

source_name: PPARg full 1 (6 nM) #3


title: Rsp 50ng - 20%

description: Hybridization of labeled and fragmented R. sphaeroides 16S rRNA gene with 20% formamide.  Total RNA in hybridization buffer is 50 ng.

value: 20% formamide


title: C.elegans_8days_GC3-1

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

country: Japan

institute: Japan Aerospace Exploration Agency

hyb_protocol: Labeled cRNA (1.65 µg/sample) was hybridized to a C. elegans oligo microarray using a gene expression hybridization kit at 65 °C for 17 hours.

scan_protocol: Array were scanned with an Agilent Scanner and processed with Agilent Feature Extraction Software.

data_processing: Microarray data were analyzed using Gene Spring software (Agilent Technologies). Normalized data were produced by "Normalize to 75 percentile sift protocol’’ and "baseline to median of control sample protocol’’. Arrays were filtered on expression (20-100)th percentile in raw data.

organism: Caenorhabditis elegans

source_name: Ground control

label_protocol: Total RNA was amplified using the Low Input Quick Amp Labeling Kit protocol. Cy3 labeled cRNA was produced according to manufacturer's protocol.

growth_protocol: Approximately 50 L1 larvae were grown in 2 mL M9. Worms were cultured in 12 mL S basal medium contained bacterial feeds for 8days.

extract_protocol: Worms were homogenized with four rounds of 20-second beating at 5000 rpm in a Micro Smash TM MS-100 bead beater with 3 minutes of cooling on ice between rounds. Total RNA was extracted using an Isogen RNA purification kit following the manufacturer’s protocol.

tag: strain

value: N2 wild type

tag: developmental stage

value: adult