title: Liver_saline injected chicken fed MOS (prebiotic)_ replica 5

source_name: Total RNA from liver of saline injected chicken fed MOS (prebiotic) labeled with Cyanine-3 (green).


title: Genomic DNA from normal fetal skin 3

status: Public on May 06 2011

type: genomic

city: Vancouver

first: Ryan

last: Yuen

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
FT5_N_skin
Normal skin sample.

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using the standard recommended Illumina scanner setting.

data_processing: Data were background-normalized using BeadStudio software v3.1.3.0, which subtracts a background value derived by averaging the signals of built-in negative control bead types.

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal skin, normal

label_protocol: DNA was bisulfite converted, amplified, and fragmented.

extract_protocol: Genomic DNA was extracted using standard techniques and purified using the Qiagen DNeasy Kit according to standard instructions.

tag: gender

value: male

tag: tissue

value: skin

tag: developmental stage

value: fetal

tag: disease state

value: normal


title: Genomic DNA from normal fetal skin 4

description:
FT6_N_skin
Normal skin sample.


title: Liver_LPS injected chicken fed VIRG (antibiotic)_ replica 4

type: RNA

city: Ste Anne de Bellevue

first: Bushansingh

middle: Shyam

last: Baurhoo

state: Quebec

address: 21111, Lakeshore Road

department: Animal Science

institute: McGill University

description:
raw data file: Liver Array_4.DAT
Slide 4_LPS chicken_antibiotic group_ replica 4 (Cy3) vs LPS chicken_prebiotic group_ replica 2 (Cy5)

hyb_protocol: mix of 33 pmol of both samples was resuspended with 33 µl Pronto! Long Oligo Hybridization solution and applied to pre-hybrydized microarray slides with spotted area coved with a 25 X 40 mm glass coverslip; slides were hybridized in Corning Hybridization Chambers immersed in 42C water bath, protected from light, for 16h. After hybridization, slides were sequencenly washed according to manufacturer's instructions (Pronto! Universal Microarray Hybridization Kit, Corning Inc.)

scan_protocol: scanned on ScanArray Gx Plus (PerkinElmer) set to 65% lazer power Images were quantified using ScanAlyze Software (version 2.50).

data_processing: Log2 transformed data was submitted to ratio analysis and LOWESS normalization using JMP Genomics Software (SAS Institute)

molecule: total RNA

organism: Gallus gallus

source_name: Total RNA from liver of LPS injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).

label_protocol: 5µg of total RNA were primed with 3µg of random primers and 2µg of oligo(dt) primer, heated at 70 oC for 10 min, then reverse transcribed at 42 oC for 2h with 3.2 µl ChipShot Reverse Transcriptase and 4 µl aminoallyl-sNTPs; cDNA was indirectly labeled with CyDye NHS Esters (Cy3 or Cy5) by adding 60 µl of cDNA eluted to dried 40,000 pmol CyDye aliquot and hybrydized at room temperature for 1h, followed by purification steps as indicated by manufacturer's instructions (ChipShot Indirect Labeling System and Membrane Clean-Up System, Promega Corp)

growth_protocol: broiler chicks raised under standard conditions and fed prebiotic or antibiotic diet ad libitum

extract_protocol: Total RNA from liver, intestine and skeletal muscle tissues was extracted using Trizol reagent and Prelink RNA Mini Kit following manufacturer's instructions (Invitrogen)

treatment_protocol: at 14 d of age, chicks were injected i.p. with saline or Salmonella LPS. At 24 h post-injection, liver, intestine (jejunum) and skeletal muscle (breast) tissue samples were snap frozen in liquid nitrogen and stored at -80 oC for later RNA extraction and microarray analysis.

value: liver

tag: status

value: VIRG birds

tag: breed

value: cobb 500 broiler chicken

tag: age

value: 14 days


title: Liver_saline injected chicken fed VIRG (antibiotic)_ replica 4

description:
raw data file: Liver Array_8.DAT
Slide 8_saline chicken_antibiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 4 (Cy5)

source_name: Total RNA from liver of saline injected chicken fed VIRG (antibiotic) labeled with Cyanine-3 (green).


title: Liver_saline injected chicken fed MOS (prebiotic)_ replica 3

description:
raw data file: Liver Array_7.DAT
Slide 7_saline chicken_prebiotic group_ replica 3 (Cy3) vs saline chicken_antibiotic group_ replica 3 (Cy5)

value: MOS birds


title: CLL_del11q rep4_case52

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

country: USA

institute: University of Michigan

description: 50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 48 deg C with rotation at 60 rpm.  Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix GeneChip data were analyzed as described (Ouillette et al., Cancer Res. 2008;68:1012-21).  Raw probe-level data were converted to expression measures using the Robust Multi-array Average (RMA) method, which is implemented in the Affymetrix package of  Bioconductor (Izarry et al., Biostatistics. 2003;4:249-64; R version 2.7.0, Bioconductor Affymetrix package version 1.17.5). Briefly, the raw perfect match (PM) probes are first quartile normalized to reduce array-to-array variation. The normalized probe data are then converted to an expression measure (log scale) for each gene on each chip. For differential expression analysis relating to 11q deletion status, we used two-sample Z-tests to compare the mean log-scale expression level between del11q and non-del11q samples.  Genes with a False Discovery Rate (33) below 0.1 were selected, then fold-changes, FDR values, and Z-scores were used to identify genes having a strong association with 11q deletion status.
Robust multi-array average (RMA)-computed expression values (Izarry et al., Biostatistics, 4:249-64, 2003).  Note that the expression values are log2-transformed data.

label: biotin

source_name: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.

label_protocol: 50ng total RNA was amplified using the Ovation RNA Amplification system (NuGen, Inc.), labeled with the FL-Ovation cDNA Biotin module (NuGen, Inc.) and hybridized to the Human 133 2.0 plus GeneChip (Affymetrix) following the manufacturer's recommended protocols.

growth_protocol: Material used was cryopreserved primary human peripheral blood cells, prepared as below.

extract_protocol: CLL peripheral blood mononuclear cells were stained with propidium iodide and CD19*PE, then sorted  using a high-speed FACS Aria (Becton Dickinson) sorter to purity. RNA was extracted using the Trizol reagent. RNA was further purified using the RNAeasy kit (Qiagen).

tag: cell type

tag: del11q status

value: del11q present

tag: treatment status prior to enrollment [ut = untreated; t = treated]

value: UT

tag: net insr expression by facs

tag: delta ctm insr-gapd

tag: zap70%+ mean

tag: igvh (98%) [um = unmutated; m = mutated]

value: UM

tag: FISH (>25% of nuclei)

tag: FISH-all

tag: snp 6.0 total subchromosomal and chromosomal lesions


title: Liver_saline injected chicken fed MOS (prebiotic)_ replica 1

description:
raw data file: Liver Array_5.DAT
Slide 5_saline chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_prebiotic group_ replica 3 (Cy5)

tag: gender


title: Liver_LPS injected chicken fed MOS (prebiotic)_ replica 4

description:
raw data file: Liver Array_6.DAT
Slide 6_LPS chicken_prebiotic group_ replica 4 (Cy3) vs saline chicken_prebiotic group_ replica 2 (Cy5)

source_name: Total RNA from liver of LPS injected chicken fed MOS (prebiotic) labeled with Cyanine-3 (green).

tag: tissue


title: Genomic DNA from normal fetal skin 1

description:
FT3_N_skin
Normal skin sample.

value: female

tag: developmental stage


title: Genomic DNA from normal fetal skin 2

description:
FT4_N_skin
Normal skin sample.

tag: disease state


title: Liver_LPS injected chicken fed MOS (prebiotic)_ replica 1

description:
raw data file: Liver Array_3.DAT
Slide 3_LPS chicken_prebiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 3 (Cy5)

tag: status


title: CLL_del11q rep3_case32

value: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient

value: T

value: 11q, trisomy 12


title: CLL_del11q rep2_case24


title: Genomic DNA from normal fetal muscle 6

description:
mT4-5_N_muscle
Normal muscle sample.

source_name: Fetal muscle, normal

value: muscle


title: CLL_del11q rep1_case22

data_processing:
Affymetrix GeneChip data were analyzed as described (Ouillette et al., Cancer Res. 2008;68:1012-21).  Raw probe-level data were converted to expression measures using the Robust Multi-array Average (RMA) method, which is implemented in the Affymetrix package of Bioconductor (Izarry et al., Biostatistics. 2003;4:249-64; R version 2.7.0, Bioconductor Affymetrix package version 1.17.5). Briefly, the raw perfect match (PM) probes are first quartile normalized to reduce array-to-array variation. The normalized probe data are then converted to an expression measure (log scale) for each gene on each chip. For differential expression analysis relating to 11q deletion status, we used two-sample Z-tests to compare the mean log-scale expression level between del11q and non-del11q samples.  Genes with a False Discovery Rate (33) below 0.1 were selected, then fold-changes, FDR values, and Z-scores were used to identify genes having a strong association with 11q deletion status.
Robust multi-array average (RMA)-computed expression values (Izarry et al., Biostatistics, 4:249-64, 2003).  Note that the expression values are log2-transformed data.

value: 11q,trisomy 12, 13q


title: Genomic DNA from normal fetal muscle 5

description:
FT13_N_muscle
Normal muscle sample.


title: Liver_saline injected chicken fed VIRG (antibiotic)_ replica 1

description:
raw data file: Liver Array_1.DAT
Slide 1_saline chicken_antibiotic group_ replica 1 (Cy3) vs LPS chicken_antibiotic group_ replica 1 (Cy5)

tag: breed

value: male


title: Genomic DNA from normal fetal muscle 4

description:
FT6_N_muscle
Normal muscle sample.

value: fetal


title: Genomic DNA from normal fetal muscle 2

description:
FT4_N_muscle
Normal muscle sample.

value: normal


title: Genomic DNA from normal fetal muscle 1

description:
FT3_N_muscle
Normal muscle sample.


title: Genomic DNA from normal fetal lung 6

description:
mT16-62_UPD_lung
Normal lung sample.

source_name: Fetal lung, normal

value: lung


title: HSCR patient sample 354.3, rep2

city: Baltimore

first: Qian

last: Jiang

address: 733 N Broadway Street

institute: JHMI

description: Isolated HSCR patient.

hyb_protocol: Hybridization buffer, human Cot-1 DNA and blocking agent were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent High-Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing:
After image analysis, the raw intensities from the red and green channels were adjusted by subtraction of the background intensity and preprocessed using a variance stabilizing normalization procedure. This procedure, called vsn2, provides straightforward methods for preprocessing two-channel arrays by calibrating the dependency between the mean and variance of the raw intensity measurements while accounting for both the foreground and background intensities, within a model framework. This analysis was performed for each array analyzed. To avoid the influence of outliers in the raw intensities, we trimmed the largest 10% of the residuals when estimating the parameters in vsn2.  Consequently, we performed the locally weighted linear regression using the lowess function in R, for the red and green channels separately to smooth out the systematic effect caused by the GC-content variation in the probe sequences. These final residuals from the lowess regression were used for further analysis. To control for batch effects during experimental array processing, we utilized the 1,262 normalization probes from Agilent and our 8,000 control probes. We performed quantile normalization on each array so that the red and green intensities of the control probes had the same mean absolute difference (MAD) and the log2 ratio of the red over green intensities had their median centered at zero. The between array normalization procedure was performed using the marray R package available through www.bioconductor.org.

The post-normalization relative intensity data log2R, where R = red/green intensity, were plotted against their genomic location, and outliers were smoothed using a sliding window of five probes. For a given smoothed region, we calculated its median (m) from the local observations. We also trimmed the most extreme 2.5% of observations to calculate the standard deviation ( ) for the entire data set. For a given smoothed region, an outlier was determined and smoothed if the difference between maximum or minimum intensity and its closest neighboring probe exceeded 4 : we d these observations by m ± 2 .  After smoothing of outliers, we used the circular binary segmentation procedure (CBS) to detect copy number with a Type-I error (α) of 0.01. For the segmented region reported by CBS, we examined the intensities across ≥10 probes and used a stringent criterion to call a duplication if log2R ≥ log2(1.5) = +0.58, a deletion if log2R ≤ log2(0.5) = -1, and a normal diploid dosage if -1 < log2R < 0.58.  Although the stringent criterion can reduce false positive CNV identification, it can also increase the false negative rate. Thus, we also analyzed our results using the following relaxed criterion: call a duplication if log2R ≥ log2(1.5) = +0.40, a deletion if log2R ≤ log2(0.5) = -0.80, and a normal diploid dosage if -0.80 < log2R < 0.40. Finally, we also used the commercial proprietary software provided by Agilent (Genomic Workbench, Standard Edition, V 5.0.14) to call CNVs. Nevertheless, the actual duplication and deletion calls utilized the identical stringent and relaxed criteria indicated earlier.

source_name: Genomic DNA from HSCR patient sample 354.3

label_protocol: Test DNAs were labeled with Cy5-dCTP (red fluorescence) and the sex-matched control DNA with Cy3-dCTP (green fluorescence) using the Invitrogen BioPrime Array CGH genomic labeling kit (Invitrogen Corporation, Carlsbad, CA).

extract_protocol: Genomic DNA was extracted from whole blood according to a standard salting-out procedure.

value: whole blood

value: Hirschsprung disease (HSCR)

tag: patient identifier

source_name: Genomic DNA from pooled sex-matched control

value: control


title: HSCR patient sample 63.3, rep3

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 63.3

value: Hirschsprung disease (HSCR) with additional anomaly


title: HSCR patient sample 242.4

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 242.4


title: HSCR patient sample 122.7, rep3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 122.7


title: HSCR patient sample 300.3, rep2

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 300.3


title: HSCR patient sample 355.3, rep2

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 355.3


title: Genomic DNA from normal fetal lung 4

description:
FT6_N_lung
Normal lung sample.


title: Genomic DNA from normal fetal lung 3

description:
FT5_N_lung
Normal lung sample.


title: Genomic DNA from normal fetal lung 5

description:
mT4-5_N_lung
Normal lung sample.


title: HSCR patient sample 122.7, rep2

description: Isolated HSCR patient.


title: Genomic DNA from normal fetal muscle 3

description:
FT5_N_muscle
Normal muscle sample.


title: HSCR patient sample 408.3, rep2

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 408.3


title: HSCR patient sample 413.3, rep3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 413.3


title: Genomic DNA from normal fetal lung 2

description:
FT4_N_lung
Normal lung sample.


title: HSCR patient sample 413.3, rep2

description: Isolated HSCR patient.


title: Genomic DNA from normal fetal kidney 6

description:
mT4-5_N_kidney
Normal kidney sample.

source_name: Fetal kidney, normal

value: kidney


title: Genomic DNA from normal fetal lung 1

description:
FT3_N_lung
Normal lung sample.


title: Genomic DNA from normal fetal kidney 4

description:
FT6_N_kidney
Normal kidney sample.


title: Genomic DNA from normal fetal kidney 5

description:
FT13_N_kidney
Normal kidney sample.


title: HSCR patient sample 122.7, rep1

description: Isolated HSCR patient.


title: Genomic DNA from normal fetal kidney 3

description:
FT5_N_kidney
Normal kidney sample.


title: Genomic DNA from normal fetal kidney 1

description:
FT3_N_kidney
Normal kidney sample.


title: Genomic DNA from normal fetal brain 6

description:
CPM16-36_BPD_brain
Normal brain sample.

source_name: Fetal brain, normal

value: brain


title: HSCR patient sample 63.3, rep2

description: HSCR patient with additional anomaly.


title: Genomic DNA from normal fetal kidney 2

description:
FT4_N_kidney
Normal kidney sample.


title: Genomic DNA from normal fetal brain 4

description:
mT4-5_N_brain
Normal brain sample.


title: HSCR patient sample 413.3, rep1

description: Isolated HSCR patient.


title: HSCR patient sample 348.3

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 348.3


title: HSCR patient sample 355.3, rep1

description: Isolated HSCR patient.


title: Genomic DNA from normal fetal brain 5

description:
mT16-62_UPD_brain
Normal brain sample.


title: HSCR patient sample 359.3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 359.3


title: Genomic DNA from normal fetal brain 2

description:
FT5_N_brain
Normal brain sample.


title: HSCR patient sample 300.3, rep1

description: HSCR patient with additional anomaly.


title: HSCR patient sample 384.3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 384.3


title: HSCR patient sample 63.3, rep1

description: HSCR patient with additional anomaly.


title: HSCR patient sample 423.3

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 423.3


title: HSCR patient sample 150.3

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 150.3


title: HSCR patient sample 354.3, rep1

description: Isolated HSCR patient.


title: HSCR patient sample 47.3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 47.3


title: HSCR patient sample 372.3

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 372.3


title: Genomic DNA from normal fetal brain 1

description:
FT4_N_brain
Normal brain sample.


title: Genomic DNA from normal fetal brain 3

description:
FT13_N_brain
Normal brain sample.


title: Slide 171167

status: Public on May 05 2011

city: Groningen

first: Jetta

last: Bijlsma

address: Hanzeplein 1

department: Medical Microbiology

country: Netherlands

institute: University Medical Center Groningen

description: Sample 2

hyb_protocol: The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519)

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Net{A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to OD600 of 0.25 in GM17 media

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype/variation

value: wild type

source_name: Net{B}

value: mutant


title: HSCR patient sample 252.3

description: HSCR patient with additional anomaly.

source_name: Genomic DNA from HSCR patient sample 252.3

source_name: Genomic DNA from pooled sex-matched control


title: Slide 171336

description: Sample 1


title: Slide 171337

description: Sample 3


title: Naringenin vs Control Replicate 6

city: College Station

first: Bhimanagouda

middle: S

last: Patil

state: TX

address: 1500 Research Pkwy, Ste A120

institute: Texas A&M University

hyb_protocol: A total of six slides were used. S. Typhimurium treated with naringenin cDNA was labeled with Cy3 and control cDNA labeled with Cy5 were mixed and applied to three slides while the labeling was reversed for remaining three slides. This strategy was used to avoid any bias arising due to dye labeling activity of Cy3 versus Cy5. The labeled mixtures were cleaned again using QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from  S. Typhimurium treatment and control were used to hybridize on the microarray slides. Hybridization was carried out at 42°C for 18 h in the dark.

scan_protocol: Scanned on a GenePix Scanner 4100A

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed test signal/processed reference signal. Acuity 4.0 (Molecular Devices) was used for analysis.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Salmonella Typhimurium LT2 cells

label_protocol: Total RNA (10 µg) from treatment and control was used to synthesis cDNA using random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and then centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and Aminoallyl-deoxyuridine triphosphate mix) was then incubated with Superscript II reverse transcriptase (Invitrogen) at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs were labeled with Cy-3 mono-Reactive Dye and Cy-5 mono-Reactive Dye (GE Health Care)

growth_protocol: Overnight culture of Salmonella Typhimurium LT2 was  diluted 1000 fold in LG-glu (0.5% ) and grown to OD600 ≈ 1.0 at 37oC and 200 rpm in waterbath

extract_protocol: Total RNA was stabilized with RNAprotect bacteria reagent (Qiagen Inc., Valencia, CA, USA) and RNA was isolated with RNeasy minikit (Qiagen Inc.) according to manufacturer’s instructions.

treatment_protocol: The diluted culture was treated with 100 µg/ml (2.5 µl of 40 mg/ml stock) naringenin or equivalent volume of DMSO.

tag: growth stage

tag: treatment

value: 100 µg/ml naringenin

tag: growth satge

value: 2.5 µl DMSO


title: Naringenin vs Control Replicate 3


title: Naringenin vs Control Replicate 2


title: HSCR patient sample 408.3, rep1

description: Isolated HSCR patient.


title: Naringenin vs Control Replicate 4


title: HSCR patient sample 370.3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 370.3


title: Naringenin vs Control Replicate 1


title: Naringenin vs Control Replicate 5


title: HSCR patient sample 346.3

description: Isolated HSCR patient.

source_name: Genomic DNA from HSCR patient sample 346.3


title: SU-DHL4, untreated, rep2

city: Berlin

first: Volkhard

last: Seitz

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Charité Universitätsmedizin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Expression arrays were analyzed using the statistical programming environment R and Bioconductor. Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
We defined a probe set as significantly regulated if (a) at least a two-fold change was observed and (b) the BH-corrected p-value was below 0.05.

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

growth_protocol: Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.

extract_protocol: RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).

tag: cell line

tag: cell type

value: B-cell lymphoma cells


title: SU-DHL6, untreated, rep2


city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
P9_Nov24

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio_2010.1

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period,biological rep10

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit in accordance with the prescribed protocol provided with the kit

extract_protocol: RNA was extracted with PAXgene Blood RNA Kit in accordance with the prescribed protocol provided with the kit.

tag: patient

tag: virus strain

value: Pandemic influenza (A/H1N1 new subtype)

value: Blood

tag: mechanical ventilation

value: no

tag: disease phase

value: late period


title: SU-DHL6 untreated, rep2

data_processing:
Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.

source_name: SU-DHL6, untreated

treatment_protocol: A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.

value: untreated


title: Namalwa, untreated, rep2

source_name: Namalwa

value: Namalwa


title: U266

value: plasma cell myeloma cells


title: SU-DHL6, untreated, rep1


title: LP1


title: SU-DHL4, untreated, rep1


title: HepG2 cells, HNF4a RNAi treated, rep2

city: Riverside

first: Eugene

middle: L

last: Bolotin

state: CA

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

description: Expression profiling from HepG2 cells,  with reduced HNF4a

scan_protocol: Standard Affymetrix Scanner M10

data_processing: Limma (Bioconductor) and GCRMA

source_name: Cultured HepG2 cells,  ATCC# HB-8065

label_protocol: Standard Affymetrix Biotin Labeling

growth_protocol: DMEM containing 10% Fetal Bovine Serum (FBS), 1% non-essential amino acids, and 1% sodium pyruvate. All cell lines were  supplemented with 1%

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA) and reverse transcribed using the Reverse Transcription System kit (Promega, Madison, WI). PCR amplification was performed in the linear range using a PTC-100 TM programmable thermal controller (MJ Research, Inc., Hercules, CA). One-fifth of each reaction was electrophoresed on a 2% agarose gel, stained with ethidium bromide and visualized by UV light (see Supplementary Table S3B for a list of PCR primers used).

treatment_protocol: RNA interference (RNAi) against HNF4a1 was performed in HepG2 cells using siRNAs corresponding to nucleotides +179 to +197 of human HNF4A (NM_178849, sense siRNA: 5’-UGUGCAGGUGUUGACGAUGdTdT-3’, antisense siRNA 5’-CAUCGUCAACACCUGCACAdTdT-3’) purchased from Dharmacon Research, Inc. (An NCBI Blast search indicated that this sequence is unique to HNF4A). Approximately 24 hr prior to transfection, cells were plated at a density of ~1.5 x105 or  ~2.5 x105 cells/well in a 12- or 6-well plate, respectively (~50-70% confluency) without antibiotics. The siRNAs (100 or 200 pmol, respectively) were introduced into the cells using TransIT-TKO transfection reagent purchased from Mirus Bio Corporation (Madison, WI). Each experiment included a control containing just the transfection reagent as well as a nonspecific siRNA control against firefly luciferase (PGL3: sense siRNA 5’-CUUACGCUGAGUACUUCGAdTdT-3’; antisense siRNA 5’-dTdTGAAUGCGACUCAUGAAGCU). To verify HNF4a protein levels, cells were lysed in RIPA buffer purchased from Santa Cruz Biotechnology and analyzed by SDS-PAGE followed by immunoblotting

value: HNF4a knockdown


title: L363


title: Namalwa, untreated, rep1


title: HepG2 cells, HNF4a RNAi treated,  rep1

description: Expression profiling from HepG2 cells, with reduced HNF4a


title: HT

source_name: HT, untreated

value: HT


title: HepG2 cells, control, rep2

description: Expression profiling from HepG2 cells

value: control


title: HT + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)

source_name: HT, A/T treatment

value: 5-aza-dC, trichostatin A


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
HURH 4D7

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep14

value: yes


title: SU-DHL6 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2

source_name: SU-DHL6, A/T treatment


title: SU-DHL6 untreated, rep1


title: HepG2 cells, control, rep1

description: Expression profiling from HepG2 cells


title: SU-DHL4 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1

source_name: SU-DHL4, A/T treatment


title: SU-DHL6 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1


title: SU-DHL4 untreated, rep2

source_name: SU-DHL4, untreated


title: SU-DHL4 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2


title: SU-DHL4 untreated, rep1


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
HURH 6D7

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep13


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period.
HLF 11.1

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep6

value: early period


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in early period.
P9_Nov22

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep6


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
HURH 7D7

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep12


title: Raji + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2

source_name: Raji, A/T treatment

value: Raji


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in early period.
HLF 7.1

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep5


title: Raji untreated, rep2

source_name: Raji, untreated


title: Namalwa untreated, rep2

source_name: Namalwa, untreated


title: Raji untreated, rep1


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
HLF 5.3

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep10


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
HURH 7D3

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep11


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
MA.S.A_Nov 9/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep8


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
STS_Nov 14/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep9


title: Raji + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1


title: Namalwa + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1

source_name: Namalwa, A/T treatment


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in early period.
P13_Nov 27/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep3


title: Namalwa + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2


title: Namalwa untreated, rep1


title: Daudi untreated, rep2

source_name: Daudi, untreated

value: Daudi


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
HLF 6.3

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep8


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in early period.
HLF 6.1

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep4


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
P6_Nov 15/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep7


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period.
P12_Nov 26/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep5


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
DED_Nov 7/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep7


title: Daudi untreated, rep1


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
P11_Nov 29/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep6


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
DED_Nov 4/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep5


title: Daudi + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1

description: Daudi_A/T-treated _1

source_name: Daudi, A/T treatment


title: KM-H2, rep2

treatment_protocol: Untreated.

value: Hodgkin cells


title: Daudi + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2

value: B-cell lymphoma cells


title: SU-DHL6, rep2


title: L428, rep2


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
P6_Nov 13/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep6

value: Pandemic influenza (A/H1N1 new subtype)


title: KM-H2, rep1


title: [delta smelt]-[Control1 vs NH3 exposed1]-[1]

city: Davis

first: Richard

middle: Edward

last: Connon

address: One Shields Avenue

department: Anatomy, Physiology and Cell Biology

institute: University of California at Davis

description: Sample 8: Log-2 ratio, [Control1 vs NH3 exposed1]-[1], 555/647

hyb_protocol: Hybridization was carried out in an automated tecan HS4800 hybridization station (Tecan, San Jose, Ca, USA)

scan_protocol: Slides were scanned using a GenePix 4000B scanner instrument (Axon Instruments, Sunnyvale, Ca, USA)

data_processing: Data analysis: Two color microarray assessments were carried out on quadruplicate treatments, using 1µg of amplified cDNA for each control vs exposed sample, incorporating dye swaps for each (total 8 samples). Microarray hybridizations were performed using an automated Tecan HS4800 hybridization station. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment

label: Alexa Fluor 555

organism: Hypomesus transpacificus

source_name: Whole organism, exposed

label_protocol: Fifteen micrograms of total RNA was labeled with Alexa Fluor dyes using Superscript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, Ca, USA)

growth_protocol: Juveniles obtained from the Fish Culture Conservation Facility (FCCL) at the University of California at Davis.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, Ca, USA) as per manufacturer's protocol

treatment_protocol: 57-old juveniles were exposed for 7 days to 10 mg/L Ammonium chloride

value: larva

tag: age

value: 57-days old

tag: stress

value: ammonium chloride

label: Alexa Fluor 647

source_name: Whole organism, control

treatment_protocol: control

tag: control composition

value: Pooled mixed age


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
MA.S.A_Nov 14/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep3

tag: tissue

value: Blood

value: late period


title: L428, rep1


title: SU-DHL4, rep1


title: L1236, rep1


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
P11_Nov 27/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep4


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period.
P7_Nov 18/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep4


title: SU-DHL6, rep1


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
DED_Nov 3/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep2


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in early period.
P6_Nov 11/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep2

value: no


title: L1236, rep2


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
P13_Nov 29/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep5


title: Light, biological rep3

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: Gene expression data from Arabidopsis Thaliana under high light

hyb_protocol: Technical steps as target hybridization, washing and staining of the arrays were performed sequentially as described in the Affymetrix GeneChip expression analysis technical manual using the Affymetrix once-cycle target labelling and control reagents, an Affymetrix GeneChip hybridization oven 640, and Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using Affymetrix GenChip Scanner 3000 7G.

data_processing: Data was standardized from R  using the affy Bioconductor package. Methods: Robust Multi-array Average and quantile normalization.

organism: Arabidopsis thaliana

source_name: Arabidopsis Thaliana under high light

label_protocol: Biotin-labelled cRNA was produced by in vitro transcription using GeneChip® 3' IVT Express Kit. The biotin-labelled cRNA was degraded by alkaline digestion and used for hybridization with ATH1 arrays.

growth_protocol: Arabidopsis cell suspension culture was maintained in 200 mL of liquid growth medium (Jouannea and Peaudlen, 1967; Axelos et al., 1992) by gentle agitation at 120 rpm at 24 ºC under continuous illumination (50 microE/m2/s) in an incubator shaker. Cells were sub-cultured with a 1/20 dilution factor every 7 days.

extract_protocol: Total RNA was extracted with the acid guanidine isothiocyanate-phenol-chloroform method using Trizol reagent. Total RNA was treated with TURBO DNase  to eliminate traces of contaminating genomic DNA.

treatment_protocol: An incubation of 30 min at high light or 1-h at dark were selected as the optimum time to monitor the changes in the transcription profile in the microarray experiments.

value: Light

tag: sample type

value: cell suspension culture


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period.
P12_Nov 30/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, late period, biological rep1


title: SU-DHL4, rep2


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
P6_Nov 17/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep4


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period.
P12_Nov 24/09

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep3


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in early period.
HUV_7d1

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, early period, biological rep1


title: Light, biological rep2


title: [delta smelt]-[NH3 exposed3 vs Control4]-[3]

description:
Dye swap
Sample 7: Log-2 ratio, [NH3 exposed3 vs Control4]-[3], 647/555

tag: developmental stage


title: Namalwa, rep1

source_name: Namalwa

value: Namalwa


title: Dark, biological rep3

description: Gene expression data from Arabidopsis Thaliana under dark

source_name: Arabidopsis Thaliana under dark

value: Dark


title: [delta smelt]-[NH3 exposed2 vs Control1]-[2]

description:
Dye swap
Sample 4: Log-2 ratio, [NH3 exposed2 vs Control1]-[2], 647/555


title: [delta smelt]-[NH3 exposed4 vs Control3]-[4]

description:
Dye swap
Sample 6: Log-2 ratio, [NH3 exposed4 vs Control3]-[4], 647/555


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period.
HUV_6d1

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep1

value: yes

value: early period


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period.
HUV_6d3

source_name: Blood of Pandemic H1N1 positive critical patient under mechanical ventilation, early period, biological rep2


title: [delta smelt]-[Control2 vs NH3 exposed2]-[2]

description: Sample 5: Log-2 ratio, [Control2 vs NH3 exposed2]-[2], 555/647

source_name: Whole organism, exposed


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
FCC_Nov 10/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep3


title: Namalwa, rep2


title: [delta smelt]-[Control4 vs NH3 exposed4]-[4]

description: Sample 2: Log-2 ratio, [Control4 vs NH3 exposed4]-[4], 555/647

source_name: Whole organism, control


title: Light, biological rep1


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
HLF 7.3

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep9


title: Dark, biological rep2


title: H1299 DAC 1 uM (3239)

city: San Diego

first: Helen

last: Brady

address: 4550 Towne Centre Ct

institute: Celgene

description:
decitabine treated 48h
3239_H1299_1uM-Dac_2.CHP
H1299 1D
3239_H1299_1uM-Dac_2.CEL

hyb_protocol: Biotin-labeled cRNA (10 μg) was fragmented and hybridized to each human U133A 2.0 genechip (Affymetrix, Santa Clara, CA).

scan_protocol: Standard Affymetrix protocol

source_name: H1299 cells

label_protocol: Double-stranded cDNA and biotinlabeled cRNA were synthesized using 100 ng of total RNA with Ambion’s MessageAmp Premier RNA Amplification Kit (ABI, Foster City, CA).

growth_protocol: Cells were seeded 24 hours before drug treatment and incubated at 37°C and 5% CO2. Cells were seeded at 0.6–1.2 × 105 cells per well, in 6-well plates,using 4 mL of medium per well, with fresh drug added directly to the medium every 24 hours. At this seeding density, cells are30%–40%confluent at the start of drug treatments.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen)

tag: agent

value: decitabine

tag: dose

value: 1 uM


title: [delta smelt]-[NH3 exposed1 vs Control2]-[1]

description:
Dye swap
Sample 3: Log-2 ratio, [NH3 exposed1 vs Control2]-[1], 647/555


title: Control, biological rep2

description: Gene expression data from Arabidopsis Thaliana control

source_name: Arabidopsis Thaliana control

value: Control


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
FCC_Nov 4/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep1

value: Pandemic influenza (A/H1N1 new subtype)


title: H1299 DAC 3 uM (3241)

description:
decitabine treated 48h
3241_H1299_3uM-Dac_2.CHP
H1299 3D
3241_H1299_3uM-Dac_2.CEL

value: 3 uM


description:
Gene expression data from blood of Pandemic H1N1 positive critical patient with no mechanical ventilation in late period.
FCC_Nov 6/09

source_name: Blood of Pandemic H1N1 positive critical patient with no mechanical ventilation, late period, biological rep2


title: H1299 DAC 1 uM (3238)

description:
decitabine treated 48h
3238_H1299_1uM-Dac_1.CHP
H1299 1D
3238_H1299_1uM-Dac_1.CEL


title: Healthy Control, biological rep4

description:
Gene expression data from healthy control blood.
Ctrl4

source_name: Blood of Healthy Control, biological rep4

value: control


title: Healthy Control, biological rep3

description:
Gene expression data from healthy control blood.
Ctrl3

source_name: Blood of Healthy Control, biological rep3


title: H1299 DAC 0.3 uM (3237)

description:
decitabine treated 48h
3237_H1299_0.3uM-Dac_2.CHP
H1299 0.3D
3237_H1299_0.3uM-Dac_2.CEL


title: Dark, biological rep1

description: Gene expression data from Arabidopsis Thaliana under dark


title: H1299 DAC 3 uM (3240)

description:
decitabine treated 48h
3240_H1299_3uM-Dac_1.CHP
H1299 3D
3240_H1299_3uM-Dac_1.CEL


title: [delta smelt]-[Control3 vs NH3 exposed3]-[3]

description: Sample 1: Log-2 ratio, [Control3 vs NH3 exposed3]-[3], 555/647

value: larva

value: 57-days old

value: ammonium chloride


title: Control, biological rep1


title: Healthy Control, biological rep2

description:
Gene expression data from healthy control blood.
Ctrl2

source_name: Blood of Healthy Control, biological rep2

value: Blood


title: Control, biological rep3


title: lymphatic endothelial cells 2 [exon-level]

city: Taipei

first: Ting-Yu

last: Chang

address: No155, LiNong St

country: Taiwan

institute: National Yang-Ming University

description:
LEC2
control lymphatic endothelial cells
exon-level data

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console with RMA normalization on both exon and gene levels.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

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

growth_protocol: Human dermal lymphatic endothelial cells cultured with Promocell Endothelial Cell Growth Medium MV

extract_protocol: Total RNA were extracted with Qiagen RNeasy kit

treatment_protocol: Infectd with KSHV at 30 MOI or mock infection and cultured for 2 days

value: dermis

value: lymphatic endothelial cells

tag: infection

value: uninfected


title: lymphatic endothelial cells 2 [gene-level]

description:
LEC2
control lymphatic endothelial cells
gene(transcript)-level data

source_name: Human dermal lymphatic endothelial cells


title: H1299 AZA 1 uM (3231)

description:
azacitidine treated 48h
3231_H1299_1uM-Aza_2.CHP
H1299 1A
3231_H1299_1uM-Aza_2.CEL

value: azacitidine


title: H1299 DAC 0.3 uM (3236)

description:
decitabine treated 48h
3236_H1299_0.3uM-Dac_1.CHP
H1299 0.3D
3236_H1299_0.3uM-Dac_1.CEL


title: lymphatic endothelial cells 1 [gene-level]

description:
LEC1
control lymphatic endothelial cells
gene(transcript)-level data


title: lymphatic endothelial cells 1 [exon-level]

description:
LEC1
control lymphatic endothelial cells
exon-level data


title: H1299 AZA 3 uM (3232)

description:
azacitidine treated 48h
3232_H1299_3uM-Aza_1.CHP
H1299 3A
3232_H1299_3uM-Aza_1.CEL


title: KSHV infected lymphatic endothelial cells 2 [gene-level]

description:
KLEC2
KSHV infected lymphatic endothelial cells (2d)
gene(transcript)-level data

source_name: Human dermal lymphatic endothelial cells, KSHV infected

value: KSHV


title: KSHV infected lymphatic endothelial cells 3 [exon-level]

description:
KLEC3
KSHV infected lymphatic endothelial cells (2d)
exon-level data


title: Healthy Control, biological rep1

description:
Gene expression data from healthy control blood.
Ctrl1

source_name: Blood of Healthy Control, biological rep1


title: H1299 AZA 1 uM (3230)

description:
azacitidine treated 48h
3230_H1299_1uM-Aza_1.CHP
H1299 1A
3230_H1299_1uM-Aza_1.CEL


title: KSHV infected lymphatic endothelial cells 1 [gene-level]

description:
KLEC1
KSHV infected lymphatic endothelial cells (2d)
gene(transcript)-level data


title: mESC, biological Zebularine rep9

city: Sevilla

first: Abdelkrim

last: Hmadcha

address: Avda Américo Vespucio 24, Parque Científico y Tecnológico Cartuja

department: Regeneration and Cell Therapy

institute: CABIMER

description: Mouse gene expression.

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip®  Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G.

data_processing:
The images were processed with Microarray Analysis Suite 5.0 (Affymetrix). All samples demonstrated characteristics of high-quality cRNA (3’/5’ ratio of probe sets for glyceraldehyde-3-phosphate dehydrogenase and beta-actin of <1.5) and were subjected to subsequent analysis.  Raw expression values obtained directly from .CEL files were pre-processed using the RMA method (Irizarry et al. [1]), a three-step process which integrates background correction, normalization and summarization of probe values. All the statistical analysis were done using the free statistical language R and the libraries developed for microarray data analysis by the Bioconductor Project (www.bioconductor.org). The main methods and tools used are described in the monograph by Gentleman et al. [2].

Analysis methods: The selection of differentially expressed genes was performed using a linear model approach following the methodology (“Empirical Bayes and Linear Models for Microarrays”) described by G. Smyth in [3] and implemented in the limma Bioconductor package. Briefly, the method consists of fitting a linear model for each gene and performing a variance regularization based on empirical Bayes modelling. The empirical Bayes analysis performed yields several performance measures which help to decide which genes appear as differentially expressed.

References:
1- R. A. Irizarry, B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, and T. P. Speed. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249–264, 2003.
2- Robert Gentleman, Vince Carey, Wolfgang Huber, Rafael Irizarry, and Sandrine Dudoit. Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, 2005.
3- G.K. Smyth. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology, 3, 2004.

organism: Mus musculus

source_name: mouse embryonic stem cells, zebularine

label_protocol: cRNA were labeled according to the standard Affymetrix protocol.

growth_protocol: Mouse ESCs (D3 cell line) were cultured in DMEM (Dulbecco´s) with 15% FBS, 10.000 U/ml Penicillin, 10.000 µg/ml Streptomycin, 2mM Glutamine, 10-4 M β-mercaptoethanol, non-essential amino-acids 1x and 103 U/ml Leukaemia Inhibitory Factor (LIF), at 37ºC and 5% CO2.

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

treatment_protocol: Embryoid bodies (EBs) were generated by hanging drop culture during 3 days in DMEM in the absence of LIF. Then, 9 cultures were left untreated while the rest were treated with 30 μM of zebularine during 7 days.

value: embryonic stem cells

tag: treatment

value: zebularine

tag: treatment duration

value: 7 days


title: H1299 AZA 0.3 uM (3229)

description:
azacitidine treated 48h
3229_H1299_0.3uM-Aza_2.CHP
H1299 0.3A
3229_H1299_0.3uM-Aza_2.CEL

tag: cell line


title: H1299 AZA 0.3 uM (3228)

description:
azacitidine treated 48h
3228_H1299_0.3uM-Aza_1.CHP
H1299 0.3A
3228_H1299_0.3uM-Aza_1.CEL


title: H1299 AZA 3 uM (3233)

description:
azacitidine treated 48h
3233_H1299_3uM-Aza_2.CHP
H1299 3A
3233_H1299_3uM-Aza_2.CEL


title: KSHV infected lymphatic endothelial cells 2 [exon-level]

description:
KLEC2
KSHV infected lymphatic endothelial cells (2d)
exon-level data

tag: cell type


title: KSHV infected lymphatic endothelial cells 3 [gene-level]

description:
KLEC3
KSHV infected lymphatic endothelial cells (2d)
gene(transcript)-level data


title: LP1_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-2, LP-1

hyb_protocol: Reaction mixtures were hybridized to the GeneChip® Human Promoter 1.0R Arrays for 16 h at 45 °C at 60 rpm and stained with streptavidin/phycoerythrin, followed by a biotin-conjugated anti-streptavidin antibody and a second streptavidin/phycoerythrin staining. All liquid handling was carried out by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) and CEL files were generated with the GCOS 1.3 software (Affymetrix).

data_processing:
Resulting CEL files were analyzed using the Model-based Analysis of Tiling arrays (MAT) algorithm. We used default parameters except for the MaxGap parameter, which was reduced to 50 bp to find acetylated regions at higher resolution. Instead of working with the original Affymetrix BPMAP files, we used the microarray probe mapping to NCBI build 36 provided by the MAT homepage (http://liulab.dfci.harvard.edu/MAT/). This analysis resulted in a list of significantly acetylated regions for each of the nine cell lines.
Bar and Bed files were generated with the Model-based Analysis of Tiling arrays (MAT) software.

source_name: LP1 H3 K9/14 ChIP-DNA

label_protocol: Approximately 250 ng of ChIP-DNA was used as a template for ligation-mediated linear amplification according to the protocol of Young et al. to obtain a sufficient amount of labeled DNA for chip hybridization. The GeneChIP WT double-stranded DNA terminal labeling kit (Affymetrix) was used for DNA-fragmentation according to the manufacturer’s instructions.

growth_protocol: Three Hodgkin lymphoma cell lines (L1236, KM-H2, L428), three plasma cell myeloma cell lines (L363, U266, LP-1), and three B-cell lines (SU-DHL4, SU-DHL6, Namalwa) were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.

extract_protocol: The cell lines were used for ChIP following the protocol developed by the group of Young (PMID 17406303) with minor modifications. For each ChIP experiment, 10 µg of anti-acetyl-histone H3 (Lys9 + Lys14) antibody (06-599; Upstate Chemicon, Temecula, CA, USA) was employed. All experiments were performed in duplicates or triplicates. A detailed protocol is provided as supplementary information (Supplementary protocol S1) in our publication related to this GEO data.

value: plasma cell myeloma cells

tag: antibody

value: anti-acetyl H3K9/14 rabbit polyclonal

tag: antibody manufacturer

value: Upstate Chemicon

tag: antibody catalog #

source_name: LP1 Input DNA


title: U266_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-2, U266

source_name: U266 H3 K9/14 ChIP-DNA

source_name: U266 Input DNA


title: mESC, biological Zebularine rep8

description: Mouse gene expression.


title: L363_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-2, L366

source_name: L363 H3 K9/14 ChIP-DNA

source_name: L363 Input DNA


title: KSHV infected lymphatic endothelial cells 1 [exon-level]

description:
KLEC1
KSHV infected lymphatic endothelial cells (2d)
exon-level data


title: H1299 vehicle control (3225)

description:
DMSO treated
3225_H1299_VEH_2.CHP
H1299 VEH
3225_H1299_VEH_2.CEL

source_name: H1299 cells

value: DMSO


title: mESC, biological Zebularine rep7

description: Mouse gene expression.


title: SU-DHL6-Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-3, SU-DHL6

source_name: SU-DHL6 H3 K9/14 ChIP-DNA

value: B-cell lymphoma cells

source_name: SU-DHL6 Input DNA


title: SU-DHL4-Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-3, SU-DHL4

source_name: SU-DHL4 H3 K9/14 ChIP-DNA

source_name: SU-DHL4 Input DNA


title: mESC, biological Zebularine rep6

description: Mouse gene expression.


title: mESC, biological Zebularine rep5

description: Mouse gene expression.


title: Namalwa_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-3, Namalwa

source_name: Namalwa H3 K9/14 ChIP-DNA

value: Namalwa

source_name: Namalwa Input DNA


title: H1299 vehicle control (3224)

description:
DMSO treated
3224_H1299_VEH_1.CHP
H1299 VEH
3224_H1299_VEH_1.CEL

value: control


title: mESC, biological Zebularine rep3

description: Mouse gene expression.


title: A549 DAC 1 uM (3221)

description:
decitabine treated 48h
3221_A549_1uM-Dac_2.CHP
A549 1D
3221_A549_1uM-Dac_2.CEL

source_name: A549 cells

value: decitabine

value: 1 uM


title: mESC, biological Zebularine rep1

description: Mouse gene expression.


title: A549 DAC 3 uM (3222)

description:
decitabine treated 48h
3222_A549_3 uM Dac_1_REPEAT.CHP
A549 3D
3222_A549_3 uM Dac_1_REPEAT.CEL

value: 3 uM


title: L428_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-3, L428

source_name: L428 H3 K9/14 ChIP-DNA

value: Hodgkin lymphoma cells

source_name: L428 Input DNA


title: A549 DAC 3 uM (3223)

description:
decitabine treated 48h
3223_A549_3uM-Dac_2.CHP
A549 3D
3223_A549_3uM-Dac_2.CEL


title: A549 DAC 0.3 uM (3219)

description:
decitabine treated 48h
3219_A549_0.3uM-Dac_2.CHP
A549 0.3D
3219_A549_0.3uM-Dac_2.CEL


title: mESC, biological Zebularine rep4

description: Mouse gene expression.

source_name: mouse embryonic stem cells, zebularine


title: L1236_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-3, L1236

source_name: L1236 H3 K9/14 ChIP-DNA

source_name: L1236 Input DNA


title: mESC, biological Zebularine rep2

description: Mouse gene expression.


title: A549 DAC 1 uM (3220)

description:
decitabine treated 48h
3220_A549_1uM-Dac_1.CHP
A549 1D
3220_A549_1uM-Dac_1.CEL


title: A549 DAC 0.3 uM (3218)

description:
decitabine treated 48h
3218_A549_0.3uM-Dac_1.CHP
A549 0.3D
3218_A549_0.3uM-Dac_1.CEL


title: mESC, biological Control rep7

description: Mouse gene expression.

source_name: mouse embryonic stem cells, control


title: A549 AZA 3 uM (3215)

description:
azacitidine treated 48h
3215_A549_3uM_Aza_2.CHP
A549 3A
3215_A549_3uM_Aza_2.CEL


title: mESC, biological Control rep6

description: Mouse gene expression.


title: mESC, biological Control rep9

description: Mouse gene expression.


title: ER:Ras-IMR90 cells day 4 replicate 3

city: Cambridge

first: Shamith

last: Samarajiwa

address: Robinson way

country: United Kingdom

institute: Cambridge Research Institute

description:
replicate 3
bead level data file: 1881436325_A

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: IMR90 cell

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

growth_protocol: IMR90 human diploid fibroblasts were cultured in DMEM and supplimented with 10% FBS and antibiotics. Cells were maintained in 21% oxygen.

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: To induce senescence IMR90 cells expressing ER:H-RasV12 were given 100 nM 4-hydroxytamoxifen (4OHT)

value: human diploid fibroblast

tag: time point

value: day 4

value: 100 nM 4-hydroxytamoxifen


title: A549 AZA 3 uM (3214)

description:
azacitidine treated 48h
3214_A549_3uM_Aza_1.CHP
A549 3A
3214_A549_3uM_Aza_1.CEL

value: azacitidine


title: mESC, biological Control rep8

description: Mouse gene expression.

value: embryonic stem cells


title: A549 AZA 1 uM (3213)

description:
azacitidine treated 48h
3213_A549_1uM_Aza_2.CHP
A549 1A
3213_A549_1uM_Aza_2.CEL


title: A549 AZA 1 uM (3212)

description:
azacitidine treated 48h
3212_A549_1uM_Aza_1.CHP
A549 1A
3212_A549_1uM_Aza_1.CEL


title: ER:Ras-IMR90 cells day 4 replicate 2

description:
replicate 2
bead level data file: 1881436313_F


title: KM-H2_Acet_ChIP

description: Acet H3 K9/14 ChIP, Biological Rep 1-3, KM-H2

source_name: KM-H2 H3 K9/14 ChIP-DNA

source_name: KM-H2 Input DNA


title: A549 AZA 0.3uM (3211)

description:
azacitidine treated 48h
3211_A549_0.3uM_Aza_2.CHP
A549 0.3A
3211_A549_0.3uM_Aza_2.CEL


title: mESC, biological Control rep4

description: Mouse gene expression.


title: ER:Ras-IMR90 cells day 4 replicate 1

description:
replicate 1
bead level data file: 1881436294_B


title: ER:Ras-IMR90 cells day 0 replicate 3

description:
replicate 3
bead level data file: 1881436294_C

value: day 0


title: Case 13 Xenograft

city: Boston

first: Chiara

last: Grisanzio

address: 44 Binney Street

department: Medical Oncology

institute: DFCI

description:
X13
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C12_238232.CEL

hyb_protocol: Following fragmentation, 40 ug of cRNA were hybridized for 16 hr at 48C on GeneChip 250K StyI Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Probe-level signal intensities (i.e. copy number data)  were normalized to a baseline array with median intensity using invariant set normalization and SNP-level signal intensities were obtained using a model-based (PM/MM) method. Significant regions of copy-number variation were determined using the Genomic Identification of Significant Targets In Cancer (GISTIC) method. SN, gene, and cytogenetic band locations are based on the hg18 genome build (http://genome.ucsc.edu). For the comparison between the Euclidean distance distributions among profiles of different subgroups, p-values were calculated by permuting group labels.

source_name: renal cell carcinoma

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 250 ng genomic DNA

extract_protocol: Extraction of genomic DNA was performed using SDS with proteinase K, followed by phenol/chloroform and ethanol precipitation

treatment_protocol: Frozen tissue was needle-dissected, lysed in SDS, and purified using phenol/chloroform

tag: disease state

value: renal cell carcinoma (RCC)

tag: case

value: xenograft


title: A549 AZA 0.3uM (3210)

description:
azacitidine treated 48h
3210_A549_0.3 uM_Aza_1.CHP
A549 0.3A
3210_A549_0.3 uM_Aza_1.CEL


title: mESC, biological Control rep3

description: Mouse gene expression.


title: mESC, biological Control rep2

description: Mouse gene expression.


title: mESC, biological Control rep5

description: Mouse gene expression.


title: Case 19 Xenograft

description:
X19
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_D02_238236.CEL


title: mESC, biological Control rep1

description: Mouse gene expression.


title: A549 vehicle control (3207)

description:
DMSO treated
3207_A549_VEH_2.CHP
A549 VEH
3207_A549_VEH_2.CEL


title: Case 12 Xenograft

description:
X12
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C09_238226.CEL


title: ER:Ras-IMR90 cells day 0 replicate 2

description:
replicate 2
bead level data file: 1881436250_B


title: ER:Ras-IMR90 cells day 0 replicate 1

description:
replicate 1
bead level data file: 1881436132_A


title: ovarian cancer sample 19

status: Public on May 04 2011

city: Aachen

first: Qiong

last: Lin

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2. Raw data were processed using the BioConductor software package (www.bioconductor.org). Normalization was done by quantile normalization.

label: Cy5 and Cy3

source_name: ovarian cancer sample

label_protocol: Standard Illumina Protocol

extract_protocol: Tumor material was subjected to pathological frozen section; and immediately snaps frozen. 0.5 cm3 of tissue was lysed using Lysing Matrix A (Q-BIOgene) and were homogenized (BIO101/Savant FastPrep Homogenizer). After an overnight incubation with SDS and proteinkinase K, DNA was precipitated by adding ice-cold isopropanol, collected and dried. Concentration and quality of dissolved DNA was measured using Nanodrop Spectrophotometer (Parmacia Biotech).

value: Human ovarian cancer

tag: pfi (months)

tag: grading

tag: age (years)


title: ovarian cancer sample 16

tag: tissue


title: Case 13 Original

description:
O13
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C11_238230.CEL

value: original RCC


title: Case 19 Original

description:
O19
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_D01_238234.CEL


title: ovarian cancer sample 20


title: Case 12 Original

description:
O12
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C10_238228.CEL


title: ovarian cancer sample 17


title: Case 11 Xenograft

description:
X11
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C08_238224.CEL


title: ovarian cancer sample 15


title: Case 9 Xenograft

description:
X9
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C04_238216.CEL


title: A549 vehicle control (3206)

description:
DMSO treated
3206_A549_VEH_1.CHP
A549 VEH
3206_A549_VEH_1.CEL

tag: agent

value: DMSO


title: ovarian cancer sample 14


title: ovarian cancer sample 13


title: ovarian cancer sample 18


title: Case 8 Original

description:
O8
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C01_238210.CEL


title: ovarian cancer sample 9


title: ovarian cancer sample 12


title: ovarian cancer sample 8


title: ovarian cancer sample 7


title: Case 8 Xenograft

description:
X8
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C02_238212.CEL


title: ovarian cancer sample 11


title: ovarian cancer sample 6


title: ovarian cancer sample 10


title: Case 9 Original

description:
O9
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C03_238214.CEL


title: ovarian cancer sample 3


title: Case 11 Original

description:
O11
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C07_238222.CEL


title: Case 10 Xenograft

description:
X10
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C06_238220.CEL


title: ovarian cancer sample 2


title: ovarian cancer sample 1


title: ovarian cancer sample 4


title: ovarian cancer sample 5


title: Blood cells of subject S3 exposed to 200µM FA for 4 hours

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

hyb_protocol: According to Affymetrix. GeneChip Fluidics Station 450 was used for washing.

scan_protocol: GeneChip Scanner 3000 was used for scanning.

data_processing: BRB Array Tools. Data were normalized using RMA. The different tissue groups were normalized separately.

source_name: Blood cells after exposure to 200µM FA for 4 hours

label_protocol: One Cycle Target Labelling Protocol.

extract_protocol: RNeasy Mini Kit (Qiagen) for nasal biopsies;  PAXGene RNA Kit and QIAmp RNA Blood Mini Kit (Qiagen) for blood samples.

treatment_protocol: Male non-smokers were exposed to formaldehyde (FA) vapors for 4 h per day over a period of 5 working days under strictly controlled conditions. For each exposure day, different exposure concentrations were used in a random order ranging from 0 up to 0.7 ppm. During exposure, subjects had to perform bicycle exercises (about 80 W) four times for 15 min. Samples were taken before the first and after the last exposure.

value: blood cells

tag: gender

value: male

tag: smoking status

value: non-smoker

value: formaldehyde vapors

tag: treatment dosage

tag: exposure time

value: 4 h

tag: subject


title: Case 10 Original

description:
O10
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_C05_238218.CEL


title: Case 6 Original

description:
O6
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B11_238206.CEL


title: Blood cells of subject S3 control

source_name: Blood cells before exposure

tag: treatment


title: Blood cells of subject S5 control


title: Blood cells of subject S4 exposed to 200µM FA for 4 hours


title: Blood cells of subject S5 exposed to 200µM FA for 4 hours


title: Blood Sample of subject 26 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling

source_name: Blood sample after inhalation, 0.7 ppm FA 0 hr before sampling

value: blood

value: 0.7 ppm

tag: time before sampling

value: 0 h

tag: group

value: C


title: Blood cells of subject S1 exposed to 200µM FA for 4 hours


title: Blood cells of subject S1 control


title: Blood cells of subject S2 control


title: Blood Sample of subject 34 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Blood cells of subject S4 control


title: Blood Sample of subject 33 before inhalation; Group C

source_name: Blood sample before inhalation


title: Blood Sample of subject 34 before inhalation; Group C


title: Blood Sample of subject 32 before inhalation; Group C


title: Blood Sample of subject 32 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Blood cells of subject S2 exposed to 200µM FA for 4 hours


title: Blood Sample of subject 26 before inhalation; Group C


title: Blood Sample of subject 33 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Case 6 Xenograft

description:
X6
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B12_238208.CEL


title: Case 3 Xenograft

description:
X3
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B07_238198.CEL


title: Blood Sample of subject 4 before inhalation; Group C


title: Blood Sample of subject 2 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Blood Sample of subject 1 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Blood Sample of subject 3 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Blood Sample of subject 36 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling

source_name: Blood sample after inhalation, 0.7 ppm FA 24 hr before sampling

value: B


title: Blood Sample of subject 40 before inhalation; Group B


title: Blood Sample of subject 40 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: Blood Sample of subject 2 before inhalation; Group C


title: Blood Sample of subject 41 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: Blood Sample of subject 39 before inhalation; Group B


title: Blood Sample of subject 3 before inhalation; Group C


title: Case 5 Xenograft

description:
X5
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B10_238204.CEL


title: Blood Sample of subject 41 before inhalation; Group B


title: Case 5 Original

description:
O5
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B09_238202.CEL


title: Blood Sample of subject 4 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: Blood Sample of subject 1 before inhalation; Group C


title: Blood Sample of subject 29 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: Blood Sample of subject 28 before inhalation; Group B


title: DG_HAB_09

city: München

first: Ludwig

last: Czibere

address: Kraepelinstrasse 2

institute: Max Planck Institute of Psychiatry

description:
Biological replicate of HAB 5
This sample has been identified as inadequate during the scan process and has therefore been excluded from further analysis.

hyb_protocol: Each microarray slide had the capacity for six samples, same brain regions were hybridized in the same batch comparing a maximum of six individual mice of each breeding line. Reagents and material were provided by Illumina, the procedure was strictly conducted according to the manufacturer’s protocol. In brief, each sample was mixed with hybridization buffer, loaded onto the designated array field and the slides were put into hybridization chambers and incubated for 17h in incubation chambers provided by Illumina. Arrays were washed in several steps, incubated with Cy3, washed several times again and dried by centrifugation.

scan_protocol: Fluorescence signals were detected on a BeadStation scanner (Illumina) and analyzed by the BeadStudio (Illumina) software. The manufacturer's built-in controls have been analyzed including hybridization controls and sample dependent parameters. Only microarrays fulfilling Illumina's recommendations for quality control have been used for further evaluation.

data_processing: Illumina BeadStudio gene expression results were further analyzed using R-packages, based on ‘beadarray’ system as described by Dunning et al. (2007), which simplifies the comparison between a high number of arrays. First, pair wise box plots were generated to compare mean expression within each line and brain region. Normalization for expression values has been applied to all samples with the ‘QSpline’ function. Each sample has been clustered to ensure that each brain region per line shows similar expression patterns using the ‘hclust’ function. Three samples from different brain regions have been identified as inadequate during the scan process and have therefore been excluded from further analysis. For differential expression analysis, functions of the ‘LIMMA’ package have been applied on log2-transformed values. The resulting matrix has been used for all subsequent analyses. Significantly regulated genes were ranked using an empirical BAYES method implemented in the LIMMA R-package (Lonnstedt and Speed, 2002; Smyth, 2004).

label: biotin, Cy3

source_name: Dentate gyrus, HAB mouse  09

label_protocol: RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion) with only one round of in vitro transcription, where biotinylated uracyl bases were built in to the newly synthesized aRNA. 5µg per sample were required for loading to the microarray slides. Correct quantification was ensured by measurement of optic density in a NanoPhotometer (Implen, Munich, Germany) and additional analysis on agarose gel. Samples not fulfilling all criteria of homogeneity (inadequate concentrations, too many small but few larger aRNA fragments) were excluded from further analysis.

extract_protocol: From all samples, total RNA was extracted individually (one sample per mouse and brain region) in presterilized 1.5ml Safelock tubes (Eppendorf, Hamburg, Germany) using a TRIzol (Invitrogen, Karlsruhe, Germany) chloroform standard protocol. After tissue homogenization in 300µl of TRIzol by pipetting, 1µl linear acrylamide (5mg/ml, Ambion, Austin, TX) and 60µl of chloroform (Carl Roth, Karlsruhe, Germany) were added and the samples vortexed. Centrifugation for 5min at 18°C and 13,000rpm followed, then RNA was precipitated with 180µl isopropanol (Carl Roth) overnight at -20°C, centrifuged at 4°C and 13,000rpm for 30min and washed twice in 500µl 70% ethanol (Carl Roth) with centrifugation steps at 4°C and 13,000rpm of 10min in between. Following the last centrifugation step, all remaining liquid was removed with a pipet, pellets were dried in an incubator for 15min at 45°C and resolved in 13µl of autoclaved bidistilled water.

treatment_protocol: Brains were collected, dissected in slices of 25µm and mounted to Superfrost microscope slides (Menzel, Braunschweig, Germany) or onto LMD6000 metallic frame slides covered with a membrane of polyethylene terephthalate (Leica Microsystems Deutschland, Bensheim, Germany) in a cryostat (Microm MH50, Microm, Walldorf, Germany) from rostral to caudal.  Only brain slices containing the brain areas of interest were sampled, including the anterior part of the cingulate cortex (Cg), the hypothalamic paraventricular nucleus (PVN), the anterior dentate gyrus (DG), the basolateral (BLA) and the central amygdala (CeA). For the DG, the same coordinates as for the PVN were applied. To cover the whole area of interest an overall depth of 400µm per region was chosen. While sampling the CG, BLA and CeA four brain slices were mounted onto an LMD6000 metallic frame slide (Leica Microsystems), the following four to Superfrost slides (Menzel). This procedure was repeated for the next eight slices. For the region containing the PVN and DG only two slices were mounted to one slide always alternating the LMD6000 frame and the Superfrost microscope slides. Only the LMD6000 slides were used for further processing and stored at -80°C. Right before laser-microdissection, brain slices on the LMD6000 frame slides were stained with cresyl violet applying a modified staining protocol that included 1.5min staining in cresyl violet, followed by washing in 70% and 96% ethanol for 20s each and in isopropanol for 5min. The slides were refrozen and processed at the laser-microdissection microscope (AS LMD, Leica). For the dissection procedure of the required brain areas, a magnification of 100x was chosen with laser power between 80-100% and speed varying between 1 and 4. Cut-out brain areas were captured in the caps of 0.2ml PCR soft tubes (Biozym Scientific, Hessisch Oldendorf, Germany) and cooled on dry ice immediately after completion of one brain region. Pictures of the processed brain slices were acquired by means of the IM1000 software.  Microm, Walldorf, Germany) from rostral to caudal.

tag: strain

tag: age

value: 10 weeks

tag: source tissue

value: brain


title: Blood Sample of subject 44 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling

source_name: Blood sample after inhalation, 0.7 ppm FA 72 hr before sampling

value: A


title: Blood Sample of subject 25 before inhalation; Group B


title: Blood Sample of subject 45 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: Blood Sample of subject 36 before inhalation; Group B


title: Blood Sample of subject 25 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: Blood Sample of subject 29 before inhalation; Group B


title: Blood Sample of subject 45 before inhalation; Group A


title: Blood Sample of subject 39 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: Blood Sample of subject 28 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: DG_HAB_05

description:
Biological replicate of HAB 3
This sample has been identified as inadequate during the scan process and has therefore been excluded from further analysis.

source_name: Dentate gyrus, HAB mouse  05


title: DG_LAB_06

description:
Biological replicate of LAB 2
This sample has been identified as inadequate during the scan process and has therefore been excluded from further analysis.

source_name: Dentate gyrus, LAB mouse  06


title: Blood Sample of subject 44 before inhalation; Group A


title: Blood Sample of subject 42 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: Blood Sample of subject 10after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: DG_NAB_02

description: Biological replicate of NAB 2

source_name: Dentate gyrus, NAB mouse  02


title: Blood Sample of subject 43 before inhalation; Group A


title: DG_NAB_04

description: Biological replicate of NAB 3

source_name: Dentate gyrus, NAB mouse  04


title: DG_LAB_10

description: Biological replicate of LAB 3

source_name: Dentate gyrus, LAB mouse  10


title: Blood Sample of subject 10 before inhalation; Group A


title: Nasal Biopsy of subject 34 before inhalation; Group C

source_name: Nasal biopsy before inhalation

value: nasal biopsy


title: Blood Sample of subject 9 before inhalation; Group A


title: Blood Sample of subject 42 before inhalation; Group A


title: Case 3 Original

description:
O3
SNP array data from renal cell carcinoma
PUNAS_p_Kinome_misc_AFFX_n_GenomeWideSNP_6_B08_238200.CEL

tag: disease state

value: renal cell carcinoma (RCC)

tag: case


title: Blood Sample of subject 9 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: DG_LAB_14

description: Biological replicate of LAB 1

source_name: Dentate gyrus, LAB mouse  14


title: DG_HAB_17

description: Biological replicate of HAB 4

source_name: Dentate gyrus, HAB mouse  17


title: DG_LAB_16

description: Biological replicate of LAB 4

source_name: Dentate gyrus, LAB mouse  16


title: Nasal Biopsy of subject 34 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 0 hr before sampling


title: DG_HAB_01

description: Biological replicate of HAB 2

source_name: Dentate gyrus, HAB mouse  01


title: Nasal Biopsy of subject 32 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: BLA_NAB_08

description: Biological replicate of NAB 5

source_name: Basolateral amygdala, NAB mouse  08


title: Blood Sample of subject 43 after inhalation; Group A: inhalation with 0.7 ppm FA 72 h before sampling


title: DG_NAB_15

description: Biological replicate of NAB 1

source_name: Dentate gyrus, NAB mouse  15


title: DG_HAB_11

description: Biological replicate of HAB 1

source_name: Dentate gyrus, HAB mouse  11


title: Nasal Biopsy of subject 33 before inhalation; Group C


title: Nasal Biopsy of subject 33 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: BLA_NAB_15

description: Biological replicate of NAB 6

source_name: Basolateral amygdala, NAB mouse  15


title: Nasal Biopsy of subject 26 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: BLA_NAB_04

description: Biological replicate of NAB 4

source_name: Basolateral amygdala, NAB mouse  04


title: LungTumour_stage2_258

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

institute: National Research Council

description: Clontech Universal Reference Total RNAs are total RNA controls derived from whole tissue sources. Each species-specific Reference Total RNA is made by pooling the total RNA extracts from a collection of different tissues, thus providing the broadest coverage of expressed genes (from Clontech)

hyb_protocol: Hybridization was completed using the 3DNA kit from Genisphere, (60 uL) was carefully applied to one corner of the Lifter Slip on the slide and immediately placed in the hybridization chamber (Die Tech, San Jose, CA, USA) for ON hyb. The hybridization process is 2 step where the initial hyb is cDNA only, and the second hyb is to couple the fluorophore. After hybridization slides were washed.

scan_protocol: Scanned on Molecular Dynamics Axon 4200A, GenePix 6.1 software.

data_processing:
Limma LOWESS normalized, background subtracted data obtained from log2 of processed Experimental signal/processed Reference signal. Arraypipe software was used.
Ratio, based on the highest level intensity values available (normalized over background corrected over foreground intensities and merged over log-transformed over natural values). A value of 1 is equal to no change. Everything greater than 1 means a positive change (up-regulation) and everything smaller than 1 means a negative change (down-regulation) from one condition to another (usually from CH1 to CH2).

source_name: Stage 2 lung carcinoma

label_protocol: RNA (1 ug) from control RNA reference and experimental samples was reverse transcribed and labeled using the 3DNA Genisphere Array 900 expression array detection kit (Genisphere Inc,Hatfield PA, USA) with Alexa fluorophores according to manufacturers instructions.

extract_protocol: Tissue frozen in liquid nitrogen and pulverized with BioPulverizer from BioSpec. Total RNA extracted using Triazole according to the manufactures protocol

value: Lung Adenocarcinoma

tag: Stage

tag: patient age

value: > 50 years of age

source_name: Human Reference RNA

tag: reference

value: Clontech Universal Reference Total RNA at 1mg/ml


title: Nasal Biopsy of subject 32 before inhalation; Group C

tag: tissue

value: male


title: LungTumour_stage2_300


title: BLA_HAB_05

description: Biological replicate of HAB 5

source_name: Basolateral amygdala, HAB mouse  05

tag: gender


title: BLA_LAB_07

description: Biological replicate of LAB 5

source_name: Basolateral amygdala, LAB mouse  07


title: Nasal Biopsy of subject 26 before inhalation; Group C

tag: smoking status

value: non-smoker


title: BLA_NAB_13

description: Biological replicate of NAB 2

source_name: Basolateral amygdala, NAB mouse  13


title: LungTumour_stage2_262


title: Nasal Biopsy of subject 4 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling

value: formaldehyde vapors

tag: treatment dosage


title: BLA_NAB_12

description: Biological replicate of NAB 1

source_name: Basolateral amygdala, NAB mouse  12


title: LungTumour_stage2_240


title: Nasal Biopsy of subject 4 before inhalation; Group C

source_name: Nasal biopsy before inhalation


title: LungTumour_stage2_229


title: BLA_LAB_06

description: Biological replicate of LAB 4

source_name: Basolateral amygdala, LAB mouse  06


title: LungTumour_stage1_272

source_name: Stage 1 lung carcinoma


title: BLA_LAB_10

description: Biological replicate of LAB 3

source_name: Basolateral amygdala, LAB mouse  10


title: BLA_HAB_01

description: Biological replicate of HAB 2

source_name: Basolateral amygdala, HAB mouse  01


title: BLA_LAB_14

description: Biological replicate of LAB 1

source_name: Basolateral amygdala, LAB mouse  14


title: BLA_HAB_09

description: Biological replicate of HAB 3

source_name: Basolateral amygdala, HAB mouse  09


title: BLA_HAB_11

description: Biological replicate of HAB 1

source_name: Basolateral amygdala, HAB mouse  11


title: Nasal Biopsy of subject 3 before inhalation; Group C


title: BLA_HAB_17

description: Biological replicate of HAB 4

source_name: Basolateral amygdala, HAB mouse  17


title: LungTumour_stage1_278


title: PVN_LAB_10

description: Biological replicate of LAB 5

source_name: Hypothalamic paraventricular nucleus, LAB mouse  10


title: LungTumour_stage1_218


title: PVN_HAB_17

description: Biological replicate of HAB 6

source_name: Hypothalamic paraventricular nucleus, HAB mouse  17


title: BLA_LAB_03

description: Biological replicate of LAB 2

source_name: Basolateral amygdala, LAB mouse  03


title: Nasal Biopsy of subject 2 before inhalation; Group C


title: Nasal Biopsy of subject 3 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 0 hr before sampling


title: Nasal Biopsy of subject 2 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: PVN_NAB_04

description: Biological replicate of NAB 5

source_name: Hypothalamic paraventricular nucleus, NAB mouse  04


title: BLA_NAB_02

description: Biological replicate of NAB 3

source_name: Basolateral amygdala, NAB mouse  02


title: LungTumour_stage1_202

source_name: Human Reference RNA


title: LungTumour_stage1_252


title: Nasal Biopsy of subject 1 after inhalation; Group C: inhalation with 0.7 ppm FA 0h before sampling


title: PVN_HAB_20

description: Biological replicate of HAB 5

source_name: Hypothalamic paraventricular nucleus, HAB mouse  20


title: PVN_HAB_01

description: Biological replicate of HAB 4

source_name: Hypothalamic paraventricular nucleus, HAB mouse  01


title: PVN_HAB_09

description: Biological replicate of HAB 2

source_name: Hypothalamic paraventricular nucleus, HAB mouse  09


title: Nasal Biopsy of subject 41 before inhalation; Group B

source_name: Nasal biopsy before inhalation


title: PVN_LAB_03

description: Biological replicate of LAB 3

source_name: Hypothalamic paraventricular nucleus, LAB mouse  03


title: Hdh knock-in embryonic stem cells, Q111 line, biological replicate 3

first: Jong-Min

last: Lee

state: MA

address: 185 Cambridge Street

department: Center for Human Genetic Research

institute: Massachusetts General Hospital

description: Gene expression data from Hdh knock-in embryonic stem cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: gcRMA

source_name: mouse embryonic stem cells

label_protocol: IVT labeling kit from the Affy company

growth_protocol: Standard growth condition for mouse embryonic stem cells

extract_protocol: Trizol extraction and Qiagen Rneasy mini coulmn clean up

value: knock-in

tag: genotype (hdh cag repeat length)

tag: differentiation status

value: undifferentiated

tag: cell line


title: Nasal Biopsy of subject 1 before inhalation; Group C

tag: treatment

tag: subject


title: PVN_HAB_11

description: Biological replicate of HAB 3

source_name: Hypothalamic paraventricular nucleus, HAB mouse  11

tag: strain


title: PVN_LAB_06

description: Biological replicate of LAB 4

source_name: Hypothalamic paraventricular nucleus, LAB mouse  06

tag: age


title: Nasal Biopsy of subject 40 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling

source_name: Nasal biopsy after inhalation, 0.7 ppm FA 24 hr before sampling

value: 0.7 ppm

tag: time before sampling

tag: group


title: PVN_LAB_14

description: Biological replicate of LAB 2

source_name: Hypothalamic paraventricular nucleus, LAB mouse  14

tag: source tissue


title: Nasal Biopsy of subject 41 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: Hdh knock-in embryonic stem cells, Q111 line, biological replicate 2


title: Hdh knock-in embryonic stem cells, Q91 line, biological replicate 3


title: Nasal Biopsy of subject 40 before inhalation; Group B


title: PVN_NAB_02

description: Biological replicate of NAB 3

source_name: Hypothalamic paraventricular nucleus, NAB mouse  02


title: Nasal Biopsy of subject 39 after inhalation; Group B: inhalation with 0.7 ppm FA 24 h before sampling


title: PVN_HAB_05

description: Biological replicate of HAB 1

source_name: Hypothalamic paraventricular nucleus, HAB mouse  05


title: Hdh knock-in embryonic stem cells, Q111 line, biological replicate 1


title: Hdh knock-in embryonic stem cells, Q91 line, biological replicate 2


title: CeA_HAB_09

description: Biological replicate of HAB 6

source_name: Central amygdala, HAB mouse  09


title: PVN_NAB_12

description: Biological replicate of NAB 2

source_name: Hypothalamic paraventricular nucleus, NAB mouse  12


title: CeA_LAB_21

description: Biological replicate of LAB 5

source_name: Central amygdala, LAB mouse  21


title: CeA_HAB_11

description: Biological replicate of HAB 5

source_name: Central amygdala, HAB mouse  11


title: PVN_NAB_13

description: Biological replicate of NAB 1

source_name: Hypothalamic paraventricular nucleus, NAB mouse  13


title: PVN_LAB_07

description: Biological replicate of LAB 1

source_name: Hypothalamic paraventricular nucleus, LAB mouse  07


title: Nasal Biopsy of subject 39 before inhalation; Group B


title: Hdh knock-in embryonic stem cells, Q50 line, biological replicate 3


title: PVN_NAB_18

description: Biological replicate of NAB 4

source_name: Hypothalamic paraventricular nucleus, NAB mouse  18


title: CeA_NAB_13

description: Biological replicate of NAB 6

source_name: Central amygdala, NAB mouse  13


title: Hdh knock-in embryonic stem cells, Q91 line, biological replicate 1


title: Hdh knock-in embryonic stem cells, Q50 line, biological replicate 2


title: CeA_HAB_17

description: Biological replicate of HAB 4

source_name: Central amygdala, HAB mouse  17


title: CeA_HAB_05

description: Biological replicate of HAB 2

source_name: Central amygdala, HAB mouse  05


title: Hdh knock-in embryonic stem cells, Q50 line, biological replicate 1

source_name: mouse embryonic stem cells


title: Nasal Biopsy of subject 36 before inhalation; Group B

source_name: Nasal biopsy before inhalation


title: CeA_NAB_04

description: Biological replicate of NAB 3

source_name: Central amygdala, NAB mouse  04


title: Hdh knock-in embryonic stem cells, Q20 line, biological replicate 3


title: CeA_NAB_15

description: Biological replicate of NAB 5

source_name: Central amygdala, NAB mouse  15