title: LCL MZ 34b


title: LCL MZ 30b

status: Public on Oct 29 2011

type: RNA

city: Brisbane

first: Joseph

middle: E

last: Powell

state: Qld

address: St lucia

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

description: Whole blood samples were collected from MZ twin pairs and processed within 24 hours of collection

hyb_protocol: Expression profiles were generated by hybridising 750ng of cRNA to Illumina HumanHT-12 v3.0 Beadchip according to Illumina whole-genome gene expression direct hybridization assay guide (Illumina Inc, San Diego, USA). Briefly, 500 ng of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridised to an Illumina whole genome expression chip, HumanHT-12 v3.0 for 18 h at 58oC.

scan_protocol: Beadchips were then washed and stained and subsequently scanned to obtain fluorescence intensities using an Illumina Bead Array Reader (BAR). A Latin square design was used to randomise the samples on the chips and chip positions.

data_processing:
Relative expression values were generated for each transcript using Illumina Genome Studio software (Illumina Inc., San Diego). To minimise the influence of overall signal levels, which may reflect RNA quantity and quality rather than a true biological difference between individuals, the following standardisation procedures were used. Background noise detected from negative control beads was subtracted from raw expression values for each transcript. Data were then filtered for gene transcripts that were present in at least 50% of samples at p < 0.05 according to the global-error threshold calculated by Genome Studio’s cross-gene error model. To prevent the introduction of bias between the LCL and WB samples, the raw microarray data from both tissue samples were quantile normalised together. Adjusted expression levels for each transcript were transformed using a quantile transformation to achieve a stabilized variance distribution across average expression levels.
Non-normalised data have just background subtraction from the raw signals. Normalised data has been filtered for  genes significantly expressed in greater than 50% of samples. Values have then been quantile normalized.

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood was collected directly into ACD (Acid Citrate Dextrose) vacuum tube. Mononucleated cells were isolated using a ficoll gradient and LCL established by Epstein-Barr virus transformation of lymphocytes and stored in liquid nitrogen.

label_protocol: standard Illumina protocol

extract_protocol: Whole blood was collected directly into ACD (Acid Citrate Dextrose) vacuum tube. Mononucleated cells were isolated using a ficoll gradient and LCL established by Epstein-Barr virus transformation of lymphocyte and stored in liquid nitrogen. For RNA isolation, established cell lines were regrown under tightly controlled growth conditions in the same batch of RPMI 1640 media with 10% FCS and antibiotics, to limit the cell culture effects on RNA preparation. Total RNA was extracted from samples using Qiagen RNeasy Midi-Kits (QIAGEN, Valencia, CA), when cells were in log phase growth.

tag: cell type

value: Lymphoblastoid Cell Line

tag: twin


title: LCL MZ 29b


title: LCL MZ 29a


title: LCL MZ 30a


title: LCL MZ 31a


title: LCL MZ 23b


title: LCL MZ 26b


title: LCL MZ 27b


title: LCL MZ 22b


title: LCL MZ 26a


title: LCL MZ 24a


title: LCL MZ 28a


title: LCL MZ 24b


title: LCL MZ 21b


title: LCL MZ 20b


title: LCL MZ 28b


title: LCL MZ 27a


title: LCL MZ 20a


title: LCL MZ 21a


title: LCL MZ 23a


title: LCL MZ 22a


title: LCL MZ 25a


title: LCL MZ 18a


title: LCL MZ 19a


title: LCL MZ 25b


title: LCL MZ 19b


title: LCL MZ 18b


title: LCL MZ 17b


title: LCL MZ 17a


title: LCL MZ 16a


title: LCL MZ 15b


title: LCL MZ 16b


title: LCL MZ 14a


title: LCL MZ 12a


title: LCL MZ 13a


title: LCL MZ 10a


title: LCL MZ 8b


title: LCL MZ 14b


title: LCL MZ 9b


title: LCL MZ 15a


title: LCL MZ 7b


title: LCL MZ 6b


title: LCL MZ 9a


title: LCL MZ 10b


title: LCL MZ 11a


title: LCL MZ 8a


title: LCL MZ 11b


title: LCL MZ 6a


title: LCL MZ 4a


title: LCL MZ 12b


title: LCL MZ 5a


title: LCL MZ 13b


title: LCL MZ 7a


title: LCL MZ 4b


title: LCL MZ 5b


title: WB MZ 45a

extract_protocol: Whole blood samples were collected from MZ twin pairs and processed within 24 hours of collection. Whole blood was collected directly into PAXgeneTM tubes (QIAGEN, Valencia, CA). Total RNA was extracted from PAXgeneTM tubes using the WB gene RNA purification kit (QIAGEN, Valencia, CA).

tag: tissue

value: Whole Blood


title: WB MZ 46a

source_name: Whole blood was collected directly into PAXgeneTM tubes (QIAGEN, Valencia, CA).


title: LCL MZ 2a


title: WB MZ 43a


title: WB MZ 42a


title: LCL MZ 1a


title: LCL MZ 3a


title: WB MZ 45b


title: LCL MZ 3b


title: WB MZ 44a


title: WB MZ 47a


title: WB MZ 41a


title: LCL MZ 1b


title: WB MZ 47b


title: LCL MZ 2b


title: WB MZ 42b


title: WB MZ 46b


title: WB MZ 40a


title: WB MZ 39a


title: WB MZ 40b


title: WB MZ 38b


title: WB MZ 39b


title: WB MZ 41b


title: WB MZ 43b


title: WB MZ 37b


title: WB MZ 38a


title: WB MZ 44b


title: WB MZ 35b


title: WB MZ 36b


title: WB MZ 36a


title: WB MZ 29a


title: WB MZ 30b


title: WB MZ 28a


title: WB MZ 29b


title: WB MZ 31b


title: WB MZ 33b


title: WB MZ 32b


title: WB MZ 27b


title: WB MZ 37a


title: WB MZ 35a


title: WB MZ 34a


title: WB MZ 27a


title: WB MZ 28b


title: WB MZ 33a


title: WB MZ 34b


title: WB MZ 23a


title: WB MZ 32a


title: WB MZ 31a


title: WB MZ 30a


title: WB MZ 24a


title: WB MZ 25b


title: WB MZ 26a


title: WB MZ 22b


title: WB MZ 24b


title: WB MZ 25a


title: WB MZ 26b


title: WB MZ 23b


title: Ypk1 time 30

city: Davis

first: Ted

last: Powers

state: CA

address: One Shields Ave

department: Molecular and Cellular Biology

country: USA

institute: UC Davis

description: background strain is deleted for both Ypk1 and Ypk2 (ypk1 delta ypk2 delta)

hyb_protocol: from microarrays.org

scan_protocol: scanned using GenePix 4000a

data_processing: data analyzed using GenePix Pro 3.0

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: WT Ypk1; 2,3-DMB-PPI, 30 min

label_protocol: from microarrays.org

growth_protocol: grown in SCD-Leu

extract_protocol: polyA mRNA

treatment_protocol: Treated with inhibitor 2,3-DMB-PP1 at 0.5 uM or 3-MB-PPI at 1 uM

tag: plasmid

value: WT Ypk1

tag: treatment agent

tag: treatment time

value: 30 min

source_name: AS Ypk1; 2,3-DMB-PPI, 30 min

value: AS Ypk1


title: Ypk2 time 30

source_name: WT Ypk2; 3-MB-PPI, 30 min

value: WT Ypk2

source_name: AS Ypk2; 3-MB-PPI, 30 min

value: AS Ypk2


title: Ypk1 vs Ypk2

source_name: WT Ypk1; no inhibitor

value: no inhibitor

source_name: WT Ypk2; no inhibitor


title: Ypk2 time 15

source_name: WT Ypk2; 3-MB-PPI, 15 min

value: 15 min

source_name: AS Ypk2; 3-MB-PPI, 15 min


title: Ypk1 time 60

source_name: WT Ypk1; 2,3-DMB-PPI, 60 min

value: 60 min

source_name: AS Ypk1; 2,3-DMB-PPI, 60 min


title: Ypk2 time 0

source_name: WT Ypk2; 3-MB-PPI, 0 min

value: 0 min

source_name: AS Ypk2; 3-MB-PPI, 0 min


title: Ypk2 time 60

source_name: WT Ypk2; 3-MB-PPI, 60 min

source_name: AS Ypk2; 3-MB-PPI, 60 min


title: WB MZ 21b


title: WB MZ 22a


title: WB MZ 19b


title: WB MZ 20b


title: WB MZ 21a


title: WB MZ 20a


title: WB MZ 18b


title: WB MZ 16a


title: WB MZ 17a


title: WB MZ 15a


title: zeb-con2

city: beijing

first: zhonghua

last: dai

state: beijing

address: no.3 nan-yi-tiao

country: China

institute: chinese academy of sciences

description: gene expression data of normal zebrafish brains

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

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

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

label: biotin

organism: Danio rerio

source_name: adult zebrafish

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

growth_protocol: Adult zebrefish were raised under the standard laboratory breeding condition(28C).

extract_protocol: Total RNAs were extracted from brains using the total RNA isolation kit (Promega, Madison, USA).

treatment_protocol: Adult zebrefish were subjected to cold(10C) stress.

value: adult zebrafish brain

tag: treatment group

value: normal


title: Ypk1 time 0

source_name: WT Ypk1; 2,3-DMB-PPI, 0 min

source_name: AS Ypk1; 2,3-DMB-PPI, 0 min


title: zeb-exp2

description: gene expression data of cold-stressed zebrafish brains

value: cold-stressed


title: WB MZ 19a

source_name: Whole blood was collected directly into PAXgeneTM tubes (QIAGEN, Valencia, CA).


title: WB MZ 18a


title: WB MZ 16b


title: WB MZ 17b


title: WB MZ 15b


title: WB MZ 14a


title: Ypk1 time 15

source_name: WT Ypk1; 2,3-DMB-PPI, 15 min

source_name: AS Ypk1; 2,3-DMB-PPI, 15 min


title: Hypo_male_rep2_amp

city: San Francisco

first: Xiaohong

last: Xu

address: 1550 4th Street, Rock Hall 345 Mission Bay

department: Anatomy

institute: University of California at San Francisco

description: Technical Replicate 2 of 2

hyb_protocol: Probes were added to hybridization buffer and denatured at 100C for 5 minutes. After cooling, probes were added to array slides and allowed to hybridized in sealed chambers for 48 hours in a 65C water bath. Slides were washed in a high salt solution at 65C, followed by low salt washes at room temperature. Slides were then dried by centrifugation in a low ozone environment.

scan_protocol: Slides were scanned with an Axon Slide Scanner 4000B in a low ozone environment.

data_processing:
Genepix 4.0 was used to grid arrays and obtain gpr files. Normalization and data analysis were performed in MatLab.
Ratio Calculation (GSE33307_AMP_samples_ratio_matrix.txt): Male to female expression ratios were generated in the following way. Male or female intensity values were first divided by the whole brain intensity vales, and the male to brain ratio was then divided by the female to brain ratio to calculate the male to female ratio. First 4 columns of metadata are hypothalamus to whole brain ratios. Next 4 columns are the calculated male hypothalamus to female hypothalamus ratios.
No normalization was performed on the data. Signals are provided in the GSE33307_AMP_samples_signals_matrix.txt supplementary file

organism: Mus musculus

source_name: adult male hypothalamus and BNST

label_protocol: The mRNA was incubated with DnaseI (Invitrogen) to remove residual genomic DNA and used for the T7 based amplification method (Amino allyl message AmpII, Invitrogen). 10ug of the amplified hypothalamus mRNA and 20ug of the whole brain mRNA were coupled to Cy3 and Cy5 respectively using standard protocol (Amersham).

growth_protocol: Four adult (10-12 weeks old) male and four adult female mice were individually housed one week prior to tissue dissection. (All were group housed by sex after weaning and sexually naïve.)

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions and column purified (Micro-to-Midi columns, Invitrogen). mRNA was isolated using the Fast Track mRNA isolation kit (Invitrogen).

treatment_protocol: Freshly dissected brains were sectioned into 1mm coronal slices using a tissue chopper. The hypothalamus, including the BNST was idenified by landmarks and coordinates from the mouse brain atlas and dissected out under a stereomicroscope.

value: Hypothalamus and bed nucleus of the stria terminalis

tag: Sex

value: 4 males

tag: strain

tag: age

value: 10-12 weeks

source_name: adult male and female whole brain and pituitary

value: whole brain and pituitary

value: 1 male and 1 female

tag: sample set

value: Set 1


title: Hypo_female_rep1_amp

description: Technical Replicate 1 of 2

source_name: adult female hypothalamus and BNST

value: 4 females


title: Hypo_female_rep2_amp

description: Technical Replicate 2 of 2


title: WB MZ 14b

value: Whole Blood


title: zeb-con1


title: zeb-exp1


title: Hypo_female_rep5

description: Biological Replicate 3 of 3; Technical Replicate 1 of 2

data_processing:
Genepix 4.0 was used to grid arrays and obtain gpr files. Normalization and data analysis were performed in MatLab.
Ratio Calculation:Male to female expression ratios were generated two different ways. Male or female intensity values were first divided by the whole brain intensity vales, and the male to brain ratio was then divided by the female to brain ratio to calculate the male to female ratio. Or male to female ratios were also calculated by directly dividing the male intensity by the female intensity without normalizing to the whole brain sample (treating the arrays as single color arrays) (labeled as Grn). For each method of ratio calculation, intensities from either within only a single experiment or across all three experiments were compared (Within: labeled as x12; Across: labeled as x36).  Male to female expression ratios were generated two different ways. Male or female intensity values were first divided by the whole brain intensity vales, and the male to brain ratio was then divided by the female to brain ratio to calculate the male to female ratio. Or male to female ratios were also calculated by directly dividing the male intensity by the female intensity without normalizing to the whole brain sample (treating the arrays as single color arrays). For each method of ratio calculation, intensities from either within only a single experiment or across all three experiments were compared.
Several Normalization methods were used and are described below. Matrix files are provided for each normalization method, ratio calculation method, and two-color or one-color treatment (44 total). Gpr files are also provided.
Normalization:Global Normalization—Global normalization assumes that the majority of the transcripts on the array are not different between the two samples and adjusts the calculated ratios according to this assumption. The hypothalamus to brain ratio from each array was normalized and the male to female ratios calculated. Or the male to female ratio were normalized directly. The MatLab manorm function was used to execute global normalization.
Ubiquitin C Normalizations—The MEEBO platform contains 260 Ubiquitin C (Ubc) spots for normalization purposes. It is assumed that since Ubc is a housekeeping gene the expression should not be different between the samples being compared. Ubiquitin C normalization was used to adjust raw intensity values. In our experiment, the arrays were normalized to Ubc in two different ways. In the first, all Cy3 intensities of an array were divided by the average Ubc Cy3 intensity and the same was done for the Cy5 intensities. This effectively normalized within the array (Global Ubc). For the second method, the average Cy3 and Cy5 intensities were calculated for each array and the intensity values for every array were adjusted by a multiplicative factor so that the average Ubc Cy3 and Cy5 intensities were the same for every array (Quantile Ubc). This effectively normalized across arrays.
Intensity Sum Normalization—Intensity sum normalization assumes that since equal amounts of labeled sample are hybridized onto the arrays, the overall intensities of the arrays should be the same. Intensity sum normalization was used to adjust the raw intensity values. While every effort is made during the scanning process to ensure that the arrays are within the same ranges of intensities, arrays will have overall higher or lower intensity values than others due to experimental variability. To correct for this, the intensities of the arrays were adjusted by a multiplicative factor so that the sum of all intensities on an array was now equal to the average of the sum of the intensities of all arrays.
Quantile Normalization—Quantile normalization assumes that the same ranges of values exist among the samples. The quantile normalization method can be used to adjust the raw intensities on each array so that all arrays will have the same range of intensity values. Quantile normalization can also be used to adjust the ratios for each array so that the range of ratio values for each array is the same. In our experiment, quantile normalization was performed separately on the raw intensities or the ratios from the arrays, normalizing across arrays. The MatLab quantilenorm function was used to perform the quantile normalization.
No normalization—In addition to the methods described above, data was also processed without any normalization in parallel.
First 12 columns of metadata are hypothalamus to whole brain ratios. Next columns are the calculated male hypothalamus to female hypothalamus ratios.
Please see readme.txt supplementary file on the Series record for a description of the various normalized data matrix file contents.

label_protocol: 0.5ug of hypothalamus mRNA and 2 ug of whole brain mRNA were primed with 5ug of random nonamers and oligo dT at 70C for 10 mins, then reverse transcribed at 42C for 2 hours in the presence of 150U of Stratascript reverse transcriptase and 500 uM each dATP, dCTP, and dGTP, 300uM aminoallyl-dUTP, and 200uM dTTP. After transcription, the cDNA was coupled to either Cy3 or Cy5 (Amersham) and then excess dye was removed with the Zymo Clean and Concentrator-5 columns according to the manufacturer's instructions.

growth_protocol: Four adult (10-12 weeks old) male and four adult female mice were individually housed one week prior to tissue dissection. (All were group housed by sex after weaning and sexually naïve.) The hypothalamus and bed nucleus of the stria terminalis were dissected from 1 mm brain slices.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions. mRNA was isolated using the Invitrogen Fast Track mRNA isolation kit.

value: Set 3


title: Hypo_female_rep6

description: Biological Replicate 3 of 3; Technical Replicate 2 of 2


title: Hypo_male_rep1_amp

description: Technical Replicate 1 of 2


title: WB MZ 13b


title: WB MZ 13a


title: Hypo_male_rep3

description: Biological Replicate 2 of 3; Technical Replicate 1 of 2

value: Set 2


title: Hypo_female_rep3


title: Hypo_female_rep4

description: Biological Replicate 2 of 3; Technical Replicate 2 of 2


title: Hypo_male_rep4


title: Hypo_female_rep1

description: Biological Replicate 1 of 3; Technical Replicate 1 of 2


title: Hypo_male_rep2

description: Biological Replicate 1 of 3; Technical Replicate 2 of 2


title: Hypo_male_rep1


title: Hypo_male_rep5


title: WB MZ 12b


title: WB MZ 11b


title: WB MZ 11a


title: Hypo_female_rep2


title: Hypo_male_rep6


title: WB MZ 10b


title: WB MZ 9a


title: WB MZ 10a


title: WB MZ 9b


title: WB MZ 7b


title: WB MZ 12a


title: WB MZ 8b


title: WB MZ 4a


title: WB MZ 5a


title: WB MZ 6a


title: WB MZ 7a


title: WB MZ 8a


title: WB MZ 2b


title: MSC-AT_donor11_P10

status: Public on Oct 28 2011

type: genomic

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

description: alternatively named mesenchymal stromal cells

hyb_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was hybridized with 200ng DNA.

scan_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.

data_processing: Initial data analysis was performed with the BeadStudio Methylation software from Illumina (ie, BeadStudio Methylation Analysis Module 3.2.0). Raw data were background normalized.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor11 - passage 10

label_protocol: Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo research Corporation, Orange, US). This step leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine. After bisulfate conversion each sample was whole genome amplified and enzymatically fragmented.

extract_protocol: Genomic DNA of 10(6) MSC was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.

tag: cell passage

tag: gender

value: female


title: WB MZ 4b


title: WB MZ 3a


title: WB MZ 3b


title: WB MZ 5b


title: WB MZ 6b


title: WB MZ 1a


title: WB MZ 2a


title: MSC-AT_donor10_P10

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor10 - passage 10

value: male


title: MSC-AT_donor4_P10

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor4 - passage 10


title: MSC-AT_donor8_P10

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor8 - passage 10


title: WB MZ 1b


title: MSC-AT_donor10_P5

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor10 - passage 5


title: MSC-AT_donor8_P5

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor8 - passage 5


title: Blood 213

city: Providence

first: Graham

middle: M

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

description: Blood sample from control patient.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to the Illumina Infinium Human Methylation27 BeadChip using the standard Illumina protocol.

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

data_processing: BeadStudio software v3.2. The Sample table values were generated by reporting the raw data (normalization was not recommended by Illumina) and subsetting the full 27,578 loci to 26,486 autosomal probes in order to minimize gender biases in the analysis.

source_name: blood

label_protocol: Standard Illumina labeling protocol.

extract_protocol: Genomic DNA was extracted using the DNeasy blood and tissue kit according to standard instructions.

value: peripheral blood

tag: disease state


title: Blood 211

description: Blood sample from control patient.


title: Blood 210

description: Blood sample from control patient.


title: Blood 208

description: Blood sample from control patient.


title: Blood 212

description: Blood sample from control patient.


title: Blood 204

description: Blood sample from control patient.


title: Blood 207

description: Blood sample from control patient.


title: Blood 203

description: Blood sample from control patient.


title: MSC-AT_donor4_P5

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor4 - passage 5


title: Blood 205

description: Blood sample from control patient.


title: Blood 199

description: Blood sample from control patient.


title: Blood 201

description: Blood sample from control patient.


title: Blood 206

description: Blood sample from control patient.


title: Blood 202

description: Blood sample from control patient.


title: Blood 200

description: Blood sample from control patient.


title: Blood 209

description: Blood sample from control patient.


title: Blood 192

description: Blood sample from control patient.


title: Blood 193

description: Blood sample from control patient.


title: NSL1_ChIP_males_rep3

city: Munich

first: Christian

last: Feller

address: Schillerstraße 44

department: Molecular Biology

institute: Adolf-Butenandt Institute at the LMU University Munich

description:
303313
Replicate 3 of 3.

hyb_protocol: Performed by imaGenes (www.imaGenes-bio.de).

data_processing: Raw signals of all channels in all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor.

organism: Drosophila melanogaster

source_name: DNA from males, input DNA

extract_protocol:
Chromatin extract preparation and chromatin immunoprecipitation were performed as described in Prestel et al. (2010). Briefly, chromatin extracts from sex-sorted adult flies were prepared according to the protocol of Negre et al. (2008) and with the modifications described in Prestel et al. (2010). DNA concentration of the chromatin extract was determined and 7.5 to 15µg of DNA was used for a single ChIP experiment. The IP was performed using 5 µl of custom anti-NSL1 serum. After the pull down and extensive washing, DNA was extracted with phenol-chloroform, ethanol precipitated and further cleaned using the GenElute PCR clean-up kit (SIGMA). DNA was amplified using the whole-genome amplification kit (WGA, SIGMA). Labeling, hybridization to customized high-resolution NimbleGen tiling arrays (comprising the euchromatic part of the entire X chromosome, 5 Mb of 2L, 2R and 3L, respectively, as well as 10 Mb of 3R), scanning and feature extraction was performed by ImaGenes (Berlin).

Generation of NSL1-specific antibody: For generating epitopes to raise antibodies against NSL1, a cDNA fragment (#LP09056) was ordered at the Drosophila Genomics Resource Center.  The NSL1 fragment corresponding to the amino acids 1271 to 1550 was amplified by PCR and cloned into the pGEX2TKN. The N-terminal GST-tagged NSL1 fragment was expressed in E. coli BL21 cells, purified on glutathione beads, and used to raise antibodies in rabbit.

value: whole body

tag: developmental stage

value: adult

tag: chip antibody

source_name: DNA from males, NSL1 ChIP

value: rabbit anti-NSL1 polyclonal


title: Blood 198

description: Blood sample from control patient.

value: normal


title: Blood 197

description: Blood sample from control patient.


title: Blood 194

description: Blood sample from control patient.


title: Blood 195

description: Blood sample from control patient.


title: Blood 196

description: Blood sample from control patient.


title: Blood 186

description: Blood sample from control patient.


title: Blood 189

description: Blood sample from control patient.


title: Blood 184

description: Blood sample from control patient.


title: NSL1_ChIP_females_rep2

description:
226250
Replicate 2 of 3.

scan_protocol: Performed by imaGenes (www.imaGenes-bio.de).

source_name: DNA from females, NSL1 ChIP

source_name: DNA from females, input DNA


title: Blood 185

description: Blood sample from control patient.


title: Blood 190

description: Blood sample from control patient.


title: NSL1_ChIP_females_rep3

description:
3047722
Replicate 3 of 3.

label_protocol: Performed by imaGenes (www.imaGenes-bio.de).


title: Blood 178

description: Blood sample from control patient.


title: Blood 187

description: Blood sample from control patient.


title: Blood 179

description: Blood sample from control patient.


title: Blood 191

description: Blood sample from control patient.


title: Blood 182

description: Blood sample from control patient.


title: Blood 180

description: Blood sample from control patient.


title: NSL1_ChIP_S2_rep1

description:
303315
Replicate 1 of 2.

source_name: DNA from S2, input DNA

tag: cell line

source_name: DNA from S2, NSL1 ChIP


title: NSL1_ChIP_females_rep1

description:
311160
Replicate 1 of 3.


title: MSC-AT_donor11_P5

source_name: mesenchymal stem cells (MSC) from human adipose tissue of donor11 - passage 5

tag: cell type


title: NSL1_ChIP_males_rep2

description:
225790
Replicate 2 of 3.


title: NSL1_ChIP_males_rep1

description:
181078
Replicate 1 of 3.


title: Blood 188

description: Blood sample from control patient.


title: NSL1_ChIP_S2_rep2

description:
317125
Replicate 2 of 2.


title: Blood 181

description: Blood sample from control patient.


title: Blood 175

description: Blood sample from control patient.


title: Blood 183

description: Blood sample from control patient.


title: Blood 173

description: Blood sample from control patient.


title: Blood 171

description: Blood sample from control patient.


title: Blood 170

description: Blood sample from control patient.


title: Blood 174

description: Blood sample from control patient.


title: Blood 172

description: Blood sample from control patient.


title: Blood 176

description: Blood sample from control patient.


title: Blood 167

description: Blood sample from control patient.


title: Blood 169

description: Blood sample from control patient.


title: Blood 163

description: Blood sample from control patient.


title: Blood 164

description: Blood sample from control patient.


title: Blood 165

description: Blood sample from control patient.


title: Blood 162

description: Blood sample from control patient.


title: Blood 157

description: Blood sample from control patient.


title: Blood 158

description: Blood sample from control patient.


title: Blood 166

description: Blood sample from control patient.


title: Blood 161

description: Blood sample from control patient.


title: Blood 154

description: Blood sample from control patient.


title: Blood 153

description: Blood sample from control patient.


title: Blood 155

description: Blood sample from control patient.


title: Blood 159

description: Blood sample from control patient.


title: Blood 156

description: Blood sample from control patient.


title: Blood 160

description: Blood sample from control patient.


title: Blood 177

description: Blood sample from control patient.


title: Blood 152

description: Blood sample from control patient.


title: Blood 139

description: Blood sample from control patient.


title: Blood 150

description: Blood sample from control patient.


title: Blood 143

description: Blood sample from control patient.


title: Blood 145

description: Blood sample from control patient.


title: Blood 144

description: Blood sample from control patient.


title: Blood 168

description: Blood sample from control patient.


title: Blood 151

description: Blood sample from control patient.


title: Blood 146

description: Blood sample from control patient.


title: Blood 141

description: Blood sample from control patient.


title: Blood 148

description: Blood sample from control patient.


title: Blood 147

description: Blood sample from control patient.


title: Blood 140

description: Blood sample from control patient.


title: Blood 149

description: Blood sample from control patient.


title: Blood 136

description: Blood sample from control patient.


title: Blood 135

description: Blood sample from control patient.


title: Blood 137

description: Blood sample from control patient.


title: Blood 133

description: Blood sample from control patient.


title: Blood 132

description: Blood sample from control patient.


title: Blood 129

description: Blood sample from control patient.


title: Blood 142

description: Blood sample from control patient.


title: Blood 130

description: Blood sample from control patient.


title: Blood 138

description: Blood sample from control patient.


title: Blood 128

description: Blood sample from control patient.


title: Blood 131

description: Blood sample from control patient.


title: Blood 126

description: Blood sample from control patient.


title: Blood 124

description: Blood sample from control patient.


title: Blood 127

description: Blood sample from control patient.


title: Blood 125

description: Blood sample from control patient.


title: Blood 123

description: Blood sample from control patient.


title: Blood 122

description: Blood sample from control patient.


title: Blood 121

description: Blood sample from control patient.


title: Blood 118

description: Blood sample from control patient.


title: Blood 120

description: Blood sample from control patient.


title: Blood 114

description: Blood sample from control patient.


title: Blood 110

description: Blood sample from control patient.


title: Blood 113

description: Blood sample from control patient.


title: Blood 116

description: Blood sample from control patient.


title: Blood 115

description: Blood sample from control patient.


title: Blood 112

description: Blood sample from control patient.


title: Blood 117

description: Blood sample from control patient.


title: Blood 134

description: Blood sample from control patient.


title: Blood 109

description: Blood sample from control patient.


title: Blood 111

description: Blood sample from control patient.


title: Blood 119

description: Blood sample from control patient.


title: Blood 108

description: Blood sample from control patient.


title: Blood 106

description: Blood sample from control patient.


title: Blood 100

description: Blood sample from control patient.


title: Blood 101

description: Blood sample from control patient.


title: Blood 104

description: Blood sample from control patient.


title: Blood 99

description: Blood sample from control patient.


title: Blood 105

description: Blood sample from control patient.


title: Blood 98

description: Blood sample from control patient.


title: Blood 95

description: Blood sample from control patient.


title: Blood 97

description: Blood sample from control patient.


title: Blood 102

description: Blood sample from control patient.


title: Blood 94

description: Blood sample from control patient.


title: Blood 103

description: Blood sample from control patient.


title: Blood 87

description: Blood sample from control patient.


title: Blood 89

description: Blood sample from control patient.


title: Blood 91

description: Blood sample from control patient.


title: Blood 90

description: Blood sample from control patient.


title: Blood 92

description: Blood sample from control patient.


title: Blood 107

description: Blood sample from control patient.


title: Blood 93

description: Blood sample from control patient.


title: Blood 96

description: Blood sample from control patient.


title: Blood 86

description: Blood sample from control patient.


title: Blood 84

description: Blood sample from control patient.


title: Blood 83

description: Blood sample from control patient.


title: Blood 85

description: Blood sample from control patient.


title: Blood 88

description: Blood sample from control patient.


title: Blood 81

description: Blood sample from control patient.


title: Blood 80

description: Blood sample from control patient.


title: Blood 82

description: Blood sample from control patient.


title: Blood 76

description: Blood sample from control patient.


title: Blood 77

description: Blood sample from control patient.


title: Blood 73

description: Blood sample from control patient.


title: Blood 66

description: Blood sample from control patient.


title: Blood 58

description: Blood sample from control patient.


title: Blood 78

description: Blood sample from control patient.


title: Blood 70

description: Blood sample from control patient.


title: Blood 74

description: Blood sample from control patient.


title: Blood 55

description: Blood sample from control patient.


title: Blood 61

description: Blood sample from control patient.


title: Blood 62

description: Blood sample from control patient.


title: Blood 54

description: Blood sample from control patient.


title: Blood 59

description: Blood sample from control patient.


title: Blood 51

description: Blood sample from control patient.


title: Blood 63

description: Blood sample from control patient.


title: Blood 67

description: Blood sample from control patient.


title: Blood 69

description: Blood sample from control patient.


title: Blood 65

description: Blood sample from control patient.


title: Blood 71

description: Blood sample from control patient.


title: Blood 72

description: Blood sample from control patient.


title: Blood 52

description: Blood sample from control patient.


title: Blood 53

description: Blood sample from control patient.


title: Blood 40

description: Blood sample from control patient.


title: Blood 75

description: Blood sample from control patient.


title: Blood 44

description: Blood sample from control patient.


title: Blood 48

description: Blood sample from control patient.


title: Blood 56

description: Blood sample from control patient.


title: Blood 39

description: Blood sample from control patient.


title: Blood 50

description: Blood sample from control patient.


title: Blood 64

description: Blood sample from control patient.


title: Blood 47

description: Blood sample from control patient.


title: Blood 79

description: Blood sample from control patient.


title: Blood 49

description: Blood sample from control patient.


title: Blood 38

description: Blood sample from control patient.


title: Blood 43

description: Blood sample from control patient.


title: Blood 60

description: Blood sample from control patient.


title: Blood 68

description: Blood sample from control patient.


title: Blood 57

description: Blood sample from control patient.


title: Blood 37

description: Blood sample from control patient.


title: Blood 36

description: Blood sample from control patient.


title: Blood 41

description: Blood sample from control patient.


title: Blood 42

description: Blood sample from control patient.


title: Blood 45

description: Blood sample from control patient.


title: Blood 46

description: Blood sample from control patient.


title: Blood 34

description: Blood sample from control patient.


title: Blood 35

description: Blood sample from control patient.


title: Blood 31

description: Blood sample from control patient.


title: Blood 32

description: Blood sample from control patient.


title: Blood 30

description: Blood sample from control patient.


title: Blood 28

description: Blood sample from control patient.


title: Blood 24

description: Blood sample from control patient.


title: Blood 26

description: Blood sample from control patient.


title: Blood 27

description: Blood sample from control patient.


title: Blood 17

description: Blood sample from control patient.


title: Blood 21

description: Blood sample from control patient.


title: Blood 19

description: Blood sample from control patient.


title: Blood 23

description: Blood sample from control patient.


title: Blood 14

description: Blood sample from control patient.


title: Blood 12

description: Blood sample from control patient.


title: Blood 25

description: Blood sample from control patient.


title: Blood 20

description: Blood sample from control patient.


title: Blood 8

description: Blood sample from control patient.


title: Blood 10

description: Blood sample from control patient.


title: Blood 33

description: Blood sample from control patient.


title: Blood 22

description: Blood sample from control patient.


title: Blood 18

description: Blood sample from control patient.


title: Blood 29

description: Blood sample from control patient.


title: Blood 7

description: Blood sample from control patient.


title: Blood 13

description: Blood sample from control patient.


title: Blood 16

description: Blood sample from control patient.


title: Blood 11

description: Blood sample from control patient.


title: Blood 6

description: Blood sample from control patient.


title: Blood 15

description: Blood sample from control patient.


title: Blood 9

description: Blood sample from control patient.


title: Blood 4

description: Blood sample from control patient.


title: HNSCC 89

description: Tumor sample.

source_name: head and neck squamous cell carcinoma

value: head and neck squamous cell carcinoma (HNSCC)

tag: sample type

value: fresh-frozen tumor


title: Blood 3

description: Blood sample from control patient.

tag: tissue


title: HNSCC 87

description: Tumor sample.


title: HNSCC 86

description: Tumor sample.


title: HNSCC 90

description: Tumor sample.


title: HNSCC 82

description: Tumor sample.

value: oral


title: HNSCC 70

description: Tumor sample.


title: HNSCC 91

description: Tumor sample.


title: HNSCC 74

description: Tumor sample.


title: Blood 1

description: Blood sample from control patient.


title: HNSCC 78

description: Tumor sample.


title: HNSCC 88

description: Tumor sample.


title: HNSCC 83

description: Tumor sample.


title: HNSCC 79

description: Tumor sample.


title: HNSCC 71

description: Tumor sample.


title: HNSCC 84

description: Tumor sample.


title: HNSCC 76

description: Tumor sample.

value: pharynx


title: HNSCC 85

description: Tumor sample.


title: Blood 2

description: Blood sample from control patient.


title: HNSCC 75

description: Tumor sample.


title: Blood 5

description: Blood sample from control patient.


title: HNSCC 81

description: Tumor sample.


title: HNSCC 77

description: Tumor sample.


title: HNSCC 73

description: Tumor sample.


title: HNSCC 69

description: Tumor sample.

value: larynx


title: HNSCC 80

description: Tumor sample.


title: HNSCC 72

description: Tumor sample.


title: HNSCC 68

description: Tumor sample.


title: HNSCC 56

description: Tumor sample.


title: HNSCC 67

description: Tumor sample.


title: HNSCC 66

description: Tumor sample.


title: HNSCC 52

description: Tumor sample.


title: HNSCC 48

description: Tumor sample.


title: HNSCC 44

description: Tumor sample.


title: HNSCC 62

description: Tumor sample.


title: HNSCC 49

description: Tumor sample.


title: HNSCC 45

description: Tumor sample.


title: HNSCC 63

description: Tumor sample.


title: HNSCC 40

description: Tumor sample.


title: HNSCC 42

description: Tumor sample.


title: HNSCC 61

description: Tumor sample.


title: HNSCC 46

description: Tumor sample.


title: HNSCC 59

description: Tumor sample.


title: HNSCC 57

description: Tumor sample.


title: HNSCC 58

description: Tumor sample.


title: HNSCC 50

description: Tumor sample.


title: HNSCC 60

description: Tumor sample.


title: HNSCC 53

description: Tumor sample.


title: HNSCC 54

description: Tumor sample.


title: HNSCC 55

description: Tumor sample.


title: HNSCC 38

description: Tumor sample.


title: HNSCC 64

description: Tumor sample.


title: HNSCC 41

description: Tumor sample.


title: HNSCC 51

description: Tumor sample.


title: HNSCC 65

description: Tumor sample.


title: HNSCC 36

description: Tumor sample.


title: HNSCC 37

description: Tumor sample.


title: HNSCC 47

description: Tumor sample.


title: HNSCC 33

description: Tumor sample.


title: HNSCC 34

description: Tumor sample.


title: HNSCC 30

description: Tumor sample.


title: HNSCC 43

description: Tumor sample.


title: HNSCC 29

description: Tumor sample.


title: HNSCC 39

description: Tumor sample.


title: HNSCC 35

description: Tumor sample.


title: HNSCC 26

description: Tumor sample.


title: HNSCC 22

description: Tumor sample.


title: HNSCC 32

description: Tumor sample.


title: HNSCC 18

description: Tumor sample.


title: HNSCC 20

description: Tumor sample.


title: HNSCC 25

description: Tumor sample.


title: HNSCC 27

description: Tumor sample.


title: HNSCC 31

description: Tumor sample.


title: HNSCC 28

description: Tumor sample.


title: HNSCC 21

description: Tumor sample.


title: HNSCC 23

description: Tumor sample.


title: HNSCC 19

description: Tumor sample.


title: HNSCC 15

description: Tumor sample.


title: HNSCC 16

description: Tumor sample.


title: HNSCC 24

description: Tumor sample.


title: HNSCC 7

description: Tumor sample.


title: HNSCC 11

description: Tumor sample.


title: HNSCC 14

description: Tumor sample.


title: HNSCC 12

description: Tumor sample.


title: HNSCC 17

description: Tumor sample.


title: HNSCC 3

description: Tumor sample.


title: HNSCC 8

description: Tumor sample.


title: HNSCC 4

description: Tumor sample.


title: HNSCC 13

description: Tumor sample.


title: HNSCC 6

description: Tumor sample.


title: Normal head and neck tissue 18

description:
ndri 18
Normal tissue sample.

source_name: normal head and neck tissue


title: HNSCC 9

description: Tumor sample.


title: HNSCC 10

description: Tumor sample.


title: HNSCC 5

description: Tumor sample.


title: Normal head and neck tissue 12

description:
ndri 12
Normal tissue sample.


title: Normal head and neck tissue 15

description:
ndri 15
Normal tissue sample.


title: Normal head and neck tissue 16

description:
ndri 16
Normal tissue sample.


title: Normal head and neck tissue 11

description:
ndri 11
Normal tissue sample.


title: Normal head and neck tissue 13

description:
ndri 13
Normal tissue sample.


title: HNSCC 2

description: Tumor sample.


title: Normal head and neck tissue 17

description:
ndri 17
Normal tissue sample.


title: Normal head and neck tissue 14

description:
ndri 14
Normal tissue sample.


title: Normal head and neck tissue 10

description:
ndri 10
Normal tissue sample.


title: Normal head and neck tissue 4

description:
ndri 4
Normal tissue sample.


title: Normal head and neck tissue 7

description:
ndri 7
Normal tissue sample.


title: HNSCC 1

description: Tumor sample.


title: Normal head and neck tissue 9

description:
ndri 9
Normal tissue sample.


title: Normal head and neck tissue 8

description:
ndri 8
Normal tissue sample.


title: Normal head and neck tissue 1

description:
ndri 1
Normal tissue sample.


title: Normal head and neck tissue 6

description:
ndri 6
Normal tissue sample.


title: Normal head and neck tissue 5

description:
ndri 5
Normal tissue sample.


title: Normal head and neck tissue 3

description:
ndri 3
Normal tissue sample.


title: Normal head and neck tissue 2

description:
ndri 2
Normal tissue sample.


title: Adenocarcinoma_sample_37A

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

description:
37A_070228
Hybridized to HG-U133 Plus 2.0

hyb_protocol: Sample hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 5).

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.

data_processing: Analyses of the gene expression data were carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.

source_name: Non-small cell lung cancer tissue, long-term survival, adenocarcinoma

label_protocol: Sample preparation was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 5).

extract_protocol: RNA was extracted from 2-10 frozen tissue sections (10mm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) and the RNeasy Mini Kit (Qiagen), respectively.

value: non-small cell lung cancer

tag: histology

value: adenocarcinoma

tag: survival

value: long

tag: registry year


title: HUVEC cells, COUP-TFII siRNA for 48 hr, rep1

city: Houston

first: Xinpu

last: Chen

address: One baylor Plaza

institute: Baylor College of Medicine

description: HUVEC_COUP-TFII siRNA1

hyb_protocol: hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto a GeneChip® Human U133 Plus 2.0 array.  The array was hybridized overnight at 45°C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain.  Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix GCOS software version 1.4.

data_processing: The data were analyzed with dCHIP using Affymetrix default analysis settings and global scaling as normalization method. We selected differentially expressed genes using three sample comparisons according to the following criteria: lower bound of 90% confidence interval of fold change greater than 1.2 [available as a Series Supplementary file, differentially_expressed.txt].

source_name: HUVEC_COUP-TFII siRNA_48 hr

label_protocol: Samples were labeled using the standard Affymetrix T7 oligo(dT) primer protocol.  Using our GCAS automated system, five µg of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA.  The labeled cRNA was quantified using the NanoDrop® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration

growth_protocol: HUVEC cells are cultured in EGM-2 medium

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

treatment_protocol: Control or COUP-TFII siRNA knockdown

value: primary human vein endothelial cell

tag: transfected with

value: COUP-TFII siRNA


title: Squamous_cell_carcinoma_sample_6A

description:
6A_070228
Hybridized to HG-U133 Plus 2.0

source_name: Non-small cell lung cancer tissue, long-term survival, squamous cell carcinoma

value: squamous cell carcinoma


title: HUVEC cells, control siRNA for 48 hr, rep1

description: HUVEC_control siRNA1

source_name: HUVEC_control siRNA_48 hr

value: control siRNA


title: Large_cell_carcinoma_sample_87A

description:
87A_070228
Hybridized to HG-U133 Plus 2.0

source_name: Non-small cell lung cancer tissue, short-term survival, large cell carcinoma

value: large cell carcinoma

value: short


title: Adenocarcinoma_sample_81A

description:
81A_070509
Hybridized to HG-U133 Plus 2.0

source_name: Non-small cell lung cancer tissue, short-term survival, adenocarcinoma


title: Large_cell_carcinoma_sample_361A

description:
361A_070907
Hybridized to HG-U133 Plus 2.0

source_name: Non-small cell lung cancer tissue, long-term survival, large cell carcinoma


title: HUVEC cells, COUP-TFII siRNA for 48 hr, rep2

description: HUVEC_COUP-TFII siRNA2


title: Squamous_cell_carcinoma_sample_39A

description:
39A_070509
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_48A

description:
48A_070509
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_88A

description:
88A_070228
Hybridized to HG-U133 Plus 2.0

source_name: Non-small cell lung cancer tissue, short-term survival, squamous cell carcinoma


title: HUVEC cells, control siRNA for 48 hr, rep2

description: HUVEC_control siRNA2


title: Squamous_cell_carcinoma_sample_365A

description:
365A_070907
Hybridized to HG-U133 Plus 2.0


title: HUVEC cells, COUP-TFII siRNA for 48 hr, rep3

description: HUVEC_COUP-TFII siRNA3


title: Adenocarcinoma_sample_35A

description:
35A_070912
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_373B

description:
373B_070907
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039549_1_3

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

description: LTBI whole blood RNA

hyb_protocol: Quantity and labelling efficiency were verified before hybridization of the samples to whole-genome oligonucleotide microarray (Agilent Technologies).

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Agilent Feature Extraction Software (v 6.1.1) was used for background subtraction and LOWESS normalization.

source_name: Peripheral blood LTBI

label_protocol: Total RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was isolated from 2,5 ml of peripheral whole blood collected in PAXgene tubes, using the PAXgene Blood RNA Kit (PreAnalystics, Europe BD, Belgium).

tag: group

value: healthy donors latently infected with M. tuberculosis

value: Female


title: Adenocarcinoma_sample_359A

description:
359A_070907
Hybridized to HG-U133 Plus 2.0


title: Whole blood NID_251485039548_1_4

description: NID whole blood RNA

source_name: Peripheral blood NID

value: healthy non-infected donors

value: Male


title: Squamous_cell_carcinoma_sample_370A

description:
370A_070907
Hybridized to HG-U133 Plus 2.0


title: HUVEC cells, control siRNA for 48 hr, rep3

description: HUVEC_control siRNA3


title: Whole blood NID_251485039549_1_4

description: NID whole blood RNA


title: Squamous_cell_carcinoma_sample_367A

description:
367A_070907
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039549_1_1

description: LTBI whole blood RNA


title: Whole blood LTBI_251485039549_1_2

description: LTBI whole blood RNA


title: Squamous_cell_carcinoma_sample_342A

description:
342A_070907
Hybridized to HG-U133 Plus 2.0


title: Whole blood NID_251485039548_1_2

description: NID whole blood RNA


title: Whole blood NID_251485039548_1_3

description: NID whole blood RNA


title: Large_cell_carcinoma_sample_33A

description:
33A_070509
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_338A

description:
338A_071005
Hybridized to HG-U133 Plus 2.0


title: Large_cell_carcinoma_sample_314A

description:
314A_070921
Hybridized to HG-U133 Plus 2.0


title: Large_cell_carcinoma_sample_331A

description:
331A_070914
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_347A

description:
347A_070907
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_317A

description:
317A_070926
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039517_1_1

description: TB whole blood RNA

source_name: Peripheral blood TB

value: tuberculosis patients


title: Whole blood NID_251485039518_1_4

description: NID whole blood RNA


title: Whole blood NID_251485039548_1_1

description: NID whole blood RNA


title: Whole blood NID_251485039518_1_1

description: NID whole blood RNA


title: Whole blood TB_251485039518_1_2

description: TB whole blood RNA


title: Whole blood NID_251485039518_1_3

description: NID whole blood RNA


title: Squamous_cell_carcinoma_sample_297A

description:
297A_070912
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_319A

description:
319A_070914
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_32A

description:
32A_070509
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_305A

description:
305A_070912
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039517_1_4

description: TB whole blood RNA


title: Adenocarcinoma_sample_310A

description:
310A_070912
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039516_1_2

description: TB whole blood RNA


title: Whole blood TB_251485039517_1_3

description: TB whole blood RNA


title: Whole blood TB_251485039516_1_3

description: TB whole blood RNA


title: Whole blood TB_251485039517_1_2

description: TB whole blood RNA


title: Whole blood TB_251485039516_1_1

description: TB whole blood RNA


title: Whole blood TB_251485039516_1_4

description: TB whole blood RNA


title: Large_cell_carcinoma_sample_295B

description:
295B_070912
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_300A

description:
300A_070919
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_299B

description:
299B_070912
Hybridized to HG-U133 Plus 2.0


title: Large_cell_carcinoma_sample_309A

description:
309A_070921
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_271A

description:
271A_071005
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_256A

description:
256A_070926
Hybridized to HG-U133 Plus 2.0


title: Whole blood NID_251485039515_1_4

description: NID whole blood RNA


title: Whole blood NID_251485039514_1_1

description: NID whole blood RNA


title: Whole blood LTBI_251485039515_1_1

description: LTBI whole blood RNA


title: Adenocarcinoma_sample_255A

description:
255A_070926
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039513_1_4

description: LTBI whole blood RNA


title: Whole blood NID_251485039515_1_3

description: NID whole blood RNA


title: Large_cell_carcinoma_sample_265A

description:
265A_071005
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_27A

description:
27A_070509
Hybridized to HG-U133 Plus 2.0


title: Whole blood NID_251485039514_1_4

description: NID whole blood RNA


title: Whole blood LTBI_251485039514_1_2

description: LTBI whole blood RNA


title: Whole blood NID_251485039513_1_3

description: NID whole blood RNA


title: Adenocarcinoma_sample_247A

description:
247A_070926
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_288A

description:
288A_070914
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039513_1_2

description: TB whole blood RNA


title: Whole blood NID_251485039515_1_2

description: NID whole blood RNA


title: Adenocarcinoma_sample_229A

description:
229A_070912
Hybridized to HG-U133 Plus 2.0


title: Large_cell_carcinoma_sample_234A

description:
234A_070912
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_235A

description:
235A_070912
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_258A

description:
258A_071005
Hybridized to HG-U133 Plus 2.0


title: Large_cell_carcinoma_sample_207A

description:
207A_070912
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_278A_2

description:
278A-2_070912
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_284A

description:
284A_070912
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039512_1_4

description: TB whole blood RNA


title: Whole blood LTBI_251485039514_1_3

description: LTBI whole blood RNA


title: Whole blood TB_251485039513_1_1

description: TB whole blood RNA


title: Whole blood TB_251485039512_1_3

description: TB whole blood RNA


title: Adenocarcinoma_sample_197B

description:
197B_070509
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_175B

description:
175B_070228
Hybridized to HG-U133 Plus 2.0


title: Large_cell_carcinoma_sample_196A

description:
196A_070228
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039512_1_2

description: LTBI whole blood RNA


title: Whole blood TB_251485039511_1_3

description: TB whole blood RNA


title: Whole blood TB_251485039512_1_1

description: TB whole blood RNA


title: Whole blood LTBI_251485039511_1_4

description: LTBI whole blood RNA


title: Adenocarcinoma_sample_165C

description:
165C_070509
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_169D

description:
169D_070228
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_189A

description:
189A_070509
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039511_1_2

description: TB whole blood RNA


title: 6 week old aorta 48_young microRNA

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Agilent Feature Extraction Software

source_name: aorta

label_protocol: standard Agilent protocol

extract_protocol: RNA was extracted with Trizol

value: 6 weeks

value: aorta

tag: genetic background


title: Large_cell_carcinoma_sample_195B

description:
195B_070912
Hybridized to HG-U133 Plus 2.0


title: Whole blood NID_251485039511_1_1

description: NID whole blood RNA


title: 6 week old aorta 47_young microRNA

tag: age


title: Adenocarcinoma_sample_172C

description:
172C_070912
Hybridized to HG-U133 Plus 2.0


title: 6 week old aorta 46_young microRNA


title: 18 month old aorta 38_old microRNA

value: 18 months


title: 18 month old aorta 37_old microRNA


title: 18 month old aorta 36_old microRNA


title: Whole blood TB_251485039510_1_3

description: TB whole blood RNA


title: Whole blood NID_251485039510_1_4

description: NID whole blood RNA


title: Whole blood NID_251485039510_1_2

description: NID whole blood RNA


title: 6 week old aorta 45_young microRNA


title: Squamous_cell_carcinoma_sample_14A

description:
14A_070228
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer


title: peritumoral HCC, no bone metastasis, patient 48

city: Shanghai

first: Zuolin

last: Xiang

address: 136 Yi Xue Yuan Road

institute: Zhongshan Hospital, Fudan University

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 48
peritumoral tissues NBM

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Scanned data were uploaded into GenomeStudio for further analysis.

label: Cy3, Cy5

label_protocol: RNA with a cycle threshold (Ct) value ≤28 was used for the DASL assay.

extract_protocol: Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit (Roche Diagnostics, Germany) according to the manufacturer’s protocol.Proteinase K digestion time was 12 hours for each sample. RNA samples were stored at -80°C until use.

tag: disease progression

value: no bone metastasis

value: peritumoral hepatocellular carcinoma tissues

tag: individual

value: patient 48

value: hepatocellular carcinoma


title: peritumoral HCC, no bone metastasis, patient 47

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 47
peritumoral tissues NBM

value: patient 47


title: 18 month old aorta 35_old microRNA


title: peritumoral HCC, no bone metastasis, patient 46

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 46
peritumoral tissues NBM

value: patient 46


title: Whole blood TB_251485039509_1_3

description: TB whole blood RNA

tag: gender


title: intratumoral HCC, no bone metastasis, patient 46

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 46
intratumoral tissues NBM

value: intratumoral hepatocellular carcinoma tissues

tag: disease state


title: intratumoral HCC, no bone metastasis, patient 48

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 48
intratumoral tissues NBM


title: Whole blood NID_251485039509_1_4

description: NID whole blood RNA


title: intratumoral HCC, no bone metastasis, patient 43

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 43
intratumoral tissues NBM

value: patient 43


title: peritumoral HCC, no bone metastasis, patient 44

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 44
peritumoral tissues NBM

value: patient 44


title: peritumoral HCC, no bone metastasis, patient 45

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 45
peritumoral tissues NBM

value: patient 45


title: intratumoral HCC, no bone metastasis, patient 47

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 47
intratumoral tissues NBM


title: Adenocarcinoma_sample_12B

description:
12B_070912
Hybridized to HG-U133 Plus 2.0

value: adenocarcinoma

value: short


title: intratumoral HCC, no bone metastasis, patient 42

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 42
intratumoral tissues NBM

value: patient 42


title: intratumoral HCC, no bone metastasis, patient 45

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 45
intratumoral tissues NBM


title: Adenocarcinoma_sample_162A

description:
162A_070509
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039470_1_3

description: TB whole blood RNA

value: tuberculosis patients

value: Female


title: Whole blood NID_251485039510_1_1

description: NID whole blood RNA

value: healthy non-infected donors

value: Male


title: Squamous_cell_carcinoma_sample_131A

description:
131A_070228
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer

value: squamous cell carcinoma


title: peritumoral HCC, no bone metastasis, patient 41

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 41
peritumoral tissues NBM

value: no bone metastasis

value: peritumoral hepatocellular carcinoma tissues

value: patient 41


title: Whole blood TB_251485039470_1_4

description: TB whole blood RNA


title: peritumoral HCC, no bone metastasis, patient 43

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 43
peritumoral tissues NBM

value: hepatocellular carcinoma


title: Whole blood TB_251485039509_1_2

description: TB whole blood RNA


title: Squamous_cell_carcinoma_sample_13A

description:
13A_070509
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_112B

description:
112B_070912
Hybridized to HG-U133 Plus 2.0


title: intratumoral HCC, no bone metastasis, patient 40

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 40
intratumoral tissues NBM

value: intratumoral hepatocellular carcinoma tissues

value: patient 40


title: peritumoral HCC, no bone metastasis, patient 42

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 42
peritumoral tissues NBM


title: intratumoral HCC, no bone metastasis, patient 44

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 44
intratumoral tissues NBM

value: patient 44


title: Whole blood LTBI_251485039469_1_4

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis


title: peritumoral HCC, no bone metastasis, patient 38

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 38
peritumoral tissues NBM

value: patient 38


title: Squamous_cell_carcinoma_sample_98A

description:
98A_081029
Hybridized to HG-U133 Plus 2.0

value: short


title: Large_cell_carcinoma_sample_375A

description:
375A_081028
Hybridized to HG-U133 Plus 2.0

value: large cell carcinoma

value: long


title: Whole blood TB_251485039470_1_1

description: TB whole blood RNA

value: tuberculosis patients

value: Female


title: intratumoral HCC, no bone metastasis, patient 41

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 41
intratumoral tissues NBM


title: Whole blood TB_251485039509_1_1

description: TB whole blood RNA

value: Male


title: peritumoral HCC, no bone metastasis, patient 40

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 40
peritumoral tissues NBM


title: intratumoral HCC, no bone metastasis, patient 39

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 39
intratumoral tissues NBM

value: patient 39


title: peritumoral HCC, no bone metastasis, patient 39

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 39
peritumoral tissues NBM


title: peritumoral HCC, no bone metastasis, patient 37

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 37
peritumoral tissues NBM

value: patient 37


title: Whole blood TB_251485039469_1_2

description: TB whole blood RNA


title: peritumoral HCC, no bone metastasis, patient 36

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 36
peritumoral tissues NBM

value: no bone metastasis

value: patient 36


title: Whole blood TB_251485039470_1_2

description: TB whole blood RNA


title: intratumoral HCC, no bone metastasis, patient 35

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 35
intratumoral tissues NBM

value: patient 35


title: Adenocarcinoma_sample_61A

description:
61A_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer

value: adenocarcinoma


title: intratumoral HCC, no bone metastasis, patient 38

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 38
intratumoral tissues NBM

value: intratumoral hepatocellular carcinoma tissues

value: hepatocellular carcinoma


title: intratumoral HCC, no bone metastasis, patient 37

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 37
intratumoral tissues NBM


title: Adenocarcinoma_sample_369A

description:
369A_081028
Hybridized to HG-U133 Plus 2.0


title: peritumoral HCC, no bone metastasis, patient 35

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 35
peritumoral tissues NBM

value: peritumoral hepatocellular carcinoma tissues


title: Squamous_cell_carcinoma_sample_357A

description:
357A_081106
Hybridized to HG-U133 Plus 2.0

value: squamous cell carcinoma


title: intratumoral HCC, no bone metastasis, patient 36

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 36
intratumoral tissues NBM


title: Adenocarcinoma_sample_11C

description:
11C_070509
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039469_1_3

description: TB whole blood RNA


title: intratumoral HCC, no bone metastasis, patient 34

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 34
intratumoral tissues NBM

value: patient 34


title: Adenocarcinoma_sample_341A

description:
341A_081106
Hybridized to HG-U133 Plus 2.0

value: short


title: peritumoral HCC, no bone metastasis, patient 34

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 34
peritumoral tissues NBM


title: Adenocarcinoma_sample_302A

description:
302A_081106
Hybridized to HG-U133 Plus 2.0

value: long


title: Squamous_cell_carcinoma_sample_344A

description:
344A_081106
Hybridized to HG-U133 Plus 2.0


title: intratumoral HCC, no bone metastasis, patient 32

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 32
intratumoral tissues NBM

value: patient 32


title: peritumoral HCC, no bone metastasis, patient 33

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 33
peritumoral tissues NBM

value: patient 33


title: peritumoral HCC, no bone metastasis, patient 32

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 32
peritumoral tissues NBM


title: intratumoral HCC, no bone metastasis, patient 33

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 33
intratumoral tissues NBM


title: Whole blood NID_251485039468_1_3

description: NID whole blood RNA

value: healthy non-infected donors

value: Male


title: peritumoral HCC, no bone metastasis, patient 31

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 31
peritumoral tissues NBM

value: patient 31


title: Whole blood TB_251485039468_1_4

description: TB whole blood RNA

value: tuberculosis patients

value: Female


title: Large_cell_carcinoma_sample_332Y

description:
332Y_081029
Hybridized to HG-U133 Plus 2.0

value: large cell carcinoma


title: Adenocarcinoma_sample_292B

description:
292B_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer


title: Adenocarcinoma_sample_311C

description:
311C_081106
Hybridized to HG-U133 Plus 2.0

value: adenocarcinoma


title: peritumoral HCC, no bone metastasis, patient 30

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 30
peritumoral tissues NBM

value: no bone metastasis

value: patient 30


title: intratumoral HCC, no bone metastasis, patient 31

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 31
intratumoral tissues NBM

value: intratumoral hepatocellular carcinoma tissues

value: hepatocellular carcinoma


title: Whole blood LTBI_251485039469_1_1

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis


title: Squamous_cell_carcinoma_sample_296A

description:
296A_081211
Hybridized to HG-U133 Plus 2.0

value: squamous cell carcinoma


title: Adenocarcinoma_sample_301A

description:
301A_081029
Hybridized to HG-U133 Plus 2.0

value: long


title: peritumoral HCC, no bone metastasis, patient 29

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 29
peritumoral tissues NBM

value: peritumoral hepatocellular carcinoma tissues

value: patient 29


title: Whole blood TB_251485039468_1_1

description: TB whole blood RNA


title: intratumoral HCC, no bone metastasis, patient 30

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 30
intratumoral tissues NBM


title: Whole blood NID_251485039467_1_4

description: NID whole blood RNA

value: healthy non-infected donors


title: Whole blood TB_251485039467_1_3

description: TB whole blood RNA


title: peritumoral HCC, no bone metastasis, patient 27

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 27
peritumoral tissues NBM

value: patient 27


title: Whole blood NID_251485039468_1_2

description: NID whole blood RNA


title: peritumoral HCC, no bone metastasis, patient 26

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 26
peritumoral tissues NBM

value: patient 26


title: intratumoral HCC, no bone metastasis, patient 29

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 29
intratumoral tissues NBM


title: intratumoral HCC, no bone metastasis, patient 26

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 26
intratumoral tissues NBM


title: Whole blood TB_251485039467_1_2

description: TB whole blood RNA

value: tuberculosis patients

value: Male


title: intratumoral HCC, no bone metastasis, patient 28

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 28
intratumoral tissues NBM

value: patient 28


title: Squamous_cell_carcinoma_sample_291A

description:
291A_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer

value: short


title: peritumoral HCC, no bone metastasis, patient 28

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 28
peritumoral tissues NBM

value: no bone metastasis


title: Large_cell_carcinoma_sample_260A

description:
260A_081029
Hybridized to HG-U133 Plus 2.0

value: large cell carcinoma


title: Adenocarcinoma_sample_272B

description:
272B_081029
Hybridized to HG-U133 Plus 2.0

value: adenocarcinoma


title: peritumoral HCC, no bone metastasis, patient 25

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 25
peritumoral tissues NBM

value: patient 25

value: hepatocellular carcinoma


title: intratumoral HCC, no bone metastasis, patient 27

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 27
intratumoral tissues NBM

value: intratumoral hepatocellular carcinoma tissues


title: Adenocarcinoma_sample_282A

description:
282A_081029
Hybridized to HG-U133 Plus 2.0


title: Squamous_cell_carcinoma_sample_274B

description:
274B_081029
Hybridized to HG-U133 Plus 2.0

value: squamous cell carcinoma

value: long


title: intratumoral HCC, no bone metastasis, patient 25

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 25
intratumoral tissues NBM


title: Squamous_cell_carcinoma_sample_249A

description:
249A_081029
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039467_1_1

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis

value: Female


title: Whole blood TB_251485039466_1_2

description: TB whole blood RNA


title: Large_cell_carcinoma_sample_243A

description:
243A_081028
Hybridized to HG-U133 Plus 2.0


title: intratumoral HCC, bone metastasis, patient 24

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 24
intratumoral tissues BM

value: bone metastasis

value: patient 24


title: intratumoral HCC, bone metastasis, patient 22

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 22
intratumoral tissues BM

value: patient 22


title: peritumoral HCC, bone metastasis, patient 23

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 23
peritumoral tissues BM

value: peritumoral hepatocellular carcinoma tissues

value: patient 23


title: peritumoral HCC, bone metastasis, patient 24

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 24
peritumoral tissues BM


title: Adenocarcinoma_sample_23A

description:
23A_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer


title: Whole blood NID_251485039466_1_1

description: NID whole blood RNA

value: healthy non-infected donors


title: Whole blood TB_251485039466_1_3

description: TB whole blood RNA

value: tuberculosis patients

value: Male


title: Whole blood NID_251485039465_1_3

description: NID whole blood RNA


title: peritumoral HCC, bone metastasis, patient 22

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 22
peritumoral tissues BM


title: intratumoral HCC, bone metastasis, patient 21

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 21
intratumoral tissues BM

value: patient 21


title: peritumoral HCC, bone metastasis, patient 21

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 21
peritumoral tissues BM


title: intratumoral HCC, bone metastasis, patient 20

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 20
intratumoral tissues BM

value: patient 20


title: intratumoral HCC, bone metastasis, patient 23

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 23
intratumoral tissues BM

value: hepatocellular carcinoma


title: peritumoral HCC, bone metastasis, patient 20

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 20
peritumoral tissues BM


title: Whole blood LTBI_251485039466_1_4

description: LTBI whole blood RNA


title: intratumoral HCC, bone metastasis, patient 19

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 19
intratumoral tissues BM

value: intratumoral hepatocellular carcinoma tissues

value: patient 19


title: Whole blood TB_251485039465_1_1

description: TB whole blood RNA


title: Whole blood TB_251485039465_1_4

description: TB whole blood RNA


title: Whole blood TB_251485039465_1_2

description: TB whole blood RNA


title: peritumoral HCC, bone metastasis, patient 16

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 16
peritumoral tissues BM

value: patient 16


title: intratumoral HCC, bone metastasis, patient 15

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 15
intratumoral tissues BM

value: patient 15


title: peritumoral HCC, bone metastasis, patient 17

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 17
peritumoral tissues BM

value: patient 17


title: intratumoral HCC, bone metastasis, patient 17

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 17
intratumoral tissues BM

value: bone metastasis


title: intratumoral HCC, bone metastasis, patient 18

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 18
intratumoral tissues BM

value: patient 18


title: Whole blood LTBI_251485039464_1_2

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis

value: Female


title: Adenocarcinoma_sample_224A

description:
224A_081028
Hybridized to HG-U133 Plus 2.0

value: adenocarcinoma

value: long


title: Whole blood TB_251485039464_1_3

description: TB whole blood RNA


title: Squamous_cell_carcinoma_sample_217A

description:
217A_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer

value: squamous cell carcinoma

value: short


title: Adenocarcinoma_sample_223A

description:
223A_081028
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_228B

description:
228B_081028
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_215A

description:
215A_090128
Hybridized to HG-U133 Plus 2.0


title: peritumoral HCC, bone metastasis, patient 18

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 18
peritumoral tissues BM

value: peritumoral hepatocellular carcinoma tissues


title: Adenocarcinoma_sample_22B

description:
22B_081028
Hybridized to HG-U133 Plus 2.0


title: intratumoral HCC, bone metastasis, patient 14

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 14
intratumoral tissues BM

value: patient 14


title: intratumoral HCC, bone metastasis, patient 16

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 16
intratumoral tissues BM

value: hepatocellular carcinoma


title: peritumoral HCC, bone metastasis, patient 15

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 15
peritumoral tissues BM


title: Whole blood NID_251485039463_1_3

description: NID whole blood RNA

value: healthy non-infected donors


title: peritumoral HCC, bone metastasis, patient 14

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 14
peritumoral tissues BM


title: Whole blood NID_251485039463_1_4

description: NID whole blood RNA


title: Whole blood LTBI_251485039464_1_1

description: LTBI whole blood RNA


title: Adenocarcinoma_sample_213A

description:
213A_081029
Hybridized to HG-U133 Plus 2.0


title: intratumoral HCC, bone metastasis, patient 12

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 12
intratumoral tissues BM

value: intratumoral hepatocellular carcinoma tissues

value: patient 12


title: peritumoral HCC, bone metastasis, patient 13

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 13
peritumoral tissues BM

value: patient 13


title: intratumoral HCC, bone metastasis, patient 13

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 13
intratumoral tissues BM


title: peritumoral HCC, bone metastasis, patient 12

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 12
peritumoral tissues BM


title: intratumoral HCC, bone metastasis, patient 11

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 11
intratumoral tissues BM

value: patient 11


title: Large_cell_carcinoma_sample_212A

description:
212A_081029
Hybridized to HG-U133 Plus 2.0

value: large cell carcinoma


title: Whole blood NID_251485039463_1_2

description: NID whole blood RNA


title: Large_cell_carcinoma_sample_214A

description:
214A_081029
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039463_1_1

description: LTBI whole blood RNA


title: Whole blood LTBI_251485039462_1_4

description: LTBI whole blood RNA


title: intratumoral HCC, bone metastasis, patient 10

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 10
intratumoral tissues BM

value: bone metastasis

value: patient 10


title: Whole blood NID_251485039464_1_4

description: NID whole blood RNA

value: Male


title: Whole blood TB_251485039462_1_3

description: TB whole blood RNA

value: tuberculosis patients

value: Female


title: peritumoral HCC, bone metastasis, patient 11

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 11
peritumoral tissues BM


title: peritumoral HCC, bone metastasis, patient 10

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 10
peritumoral tissues BM


title: Whole blood NID_251485039462_1_2

description: NID whole blood RNA


title: Large_cell_carcinoma_sample_203B

description:
203B_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer

value: long


title: intratumoral HCC, bone metastasis, patient 9

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 9
intratumoral tissues BM

value: patient 9


title: Adenocarcinoma_sample_201A

description:
201A_090109
Hybridized to HG-U133 Plus 2.0

value: adenocarcinoma

value: short


title: peritumoral HCC, bone metastasis, patient 9

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 9
peritumoral tissues BM

value: peritumoral hepatocellular carcinoma tissues

value: hepatocellular carcinoma


title: Squamous_cell_carcinoma_sample_202A

description:
202A_081029
Hybridized to HG-U133 Plus 2.0

value: squamous cell carcinoma


title: intratumoral HCC, bone metastasis, patient 8

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 8
intratumoral tissues BM

value: intratumoral hepatocellular carcinoma tissues

value: patient 8


title: peritumoral HCC, bone metastasis, patient 19

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 19
peritumoral tissues BM

value: patient 19


title: Whole blood TB_251485039461_1_4

description: TB whole blood RNA


title: Whole blood NID_251485039462_1_1

description: NID whole blood RNA

value: healthy non-infected donors


title: Adenocarcinoma_sample_192C

description:
192C_081106
Hybridized to HG-U133 Plus 2.0


title: Adenocarcinoma_sample_171A

description:
171A_081211
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039461_1_3

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis


title: Whole blood TB_251485039461_1_2

description: TB whole blood RNA


title: peritumoral HCC, bone metastasis, patient 5

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 5
peritumoral tissues BM

value: bone metastasis

value: patient 5


title: peritumoral HCC, bone metastasis, patient 4

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 4
peritumoral tissues BM

value: patient 4


title: intratumoral HCC, bone metastasis, patient 5

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 5
intratumoral tissues BM


title: intratumoral HCC, bone metastasis, patient 6

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 6
intratumoral tissues BM

value: patient 6


title: peritumoral HCC, bone metastasis, patient 8

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 8
peritumoral tissues BM


title: intratumoral HCC, bone metastasis, patient 7

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 7
intratumoral tissues BM

value: patient 7


title: intratumoral HCC, bone metastasis, patient 3

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 3
intratumoral tissues BM

value: patient 3


title: intratumoral HCC, bone metastasis, patient 4

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 4
intratumoral tissues BM


title: peritumoral HCC, bone metastasis, patient 6

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 6
peritumoral tissues BM


title: peritumoral HCC, bone metastasis, patient 7

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 7
peritumoral tissues BM


title: Whole blood NID_251485039459_1_4

description: NID whole blood RNA

value: Female


title: Large_cell_carcinoma_sample_174A

description:
174A_081029
Hybridized to HG-U133 Plus 2.0

value: non-small cell lung cancer

value: large cell carcinoma


title: Adenocarcinoma_sample_19A

description:
19A_081028
Hybridized to HG-U133 Plus 2.0

value: adenocarcinoma

value: short


title: Adenocarcinoma_sample_200A

description:
200A_081029
Hybridized to HG-U133 Plus 2.0

value: long


title: peritumoral HCC, bone metastasis, patient 3

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 3
peritumoral tissues BM

value: peritumoral hepatocellular carcinoma tissues

value: hepatocellular carcinoma


title: Adenocarcinoma_sample_193B

description:
193B_081106
Hybridized to HG-U133 Plus 2.0


title: Whole blood TB_251485039459_1_3

description: TB whole blood RNA

value: tuberculosis patients

value: Male


title: Large_cell_carcinoma_sample_158A

description:
158A_081029
Hybridized to HG-U133 Plus 2.0


title: Whole blood LTBI_251485039461_1_1

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis


title: Whole blood LTBI_251485039459_1_1

description: LTBI whole blood RNA


title: Large_cell_carcinoma_sample_133A

description:
133A_081106
Hybridized to HG-U133 Plus 2.0


title: Whole blood NID_251485039459_1_2

description: NID whole blood RNA

value: healthy non-infected donors


title: peritumoral HCC, bone metastasis, patient 2

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 2
peritumoral tissues BM

value: bone metastasis

value: patient 2


title: intratumoral HCC, bone metastasis, patient 1

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 1
intratumoral tissues BM

value: intratumoral hepatocellular carcinoma tissues

value: patient 1


title: intratumoral HCC, bone metastasis, patient 2

description:
formalin-fixed, paraffin-embedded specimen
intratumoral tissuesof patient 2
intratumoral tissues BM


title: peritumoral HCC, bone metastasis, patient 1

description:
formalin-fixed, paraffin-embedded specimen
peritumoral tissues of patient 1
peritumoral tissues BM


title: nsrR mutant treated with NO replicate 1

city: Beaverton

first: Michiko

last: Nakano

state: OR

address: 20000 NW Walker Rd

institute: OHSU

description: gene expression from nsrR mutant treated with spermineNONOate

hyb_protocol: Crosslink arrays in UV Stratalinker and incubate in prehybridization buffer (5xSSC, 0.1% SDS, 1%BSA) at 42°C for 45 min.  Incubate with hybridization buffer (10xSSC, 0.1% SDS, 50% formamide, yeast tRNA, salmon testes DNA) overnight in hybridization chamber (Corning) in 42°C water bath. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on GenePix 4000B scanner (Axon Instruments Inc.) and images were processed and analyzed with Gene 3.0 software (Axon Instruments Inc.).

data_processing: Cy3 and Cy5 signals for each spot were normalized to the total Cy3 and Cy5 signals of the array. The total signal for each channel was calculated by summing the values of the total signals for each spot, which was calculated by multiplying the mean signal intensity (per pixel) by the number of pixels. Ratios were calculated only when the spot had a signal 1 standard deviation above background for 50% of pixels in each channel.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: anaerobic growth with pyruvate, treated with NO

label_protocol: 10 mg of total RNA were primed with 2.5 mg randome hexamers at 70°C for 10 min, cooled on ice for 5 min. Then add 500 mM each dATP, dCTP, dUTP with 100 mM dTTP, 400 mM aminoallyl-dUTP (Ambion), and 300 units SuperScript II Rtase (Invitrogen). Incubate at 25°C for 10 min, 42°C for 70 min, and 70°C for 15 min. After RNA hydrolysis and cleanup by Qiagen MinElute Purfication kit, pool an aliquote of each sample into one tube as reference. Add Cy3 to reference and Cy5 to sample reactions and incubate at room temperature in the dark for 1 hr.

growth_protocol: Cells were grown anaerobically until mid-log in 2xYT supplemented with 1% glucose and 0.2% nitrate (called NO3) or with 0.5% glucose and 0.5% pyruvate (called pyr)

extract_protocol: Qiagen Rneasy kit was used according to the manufacturer's instruction

treatment_protocol: One of pyruvate cultures above will be treated with 100mM spermine NONOate (called NO) for 1 hr

tag: genotype/variation

value: nsR

tag: treatment

source_name: pooled samples

value: Pooled all samples as reference


title: nsrR mutant grown with pyruvate replicate 3

description: gene expression from nsrR mutant during anaerobic fermentaion that does not generate endogenous NO

source_name: anaerobic growth with pyruvate until mid-log

value: anaerobic growth with pyruvate


title: nsrR mutant grown with pyruvate replicate 2


title: nsrR mutant grown with pyruvate replicate 1


title: EA.hy296_K12_rep2

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.

data_processing: We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).

source_name: EA.hy296 cells transduced with the K12/12 construct

label_protocol: GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.

growth_protocol: DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.

tag: cell line

tag: construct


title: EA.hy296_GFP_rep3

source_name: EA.hy296 cells transduced with the GFP construct

value: GFP


title: nsrR mutant grown with nitrate replicate 3

description: gene expression from nsrR mutant during nitrate respiration that generates endogenous NO

source_name: anaerobic growth with nitrate until mid-log

value: anaerobic growth with nitrate

tag: sample type


title: nsrR mutant grown with nitrate replicate 2


title: nsrR mutant treated with NO replicate 2

value: anaerobic growth with pyruvate, treated with NO


title: nsrR mutant treated with NO replicate 3


title: EA.hy296_K10_rep3

source_name: EA.hy296 cells transduced with the K10/12 construct


title: Whole blood TB_251485039458_1_3

description: TB whole blood RNA

value: Female


title: nsrR mutant grown with nitrate replicate 1


title: EA.hy296_K10_rep2


title: Whole blood TB_251485039458_1_2

description: TB whole blood RNA


title: Whole blood NID_251485039458_1_4

description: NID whole blood RNA


title: Whole blood NID_251485039457_1_3

description: NID whole blood RNA


title: EA.hy296_K12_rep3


title: Double_KO_Crush_Rep3

city: Boston

first: Tao

last: Lu

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

hyb_protocol: Cocktails containing 2.5ug fragmentated and biotin-labeled cDNA were hybridazed to the GeneChip@ Mouse Gene 1.0ST arrays for 16 hours. Arrays were washed and stained with the GeneChip Fludics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GCS 3007G

data_processing: Data from microarrays were log2 transformed at probe level and normalized using dChip. Statistical significance of gene expression differences between groups was determined by SAM (Significance Analysis of Microarrays) software.

source_name: Pten/Socs3 double KO_YFP17 mouse retinal neuron after crush

label_protocol: 0.05ug of total RNA from each sample was processed using Nugen Ovation WTA System

growth_protocol: In vivo YFP17 labeled mouse brain retinal cells, floxed with Rosa-lox-STOP-lox-Tomato at targeted genes (PTEN, SOCS3, or both)

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit

treatment_protocol: Two weeks following AAV-Cre injection, the left optic nerve was exposed intraorbitally and crushed with jeweler’s forceps for 5 seconds approximately 1 mm behind the optic disc.

tag: cell type

value: retinal neuron

tag: strain

value: Pten/Socs3 double KO

tag: protocol

value: left optic nerve was exposed intraorbitally and crushed ~1 mm behind optic disc


title: EA.hy296_K12_rep1


title: Whole blood LTBI_251485039458_1_1

description: LTBI whole blood RNA

value: Male


title: EA.hy296_K10_rep1


title: EA.hy296_GFP_rep2


title: Double_KO_Crush_Rep2


title: Double_KO_Crush_Rep1


title: Whole blood TB_251485039457_1_2

description: TB whole blood RNA

value: tuberculosis patients


title: Whole blood TB_251485039457_1_1

description: TB whole blood RNA


title: Whole blood TB_251485039457_1_4

description: TB whole blood RNA


title: wild type treated with NO replicate 2

description: gene expression from wild type treated with spermineNONOate


title: wild type treated with NO replicate 1


title: wild type treated with NO replicate 3


title: wild type grown with pyruvate replicate 3

description: gene expression from wild type during anaerobic fermentaion that does not generate endogenous NO


title: Whole blood LTBI_251485039456_1_3

description: LTBI whole blood RNA

value: healthy donors latently infected with M. tuberculosis


title: Whole blood NID_251485039456_1_4

description: NID whole blood RNA

value: healthy non-infected donors


title: wild type grown with pyruvate replicate 2


title: DG75_K12_rep3

source_name: DG75 cells transduced with the K12/12 construct


title: DG75_K12_rep1


title: Socs3_KO_Crush_Rep2

source_name: Socs3_KO_YFP17 mouse retinal neuron after crush