title: Donor 3, wt vs. Co

city: Konstanz

first: Sonja

last: von Aulock

address: POB M668

department: Biochemical Pharmacology

country: Germany

institute: University of Konstanz

description:
Donor 3. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450005

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQOR (TM) Immunology Microarrays Human Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) microarrays were done with the ScanArrayLite4000 Microarray Scanner (Packard-Biosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Median method. For normalisation, only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: whole blood, unstimulated

label_protocol: 1 µg T7-amplified RNA was labeled by reverse transcription with either Cy3-dCTPs or Cy5-dCTPs as described elsewhere (PMID: 8800675).

growth_protocol: Human blood was drawn from healthy volunteers into heparinized S-monovettes® (Sarstedt,Nümbrecht, Germany), diluted five-fold in RPMI 1640 medium (Biochrom, Berlin, Germany) and stimuli were added. The final volume was adjusted to 500 µl and the incubations were carried out in open polypropylene vials for 7 h at 37°C and 5% CO2. After 7 h incubation time, samples were resuspended by gentle shaking, and centrifuged at 400 x g for 2 min. The remaining cell pellet was resuspended and transferred to a 15 ml centrifugation tube (Greiner Bio-One) on ice. 5 ml erythrocyte lysis buffer (EL buffer, Qiagen, Hilden, Germany) was added to each sample and incubated for 10 min on ice. Samples were briefly vortexed twice during this time. The samples were centrifuged at 400 x g for 10 min at 4°C and the supernatant was discarded. The remaining leukocyte pellet was washed twice with PBS and stored at -80°C until RNA preparation.

extract_protocol: RNA was isolated following the NucleoSpin® RNA II protocol (Macherey-Nagel).

treatment_protocol: Human whole blood were either left unstimulated or treated for 7 hrs with 10 µg of LTA from SA113 wt, 10 µg of LTA from SA113 delta-lgt or 10 µg of PAM2Cys.

value: whole blood

value: peripheral blood mononuclear cells (PBMCs)

tag: stimulation

value: unstimulated control

tag: donor

source_name: whole blood, stimulated, LTA, wt

value: 10 µg of LTA from SA113 wt


title: Donor 3, lgt vs. Co

status: Public on Apr 05 2015

type: RNA

description:
Donor 3. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450006

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

source_name: whole blood, stimulated, LTA, delta-lgt mutant

value: 10 µg of LTA from SA113 delta-lgt mutant


title: Donor 3, PAM vs. Co

description:
Donor 3. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450012

source_name: whole blood, stimulated, PAM2Cys

value: 10 µg of PAM2Cys


title: Donor 1, wt vs. Co

description:
Donor 1. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 808.
6310078


title: Donor 4, wt vs. Co

description:
Donor 4. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450007


title: Donor 1, PAM vs. Co

description:
Donor 1. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450010


title: Donor 2, PAM vs. Co

description:
Donor 2. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450009


title: Donor 4, lgt vs. Co

description:
Donor 4. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450008


title: Donor 2, lgt vs. Co

description:
Donor 2. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450004


title: Donor 4, PAM vs. Co

description:
Donor 4. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450011


title: Donor 1, lgt vs. Co

description:
Donor 1. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 808.
6310080


title: Donor 2, wt vs. Co

description:
Donor 2. Stimulation for 7h, lysis of erythrocytes after 7h. RNA extraction done by Miltenyi Biotech.
Hybridized to array from batch 821.
6450002


title: AGM WSS-indo 36hrs rep3

city: Houston

first: Pamela

middle: L

last: Wenzel

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

country: USA

institute: University of Texas Health Science Center at Houston

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw signals of all the build-in controls were checked as quality control for the performance of the arrays. Sample-independent controls were used to check: a. Hybridization (control molecules at low, medium and high concentrations); b. Signal generation (background, noise, biotin labeling and hybridization at high and low stringency). Housekeeping genes were used as sample-dependent controls.  Background was subtracted and arrays were quantile normalized.

label: biotin

organism: Mus musculus

source_name: AGM WSS-indo 36hrs rep3

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

growth_protocol: Embryos from C57BL/6J timed pregnancies were microdissected for isolation of E10.5 AGM regions. Tissues were dissociated by treatment with Accutase (STEMCELL Technologies) at room temperature with gentle agitation for 20 minutes. Cells were resuspended in M5300 Myelocult medium (STEMCELL Technologies) enriched with HEPES (Invitrogen, 12.5 ml 1M HEPES/500 ml of Myelocult medium), non-Essential Amino Acids (Gibco), Sodium Pyruvate (Gibco), Penicillin 10 units/ml (Lonza) and Streptomycin 10 µg/ml (Lonza) without addition of hydrocortisone.

extract_protocol: Cells were directly lysed on microfluidic slides with RLT lysis buffer. Total RNA was immediately extracted with the QIAGEN RNeasy kit.

treatment_protocol: Microfluidics consisted of IBIDI VI^0.4 channel slides in line with a recirculating medium system driven by a single Harvard Apparatus PHD ULTRA 4400 with Remote syringe pump, 0.27 PSI crack pressure check valves (Qosina), and female luer lock three-way stop cocks (Qosina). After 6 to 8 hours of incubation, non-adherent cells were washed away and cells were cultured for 6 or 36 hours in static/low-flow conditions (0.0001 dyne/cm^2) or in the presence of WSS (5 dyne/cm^2).

tag: strain

tag: developmental stage

value: AGM

tag: duration of fluid flow

value: 36 hours

tag: force

value: 5 dyne/cm^2

tag: drug

value: indomethacin


title: AGM WSS 36hrs rep3

source_name: AGM WSS 36hrs rep3

value: vehicle


title: AGM WSS-indo 36hrs rep1

source_name: AGM WSS-indo 36hrs rep1


title: AGM WSS-indo 36hrs rep2

source_name: AGM WSS-indo 36hrs rep2


title: AGM WSS 36hrs rep2

source_name: AGM WSS 36hrs rep2


title: AGM static-indo 36hrs rep1

source_name: AGM static-indo 36hrs rep1


title: AGM WSS 36hrs rep1

source_name: AGM WSS 36hrs rep1


title: AGM static 36hrs rep1

source_name: AGM static 36hrs rep1


title: AGM static-indo 36hrs rep2

source_name: AGM static-indo 36hrs rep2


title: AGM static 36hrs rep2

source_name: AGM static 36hrs rep2


title: AGM WSS-indo 6hrs rep2

source_name: AGM WSS-indo 6hrs rep2

value: 6 hours


title: AGM WSS 6hrs rep3

source_name: AGM WSS 6hrs rep3


title: AGM static 6hrs rep2

source_name: AGM static 6hrs rep2


title: AGM static-indo 6hrs rep2

source_name: AGM static-indo 6hrs rep2


title: AGM WSS 6hrs rep1

source_name: AGM WSS 6hrs rep1


title: AGM static-indo 6hrs rep3

source_name: AGM static-indo 6hrs rep3


title: AGM WSS-indo 6hrs rep1

source_name: AGM WSS-indo 6hrs rep1


title: AGM static 36hrs rep3

source_name: AGM static 36hrs rep3


title: AGM WSS 6hrs rep2

source_name: AGM WSS 6hrs rep2


title: AGM static-indo 6hrs rep1

source_name: AGM static-indo 6hrs rep1


title: AGM WSS-indo 6hrs rep3

source_name: AGM WSS-indo 6hrs rep3


title: Blood_BASE Challenged_1

status: Public on Apr 04 2015

city: Lodi

first: Andrea

last: Trovato

address: Via Einstein

country: Italy

institute: Parco Tecnologico Padano

description: Bovine blood 12MPC 01

hyb_protocol: Four micrograms of labeled RNA were fragmented to a uniform size and hybridized to the custom array following the CustomArray 90K Microarray Hybridization and Imaging Protocol. Arrays were stripped and rehybridized using the CustomArray Stripping Kit for 90K (catalog number 610049) following the protocols of the manufacturer. Each array was used up to four times with no deterioration in signal or increase in background.

scan_protocol: The hybridized arrays were scanned with a GenePix 4000B microarray scanner (Axon, Toronto, CA), and images (TIF format) were exported to the CombiMatrix Microarray Imager Software, to perform a quality check of the hybridizations and the spots on the slide.

data_processing: Data were extracted and loaded into R using the Limma analysis package from Bioconductor, and the signal intensities were processed and normalized using standard procedures. Limma performs a linear regressionanalysis on the hybridizations, using a group means parameterization approach to compare the different conditions and perform a false discovery rate adjustment with Benjamini–Hochberg correction for multiple testing. DE genes were selected using an adjusted p value cutoff equal to .01.

organism: Bos taurus

source_name: Buffy Coat_BASE Challenged 1

label_protocol: 1 μg of total RNA was amplified and labeled with Cy5-ULS using the RNA Amplification and Labelling Kit from CombiMatrix (ampULSe catalog number GEA-022; Kreatech Biotechnology, Amsterdam, the Netherlands). All procedures were carried out according to the manufacturer’s protocols

extract_protocol: RNA was extracted using TRI-reagent (Sigma-Aldrich) following the instructions of the supplier.

treatment_protocol: The fresh blood was centrifuged at 250 × g for 20 min, the buffy coat was transferred to a new tube and contaminating red blood cells were lysed with 10ml of RBC Lysis Solution.

tag: breed

value: Holstein

tag: age

value: 16 Months

tag: gender

value: Female


title: MHCC97L with PML knockdown (replicate)

city: Shanghai

first: Xin

last: Zhang

state: -- Please select an option --

address: No.180 Fenglin Road, Zhongshan Hospital

country: China

institute: Liver Cancer Institution

description: Analysis used total RNA of control-siRNA transfected cells for comparison to the experimental samples with PML-siRNA.

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

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

source_name: PML knockdown using siRNA

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: MHCC97H/L cells were maintained in high-glucose Dulbecco’s modified Eagle medium (DMEM) or Minimum Essential Media (MEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin at 37°C in a humidified incubator under 5% carbon dioxide.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Transfection of PML-siRNA in MHCC97H/L cells was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions.

tag: cell line

source_name: control cells transfected with empty vector


title: Blood_Neg_2

description: Bovine blood 02

source_name: Buffy Coat_Neg_2


title: Blood_BASE Challenged_5

description: Bovine blood 12MPC 05

source_name: Buffy Coat_BASE Challenged 5


title: Blood_BASE Challenged_3

description: Bovine blood 12MPC 03

source_name: Buffy Coat_BASE Challenged 3


title: AGM static 6hrs rep1

source_name: AGM static 6hrs rep1


title: Blood_Neg_4

description: Bovine blood 04

source_name: Buffy Coat_Neg_4


title: Blood_Neg_5

description: Bovine blood 05

source_name: Buffy Coat_Neg_5


title: Blood_BASE Challenged_4

description: Bovine blood 12MPC 04

source_name: Buffy Coat_BASE Challenged 4


title: Blood_Neg_3

description: Bovine blood 03

source_name: Buffy Coat_Neg_3


title: Blood_Neg_1

description: Bovine blood 01

source_name: Buffy Coat_Neg_1


title: AGM static 6hrs rep3

source_name: AGM static 6hrs rep3


title: Blood_BASE Challenged_2

description: Bovine blood 12MPC 02

source_name: Buffy Coat_BASE Challenged 2


title: AGM static-indo 36hrs rep3

source_name: AGM static-indo 36hrs rep3


title: MHCC97L with PML knockdown


title: CB from bx mouse #125

status: Public on Apr 03 2015

city: San Francisco

first: William

middle: A.

last: Weiss

state: CA

address: 1450 3rd Street, HD-220

department: Neurology

institute: University of California, San Francisco

hyb_protocol: 200 ul of hybridization cocktail were injected into microarrays and hybridized at 45°C for 16 hr at 60 rpm.  Arrays were washed with fluidics station protocol: FS450_0001

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Expression was based on RMA values assessed using the Bioconductor XPS package in R on only core probes
RMA normalized values provided by XPS. Data are available in Series supplementary file "normalized.txt". The identifiers in the first column were matched to the Exon Cluster IDs (exon_id column of the GPL6193 platform table).

label: Biotin

source_name: backcrossed mouse, CB

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual using kit 900652.

growth_protocol: Superior Cervical Ganglia and Cerebellum were dissected from backcrossed mice at time of tumor harvest or 1 year of age

extract_protocol: Total RNA was extracted using Trizol and purified using the RNeasy mini kit.

value: Cerebellum, Right-Half

value: N1 generation of a backcross between TH-MYCN (FVB/NJ background) and wild-type 129/SvJ


title: CB from bx mouse #124


title: CB from bx mouse #123


title: Heart_day 2_rep3

city: Hong Kong

first: Lee

middle: Kenneth

last: Ka Ho

address: Rm126, Lo Kwee Seong Integrated Biomedical Science Building, CUHK, Shatin, N.T.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

hyb_protocol: Hybridization was performed on the microarray at 42℃ for 16 h and the slide was washed using the NimbleGen wash buffer kits

scan_protocol: The array slide was scanned using a NimbleGen MS 200 Microarray Scanner, which produced 532 nm TIFF images.

data_processing: The scanned images were imported into the DEVA software (Roche) to quantify the signal intensities of corresponding probes in the microarray

source_name: Heart, day 2 of postnatal stage

label_protocol: The resulting cDNA samples were labelled with Cy3 random nanomers using the NimbleGen One-Color DNA labelling kit (Roche NimbleGen, Madison, WI, USA) according to manufacturer’s instruction.

extract_protocol: Total RNA was isolated from mouse heart (three heart samples from 2- and 13-day-old mice) using an RNeasy Fibrous Tissue Mini Kit (Qiagen, USA), according to the manufacturer’s instructions.

value: ICR

value: Heart

value: day 2 of postnatal stage


title: Heart_day 13_rep3

source_name: Heart, day 13 of postnatal stage

value: day 13 of postnatal stage


title: CB from bx mouse #122


title: Heart_day 13_rep1


title: CB from bx mouse #121


title: Heart_day 2_rep1


title: U17 KD biological replicate 2

city: St Louis

first: Daniel

last: Ory

state: MO

address: Box 8086 660 S Euclid Ave

institute: Washington University

data_processing:
The Illumina GenomeStudio software (v2010) was used to generate signal intensity data and normalization with  including cubic spline method.
Cubic spline normalization is implemented to remove curvatures observed in scatter plots that arise from nonlinear relationships between samples or groups of samples when plotted in log space. This method initially divides the intensity distribution into a group of quantiles consisting of a similar number of gene intensities. Quantiles (q) are determined by letting where i equals array 1,2,3,...m and N is equal to total number of quantiles. By letting qi be a vector of N quantiles, then N = max (15, Nprobes/100) where Nprobes is the number of probes represented on a sample array. Using the scaling factor, the intensities from the sample array in a given quantile are adjusted to match the intensities from the virtual array. For two samples to be normalized to each other, cubic spline normalization scales the kth quantile of the sample array such that it is equal to the kth quantile of the virtual array. This scaling is repeated for each quantile. Genes with values that lie between quantiles are adjusted by interpolation of the neighboring quantiles. While this normalization is meant to address nonlinear relationships between samples in log space, it can also be used as a general normalization method.

source_name: NIH-3T3 cells

label_protocol: cDNA was prepared with oligodeoxyribose thymidine (oligo-dT) to select for poly-A RNA

extract_protocol: Total RNA were isolated by TRIzol reagent (Invitrogen) from WT, U17 snoRNA KD (ShSnhg3 stable clone), and U17 snoRNA OE (pMDβglobinU17b stable clone) cells grown in LPDS media for 24 hours, and integrity of RNA was assessed by BioAnalyzer 2100 (Agilent Technolgies)

tag: genotype/variation

value: U17 snoRNA knockdown


title: U17 KD biological replicate 3


title: CB from bx mouse #120


title: HM20 cells_untreated_rep1

city: Hsinchu

first: Jia-Lin

last: Lee

address: 101, Sec. 2, Kuang Fu Road

country: Taiwan

institute: National Tsing Hua University

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Lung cancer cell line A549_spheres_HM20_untreated

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit

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

value: Lung cancer

value: Mesenchymal type


title: Heart_day 2_rep2


title: LM cells_untreated_rep1

source_name: Lung cancer cell line A549_spheres_LM_untreated

value: Epithelial type


title: HTO_NIPP1-Pa_cell line Pa n°1_rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
Sample name: 6073
Cells: Hela-Tet-Off (Clontech) stably transfected with Flag-NIPP1_Pa_mut (deletion of the C-terminal part of NIPP1, AA330-351)

hyb_protocol: 28 pmol Cy3 incorporated dye was fragmented and resuspended in hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software (Agilent Technologies).

data_processing:
We use the Agilent processed signal values (i.e., feature gProcessedSignal) from Agilent Feature Extraction software and compute log2-intensities.  We remove Agilent control probes. In case of multiple probes for the same Agilent ID, log2-intensities are averaged.
The reported values are on log2-scale.

source_name: Hela-Tet-Off (Clontech) cells stably transfected with Flag-NIPP1_Pa_mut (deletion of the C-terminal part of NIPP1, AA330-351)

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

extract_protocol: HTO_parental was cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FCS and 250 Âµg/ml geneticin, HTO_NIPP1wt and HTO_NIPP1m were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FCS and 250 Âµg/ml geneticin, 200 Âµg/ml hygromycin and 50 ng/ml doxycyclin.  HTO_NIPP1wt and HTO_NIPP1m were cultured for 72 hours without doxycycline after which total RNA was isolated from all three cell lines using the Genelute Mammalian Total RNA Miniprep kit.


title: U17 KD biological replicate 4


title: HTO_NIPP1-Pa_cell line Pa n°2_rep3

description:
Sample name: 6680
Cells: Hela-Tet-Off (Clontech) stably transfected with Flag-NIPP1_Pa_mut (deletion of the C-terminal part of NIPP1, AA330-351)

value: Hela-Tet-Off (Clontech) cells stably transfected with Flag-NIPP1_Pa_mut (deletion of the C-terminal part of NIPP1, AA330-351)


title: CB from bx mouse #119


title: CB from bx mouse #118


title: CB from bx mouse #117


title: Heart_day 13_rep2


title: CB from bx mouse #115


title: CB from bx mouse #114


title: CB from bx mouse #113


title: CB from bx mouse #112


title: CB from bx mouse #111


title: HTO_NIPP1-Pa_cell line Pa n°2_rep4

description:
Sample name: 6684
Cells: Hela-Tet-Off (Clontech) stably transfected with Flag-NIPP1_Pa_mut (deletion of the C-terminal part of NIPP1, AA330-351)


title: LM cells_Wnt3A treated 24h_rep1

source_name: Lung cancer cell line A549_spheres_LM_Wnt3A_treated


title: CB from bx mouse #106


title: CB from bx mouse #105


title: CB from bx mouse #103


title: CB from bx mouse #107


title: CB from bx mouse #102


title: CB from bx mouse #104


title: CB from bx mouse #101


title: CB from bx mouse #096


title: CB from bx mouse #098


title: CB from bx mouse #116


title: CB from bx mouse #094


title: CB from bx mouse #091


title: CB from bx mouse #093


title: CB from bx mouse #092


title: CB from bx mouse #090


title: CB from bx mouse #089


title: CB from bx mouse #088


title: CB from bx mouse #087


title: CB from bx mouse #083


title: CB from bx mouse #082


title: WT biological replicate 3

value: WT


title: CB from bx mouse #080


title: CB from bx mouse #079


title: CB from bx mouse #081


title: U17 KD biological replicate 1


title: HM20 cells_Wnt3A treated 24h_rep1

source_name: Lung cancer cell line A549_spheres_HM20_Wnt3A_treated


title: CB from bx mouse #077


title: HTO_NIPP1-Pa_cell line Pa n°1_rep1

description:
Sample name: 6069
Cells: Hela-Tet-Off (Clontech) stably transfected with Flag-NIPP1_Pa_mut (deletion of the C-terminal part of NIPP1, AA330-351)


title: CB from bx mouse #076


title: CB from bx mouse #075


title: U17 OE biological replicate 3

value: U17 snoRNA overexpression


title: MHCC97H with PML knockdown (replicate)

source_name: PML knockdown using siRNA

source_name: control cells transfected with empty vector


title: WT biological replicate 1


title: U17 OE biological replicate 1


title: CB from bx mouse #073


title: WT biological replicate 2


title: MHCC97H with PML knockdown


title: CB from bx mouse #074


title: CB from bx mouse #069


title: CB from bx mouse #072


title: CB from bx mouse #068


title: WT biological replicate 4


title: CB from bx mouse #066


title: U17 OE biological replicate 4


title: CB from bx mouse #062


title: CB from bx mouse #067


title: CB from bx mouse #064


title: U17 OE biological replicate 2


title: CB from bx mouse #058


title: CB from bx mouse #059


title: CB from bx mouse #061


title: CB from bx mouse #054


title: CB from bx mouse #052


title: CB from bx mouse #050


title: CB from bx mouse #070


title: CB from bx mouse #049


title: CB from bx mouse #051


title: CB from bx mouse #046


title: CB from bx mouse #047


title: CB from bx mouse #048


title: CB from bx mouse #043


title: CB from bx mouse #065


title: CB from bx mouse #044


title: CB from bx mouse #063


title: CB from bx mouse #045


title: CB from bx mouse #041


title: CB from bx mouse #038


title: CB from bx mouse #042


title: CB from bx mouse #040


title: CB from bx mouse #057


title: CB from bx mouse #036


title: CB from bx mouse #037


title: CB from bx mouse #033


title: CB from bx mouse #031


title: CB from bx mouse #055


title: CB from bx mouse #027


title: CB from bx mouse #028


title: CB from bx mouse #030


title: CB from bx mouse #026


title: CB from bx mouse #024


title: CB from bx mouse #020


title: CB from bx mouse #018


title: CB from bx mouse #015


title: CB from bx mouse #023


title: CB from bx mouse #019


title: CB from bx mouse #014


title: CB from bx mouse #013


title: CB from bx mouse #012


title: CB from bx mouse #039


title: CB from bx mouse #008


title: CB from bx mouse #035


title: CB from bx mouse #011


title: CB from bx mouse #005


title: CB from bx mouse #004


title: SCG from bx mouse #125

source_name: backcrossed mouse, SCG

value: Total Superior Cervical Ganglia


title: CB from bx mouse #006


title: SCG from bx mouse #122


title: SCG from bx mouse #124


title: CB from bx mouse #025


title: SCG from bx mouse #123


title: SCG from bx mouse #119


title: CB from bx mouse #022


title: SCG from bx mouse #118


title: SCG from bx mouse #113


title: CB from bx mouse #010


title: SCG from bx mouse #111


title: SCG from bx mouse #112


title: SCG from bx mouse #115


title: SCG from bx mouse #107


title: SCG from bx mouse #116


title: SCG from bx mouse #114


title: CB from bx mouse #007


title: CB from bx mouse #003


title: SCG from bx mouse #104


title: SCG from bx mouse #106


title: SCG from bx mouse #105


title: SCG from bx mouse #103


title: SCG from bx mouse #121


title: SCG from bx mouse #094


title: SCG from bx mouse #098


title: SCG from bx mouse #102


title: SCG from bx mouse #101


title: SCG from bx mouse #120


title: SCG from bx mouse #096


title: SCG from bx mouse #092


title: SCG from bx mouse #089


title: SCG from bx mouse #093


title: SCG from bx mouse #088


title: SCG from bx mouse #091


title: SCG from bx mouse #117


title: SCG from bx mouse #090


title: SCG from bx mouse #083


title: SCG from bx mouse #081


title: SCG from bx mouse #082


title: SCG from bx mouse #077


title: SCG from bx mouse #076


title: SCG from bx mouse #075


title: SCG from bx mouse #074


title: SCG from bx mouse #079


title: SCG from bx mouse #072


title: SCG from bx mouse #073


title: SCG from bx mouse #069


title: SCG from bx mouse #067


title: SCG from bx mouse #063


title: SCG from bx mouse #068


title: SCG from bx mouse #061


title: SCG from bx mouse #087


title: SCG from bx mouse #055


title: SCG from bx mouse #056


title: SCG from bx mouse #058


title: SCG from bx mouse #052


title: SCG from bx mouse #066


title: SCG from bx mouse #064


title: SCG from bx mouse #065


title: SCG from bx mouse #062


title: SCG from bx mouse #070


title: SCG from bx mouse #059


title: SCG from bx mouse #057


title: SCG from bx mouse #054


title: SCG from bx mouse #043


title: SCG from bx mouse #080


title: SCG from bx mouse #051


title: SCG from bx mouse #050


title: SCG from bx mouse #049


title: SCG from bx mouse #046


title: SCG from bx mouse #048


title: Day 2 Control Replicate D vs. Box B Day 51 Replicate D

city: Kearney

first: Kimberly

middle: Ann

last: Carlson

state: NE

department: Biology

institute: University of Nebraska at Kearney

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 51 days of being in the box.

hyb_protocol: Prior to hybridization, the microarray slides were pre-hybridized for 45 minutes at 42°C in 3X SSC solution (3 M NaCl, 0.3 M sodium citrate, 1 mM EDTA) containing 1% bovine serum albumin.  The Cy3 and Cy5 probes were mixed together in 40 ul Ambion hybridization buffer #2 (Ambion). Blocking agents that included poly-dA (20 ug) and Cot-1 DNA (20 ug) were added.  Hybridization was performed overnight at 42°C.  After hybridization, the slides were washed 2x times with 2.0x SSC, 0.5% SDS at 42 degrees for 15 minutes, followed by washing 2x with 0.5x SSC, 0.50% SDS for 15 minutes each.

scan_protocol: Cy3 (532 nm) and Cy5 (635 nm) scans were performed using an ScanPix 4000B slide reader per manufacturer’s suggested conditions (Molecular Devices, Sunnyvale, CA).

data_processing: Following image capture, the overall images, as well as the individual spots, were assessed for uniformity of hybridization and individual integrity.  Problematic spots (i.e. bad morphology or those with aberrant hybridization properties) were flagged for subsequent removal from the final data set.  The intensity assessment for gene spots from 16 bit TIFF files was performed with the GenePix image analysis software (Molecular Devices).

organism: Drosophila melanogaster

source_name: Whole bodies of Drosophila melanogaster females

label_protocol: Indirect labeling with Cy3/Cy5 fluorescent dyes was performed using 12 ug of total RNA per sample using the Superscript Indirect cDNA Labeling System for DNA microarrays.

tag: population

value: Outbred population

tag: day

tag: replicate

value: D

tag: box

value: B


title: SCG from bx mouse #040


title: SCG from bx mouse #045


title: CB from bx mouse #056

value: Cerebellum, Right-Half


title: Day 2 Control Replicate D vs. Box B Day 9 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 9 days of being in the box.


title: Day 2 Control Replicate D vs. Box B Day 79 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 79 days of being in the box.


title: SCG from bx mouse #039

value: N1 generation of a backcross between TH-MYCN (FVB/NJ background) and wild-type 129/SvJ


title: Day 2 Control Replicate D vs. Box B Day 23 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 23 days of being in the box.


title: Day 2 Control Replicate D vs. Box B Day 37 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 37 days of being in the box.


title: SCG from bx mouse #044


title: SCG from bx mouse #042


title: SCG from bx mouse #047


title: Day 2 Control Replicate C vs. Box A Day 9 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 16 days of being in the box.

value: C

value: A


title: SCG from bx mouse #041


title: Day 2 Control Replicate D vs. Box B Day 72 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 72 days of being in the box.


title: Day 2 Control Replicate D vs. Box B Day 65 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 65 days of being in the box.


title: Day 2 Control Replicate D vs. Box B Day 58 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 58 days of being in the box.


title: Day 2 Control Replicate D vs. Box B Day 44 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 44 days of being in the box.


title: SCG from bx mouse #037


title: Day 2 Control Replicate D vs. Box B Day 30 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 30 days of being in the box.


title: Day 2 Control Replicate D vs. Box B Day 16 Replicate D

description: Biological Replicate D.  Collected after 2 days of being in the box vs. Box B Control Replicate D, which was collected after 16 days of being in the box.


title: Day 2 Control Replicate C vs. Box A Day 58 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 58 days of being in the box.


title: SCG from bx mouse #038


title: Day 2 Control Replicate C vs. Box A Day 30 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 30 days of being in the box.


title: SCG from bx mouse #031


title: Day 9 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 9 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: Day 2 Control Replicate C vs. Box A Day 16 Replicate C


title: Day 2 Control Replicate C vs. Box A Day 79 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 79 days of being in the box.


title: Day 9 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 9 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: Day 2 Control Replicate C vs. Box A Day 65 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 65 days of being in the box.


title: Day 2 Control Replicate C vs. Box A Day 72 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 72 days of being in the box.


title: SCG from bx mouse #036


title: Day 2 Control Replicate C vs. Box A Day 37 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 37 days of being in the box.


title: SCG from bx mouse #035


title: SCG from bx mouse #033


title: Day 2 Control Replicate C vs. Box A Day 44 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 44 days of being in the box.


title: Day 79 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 79 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.

value: combinedreplicates


title: SCG from bx mouse #026


title: eCeN11

type: genomic

city: Beijing

first: Qun

last: Gao

state: Beijing

address: Shuang Qing Road

department: Environmental sicence and engineering

institute: Tsinghua University

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 11

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

molecule: genomic DNA

organism: uncultured bacterium

source_name: Soil microbes in BioCON plots

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: carbon and nitrogen levels

value: enriched CO2, enriched N2


title: Day 2 Control Replicate C vs. Box A Day 23 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 23 days of being in the box.


title: Day 72 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 72 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 72 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 72 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: SCG from bx mouse #030

tag: tissue


title: Day 9 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 9 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: eCeN10

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 10

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.


title: SCG from bx mouse #028


title: Day 79 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 79 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: Day 9 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 9 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 2 Control Replicate C vs. Box A Day 51 Replicate C

description: Biological replicate C.  Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 51 days of being in the box.


title: Day 72 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 72 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: eCeN9

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 9


title: eCeN12

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 12


title: SCG from bx mouse #027


title: Day 79 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 79 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: Day 65 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 65 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: Day 79 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 79 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: SCG from bx mouse #022


title: eCeN6

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 6


title: SCG from bx mouse #020


title: SCG from bx mouse #025


title: SCG from bx mouse #023


title: eCeN4

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 4


title: Day 65 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 65 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: SCG from bx mouse #018


title: Day 65 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 65 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 58 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 58 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: Day 72 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 72 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: Day 51 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 51 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: Day 65 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 65 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: Day 51 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 51 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: eCeN8

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 8


title: eCeN3

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 3


title: Day 58 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 58 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: eCeN7

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 7


title: Day 44 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 44 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 58 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 58 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: SCG from bx mouse #015


title: Day 51 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 51 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: Fibroblast_control4_rep1

city: SAO PAULO

first: JOAO PAULO

last: KITAJIMA

state: SP

address: RUA CUBATAO 86 CJ 1602

country: Brazil

institute: MENDELICS

hyb_protocol: 10ug de cRNA were hybridized for 17h at 45˚C. GeneChips were washed and stained in Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console using Sketch-Quantile as normalization method. Analysis was performed using rma-gene-default as parameter for affymetrix-algorithm-param-apt-opt-analysis-name. #%affymetrix-algorithm-param-apt-opt-analysis-spec was specified as rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true.subsetmd5=5d3721419adb28afd03b764858482c6b,pm-only,med-polish.expon=false.attenuate=true.l=0.005.h=-1,expr.genotype=false.strand=false.

source_name: Fibroblast control

label_protocol: Not provided.

extract_protocol: TRIZOL® reagent (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: Healthy

value: Skin fibroblast


title: Day 44 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 44 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: eCeN1

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 1


title: Fibroblast_control2_rep1


title: aCeN12

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 12

value: ambient CO2, enriched N2


title: SCG from bx mouse #019

tag: strain


title: Day 58 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 58 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 51 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 51 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: SCG from bx mouse #010


title: Day 37 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 37 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 44 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 44 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: Fibroblast_control1_rep1


title: Day 37 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 37 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: SCG from bx mouse #008


title: SCG from bx mouse #014


title: Day 44 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 44 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: eCeN2

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 2


title: SCG from bx mouse #013


title: aCeN9

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 9


title: eCeN5

description: GeoChip data for soil sample collected at enriched CO2, enriched N2, replicate 5


title: SCG from bx mouse #012


title: SCG from bx mouse #011


title: aCeN8

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 8


title: aCeN11

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 11


title: Day 37 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 37 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: Day 37 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 37 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: aCeN6

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 6


title: SCG from bx mouse #005


title: Fibroblast_patient3_rep1

source_name: Fibroblast SPOAN patient

value: SPOAN (spastic paraplegia, optic atrophy, and neuropathy) syndrome


title: Fibroblast_patient2_rep1


title: aCeN10

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 10


title: Fibroblast_patient1_rep1


title: SCG from bx mouse #007


title: SCG from bx mouse #004


title: aCeN5

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 5


title: Fibroblast_patient4_rep1


title: Day 30 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 30 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: SCG from bx mouse #006


title: aCeN2

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 2


title: aCeN7

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 7


title: Day 30 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 30 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: Day 23 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 23 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: Day 30 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 30 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: SCG from bx mouse #003


title: aCeN4

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 4


title: SCG from bx mouse #024


title: Day 23 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 23 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.


title: aCeN1

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 1


title: Day 23 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 23 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: Day 30 All replicates combined vs. Box A Day 2 Control Replicate B

description: All replicates collected after 30 days of being in the box were combined vs. Box A Control Replicate B, which was collected after 2 days of being in the box.


title: aCeN3

description: GeoChip data for soil sample collected at ambient CO2, enriched N2, replicate 3


title: eCaN11

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 11

value: enriched CO2, ambient N2


title: eCaN12

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 12


title: Day 23 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 23 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: eCaN8

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 8


title: Day 16 Replicate C vs. Box B Day 2 Control Replicate C

description: Biological replicate C.  Collected after 16 days of being in the box vs. Box B Control Replicate C, which was collected after 2 days of being in the box.


title: eCaN7

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 7


title: C-CAFs_Late_ICI_rep1

city: Bangalore

last: Jayshree

state: Karnataka

address: Dr. M.H Marigowda Road, Hombegowda Nagar

department: Department of Microbiology

country: India

institute: Kidwai Memorial Institute of Oncology

description: Sample name: Late_ICI_NI3

hyb_protocol: Labeled cRNA  of 600 ηg were fragmented at 60 ºC and hybridized onto a Agilent designed Custom Human GXP 8x60K (AMADID No: 027114) arrays. Fragmentation and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, Insitu Hybridization kit, Part Number 5190-0404). Hybridization was performed in Agilent’s Surehyb Chambers at 65 ºC for 16 hours.

scan_protocol: The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327), and scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Data extraction from scanned images was done using Agilent Feature Extraction software. Using R-package (version2.1.2.1), the Feature Extraction result files were subjected to background correction using normexp function, Quantile normalization was performed, and the replicate probes were averaged. Normalization, pre-processing and differential analysis was implemented in the Bioconductor package Linear Models for MicroArray (LIMMA). Genes expressed differentially with a p-value threshold of 0.05 were considered significant.

source_name: Late stage cervical cancer associated fibroblasts, ICI treated, replicate 1

label_protocol: The samples were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA of 500ηg was reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. The double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated. The cDNA synthesis and in-vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned using Qiagen RNesay columns (Qiagen, Cat No: 74106), and the quality was assessed using Nanodrop ND-1000.

growth_protocol: Tumor tissues of SCC cervix were minced into small, fine pieces of 1mm to 5mm using sterile scalpel and tweezers. The pieces were placed in 35mmx15mm culture dishes and incubated at 37°C for 30 minutes for adherence. After 30 min incubation, 2ml of DMEM (Catalogue No. D7777, Sigma) and 10% Fetal Bovine Serum (FBS) (Catalogue. No. 10099-141, Gibco®, N.Y, USA) was added. These tissue pieces were cultured for 7 days at 37°C in the presence of 5% CO2. After 7 days, the non-adherent cells were removed from the culture dish and adherent cells were dispersed by adding 0.025% trypsin (Catalogue No. 25200-056, Gibco®) for 2min, and the loosely adhered fibroblasts were dispersed easily. The dispersed fibroblast cells were collected and seeded into fresh 60x15mm tissue culture dishes and incubated for 5 days. A 3rd passage of fibroblasts culture was done similarly.

extract_protocol: Total RNA was isolated from C-CAFs using the total RNA isolation kit (Catalogue No. 80204; Qiagen, Valencia, CA). RNA was reverse transcribed using oligodT and Moloney Murine Leukaemia Virus reverse transcriptase (Catalogue No. 210210; Qiagen).

treatment_protocol: Cervical cancer CAFs were seeded into 60x15mm tissue culture dishes, and were allowed to reach 60-70% confluency. The cultured C-CAFs were incubated for 3 days either of the ER antagonists, ICI 182,780 (1.835μM) or MPP (1μM), while E2 (3.67ηM) cultured C-CAFs served as a control.

value: Cervical cancer - SCC

tag: disease stage

value: Stage IIIA

tag: cell-type

value: Cancer Associated Fibroblasts (CAFs)

tag: treatment

value: ICI (ER-alpha antagonist)


title: C-CAFs_Late_ICI_rep2

description: Sample name: Late_ICI_NI4

source_name: Late stage cervical cancer associated fibroblasts, ICI treated, replicate 2


title: C-CAFs_Early_ICI_rep2

description: Sample name: Early_ICI_NI2

source_name: Early stage cervical cancer associated fibroblasts, ICI treated, replicate 2

value: Stage IB2


title: Day 16 Replicate A vs. Box A Day 2 Control Replicate A

description: Biological replicate A.  Collected after 16 days of being in the box vs. Box A Control Replicate A, which was collected after 2 days of being in the box.

value: Outbred population

value: B


title: C-CAFs_Early_ICI_rep1

description: Sample name: Early_ICI_NI1

source_name: Early stage cervical cancer associated fibroblasts, ICI treated, replicate 1


title: eCaN10

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 10


title: Day 16 Replicate B vs. Box B Day 2 Control Replicate B

description: Biological replicate B.  Collected after 16 days of being in the box vs. Box B Control Replicate B, which was collected after 2 days of being in the box.


title: C-CAFs_Early_MPP_rep1

description: Sample name: Early_MPP_MJA2

source_name: Early stage cervical cancer associated fibroblasts, MPP treated, replicate 1

value: MPP (ER-alpha antagonist)


title: eCaN5

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 5


title: eCaN9

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 9


title: Fibroblast_control3_rep1


title: eCaN4

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 4


title: C-CAFs_Early_MPP_rep2

description: Sample name: Early_MPP_MJB2

source_name: Early stage cervical cancer associated fibroblasts, MPP treated, replicate 2


title: eCaN3

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 3


title: Day 16 All replicates combined vs. Box A Day 2 Control Replicate B


title: C-CAFs_Early_E2_rep4

description: Sample name: Early_E2_EJB1

source_name: Early stage cervical cancer associated fibroblasts, E2 treated (control), replicate 4

value: Estrogen (E2)


title: C-CAFs_Late_E2_rep2

description: Sample name: Late_E2_NS6

source_name: Late stage cervical cancer associated fibroblasts, E2 treated (control), replicate 2


title: C-CAFs_Early_E2_rep1

description: Sample name: Early_E2_NS3

source_name: Early stage cervical cancer associated fibroblasts, E2 treated (control), replicate 1


title: LNCaP-ABL KD1 Biological replicate 4

first: Akash

middle: Kumar

last: Kaushik

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Standard Affimatrix protocol were used at Affymetrix and Microarray Core Facility at UMICH using IVT express kit.

scan_protocol: Standard Affimatrix protocol were used at Affymetrix and Microarray Core Facility at UMICH.

data_processing: calculated expression values for each gene using a robust multi-array average (RMA) Irizarry et al. (2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data.

source_name: LNCaP-ABL cells with GNPNAT1 shRNA 1

growth_protocol: 22RV1 and LNCaP-ABL were grown in RPMI 1640 medium with 10 % full or charcoal stripped FBS  and with or without phenol red respectively. 100 ug/ml of Normocin was added to all the cell culture media

extract_protocol: We used RNeasy Mini Kit from QIAGEN for total RNA extraction according to the manusfacturer's protocol

treatment_protocol: To generate stable GNPNAT1 KD in 22RV1, LNCaP-ABL and C42 cells, lentiviral transduction of GNPNAT1 shRNA (Sigma Aldrich (Product# CSTVRS), two independent shRNA clones) was carried out using a virus titer of 5 MOI and cells were selected using 0.5ug/ml puromycin

value: LNCaP-ABL

tag: lentivirus

value: GNPNAT1 shRNA 1

tag: sample type

value: CRPC, contains AR-FL


title: LNCaP-ABL KD5 Biological replicate 1

source_name: LNCaP-ABL cells with GNPNAT1 shRNA 5

label_protocol: Standard Affimatrix protocol were used at Affymetrix and Microarray Core Facility at UMICH using IVT express kit.

value: GNPNAT1 shRNA 5


title: LNCaP-ABL KD5 Biological replicate 2


title: eCaN1

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 1


title: LNCaP-ABL KD1 Biological replicate 3


title: LNCaP-ABL KD1 Biological replicate 2


title: eCaN6

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 6


title: D_rep3

city: Vienna

first: Pawel

middle: P.

last: Labaj

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: Boku University Vienna

description: MAQC-III sample D

hyb_protocol: 10 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) were fragmented at 70°C for 5 minutes in a reaction volume of 250 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 µl of 2x GExAgilent hybridization buffer were added to the fragmentation mixture and hybridized to Agilent SurePrint Custom GE 1 Million microarrays (Agilent # G4860A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). The slides were dried after removing them slowly from Wash buffer 2 solution.

scan_protocol: Microarrays were scanned with an Agilent G2505C Microarray scanner using one color scan settings (scan area 61mmx21.6 mm) at a resolution of 2 µm  in double pass scanning. The dye channel was set to Green and Green PMT was set to 100% to yield a high-sensitivity 20 bit TIFF image. A second scan at a lower PMT yield proved unnecessary for these hybridizations.

data_processing: Agilent Feature Extraction Software (v10.10.1.1) was applied with the default parameters appropriate for the chip type (1M feature array; protocol GE1_1010_Sep10 and Grid 039825_D_F_20120329), unprocessed median spot intensities without background subtraction were exported. We applied the published HOOK algorithm for saturation detrending and the FARMS algorithm for expression level estimates from probe groups.

source_name: mix of total RNA of samples A and B in ratio 1:3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng total RNA using the Agilent kit for One-Color Microarray-Based Exon Analysis Low Input Quick Amp WT labeling (Agilent V 1.0, November 2010) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.

extract_protocol: mixing of total RNA in known ratios

tag: seqc sample

value: D

tag: mixing ratio


title: D_rep4

description: MAQC-III sample D


title: aCaN12

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 12

value: ambient CO2, ambient N2


title: eCaN2

description: GeoChip data for soil sample collected at enriched CO2, ambient N2, replicate 2


title: aCaN11

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 11


title: D_rep2

description: MAQC-III sample D


title: aCaN10

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 10


title: C-CAFs_Early_E2_rep3

description: Sample name: Early_E2_EJA1

source_name: Early stage cervical cancer associated fibroblasts, E2 treated (control), replicate 3


title: C_rep4

description: MAQC-III sample C

source_name: mix of total RNA of samples A and B in ratio 3:1

value: C


title: D_rep1

description: MAQC-III sample D


title: C-CAFs_Late_E2_rep1

description: Sample name: Late_E2_NS5

source_name: Late stage cervical cancer associated fibroblasts, E2 treated (control), replicate 1


title: aCaN9

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 9

source_name: Soil microbes in BioCON plots


title: aCaN8

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 8


title: aCaN7

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 7


title: aCaN6

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 6


title: C_rep2

description: MAQC-III sample C


title: C_rep3

description: MAQC-III sample C


title: aCaN5

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 5


title: LNCaP-ABL KD1 Biological replicate 1


title: B_rep4

description: MAQC-III sample B

source_name: Human Brain Reference RNA (HBRR, Ambion) + ERCC Mix2 = Sample B


title: C_rep1

description: MAQC-III sample C


title: B_rep3

description: MAQC-III sample B


title: LNCaP-ABL NT Biological replicate 3

source_name: LNCaP-ABL cells with scrambled shRNA

value: scrambled shRNA


title: B_rep2

description: MAQC-III sample B


title: LNCaP-ABL NT Biological replicate 2


title: C-CAFs_Early_E2_rep2

description: Sample name: Early_E2_NS4

source_name: Early stage cervical cancer associated fibroblasts, E2 treated (control), replicate 2

value: Cervical cancer - SCC


title: 22Rv1 KD5 Biological replicate 4

source_name: 22Rv1 cells with GNPNAT1 shRNA 5

value: CRPC, contains AR-V7


title: 22Rv1 KD5 Biological replicate 2


title: LNCaP-ABL NT Biological replicate 4


title: 22Rv1 KD5 Biological replicate 3


title: B_rep1

description: MAQC-III sample B


title: 22Rv1 KD1 Biological replicate 3

source_name: 22Rv1 cells with GNPNAT1 shRNA 1


title: 22Rv1 KD1 Biological replicate 4


title: 22Rv1 KD5 Biological replicate 1


title: A_rep4

description: MAQC-III sample A

source_name: Universal Human Reference RNA (UHRR, Stratagene) + ERCC Mix1 = Sample A

value: A


title: aCaN3

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 3


title: aCaN1

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 1


title: aCaN4

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 4


title: 22RV1 NT Biological replicate 4

source_name: 22Rv1 cells with scrambled shRNA


title: 22Rv1 KD1 Biological replicate 2


title: A_rep3

description: MAQC-III sample A


title: A_rep2

description: MAQC-III sample A


title: A_rep1

description: MAQC-III sample A


title: 22Rv1 KD1 Biological replicate 1


title: 22RV1 NT Biological replicate 3


title: 22RV1 NT Biological replicate 2


title: 22RV1 NT Biological replicate 1


title: B2bex

status: Public on Apr 02 2015

city: Tokyo

first: Naoomi

last: Tominaga

address: 5-1-1 Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research institute

hyb_protocol: Agilent miRNA expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies Scanner G2505C at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 046064_D_F_20121223) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: extracellular vesicles from breast cancer cell line

label_protocol: 100 ng of total RNA was used by Agilent’s miRNA Complete Labeling and Hybridization Kit

extract_protocol: Total RNA was extracted using the QIAzol reagent and the miRNeasy Mini Kit (Qiagen)

treatment_protocol: miRNA expression in extracellular vesicles was collected from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.

tag: cell line

tag: collected from cell line

value: extracellular vesicles


title: H1ex


title: PBMC_85

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: Sample name: 8473515044_K

hyb_protocol: After a second Ribogreen quant and normalization step, amplified and labeled cRNA is  hybridized overnight at 58C to the expression arrays. Hybridization is followed by washing, blocking, staining (Cy3-Streptavidin) and drying on the Little Dipper processor.

scan_protocol: Array chips were scanned on the iScan reader.

data_processing:
Expression data is extracted and compiled using BeadStudio software (Illumina) and extracted (un-normalized) data are reported.  See 'non-normalized_data.txt' linked as supplementary file on Series record.
Illumina BeadStudio software outputs the average read intensity for beads corresponding to each probe.

source_name: Peripheral blood monocytes

label_protocol: All total RNA samples are quanted using a Ribogreen fluorescent assay and normalized to 10 ng/ul prior to amplification. Amplified and labeled cRNA is produced using the Illumina specific Ambion TotalPrep kit. 1st and 2nd strand cDNA is produced using the Ambion kit and purified using a robotic assisted magnetic capture step. Biotinylated cRNA is produced from the cDNA template in a reverse transcription reaction. Typical yields are in excess of 1.5 ug.

extract_protocol: 24ml of fresh blood was collected from participants. Blood was drawn into three 8 mL Cell Preparation Tubes (CPT) containing sodium citrate. Peripheral blood mononuclear cells (PBMCs) were then isolated through centrifugation within 6 hours of collection (Salazar-Gonzalez et al., 1997). PBMCs were washed with phosphate buffered saline, and then monocytes were isolated through Rosette separation (RosetteSep®; Stem Cell Technologies) according to the manufacturer instructions). Monocytes were then pelleted, lysed, and RNA extracted using the Qiagen RNeasy kit including a DNase treatment to eliminate any potentially confounding genomic DNA contamination(Shay et al., 2003). RNA was stored at -80°C

tag: developmental stage

value: adult

tag: disease state

value: HIV+

value: Peripheral blood monocytes

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: B2aex

tag: cell line

tag: collected from cell line


title: PBMC_80

description: Sample name: 8473515044_C

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: artdate

tag: vload

tag: cnspengrp


title: PBMC_82

description: Sample name: 8473515044_E

tag: developmental stage

tag: disease state

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_79

description: Sample name: 8473515044_B

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: artdate

tag: vload

tag: cnspengrp


title: H2LNex

tag: cell line

tag: collected from cell line


title: PBMC_78

description: Sample name: 8473515041_L

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_84

description: Sample name: 8473515044_I

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: artdate

tag: vload

tag: cnspengrp


title: PBMC_77

description: Sample name: 8473515041_K

tag: cell type

tag: batch

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_81

description: Sample name: 8473515044_D

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: artdate

tag: vload

tag: cnspengrp


title: PBMC_76

description: Sample name: 8473515041_J

tag: cell type

tag: batch

tag: bmi

tag: weight

tag: cesd

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc


title: PBMC_86

description: Sample name: 8473515044_L

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_73

description: Sample name: 8473515041_G

tag: cell type

tag: batch

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_74

description: Sample name: 8473515041_H

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: height

tag: osteodt

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_75

description: Sample name: 8473515041_I

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_68

description: Sample name: 8473515041_A

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_69

description: Sample name: 8473515041_B

tag: cell type

tag: batch

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_72

description: Sample name: 8473515041_F

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_64

description: Sample name: 8292044074_I

tag: cell type

tag: batch

tag: bmi

tag: weight

tag: cesd

tag: pddate

tag: osteodt

tag: haartdate

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_62

description: Sample name: 8292044074_G

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_67

description: Sample name: 8292044074_L

tag: developmental stage

tag: disease state

tag: cell type

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_70

description: Sample name: 8473515041_C

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_60

description: Sample name: 8292044074_E

tag: developmental stage

tag: disease state

tag: cell type

tag: cesd

tag: pddate

tag: haartdate

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_71

description: Sample name: 8473515041_E

tag: developmental stage

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: osteodt

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_66

description: Sample name: 8292044074_K

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club

tag: hash

tag: cocaine


title: PBMC_63

description: Sample name: 8292044074_H

tag: developmental stage

tag: date

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_65

description: Sample name: 8292044074_J

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club


title: PBMC_61

description: Sample name: 8292044074_F

tag: developmental stage

tag: date

tag: lastedcat

tag: age

tag: height

tag: pddate

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_56

description: Sample name: 8292044073_L

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club


title: PBMC_55

description: Sample name: 8292044073_K

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: pddate

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_54

description: Sample name: 8292044073_J

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club


title: aCaN2

description: GeoChip data for soil sample collected at ambient CO2, ambient N2, replicate 2

tag: carbon and nitrogen levels


title: PBMC_53

description: Sample name: 8292044073_I

tag: developmental stage

tag: disease state

tag: cell type

tag: lastedcat

tag: age

tag: height

tag: pddate

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_58

description: Sample name: 8292044074_C

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: club


title: PBMC_47

description: Sample name: 8292044073_B

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_50

description: Sample name: 8292044073_F

tag: cell type

tag: batch

tag: svisit

tag: date

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol


title: PBMC_45

description: Sample name: 8292044059_K

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc


title: PBMC_52

description: Sample name: 8292044073_H

tag: cell type

tag: batch

tag: svisit

tag: date

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_48

description: Sample name: 8292044073_C

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc


title: PBMC_46

description: Sample name: 8292044059_L

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor


title: PBMC_49

description: Sample name: 8292044073_E

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: ghb

tag: anycancer


title: PBMC_41

description: Sample name: 8292044059_E

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor


title: PBMC_57

description: Sample name: 8292044074_B

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: ghb

tag: anycancer


title: PBMC_51

description: Sample name: 8292044073_G

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor


title: PBMC_38

description: Sample name: 8292044059_B

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: osteodt

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: ghb

tag: anycancer


title: PBMC_42

description: Sample name: 8292044059_F

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor


title: PBMC_40

description: Sample name: 8292044059_D

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc

tag: ghb

tag: anycancer


title: PBMC_29

description: Sample name: 7649540069_A

tag: cell type

tag: batch

tag: svisit

tag: date

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor


title: PBMC_33

description: Sample name: 7649540069_F

tag: developmental stage

tag: disease state

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc


title: PBMC_35

description: Sample name: 7649540069_H

tag: cell type

tag: batch

tag: svisit

tag: date

tag: cesd

tag: pddate

tag: haartdate

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_32

description: Sample name: 7649540069_E

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc


title: PBMC_44

description: Sample name: 8292044059_I

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_39

description: Sample name: 8292044059_C

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: heroin

tag: halluc


title: PBMC_27

description: Sample name: 7602346090_K

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: echlor


title: PBMC_43

description: Sample name: 8292044059_H

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: height

tag: pddate

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: club

tag: hash

tag: cocaine

tag: ghb

tag: anycancer


title: PBMC_83

description: Sample name: 8473515044_F

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor


title: PBMC_36

description: Sample name: 7649540069_J

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: ghb

tag: anycancer


title: PBMC_34

description: Sample name: 7649540069_G

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor


title: PBMC_28

description: Sample name: 7602346090_L

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: ghb

tag: anycancer


title: PBMC_31

description: Sample name: 7649540069_C

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor


title: PBMC_24

description: Sample name: 7602346090_H

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: height

tag: pddate

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: club

tag: hash

tag: cocaine

tag: ghb

tag: anycancer


title: PBMC_22

description: Sample name: 7602346090_D

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor


title: PBMC_21

description: Sample name: 7602346090_B

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: ghb

tag: anycancer


title: PBMC_30

description: Sample name: 7649540069_B

tag: svisit

tag: date

tag: bmi

tag: weight

tag: cesd

tag: pddate

tag: haartdate

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor


title: PBMC_37

description: Sample name: 8292044059_A

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: height

tag: race

tag: hivdate

tag: fromscyr

tag: vload

tag: club

tag: hash

tag: cocaine

tag: ghb

tag: anycancer


title: PBMC_25

description: Sample name: 7602346090_I

tag: developmental stage

tag: disease state

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor


title: PBMC_17

description: Sample name: 7602346077_H

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: pddate

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: club

tag: hash

tag: cocaine


title: PBMC_12

description: Sample name: 7602346077_C

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: cesd

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: smoke

tag: cnsinf

tag: hivneuro

tag: alcohol

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_15

description: Sample name: 7602346077_F

tag: developmental stage

tag: disease state

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: osteodt

tag: race

tag: hivdate

tag: fromscyr

tag: haartdate

tag: vload

tag: club

tag: hash

tag: cocaine


title: PBMC_11

description: Sample name: 7602346077_A

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: artdate

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: anycancer


title: PBMC_23

description: Sample name: 7602346090_G

tag: svisit

tag: date

tag: lastedcat

tag: age

tag: bmi

tag: height

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: heroin

tag: halluc

tag: echlor

tag: ghb


title: PBMC_16

description: Sample name: 7602346077_G

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash

tag: cocaine

tag: anycancer


title: PBMC_20

description: Sample name: 7602346090_A

tag: date

tag: lastedcat

tag: age

tag: height

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: heroin

tag: halluc

tag: echlor

tag: ghb


title: PBMC_26

description: Sample name: 7602346090_J

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: bmi

tag: weight

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBMC_59

description: Sample name: 8292044074_D

tag: date

tag: lastedcat

tag: age

tag: height

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_19

description: Sample name: 7602346077_L

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: bmi

tag: weight

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBMC_9

description: Sample name: 7602346063_J

tag: date

tag: lastedcat

tag: age

tag: height

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_14

description: Sample name: 7602346077_E

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: bmi

tag: weight

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBM_PM_Nb25

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Standard Illumina Scanning protocol

data_processing: With GenomeStudio GX (version 1.5.4) we extracted from each array the background-corrected, summarized expression levels (AVG Signal), standard errors of the bead replicates (BEAD STERR), number of beads used (Avg NBEADS) and detection scores (Detection Pval). Subsequently, we applied a variance stabilizing transformation and a quantile normalization in R, as implemented in the lumi-package from Bioconductor.

source_name: peripheral blood monocytes, metastatic patient

label_protocol: Biotynilated cRNA was prepared with Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser, and quantification with Nanodrop.

tag: tumor stage

value: metastatic patient

tag: gender

value: F

tag: age


title: PBM_P_Nb40

source_name: peripheral blood monocytes, non-metastatic patient

value: non-metastatic patient


title: PBM_PM_Nb23


title: PBMC_18

description: Sample name: 7602346077_J

tag: developmental stage

tag: disease state

tag: cell type

tag: date

tag: lastedcat

tag: height

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_10

description: Sample name: 7602346063_L

tag: developmental stage

tag: disease state

tag: batch

tag: svisit

tag: age

tag: bmi

tag: weight

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBMC_4

description: Sample name: 7602346063_B

tag: cell type

tag: date

tag: lastedcat

tag: height

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBMC_7

description: Sample name: 7602346063_F

tag: developmental stage

tag: disease state

tag: batch

tag: svisit

tag: age

tag: bmi

tag: weight

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBMC_2

description: Sample name: 7602346012_K

tag: cell type

tag: date

tag: lastedcat

tag: height

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBM_P_Nb21

tag: tumor stage

tag: gender

value: M

tag: age


title: PBM_P_Nb39


title: PBM_PM_Nb28


title: PBMC_6

description: Sample name: 7602346063_E

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBMC_5

description: Sample name: 7602346063_D

tag: age

tag: bmi

tag: height

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBM_P_Nb31

tag: tumor stage

tag: gender


title: PBM_P_Nb24

tag: age


title: PBM_P_Nb18


title: PBM_P_Nb4


title: PBM_P_Nb22


title: PBM_P_Nb20


title: PBMC_13

description: Sample name: 7602346077_D

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: bmi

tag: height

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash


title: PBM_P_Nb14

tag: tumor stage

tag: gender

tag: age


title: PBM_PM_Nb1


title: PBM_PM_Nb27


title: PBMC_8

description: Sample name: 7602346063_H

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBM_PM_Nb16

tag: tumor stage

tag: gender

tag: age


title: PBM_PM_Nb11


title: PBM_P_Nb6


title: PBMC_3

description: Sample name: 7602346012_L

tag: developmental stage

tag: disease state

tag: cell type

tag: batch

tag: svisit

tag: date

tag: lastedcat

tag: height

tag: artdate

tag: vload

tag: cnspengrp

tag: handd

tag: nlang

tag: cnsinf

tag: hivneuro

tag: club

tag: hash