title: control, biological replicate 4

scan_protocol: Performed by Source Bioscience according to the manufacturer's instructions.

source_name: HeLa, control treatment


title: Heart.Placebo.Norm.2

status: Public on Oct 01 2012

type: RNA

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

description:
SAMPLE 20
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance stabilized and robust spline normalized using the ‘lumi’ package in R/BioConductor

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: ventricular myocardium, 5 days placebo,normoxic

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

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

treatment_protocol: Mature male C57Bl/6 mice were briefly anesthetized with halothane, a small incision made at the base of the neck, and placebo or 75-mg morphine pellets were inserted into the dorsal subcutaneous space before closure with 9-mm wound clips. Pellets were left in place for 5 days before analysis of cardiac I-R tolerance ex vivo. Briefly mice were anesthetized with sodium pentobarbital and hearts excised and perfused in a Langendorff mode. After 30 min stabilization control (placebo) and SLP hearts were subjected to either 25 min of global normothermic ischemia and 45 minutes of aerobic reperfusion, or time-matched normoxic perfusion. Hearts were collected in RNAlater and the left ventricular tissue dissected from the heart.

tag: strain

tag: gender

value: male

tag: age

value: 10-14 weeks

tag: agent

value: placebo

tag: treatment protocol (post-agent)

value: normoxic perfusion

tag: tissue

value: ventricular myocardium


title: Pediatric diarrheal sample from Mexico, #8

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

country: USA

institute: University of California, San Francisco

description:
Sample8
Amplified cDNA.

hyb_protocol: Microarrays were hybridized overnight at 65C according to the manufacturer's protocol (Agilent Technologies) using the Agilent Gene Expression Hybridization kit.

scan_protocol: Microarrays were scanned at 2 um resolution on an Agilent DNA Microarray Scanner.

data_processing:
Background-subtracted output intensities from Agilent's Feature Extraction software from 37,432 V3/V4 viral probes were sum normalized and then used for cluster and Z-score analysis (Eisen, et al., 1998; Chiu, et al., 2006; Chen, et al., 2011). Samples were declared positive for a diarrheal virus by microarray if positive by both cluster and Z-score analysis.

The background-subtracted output intensities from Agilent's Feature Extraction Software are available in 'GSE40008_raw_matrix.txt', which is linked to the Series record as a supplementary file.
The sum-normalized intensities are in the Sample data tables.

organism: Homo sapiens

source_name: Diarrheal stool

label_protocol: Randomly amplified cDNA was labelled using a Cy3 fluorescent dye via aa-dNTP incorporation (Wang, et al, 2002; Chiu, et al, 2006; Chiu, et al, 2008).

growth_protocol: Viral particles were purified from stool samples by shaking 1 mL phosphate-buffered saline, 0.1 g glass beads, 100 uL chloroform, and 0.2 g feces using a mechanical shaker, spinning x 20 min x 1000g in a centrifuge, and recovering the supernatant.

extract_protocol: Total nucleic acid was extracted using the PureLink 96 Viral RNA/DNA kit.

treatment_protocol: 500 uL of supernatant were passed through a 0.45 um filter and treated with a cocktail of nucleases (Turbo DNAse, Ambion, and RANseA, Invitrogen)

tag: developmental stage

value: child

tag: disease state

value: acute gastroenteritis

value: diarrhea

tag: polyomavirus (mxpyv) status

value: positive


title: control, biological replicate 3

city: Oxford

first: Martin

last: Dienstbier

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

hyb_protocol: Performed by Source Bioscience according to the manufacturer's instructions.

data_processing:
Microarray data from 4 biological repeats (each for vU1.8 knock-down and control) were processed by Affymetrix Power tools (http://www.affymetrix.com) using DABG and RMA algorithms for background correction and quantile normalization. Signal values were expressed in log2-scale.
HuEx-1_0-st-v2.r2.pgf

growth_protocol: HeLa cells were grown in Dulbecco's Modified Eagle Media (Invitrogen) supplemented with 10% fetal calf serum, 50  g of Penicillin per ml and 4 uM L-glutamine.

extract_protocol: Total RNA was isolated from HeLa cells using Trizol (Invitrogen), according to manufacturers’ instructions.

treatment_protocol: Knockdown experiments were performed in HeLa cells with lipofectAMINE 2000 reagent (Invitrogen) according to manufacturers' instructions. Typically, 1 × 107 cells were transfected with 600 pmoles of the 2-OMe oligonucleotide and cells harvested 18 hrs later. The control oligonucleotide is sense to the tU1 at position 11 to 32, the vU1.8-specific oligonucleotide is antisense to vU1.8 at position 11 to 33, where 1 is the first base of the U1/vU1 sequence.

tag: cell line

value: HeLa


title: vU1.8 snRNA knock-down, biological replicate 1

source_name: HeLa, vU1.8 snRNA knock-down

label_protocol: Performed by Source Bioscience according to the manufacturer's instructions.


title: vU1.8 snRNA knock-down, biological replicate 4


title: control, biological replicate 2


title: GM18912_treated_2hr

city: Chicago

first: Athma

middle: A

last: Pai

state: IL

address: 920 E. 58th Street

institute: University of Chicago

hyb_protocol: mRNA was amplified from the total RNA and hybridized to the Illumina HT-12 v4.0 expression beadchip using standard Illumina protocols.

scan_protocol: Arrays were imaged using an iScan reader using standard recommended Illumina scanner settings and intensity values were compiled using BeadArray software.

data_processing: Raw intensity values were log-transformed and robust-spline normalized using the lumi package in R. For the final study, genes with low detection p-values in either the 0hr or 4hr timepoints were considered not expressed and thus not used the following analyses.

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint

label_protocol: Standard Illumina protocols.

growth_protocol: Cell lines were cultured at 37C in RPMI 1640 media (supplemented with 2mM L-glutamine and 15% fetal bovine serum) and maintained at a density of between 2-5x10^5 viable cells/ml as per Coriell recommendations.

extract_protocol: Cells were pelleted and then total RNA was extracted with an Rneasy Mini Kit (Qiagen). RNA quality was assessed using an Agilent Bioanalyzer.

treatment_protocol: Cells were treated with Actinomycin D (ActD) to arrest transcription. The treatment was done at a concentration of 750,000 cells/ml with 7.5ug/ml of ActD.

value: female

tag: hapmap population

value: YRI

tag: ethnicity

value: Yoruba

tag: treatment

value: ActD

tag: time point


title: vU1.8 snRNA knock-down, biological replicate 2


title: Pediatric diarrheal sample from Mexico, #7

description:
Sample7
Amplified cDNA.


title: Heart.Placebo.IR.6

description:
SAMPLE 18
replicate 6

source_name: ventricular myocardium, 5 days placebo, ischemia-reperfused

value: global normothermic ischemia and aerobic reperfusion


title: GM18916_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: GM18912_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: Pediatric diarrheal sample from Mexico, #6

description:
Sample6
Amplified cDNA.


title: Heart.Placebo.Norm.3

description:
SAMPLE 21
replicate 3


title: Pediatric diarrheal sample from Mexico, #5

description:
Sample5
Amplified cDNA.


title: GM18909_treated_2hr


title: GM18909_treated_0.5hr


title: GM18912_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint


title: Pediatric diarrheal sample from Mexico, #3

description:
Sample3
Amplified cDNA.


title: GM18912_treated_1hr


title: GM18912_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint


title: control, biological replicate 1


title: Heart.Placebo.IR.4

description:
SAMPLE 16
replicate 4


title: GM18909_untreated_0hr


title: GM18909_treated_4hr


title: GM18907_treated_4hr


title: Heart.Placebo.IR.5

description:
SAMPLE 17
replicate 5


title: Heart.Placebo.IR.2

description:
SAMPLE 14
replicate 2


title: GM18909_treated_1hr


title: GM18907_treated_2hr


title: Heart.Placebo.IR.3

description:
SAMPLE 15
replicate 3


title: Pediatric diarrheal sample from Mexico, #4

description:
Sample4
Amplified cDNA.


title: Heart.Placebo.IR.1

description:
SAMPLE 13
replicate 1


title: Pediatric diarrheal sample from Mexico, #2

description:
Sample2
Amplified cDNA.


title: Heart.SLP.Norm.6

description:
SAMPLE 12
replicate 6

source_name: ventricular myocardium, 5 days SLP, normoxic

value: SLP


title: GM18907_untreated_0hr


title: GM18907_treated_1hr


title: GM18907_treated_0.5hr


title: Pediatric diarrheal sample from Mexico, #1

description:
Sample1
Amplified cDNA.


title: GM18870_treated_2hr


title: DNA normozospermic 103

type: genomic

city: Florence

first: Chiara

last: Chianese

address: viale Pieraccini. 6

country: Italy

institute: Univerity of Florence

description: normozoospermia

hyb_protocol: After sample denaturation and pre-annealing with 5µl of Human Cot-1 DNA (Invitrogen, Carlsbad, CA), hybridization was performed at 65°C with shaking for 24 hours. After two washing steps, the array was analyzed through the Agilent scanner and the Feature Extraction software (v10 1.1.1).

scan_protocol: Scanned on an Agilent G2539A scanner. Images were quantified using Agilent Feature Extraction Software (version 10 1.1.1).

data_processing: Agilent Feature Extraction Software (version 10 1.1.1) was used for background subtraction and LOWESS normalization. Graphical overview was obtained using the DNA Analytics (v4.0.73). All the array experiments were analysed using the ADM-2 algorithm at threshold 5. Text aberration summaries were analyzed to calculate the average log2 ratios of each Copy Number Variation and we considered at least 3 adjacent oligonucleotides needed for a reliable call. The positions of oligomeres refer to the Human Genome March 2006 assembly (hg18).

molecule: genomic DNA

source_name: genomic DNA extracted from lymphocytes of a normozospermic subject

label_protocol: 300ng of test DNA and control DNA  were double-digested with RsaI and AluI (Promega) for 1 hour at 37°C. After digestion, samples were incubated at 65°C for 20 minutes to inactivate the enzymes, then labeled by random priming (Agilent Technologies) for 2 hours using Cy5-dUTP for the test DNA and Cy3-dUTP (Agilent Technologies) for the control DNA. Labeled DNAs were incubated at 65°C for 10 minutes and then purified with Microcon YM-30 filter units (Millipore, Billerica, USA). Every purified sample was brought to a total volume of 9.5µl in 1XTE (pH 8.0, Promega), and yield and specific activity were determined for each sample using a NanoDrop ND-1000 UV-VIS Spectrophotometer (Labtech International LTD). The appropriate cyanine 5- and cyanine 3-labeled samples were combined in a total volume of 16μl.

extract_protocol: Genomic DNA extracted using QIAamp DNA mini kit or Salting out procedure following manufacturer's instructions

value: Male

tag: phenotype

value: normozoospermia

tag: cell type

value: lymphocyte

tag: cnv count

tag: cnv code

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject

value: normozoospermic


title: GM18862_treated_0.5hr

tag: gender

value: male


title: GM18861_treated_4hr


title: Heart.SLP.Norm.5

description:
SAMPLE 11
replicate 5

tag: strain

tag: age

value: 10-14 weeks

value: normoxic perfusion

value: ventricular myocardium


title: GM18870_untreated_0hr


title: Heart.SLP.Norm.3

description:
SAMPLE 9
replicate 3

tag: agent

tag: treatment protocol (post-agent)


title: Heart.SLP.Norm.1

description:
SAMPLE 7
replicate 1

tag: tissue


title: DNA normozospermic 102

description: normozoospermia


title: GM18870_treated_0.5hr


title: DNA normozospermic 104

description: normozoospermia


title: GM18862_untreated_0hr


title: GM18862_treated_2hr


title: GM18870_treated_1hr


title: DNA normozospermic 101

description: normozoospermia


title: Heart.SLP.Norm.4

description:
SAMPLE 10
replicate 4


title: GM18862_treated_4hr


title: DNA normozospermic 100

description: normozoospermia


title: GM18862_treated_1hr


title: GM18870_treated_4hr


title: GM18861_untreated_0hr


title: Heart.SLP.IR.6

description:
SAMPLE 6
replicate 6

source_name: ventricular myocardium, 5 days SLP, ischemia-reperfused


title: GM18861_treated_2hr


title: DNA normozospermic 99

description: normozoospermia


title: DNA normozospermic 98

description: normozoospermia


title: GM18861_treated_1hr


title: Heart.SLP.Norm.2

description:
SAMPLE 8
replicate 2


title: Heart.SLP.IR.5

description:
SAMPLE 5
replicate 5


title: GM18861_treated_0.5hr


title: GM18859_treated_2hr


title: Heart.SLP.IR.2

description:
SAMPLE 2
replicate 2


title: GM18859_treated_0.5hr


title: GM18858_treated_4hr


title: Heart.SLP.IR.3

description:
SAMPLE 3
replicate 3


title: DNA normozospermic 95

description: normozoospermia


title: DNA normozospermic 97

description: normozoospermia


title: GM18859_treated_4hr


title: Heart.SLP.IR.4

description:
SAMPLE 4
replicate 4


title: GM18858_untreated_0hr


title: DNA normozospermic 96

description: normozoospermia


title: GM18858_treated_1hr


title: SH-SY5Y cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: EMEM:F-12 = 1:1 / non-essential amino acids / 15% heat-inactivated FBS

extract_protocol: Total RNA extracted using Rneasy Plus Mini kit (QIAGEN) following manufacturer's instructions

treatment_protocol: add 1/1000 vol. of DMSO or 50 mM clioquinol (dissolved in DMSO)

value: DMSO

value: 50 mM clioquinol


title: DNA normozospermic 94

description: normozoospermia


title: GM18856_treated_2hr


title: DNA normozospermic 93

description: normozoospermia


title: GM18858_treated_0.5hr


title: GM18859_treated_1hr


title: GM18856_treated_4hr


title: FG versus L3.6 Replicate 3

city: Houston

first: Mark

last: Truty

address: 1515 Holcombe Blvd.

department: Surgical Oncology

institute: University of Texas, MD Anderson Cancer Center

description:
Replicate #3 of FGvsL3.6
FGvsL3.6-rep3

hyb_protocol: Hybridization was performed using Agilent Gene Expression Hybridization Kit #5188-5242 containing 2x Hi-RPM Hybridization Buffer, 25x Fragmentation Buffer, and 10x Gene Expression Blocking Agent.Samples were applied per instructions to microarrays and enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were sequentially washed and prepared for scanning.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Feature Extraction Software 9.5.3.1 was used and data was background subtraction/corrected and normalized using loess (within arrays).
Normalized LogRatios and the significance value of the Log Ratio were used. Both the magnitude and the significance threshold of the logratio were used representing test/reference with  PValueLogRatio of <0.0001 and 10-fold differential expression Cy5 over Cy3 higher in Cy5 channel.

source_name: FG

label_protocol: Labeling system for incorporating dye into samples was performed with Low Input Quick Amp Labeling Kit, two-color cat # 5190-2306 containing: T7 Primer, 5x First Strand Buffer, 0.1M DTT, 10 mM dNTP Mix, AffinityScript RNase Block Mix, 5x Transcription Buffer, NTP Mix, T7 RNA Polymerase Blend, Nuclease-free Water, Cyanine 3-CTP (green), and Cyanine 5-CTP (red).

growth_protocol: Both cell lines grown under identical standard conditions. No treatments.

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

value: subcloned cell line FG

tag: metastatic potential

value: poorly metastatic

value: subcloned cell line L3.6

value: highly metastatic


title: FG versus L3.6 Replicate 2

description:
Replicate #2 of FGvsL3.6
FGvsL3.6-rep2


title: FG versus L3.6 Replicate 1

description:
Replicate #1 of FGvsL3.6
FGvsL3.6-rep1


title: GM18856_treated_1hr

value: YRI

value: Yoruba

value: ActD


title: GM18856_treated_0.5hr


title: Heart.SLP.IR.1

description:
SAMPLE 1
replicate 1

value: SLP

value: global normothermic ischemia and aerobic reperfusion


title: GM18859_untreated_0hr


title: GM18858_treated_2hr

value: female


title: DNA normozospermic 91

description: normozoospermia

value: Male

value: normozoospermia

value: lymphocyte

value: normozoospermic


title: DNA normozospermic 92

description: normozoospermia

value: male


title: GM18856_untreated_0hr


title: daptomycin resistant strain CB1541 vs. parent strain CB1118-rep2

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

description: Analysis used CB1118 RNA as control samples for comparison to CB1541 S. aureus RNA samples.

hyb_protocol: Arrays were blocked in 1% SDS, 5 X SSC and 1 mg/ml BSA at 42C for 1 h.  Arrays were then washed 2X for 5 min in 0.1X SSC and 2X for 30 sec in sterile double-distilled water.  Arrays were hybirdized to Cy-labeled cDNAs denatured at 05C in 10 mM EDTA for 5 min and mixed with 40 ul hybridization buffer (Ambion) before loading under a caverslip on the array and sealing in hybridization cassettes.  Hybridization was carried out at 47C for 18 h.  Afterwards, array slides were washed in 2X SSC, 0.5% SDS at 37C for 5 min, followed by stringency washes 2X in 0.1X SSC at 37C for 2.5 min each, and 2X in 0.1X SSC at room temperature for 2.5 min each.

scan_protocol: Arrays were scanned using an Axon 4000b, and images analyzed using GenePix 6.0.

data_processing: Intensity of spots are quantified by using Spotfinder. Low intensity filter in MIDAS is used to filter out points with intensity less than 1000. Array intensity data was log2-transformed, and normalized using the Lowess algorithm.  Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast.  A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

organism: Staphylococcus aureus

source_name: sample collected at OD600 at 0.4

label_protocol: Amino-allyl labeled cDNA was dried and then suspended in 0.1 M sodium carbonate (pH 9.3) and coupled with either Cy3 or Cy5 (swapped between balanced samples, N=4).  Uncoupled dye was removed by column purification (Qiagen).

growth_protocol: Cultures were initiated from overnight cultures in MHB into fresh MHB at 1:100 and grown to OD600=0.4.

extract_protocol: Samples were added to RNA Protect (Qiagen, Valencia, CA) and processed according to the manufacturer's instructions.  Cells were harvested by centrifugation (8,000 X g, 20 min, 4C) and then resuspended in 1 ml Trizol (Invitrogen, Carlsbad, CA) and processed in an FP120 FastPrep cell disruptor (MP Biomedicals, Irvine, CA).  Chloroform was subsequently added to the lysates, followed by centrifugation (16,000 X g, 15 min, 4C) and RNA was precipitated 1:1 (vol/vol) in 100% ethyl alcohol.  The RNA was then purified using the RNeasy™ kit (Qiagen) according to the manufacturer's instructions. Contaminating DNA was removed from purified RNA using DNAfree (Ambion, Austin, TX).  cDNA was produced using SuperScript II Reverse Transcriptase (Invitrogen) from 2 µg of total RNA combined with random hexamers, 0.25 mM deoxynucleoside triphosphate, and 0.25 mM aminoallyl-dUTP.

treatment_protocol: Cultures in MHB grown to OD600=0.4


title: daptomycin resistant strain CB1541 vs. parent strain CB1118-rep3


title: C5 versus C5LM2 Replicate 3

description:
Replicate #3 of C5vsC5LM2
C5vsC5LM2-rep3

value: subcloned cell line C5

value: subcloned cell line C5LM2


title: DNA normozospermic 88

description: normozoospermia


title: RWV_5

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

institute: Dstl

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours

scan_protocol: scanned using the Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and data was extracted using GenePix® pro 6.1

data_processing: 75th percentile normalisation

source_name: A549 Cell Culture from RWVs

label_protocol: RNA was labelled with Cy3 using the Quick Amp Labelling kit (Agilent) as per the manufacturer’s instructions.

growth_protocol: Grown in RWVs in Dulbeccos modified eagle's media with 10% foetal calf serum and 4mM l-glutamine

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: Cells extracted from RWVs or Monolayers and placed into Qiagen RLT (lysis buffer) containing B-mercaptoethanol


title: C5 versus C5LM2 Replicate 1

description:
Replicate #1 of C5vsC5LM2
C5vsC5LM2-rep1


title: GM18855_treated_2hr


title: GM18852_treated_4hr


title: DNA normozospermic 86

description: normozoospermia


title: GM18852_treated_1hr


title: GM18855_treated_0.5hr


title: daptomycin resistant strain CB1540 vs. parent strain CB1118-rep3

description: Analysis used CB1118 RNA as control samples for comparison to CB1540 S. aureus RNA samples.


title: DNA normozospermic 90

description: normozoospermia


title: GM18855_untreated_0hr


title: GM18852_treated_2hr


title: DNA normozospermic 89

description: normozoospermia


title: C5 versus C5LM2 Replicate 2

description:
Replicate #2 of C5vsC5LM2
C5vsC5LM2-rep2


title: DNA normozospermic 87

description: normozoospermia


title: RWV_4


title: RWV_2


title: DNA normozospermic 85

description: normozoospermia


title: DNA normozospermic 84

description: normozoospermia


title: GM18855_treated_4hr


title: GM18852_untreated_0hr


title: GM18852_treated_0.5hr


title: daptomycin resistant strain CB1541 vs. parent strain CB1118-rep1


title: daptomycin resistant strain CB1540 vs. parent strain CB1118-rep2


title: RWV_3


title: daptomycin resistant strain CB1540 vs. parent strain CB1118-rep1


title: GM18846_treated_4hr


title: DNA normozospermic 83

description: normozoospermia


title: RWV_1


title: Mono_2

source_name: A549 Cell Culture From Monolayer


title: DNA normozospermic 82

description: normozoospermia


title: Mono_3


title: Alcohol liquid diet, biological replicate 3

city: TAIPEI

first: Lee-Yan

last: Sheen

address: No. 1, Sec 4, Roosevelt Road,

department: Institute of Food Science and Technology

country: Taiwan

institute: National Taiwan University

hyb_protocol: 1.5µg cRNA were subsequently hybridized to Illumina MouseRef-8 v2.0 expression beadchip (Illumina, San Diego, CA) at 58 C. After 14-20 hours hybridization, the BeadChip were stained by Cy3 and washed.

scan_protocol: Intensities of bead fluorescence were detected by the Illumina BeadArray Reader.

data_processing: Raw intensity values were exported from GenomeStudio software for data processing and statistical computing in R (http://www.R-project.org) and Bioconductor (http://www.bioconductor.org). Microarray probes with detection p-value less than 0.05 were considered to be present in the analysis. Data quality of the probes was assessed using the Lumi - a Bioconductor package to process Illumina microarray data (Du et al., 2008).  A robust spline normalization (RSN) method in the Lumi package that combines the features of the quantile and loess normalization methods was used for normalization of the data. Limma – a Bioconductor R package was used to identify differentially expressed genes among groups.

label: Biotin

source_name: Alcohol, biological replicate 3

label_protocol: 500 ng RNA is converted to double-stranded cDNA, followed by an amplification step (in vitro transcription, IVT) to generate biotin labeled cRNA.

extract_protocol: Total RNA extracted from frozen liver tissue using TRIzol reagent (Invitrogen) and purified by RNeasy MinElute Cleanup (Qiagen, GmbH).

value: Alcohol liquid diet

tag: genetic background

value: liver


title: Alcohol liquid diet, biological replicate 2

source_name: Alcohol, biological replicate 2


title: DNA normozospermic 81

description: normozoospermia


title: Alcohol liquid diet, biological replicate 4

source_name: Alcohol, biological replicate 4


title: GM18846_treated_1hr

tag: cell line


title: DNA normozospermic 80

description: normozoospermia


title: GM18846_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint

tag: hapmap population


title: GM18846_treated_0.5hr

tag: ethnicity


title: DNA normozospermic 78

description: normozoospermia


title: Mono_5


title: GM18522_treated_4hr

tag: treatment


title: Alcohol liquid diet, biological replicate 1

source_name: Alcohol, biological replicate 1


title: Control liquid diet, biological replicate 4

source_name: Control, biological replicate 4

value: Lieber-DeCarli liquid control diet


title: Mono_4


title: DNA normozospermic 77

description: normozoospermia


title: GM18846_untreated_0hr

tag: time point


title: GM18522_treated_2hr


title: Mono_1


title: GM18855_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: Control liquid diet, biological replicate 3

source_name: Control, biological replicate 3


title: DNA normozospermic 76

description: normozoospermia

tag: phenotype


title: GM18522_treated_1hr


title: DNA normozospermic 79

description: normozoospermia

tag: cell type


title: DNA normozospermic 75

description: normozoospermia

tag: cnv count


title: DNA normozospermic 74

description: normozoospermia


title: Control liquid diet, biological replicate 1

source_name: Control, biological replicate 1


title: GM18519_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint


title: Control liquid diet, biological replicate 2

source_name: Control, biological replicate 2


title: GM18522_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint


title: GM18522_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: Garlic oil and alcohol liquid diet, biological replicate 4

source_name: Garlic Oil, biological replicate 4

value: Garlic oil and alcohol liquid diet


title: DNA normozospermic 73

description: normozoospermia

source_name: genomic DNA extracted from lymphocytes of a normozospermic subject

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: DNA normozospermic 72

description: normozoospermia

tag: cnv code


title: Garlic oil and alcohol liquid diet, biological replicate 2

source_name: Garlic Oil, biological replicate 2

tag: gender


title: Garlic oil and alcohol liquid diet, biological replicate 1

source_name: Garlic Oil, biological replicate 1


title: GM18519_treated_1hr

value: YRI


title: Garlic oil and alcohol liquid diet, biological replicate 3

source_name: Garlic Oil, biological replicate 3


title: DNA normozospermic 70

description: normozoospermia


title: Diallyl disulfide and alcohol liquid diet, biological replicate 4

source_name: DADS, biological replicate 4


title: DNA normozospermic 66

description: normozoospermia


title: DNA normozospermic 68

description: normozoospermia


title: Diallyl disulfide and alcohol liquid diet, biological replicate 2

source_name: DADS, biological replicate 2


title: GM18519_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint

value: Yoruba


title: GM18519_untreated_0hr


title: Diallyl disulfide and alcohol liquid diet, biological replicate 3

source_name: DADS, biological replicate 3


title: GM18519_treated_0.5hr

value: ActD


title: GM18517_treated_4hr


title: GM18517_treated_2hr


title: GM18517_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: DNA normozospermic 67

description: normozoospermia


title: Diallyl disulfide and alcohol liquid diet, biological replicate 1

source_name: DADS, biological replicate 1


title: DNA normozospermic 69

description: normozoospermia


title: DNA normozospermic 65

description: normozoospermia


title: Ox-ARP, rep4

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
5541914039_H
Replicate 4 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using average normalization in GenomeStudio v2010.2.

source_name: Neuro 2a cells, H2O2, ARP-derivatized RNA

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays. Cy3-Streptavidin was incorporated during the Wash and Block protocol as a fluor for scanning.

extract_protocol: Total RNA isolated by TRIzol was derivatized with ARP on abasic sites. After the RNA was incubated with streptavidin magnetic beads and then washed with stringent buffer conditions, oxidized RNA was specifically isolated by pull-down.

treatment_protocol: Neuro 2a cells received hydrogen peroxide treatment or no treatment as a control.

value: Neuro 2a

tag: strain

value: hydrogen peroxide

tag: pull-down process

value: yes


title: GM18517_treated_0.5hr

value: female


title: Ox-ARP, rep3

description:
5541914039_G
Replicate 3 of 4.


title: Ox-ARP, rep2

description:
5541914022_H
Replicate 2 of 4.


title: Ox-ARP, rep1

description:
5541914022_G
Replicate 1 of 4.


title: Amplified single cell DNA_Embryo_Family4_Blastomere1

city: Leuven

first: Thierry

last: Voet

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KULeuven

description:
Hybridized to 250K_Nsp
Computed genotypes are provided the CHP files

hyb_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

data_processing: The 12 amplified single lymphoblastoid cell DNA samples were genotyped using (1) the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12, (2) the BRLMM algorithm within the ‘Genotyping console 3.0.1’ software (Affymetrix) using a scoring threshold of 0.1 and (3) the Birdseed algorithm of the APT-1.10.1 package (Affymetrix Power Tools) using the ‘birdseed-dev’ command which is the most recently incorporated development version of birdseed from The Broad Institute (http://www.broadinstitute.org/mpg/birdsuite/birdseed.html).  The 3 amplified single human blastomere DNA samples were genotyped using the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12.  The 19 non-amplified genomic DNA samples extracted from blood were genotyped using the dynamic model algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12.

source_name: multiple displacement amplified (MDA)-DNA of a single human blastomere biopsied from a human IVF embryo

extract_protocol: Single cells were transferred to a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (MidAtlantic Diagnostics, Mount Laurel, USA). The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with Genomi Phi V2 (GE Healthcare, Piscataway, NJ). The MDA products were purified and resuspended in 100 µl of elution buffer (High Pure PCR Product Purification Kit, Roche, Basel, Switzerland). All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies, Rockland, DE). SC-amplifications yielding less than 2 µg DNA were not further used.

value: Male

value: single cell from a 3-day-old human IVF embryo

tag: embryo

value: IVF protocol:controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF (n=8) or ICSI (n=1) with ejaculated sperm. Embryos were cultured in Global Medium (GlobalLife) and the morphology was daily assessed. Only genetically normal embryos of good morphology (with compaction or blastocyst formation) were transferred on day 4 or 5. Supernumerary genetically normal embryos of good morphology were frozen at day 4 or 5. Day 3 (evening) or day 4 (morning) embryos diagnosed with a microdeletion or with a normal sex but not suitable for transfer due to a familial genetic reason were used for this study if fulfilling all inclusion criteria (see patient info).  Patient info:Couples entering the IVF-PGD-program for sex selection due to X-linked disorders or BRCA mutations or for familial microdeletion syndromes were asked to participate. Inclusion criteria were:(1) written informed consent from each couple, (2) maternal and paternal age ≤ 35 years, (3) normal karyotype for both partners, (4) a maternal body mass index of 18-30 kg/m², (5) initial normal semen parameters according to WHO regulation, (6) good quality embryos:2-5 blastomeres on day 2, 6-10 blastomeres on day 3, <20% fragmentation, equal sized blastomeres, (7) no recurrent miscarriages. The study was approved by the Ethical Committee of the University Hospital (registration number NCT00614367).  Treatment protocol:Embryos were incubated briefly in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO) to remove the zona pellucida (ZP) by mouth controlled pipetting using Flexipet micromanipulation pipettes (130 µm, Cook, IVF Queensland, Australia). They were then transferred to Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium) and gently pipetted to disaggregate the individual blastomeres. Single blastomeres were washed three times in the dissociation medium.


title: GM18516_treated_2hr

value: male


title: GM18517_untreated_0hr


title: DNA normozospermic 62

description: normozoospermia

value: normozoospermia

value: lymphocyte

value: normozoospermic


title: GM18516_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint


title: DNA normozospermic 63

description: normozoospermia


title: Amplified single cell DNA_Embryo_Family4_Blastomere2

scan_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual


title: GM18516_treated_1hr


title: Basal-ARP, rep4

description:
5541914039_F
Replicate 4 of 4.

source_name: Neuro 2a cells, untreated, ARP-derivatized RNA


title: Amplified single cell DNA_Embryo_Family4_Blastomere3

label_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual


title: DNA normozospermic 60

description: normozoospermia


title: Basal-ARP, rep3

description:
5541914039_E
Replicate 3 of 4.


title: GM18516_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: Basal-ARP, rep2

description:
5541914022_F
Replicate 2 of 4.


title: DNA normozospermic 64

description: normozoospermia


title: DNA normozospermic 71

description: normozoospermia


title: GM18516_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint


title: Ox-total, rep4

description:
5541914039_D
Replicate 4 of 4.

source_name: Neuro 2a cells, H2O2

value: no


title: DNA normozospermic 59

description: normozoospermia

source_name: genomic DNA extracted from lymphocytes of a normozospermic subject

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject


title: DNA normozospermic 58

description: normozoospermia


title: DNA normozospermic 57

description: normozoospermia


title: Amplified single cell DNA_EBV cell line_Family3_Individual4_SingleCell1

source_name: multiple displacement amplified (MDA)-DNA of a single human Epstein-Barr virus (EBV)-transformed lymphoblastoid cell

value: single cell from a human Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line of person Family3_Individual4


title: GM18511_treated_2hr


title: Amplified single cell DNA_EBV cell line_Family3_Individual4_SingleCell2


title: Ox-total, rep3

description:
5541914039_C
Replicate 3 of 4.


title: DNA normozospermic 56

description: normozoospermia


title: DNA normozospermic 61

description: normozoospermia


title: GM18511_treated_1hr


title: Basal-ARP, rep1

description:
5541914022_E
Replicate 1 of 4.


title: Amplified single cell DNA_EBV cell line_Family3_Individual4_SingleCell3.


title: DNA normozospermic 55

description: normozoospermia


title: GM18511_treated_0.5hr


title: Ox-total, rep2

description:
5541914022_D
Replicate 2 of 4.


title: DNA normozospermic 54

description: normozoospermia


title: Ox-total, rep1

description:
5541914022_C
Replicate 1 of 4.


title: Amplified single cell DNA_EBV cell line_Family2_Individual2_SingleCell3

value: Female

value: single cell from a human Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line of person Family2_Individual2


title: Amplified single cell DNA_EBV cell line_Family3_Individual3_SingleCell2

value: single cell from a human Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line of person Family3_Individual3


title: Genomic DNA_Blood_Family4_PaternalGrandfather

source_name: genomic DNA isolated from blood

value: Blood


title: DNA normozospermic 53

description: normozoospermia


title: GM18511_untreated_0hr

value: YRI

value: Yoruba


title: DNA normozospermic 52

description: normozoospermia


title: Basal-total, rep2

description:
5541914022_B
Replicate 2 of 4.

source_name: Neuro 2a cells, untreated

value: Neuro 2a


title: Basal-total, rep3

description:
5541914039_A
Replicate 3 of 4.


title: Amplified single cell DNA_EBV cell line_Family3_Individual3_SingleCell1


title: GM18510_treated_4hr

value: ActD


title: DNA normozospermic 51

description: Control subject 10-329 excluded from the study because of inappropriate sperm parameters

value: Male


title: GM18510_treated_2hr


title: GM18511_treated_4hr

value: female


title: Genomic DNA_Blood_Family4_PaternalGrandmother


title: Amplified single cell DNA_EBV cell line_Family2_Individual2_SingleCell2


title: Basal-total, rep4

description:
5541914039_B
Replicate 4 of 4.


title: Amplified single cell DNA_EBV cell line_Family2_Individual2_SingleCell1


title: GM18510_treated_1hr


title: Amplified single cell DNA_EBV cell line_Family3_Individual3_SingleCell3


title: Genomic DNA_Blood_Family3_MaternalGrandfather


title: Basal-total, rep1

description:
5541914022_A
Replicate 1 of 4.


title: GM18510_treated_0.5hr


title: Genomic DNA_Blood_Family4_father


title: Amplified single cell DNA_EBV cell line_Family1_Individual1_SingleCell2

value: single cell from a human Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line of person Family1_Individual1


title: DNA normozospermic 50

description: normozoospermia

value: male


title: Amplified single cell DNA_EBV cell line_Family1_Individual1_SingleCell3


title: crel-/-relb-/- BMDCs Pam3CSK4 24h

city: La Jolla

first: Vincent

middle: Feng-Sheng

last: Shih

address: UCSD m/c 0375, NSB 3318 9500, Gilman Dr.

department: Chemistry and Biochemistry

institute: UCSD

description: BMDCs gene expression in response to CpG or Pam3CSK4

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

source_name: Bone marrow derived dendritic cells

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

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

tag: genotype

value: crel-/-relb-/-

tag: agent

tag: time


title: GM18510_untreated_0hr


title: crel-/-relb-/- BMDCs Pam3CSK4 8h


title: DNA normozospermic 47

description: normozoospermia

value: normozoospermia

value: lymphocyte


title: Genomic DNA_Blood_Family3_MaternalGrandmother

tag: tissue


title: DNA normozospermic 48

description: normozoospermia

value: normozoospermic


title: Genomic DNA_Blood_Family4_mother


title: DNA normozospermic 49

description: normozoospermia


title: crel-/-relb-/- BMDCs Pam3CSK4 1h


title: Genomic DNA_Blood_Family3_father


title: Amplified single cell DNA_EBV cell line_Family1_Individual1_SingleCell1


title: GM18507_treated_2hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 2hr timepoint

tag: cell line


title: DNA normozospermic 46

description: normozoospermia


title: crel-/-relb-/- BMDCs CpG 8h

value: CpG


title: crel-/-relb-/- BMDCs CpG 1h


title: crel-/-relb-/- BMDCs CpG 24h


title: Genomic DNA_Blood_Family3_mother

value: Female


title: GM18507_treated_1hr

tag: hapmap population


title: crel-/-relb-/- BMDCs CpG 0h

value: unstimulated


title: Genomic DNA_Blood_Family3_Individual4


title: GM18507_treated_0.5hr

tag: ethnicity


title: DNA normozospermic 45

description: normozoospermia


title: DNA normozospermic 44

description: normozoospermia


title: DNA normozospermic 43

description: normozoospermia


title: GM18507_untreated_0hr

tag: treatment


title: relb-/- BMDCs Pam3CSK4 24h

value: relb-/-


title: 12h uninfested control incompatible rep2

city: Lincoln

first: Chitvan

last: Khajuria

state: NE

address: 103 Entomology Hall

institute: University of Nebraska-Lincoln

description: Gene expression data from 1.5-2 cm of the second leaf sheath of Molly without hessian fly larvae

hyb_protocol: Hybridization on the wheat microarrays were performed according Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix)

scan_protocol: After hybridization and washing, the arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: MAS 5.0

organism: Triticum aestivum

source_name: Wheat, 1.5-2 cm of the second leaf sheath

label_protocol: Biotinylated cRNA were prepared according to Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix)

growth_protocol: Wheat seedlings were grown in a growth chamber set at 20±1°C in daytime and 18±1°C at night with a 14:10 h (L/D) photoperiod

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

treatment_protocol: Wheat seedlings were infested at two-leaf stage with eggs from 10 mated females per 10 plants. Larval hatching time was monitored with additional infested plants under the same growth chamber.

value: 1.5-2 cm of the second leaf sheath

tag: cultivar

value: Molly

value: 12h control

value: uninfested


title: DNA normozospermic 42

description: normozoospermia

tag: phenotype


title: GM18505_treated_4hr

value: YRI

value: Yoruba

value: ActD

tag: time point


title: relb-/- BMDCs Pam3CSK4 8h


title: DNA normozospermic 41

description: normozoospermia

value: Male

tag: cell type

tag: cnv count


title: 12h uninfested control incompatible rep3


title: GM18505_treated_2hr

tag: gender

value: female


title: Genomic DNA_Blood_Family3_Individual3

value: Blood


title: relb-/- BMDCs Pam3CSK4 1h

tag: strain


title: relb-/- BMDCs CpG 24h


title: relb-/- BMDCs CpG 8h


title: GM18505_treated_0.5hr


title: GM18505_treated_1hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 1hr timepoint


title: 12h uninfested control incompatible rep1


title: GM18507_treated_4hr

value: male


title: GM18505_untreated_0hr


title: DNA normozospermic 39

description: normozoospermia

value: normozoospermia

value: lymphocyte

tag: cnv code


title: 12h uninfested control compatible rep2

description: Gene expression data from 1.5-2 cm of the second leaf sheath of Newton without hessian fly larvae

value: Newton


title: DNA normozospermic 37

description: normozoospermia

value: normozoospermic


title: DNA normozospermic 38

description: normozoospermia


title: Genomic DNA_Blood_Family2_MaternalGrandmother

value: Female


title: GM18504_treated_4hr


title: relb-/- BMDCs CpG 1h

value: relb-/-

value: CpG


title: Genomic DNA_Blood_Family2_mother


title: Genomic DNA_Blood_Family2_Individual2


title: GM18504_treated_2hr


title: 24h incompatible interaction biological rep3

description: Gene expression data from 1.5-2 cm of the second leaf sheath of Molly infested with Hessian fly larvae

value: 1.5-2 cm of the second leaf sheath

value: Molly

value: 24h after Hessian fly egg hatching

value: infested with Hessian fly larvae


title: 12h uninfested control compatible rep1

value: 12h control

value: uninfested


title: Genomic DNA_Blood_Family2_father

value: Male


title: WT BMDCs Pam3CSK4 24h

value: wild type


title: relb-/- BMDCs CpG 0h

value: unstimulated


title: DNA normozospermic 36

description: normozoospermia

value: male


title: 12h uninfested control compatible rep3


title: 24h incompatible interaction biological rep1


title: Genomic DNA_Blood_Family1_father

value: Blood


title: WT BMDCs Pam3CSK4 8h


title: 24h incompatible interaction biological rep2


title: GM18504_treated_1hr

value: YRI

value: Yoruba

value: ActD


title: GM18504_treated_0.5hr


title: DNA normozospermic 40

description: normozoospermia

value: normozoospermia

value: lymphocyte

value: normozoospermic


title: DNA normozospermic 35

description: normozoospermia


title: 24h compatible interaction biological rep3

description: Gene expression data from 1.5-2 cm of the second leaf sheath of Newton infested with Hessian fly larvae

value: 1.5-2 cm of the second leaf sheath

value: Newton


title: DNA normozospermic 34

description: normozoospermia


title: WT BMDCs Pam3CSK4 1h


title: Genomic DNA_Blood_Family1_MaternalGrandmother

value: Female


title: DNA normozospermic 32

description: normozoospermia


title: DNA normozospermic 33

description: normozoospermia


title: 24h compatible interaction biological rep1

value: 24h after Hessian fly egg hatching

value: infested with Hessian fly larvae


title: GM18502_treated_2hr

value: female


title: WT BMDCs CpG 24h

value: CpG


title: GM18502_treated_4hr


title: Genomic DNA_Blood_Family2_MaternalGrandfather

value: Male


title: GM18502_treated_1hr


title: Genomic DNA_Blood_Family1_Individual1


title: WT BMDCs CpG 1h

value: wild type


title: WT BMDCs CpG 8h


title: DNA normozospermic 31

description: normozoospermia

value: male


title: 24h compatible interaction biological rep2


title: Genomic DNA_Blood_Family1_mother

value: Blood


title: WT BMDCs CpG 0h

value: unstimulated


title: DNA normozospermic 30

description: normozoospermia


title: DNA normozospermic 29

description: normozoospermia


title: GM18504_untreated_0hr

value: YRI

value: Yoruba


title: experiment 7 UVC- and EtBr-exposed samples at 51 h 7eu51

city: Durham

first: Joel

last: Meyer

state: NC

address: Box 90328 LSRC A354

institute: Duke University

hyb_protocol: Affymetrix GeneChip Hybridization, Wash protocol (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix GeneChip Scan protocol (Affymetrix, Santa Clara, CA)

data_processing: Data were normalized using RMA (quantile normalization) in both Rosetta Resolver and GeneSpring (GX 11). Next, using nonfiltered Rosetta Resolver RMA-normalized data, six samples were excluded from the analysis based on their identification as outliers using PCA: 18630_6C48, 18634_6c51, 18631_6u48, 18636_6u51, 18616_5e48, 15921_7e51. The Matrix spreadsheet contains the data generated by and analyzed in GeneSpring for the remaining 69 samples.

organism: Caenorhabditis elegans

label_protocol: MessageAmp Premier RNA  Amplification Kit Cat#4385821

growth_protocol: Age-synchronized L1-stage wildtype (N2 Bristol strain) C. elegans were prepared by egg prep and overnight hatch, plated on K agar plates without food (to continue L1 arrest), and after the third UVC exposure placed on K agar plates with a lawn of OP50 bacteria.

extract_protocol: Nematodes were frozen by dripping 3,000-5,000 pelleted nematodes suspended in about 500 μl K-medium into liquid nitrogen, and stored at -80°C. The pellets were ground into fine powder with a liquid nitrogen-cooled mortar and pestle and RNA was extracted using an RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: The growth-arrested L1 larvae were exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total), or maintained under normal lab light (mostly dark, in incubators). Half of the UVC and no-UVC samples were also exposed to EtBr (5ug/mL in agar). Nematodes were sampled for RNA 3 h after the first UVC dose (3 h), just prior to the second dose (24 h), just prior to the third dose (48 h), and 3 h after the final dose (51 h), which is also 3 h after being placed on food. The entire experiment was repeated 7 times, with a subset of samples (final n = 4-6 per time and treatment) chosen for microarray analysis based on yield and quality of RNA.

value: pooled whole-body extracts

value: UVC- and EtBr-exposed

value: N2 Bristol


title: GM18502_untreated_0hr


title: 12h incompatible interaction biological rep2

value: 1.5-2 cm of the second leaf sheath

value: Molly

value: 12h after Hessian fly egg hatching


title: experiment 7 UVC-exposed samples at 51 h 7u51

value: UVC-exposed


title: GM18501_treated_4hr

value: ActD


title: GM18502_treated_0.5hr

value: female


title: DNA normozospermic 28

description: normozoospermia

value: normozoospermia

value: lymphocyte

value: normozoospermic


title: 12h incompatible interaction biological rep1

value: infested with Hessian fly larvae


title: 12h compatible interaction biological rep3

value: Newton


title: GM18501_treated_2hr

value: male


title: 12h compatible interaction biological rep2


title: DNA normozospermic 27

description: normozoospermia

value: Male


title: GM18501_treated_1hr

value: YRI

value: Yoruba


title: 12h compatible interaction biological rep1


title: experiment 7 control samples at 51 h 7c51

source_name: experiment 7 control samples at 51 h

value: pooled whole-body extracts

value: control


title: GM18501_treated_0.5hr


title: 6h incompatible interaction biological rep3

value: 1.5-2 cm of the second leaf sheath

value: 6h after Hessian fly egg hatching


title: experiment 7 EtBr-exposed samples at 48 h 7e48

value: EtBr-exposed

value: N2 Bristol


title: DNA normozospermic 25

description: normozoospermia


title: 6h incompatible interaction biological rep2

value: Molly


title: DNA normozospermic 26

description: normozoospermia


title: DNA normozospermic 24

description: normozoospermia


title: experiment 7 UVC- and EtBr-exposed samples at 48 h 7eu48

value: UVC- and EtBr-exposed


title: DNA normozospermic 23

description: normozoospermia

value: normozoospermia


title: experiment 7 UVC- and EtBr-exposed samples at 24 h 7eu24


title: 6h incompatible interaction biological rep1


title: GM18501_untreated_0hr


title: DNA normozospermic 22

description: normozoospermia

value: lymphocyte


title: experiment 7 control samples at 48 h 7c48

source_name: experiment 7 control samples at 48 h


title: 6h compatible interaction biological rep2


title: GM18499_treated_2hr

value: female

value: ActD


title: experiment 7 UVC-exposed samples at 48 h 7u48

value: UVC-exposed


title: GM18499_treated_1hr


title: experiment 7 UVC-exposed samples at 24 h 7u24


title: GM18499_treated_4hr


title: DNA normozospermic 20

description: normozoospermia

value: normozoospermic

value: male


title: GM18499_treated_0.5hr

value: YRI


title: DNA normozospermic 19

description: normozoospermia

value: Male


title: 6h compatible interaction biological  rep1

value: Newton

value: infested with Hessian fly larvae


title: Patient 2 -Pre-therapy Dose 0 -tumor -repeat 2 - mAdbID:107521

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 107521

hyb_protocol: Sample Hybridization Protocol Other: Combine Cy3 and Cy5 labeled target (adjust the color to purple), add 1/10 volume of 10 X fragmentation buffer (Ambion # 8740) and incubate for 15 min at 70 C. Add 3 ul of stop solution (Ambion # 8730) and complete dry the sample by speed vacuum. Add 19 ul of the following mixture to the dried target: 15 ul Kreatech hybridization buffer (Kraetech Diagnostics), 2 ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 2 ul yeast tRNA (4mg/ml Sigma Cat# R8759). Incubate for 3 min at 99 C and subsequently add 44.5 ul of the following mixture: 12.5 ul 20X SSC, 2ul 10% SDS, 30 ul formamide. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 42C for 20 hrs.

scan_protocol: Scan_MicronsPerPixelX: 10 Scan_MicronsPerPixelY: 10 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B US45103062, Agilent).

data_processing:
BRB Array Tools Data Processing Protocol
Calculation Method: Gene expression analysis was performed using NCI BRB-Array Tools Version 4.1.0 developed by the NCI Biometric Research Branch (Bethesda, MD). Each array was normalized using a median over the entire array. The data were filtered by intensity>=100 in both channel or override if one channel <100. Spot size>10um. Minimum fold change: less than 5% of expression data values have at least a 1.5 fold change in either direction from the gene median value. Excluded missing values present in less than 50% of samples across the entire data set.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-NonAT_95_Feb07 (Read Only)

source_name: Tumor Biopsy - Pre-therapy - Dose 0

label_protocol:
Cy5 Labeling Protocol
Other: Sample aRNA was labelled with cy5 using ULS aRNA Fluorescent Labeling kit (Kreatech).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen or Gibco BRL).

value: blood

tag: disease state

value: metastatic malignant melanoma

tag: other

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Labeling Protocol
Other: Reference aRNA was labelled with cy3 using ULS aRNA Fluorescent Labeling kit (Kreatech).

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 2 -Pre-therapy Dose 0 -blood -repeat 2 - mAdbID:107522

description: mAdb experiment ID: 107522

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B US45103062, Agilent).

source_name: Blood Specimen - Pre-therapy - Dose 0

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: experiment 7 control samples at 24 h 7c24

source_name: experiment 7 control samples at 24 h

value: pooled whole-body extracts

value: control

value: N2 Bristol


title: DNA normozospermic 18

description: normozoospermia

value: normozoospermia

value: lymphocyte


title: experiment 7 EtBr-exposed samples at 24 h 7e24

value: EtBr-exposed


title: experiment 7 UVC- and EtBr-exposed samples at 3 h 7eu3

value: UVC- and EtBr-exposed

value: 3 h


title: DNA normozospermic 21

description: normozoospermia

value: Male

value: normozoospermic

value: male


title: Patient 2 -Pre-therapy Dose 0 -tumor -repeat 1 - mAdbID:107520

description: mAdb experiment ID: 107520

value: blood

value: metastatic malignant melanoma


title: Patient 13 -Pre-therapy Dose 0 -tumor - mAdbID:107519

description: mAdb experiment ID: 107519

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.

value: Blood


title: Patient 12 -Dose 6 -tumor - mAdbID:107518

description: mAdb experiment ID: 107518

source_name: Tumor Biopsy - Dose 6 - 3 hours later

treatment_protocol:
Treatment type: compound
Agent: rIL-2 (Proleukin,®Prometheus Laboratories, San Diego, CA)
Treatment dose: 600,000 International Units/kg (0.037 mg
Treatment time: every 8 hours by a 15-minute intravenous
In-vitro treatment: Patients were hospitalized in a monitored hematology-oncology unit at the University of Virginia Medical Center and received 600,000 International Units/kg (0.037 mg/kg) of rIL-2 (Proleukin,®Prometheus Laboratories, San Diego, CA) every 8 hours by a 15-minute intravenous infusion for a maximum of 14 doses. Following 9 days of rest, the schedule was repeated for up to 14 doses, for a maximum of 28 doses per course, as tolerated. During administration of therapy, doses were frequently withheld for severe toxicity. Patients were medicated with cephalexin, famotidine, ibuprofen and acetaminophen on a scheduled basis to reduce the risk of infection and cytokine-release symptoms.

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the sixth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: GM18498_treated_4hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 4hr timepoint

value: YRI

value: Yoruba

value: ActD


title: DNA normozospermic 16

description: normozoospermia

source_name: genomic DNA extracted from lymphocytes of a normozospermic subject

value: normozoospermia

value: lymphocyte


title: GM18499_untreated_0hr

source_name: HapMap lymphoblastoid cell line, untreated, 0hr timepoint

value: female


title: 6h compatible interaction biological rep3

value: 1.5-2 cm of the second leaf sheath

value: Newton

value: 6h after Hessian fly egg hatching

value: infested with Hessian fly larvae


title: GM18498_treated_2hr

value: male


title: DNA normozospermic 17

description: normozoospermia

value: Male

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject

value: normozoospermic


title: GM18498_treated_0.5hr

source_name: HapMap lymphoblastoid cell line, treated with ActD, 0.5hr timepoint


title: GM18498_treated_1hr


title: experiment 7 EtBr-exposed samples at 3 h 7e3

value: pooled whole-body extracts

value: EtBr-exposed

value: 3 h

value: N2 Bristol


title: GM18498_untreated_0hr

value: YRI


title: experiment 7 UVC-exposed samples at 3 h 7u3

source_name: experiment 7 UVC-exposed samples at 3 h

value: UVC-exposed


title: Gene expression in virX mutant rep4

city: Kanazawa

first: Tohru

last: Shimizu

state: Ishikawa

address: 13-1, Takara-machi

department: Department of Bacteriology

institute: Kanazawa University

hyb_protocol: Hybridization solution (25 μl of Cy-dye-labeled cDNA solution, 10 μl of x20 SSC, 3 μl of water, and 2 μl of 10% SDS) was poured onto the slide glass and covered with a cover-glass with a gap (Matsunami Glass). The slide was inserted into the hybridization chamber, and hybridization was performed at 60 °C overnight.

scan_protocol: Scanned on an FLA-8000 scanner (Fuji Film, Japan). The density of the scanned spots was measured by ArrayVision software (Imaging Research, USA)

data_processing: Normalized by the median of the raw intensities for all spots in each control and sample. LOWESS normalization was performed. GeneSpring software was used.

organism: Clostridium perfringens str. 13

source_name: wild-type strain 13 durin exponential growth

label_protocol: 15 µg of total RNA from was mixed with 2 µl of random primers (d(N)6, d(N)9, 0.5 µg/µl each, Takara, Japan) and adjusted to 22 µl with water. The solution was kept at 65°C for 5 min to denature the RNA. The annealing reaction was performed at 42°C for 5 min. The premix solution (18 µl) was mixed into RNA solution, and reverse transcription was performed at 42 °C for 60 min. The premix solution was a mixture of 8 µl of x5 power script reaction buffer, 4 µl of dNTPs (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP, 3 mM amino-allyl dUTP (Sigma, USA)), 4 µl of 0.1 M DTT, 0.1 µl of RNase inhibitor (TakaRa, Japan), and 2 µl of Powerscript reverse transcriptase (BD Biosciences, USA). After incubation, 5 µl of 0.5M EDTA (pH 8.0) and 10 µl of 1 N NaOH were mixed, and the mixture was incubated at 65°C for 30 min to stop the reaction and remove the RNA templates, followed by the addition of 25 µl of 1 M Tris-Cl (pH 7.5) for neutralization. The mixture was transferred to a Microcon-30 filter (Millipore, USA) and centrifuged. The filter was washed with 100 µl of water 4 times, and the sample was eluted in 25 µl of water. The solution was completely dried, re-suspended in 10 µl of 50 mM NaCO3, and incubated at room temperature (RT) for 3 min. Ten microliters of Cy3 or Cy5 (GE Healthcare, USA) was mixed and incubated at RT for 60 min in a dark place. Ten microliters of Na2OH (Sigma) was added to remove un-reacted Cy-dye. Finally, the labeled product was purified by a QIAquick column (Qiagen, Germany).

growth_protocol: strains were cultured in GAM (Gifu Anaerobic Medium)

extract_protocol: Total RNA extracted using hot-phenol method

tag: genotype

value: wild-type

source_name: virX mutant (TS186) during exponential growth

value: virX mutant


title: Gene expression in virX mutant rep3


title: Patient 12 -Pre-therapy Dose 0 -blood -repeat 2 - mAdbID:107516

description: mAdb experiment ID: 107516

value: blood

value: metastatic malignant melanoma

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: experiment 7 control samples at 3 h 7c3

source_name: experiment 7 control samples at 3 h

value: control

tag: time


title: DNA normozospermic 13

description: normozoospermia

value: Male

value: normozoospermia

value: lymphocyte

value: male


title: Patient 12 -Pre-therapy Dose 0 -tumor - mAdbID:107517

description: mAdb experiment ID: 107517

tag: tissue

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: Patient 11 -Pre-therapy Dose 0 -tumor -repeat 2 - mAdbID:107514

description: mAdb experiment ID: 107514


title: DNA normozospermic 14

description: normozoospermia

value: normozoospermic


title: DNA normozospermic 15

description: normozoospermia


title: experiment 6 UVC- and EtBr-exposed samples at 48 h 6Eu48

value: pooled whole-body extracts

value: UVC- and EtBr-exposed

value: N2 Bristol


title: Patient 12 -Pre-therapy Dose 0 -blood -repeat 1 - mAdbID:107515

description: mAdb experiment ID: 107515


title: experiment 6 UVC- and EtBr-exposed samples at 51 h 6Eu51


title: DNA normozospermic 12

description: normozoospermia


title: DNA normozospermic 11

description: normozoospermia


title: experiment 6 EtBr-exposed samples at 51 h 6e51

value: EtBr-exposed


title: 12h incompatible interaction biological rep3

source_name: Wheat, 1.5-2 cm of the second leaf sheath

value: 1.5-2 cm of the second leaf sheath

value: Molly

value: 12h after Hessian fly egg hatching

value: infested with Hessian fly larvae


title: experiment 6 EtBr-exposed samples at 48 h 6e48


title: Gene expression in virX mutant rep2

value: wild-type

value: virX mutant


title: Gene expression in virX mutant rep1


title: Patient 10 -Pre-therapy Dose 0 -tumor -repeat 2 - mAdbID:107512

description: mAdb experiment ID: 107512

value: blood

value: metastatic malignant melanoma

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 9 -Dose 6 -tumor - mAdbID:107511

description: mAdb experiment ID: 107511

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the sixth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: Patient 10 -Dose 4 -tumor - mAdbID:107513

description: mAdb experiment ID: 107513

source_name: Tumor Biopsy - Dose 4 - 3 hours later

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the fourth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: NHBE_day28_1 [miRNA]

city: Bethesda

first: Steven

last: Kern

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

description: CCL100415_ALI_day 28_1

hyb_protocol: Following fragmentation, labeled RNA was hybridized to the Affymetrix miRNA GeneChip at 46 ⁰C and 60 rpm for 16h. The microarrays were washed and stained in the Affymetrix Fluidics Station 450 using the standard format as describe by Affymetrix.

scan_protocol: MicroRNA chips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Expression values for miRNA were summarized using Affymetrix’s QC toolbox. All statistical analysis were performed using the Mathematical and Statistical Computing Laboratory (MSCL) Analyst's Toolbox (http://abs.cit.nih.gov/MSCLtoolbox/)

source_name: NHBE cells_Day 28

label_protocol: Total RNA (300ng) was processed and labeled using the FlashTag Biotin RNA Labeling Kit following manufacturer's instruction

growth_protocol: Normal human bronchial epithelial cells were grown in 6.5-mm transwell-clear membrane supports coated with rat tail collagen inserted in 24-well plates. Undifferentiated cells were grown under submerged conditions until they reached confluence. At that point, an air-liquid interface culture was created by removing the apical medium and replacing the medium of the basal compartment with B-ALI differentiation medium. Medium was changed every 48h throughout the ALI culture period (4 weeks).

extract_protocol: Trizol extraction of total RNA (including small RNAs) was combined with spin column extraction following manufacturer's instructions (miRNeasy  Mini kit, Qiagen).

treatment_protocol: Cells were harvested for total RNA extraction when they were subconfluent or confluent, and after 28 days of ALI culture.

value: normal human bronchial epithelial (NHBE) cells

tag: culture stage

value: Day 28


title: experiment 6 EtBr-exposed samples at 24 h 6e24

value: pooled whole-body extracts

value: N2 Bristol


title: Patient 9 -Pre-therapy Dose 0 -tumor - mAdbID:107510

description: mAdb experiment ID: 107510

source_name: Tumor Biopsy - Pre-therapy - Dose 0

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: DNA normozospermic 9

description: normozoospermia

value: Male

value: normozoospermia

value: lymphocyte

value: normozoospermic

value: male


title: Patient 8 -Dose 6 -tumor - mAdbID:107509

description: mAdb experiment ID: 107509

value: blood

source_name: Pooled Normal Donor PBMC


title: Patient 6 -Dose 8 -3-hr-blood - mAdbID:107508

description: mAdb experiment ID: 107508

source_name: Blood Specimen - Dose 8 - 3-hour blood

value: metastatic malignant melanoma

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the 8th dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: NHBE_day28_2 [miRNA]

description: CCL100415_ALI_day 28_2


title: NHBE_Confluent_3 [miRNA]

source_name: NHBE cells_Confluent stage

value: Confluent


title: experiment 6 UVC- and EtBr-exposed samples at 24 h 6Eu24

value: UVC- and EtBr-exposed


title: NHBE_Confluent_2 [miRNA]


title: DNA normozospermic 8

description: normozoospermia


title: DNA normozospermic 10

description: normozoospermia


title: NHBE_Confluent_1 [miRNA]


title: NHBE_day28_3 [miRNA]

description: CCL100415_ALI_day 28_3


title: experiment 6 control samples at 24 h 6c24

source_name: experiment 6 control samples at 24 h

value: control


title: experiment 6 UVC-exposed samples at 24 h 6u24

value: UVC-exposed


title: experiment 6 UVC- and EtBr-exposed samples at 3 h 6Eu3

value: 3 h


title: experiment 6 EtBr-exposed samples at 3 h 6e3

value: EtBr-exposed


title: DNA normozospermic 5

description: normozoospermia


title: DNA normozospermic 4

description: normozoospermia


title: DNA normozospermic 3

description: normozoospermia


title: DNA normozospermic 6

description: normozoospermia


title: experiment 6 UVC-exposed samples at 3 h 6u3

source_name: experiment 6 UVC-exposed samples at 3 h

value: pooled whole-body extracts


title: DNA normozospermic 7

description: normozoospermia

source_name: genomic DNA extracted from lymphocytes of a normozospermic subject


title: Patient 5 -Dose 6 -tumor - mAdbID:107506

description: mAdb experiment ID: 107506

source_name: Tumor Biopsy - Dose 6 - 3 hours later

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the sixth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 6 -Pre-therapy Dose 0 -tumor - mAdbID:107507

description: mAdb experiment ID: 107507

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: DNA normozospermic 2

description: normozoospermia

value: Male

value: normozoospermia

value: lymphocyte

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject

value: normozoospermic


title: NHBE_Subconfluent_2 [miRNA]

source_name: NHBE cells_Subconfluent stage

value: normal human bronchial epithelial (NHBE) cells

value: Subconfluent


title: Patient 5 -Pre-therapy Dose 0 -tumor - mAdbID:107505

description: mAdb experiment ID: 107505

value: blood

value: metastatic malignant melanoma


title: Patient 4 -Dose 4 -tumor - mAdbID:107504

description: mAdb experiment ID: 107504

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the fourth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: Patient 4 -Dose 4 -3-hr-blood - mAdbID:107503

description: mAdb experiment ID: 107503

source_name: Blood Specimen - Dose 4 - 3-hour blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the fourth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: NHBE_Subconfluent_1 [miRNA]


title: Patient 3 -Dose 6 -tumor - mAdbID:107501

description: mAdb experiment ID: 107501


city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: human peripheral blood B cells  N10 Normal bone marrow plasma cells_GPL91

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard affymetrix protocol

extract_protocol: RNeasy Mini Kit(50)


description: human peripheral blood B cells  N09 Normal bone marrow plasma cells_GPL91


title: Patient 4 -Pre-therapy Dose 0 -tumor - mAdbID:107502

description: mAdb experiment ID: 107502


title: experiment 5 UVC- and EtBr-exposed samples at 51 h 5Eu51

value: UVC- and EtBr-exposed

value: N2 Bristol


title: Patient 3 -Dose 6 -3-hr-blood -repeat 2 - mAdbID:107500

description: mAdb experiment ID: 107500

source_name: Blood Specimen - Dose 6 - 3-hour blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the sixth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: DNA infertile 94

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

value: azoospermia

value: male


title: Patient 3 -Pre-therapy Dose 0 -tumor - mAdbID:107499

description: mAdb experiment ID: 107499

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: DNA infertile 96

description: azoospermia

value: Male


title: NHBE_Subconfluent_3 [miRNA]


description: human peripheral blood B cells  N08 Normal bone marrow plasma cells_GPL91


description: human peripheral blood B cells  N07 Normal bone marrow plasma cells_GPL91


title: DNA normozospermic 1

description: normozoospermia

value: normozoospermia

value: lymphocyte


title: experiment 5 EtBr-exposed samples at 51 h 5e51

value: pooled whole-body extracts

value: EtBr-exposed


title: experiment 5 control samples at 51 h 5c51

source_name: experiment 5 control samples at 51 h

value: control


title: experiment 5 UVC- and EtBr-exposed samples at 48 h 5Eu48


title: experiment 5 UVC-exposed samples at 48 h 5u48

value: UVC-exposed


title: DNA infertile 93

description: severe oligozoospermia

value: severe oligozoospermia

value: normozoospermic


title: DNA infertile 95

description: azoospermia


title: Patient 2 -Dose 6 -tumor -repeat 2 - mAdbID:107498

description: mAdb experiment ID: 107498

value: blood

value: metastatic malignant melanoma

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the sixth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: experiment 5 UVC-exposed samples at 51 h 5u51

value: N2 Bristol


title: experiment 6 control samples at 3 h 6c3

source_name: experiment 6 control samples at 3 h

value: 3 h


title: DNA infertile 92

description: mild oligozoospermia

value: mild oligozoospermia

value: male


description: human peripheral blood B cells  N05 Normal bone marrow plasma cells_GPL91


title: experiment 5 control samples at 48 h 5c48

source_name: experiment 5 control samples at 48 h


description: human peripheral blood B cells  N06 Normal bone marrow plasma cells_GPL91


title: DNA infertile 91

description: azoospermia

value: azoospermia


title: Patient 13 -Pre-therapy Dose 0 -blood - mAdbID:107490

description: mAdb experiment ID: 107490

source_name: Blood Specimen - Pre-therapy - Dose 0

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.

value: Blood

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: Patient 2 -Dose 6 -tumor -repeat 1 - mAdbID:107497

description: mAdb experiment ID: 107497


description: human peripheral blood B cells  N01 Normal bone marrow plasma cells_GPL91


title: Patient 12 -Dose 6 -3-hr-blood - mAdbID:107487

description: mAdb experiment ID: 107487

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the sixth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: DNA infertile 90

description: severe oligozoospermia

value: Male

value: lymphocyte


description: human peripheral blood B cells  N03 Normal bone marrow plasma cells_GPL91


title: experiment 5 EtBr-exposed samples at 24 h 5e24

value: pooled whole-body extracts

value: EtBr-exposed


title: Patient 12 -Pre-therapy Dose 0 -tumor - mAdbID:107486

description: mAdb experiment ID: 107486

source_name: Tumor Biopsy - Pre-therapy - Dose 0

value: blood

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


description: human peripheral blood B cells  N04 Normal bone marrow plasma cells_GPL91


title: experiment 5 UVC- and EtBr-exposed samples at 3 h 5eu3

value: UVC- and EtBr-exposed


title: DNA infertile 86

description: azoospermia

value: normozoospermic


title: T9 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T9 tonsil plasma cells_GPL91

source_name: T9 tonsil plasma cells_GPL91

tag: T9 tonsil plasma cells_GPL91


title: experiment 5 EtBr-exposed samples at 3 h 5e3

value: 3 h

value: N2 Bristol


title: experiment 5 UVC-exposed samples at 24 h 5u24

value: UVC-exposed


title: T7 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T7 tonsil plasma cells_GPL91

source_name: T7 tonsil plasma cells_GPL91

tag: T7 tonsil plasma cells_GPL91


title: experiment 5 UVC- and EtBr-exposed samples at 24 h 5eu24

tag: treatment


description: human peripheral blood B cells  N002 Normal bone marrow plasma cells_GPL91


title: Patient 11 -Dose 5 -21-hr-blood - mAdbID:107481

description: mAdb experiment ID: 107481

source_name: Pooled Normal Donor PBMC

source_name: Blood Specimen - Dose 5 - 21-hour blood

value: metastatic malignant melanoma

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 21 hours after the 5th dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: Patient 11 -Dose 4 -tumor - mAdbID:107480

description: mAdb experiment ID: 107480

value: Blood

source_name: Tumor Biopsy - Dose 4 - 3 hours later

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the fourth dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: experiment 5 control samples at 24 h 5c24

source_name: experiment 5 control samples at 24 h

value: control


title: Patient 11 -Dose 5 -tumor - mAdbID:107482

description: mAdb experiment ID: 107482

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.

source_name: Tumor Biopsy - Dose 5 - 3 hours later

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained 3 hours after the 5th dose of rIL-2. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: T5 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T5 tonsil plasma cells_GPL91

source_name: T5 tonsil plasma cells_GPL91

tag: T5 tonsil plasma cells_GPL91


title: DNA infertile 87

description: severe oligozoospermia

value: Male

tag: phenotype

value: severe oligozoospermia

value: lymphocyte

source_name: genomic DNA extracted from lymphocytes of the reference normozoospermic control subject

value: male


title: DNA infertile 85

description: mild oligozoospermia

value: mild oligozoospermia


title: DNA infertile 89

description: azoospermia

value: azoospermia

value: normozoospermic


title: DNA infertile 83

description: azoospermia


title: Patient 11 -Dose 4 -3-hr-blood - mAdbID:107479

description: mAdb experiment ID: 107479

source_name: Blood Specimen - Dose 4 - 3-hour blood

value: blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the fourth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: T6 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T6 tonsil plasma cells_GPL91

source_name: T6 tonsil plasma cells_GPL91

tag: T6 tonsil plasma cells_GPL91


title: experiment 5 control samples at 3 h 5c3

source_name: experiment 5 control samples at 3 h

value: pooled whole-body extracts

value: 3 h

value: N2 Bristol


title: T4 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T4 tonsil plasma cells_GPL91

source_name: T4 tonsil plasma cells_GPL91

tag: T4 tonsil plasma cells_GPL91


title: Patient 11 -Pre-therapy Dose 0 -tumor -repeat 1 - mAdbID:107477

description: mAdb experiment ID: 107477

value: metastatic malignant melanoma

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.

value: Blood

tag: cell type


title: Patient 12 -Dose 6 -20-hr-blood - mAdbID:107488

description: mAdb experiment ID: 107488

value: PBMC

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.

source_name: Blood Specimen - Dose 6 - 20-hour blood

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 20 hours after the sixth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: Patient 11 -Pre-therapy Dose 0 -blood -repeat 2 - mAdbID:107475

description: mAdb experiment ID: 107475

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: experiment 5 UVC-exposed samples at3 h 5u3

source_name: experiment 5 UVC-exposed samples at3 h

value: UVC-exposed


title: DNA infertile 81

description: azoospermia

source_name: genomic DNA extracted from lymphocytes of an infertile patient

tag: gender

value: Male

value: lymphocyte

tag: cnv count

value: male


title: T2 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T2 tonsil plasma cells_GPL91

source_name: T2 tonsil plasma cells_GPL91

tag: T2 tonsil plasma cells_GPL91


title: DNA infertile 88

description: severe oligozoospermia

value: severe oligozoospermia

tag: cnv code

value: normozoospermic


title: experiment 4 UVC- and EtBr-exposed samples at 51 h 4eu51

value: UVC- and EtBr-exposed

tag: strain


title: experiment 4 EtBr-exposed samples at 51 h 4e51

value: pooled whole-body extracts

value: EtBr-exposed


title: Patient 11 -Pre-therapy Dose 0 -blood -repeat 1 - mAdbID:107474

description: mAdb experiment ID: 107474

source_name: Blood Specimen - Pre-therapy - Dose 0

value: blood

tag: disease state

tag: other


title: experiment 4 UVC-exposed samples at 51 h 4u51

tag: tissue

tag: time

value: N2 Bristol


title: Patient 10 -Pre-therapy Dose 0 -tumor -repeat 1 - mAdbID:107471

description: mAdb experiment ID: 107471

source_name: Tumor Biopsy - Pre-therapy - Dose 0

value: metastatic malignant melanoma

value: FNA (fine needle aspiration biopsy) of melanoma metastases were obtained pre-therapy. A 23 Gauge hypodermic needle was inserted into the tumor. After insertion, multiple passes at changing angles of insertion were made through all quadrants of the tumor. Tissue collected into the needle was suspended in 10 ml cold RPMI and centrifuged at 1500 rpm for 5 minutes at 4oC. The cell pellet was harvested and red blood cells were eliminated with ACK lysis buffer. Cells were resuspended in 1 ml cold RPMI, transferred to a 1.5 ml Eppendorf tube, spun at 1500 rpm for 5 minutes and the supernatant was discarded. The cell pellet was resuspended in 500 ul of Trizol (Gibco BRL) and mixed thoroughly in the lysis buffer to ensure lysis of all cells. Lysates were frozen at -80oC until use.


title: T10 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T10 tonsil plasma cells_GPL91

source_name: T10 tonsil plasma cells_GPL91

tag: T10 tonsil plasma cells_GPL91


title: T11 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T11 tonsil plasma cells_GPL91

source_name: T11 tonsil plasma cells_GPL91

tag: T11 tonsil plasma cells_GPL91


title: Patient 10 -Dose 4 -3-hr-blood - mAdbID:107472

description: mAdb experiment ID: 107472

source_name: Pooled Normal Donor PBMC

value: Blood

value: PBMC

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) 3 hours after the fourth dose of rIL-2 to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.


title: DNA infertile 84

description: azoospermia

value: azoospermia


title: DNA infertile 79

description: azoospermia


title: experiment 4 UVC- and EtBr-exposed samples at 48 h 4eu48

tag: treatment


title: Patient 10 -Pre-therapy Dose 0 -blood - mAdbID:107469

description: mAdb experiment ID: 107469

value: Blood specimens were collected in CPT tubes containing sodium heparin, gel and density gradient media (8 ml) (BD bioscience) pre-therapy to separate PBMC for RNA preparation. PBMC were pelleted by centrifugation, lysed in 700 ul of Trizol reagent (Invitrogen) and stored at -80 till use.

value: Sample Pooling Protocol:Pooled PBMC from 5 normal donors obtained from aphereses.


title: experiment 4 EtBr-exposed samples at 48 h 4e48


title: T1 tonsil plasma cells_GPL91

description: human peripheral blood B cells  T1 tonsil plasma cells_GPL91

source_name: T1 tonsil plasma cells_GPL91

tag: T1 tonsil plasma cells_GPL91


title: W2 WM plasma cells_GPL91

description: human peripheral blood B cells  W2 WM plasma cells_GPL91

source_name: W2 WM plasma cells_GPL91

tag: W2 WM plasma cells_GPL91


title: DNA infertile 82

description: azoospermia

value: Male

tag: phenotype

value: lymphocyte


title: DNA infertile 77

description: azoospermia

value: male


title: DNA infertile 78

description: azoospermia

value: normozoospermic