title: HeLa_sodium butyrate_2

description: HeLa_sodium butyrate_2

source_name: HeLa 15 hrs NaB treatment

label_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay (P/N 701880 Rev. 5)

value: sodium butyrate


title: Non-smokers 4

status: Public on Feb 03 2011

type: RNA

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

country: USA

institute: University of Iowa

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST arrays (Part No. 900650), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 GeneChip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), and signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade.

data_processing:
Data were collected using the GeneChip Operating Software (GCOS) v1.4. Data were normalized by RMA using PartekGS v 6.5.

Genome build: hg18
Exons used in analysis: core
Probe group file: HuEx-1_-st-v2.r2pgf
Meta-probeset file: HuEx-1_0-st-v2.rx.dt1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bronchoalveolar lavage, non-smoker

label_protocol: Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  Four ug of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: After informed consent was obtained, subjects underwent standard flexible bronchoscopy.  After the application of local anesthesia, bronchoalveolar lavage was performed by instilling 20 ml of normal saline into a tertiary bronchus up to five times in three different lung segments.  The first collection out of five was discarded for possible contamination from upper airway secretions or by lidocaine, which is used to locally anesthetize the subject during the procedure.  The remaining lavage was transported to the laboratory where fluid was filtered through sterile gauze and centrifuged at 200 x g for 5 min to pellet cellular material. The resulting pellet was suspended in phosphate-buffered saline and centrifuged at 16,000 x g for one minute.  The macrophages were suspended in medium, labeled with Wright stain and microscopically examined to ensure that greater than 95% of the cells were macrophages.  Following validation, 5x10^6 cell aliquots were frozen at -80°C for later DNA and RNA isolation.

tag: cell type

value: alveolar macrophages

tag: sample type

value: non-smoker


title: Non-smokers 9


title: HeLa_control_1

city: Prague

first: David

last: Stanek

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

hyb_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay (P/N 701880 Rev. 5)

scan_protocol: Affymetrix GeneChip Expression Wash, Stain, and Scan User Manual (P/N 702731)

data_processing: Data were analysed using Partek Genomics Suite 6.4 software (RMA, quantile normalization). Only  ‘core’ meta-probe sets were used to identify alternative splicing events.

source_name: HeLa control

growth_protocol: HeLa cells cultured in DMEM supplemented with 10% fetal calf serum, penicillin, and streptomycin.

extract_protocol: Total RNA isolated with TRIzol

treatment_protocol: 15 hrs treatment with 5mM sodium butyrate

tag: cell line

value: HeLa

tag: agent


title: Non-smokers 10


title: HeLa_sodium butyrate_1

description: HeLa_sodium butyrate_1


title: Non-smokers 8


title: Non-smokers 5


title: Non-smokers 2


title: Skin, day 15, fish 4

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: Time-point 5 of 5, biological replicate 4 of 4

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned GenePix 4100A at a resolution of 5 microns

data_processing: GenePix Pro 6.0 was used for spot to grid alignment, feature extraction and quantification. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Skin of infected salmon

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Salmon (100-200 g) was kep in tanks with sea water

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)

treatment_protocol: Salmon louse of LsGulen strain were reared in the hatchery and egg strings were collected and placed into an incubator until they reached the copepodid stage. Atlantic salmon were challenged with L. salmonis (approximately 100 copepodids per fish).

tag: disease state

value: challenged with L. salmonis

source_name: Skin of control salmon


title: Lovo cells infected with LntA-V5+ Listeria, biological rep1

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Cell intensity files were generated with GeneChipOperating Software. Raw data were processed by the Robust Multichip Analysis (RMA) algorithm.
probe group file: HuGene-1_0-st-v1.r3.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: 300 ng of total RNA were analysed using the Affymetrix Human Gene1.0 ST Array (exon array), according to the GeneChip whole transcript sense target labeling assay manual, using the GeneChip WT cDNA Synthesis and amplification Kit and WT terminal labeling Kit.

growth_protocol: LoVo cells grown in 6-well plates following ATCC  recommendations, to confluency. All cells were cultured at 37°C in a humidified atmosphere containing 10% CO2.

extract_protocol: RNA  was extracted using the RNeasy Mini Kit (Qiagen). RNA quality was monitored on Agilent RNA Pico LabChips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were infected  with either lntA-V5+ or DlntA Listeria strains

tag: infection

value: LntA-V5+ Listeria

tag: human cell line

value: Lovo epithelial cells ATCC CCL-229

tag: listeria strain


title: Lovo cells infected with LntA-V5+ Listeria, biological rep2


title: Lovo cells infected with mutant DLntA Listeria, biological rep1

value: Mutant DlntA Listeria


title: Lovo cells infected with mutant DLntA Listeria, biological rep3


title: HeLa_control_2


title: Fe-CRE+, Biological Rep 3

city: ANN Arbor

first: wenbo

last: xu

state: MI

address: MSR BILD II

institute: university of michigan

description: Gene expression data from livers of the Ire1α null mice under the non-stressed condition.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430_2 expression Array. GeneChips were washed and stained according to the standard procedures

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

data_processing: The data was anaylysed using D-chip and Genespring software

organism: Mus musculus

source_name: mouse liver tissue without ER stress challenge

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The Ire1α conditional null or control mice (C57Bl/6J strain background) of 3-months old were used for the experiment.

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

treatment_protocol: Mice were injected intraperitoneally with TM (2µg/gram body weight) or vehicle (150 µM dextrose), and liver tissue was isolated at 8 hours after the injection.

tag: tissue

value: liver

tag: age

value: 3-months old

tag: genotype/variation

value: Ire1α null

tag: strain

value: vehicle


title: Fe+CRE+, Biological Rep 2

description: Gene expression data from livers of the control mice under the non-stressed condition.

value: control


title: Fe-CRE+, Biological Rep 2


title: Skin, day 15, fish 2

description: Time-point 5 of 5, biological replicate 2 of 4


title: Fe-CRE+Tm, Biological Rep 3

description: Gene expression data from livers of the Ire1α null mice at 8 hours after tunicamycin treatment.

source_name: mouse liver tissue after ER stress challenge

value: tunicamycin


title: Fe-CRE+, Biological Rep 1


title: Skin, day 15, fish 3

description: Time-point 5 of 5, biological replicate 3 of 4


title: Fe+CRE+, Biological Rep 3


title: HeLa_sodium butyrate_3

description: HeLa_sodium butyrate_3


title: Lovo cells infected with mutant DLntA Listeria, biological rep2


title: Skin, day 15, fish 1

description: Time-point 5 of 5, biological replicate 1 of 4


title: Spleen, day 15, fish 2

source_name: Spleen of infected salmon

source_name: Spleen of control salmon


title: Spleen, day 15, fish 3


title: Lovo cells infected with LntA-V5+ Listeria, biological rep3


title: Fe-CRE+Tm, Biological Rep 1


title: Skin, day 10, fish 4

description: Time-point 4 of 5, biological replicate 4 of 4


title: Skin, day 10, fish 2

description: Time-point 4 of 5, biological replicate 2 of 4


title: Spleen, day 10, fish 4


title: Spleen, day 5, fish 4

description: Time-point 3 of 5, biological replicate 4 of 4


title: Fe+CRE+, Biological Rep 1


title: Skin, day 10, fish 3

description: Time-point 4 of 5, biological replicate 3 of 4


title: Skin, day 5, fish 3

description: Time-point 3 of 5, biological replicate 3 of 4


title: Spleen, day 10, fish 3


title: Spleen, day 10, fish 2


title: Spleen, day 5, fish 3


title: Spleen, day 5, fish 2

description: Time-point 3 of 5, biological replicate 2 of 4


title: Spleen, day 15, fish 4


title: Fe-CRE+Tm, Biological Rep 2


title: Skin, day 10, fish 1

description: Time-point 4 of 5, biological replicate 1 of 4


title: Spleen, day 15, fish 1


title: Skin, day 5, fish 4


title: CD8 T-Cell no treatment #1

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

description: Gene expression data from CD8 T-cells isolated from the MLR with nothing additional added to the media

hyb_protocol: Following fragmentation, aRNA was hybridized on GeneChip Mouse Genome 430 2.0 Array in a GeneChip Hybridization Oven 640. Whshing and Labeled by using GeneChip Fluidicas Station 450.

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

data_processing: The data were analyzed with AGCC (Affymetrix Genechip Command Console).  Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.

label: Biotin

label_protocol: aRNA was prepared according to the protocol for GeneChip 3 IVT Express Kit, Revision 7.

growth_protocol: Splenocytes were harvested from either FVB/N (stimulator) or C57BL/6 (responder) mice (Jackson Laboratories) and processed in PBS supplemented with 2% FCS (Invitrogen), n = 4 mice per group. After ACK red blood cell lysis of single cell suspensions, cells were placed in cRPMI media with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen), and 5 µg/mL 2-mercaptoethanol (Sigma-Aldrich). Responder cells were labeled with 5 µM CFSE from CellTrace™ CFSE Cell Proliferation Kit (Invitrogen). MLR was conducted by placing 8x105 FVB/N splenocytes, which had been irradiated with 30 Gy, into each well of a 96-well plate together with 2x105 CFSE-labeled C57BL/6 cells in a total volume of 250 μL cRPMI.  Proliferation of C57BL/6 responders was assessed by FACS analysis after 5 days of incubation with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L. Assays were performed in triplicate.

extract_protocol: Following the MLR, responder splenocytes were washed, resuspended in FACS buffer, and incubated with mouse-anti-human CD4+ and CD8+ antibodies (BD Biosciences) for 30 min at 4°C. Responder T-cell subsets were then isolated by FACS on a Vantage SE cell sorter (Becton Dickinson Immunocytometry Systems) analyzing for cells which were double positive for FITC (CFSE) and either CD4 or CD8. Sorted cells were collected and 3x105 cells were counted using a hemocytometer, and total RNA was immediately extracted using the RNeasy micro kit (Qiagen) per manufacturer’s instructions.

treatment_protocol: C57BL/6 responder splenocytes were incubated for 5 days with or without 50 µg CTLA4-Ig, 50 µg anti-LFA-1, and 50 µg anti-CD40L.

value: CD8 T-cells


title: CD8 T-Cell no treatment #2

source_name: CD8 T-cells isolated from the MLR with nothing additional added to the media


title: Skin, day 5, fish 2


title: Fe+CRE+Tm, Biological Rep 3

description: Gene expression data from livers of the control mice at 8 hours after tunicamycin treatment.


title: Sim2s transgenic replicate 1

city: College Station

first: Weston

last: Porter

state: Texas

department: Integrative Biosciences

institute: Texas A&M University

hyb_protocol: 1. Fragment cRNA. In 25 μl total volume, add 10 μg of cRNA to 5 μl of 5Å~ fragmentation buffer and incubate at 94 ºC for 20 min. 2. Prepare hybridization reaction mixture. Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 ºC for 5 min and immediately chill on ice for 5–30 min. 3. Loading reaction mixtures into array chambers. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. 4. Hybridization. Set the shaker speed to 300 rpm and incubate slides for 18–24 h at 37 ºC, maintaining a consistent hybridization time for comparative experiements. 5. Post-hybridization wash. Remove the Flex Chamber using the hybridization removal tool to hold the bioarray in place while peeling the Flex Chamber off at a 60º angle. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75Å~ TNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75Å~ TNT, and incubate at 46 °C for exactly 1 h. Do not exceed 1 h incubation. 6. Detection with streptavidin-dye conjugate. Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir into the small reagent reservoir and incubate bioarrays at ambient temperature for 30 min. Wash the bioarrays four times with 1Å~ TNT (5 min each wash) in large reagent reservoirs. Rinse the bioarrays in 0.1Å~ SSC/0.05% Tween™ for 30 s. Immediately follow the rinse with centrifugation to dry bioarrays, and store dried bioarrays in the dark.

scan_protocol: Images were captured on anAxon GenePix Scanner (Arlington, TX) using CodeLink Expression Scanning Software and were analyzed using CodeLink Expression Analysis Software

data_processing: Raw microarray data was normalized and analyzed using CodeLink Expression Analysis Software version 4.1.0.29054 (GE Healthcare). A median normalization method was used, with a 20% threshold trim percentage.

source_name: fourth inguinal mammary gland

label_protocol: 1. Assessment of total RNA concentration and quality. Assess the concentration and quality of the total RNA sample by spectrophotometry and electrophoresis (Appendixes 2 and 3), or by another  analytical method such as use of the Agilent™ Bioanalyzer. 2. Synthesis of first-strand cDNA. Incubate total RNA (0.2–2 μg), diluted bacterial control mRNAs and T7 oligo(dT) primer for 10 min at 70 ºC. Add first-strand reaction components and incubate for 2 h at 42 °C. 3. Synthesis of second-strand cDNA. Add the first-strand cDNA product to the secondstrand reaction components and incubate for 2 h at 16 °C in a refrigerated incubator. 4. Purification of double-stranded cDNA. Purify and elute twice with 30 μl EB buffer each time. Dry the purified cDNA. 5. Synthesis of cRNA by IVT. Resuspend cDNA pellet in resuspension solution. Add biotinylated UTP, ribonucleotides, and the 10Å~ T7 enzyme mix to the resuspended cDNA and incubate at 37 °C for 14 h. 6. Recovery of biotin-labelled cRNA. Purify cRNA and elute the cRNA twice—each time with 50 μl nuclease-free water. 7. Assessment of cRNA concentration, yield, and quantity. Measure the absorbance at 260 nm of a 2 μl aliquot of cRNA diluted in 98 μl water. Add 11 μl of 0.1 M Tris- HCl to the sample and read the sample again at 260 nm and 280 nm to determine the A260:A280 ratio. If the ratio is less than 1.8, precipitate the cRNA according to Appendix 7. Do not proceed with bioarray processing unless the A260:A280 ratio is greater than 1.8.

growth_protocol: Pups were removed from both wild-type and MMTV-Sim2s mice at lactation day 10.  Mammary tissue was harvested from dams 72 hours post weaning.  The fourth inguinal mammary glands were used for RNA isolation.  All animals were housed in solitary caging after parturition (with litter) under a standard 12 hour photoperiod.  The animals were given access to food and water ad libitum.

extract_protocol: RNA was isolated from tissues using Trizol Reagent (Invitrogen), followed by purification using a Qiagen RNEasy Mini Kit (Qiagen, Valencia, CA) .  There was no deviation from the manufacturer's protocol

value: 10 week

tag: gender

value: female

tag: genetic background

value: FVB

value: fourth inguinal mammary gland

tag: genotype

value: Sim2s transgenic


title: Spleen, day 1, fish 3

description: Time-point 1 of 5, biological replicate 3 of 4


title: Spleen, day 1, fish 4

description: Time-point 1 of 5, biological replicate 4 of 4


title: Fe+CRE+Tm, Biological Rep 2


title: Spleen, day 5, fish 1

description: Time-point 3 of 5, biological replicate 1 of 4


title: Fe+CRE+Tm, Biological Rep 1


title: Skin, day 5, fish 1


title: Skin, day 3, fish 4

description: Time-point 2 of 5, biological replicate 4 of 4


title: Skin, day 1, fish 3


title: Skin, day 3, fish 3

description: Time-point 2 of 5, biological replicate 3 of 4


title: wild-type replicate 2

value: wild-type


title: Spleen, day 10, fish 1

value: challenged with L. salmonis


title: Spleen, day 3, fish 4


title: Spleen, day 3, fish 3


title: Spleen, day 3, fish 2

description: Time-point 2 of 5, biological replicate 2 of 4


title: CD4 T-Cell Costimulatory blockade treated #2

description: Gene expression data from CD4 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media

value: CD4 T-cells

value: leuckocyte costimulatory blocking antibodies anti-LFA-1, CTLA4Ig, anti-CD40-ligand


title: Skin, day 3, fish 2


title: Spleen, day 3, fish 1

description: Time-point 2 of 5, biological replicate 1 of 4


title: Sim2s transgenic replicate 3


title: Skin, day 3, fish 1


title: CD4 T-Cell Costimulatory blockade treated #1

source_name: CD4 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media


title: CD8 T-Cell Costimulatory blockade treated #2

description: Gene expression data from CD8 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media


title: Sim2s transgenic replicate 2


title: CD8 T-Cell Costimulatory blockade treated #1

source_name: CD8 T-cells isolated from the MLR with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies added to the media


title: Skin, day 1, fish 4


title: CD4 T-Cell no treatment #2

description: Gene expression data from CD4 T-cells isolated from the MLR with nothing additional added to the media


title: flower_athd1_rep4

status: Public on Feb 02 2011

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

description:
7-37-ws_cy5,athd1_cy3
Biological replicate 2 of 4.

hyb_protocol: Each lyophilized probe was re-suspended in 40 μL of hybridization solution (0.25 M Na2HPO4, 0.25 M NaH2PO4, pH 7.4, and 3.5% SDS, w/v). The solution was heated for 2 min at 95 °C, chilled immediately in ice, and applied directly to the array. After covering the array with a 24 × 40 mm coverslip (Sigma, St Louis, MO), the slide was placed in a microarray hybridization chamber (Corning Incorporated, Corning, NY). Hybridization was performed overnight (16 h) at 60 °C in a hybridization oven. After hybridization, the slides were washed for 2 min in 2× SSC, 0.03% (w/v) SDS, 2 min in 0.2× SSC, and 2 min in 0.05× SSC. Immediately after the last wash, the slides were dried by centrifugation (3 min at 500 r.p.m.).

scan_protocol: Slides were scanned using GenePix 4000B.

data_processing:
We applied a linear model to exclude technical variation by arrays and dyes and biological variation by different plant populations. The linear model is:
Log (Yigkl) = µ + Gi + Tj + Ak + Dl + (G*T)ij + (G*A)ik + (G*D)il + (G*T*D)ijl + ɛijkl
where Y represents raw intensity after background level is subtracted; G, T, A, and D are main sources of variation from gene (G), treatment (plant species, T), array (A) and dye (D); i = 1,…, 31818; j = 1, 2; k = 1, 2, 3, 4;l = 1,2; µ represents the overall mean. The interaction terms, G*T, G*A, G*D, and G*T*D mean gene-by-species, gene-by-array, gene-by-dye and gene-by-species-by-dye. ɛijkl represents random error.

organism: Arabidopsis thaliana

source_name: wild type, flower

label_protocol: We used 500 ng of mRNA in each labeling reaction using Cy3- or Cy5-dCTP (Amersham Biosciences). The Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization, and then an equal amount of RNA samples was reversely labeled for another hybridization.

growth_protocol: The plants were grown in a growth chamber under growth conditions of 22°/18° (day/night) and 14 hr of illumination per day. RNA were isolated from tissues collected from a pool of 32 plants in each line. Rosette leaves were collected at the prebolting stage (~3 weeks), while flower buds were harvested after the first flower bloomed.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen, San Diego). The mRNA was isolated from 500 µg of total RNA with the FastTrack 2.0 mRNA isolation kit (Invitrogen).

treatment_protocol: Arabidopsis thaliana ecotype Ws (AtHD1/AtHD1, +/+), AtHD1/athd1-t1 (+/–), and athd1-t1/athd1-t1 (–/–) plants were produced.

tag: ecotype

value: Ws

value: flower

value: wild type

source_name: AtHD1 mutant, flower

value: AtHD1 mutant


title: wild-type replicate 3


title: Spleen, day 1, fish 2

description: Time-point 1 of 5, biological replicate 2 of 4


title: leaf_athd1_rep5

description:
7-21-ws_cy3,athd1_cy5
Biological replicate 3 of 4.

source_name: AtHD1 mutant, leaf

value: leaf

source_name: wild type, leaf


title: Skin, day 1, fish 2


title: leaf_athd1_rep6

description:
7-22-ws_cy5,athd1_cy3
Biological replicate 3 of 4.


title: leaf_athd1_rep3

description:
7-19-ws_cy3,athd1_cy5
Biological replicate 2 of 4.


title: CD4 T-Cell no treatment #1

source_name: CD4 T-cells isolated from the MLR with nothing additional added to the media

value: control


title: leaf_athd1_rep4

description:
7-20-ws_cy5,athd1_cy3
Biological replicate 2 of 4.


title: Skin, day 1, fish 1

description: Time-point 1 of 5, biological replicate 1 of 4


title: flower_athd1_rep7

description:
7-42-ws_cy3,athd1_cy5
Biological replicate 4 of 4.


title: wild-type replicate 1


title: leaf_athd1_rep1

description:
7-17-ws_cy3,athd1_cy5
Biological replicate 1 of 4.


title: RCH_KIDNEY_14_Snp_Hind

type: genomic

city: GrandRapids

first: Naga Manjari

last: Vadlapatla

address: 333 Bostwick Avenue Northeast

institute: Vanandel research Institute

hyb_protocol: Affymetrix procedures

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

data_processing: Files were processed by Affymetrix  GCOS  with default analysis setting

molecule: genomic DNA

source_name: Chromophobe renal tumor tissue

label_protocol: Fragmented DNA labeled by 2 ul of GeneChip DNA labeling Reagent(30mM)

extract_protocol: Jet quick kit according to maufacturers protocol

tag: tissue type

value: Chromophobe renal tumor tissue


title: flower_athd1_rep6

description:
7-41-ws_cy5,athd1_cy3
Biological replicate 3 of 4.


title: ON_KIDNEY_13_Snp_Hind

source_name: Oncocytoma renal tumor tissue

value: Oncocytoma renal tumor tissue


title: flower_athd1_rep5

description:
7-39-ws_cy3,athd1_cy5
Biological replicate 3 of 4.


title: Spleen, day 1, fish 1


title: ON_KIDNEY_11_Snp_Hind


title: flower_athd1_rep2

description:
7-33-ws_cy5,athd1_cy3
Biological replicate 1 of 4.


title: flower_athd1_rep3

description:
7-36-ws_cy3,athd1_cy5
Biological replicate 2 of 4.


title: flower_athd1_rep1

description:
7-32-ws_cy3,athd1_cy5
Biological replicate 1 of 4.


title: flower_athd1_rep8

description:
7-43-ws_cy5,athd1_cy3
Biological replicate 4 of 4.


title: leaf_athd1_rep8

description:
7-24-ws_cy5,athd1_cy3
Biological replicate 4 of 4.


title: ON_KIDNEY_10_Snp_Hind


title: ON_KIDNEY_11_Snp_Xba


title: ON_KIDNEY_12_Snp_Hind


title: ON_KIDNEY_9_Snp_Hind


title: ON_KIDNEY_13_Snp_Xba


title: leaf_athd1_rep7

description:
7-23-ws_cy3,athd1_cy5
Biological replicate 4 of 4.


title: WT Mem CD4 2

city: new haven

first: xing

last: chang

address: 10 Amistad street, RM414

institute: Yale University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: WT mice spleen and lymph nodes CD4 T cells

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

growth_protocol: cells with indicated surface marker were FACS sorted from spleen and lymph nodes of the mice

extract_protocol: Total RNA was extracted with TRIZOL and further cleaned up with Qiagen RNeasy cleanup kit

tag: cell surface marker

value: spleen and lymph nodes CD4 T cells


title: leaf_athd1_rep2

description:
7-18-ws_cy5,athd1_cy3
Biological replicate 1 of 4.


title: NUGC3_SOX2vsGFP_72h

city: Tokyo

first: Takeshi

last: Otsubo

address: 1-5-45 Yushima Bunkyo-ku

department: Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: 72 hours after infection

hyb_protocol: Standard Agilent protocol

scan_protocol: Agilent DNA Microarray scanner and Agilent scan control software

data_processing: Agilent Feature Extraction Software version 9.5.3

source_name: Gastric carcinoma cell line, infected with Adeno-GFP

label_protocol: Standard Agilent protocol

growth_protocol: NUGC3 cells were cultured in RPMI1640 medium.

extract_protocol: Total RNA was extracted by using Trizol reagent and treated with DNA-free.

treatment_protocol: NUGC3 cells were infected with the optimum 20 MOI (infectious units/cell) of SOX2- or control GFP-expressing adenoviral vectors. At 72 h after infection, the total RNAs were extracted.

tag: vector

value: Adenoviral GFP

source_name: Gastric carcinoma cell line, infected with Adeno-SOX2

value: Adenoviral SOX2


title: ON_KIDNEY_12_Snp_Xba


title: ON_KIDNEY_10_Snp_Xba


title: RCH_KIDNEY_14_Snp_Xba


title: ON_KIDNEY_6_Snp_Hind


title: RCH_KIDNEY_3_Snp_Hind


title: ON_KIDNEY_8_Snp_Hind


title: RCH_KIDNEY_1_Snp_Hind


title: WT Mem CD4 1

description: replicate 1


title: ON_KIDNEY_9_Snp_Xba


title: ON_KIDNEY_7_Snp_Hind


title: MEKK2/3 dKO Mem CD4 2

description: replicate 2

source_name: MEKK2/3 dKO mice spleen and lymph nodes CD4 T cells

value: MEKK2/3 dKO


title: RCH_KIDNEY_5_Snp_Hind


title: MEKK2/3 dKO Mem CD4 1

description: replicate 1


title: Abcb4 knockout mouse treated with norUDCA for 3 days 2

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Microarrays were hybridized in a volume of 1.5 ml at 55°C for 16 hours. After hybridization, arrays were washed with hybridization wash buffer and chemiluminescence rinse buffer. Enhanced chemiluminescent signals were generated by incubating arrays with alkaline phosphatase conjugated anti-digoxigenin antibody followed by incubation with chemiluminescence enhancing solution and a final addition of chemiluminescence substrate.

scan_protocol: Four images were collected for each microarray using the ABI 1700 Chemiluminescent Microarray Analyzer.

data_processing:
Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background and spot, and spatially normalized.
Expression values were imported into GeneSpring 6.2.1 (Silicon Genetics, Redwood, CA, USA) and processed according to Applied Biosystems standard procedure ("per chip" and "per gene" normalization). Data were filtered using the Cross-Gene Error Model (CEM); S/N >3 and Flag = 0.

label: Applied Biosystems Chemiluminescent RT Labeling Kit

source_name: mouse liver RNA

label_protocol: Each microarray was first pre-hybridized at 55°C for 1 hour in hybridization buffer with blocking reagent. Oligo(dT)-primed, DIG-labeled cDNA targets were fragmented, mixed with internal control target.

extract_protocol: Tissues were immediately snap-frozen in pre-chilled 2-methylbutane after excision and stored in liquid nitrogen. RNA was isolated using TrizolTM reagent according to the manufacturer’s protocol. RNA samples were analyzed using Agilent Bioanalyzer Lab-on-chip Nano 6000 to determine integrity, quality, and concentration of the samples. Only samples fulfilling the quality criteria (Ratio of 28S to 18S rRNA of >2.0) were used for further microarray analysis.

value: FVB/N

value: 3 months

value: male

value: liver

value: Abcb4 KO

tag: treatment

value: side-chain modified bile acid "norUDCA" for 3 days


title: RCH_KIDNEY_4_Snp_Hind


title: ON_KIDNEY_8_Snp_Xba


title: ON_KIDNEY_7_Snp_Xba


title: Abcb4 knockout mouse FVBN 2

value: untreated


title: Abcb4 knockout mouse treated with norUDCA for 3 days 1


title: Wildtype mouse FVBN 1

value: wild type

value: untreated control


title: RCH_KIDNEY_5_Snp_Xba


title: RCH_KIDNEY_4_Snp_Xba


title: Wildtype mouse FVBN 2


title: ON_KIDNEY_6_Snp_Xba


title: RCH_KIDNEY_2_Snp_Xba


title: RCH_KIDNEY_3_Snp_Xba


title: RCH_KIDNEY_1_Snp_Xba


title: Liver F2 Control Pool (n=294) vs. 530417_F2_232

city: Boston

first: Sergey

last: Lezhnin

state: MA

address: 33 AVENUE LOUIS PASTEUR

department: Molecular Profiling

institute: Merck Research Laboratories

description: Mouse liver gene expression profiling of Cross B6/J xA/J

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

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

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

source_name: Liver F2 Control Pool (n=294)

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

value: B6/J x A/J


title: Liver F2 Control Pool (n=294) vs. 530419_F2_234


title: 530413_F2_219

description: Affymetrix Mouse liver gene expression profiling of Cross B6/J xA/J

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.


title: Liver F2 Control Pool (n=294) vs. 530418_F2_233


title: Liver F2 Control Pool (n=294) vs. 530416_F2_228


title: Liver F2 Control Pool (n=294) vs. 530433_F2_236


title: Liver F2 Control Pool (n=294) vs. 540137_F2_311


title: 540144_F2_295


title: 516127_F2_150


title: 533802_F2_246


title: 496916_F2_47


title: 522490_F2_185


title: Liver F2 Control Pool (n=294) vs. 549348_F2_313


title: Liver F2 Control Pool (n=294) vs. 549349_F2_314


title: 522495_F2_189


title: Liver F2 Control Pool (n=294) vs. 540138_F2_312


title: 522497_F2_187


title: 522499_F2_170


title: Liver F2 Control Pool (n=294) vs. 530414_F2_226


title: Liver F2 Control Pool (n=294) vs. 530431_F2_231


title: Liver F2 Control Pool (n=294) vs. 530422_F2_240


title: Liver F2 Control Pool (n=294) vs. 552556_F2_359


title: 533800_F2_244


title: 530417_F2_232


title: 505351_F2_96


title: Liver F2 Control Pool (n=294) vs. 530421_F2_239


title: Liver F2 Control Pool (n=294) vs. 530430_F2_230


title: Liver F2 Control Pool (n=294) vs. 530429_F2_229


title: Liver F2 Control Pool (n=294) vs. 530420_F2_238


title: 522492_F2_192


title: 552563_F2_346


title: RCH_KIDNEY_2_Snp_Hind


title: Liver F2 Control Pool (n=294) vs. 525930_F2_216


title: 496917_F2_48


title: 500879_F2_55


title: 549349_F2_314


title: Liver F2 Control Pool (n=294) vs. 525932_F2_214


title: Liver F2 Control Pool (n=294) vs. 533807_F2_262


title: Liver F2 Control Pool (n=294) vs. 533798_F2_260


title: 533790_F2_243


title: Liver F2 Control Pool (n=294) vs. 533811_F2_257


title: Liver F2 Control Pool (n=294) vs. 533797_F2_261


title: 530433_F2_236


title: 525927_F2_211


title: 540128_F2_299


title: 510610_F2_109


title: Liver F2 Control Pool (n=294) vs. 525931_F2_215


title: Liver F2 Control Pool (n=294) vs. 522507_F2_182


title: Liver F2 Control Pool (n=294) vs. 522506_F2_183


title: Liver F2 Control Pool (n=294) vs. 533809_F2_263


title: 516132_F2_156


title: 530430_F2_230


title: 505340_F2_90


title: Liver F2 Control Pool (n=294) vs. 533810_F2_258


title: 522509_F2_179


title: 533793_F2_252


title: Liver F2 Control Pool (n=294) vs. 522505_F2_181


title: Liver F2 Control Pool (n=294) vs. 522508_F2_180


title: 522491_F2_186


title: 496918_F2_25


title: 512424_F2_123


title: 549360_F2_322


title: Liver F2 Control Pool (n=294) vs. 552564_F2_348


title: Liver F2 Control Pool (n=294) vs. 552565_F2_347


title: Liver F2 Control Pool (n=294) vs. 540133_F2_308


title: Liver F2 Control Pool (n=294) vs. 540134_F2_309


title: 538351_F2_280


title: 530412_F2_218


title: 538356_F2_281


title: Liver F2 Control Pool (n=294) vs. 540141_F2_304


title: 510606_F2_99


title: 510609_F2_102


title: Liver F2 Control Pool (n=294) vs. 540131_F2_303


title: Liver F2 Control Pool (n=294) vs. 540132_F2_307


title: Liver F2 Control Pool (n=294) vs. 540140_F2_305


title: 525925_F2_205


title: 491029_F2_7


title: 491047_F2_24


title: Liver F2 Control Pool (n=294) vs. 540130_F2_302


title: 491028_F2_3


title: Liver F2 Control Pool (n=294) vs. 540125_F2_290


title: Liver F2 Control Pool (n=294) vs. 540129_F2_301


title: 510617_F2_104


title: 512423_F2_122


title: 512411_F2_125


title: Liver F2 Control Pool (n=294) vs. 540146_F2_293


title: Liver F2 Control Pool (n=294) vs. 540145_F2_294


title: Liver F2 Control Pool (n=294) vs. 540136_F2_310


title: Liver F2 Control Pool (n=294) vs. 540126_F2_291


title: 549352_F2_317


title: Liver F2 Control Pool (n=294) vs. 540144_F2_295


title: Liver F2 Control Pool (n=294) vs. 533808_F2_264


title: 538344_F2_279


title: 505329_F2_73


title: 491044_F2_16


title: 552546_F2_337


title: 538343_F2_278


title: Liver F2 Control Pool (n=294) vs. 533790_F2_243


title: Liver F2 Control Pool (n=294) vs. 530428_F2_225


title: Liver F2 Control Pool (n=294) vs. 530423_F2_220


title: 512410_F2_124


title: Liver F2 Control Pool (n=294) vs. 552563_F2_346


title: Liver F2 Control Pool (n=294) vs. 530424_F2_221


title: Liver F2 Control Pool (n=294) vs. 530413_F2_219


title: 512430_F2_135


title: 522502_F2_173


title: 500868_F2_67


title: Liver F2 Control Pool (n=294) vs. 533803_F2_247


title: 516136_F2_152


title: 530431_F2_231


title: 510607_F2_100


title: Liver F2 Control Pool (n=294) vs. 533801_F2_245


title: Liver F2 Control Pool (n=294) vs. 530426_F2_223


title: Liver F2 Control Pool (n=294) vs. 530427_F2_224


title: Liver F2 Control Pool (n=294) vs. 533800_F2_244


title: Liver F2 Control Pool (n=294) vs. 533802_F2_246


title: Liver F2 Control Pool (n=294) vs. 552560_F2_343


title: 549350_F2_315


title: 540124_F2_289


title: 505341_F2_76


title: Liver F2 Control Pool (n=294) vs. 552562_F2_345


title: 516134_F2_154


title: Liver F2 Control Pool (n=294) vs. 530412_F2_218


title: Liver F2 Control Pool (n=294) vs. 552549_F2_340


title: 549363_F2_328


title: Liver F2 Control Pool (n=294) vs. 552547_F2_338


title: 505334_F2_81


title: 530420_F2_238


title: Liver F2 Control Pool (n=294) vs. 530411_F2_217


title: 505348_F2_92


title: 496909_F2_34


title: Liver F2 Control Pool (n=294) vs. 533804_F2_248


title: Liver F2 Control Pool (n=294) vs. 552546_F2_337


title: 512417_F2_137


title: 522500_F2_171


title: 505331_F2_75


title: Liver F2 Control Pool (n=294) vs. 533789_F2_242


title: Liver F2 Control Pool (n=294) vs. 552558_F2_341


title: Liver F2 Control Pool (n=294) vs. 549351_F2_316


title: 549370_F2_335


title: Liver F2 Control Pool (n=294) vs. 538345_F2_283


title: Liver F2 Control Pool (n=294) vs. 538341_F2_276


title: 549364_F2_329


title: 510608_F2_101


title: Liver F2 Control Pool (n=294) vs. 549350_F2_315


title: Liver F2 Control Pool (n=294) vs. 533791_F2_250


title: 538357_F2_273


title: 525915_F2_201


title: 491041_F2_10


title: Liver F2 Control Pool (n=294) vs. 549359_F2_327


title: 552560_F2_343


title: 500877_F2_50


title: 525922_F2_196


title: 516117_F2_158


title: Liver F2 Control Pool (n=294) vs. 549364_F2_329


title: Liver F2 Control Pool (n=294) vs. 538344_F2_279


title: Liver F2 Control Pool (n=294) vs. 549363_F2_328


title: 512433_F2_144


title: Liver F2 Control Pool (n=294) vs. 549371_F2_336


title: Liver F2 Control Pool (n=294) vs. 538351_F2_280


title: 496923_F2_30


title: Liver F2 Control Pool (n=294) vs. 538355_F2_282


title: Liver F2 Control Pool (n=294) vs. 538343_F2_278


title: Liver F2 Control Pool (n=294) vs. 549370_F2_335


title: Liver F2 Control Pool (n=294) vs. 538356_F2_281


title: Liver F2 Control Pool (n=294) vs. 538342_F2_277


title: 533804_F2_248


title: 500874_F2_66


title: Liver F2 Control Pool (n=294) vs. 549361_F2_323


title: 500883_F2_64


title: 505330_F2_74


title: 496910_F2_35


title: 500873_F2_70


title: Liver F2 Control Pool (n=294) vs. 522490_F2_185


title: Liver F2 Control Pool (n=294) vs. 549355_F2_320


title: 505335_F2_82


title: Liver F2 Control Pool (n=294) vs. 549360_F2_322


title: Liver F2 Control Pool (n=294) vs. 549354_F2_319


title: Liver F2 Control Pool (n=294) vs. 549353_F2_318


title: 538359_F2_271


title: Liver F2 Control Pool (n=294) vs. 549352_F2_317


title: 491030_F2_8


title: Liver F2 Control Pool (n=294) vs. 522491_F2_186


title: 500870_F2_68


title: Liver F2 Control Pool (n=294) vs. 522495_F2_189


title: Liver F2 Control Pool (n=294) vs. 522497_F2_187


title: Liver F2 Control Pool (n=294) vs. 522494_F2_190


title: 505336_F2_83


title: 512422_F2_121


title: 538350_F2_266


title: 500886_F2_61


title: 500869_F2_69


title: Liver F2 Control Pool (n=294) vs. 522492_F2_192


title: Liver F2 Control Pool (n=294) vs. 522493_F2_191


title: Liver F2 Control Pool (n=294) vs. 525918_F2_204


title: Abcb4 knockout mouse FVBN 1


title: Liver F2 Control Pool (n=294) vs. 538352_F2_286


title: 510626_F2_119


title: 549357_F2_325


title: Liver F2 Control Pool (n=294) vs. 552554_F2_357


title: Liver F2 Control Pool (n=294) vs. 552566_F2_349


title: 491049_F2_18


title: Liver F2 Control Pool (n=294) vs. 538347_F2_285


title: 512412_F2_126


title: 512427_F2_129


title: Liver F2 Control Pool (n=294) vs. 522498_F2_169


title: 540142_F2_297


title: 516114_F2_146


title: Liver F2 Control Pool (n=294) vs. 522502_F2_173


title: 496908_F2_33


title: 516113_F2_145


title: 491039_F2_5


title: 491045_F2_17


title: Liver F2 Control Pool (n=294) vs. 522488_F2_177


title: Liver F2 Control Pool (n=294) vs. 552551_F2_354


title: Liver F2 Control Pool (n=294) vs. 522500_F2_171


title: 491033_F2_14


title: Liver F2 Control Pool (n=294) vs. 522501_F2_172


title: Liver F2 Control Pool (n=294) vs. 522486_F2_175


title: Liver F2 Control Pool (n=294) vs. 522509_F2_179


title: 496906_F2_31


title: Liver F2 Control Pool (n=294) vs. 522499_F2_170


title: 496919_F2_26


title: Liver F2 Control Pool (n=294) vs. 522487_F2_176


title: Liver F2 Control Pool (n=294) vs. 552552_F2_355


title: Liver F2 Control Pool (n=294) vs. 552568_F2_351


title: Liver F2 Control Pool (n=294) vs. 552567_F2_350


title: 500884_F2_63


title: 505343_F2_78


title: 491037_F2_20


title: 505337_F2_84


title: 538340_F2_275


title: 496921_F2_28


title: 538342_F2_277


title: Liver F2 Control Pool (n=294) vs. 552569_F2_352


title: Liver F2 Control Pool (n=294) vs. 552550_F2_353


title: 538338_F2_270


title: Liver F2 Control Pool (n=294) vs. 549362_F2_324


title: 496911_F2_36


title: 538355_F2_282


title: Liver F2 Control Pool (n=294) vs. 549358_F2_326


title: Liver F2 Control Pool (n=294) vs. 533806_F2_256


title: Liver F2 Control Pool (n=294) vs. 549357_F2_325


title: 549359_F2_327


title: 491046_F2_22


title: 525910_F2_193


title: 505342_F2_77


title: 491035_F2_19


title: Liver F2 Control Pool (n=294) vs. 533795_F2_254


title: Liver F2 Control Pool (n=294) vs. 540124_F2_289


title: Liver F2 Control Pool (n=294) vs. 522489_F2_184


title: Liver F2 Control Pool (n=294) vs. 540143_F2_296


title: Liver F2 Control Pool (n=294) vs. 538354_F2_287


title: Liver F2 Control Pool (n=294) vs. 533793_F2_252


title: Liver F2 Control Pool (n=294) vs. 540127_F2_298


title: 552547_F2_338


title: 512425_F2_127


title: 510621_F2_108


title: 516115_F2_147


title: Liver F2 Control Pool (n=294) vs. 533792_F2_251


title: 522494_F2_190


title: Liver F2 Control Pool (n=294) vs. 525933_F2_207


title: 538349_F2_265


title: 552549_F2_340


title: Liver F2 Control Pool (n=294) vs. 540142_F2_297


title: 512418_F2_138


title: Liver F2 Control Pool (n=294) vs. 525929_F2_213


title: 538348_F2_269


title: Liver F2 Control Pool (n=294) vs. 540128_F2_299


title: Liver F2 Control Pool (n=294) vs. 525926_F2_206


title: Liver F2 Control Pool (n=294) vs. 525925_F2_205


title: Liver F2 Control Pool (n=294) vs. 525919_F2_208


title: Liver F2 Control Pool (n=294) vs. 525920_F2_209


title: Liver F2 Control Pool (n=294) vs. 525921_F2_210


title: 512429_F2_134


title: Liver F2 Control Pool (n=294) vs. 525927_F2_211


title: Liver F2 Control Pool (n=294) vs. 516116_F2_157


title: 549371_F2_336


title: 505347_F2_91


title: 505332_F2_79


title: 500882_F2_65


title: Liver F2 Control Pool (n=294) vs. 516124_F2_166


title: Liver F2 Control Pool (n=294) vs. 516118_F2_159


title: 552562_F2_345


title: 549355_F2_320


title: 533789_F2_242


title: 510616_F2_103


title: Liver F2 Control Pool (n=294) vs. 516121_F2_162


title: Liver F2 Control Pool (n=294) vs. 516119_F2_160


title: Liver F2 Control Pool (n=294) vs. 516120_F2_161


title: Liver F2 Control Pool (n=294) vs. 516123_F2_167


title: Liver F2 Control Pool (n=294) vs. 516117_F2_158


title: Liver F2 Control Pool (n=294) vs. 516129_F2_163


title: Liver F2 Control Pool (n=294) vs. 516130_F2_165


title: Liver F2 Control Pool (n=294) vs. 516122_F2_168


title: 500876_F2_49


title: 510618_F2_105


title: 512421_F2_141


title: 549354_F2_319


title: 516128_F2_151


title: 491043_F2_12


title: Liver F2 Control Pool (n=294) vs. 505338_F2_88


title: Liver F2 Control Pool (n=294) vs. 505350_F2_94


title: Liver F2 Control Pool (n=294) vs. 505339_F2_89


title: 505333_F2_80


title: 500887_F2_59


title: 525924_F2_198


title: Liver F2 Control Pool (n=294) vs. 505349_F2_93


title: Liver F2 Control Pool (n=294) vs. 505348_F2_92


title: Liver F2 Control Pool (n=294) vs. 505340_F2_90


title: 538345_F2_283


title: Liver F2 Control Pool (n=294) vs. 505346_F2_87


title: 505352_F2_95


title: 516133_F2_155


title: Liver F2 Control Pool (n=294) vs. 512421_F2_141


title: 491040_F2_6


title: 549351_F2_316


title: 510620_F2_107


title: 491042_F2_11


title: Liver F2 Control Pool (n=294) vs. 505347_F2_91


title: 516126_F2_149


title: Liver F2 Control Pool (n=294) vs. 505351_F2_96


title: Liver F2 Control Pool (n=294) vs. 512419_F2_139


title: Liver F2 Control Pool (n=294) vs. 505352_F2_95


title: 510604_F2_97


title: Liver F2 Control Pool (n=294) vs. 512430_F2_135


title: 491038_F2_4


title: 510625_F2_118


title: Liver F2 Control Pool (n=294) vs. 512420_F2_140


title: Liver F2 Control Pool (n=294) vs. 512416_F2_136


title: 512420_F2_140


title: Liver F2 Control Pool (n=294) vs. 512418_F2_138


title: Liver F2 Control Pool (n=294) vs. 512417_F2_137


title: 512426_F2_128


title: Liver F2 Control Pool (n=294) vs. 516132_F2_156


title: Liver F2 Control Pool (n=294) vs. 496912_F2_37


title: 512432_F2_143


title: 549362_F2_324


title: 510627_F2_120


title: Liver F2 Control Pool (n=294) vs. 512428_F2_133


title: Liver F2 Control Pool (n=294) vs. 512429_F2_134


title: Liver F2 Control Pool (n=294) vs. 516136_F2_152


title: Liver F2 Control Pool (n=294) vs. 516135_F2_153


title: 530419_F2_234


title: 512431_F2_142


title: 491031_F2_9


title: 516123_F2_167


title: 522501_F2_172


title: Liver F2 Control Pool (n=294) vs. 516133_F2_155


title: 540138_F2_312


title: 510611_F2_110


title: Liver F2 Control Pool (n=294) vs. 516134_F2_154


title: Liver F2 Control Pool (n=294) vs. 516127_F2_150


title: 491027_F2_2


title: Liver F2 Control Pool (n=294) vs. 496913_F2_38


title: Liver F2 Control Pool (n=294) vs. 496928_F2_44


title: 512419_F2_139


title: Liver F2 Control Pool (n=294) vs. 516126_F2_149


title: 530427_F2_224


title: Liver F2 Control Pool (n=294) vs. 496929_F2_45


title: 525912_F2_195


title: 552550_F2_353


title: Liver F2 Control Pool (n=294) vs. 516128_F2_151


title: TD21_Rep2

city: Hangzhou

first: Mao

last: Youying

address: Yuhangtang Road,NO.388

country: China

institute: Zhejiang University

description: PBMC samples from acute rejection, acute tubule necrosis, renal recipients with stable function, donor tissue with stable function early after transplantation and donor tissue with stable function early after transplantation.

hyb_protocol: The hybridizations were performed overnight at 50C in a hybridization oven (Hybaid, Middlesex, UK). Subsequently, the nylon membranes were washed twice at 48C in 2xSSC and 0.1% SDS for 20 min.

scan_protocol: The signals of the array were absorbed by storage phosphor screen (Kodak, Rochester, New York, USA) for three days, and signal intensities were measured by scanning the storage phosphor screen with the Typhoon 9200 scanner (Amersham Pharmacia Biotech, Piscataway, NJ, USA).

data_processing: The signal intensity of each microarray spot on the array was quantified using the software ArrayVision6.0 (Imaging Research, Ontario, Canada). The normalization was performed by dividing a spot's signal intensity by the average signal intensity of the whole image (global normalization). Two individual hybridization experiments were performed for each probe, resulting in six replicated spots for each gene per sample.

source_name: kidney

label_protocol: The RNA samples were labeled with 33P-dCTP during the first-strand reverse transcription reactions.

extract_protocol: Total RNA was isolated by TRIZol according to manufacturer's instruction. Contaminating genomic DNA was removed by treatment with RNase-free DNase (Promega, Madison, WI, USA). RNA quality was confirmed by electropherogram. RNA was further purified using Rneasy mini kit (Qiagen).

value: kidney

tag: disease status

value: donor tissue with renal dysfunction early after transplantation


title: TD20_Rep1


title: TD20_Rep2


title: TD21_Rep1


title: TD19_Rep2


title: TD18_Rep1


title: TD18_Rep2


title: TD19_Rep1


title: TD17_Rep2


title: 522498_F2_169


title: 530411_F2_217


title: Liver F2 Control Pool (n=294) vs. 496914_F2_39


title: Liver F2 Control Pool (n=294) vs. 496927_F2_43


title: TD16_Rep2


title: TD16_Rep1


title: TD15_Rep2


title: TD17_Rep1


title: TD14_Rep2


title: TD15_Rep1


title: TD14_Rep1


title: Liver F2 Control Pool (n=294) vs. 505344_F2_85


title: 552558_F2_341


title: 552564_F2_348


title: 533791_F2_250


title: 512416_F2_136


title: 525911_F2_194


title: TD13_Rep1


title: TD13_Rep2


title: Liver F2 Control Pool (n=294) vs. 510610_F2_109


title: Liver F2 Control Pool (n=294) vs. 510611_F2_110


title: Liver F2 Control Pool (n=294) vs. 510612_F2_111


title: Liver F2 Control Pool (n=294) vs. 510614_F2_113


title: TD12_Rep2

value: donor tissue with stable function early after transplantation


title: Liver F2 Control Pool (n=294) vs. 510613_F2_112


title: 533811_F2_257


title: 522487_F2_176


title: TD12_Rep1


title: Liver F2 Control Pool (n=294) vs. 510622_F2_115


title: TD11_Rep2


title: TD10_Rep1


title: TD10_Rep2


title: TD11_Rep1


title: TD9_Rep1


title: TD9_Rep2


title: TD7_Rep1


title: TD7_Rep2


title: TD8_Rep1


title: TD6_Rep1


title: Liver F2 Control Pool (n=294) vs. 510623_F2_116


title: 496927_F2_43


title: Liver F2 Control Pool (n=294) vs. 510615_F2_114


title: Liver F2 Control Pool (n=294) vs. 500865_F2_53


title: TD5_Rep2


title: 549353_F2_318


title: Liver F2 Control Pool (n=294) vs. 500864_F2_52


title: 533792_F2_251


title: TD4_Rep2


title: TD5_Rep1


title: 530428_F2_225


title: 533808_F2_264


title: TD6_Rep2


title: TD4_Rep1


title: TD3_Rep2


title: 533797_F2_261


title: 516122_F2_168


title: Liver F2 Control Pool (n=294) vs. 500879_F2_55


title: 500881_F2_57


title: Liver F2 Control Pool (n=294) vs. 500880_F2_56


title: Liver F2 Control Pool (n=294) vs. 500881_F2_57


title: TD3_Rep1


title: Liver F2 Control Pool (n=294) vs. 512415_F2_132


title: TD2_Rep2


title: 540137_F2_311


title: 522506_F2_183


title: Liver F2 Control Pool (n=294) vs. 500866_F2_54


title: Liver F2 Control Pool (n=294) vs. 512413_F2_130


title: TD2_Rep1


title: TD1_Rep2


title: TD1_Rep1


title: Tx14_Rep1

value: stable renal function


title: Tx14_Rep2


title: Tx13_Rep1


title: Tx13_Rep2


title: Tx11_Rep1


title: Tx10_Rep2


title: Tx12_Rep1


title: 540130_F2_302


title: Liver F2 Control Pool (n=294) vs. 500871_F2_72


title: Liver F2 Control Pool (n=294) vs. 496915_F2_46


title: 540127_F2_298


title: 496913_F2_38


title: Tx9_Rep2


title: Tx10_Rep1


title: 530429_F2_229


title: Liver F2 Control Pool (n=294) vs. 500887_F2_59


title: Liver F2 Control Pool (n=294) vs. 500872_F2_71


title: Tx8_Rep2


title: Tx11_Rep2


title: Tx8_Rep1


title: Liver F2 Control Pool (n=294) vs. 500867_F2_58


title: 552556_F2_359


title: 533807_F2_262


title: Liver F2 Control Pool (n=294) vs. 496916_F2_47


title: 540125_F2_290


title: Tx9_Rep1


title: Liver F2 Control Pool (n=294) vs. 512431_F2_142


title: Liver F2 Control Pool (n=294) vs. 496917_F2_48


title: Tx6_Rep2


title: Tx7_Rep1


title: Tx7_Rep2


title: TD8_Rep2


title: Tx1_Rep2


title: Tx2_Rep1


title: Tx2_Rep2


title: Tx5_Rep1


title: Tx3_Rep2


title: Tx6_Rep1


title: Tx5_Rep2


title: Tx4_Rep2


title: Tx4_Rep1


title: 530416_F2_228


title: Liver F2 Control Pool (n=294) vs. 512433_F2_144


title: Liver F2 Control Pool (n=294) vs. 512432_F2_143


title: 525926_F2_206


title: 525920_F2_209


title: 500871_F2_72


title: 525929_F2_213


title: Liver F2 Control Pool (n=294) vs. 516115_F2_147


title: 538354_F2_287


title: Liver F2 Control Pool (n=294) vs. 516114_F2_146


title: Liver F2 Control Pool (n=294) vs. 538349_F2_265


title: Liver F2 Control Pool (n=294) vs. 538350_F2_266


title: Liver F2 Control Pool (n=294) vs. 516113_F2_145


title: Tx3_Rep1


title: ATN4_Rep1

value: acute tubular necrosis


title: ATN5_Rep2


title: ATN5_Rep1


title: ATN4_Rep2


title: Tx1_Rep1


title: ATN3_Rep2


title: ATN3_Rep1


title: ATN2_Rep1


title: ATN1_Rep2


title: ATN2_Rep2


title: ATN1_Rep1


title: AR17_Rep2

value: acute rejection


title: 538347_F2_285


title: 530423_F2_220


title: AR17_Rep1


title: AR16_Rep2


title: 516120_F2_161


title: AR16_Rep1


title: Liver F2 Control Pool (n=294) vs. 538340_F2_275


title: Liver F2 Control Pool (n=294) vs. 500886_F2_61


title: Liver F2 Control Pool (n=294) vs. 500884_F2_63


title: 510615_F2_114


title: AR15_Rep1


title: AR14_Rep2


title: AR15_Rep2


title: 522486_F2_175


title: 496915_F2_46


title: 540143_F2_296


title: 496928_F2_44


title: Liver F2 Control Pool (n=294) vs. 538338_F2_270


title: Liver F2 Control Pool (n=294) vs. 538357_F2_273


title: Liver F2 Control Pool (n=294) vs. 538359_F2_271


title: Liver F2 Control Pool (n=294) vs. 538348_F2_269


title: 549348_F2_313


title: 496914_F2_39


title: Liver F2 Control Pool (n=294) vs. 500883_F2_64


title: Liver F2 Control Pool (n=294) vs. 500882_F2_65


title: AR12_Rep2


title: AR13_Rep1


title: AR13_Rep2


title: AR14_Rep1


title: AR9_Rep2


title: AR9_Rep1


title: AR8_Rep2


title: AR8_Rep1


title: AR10_Rep1


title: AR11_Rep1


title: AR10_Rep2


title: AR12_Rep1


title: AR11_Rep2


title: AR7_Rep2


title: AR7_Rep1


title: AR6_Rep2


title: AR6_Rep1


title: 510614_F2_113


title: 552567_F2_350


title: Liver F2 Control Pool (n=294) vs. 500874_F2_66


title: 533795_F2_254


title: 500867_F2_58


title: 533803_F2_247


title: Liver F2 Control Pool (n=294) vs. 512422_F2_121


title: Liver F2 Control Pool (n=294) vs. 500868_F2_67


title: 510622_F2_115


title: 533798_F2_260


title: 525919_F2_208


title: 540134_F2_309


title: Liver F2 Control Pool (n=294) vs. 512423_F2_122


title: Liver F2 Control Pool (n=294) vs. 500876_F2_49


title: Liver F2 Control Pool (n=294) vs. 500877_F2_50


title: Liver F2 Control Pool (n=294) vs. 500869_F2_69


title: Liver F2 Control Pool (n=294) vs. 512424_F2_123


title: Liver F2 Control Pool (n=294) vs. 500870_F2_68


title: AR5_Rep2


title: AR4_Rep2


title: AR4_Rep1


title: AR3_Rep2


title: AR3_Rep1


title: AR2_Rep2


title: AR5_Rep1


title: 552569_F2_352


title: AR1_Rep2


title: AR1_Rep1


title: 505339_F2_89


title: 530426_F2_223


title: WT+Zn+Mn_vsWT_rep3

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Fluorescently-labeled cDNAs were resuspended in the manufacturer's salt-based hybridization buffer. Samples were heated for 3 min at 95C, chilled on ice for 3 min, and applied to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed for 5 min in prewarmed (30C) buffers. Buffer 1: 2X SSC, 0.1% SDS; Buffer 2: 1X SSC; Buffer 3: 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635 nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio ~ 1.0). Images were analyzed using GenePix Pro 6.0 software (Molecular Devices)

data_processing: Data were analyzed using software from the TM4 Microarray Software Suite (www.tm4.org). GenePix results files (.gpr) were converted to TIGR MultiExperiment Viewer file format (.mev) using ExpressConverter 2.1 software. Lowess (block) normalization was performed on non-background subtracted data using TIGR MIDAS 2.21 software. Spots flagged as bad (A=0 non-saturated pixels in spot; X= low spot intensity relative to background) were removed from the analysis.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae D39 rpsL1 (Winkler lab strain IU1781)

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.2

extract_protocol: Total RNA was extracted at OD620~0.2 using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification (RNAeasy mini kit, Qiagen) as described in Robertson et al., J Bact (2002) 184:3508-3520

treatment_protocol: No treatment

value: Virulent, capsule-producing serotype 2 strain D39 (NCTC 7466) transformed with the rpsL1 allele conferring streptomycin resistance

value: No treatment

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) supplemented with 200 uM Zn(II) and 300 uM Mn(II) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.2

treatment_protocol: Growth in BHI supplemented with high Zn(II) and Mn(II) concentrations


title: 530414_F2_226


title: WT+Zn+Mn_vsWT_rep1

description: Independent biological replicate

value: Growth in BHI supplemented with high Zn(II) and Mn(II) concentrations


title: Liver F2 Control Pool (n=294) vs. 512427_F2_129


title: WT+Zn+Mn_vsWT_rep2

description: Independent biological replicate


title: Liver F2 Control Pool (n=294) vs. 512426_F2_128


title: WT+Zn_vsWT_rep3

description: Independent biological replicate

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) supplemented with 200 uM Zn(II) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.2

treatment_protocol: Growth in BHI supplemented with high Zn(II) concentration


title: Liver F2 Control Pool (n=294) vs. 512425_F2_127


title: WT+Zn_vsWT_rep2

value: Growth in BHI supplemented with high Zn(II) concentration


title: MUT+Zn_vsWT+Zn_rep2

source_name: S. pneumoniae D39 rpsL1 adcR-H108Q (Winkler lab strain IU4036)

value: Virulent, capsule-producing serotype 2 strain IU1781 in which the wildtype adcR gene (SPD_2000, adc operon repressor) was replaced with a mutant adcR allele


title: 530418_F2_233

value: liver


title: WT+Zn_vsWT_rep1

description: Independent biological replicate


title: MUT+Zn_vsWT+Zn_rep1

description: Independent biological replicate


title: MUT+Zn_vsWT+Zn_rep3

description: Independent biological replicate


title: Liver F2 Control Pool (n=294) vs. 496910_F2_35


title: 505338_F2_88


title: Liver F2 Control Pool (n=294) vs. 512411_F2_125


title: 533809_F2_263


title: Liver F2 Control Pool (n=294) vs. 512412_F2_126


title: 525921_F2_210


title: 525932_F2_214


title: Liver F2 Control Pool (n=294) vs. 496911_F2_36


title: Liver F2 Control Pool (n=294) vs. 525910_F2_193


title: 505344_F2_85


title: small airways, Nsaets-008

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: no additional information

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: sex

value: F

tag: ethnic group

value: black

tag: smoking status

value: non-smoker


title: Liver F2 Control Pool (n=294) vs. 525911_F2_194


title: Liver F2 Control Pool (n=294) vs. 496909_F2_34


title: 505350_F2_94


title: small airways, Nsaets-004

description: no additional information

value: hispanic


title: small airways, SYMs-004

description: no additional information

value: smoker, 31 pack-years


title: 516130_F2_165

value: B6/J x A/J


title: small airways, Nsaets-007

description: no additional information


title: Liver F2 Control Pool (n=294) vs. 525924_F2_198


title: Liver F2 Control Pool (n=294) vs. 525922_F2_196


title: small airways, SYMs-259

description: no additional information

value: M

value: white

value: smoker, 12.5 pack-years


title: small airways, smoker 330

description: no additional information

value: smoker, 20 pack-years


title: 516121_F2_162


title: Liver F2 Control Pool (n=294) vs. 525912_F2_195


title: small airways, OcSs-002

description: no additional information

value: smoker, 1 pack-years (occasional smoker)


title: 522489_F2_184


title: 540141_F2_304


title: small airways, smoker 353

description: no additional information

value: smoker, 35 pack-years


title: 540126_F2_291


title: small airways, smoker 328

description: no additional information

value: smoker, 18 pack-years


title: small airways, smoker 341

description: no additional information

value: smoker,  16 pack-years


title: Liver F2 Control Pool (n=294) vs. 510621_F2_108


title: small airways, smoker 354

description: no additional information

value: smoker, 19 pack-years


title: Liver F2 Control Pool (n=294) vs. 525915_F2_201


title: small airways, smoker 377

description: no additional information

value: smoker,  23 pack-years


title: AR2_Rep1

value: kidney

value: acute rejection


title: 500865_F2_53

value: liver


title: small airways, smoker 327

description: no additional information

value: black

value: smoker, 45 pack-years


title: small airways, smoker 392

description: no additional information

value: smoker, 22 pack-years


title: small airways, smoker 321

description: no additional information

value: smoker, 15 pack-years


title: Liver F2 Control Pool (n=294) vs. 510607_F2_100

value: B6/J x A/J


title: Liver F2 Control Pool (n=294) vs. 510616_F2_103


title: 500864_F2_52


title: small airways, smoker 276

description: no additional information

value: M

value: smoker, 27 pack-years


title: small airways, smoker 220

description: no additional information

value: smoker, 9.3 pack-years


title: small airways, smoker 206

description: no additional information

value: hispanic

value: smoker, 51 pack-years


title: 540146_F2_293


title: small airways, smoker 269

description: no additional information

value: smoker, 14 pack-years


title: small airways, non-smoker 199

description: no additional information

value: F

value: white

value: non-smoker


title: small airways, smoker 215

description: no additional information

value: smoker, 26 pack-years


title: small airways, non-smoker 181

description: no additional information


title: 530421_F2_239


title: Liver F2 Control Pool (n=294) vs. 510604_F2_97


title: small airways, non-smoker 193

description: no additional information


title: Liver F2 Control Pool (n=294) vs. 510620_F2_107


title: small airways, non-smoker 179

description: no additional information


title: Liver F2 Control Pool (n=294) vs. 510606_F2_99


title: Liver F2 Control Pool (n=294) vs. 510609_F2_102


title: small airways, non-smoker 212

description: no additional information


title: 516118_F2_159


title: Liver F2 Control Pool (n=294) vs. 510608_F2_101


title: small airways, non-smoker 151

description: no additional information


title: small airways, non-smoker 175

description: no additional information


title: 540140_F2_305


title: 540131_F2_303


title: small airways, non-smoker 147

description: no additional information


title: small airways, non-smoker 156

description: no additional information

value: asian


title: Liver F2 Control Pool (n=294) vs. 510617_F2_104

value: liver


title: 496929_F2_45


title: 540133_F2_308


title: Liver F2 Control Pool (n=294) vs. 510618_F2_105


title: 540136_F2_310


title: Liver F2 Control Pool (n=294) vs. 510625_F2_118


title: small airways, non-smoker 155

description: no additional information


title: Liver F2 Control Pool (n=294) vs. 500873_F2_70


title: HJue-Ext-AMD-5-T-Cells-a1

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

description: HJue-Ext-AMD-5-T-Cells-U133_Plus_2-a1.CEL

hyb_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

data_processing: Microarray Suite version 5.0 (MAS 5.0). Calculated in the bioC implementation, so no absent/present calls.

source_name: T-Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The adult human RPE cell line ARPE-19 (American Type Culture Collection) was cultured in 6-well cell culture plates directly on well bottoms or on Anopore 0.2 um membrane inserts (Nunc) at 37 oC with 10% CO2 >6 weeks, until pigmented monolayers had formed. Cells were cultured in X-vivo 15 serum-free medium (Lonza BioWhittaker) with 300 ug/ml L-glutamine, 100 ug/ml penicillin and 100 ug/ml streptomycin, and 2,5 ug/ml amphotericin B.

extract_protocol: RPE cells were removed using a cell scraper. RNA was purified using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with manufacturer's instructions.

treatment_protocol: T cells were purified from fresh whole blood from healthy, young volunteers, and cultured in Anopore 0.2 um membrane inserts (Nunc) over RPE cells grown on well bottom, or under RPE cells grown in membrane inserts. A ratio of 2.5 T cells: 1 RPE cell was used. T cells were activated using Dynabeads CD3/CD28 T Cell Expander (Invitrogen), and cells were co-cultured for 48 h at 37 oC with 5% CO2.

tag: disease state

value: AMD

tag: t-cell co-culture

value: Tcells only

tag: inversion

value: basolateral


title: HJue-Ext-AMD-3-RPE-b1

scan_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

source_name: RPE

value: RPE only


title: 512415_F2_132

value: B6/J x A/J

tag: tissue


title: small airways, non-smoker 163

description: no additional information

tag: age

value: M

value: black


title: Liver F2 Control Pool (n=294) vs. 510627_F2_120

tag: strain


title: small airways, non-smoker 091

description: no additional information


title: HJue-Ext-AMD-4-RPE-CO-T-Cells-b1

description:
HJue-Ext-AMD-4-RPE-CO-T-Cells-U133_Plus_2-b1.CEL
RPE cells cultured with T cells.

value: RPE co-Tcells


title: 540129_F2_301


title: HJue-Ext-AMD-6-T-Cells-CO-RPE-a1

description:
HJue-Ext-AMD-6-T-Cells-CO-RPE-U133_Plus_2-a1.CEL
T cells cultured with RPE cells.

value: Tcells co-RPE


title: 522488_F2_177


title: small airways, non-smoker 169

description: no additional information


title: small airways, non-smoker 132

description: no additional information


title: small airways, non-smoker 140

description: no additional information

value: hispanic


title: Liver F2 Control Pool (n=294) vs. 510626_F2_119


title: 7 wt

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Gene expression data from LSK cell from Gfi1 wildtype mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned in a GeneArray Scanner (Agilent).

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: LSK cell from Gfi1 wildtype mice

label_protocol: Biotinylated cRNA were prepared according to the artus ExpressArt mRNA 2-rouind amplification protocol (nano version) from 10 ng total RNA, using the ENZO kit for labelling in the second IVT reaction

extract_protocol: RNA was extracted using the Rneasy mini kit (QIAGEN)

treatment_protocol: LSKs were sorted by FACS

tag: cell type

value: LSK

value: hematopoietic stem cell enriched fraction from bone marrow


title: 500880_F2_56


title: Liver F2 Control Pool (n=294) vs. 491042_F2_11


title: Liver F2 Control Pool (n=294) vs. 491043_F2_12


title: 500866_F2_54


title: 8 wt


title: Liver F2 Control Pool (n=294) vs. 491044_F2_16


title: 7 Ko

description: Gene expression data from LSK cell from Gfi1 knockout mice

source_name: LSK cell from Gfi1 knockout mice


title: HJue-Ext-RPE-neg-20081013-b1

description: HJue-Ext-RPE-neg-20081013-U133_Plus_2-b1.CEL

value: apical


title: 552552_F2_355


title: 8 Ko


title: Liver F2 Control Pool (n=294) vs. 491038_F2_4


title: HJue-Ext-AMD-2-RPE-CO-T-Cells-a1

description:
HJue-Ext-AMD-2-RPE-CO-T-Cells-U133_Plus_2-a1.CEL
RPE cells cultured with T cells.


title: HJue-Ext-RPE-T-20081013-b1

description:
HJue-Ext-RPE-T-20081013-U133_Plus_2-b1.CEL
T cells cultured over RPE cells.


title: HJue-Ext-RPE-neg-20080423-a1

description: HJue-Ext-RPE-neg-20080423-U133_Plus_2-a1.CEL


title: HJue-Ext-RPE-T-20080423-a1

description:
HJue-Ext-RPE-T-20080423-U133_Plus_2-a1.CEL
T cells cultured over RPE cells.


title: 5 wt


title: Liver F2 Control Pool (n=294) vs. 491039_F2_5


title: 5 Ko


title: 516135_F2_153


title: 552565_F2_347


title: HJue-Ext-AMD-1-RPE-a1


title: 516129_F2_163


title: Liver F2 Control Pool (n=294) vs. 491041_F2_10


title: Liver F2 Control Pool (n=294) vs. 491049_F2_18


title: 516124_F2_166


title: Liver F2 Control Pool (n=294) vs. 491040_F2_6


title: 510613_F2_112


title: 549361_F2_323


title: Liver F2 Control Pool (n=294) vs. 491045_F2_17


title: small airways, smoker 275

description: no additional information

value: F

value: smoker, 71 pack-years


title: Liver F2 Control Pool (n=294) vs. 491047_F2_24


title: small airways, smoker 271

description: no additional information

value: smoker, 10 pack-years


title: 533806_F2_256

value: liver


title: small airways, smoker 302

description: no additional information

value: white

value: smoker, 46 pack-years


title: small airways, smoker 303

description: no additional information

value: smoker, 10.5 pack-years


title: small airways, smoker 247

description: no additional information

value: smoker, 19.5 pack-years


title: small airways, smoker 272

description: no additional information

value: smoker, 24 pack-years


title: small airways, smoker 256

description: no additional information

value: M

value: smoker, 27 pack-years


title: small airways, smoker 317

description: no additional information

value: black

value: smoker, 26 pack-years


title: small airways, non-smoker 137

description: no additional information

value: non-smoker


title: 540132_F2_307

value: B6/J x A/J


title: 552554_F2_357


title: Liver F2 Control Pool (n=294) vs. 491028_F2_3


title: 512428_F2_133


title: small airways, smoker 229

description: no additional information

value: smoker, 47 pack-years


title: Liver F2 Control Pool (n=294) vs. 491046_F2_22


title: small airways, smoker 216

description: no additional information

value: hispanic

value: smoker, 29 pack-years


title: 525918_F2_204


title: Liver F2 Control Pool (n=294) vs. 491029_F2_7


title: 552568_F2_351


title: Liver F2 Control Pool (n=294) vs. 491033_F2_14


title: 500872_F2_71


title: 533801_F2_245


title: Liver F2 Control Pool (n=294) vs. 491030_F2_8


title: Liver F2 Control Pool (n=294) vs. 505333_F2_80


title: Liver F2 Control Pool (n=294) vs. 491031_F2_9


title: small airways, non-smoker 109

description: no additional information


title: Liver F2 Control Pool (n=294) vs. 505330_F2_74


title: small airways, non-smoker 128

description: no additional information

value: F


title: Liver F2 Control Pool (n=294) vs. 505331_F2_75


title: small airways, non-smoker 119

description: no additional information


title: Liver F2 Control Pool (n=294) vs. 505332_F2_79


title: 552551_F2_354


title: 530422_F2_240


title: 516116_F2_157


title: 522507_F2_182


title: 540145_F2_294


title: 525931_F2_215


title: small airways, smoker 240

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

value: smoker, 56.5 pack-years


title: 530424_F2_221

value: liver


title: Liver F2 Control Pool (n=294) vs. 505336_F2_83


title: Liver F2 Control Pool (n=294) vs. 505329_F2_73


title: small airways, non-smoker 103


title: 512413_F2_130


title: 538341_F2_276


title: small airways, smoker 226

value: smoker, 0.5 pack-years


title: 525933_F2_207


title: small airways, smoker 188

value: smoker, 17.5 pack-years


title: small airways, non-smoker 094


title: Liver F2 Control Pool (n=294) vs. 505335_F2_82


title: Liver F2 Control Pool (n=294) vs. 505341_F2_76


title: Liver F2 Control Pool (n=294) vs. 505343_F2_78


title: Liver F2 Control Pool (n=294) vs. 505342_F2_77


title: Liver F2 Control Pool (n=294) vs. 505334_F2_81


title: Liver F2 Control Pool (n=294) vs. 505337_F2_84


title: 525930_F2_216


title: 549358_F2_326


title: 522493_F2_191


title: Liver F2 Control Pool (n=294) vs. 491035_F2_19


title: Liver F2 Control Pool (n=294) vs. 491037_F2_20


title: Liver F2 Control Pool (n=294) vs. 496918_F2_25


title: 533810_F2_258


title: ESC E w.o-1

city: seoul

first: Eun Ju

last: Lee

address: 28 yongon dong

country: South Korea

institute: seoul natonal university

description: Gene expression of E w.o-1

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

source_name: SNUhES3 cells on autofeeder replicate 1

label_protocol: The samples were incubated at 40oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 65oC for 15 min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was preformed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40oC for 2 hours. Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: hESC-MSCs derived from SNUhES3 cells were used as autologous feeder cells for the SNUhES3 cells. SNUhES3 cells were transferred to the autofeeder layer of hESC-MSCs in 35-mm dishes (1.2X105) and cultured in DMEM/ F-12 (Invitrogen) with 20% Knock-Out SR (Invitrogen), 0.1 mmol/L β-mercaptoethanol (Sigma), non-essential amino acids (Invitrogen), 50 IU/mL penicillin, and 50 mg/mL streptomycin (Invitrogen) (autofeeder system). The culture medium was changed daily, and the hES cells were transferred using the mechanical dissociation method at 7-day intervals. The cells were incubated at 37ºC in 5% CO2. SNUhES3 cells were also cultured in an STO feeder cell layer as a control (xenofeeder system). SNUhES3 cells cultured on the STO feeder cell layer required the addition of 4 ng/mL of bFGF (Invitrogen). The other culture conditions were identical to the conditions used for the SNUhES3 culture on the autofeeder. All manipulations and cultivations were performed in a good manufacturing practice (GMP)-compliant facility.

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Invitrogen, Carlsbad, CA). The RNA were extracted with chloroform (Sigma Chemical, St. Louis, MO, USA) and followed by ethanol precipitation. RNA was quantified using NanoDrop® ND-1000 spectrophotometer(NanoDrop Technologies, Inc., Wilmington, DE, USA). And RNA quality was assessed using Agilent RNA Nano 6000 LabChip kits and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Total RNAs from SNUhES3 cells cultured on xenofeeder or autofeeder cell layer at 30 passage were isolated using TRIzol (Invitrogen, Carlsbad) and the RNeasy Mini kit (Qiagen, Valencia).

value: Embryonic stem cells

tag: gender

value: male

tag: growth condition

value: autofeeder hESC-MSCs layer

tag: cell line


title: 552566_F2_349


title: 505346_F2_87


title: 516119_F2_160


title: Liver F2 Control Pool (n=294) vs. 496923_F2_30


title: Liver F2 Control Pool (n=294) vs. 496921_F2_28


title: Liver F2 Control Pool (n=294) vs. 496919_F2_26


title: 505349_F2_93


title: ESC con-2

description: Gene expression of ESC con-2

source_name: SNUhES3 cells on xenefeeder replicate 2

value: xenofeeder STO cell layer


title: ESC con-1

description: Gene expression of ESC con-1

source_name: SNUhES3 cells on xenefeeder replicate 1


title: ESC E w.o-2

description: Gene expression of E w.o-2

source_name: SNUhES3 cells on autofeeder replicate 2


title: Liver F2 Control Pool (n=294) vs. 496906_F2_31


title: Liver F2 Control Pool (n=294) vs. 496908_F2_33


title: NA20512/NA12878

status: Public on Feb 01 2011

city: Seattle

first: Catarina

middle: D

last: Campbell

state: WA

address: 3720 15th Avenue NE

department: Genome Sciences

institute: Univerisity of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 5 ug of labelled test sample and 5 ug of labelled reference sample (NA12878)

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) except that 3000 probes through out the genome were used for dye normalization.

source_name: lymphoblast cell line DNA [test]

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: DNA was extracted from lymphoblast cell lines by Coriell Repositories (http://ccr.coriell.org/)

value: Male

value: lymphoblast cell line NA20512

tag: ethnicity

value: Toscani from Italy (HapMap code:TSI)

source_name: lymphoblast cell line DNA [reference]

value: female

value: lymphoblast cell line NA12878

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20517/NA12878

value: Female

value: lymphoblast cell line NA20517


title: NA20516/NA12878

value: lymphoblast cell line NA20516


title: NA20510/NA12878

value: lymphoblast cell line NA20510


title: NA20520/NA12878

value: lymphoblast cell line NA20520


title: NA20518/NA12878

value: lymphoblast cell line NA20518


title: NA20509/NA12878

value: lymphoblast cell line NA20509


title: NA20519/NA12878

value: lymphoblast cell line NA20519


title: NA20505/NA12878

value: lymphoblast cell line NA20505


title: NA20360/NA12878

value: lymphoblast cell line NA20360

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA20357/NA12878

value: lymphoblast cell line NA20357


title: NA20506/NA12878

value: lymphoblast cell line NA20506


title: NA20514/NA12878

value: lymphoblast cell line NA20514

value: Toscani from Italy (HapMap code:TSI)


title: NA20359/NA12878

value: lymphoblast cell line NA20359

value: female

value: lymphoblast cell line NA12878


title: NA20503/NA12878

value: Female

value: lymphoblast cell line NA20503

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20356/NA12878

value: Male

value: lymphoblast cell line NA20356


title: NA20358/NA12878

value: lymphoblast cell line NA20358


title: NA20502/NA12878

value: lymphoblast cell line NA20502


title: NA20508/NA12878

value: lymphoblast cell line NA20508


title: NA20414/NA12878

value: lymphoblast cell line NA20414


title: NA20350/NA12878

value: lymphoblast cell line NA20350

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA20349/NA12878

value: lymphoblast cell line NA20349


title: NA20363/NA12878

value: lymphoblast cell line NA20363


title: NA20504/NA12878

value: lymphoblast cell line NA20504

value: Toscani from Italy (HapMap code:TSI)


title: NA20351/NA12878

value: lymphoblast cell line NA20351

value: female


title: NA20507/NA12878

value: Female

value: lymphoblast cell line NA20507

value: lymphoblast cell line NA12878


title: NA20364/NA12878

value: lymphoblast cell line NA20364

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20412/NA12878

value: lymphoblast cell line NA20412


title: NA20344/NA12878

value: lymphoblast cell line NA20344


title: NA20345/NA12878

value: Male

value: lymphoblast cell line NA20345


title: NA20347/NA12878

value: lymphoblast cell line NA20347


title: NA20340/NA12878

value: lymphoblast cell line NA20340

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA20341/NA12878

value: lymphoblast cell line NA20341


title: NA20337/NA12878

value: lymphoblast cell line NA20337


title: NA20343/NA12878

value: lymphoblast cell line NA20343


title: NA20342/NA12878

value: lymphoblast cell line NA20342


title: NA20336/NA12878

value: lymphoblast cell line NA20336

value: female


title: NA20333/NA12878

value: Female

value: lymphoblast cell line NA20333


title: NA20335/NA12878

value: lymphoblast cell line NA20335

value: lymphoblast cell line NA12878


title: NA20515/NA12878

value: lymphoblast cell line NA20515

value: Toscani from Italy (HapMap code:TSI)

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20513/NA12878

value: Male

value: lymphoblast cell line NA20513


title: NA20339/NA12878

value: lymphoblast cell line NA20339


title: NA20317/NA12878

value: lymphoblast cell line NA20317

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA20322/NA12878

value: lymphoblast cell line NA20322


title: NA20314/NA12878

value: lymphoblast cell line NA20314


title: NA20297/NA12878

value: lymphoblast cell line NA20297


title: NA20299/NA12878

value: lymphoblast cell line NA20299


title: NA20298/NA12878

value: lymphoblast cell line NA20298

value: female


title: NA20334/NA12878

value: Female

value: lymphoblast cell line NA20334


title: NA20296/NA12878

value: lymphoblast cell line NA20296

value: lymphoblast cell line NA12878


title: NA20302/NA12878

value: lymphoblast cell line NA20302


title: NA20319/NA12878

value: lymphoblast cell line NA20319

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20301/NA12878

value: lymphoblast cell line NA20301


title: NA20332/NA12878

value: lymphoblast cell line NA20332


title: NA20316/NA12878

value: Male

value: lymphoblast cell line NA20316


title: NA20295/NA12878

value: lymphoblast cell line NA20295

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA20288/NA12878

value: lymphoblast cell line NA20288


title: NA20292/NA12878

value: lymphoblast cell line NA20292


title: NA20300/NA12878

value: lymphoblast cell line NA20300


title: NA20281/NA12878

value: lymphoblast cell line NA20281

value: female


title: NA20282/NA12878

value: Female

value: lymphoblast cell line NA20282


title: NA20290/NA12878

value: lymphoblast cell line NA20290

value: lymphoblast cell line NA12878


title: NA20291/NA12878

value: lymphoblast cell line NA20291


title: NA20348/NA12878

value: lymphoblast cell line NA20348

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20289/NA12878

value: lymphoblast cell line NA20289


title: NA20279/NA12878

value: Male

value: lymphoblast cell line NA20279


title: NA20294/NA12878

value: lymphoblast cell line NA20294


title: NA20287/NA12878

value: lymphoblast cell line NA20287

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA20278/NA12878

value: lymphoblast cell line NA20278


title: NA20284/NA12878

value: lymphoblast cell line NA20284


title: NA20129/NA12878

value: lymphoblast cell line NA20129


title: NA20277/NA12878

value: lymphoblast cell line NA20277

value: female


title: NA20276/NA12878

value: Female

value: lymphoblast cell line NA20276


title: NA20127/NA12878

value: lymphoblast cell line NA20127

value: lymphoblast cell line NA12878


title: NA20128/NA12878

value: lymphoblast cell line NA20128


title: NA20346/NA12878

value: lymphoblast cell line NA20346

value: Northwest European American from Utah (HapMap code:CEU)


title: NA20126/NA12878

value: Male

value: lymphoblast cell line NA20126


title: NA19984/NA12878

value: lymphoblast cell line NA19984


title: NA19985/NA12878

value: lymphoblast cell line NA19985


title: NA19982/NA12878

value: lymphoblast cell line NA19982

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA19983/NA12878

value: lymphoblast cell line NA19983


title: NA19904/NA12878

value: lymphoblast cell line NA19904


title: NA19918/NA12878

value: lymphoblast cell line NA19918


title: NA19917/NA12878

value: lymphoblast cell line NA19917

value: female


title: NA19836/NA12878

value: Female

value: lymphoblast cell line NA19836


title: NA19794/NA12878

value: lymphoblast cell line NA19794

value: Mexican American from Los Angeles, CA (HapMap code:MEX)

value: lymphoblast cell line NA12878


title: NA19908/NA12878

value: lymphoblast cell line NA19908

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19923/NA12878

value: lymphoblast cell line NA19923


title: NA19922/NA12878

value: Male

value: lymphoblast cell line NA19922


title: NA19900/NA12878

value: lymphoblast cell line NA19900


title: NA19920/NA12878

value: lymphoblast cell line NA19920

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA19914/NA12878

value: lymphoblast cell line NA19914


title: NA19834/NA12878

value: lymphoblast cell line NA19834


title: NA19901/NA12878

value: lymphoblast cell line NA19901


title: NA19915/NA12878

value: lymphoblast cell line NA19915

value: female


title: NA19835/NA12878

value: Female

value: lymphoblast cell line NA19835


title: NA19919/NA12878

value: lymphoblast cell line NA19919


title: NA19902/NA12878

value: lymphoblast cell line NA19902

value: lymphoblast cell line NA12878


title: NA19789/NA12878

value: lymphoblast cell line NA19789

value: Mexican American from Los Angeles, CA (HapMap code:MEX)

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19916/NA12878

value: Male

value: lymphoblast cell line NA19916


title: NA19796/NA12878

value: lymphoblast cell line NA19796


title: NA19828/NA12878

value: lymphoblast cell line NA19828

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA19790/NA12878

value: lymphoblast cell line NA19790


title: NA19795/NA12878

value: lymphoblast cell line NA19795


title: NA19909/NA12878

value: lymphoblast cell line NA19909


title: NA19788/NA12878

value: lymphoblast cell line NA19788

value: female


title: NA19921/NA12878

value: Female

value: lymphoblast cell line NA19921


title: NA19819/NA12878

value: lymphoblast cell line NA19819


title: NA19818/NA12878

value: lymphoblast cell line NA19818

value: lymphoblast cell line NA12878


title: NA19787/NA12878

value: lymphoblast cell line NA19787

value: Mexican American from Los Angeles, CA (HapMap code:MEX)


title: NA19783/NA12878

value: Male

value: lymphoblast cell line NA19783

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19782/NA12878

value: lymphoblast cell line NA19782


title: NA19785/NA12878

value: lymphoblast cell line NA19785


title: NA19784/NA12878

value: lymphoblast cell line NA19784


title: NA19786/NA12878

value: lymphoblast cell line NA19786


title: NA19776/NA12878

value: lymphoblast cell line NA19776


title: NA19773/NA12878

value: lymphoblast cell line NA19773


title: NA19778/NA12878

value: lymphoblast cell line NA19778

value: female


title: NA19770/NA12878

value: Female

value: lymphoblast cell line NA19770


title: NA19779/NA12878

value: lymphoblast cell line NA19779


title: NA19775/NA12878

value: lymphoblast cell line NA19775

value: lymphoblast cell line NA12878


title: NA19777/NA12878

value: lymphoblast cell line NA19777

value: Mexican American from Los Angeles, CA (HapMap code:MEX)


title: NA19774/NA12878

value: Male

value: lymphoblast cell line NA19774


title: NA19772/NA12878

value: lymphoblast cell line NA19772

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19763/NA12878

value: lymphoblast cell line NA19763


title: NA19759/NA12878

value: lymphoblast cell line NA19759


title: NA19755/NA12878

value: lymphoblast cell line NA19755


title: NA19750/NA12878

value: lymphoblast cell line NA19750


title: NA19761/NA12878

value: lymphoblast cell line NA19761


title: NA19756/NA12878

value: lymphoblast cell line NA19756

value: female


title: NA19781/NA12878

value: Female

value: lymphoblast cell line NA19781


title: NA19751/NA12878

value: lymphoblast cell line NA19751


title: NA19780/NA12878

value: lymphoblast cell line NA19780

value: lymphoblast cell line NA12878


title: NA19757/NA12878

value: lymphoblast cell line NA19757

value: Mexican American from Los Angeles, CA (HapMap code:MEX)


title: NA19752/NA12878

value: lymphoblast cell line NA19752


title: NA19771/NA12878

value: Male

value: lymphoblast cell line NA19771


title: NA19760/NA12878

value: lymphoblast cell line NA19760

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19758/NA12878

value: lymphoblast cell line NA19758


title: NA19740/NA12878

value: lymphoblast cell line NA19740


title: NA19741/NA12878

value: lymphoblast cell line NA19741


title: NA19746/NA12878

value: lymphoblast cell line NA19746


title: NA19738/NA12878

value: lymphoblast cell line NA19738

value: female


title: NA19747/NA12878

value: lymphoblast cell line NA19747


title: NA19762/NA12878

value: lymphoblast cell line NA19762


title: NA19748/NA12878

value: Female

value: lymphoblast cell line NA19748


title: NA19749/NA12878

value: lymphoblast cell line NA19749

value: lymphoblast cell line NA12878


title: NA19737/NA12878

value: lymphoblast cell line NA19737

value: Mexican American from Los Angeles, CA (HapMap code:MEX)


title: NA19735/NA12878

value: Male

value: lymphoblast cell line NA19735


title: NA19733/NA12878

value: lymphoblast cell line NA19733

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19732/NA12878

value: lymphoblast cell line NA19732


title: NA19730/NA12878

value: lymphoblast cell line NA19730


title: NA19724/NA12878

value: lymphoblast cell line NA19724


title: NA19731/NA12878

value: lymphoblast cell line NA19731


title: NA19725/NA12878

value: lymphoblast cell line NA19725

value: female


title: NA19723/NA12878

value: lymphoblast cell line NA19723


title: NA19718/NA12878

value: Female

value: lymphoblast cell line NA19718


title: NA19714/NA12878

value: lymphoblast cell line NA19714

value: African American from Southwest Unitied States (HapMap code:ASW)


title: NA19727/NA12878

value: lymphoblast cell line NA19727

value: lymphoblast cell line NA12878


title: NA19734/NA12878

value: lymphoblast cell line NA19734

value: Mexican American from Los Angeles, CA (HapMap code:MEX)


title: NA19729/NA12878

value: Male

value: lymphoblast cell line NA19729


title: NA19719/NA12878

value: lymphoblast cell line NA19719

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19722/NA12878

value: lymphoblast cell line NA19722


title: NA19721/NA12878

value: lymphoblast cell line NA19721


title: NA19720/NA12878

value: lymphoblast cell line NA19720


title: NA19712/NA12878

value: lymphoblast cell line NA19712

value: female


title: NA19711/NA12878

value: lymphoblast cell line NA19711


title: NA19713/NA12878

value: Female

value: lymphoblast cell line NA19713


title: NA19717/NA12878

value: lymphoblast cell line NA19717


title: NA19728/NA12878

value: lymphoblast cell line NA19728


title: NA19703/NA12878

value: lymphoblast cell line NA19703

value: African American from Southwest Unitied States (HapMap code:ASW)

value: lymphoblast cell line NA12878


title: NA19704/NA12878

value: lymphoblast cell line NA19704


title: NA19705/NA12878

value: Male

value: lymphoblast cell line NA19705


title: NA19726/NA12878

value: lymphoblast cell line NA19726

value: Mexican American from Los Angeles, CA (HapMap code:MEX)

value: Northwest European American from Utah (HapMap code:CEU)


title: NA19700/NA12878

value: lymphoblast cell line NA19700


title: NA19707/NA12878

value: lymphoblast cell line NA19707


title: NA19685/NA12878

value: lymphoblast cell line NA19685

value: female


title: NA19683/NA12878

value: Female

value: lymphoblast cell line NA19683


title: NA19708/NA12878

value: lymphoblast cell line NA19708


title: NA19702/NA12878

value: lymphoblast cell line NA19702


title: NA19679/NA12878

value: lymphoblast cell line NA19679


title: NA19682/NA12878

value: lymphoblast cell line NA19682


title: NA19684/NA12878

value: lymphoblast cell line NA19684

value: lymphoblast cell line NA12878


title: NA19680/NA12878

value: lymphoblast cell line NA19680


title: NA19686/NA12878

value: lymphoblast cell line NA19686


title: NA19671/NA12878

value: lymphoblast cell line NA19671


title: NA19701/NA12878

value: lymphoblast cell line NA19701

value: African American from Southwest Unitied States (HapMap code:ASW)