title: PBMC from Stable  84.2 at T0

description: STA, Biological replicate  84 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA084.2

value: PBMC from STA084

value: STA 84 of 190


title: ESCC_Biopsy_BPY148

status: Public on Feb 09 2017

type: RNA

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 12.6 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Esophageal squamous cell carcinoma

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: All esophageal squamous cell carcionma specimens were provided by the National Cancer Center Hospital and National Cancer Center Hospital East after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.

extract_protocol: Frozen biopsy specimens were placed in the ISOGEN solution and homogenised. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: All biopsy specimens were obtained before therapy and immediately frozen at -80 ﾟC until use.

tag: disease state

value: ESCC

tag: tissue

value: Biopsy before therapy

tag: therapy

value: Surgery


title: ESCC_Biopsy_BPY145


title: PBMC from Stable  83.2 at T0

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: STA, Biological replicate  83 of 190, Technical replicate 2 of 2

hyb_protocol: 1 mg of Cy5-labeled reference aRNA and 1 mg of Cy3-labeled sample aRNA were hybridized on the array for 16 h at 428C in a sealed chamber (Telechem Int., Sunnyval, CA).

scan_protocol: Hybridized slides were scanned by fluorescence confocal microscopy (ScanArray 3000,GSI-Lumonics) using independent laser excitation of the two fluorescent dyes at 532 and 633 nm at a 10 mm/pixel resolution. Fluorescence values and ratios were extracted with the GenePix Pro 5.1 software.

data_processing: The data were normalized using a lowest fit approach independently applied to each log ratio distributions.

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

label_protocol: All aRNA samples were fragmented using RNA fragmentation Reagents (Ambion) according to the manufacturer’s protocols. Fragmented aRNA  were labeled with Cyanine 3 (Cy3; Amersham Biosciences, Buckinghamshire, UK). As the reference for the hybridization, aRNA were prepared as described from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment. This referential aRNA was pooled and labeled with Cyanine 5 (Cy5). Cyanine incorporation and aRNA quantities were confirmed using a Nanodrop ND1000 spectrometer.

extract_protocol: Ten milliliters of peripheral blood were collected in EDTA tubes. Peripheral Blood Mononuclear Cells (PBMC) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and frozen in Trizol1 reagent (Invitrogen, Life Technologies, CA). One microgram of total RNA (tRNA) of each sample was subjected to amplification using the Amino Allyl MessageAmp TM II aRNA Amplification Kit (Ambion, Austin, TX) according to the manufacturer’s protocols. Quality and quantity of tRNA and amplified RNA (aRNA) was tested by an Agilent 2100 Bioanalyser.

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA083.2

value: PBMC from STA083

tag: individual replicate

value: STA 83 of 190

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: Individual 1 before exposure to high altitude

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

country: China

institute: 3rd Military Medical University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.  a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: Plasma

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.  Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: Plasma

tag: age

tag: bmi

tag: Sex

value: Male


title: ESCC_Biopsy_BPY167


title: PBMC from Stable  85.2 at T0

description: STA, Biological replicate  85 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA085.2

value: PBMC from STA085

value: STA 85 of 190


title: ESCC_Biopsy_BPY143


title: ESCC_Biopsy_BPY162


title: PBMC from Stable  83.1 at T0

description: STA, Biological replicate  83 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA083.1

value: Replicate 1 of 2


title: Individual 22 after exposure to high altitude


title: Individual 20 after exposure to high altitude


title: Individual 21 after exposure to high altitude


title: PBMC from Stable  84.1 at T0

description: STA, Biological replicate  84 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA084.1


title: ESCC_Biopsy_BPY141


title: ESCC_Biopsy_BPY136


title: Individual 19 after exposure to high altitude


title: ESCC_Biopsy_BPY131-2


title: PBMC from Stable  82.1 at T0

description: STA, Biological replicate  82 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA082.1

value: PBMC from STA082

value: STA 82 of 190


title: PBMC from Stable  81.2 at T0

description: STA, Biological replicate  81 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA081.2

value: PBMC from STA081

value: STA 81 of 190


title: ESCC_Biopsy_BPY130


title: A3

city: Beijing

first: Shuai

last: Liu

address: Dong Dan San Tiao 9, Beijing, China

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: This sample is the third of three adult worm pair biological replicates used in this experiment. Adult worm pairs were isolated from separate infected rabbits at 6 weeks post-infection.

hyb_protocol: Array hybridization, washing, scanning, and data acquisition were carried out according to the NimbleGen Arrays user’s guide.

scan_protocol: The arrays were scanned using MS200 scanner (NimbleGen Systems) with 2 µm resolution, and NimbleScan software (NimbleGen) was used to extract fluorescent intensity raw data from the scanned images.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Schistosoma japonicum

source_name: adult worm pair

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China) for producing higher yields of labeled cDNA.

growth_protocol: The freshly released cercariae were harvested from S. japonicum-infected Oncomelania hupensis purchased from Hunan Institute of Parasitic Diseases, Yueyang, China. Hepatic schistosomula were isolated from infected New Zealand rabbits at 2 weeks post-infection. Adult worms were isolated from infected rabbits at 6 weeks post-infection and manually separated under a light microscope. Eggs were purified from liver tissues of infected rabbits by enzyme digestion method.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (QIAGEN) and the contaminating genomic DNA were removed from RNA samples with Tubro DNA-free kit (Ambion, CA, USA).  The quantity and quality of the RNA samples were assessed by NanoDropND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and denaturing agarose gel electrophoresis.

treatment_protocol: Parasites of all stages were soaked in RNAlater Solution (Ambion, CA, USA), and stored at -80°C until total RNA was isolated.

tag: developmental stage

value: adult


title: PBMC from Stable  82.2 at T0

description: STA, Biological replicate  82 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA082.2


title: Individual 18 after exposure to high altitude


title: Individual 17 after exposure to high altitude


title: M1-1

description: This sample is the first of three adult male worm biological replicates (the first of two adult male worm technical replicates) used in this experiment.  Adult male worms were isolated from separate infected rabbits at 6 weeks post-infection.

source_name: adult male worm

value: adult male


title: Individual 16 after exposure to high altitude


title: ESCC_Biopsy_BPY128

value: ESCC

value: Biopsy before therapy


title: PBMC from Stable  81.1 at T0

description: STA, Biological replicate  81 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA081.1


title: ESCC_Biopsy_BPY129

value: Surgery


title: A1

description: This sample is the first of three adult worm pair biological replicates used in this experiment. Adult worm pairs were isolated from separate infected rabbits at 6 weeks post-infection.


title: Individual 14 after exposure to high altitude


title: ESCC_Biopsy_BPY127


title: Individual 15 after exposure to high altitude


title: PBMC from Stable  80.2 at T0

description: STA, Biological replicate  80 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA080.2

value: PBMC from STA080

value: STA 80 of 190


title: PBMC from Stable  79.2 at T0

description: STA, Biological replicate  79 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA079.2

value: PBMC from STA079

value: STA 79 of 190

value: Replicate 2 of 2


title: S2

description: This sample is the second of three hepatic schistosomula biological replicates used in this experiment.  Hepatic schistosomula were isolated from separate infected rabbits at 2 weeks post-infection.

source_name: hepatic schistosomula

value: hepatic schistosomula


title: A2

description: This sample is the second of three adult worm pair biological replicates used in this experiment. Adult worm pairs were isolated from separate infected rabbits at 6 weeks post-infection.


title: Individual 13 after exposure to high altitude

value: Plasma

value: Male


title: S3

description: This sample is the third of three hepatic schistosomula biological replicates used in this experiment.  Hepatic schistosomula were isolated from separate infected rabbits at 2 weeks post-infection.


title: PBMC from Stable  79.1 at T0

description: STA, Biological replicate  79 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA079.1

value: Replicate 1 of 2


title: PBMC from Stable  80.1 at T0

description: STA, Biological replicate  80 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA080.1


title: S1-1

description: This sample is the first of three hepatic schistosomula biological replicates (the first of two hepatic schistosomula technical replicates) used in this experiment. Hepatic schistosomula were isolated from separate infected rabbits at 2 weeks post-infection.


title: PBMC from Stable  78.2 at T0

description: STA, Biological replicate  78 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA078.2

value: PBMC from STA078

value: STA 78 of 190


title: ESCC_Biopsy_BPY124

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

source_name: Esophageal squamous cell carcinoma


title: Individual 12 after exposure to high altitude

source_name: Plasma


title: ESCC_Biopsy_BPY126


title: S1-2

description: This sample is the first of three hepatic schistosomula biological replicates (the second of two cercaria technical replicates) used in this experiment.   Hepatic schistosomula were isolated from separate infected rabbits at 2 weeks post-infection.


title: Individual 11 after exposure to high altitude


title: ESCC_Biopsy_BPY120


title: PBMC from Stable  78.1 at T0

description: STA, Biological replicate  78 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA078.1


title: C3

description: This sample is the third of three cercaria biological replicates used in this experiment.  The freshly released cercariae were harvested from S. japonicum-infected Oncomelania hupensis provided by Hunan Institute of Parasitic Diseases, Yueyang, China.

source_name: cercaria

value: cercaria


title: PBMC from Stable  77.2 at T0

description: STA, Biological replicate  77 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA077.2

value: PBMC from STA077

value: STA 77 of 190


title: Individual 10 after exposure to high altitude


title: ESCC_Biopsy_BPY113

value: ESCC

value: Biopsy before therapy


title: Individual 15 before exposure to high altitude


title: ESCC_Biopsy_BPY108

value: Surgery


title: C2

description: This sample is the second of three cercaria biological replicates used in this experiment.  The freshly released cercariae were harvested from S. japonicum-infected Oncomelania hupensis provided by Hunan Institute of Parasitic Diseases, Yueyang, China.


title: PBMC from Stable  77.1 at T0

description: STA, Biological replicate  77 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA077.1


title: PBMC from Stable  76.2 at T0

description: STA, Biological replicate  76 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA076.2

value: PBMC from STA076

value: STA 76 of 190


title: C1-2

description: This sample is the first of three cercaria biological replicates (the second of two cercaria technical replicates) used in this experiment.  The freshly released cercariae were harvested from S. japonicum-infected Oncomelania hupensis provided by Hunan Institute of Parasitic Diseases, Yueyang, China.


title: ESCC_Biopsy_BPY091


title: Individual 8 after exposure to high altitude


title: Individual 9 after exposure to high altitude


title: E3

description: This sample is the third of three egg biological replicates used in this experiment.  Eggs were purified from separate liver tissues of rabbits at 6 weeks post-infection.

source_name: egg

value: egg


title: Individual 7 after exposure to high altitude


title: PBMC from Stable  76.1 at T0

description: STA, Biological replicate  76 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA076.1


title: C1-1

description: This sample is the first of three cercaria biological replicates (the first of two cercaria technical replicates) used in this experiment. The freshly released cercariae were harvested from S. japonicum-infected Oncomelania hupensis provided by Hunan Institute of Parasitic Diseases, Yueyang, China.


title: E2

description: This sample is the second of three egg biological replicates used in this experiment.  Eggs were purified from separate liver tissues of rabbits at 6 weeks post-infection.


title: Individual 6 after exposure to high altitude


title: ESCC_Biopsy_BPY067


title: ESCC_Biopsy_BPY078


title: PBMC from Stable  75.2 at T0

description: STA, Biological replicate  75 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA075.2

value: PBMC from STA075

value: STA 75 of 190

value: Replicate 2 of 2


title: ESCC_Biopsy_BPY063


title: E1-2

description: This sample is the first of three egg biological replicates (the second of two egg technical replicates) used in this experiment.  Eggs were purified from separate liver tissues of rabbits at 6 weeks post-infection.


title: ESCC_Biopsy_BPY094


title: PBMC from Stable  75.1 at T0

description: STA, Biological replicate  75 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA075.1


title: Individual 5 after exposure to high altitude

value: Plasma

value: Male


title: PBMC from Stable  73.2 at T0

description: STA, Biological replicate  73 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA073.2

value: PBMC from STA073

value: STA 73 of 190


title: Individual 4 after exposure to high altitude


title: PBMC from Stable  74.1 at T0

description: STA, Biological replicate  74 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA074.1

value: PBMC from STA074

value: STA 74 of 190

value: Replicate 1 of 2


title: PBMC from Stable  74.2 at T0

description: STA, Biological replicate  74 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA074.2


title: ESCC_Biopsy_BPY059

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

value: ESCC


title: ESCC_Biopsy_BPY053

value: Biopsy before therapy


title: E1-1

description: This sample is the first of three egg biological replicates (the first of two egg technical replicates) used in this experiment. Eggs were purified from separate liver tissues of rabbits at 6 weeks post-infection.


title: ESCC_Biopsy_BPY049

value: Surgery


title: PBMC from Stable  73.1 at T0

description: STA, Biological replicate  73 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA073.1


title: Individual 3 after exposure to high altitude


title: ESCC_Biopsy_BPY032


title: Individual 1 after exposure to high altitude


title: Individual 2 after exposure to high altitude


title: ESCC_Biopsy_BPY041


title: PBMC from Stable  71.2 at T0

description: STA, Biological replicate  71 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA071.2

value: PBMC from STA071

value: STA 71 of 190


title: ESCC_Biopsy_BPY030

source_name: Esophageal squamous cell carcinoma


title: ESCC_Biopsy_BPY018


title: PBMC from Stable  72.1 at T0

description: STA, Biological replicate  72 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA072.1

value: PBMC from STA072

value: STA 72 of 190


title: PBMC from Stable  71.1 at T0

description: STA, Biological replicate  71 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA071.1


title: PBMC from Stable  72.2 at T0

description: STA, Biological replicate  72 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA072.2


title: PBMC from Stable  70.2 at T0

description: STA, Biological replicate  70 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA070.2

value: PBMC from STA070

value: STA 70 of 190


title: PBMC from Stable  69.2 at T0

description: STA, Biological replicate  69 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA069.2

value: PBMC from STA069

value: STA 69 of 190

value: Replicate 2 of 2


title: ESCC_Biopsy_BPY021


title: ESCC_Biopsy_BPY016


title: PBMC from Stable  70.1 at T0

description: STA, Biological replicate  70 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA070.1


title: ESCC_Biopsy_BPY015


title: Urea and NBPT_rep1

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description: Roots of plants treated with urea and NBPT. It is the first of urea and NBPT treated biological replicates used in this experiment.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Zea mays

source_name: 5-d-old-plants treated with urea and NBPT inhibitor

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol:
Maize seed (Zea mays L., cv. PR33T56, Pioneer Hybrid Italia S.p.A.) were germinated over aerated 0.5 mM CaSO4 solution in a dark growth chamber at 25°C. After 3 days, the seedlings were transferred into an aerated hydroponic system in a controlled climatic conditions: day/night photoperiod, 16/8 h;
light intensity, 220 µE m-2 s-1; temperature (day/night) 25/20°C; RH 70 to 80 %. 5-day-old plants were transferred to a nutrient solution containing (µM): KCl 5; CaSO4 500; MgSO4 100; KH2PO4 175; NaFe-EDTA 20; H3BO3 2.5; MnSO4 0.2; ZnSO4 0.2; CuSO4 0.05; Na2MoO4 0.05.
Nitrogen was supplied in form of: 0.5 mM urea + 0.897 NBPT inhibitor (UI treatment). The pH of solution was adjusted to pH 6.0 with potassium hydroxide.
After 8 hours (nine hours after the beginning of light phase), six plants from each treatment were pooled together and root samples were frozen in liquid nitrogen and stored at -80°C until further processing.

extract_protocol: Total RNA was isolated using the Invisorb Spin Plant RNA kit (Stratec Molecular, Berlin, Germany).

treatment_protocol:
Roots of 5-d-old maize plants were exposed for 8 hours to nutrient solution containing nitrogen in form of: 0.5 mM urea +  NBPT inhibitor (UI treatment).
Roots of six plants were pooled at the end of the experiment.

tag: hybrid

value: cv. PR33T56

value: root


title: Urea and NBPT_rep2

description: Roots of plants treated with urea and NBPT. It is the second of  urea and NBPT treated biological replicates used in this experiment.


title: ESCC_Biopsy_BPY023


title: Urea and NBPT_rep3

description: Roots of plants treated with urea and NBPT. It is the third of urea and NBPT treated biological replicates used in this experiment.


title: PBMC from Stable  69.1 at T0

description: STA, Biological replicate  69 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA069.1


title: PBMC from Stable  68.2 at T0

description: STA, Biological replicate  68 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA068.2

value: PBMC from STA068

value: STA 68 of 190


title: ESCC_Biopsy_BPY006

value: ESCC


title: ESCC_Biopsy_BPY013

value: Biopsy before therapy


title: Ts12-JM8_P4 vs JM8A3

type: genomic

first: Meili

last: Zhang

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description: CGH analysis of Ts12 vs JM8A3

hyb_protocol: Hybridization was processed for 40-72 hr at 42℃ in Roche-NimbleGen hybridization system 12. Arrays were washed with the NimbleGen Wash Buffer Kit (05584507001) and the NimbleGen Array Processing Accessories (05223539001)..

scan_protocol: Arrays were scanned on an Roche-NimbleGen MS 200 Microarray Scanner.

data_processing: Arrays were processed using NimbleScan,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio. The non-unique probes were not included.

molecule: genomic DNA

organism: Mus musculus

label_protocol: The gDNA samples were labelled using a NimbleGen Dual-Color DNA Labeling Kit (06370250001).

growth_protocol: ES cells were cultured on a layer of γ-irradiated MEFs in serum.

extract_protocol: The genomic DNA of the trisomic and wild-type ES cells were extracted using the Wizard Genomic DNA Purification Kit (Promega, A1120) according to the manufacturer’s instructions.

treatment_protocol: ES cells were collected without feeder cells.

tag: cell type

value: embryonic stem cell

tag: karyotype

value: trisomy 12

tag: strain

value: diploid


title: PBMC from Stable  67.1 at T0

description: STA, Biological replicate  67 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA067.1

value: PBMC from STA067

value: STA 67 of 190

value: Replicate 1 of 2


title: PBMC from Stable  68.1 at T0

description: STA, Biological replicate  68 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA068.1


title: PBMC from Stable  67.2 at T0

description: STA, Biological replicate  67 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA067.2


title: Ts15_P10_subclone 1 vs AB1

description: CGH analysis of Ts15 vs AB1

source_name: Ts15_P10_subclone 1

growth_protocol: ES cells were cultured on a layer of γ-irradiated SNL76/7 feeder cells in serum.

value: trisomy 15


title: ESCC_Biopsy_BPY037

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

value: Chemoradiotherapy


title: Ts15_P10_subclone 2 vs AB1

description: CGH analysis of Ts15 vs AB1

source_name: Ts15_P10_subclone 2

growth_protocol: ES cells were cultured on a layer of γ-irradiated SNL76/7 feeder cells in serum


title: PBMC from Stable  65.1 at T0

description: STA, Biological replicate  65 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA065.1

value: PBMC from STA065

value: STA 65 of 190


title: ESCC_Biopsy_BPY029

source_name: Esophageal squamous cell carcinoma


title: ESCC_Biopsy_BPY036


title: PBMC from Stable  65.2 at T0

description: STA, Biological replicate  65 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA065.2

value: Replicate 2 of 2


title: ESCC_Biopsy_BPY035


title: PBMC from Stable  66.2 at T0

description: STA, Biological replicate  66 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA066.2

value: PBMC from STA066

value: STA 66 of 190


title: ESCC_Biopsy_BPY028


title: ESCC_Biopsy_BPY026


title: ESCC_Biopsy_BPY027

tag: tumor stage

value: StageIII

tag: tnm stage


title: genomic DNA from 9407210093_R02C01

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

country: USA

institute: Yale University

description: 9407210093_R02C01: Sample 378

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNAs were extracted from whole blood using the standard protocol.

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407210063_R01C01

description: 9407210063_R01C01: Sample 377


title: Ts11_P14_subclone 1 vs AB1

description: CGH analysis of Ts11 vs AB1

source_name: Ts11_P14_subclone 1

value: trisomy 11


title: ESCC_Biopsy_BPY039

tag: disease state

value: ESCC

tag: tissue

value: Biopsy before therapy

tag: therapy


title: ESCC_Biopsy_BPY025


title: PBMC from Stable  63.2 at T0

description: STA, Biological replicate  63 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA063.2

value: PBMC from STA063

tag: individual replicate

value: STA 63 of 190

tag: techical replicate

tag: time point


title: PBMC from Stable  64.1 at T0

description: STA, Biological replicate  64 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA064.1

value: PBMC from STA064

value: STA 64 of 190


title: genomic DNA from 9407210061_R05C02

description: 9407210061_R05C02: Sample 375

value: White


title: ESCC_Biopsy_BPY019

value: Chemoradiotherapy


title: Ts11_P14_subclone 2 vs AB1

description: CGH analysis of Ts11 vs AB1

source_name: Ts11_P14_subclone 2

tag: cell type

value: embryonic stem cell

tag: karyotype

tag: strain

value: diploid


title: Ts8-JM8_P4 vs JM8A3

description: CGH analysis of Ts8 vs JM8A3

value: trisomy 8


title: Ts15_P15 vs AB1

description: CGH analysis of Ts15 vs AB1

value: trisomy 15


title: Ts11_P4 vs AB1

description: CGH analysis of Ts11 vs AB1


title: Ts15_P5 vs AB1

description: CGH analysis of Ts15 vs AB1


title: PBMC from Stable  62.1 at T0

description: STA, Biological replicate  62 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA062.1

value: PBMC from STA062

value: STA 62 of 190

value: Replicate 1 of 2


title: PBMC from Stable  62.2 at T0

description: STA, Biological replicate  62 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA062.2

value: Replicate 2 of 2


title: ESCC_Biopsy_BPY012

value: ESCC


title: genomic DNA from 9741950076_R04C01

description: 9741950076_R04C01: Sample 373

tag: hiv

tag: agebl


title: genomic DNA from 9701417123_R06C02

description: 9701417123_R06C02: Sample 374

tag: racecomg

tag: dmgsex


title: ESCC_Biopsy_BPY014

value: Biopsy before therapy


title: PBMC from Stable  66.1 at T0

description: STA, Biological replicate  66 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA066.1

value: PBMC from STA066

value: STA 66 of 190


title: genomic DNA from 9407210073_R02C02

description: 9407210073_R02C02: Sample 376

tag: gran

tag: nk


title: genomic DNA from 9701417093_R01C02

description: 9701417093_R01C02: Sample 372

value: Other

tag: bcell

tag: mono


title: Ts8_P2 vs AB1

description: CGH analysis of Ts8 vs AB1


title: Ts8_P12 vs AB1

description: CGH analysis of Ts8 vs AB1


title: PBMC from Stable  64.2 at T0

description: STA, Biological replicate  64 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA064.2

tag: tissue

value: PBMC from STA064


title: PBMC from Stable  61.2 at T0

description: STA, Biological replicate  61 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA061.2

value: PBMC from STA061

value: STA 61 of 190


title: Ts6_P6 vs AB1

description: CGH analysis of Ts6 vs AB1

value: embryonic stem cell

value: trisomy 6


title: genomic DNA from 9701417123_R04C01

description: 9701417123_R04C01: Sample 371

value: Black


title: PBMC from Stable  61.1 at T0

description: STA, Biological replicate  61 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA061.1


title: ESCC_Biopsy_BPY007

tag: disease state

tag: tumor stage

value: StageIII

tag: tnm stage

tag: therapy

value: Chemoradiotherapy


title: genomic DNA from 9741950032_R03C01

description: 9741950032_R03C01: Sample 370


title: Ts6_P16 vs AB1

description: CGH analysis of Ts6 vs AB1

value: diploid


title: ESCC_Biopsy_BPY010


title: genomic DNA from 9407210074_R06C01

description: 9407210074_R06C01: Sample 369


title: PBMC from Stable  60.2 at T0

description: STA, Biological replicate  60 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA060.2

value: PBMC from STA060

tag: individual replicate

value: STA 60 of 190

tag: techical replicate

tag: time point


title: genomic DNA from 9701417123_R05C02

description: 9701417123_R05C02: Sample 368

tag: hiv


title: ESCC_Biopsy_BPY005

value: ESCC


title: KCC-M871 0% mets

city: YOKOHAMA

first: Hiroshi

last: Hyakusoku

state: KANAGAWA

department: ENT

institute: Yokohama City University

hyb_protocol: Probe was hybridized to the DNA microarray chip, using the surePrint G3 Human GE microarray kit 8x60k ver,2.0<G4851BA>[database; hg19 : GRCh37 (Feb2009) ](Agilent Technologies, Palo Alto, CA, USA), containing a total of 50,739 spots corresponding to 28,689 unique genes followed by confocal laser scanning (Agilent Technologies Palo Alto, CA, USA).

scan_protocol: The array chip was washed and dried, and the image data was scanned. The image data was digitized by the Feature Extraction.

data_processing: The data were analyzed with GeneSpring 11.5 using Agilent default analysis settings and global scaling as normalization method.

source_name: cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I.

treatment_protocol: Adherent monolayer cultures were maintained on plastic plate and incubated at 37°C in 5% CO2 and 95% air with RPMI 1640 or DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.

tag: cell line

tag: metastatis state

tag: origin

value: Mesopharynx


title: PBMC from Stable  63.1 at T0

description: STA, Biological replicate  63 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA063.1

value: PBMC from STA063

value: STA 63 of 190

value: Replicate 1 of 2


title: Detroit562 Luci 0% mets

value: Detroit562 Luci

value: pleural effusion


title: ESCC_Biopsy_BPY004

source_name: Esophageal squamous cell carcinoma

value: Biopsy before therapy


title: PE／CA PJ34 0% mets

value: PE／CA PJ34

value: oral cavity


title: genomic DNA from 9701417123_R03C01

description: 9701417123_R03C01: Sample 366

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: genomic DNA from 9741950050_R02C02

description: 9741950050_R02C02: Sample 367

tag: nk

tag: bcell

tag: mono


title: PBMC from Stable  59.2 at T0

description: STA, Biological replicate  59 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA059.2

tag: tissue

value: PBMC from STA059

value: STA 59 of 190

value: Replicate 2 of 2


title: KCC-T871 100% mets

source_name: cell line: KCC-T871

tag: cell line:

value: Tongue


title: YCU-M862 0% mets


title: genomic DNA from 9741950076_R02C01

description: 9741950076_R02C01: Sample 365

source_name: whole blood

value: Black


title: PBMC from Stable  60.1 at T0

description: STA, Biological replicate  60 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA060.1

value: PBMC from STA060

value: STA 60 of 190


title: ESCC_Biopsy_BPY001

tag: disease state

value: ESCC

tag: therapy

value: Chemoradiotherapy


title: PBMC from Stable  59.1 at T0

description: STA, Biological replicate  59 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA059.1

tag: individual replicate

tag: techical replicate

tag: time point


title: ESCC_Biopsy_BPY003

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

tag: tumor stage

value: StageIII

tag: tnm stage


title: ESCC_Biopsy_D-2-05

value: StageIIA


title: genomic DNA from 9741950050_R06C01

description: 9741950050_R06C01: Sample 363

tag: hiv

tag: agebl


title: genomic DNA from 9741950016_R01C02

description: 9741950016_R01C02: Sample 364

tag: racecomg

tag: dmgsex


title: genomic DNA from 9701417115_R01C02

description: 9701417115_R01C02: Sample 360

tag: gran

tag: nk


title: YCU-T892 100% mets

tag: cell line

tag: metastatis state

tag: origin


title: PBMC from Stable  58.2 at T0

description: STA, Biological replicate  58 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA058.2

tag: tissue

value: PBMC from STA058

value: STA 58 of 190


title: HN30 100% mets

value: Pharynx


title: ESCC_Biopsy_D-2-01

tag: disease state

value: Biopsy before therapy

tag: therapy


title: ESCC_Biopsy_D-2-02

value: StageIIB


title: PBMC from Stable  58.1 at T0

description: STA, Biological replicate  58 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA058.1

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2


title: YCU-MS861 0% mets

value: Maxillary sinus


title: PBMC from Stable  57.2 at T0

description: STA, Biological replicate  57 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA057.2

value: PBMC from STA057

value: STA 57 of 190

value: Replicate 2 of 2

tag: time point


title: ESCC_Biopsy_D-1-11

tag: tumor stage

tag: tnm stage


title: PBMC from Stable  55.2 at T0

description: STA, Biological replicate  55 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA055.2

value: PBMC from STA055

value: STA 55 of 190


title: PBMC from Stable  56.2 at T0

description: STA, Biological replicate  56 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA056.2

value: PBMC from STA056

value: STA 56 of 190


title: PBMC from Stable  57.1 at T0

description: STA, Biological replicate  57 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA057.1


title: PBMC from Stable  55.1 at T0

description: STA, Biological replicate  55 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA055.1


title: PBMC from Stable  56.1 at T0

description: STA, Biological replicate  56 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA056.1


title: ESCC_Biopsy_D-1-07

value: ESCC

value: Chemoradiotherapy


title: genomic DNA from 9701417115_R02C02

description: 9701417115_R02C02: Sample 362

tag: hiv

tag: agebl

value: White

tag: bcell

tag: mono


title: ESCC_Biopsy_D-1-10

value: StageIIA


title: genomic DNA from 9701417112_R04C02

description: 9701417112_R04C02: Sample 361

tag: racecomg

tag: dmgsex

tag: gran

tag: nk


title: genomic DNA from 9701417123_R04C02

description: 9701417123_R04C02: Sample 358

value: Other


title: genomic DNA from 9701417112_R06C02

description: 9701417112_R06C02: Sample 357

value: Black


title: genomic DNA from 9741950076_R05C02

description: 9741950076_R05C02: Sample 359


title: genomic DNA from 9741950032_R04C02

description: 9741950032_R04C02: Sample 355


title: PBMC from Stable  54.2 at T0

description: STA, Biological replicate  54 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA054.2

value: PBMC from STA054

value: STA 54 of 190


title: genomic DNA from 9701417112_R04C01

description: 9701417112_R04C01: Sample 354


title: ESCC_Biopsy_D-1-05

tag: tissue

value: Biopsy before therapy


title: genomic DNA from 9741950032_R06C02

description: 9741950032_R06C02: Sample 353


title: ESCC_Biopsy_D-1-02

tag: disease state

value: StageIII


title: PBMC from Stable  54.1 at T0

description: STA, Biological replicate  54 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA054.1

value: Replicate 1 of 2


title: genomic DNA from 9701417112_R05C02

description: 9701417112_R05C02: Sample 352


title: ESCC_Biopsy_A-2-03

source_name: Esophageal squamous cell carcinoma

tag: therapy


title: ESCC_Biopsy_A-2-02


title: ESCC_Biopsy_BPY017


title: ESCC_Biopsy_A-1-12


title: PBMC from Stable  53.1 at T0

description: STA, Biological replicate  53 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA053.1

value: PBMC from STA053

tag: individual replicate

value: STA 53 of 190


title: genomic DNA from 9701417112_R02C01

description: 9701417112_R02C01: Sample 356


title: PBMC from Stable  52.2 at T0

description: STA, Biological replicate  52 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA052.2

value: PBMC from STA052

value: STA 52 of 190

tag: techical replicate

value: Replicate 2 of 2


title: PBMC from Stable  52.1 at T0

description: STA, Biological replicate  52 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA052.1

tag: time point


title: genomic DNA from 9741950076_R03C01

description: 9741950076_R03C01: Sample 351

source_name: whole blood


title: PBMC from Stable  53.2 at T0

description: STA, Biological replicate  53 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA053.2


title: ESCC_Biopsy_D-1-01

value: ESCC

tag: tumor stage


title: PBMC from Stable  51.1 at T0

description: STA, Biological replicate  51 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA051.1

value: PBMC from STA051

value: STA 51 of 190


title: PBMC from Stable  50.2 at T0

description: STA, Biological replicate  50 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA050.2

value: PBMC from STA050

value: STA 50 of 190


title: genomic DNA from 9701417123_R02C01

description: 9701417123_R02C01: Sample 350

value: White


title: ESCC_Biopsy_A-1-07

description: Gene expression data from biopsy of esophageal squamous cell carcinoma

value: StageIIA

tag: tnm stage

value: Chemoradiotherapy


title: ESCC_Biopsy_A-1-04

value: Biopsy before therapy


title: ESCC_Biopsy_A-1-08

value: StageIII


title: PBMC from Stable  51.2 at T0

description: STA, Biological replicate  51 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA051.2


title: ESCC_Biopsy_A-1-01


title: genomic DNA from 9701417115_R05C01

description: 9701417115_R05C01: Sample 348

tag: hiv

value: Black


title: genomic DNA from 9741950032_R02C01

description: 9741950032_R02C01: Sample 349

tag: agebl


title: genomic DNA from 9741950050_R01C02

description: 9741950050_R01C02: Sample 347

tag: bcell


title: genomic DNA from 9701417115_R06C01

description: 9701417115_R06C01: Sample 346

tag: mono


title: AAB-HT097-AT-L

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

hyb_protocol: Following fragmentation, 5 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000.

data_processing: The data were analyzed with Bioconductor/R and were GCRMA normalized and MAS5 normalized.

source_name: skin biopsy

label_protocol: NuGen Ovation Amplification System 2 and Encore Biotin Module

extract_protocol: PAXgene tissue miRNA kit

tag: patient id

tag: disease status

value: AT

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

tag: gender

value: F

tag: age

tag: registry site

value: Houston

tag: microarray batch

tag: dataset

value: Validation Dataset


title: 2. AoDILD state

type: other

city: Sagamihara

last: Furukawa

address: 18-1 Sakuradai, Minami-ku

institute: Sagamihara Hospital, National Hospital Organization

description: sera

hyb_protocol: After blocking and washing, the array was incubated with the pooled sera diluted 1:500 in 5 ml of washing buffer at 4oC for 1.5 hours. After 5 washes, the array was incubated with Alexa Fluor 647 goat anti-human IgG Abs (0.9 μg/ml) and Alexa Fluor 647 anti-V5 Ab.

scan_protocol: The data were acquired with a Microarray Scanner GenePix 4000B, quantified using GenePix Pro 5.1.

data_processing: The data were finally analyzed by ProtoArray Prospector 5.20

label: Alexa Fluor 647

molecule: other

source_name: pooled sera from 25 individuals in AoDILD state

label_protocol: The array was incubated with Alexa Fluor 647 goat anti-human IgG Abs (0.9 μg/ml).

extract_protocol: Sera were separated from blood.

tag: disease state

value: AoDILD state

tag: sample type

value: sera


title: genomic DNA from 9701417093_R06C01

description: 9701417093_R06C01: Sample 345

tag: racecomg

value: Other

tag: dmgsex

tag: gran

tag: nk


title: genomic DNA from 9741950016_R06C01

description: 9741950016_R06C01: Sample 344

tag: hiv

tag: agebl


title: PBMC from Stable  50.1 at T0

description: STA, Biological replicate  50 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA050.1

tag: tissue

value: PBMC from STA050

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: genomic DNA from 9701417112_R03C02

description: 9701417112_R03C02: Sample 343

tag: bcell

tag: mono


title: PBMC from Stable  49.1 at T0

description: STA, Biological replicate  49 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA049.1

value: PBMC from STA049

value: STA 49 of 190


title: PBMC from Stable  48.2 at T0

description: STA, Biological replicate  48 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA048.2

value: PBMC from STA048

value: STA 48 of 190

value: Replicate 2 of 2


title: AAB-HT095-AAP.T-L

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: gender

value: M

tag: age

tag: registry site


title: PBMC from Stable  47.2 at T0

description: STA, Biological replicate  47 of 190, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA047.2

value: PBMC from STA047

value: STA 47 of 190


title: genomic DNA from 9701417093_R02C02

description: 9701417093_R02C02: Sample 342

tag: racecomg

value: Black

tag: dmgsex

tag: gran


title: PBMC from Stable  48.1 at T0

description: STA, Biological replicate  48 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA048.1


title: PBMC from Stable  49.2 at T0

description: STA, Biological replicate  49 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA049.2


title: genomic DNA from 9741950016_R02C02

description: 9741950016_R02C02: Sample 341

tag: hiv

tag: agebl

value: White

tag: nk


title: AAB-N-C108-Normal-NC

value: Normal

value: NC

value: F

value: Columbia

tag: microarray batch

tag: dataset

value: Validation Dataset


title: V4

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Chlamydia-infected mice

hyb_protocol: Hybridization of Affymetrix Mouse Genome 430 PM Strip arrays were performed following the manufacturer’s recommendations.

scan_protocol: Staining and scanning of Affymetrix Mouse Genome 430 PM Strip arrays were performed following the manufacturer’s recommendations.

data_processing: Images intensities were extracted using GeneAtlas System software (Affymetrix), normalized and summarized using Robust Multi-array Average algorithm. Differential gene expression analysis assessed by fitting to an empirical Bayesian linear model. Statistical significance in differential gene expression was computed with a false discovery rate multiple testing adjustment correction. For this analysis we used the Limma package and the R statistical programming environment (Smyth, 2005).

label: Biotin

source_name: Effector lymphocytes

label_protocol: Biotinylated cRNA was prepared by terminal transferase from the GeneChip Mapping 250K Nsp Assay Kit (AffymetrixInc, Santa Clara, CA, USA).

growth_protocol: 8 week old C57BL/6 mice were purchased from the National Cancer Institute. All mice were maintained in accordance with University of California Davis Research Animal Resource guidelines. Bacteria used for vaginal infection was Chlamydia muridarum strain Nigg II, which was purchased from ATCC (Manassas, VA, USA) and cultured in HeLa 229 cells in Dulbecco’s Modified Eagle Medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal bovine serum. Elementary bodies (EBs) were purified by discontinuous density gradient centrifugation and stored at -80 degrees. The number of inclusion-forming units of purified EBs was determined by infection of HeLa 229 cells and enumeration of inclusions that were stained with anti-Chlamydia MOMP antibody. Heat-killed EBs was prepared by heating at 56ºC for 30 min. Estrus was synchronized in mice by subcutaneous injection of 2.5 mg medroxyprogesterone acetate (Greenstone LLC, Peapack, NJ, USA) five days before infection. For intravaginal infections, 1x10E5 C. muridarum in 5 mL sucrose/phosphate/glutamate buffer were deposited into vaginal vaults. To enumerate bacteria, vaginal swabs were collected, shaken with glass beads, and serial dilutions were plated on HeLa 229 cells.

extract_protocol: RNA isolation and cDNA amplification were performed as described in Gonzalez-Roca et al. (2010). In brief, 300 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt-Beckman Coulter, Indianapolis IN, USA ). RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich, Saint Louis, MO, USA). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 24 cycles when SYBR Green signal reached a plateau. cDNA was purified using GenElute PCR Clean up kit (Sigma Aldrich, Saint Louis, MO, USA).

treatment_protocol: Blood samples were immediately lysed using a RBC lysis buffer (containing 20.75 g/l NH4Cl, 2.5 g/l NaHCO3 and 0.093 g/l EDTA in distillated water). After washing twice, cells were stained with Abs against CD3-Vioblue (clone 145-2C11), CD62L-PE (clone MEL-14-H2.100) and CD44-FITC  (clone IM7.8.1; all from MiltenyiBiotec, Madrid, Spain) for 20 mins. Cells suspended in cold FACS flow buffer  (0,5% FBS-PBS with 0.5mM EDTA) were immediately sorted into 350μl of chilled RLT buffer (QIAGEN, Valencia, CA, USA) using a BD FACSAriaTM Cell Sorter. Circulating TEM cells were sorted from six 7d Chlamydia-infected mice (V group) and six contemporary sham-treated mice (C group).

tag: strain

tag: infection

value: Chlamydia-infected


title: AAB-N-C107-Normal-NC

tag: patient id


title: PBMC from Stable  47.1 at T0

description: STA, Biological replicate  47 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA047.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Stable  46.2 at T0

description: STA, Biological replicate  46 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA046.2

value: PBMC from STA046

value: STA 46 of 190


title: 1. stable state

description: sera

source_name: pooled sera from 25 individuals in stable state

tag: disease state

value: stable state

value: sera


title: AAB-SF113-AU-L

tag: disease status

value: AU

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

tag: gender

tag: age

tag: registry site

value: San Francisco


title: V5

description: Chlamydia-infected mice


title: genomic DNA from 9741950032_R05C02

description: 9741950032_R05C02: Sample 340

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: C5

description: sham mice

tag: strain

tag: infection

value: sham


title: genomic DNA from 9407210073_R06C01

description: 9407210073_R06C01: Sample 339

value: Black

tag: nk


title: AAB-C093-Normal-NC

tag: patient id

tag: microarray batch

tag: dataset


title: AAB-HT095-AAP.T-NL

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NL

value: M

value: Houston


title: C4

description: sham mice


title: PBMC from Stable  46.1 at T0

description: STA, Biological replicate  46 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA046.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: AAB-SF106-AU-L

tag: gender

tag: age

tag: registry site


title: AAB-N-C105-Normal-NC

value: Normal

value: NC

value: Columbia


title: AAB-HT101-AU-L

value: F

value: Validation Dataset


title: AAB-N-C098-Normal-NC


title: C6

description: sham mice


title: V6

description: Chlamydia-infected mice

value: Chlamydia-infected


title: genomic DNA from 9741950076_R04C02

description: 9741950076_R04C02: Sample 338

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: genomic DNA from 9701417123_R03C02

description: 9701417123_R03C02: Sample 337

tag: nk


title: PBMC from Stable  44.2 at T0

description: STA, Biological replicate  44 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA044.2

value: PBMC from STA044

value: STA 44 of 190

value: Replicate 2 of 2


title: PBMC from Stable  45.1 at T0

description: STA, Biological replicate  45 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA045.1

value: PBMC from STA045

value: STA 45 of 190

value: Replicate 1 of 2


title: genomic DNA from 9741950076_R06C02

description: 9741950076_R06C02: Sample 336

value: White


title: AAB-M110-AT-L

source_name: skin biopsy

tag: patient id

tag: disease status

value: AT

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

value: Minnesota

tag: microarray batch

tag: dataset


title: genomic DNA from 9701417112_R03C01

description: 9701417112_R03C01: Sample 335

value: Black


title: genomic DNA from 9701417123_R01C01

description: 9701417123_R01C01: Sample 334


title: PBMC from Stable  45.2 at T0

description: STA, Biological replicate  45 of 190, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA045.2

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: genomic DNA from 9701417112_R01C01

description: 9701417112_R01C01: Sample 333

tag: hiv

tag: agebl


title: genomic DNA from 9701417093_R05C01

description: 9701417093_R05C01: Sample 332

tag: racecomg

tag: dmgsex


title: AAB-C109-AU-L

value: AU

tag: gender

value: M

tag: age

tag: registry site


title: PBMC from Stable  44.1 at T0

description: STA, Biological replicate  44 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA044.1


title: genomic DNA from 9701417115_R06C02

description: 9701417115_R06C02: Sample 331

tag: gran

tag: nk

tag: bcell

tag: mono


title: AAB-C111-AU-L

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: F

value: Columbia

tag: microarray batch

tag: dataset


title: PBMC from Stable  42.1 at T0

description: STA, Biological replicate  42 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA042.1

tag: tissue

value: PBMC from STA042

tag: individual replicate

value: STA 42 of 190

tag: techical replicate

tag: time point


title: PBMC from Stable  43.2 at T0

description: STA, Biological replicate  43 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA043.2

value: PBMC from STA043

value: STA 43 of 190


title: AAB-M112-AAP-NL

value: AAP

value: NL

tag: gender

value: Validation Dataset


title: genomic DNA from 9741950016_R05C02

description: 9741950016_R05C02: Sample 329

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex


title: PBMC from Stable  41.2 at T0

description: STA, Biological replicate  41 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA041.2

value: PBMC from STA041

value: STA 41 of 190

value: Replicate 2 of 2


title: genomic DNA from 9741950016_R02C01

description: 9741950016_R02C01: Sample 328

tag: gran

tag: nk

tag: bcell


title: PBMC from Stable  41.1 at T0

description: STA, Biological replicate  41 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA041.1

value: Replicate 1 of 2


title: PBMC from Stable  43.1 at T0

description: STA, Biological replicate  43 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA043.1


title: genomic DNA from 9741950076_R03C02

description: 9741950076_R03C02: Sample 327

value: Black

tag: mono


title: AAB-SF115-AAP.T-NL

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: San Francisco


title: genomic DNA from 9741950032_R02C02

description: 9741950032_R02C02: Sample 330

value: Other


title: PBMC from Stable  42.2 at T0

description: STA, Biological replicate  42 of 190, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA042.2

tag: tissue

tag: individual replicate


title: PBMC from Stable  40.2 at T0

description: STA, Biological replicate  40 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA040.2

value: PBMC from STA040

value: STA 40 of 190

tag: techical replicate

tag: time point


title: AAB-C092-Normal-NC

value: Normal

value: NC

tag: gender

value: F

value: Columbia

tag: microarray batch

tag: dataset


title: PBMC from Stable  38.2 at T0

description: STA, Biological replicate  38 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA038.2

value: PBMC from STA038

value: STA 38 of 190


title: AAB-SF104-AAP-NL

value: AAP

value: NL

value: Validation Dataset


title: AAB-SF114-AAP-NL


title: PBMC from Stable  39.1 at T0

description: STA, Biological replicate  39 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA039.1

value: PBMC from STA039

value: STA 39 of 190


title: PBMC from Stable  40.1 at T0

description: STA, Biological replicate  40 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA040.1

value: Replicate 1 of 2


title: AAB-SF104-AAP-L

value: L

value: San Francisco


title: genomic DNA from 9741950016_R06C02

description: 9741950016_R06C02: Sample 325

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: dmgsex

tag: gran


title: AAB-M112-AAP-L

tag: patient id

tag: disease status

value: M

value: Minnesota


title: AAB-SF114-AAP-L

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age


title: PBMC from Stable  38.1 at T0

description: STA, Biological replicate  38 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA038.1


title: PBMC from Stable  39.2 at T0

description: STA, Biological replicate  39 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA039.2

tag: tissue

value: Replicate 2 of 2


title: AAB-N-C085-Normal-NC

source_name: skin biopsy

value: Normal

value: NC

tag: registry site


title: genomic DNA from 9701417115_R04C01

description: 9701417115_R04C01: Sample 326

value: Black

tag: nk

tag: bcell

tag: mono


title: AAB-N-C075-Normal-NC

tag: gender

value: Columbia

tag: microarray batch


title: AAB-N-C072-Normal-NC

value: F

tag: dataset


title: AAB-N-C074-Normal-NC


title: AAB-SF115-AAP.T-L


title: genomic DNA from 9701417112_R06C01

description: 9701417112_R06C01: Sample 323

tag: hiv

tag: agebl

value: White


title: genomic DNA from 9701417093_R05C02

description: 9701417093_R05C02: Sample 324

tag: racecomg

tag: dmgsex


title: genomic DNA from 9741950050_R02C01

description: 9741950050_R02C01: Sample 322

tag: gran


title: genomic DNA from 9701417123_R05C01

description: 9701417123_R05C01: Sample 321


title: genomic DNA from 9741950076_R01C01

description: 9741950076_R01C01: Sample 320


title: genomic DNA from 9741950016_R04C01

description: 9741950016_R04C01: Sample 318


title: PBMC from Stable  37.1 at T0

description: STA, Biological replicate  37 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA037.1

value: PBMC from STA037

tag: individual replicate

value: STA 37 of 190

tag: techical replicate

tag: time point


title: PBMC from Stable  37.2 at T0

description: STA, Biological replicate  37 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA037.2


title: PBMC from Stable  36.1 at T0

description: STA, Biological replicate  36 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA036.1

tag: tissue

value: PBMC from STA036

value: STA 36 of 190


title: PBMC from Stable  35.1 at T0

description: STA, Biological replicate  35 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA035.1

value: PBMC from STA035

value: STA 35 of 190

value: Replicate 1 of 2


title: AAB-N-C071-Normal-NC

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Validation Dataset


title: AAB-N-C070-Normal-NC

tag: gender

tag: microarray batch


title: AAB-SF100-AU-L

value: AU

value: L

value: San Francisco

tag: dataset


title: PBMC from Stable  33.2 at T0

description: STA, Biological replicate  33 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA033.2

value: PBMC from STA033

value: STA 33 of 190

value: Replicate 2 of 2


title: PBMC from Stable  35.2 at T0

description: STA, Biological replicate  35 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA035.2


title: AAB-SF090-AU-L

value: F


title: genomic DNA from 9701417093_R03C01

description: 9701417093_R03C01: Sample 317

tag: hiv

tag: agebl

value: Black

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9741950050_R05C01

description: 9741950050_R05C01: Sample 315

tag: racecomg

tag: dmgsex

tag: gran


title: AAB-N-C069-Normal-NC

value: Normal

value: NC

value: Columbia


title: genomic DNA from 9701417115_R03C02

description: 9701417115_R03C02: Sample 316


title: PBMC from Stable  33.1 at T0

description: STA, Biological replicate  33 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA033.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: genomic DNA from 9701417093_R06C02

description: 9701417093_R06C02: Sample 314


title: genomic DNA from 9701417112_R02C02

description: 9701417112_R02C02: Sample 319


title: AAB-M094-AU-L

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Minnesota


title: PBMC from Stable  34.2 at T0

description: STA, Biological replicate  34 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA034.2

value: PBMC from STA034

value: STA 34 of 190


title: PBMC from Stable  36.2 at T0

description: STA, Biological replicate  36 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA036.2

value: PBMC from STA036

value: STA 36 of 190


title: AAB-HT096-AT-L

value: AT

tag: gender

value: Houston

tag: microarray batch

tag: dataset

value: Validation Dataset


title: genomic DNA from 9741950076_R01C02

description: 9741950076_R01C02: Sample 313

tag: hiv

tag: agebl

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407201108_R03C02

description: 9407201108_R03C02: Sample 312

tag: racecomg

tag: dmgsex

tag: gran


title: AAB-SF099-AAP-NL

value: AAP

value: NL

value: San Francisco


title: PBMC from Stable  32.2 at T0

description: STA, Biological replicate  32 of 190, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA032.2

tag: tissue

value: PBMC from STA032

tag: individual replicate

value: STA 32 of 190

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: AAB-SF089-AU-L

tag: patient id

tag: disease status

value: AU

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

value: F

tag: age

tag: registry site


title: genomic DNA from 9701417115_R01C01

description: 9701417115_R01C01: Sample 309

tag: hiv

tag: agebl

value: Black


title: genomic DNA from 9407210061_R05C01

description: 9407210061_R05C01: Sample 310

value: White

tag: nk

tag: bcell


title: genomic DNA from 9741950032_R06C01

description: 9741950032_R06C01: Sample 311

tag: racecomg

tag: mono


title: genomic DNA from 9741950032_R03C02

description: 9741950032_R03C02: Sample 308

tag: dmgsex

tag: gran


title: genomic DNA from 9701417123_R01C02

description: 9701417123_R01C02: Sample 307


title: PBMC from Stable  34.1 at T0

description: STA, Biological replicate  34 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA034.1

tag: tissue

value: PBMC from STA034

value: STA 34 of 190

value: Replicate 1 of 2


title: AAB-SF078-AAP.T-NL

tag: gender

tag: microarray batch

tag: dataset


title: PBMC from Stable  31.2 at T0

description: STA, Biological replicate  31 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA031.2

value: PBMC from STA031

tag: individual replicate

value: STA 31 of 190

tag: techical replicate

tag: time point


title: PBMC from Stable  32.1 at T0

description: STA, Biological replicate  32 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA032.1


title: AAB-HT103-AAP-NL

tag: patient id

tag: disease status

value: AAP

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Houston

value: Validation Dataset


title: PBMC from Stable  31.1 at T0

description: STA, Biological replicate  31 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA031.1


title: AAB-SF099-AAP-L

value: San Francisco


title: AAB-SF078-AAP.T-L


title: AAB-HT103-AAP-L


title: PBMC from Stable  30.1 at T0

description: STA, Biological replicate  30 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA030.1

value: PBMC from STA030

value: STA 30 of 190


title: PBMC from Stable  29.2 at T0

description: STA, Biological replicate  29 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA029.2

value: PBMC from STA029

value: STA 29 of 190

value: Replicate 2 of 2


title: PBMC from Stable  29.1 at T0

description: STA, Biological replicate  29 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA029.1


title: PBMC from Stable  30.2 at T0

description: STA, Biological replicate  30 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA030.2


title: PBMC from Stable  28.2 at T0

description: STA, Biological replicate  28 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA028.2

value: PBMC from STA028

value: STA 28 of 190


title: AAB-N-C063-Normal-NC

source_name: skin biopsy

value: Normal

value: NC

value: F

value: Columbia

value: Discovery Dataset


title: AAB-N-C065-Normal-NC


title: AAB-N-C064-Normal-NC


title: genomic DNA from 9741950016_R03C01

description: 9741950016_R03C01: Sample 305

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: nk

tag: bcell


title: genomic DNA from 9741950050_R05C02

description: 9741950050_R05C02: Sample 306

tag: dmgsex

tag: gran

tag: mono


title: genomic DNA from 9701417112_R05C01

description: 9701417112_R05C01: Sample 303

value: Other


title: genomic DNA from 9741950032_R01C01

description: 9741950032_R01C01: Sample 302

value: White


title: genomic DNA from 9407210065_R04C02

description: 9407210065_R04C02: Sample 301


title: genomic DNA from 9701417093_R04C01

description: 9701417093_R04C01: Sample 300


title: genomic DNA from 9407210074_R06C02

description: 9407210074_R06C02: Sample 304


title: genomic DNA from 9701417123_R06C01

description: 9701417123_R06C01: Sample 298


title: PBMC from Stable  27.1 at T0

description: STA, Biological replicate  27 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA027.1

tag: tissue

value: PBMC from STA027

value: STA 27 of 190

value: Replicate 1 of 2


title: AAB-HT008-AU-L

value: AU

value: L

tag: gender

value: Houston

tag: microarray batch

tag: dataset


title: AAB-SF087-AU-L

tag: patient id

tag: disease status

value: San Francisco


title: PBMC from Stable  24.1 at T0

description: STA, Biological replicate  24 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA024.1

value: PBMC from STA024

tag: individual replicate

value: STA 24 of 190

tag: techical replicate

tag: time point


title: PBMC from Stable  26.1 at T0

description: STA, Biological replicate  26 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA026.1

value: PBMC from STA026

value: STA 26 of 190


title: genomic DNA from 9741950050_R03C01

description: 9741950050_R03C01: Sample 299

tag: hiv

tag: agebl


title: PBMC from Stable  28.1 at T0

description: STA, Biological replicate  28 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA028.1

value: PBMC from STA028

value: STA 28 of 190


title: PBMC from Stable  26.2 at T0

description: STA, Biological replicate  26 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA026.2

value: Replicate 2 of 2


title: AAB-SF086-AAP-L

value: AAP

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: F

tag: age

tag: registry site

value: Discovery Dataset


title: PBMC from Stable  27.2 at T0

description: STA, Biological replicate  27 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA027.2

value: PBMC from STA027


title: PBMC from Stable  24.2 at T0

description: STA, Biological replicate  24 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA024.2


title: PBMC from Stable  23.2 at T0

description: STA, Biological replicate  23 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA023.2

value: PBMC from STA023

value: STA 23 of 190


title: AAB-SF086-AAP-NL

value: NL


title: Uterine decidua isolated from Rac1 flox control mice on day 8 of pregnancy

city: Urbana

first: Juanmahel

last: Davila

state: Illinois

address: 2001 S. Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois

description:
Gene expression data from D8 decidua
D8 Flox Sample

hyb_protocol: 10 micrograms of labeled cRNA were hybridized to a Mouse Genome 430A 2.0 Affymetrix 3' Expression Analysis Array.  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_2.

source_name: Uterine decidua, Rac1 flox control mice on day 8 of pregnancy

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. Rac1 floxed mice  were crossed with PRcre mice (provided by Dr. Francceso DeMayo, (Baylor College of Medicine) to conditionally ablate Rac1 in the uterus.

extract_protocol: Trizol extraction of total RNA was performed followed by RNA cleaup using the Rneasy (Qiagen) according to the manufacturer's instructions

treatment_protocol: Rac1-null mice (n=3) and the corresponding controls (n=3) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day 1 of pregnancy. On day 8 of pregnancy, uterine horns were excised and the implantation sites were cut, separated, then placed in HBSS. The myometrium of each implantation chamber was mechanically removed and the decidua was exposed. Embryos were then removed and the decidual masses were pool and flashed freezed in liquid N2 until RNA extraction was performed.

tag: genotype/variation

value: control

tag: developmental stage

value: day 8 of pregnancy

value: decidua


title: PBMC from Stable  25.2 at T0

description: STA, Biological replicate  25 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA025.2

value: PBMC from STA025

value: STA 25 of 190


title: PBMC from Stable  25.1 at T0

description: STA, Biological replicate  25 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA025.1

tag: tissue

value: Replicate 1 of 2


title: AAB-C083-AAP-NL

tag: gender

value: M

value: Columbia


title: genomic DNA from 9741950016_R05C01

description: 9741950016_R05C01: Sample 296

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417093_R04C02

description: 9701417093_R04C02: Sample 297

value: White


title: AAB-HT079-AAP-L

tag: patient id

tag: disease status

value: AAP

value: L

value: Houston

tag: microarray batch

tag: dataset


title: genomic DNA from 9741950076_R02C02

description: 9741950076_R02C02: Sample 295

tag: hiv

tag: agebl


title: AAB-HT079-AAP-NL

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Discovery Dataset


title: genomic DNA from 9701417115_R05C02

description: 9701417115_R05C02: Sample 294


title: Uterine decidua isolated from Rac1 cKO control mice on day 8 of pregnancy

description:
Gene expression data from D8 decidua
D8 cKO sample

source_name: Uterine decidua, Rac1 cKO control mice on day 8 of pregnancy

tag: genotype/variation

value: Rac1 cKO

tag: developmental stage

tag: tissue


title: HYPOXIC FIN CONTROL2

city: PESSAC

first: Abdel-Majid

last: Khatib

address: av des Facultes

institute: INSERM

hyb_protocol: Cy3- and Cy5-labeled cRNA targets were mixed and incubated on the microarray slides in a rotating oven, at 65°C for 17 hours.

scan_protocol: After washing, slides were scanned using the Microarray Scanner (Agilent Technologies) at 5-µm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification

data_processing: Data were background corrected by the minimum method (any intensity which is zero or negative after background subtraction is set equal to half the minimum of the positive corrected intensities for that array); Lowess method was used for intra-array normalization; Quantile method was used for inter-array normalization

organism: Danio rerio

source_name: zebrafish fins_hypoxic

label_protocol: 1 µg of total RNA was labeled using the Quick Amp labeling kit (Agilent Technologies), Cy5-CTP for the reference RNA, Cy3-CTP for individual samples. Internal standards were derived from the Two-Color RNA Spike-in Kit (Agilent Technologies).

growth_protocol: zebrafish were incubated in water containing or not cobalt chloride (CoCl2, 1mM)

extract_protocol: Total RNA extracted using the NucleoSpin® RNA II kit, according to the manufacturer’s instructions.

value: adult

value: none amputated fins

tag: condition

value: hypoxic

source_name: Pooled fins including none-amputated fins and regenerated fins (blastema) under normoxic and hypoxic conditions.

tag: tisue

value: fin


title: AAB-HT009-AAP-L

source_name: skin biopsy

tag: gender

value: F


title: HYPOXIC FIN CONTROL4


title: AAB-HT091-AT-L

value: AT


title: HYPOXIC FIN CONTROL1


title: PBMC from Stable  22.1 at T0

description: STA, Biological replicate  22 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA022.1

value: PBMC from STA022

tag: individual replicate

value: STA 22 of 190

tag: techical replicate

tag: time point


title: AAB-C083-AAP-L

tag: patient id

tag: disease status

value: M

value: Columbia

tag: microarray batch


title: NORMOXIC FIN CONTROL1

source_name: zebrafish fins_normoxic

growth_protocol: zebrafish fins were allowed to regenerate following amputation

value: normoxic

source_name: Pooled fins including none amputated fins and regenerated fins (blastema) under normoxic and hypoxic conditions.


title: NORMOXIC FIN CONTROL5


title: PBMC from Stable  22.2 at T0

description: STA, Biological replicate  22 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA022.2

value: Replicate 2 of 2


title: genomic DNA from 9701417093_R03C02

description: 9701417093_R03C02: Sample 292

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: AAB-C016-AU-L

value: AU

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

tag: age

tag: registry site

tag: dataset


title: genomic DNA from 9701417093_R02C01

description: 9701417093_R02C01: Sample 293


title: AAB-N-C059-Normal-NC

value: Normal

value: NC

tag: gender

value: Discovery Dataset


title: HYPOXIC BLASTEMA 2

source_name: regenerated zebrafish fins_hypoxic

growth_protocol: following amputation of fin zebrafish, fins were allowed to regenerate and form blastema in the absence and presence of CoCl2 , 1mM

value: adult

tag: tissue

value: regenerated (blastema) fins

tag: regeneration condition

value: hypoxic (in the presence of 1mM CoCl2)

tag: harvest time point

value: after 3 days of regeneration


title: genomic DNA from 9407210063_R05C01

description: 9407210063_R05C01: Sample 291

value: Other


title: PBMC from Stable  23.1 at T0

description: STA, Biological replicate  23 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA023.1

value: PBMC from STA023

tag: individual replicate

value: STA 23 of 190

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Stable  21.2 at T0

description: STA, Biological replicate  21 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA021.2

value: PBMC from STA021

value: STA 21 of 190


title: NORMOXIC FIN CONTROL4

value: none amputated fins

tag: condition

value: normoxic

value: fin


title: HYPOXIC BLASTEMA 4


title: HYPOXIC FIN CONTROL5

value: hypoxic

tag: tisue


title: AAB-N-C054-Normal-NC

tag: patient id

tag: disease status

value: Normal

value: NC

value: F

value: Columbia

tag: microarray batch


title: AAB-M080-AU-L

value: AU

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

value: M

value: Minnesota

value: Discovery Dataset


title: AAB-N-C062-Normal-NC

tag: age


title: NORMOXIC FIN CONTROL2

value: adult


title: genomic DNA from 9701417123_R02C02

description: 9701417123_R02C02: Sample 290

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9741950076_R06C01

description: 9741950076_R06C01: Sample 289

value: White


title: HYPOXIC BLASTEMA 1

tag: tissue

value: regenerated (blastema) fins

tag: regeneration condition

value: hypoxic (in the presence of 1mM CoCl2)

tag: harvest time point

value: after 3 days of regeneration


title: AAB-HT077-AU-L

tag: gender

tag: registry site

value: Houston

tag: dataset


title: NORMOXIC BLASTEMA 4

source_name: regenerated zebrafish fins_normoxic

value: normoxic (in the absence of 1mM CoCl2)

value: fin


title: genomic DNA from 9701417115_R03C01

description: 9701417115_R03C01: Sample 288


title: PBMC from Stable  21.1 at T0

description: STA, Biological replicate  21 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA021.1

value: PBMC from STA021

tag: individual replicate

value: STA 21 of 190

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: NORMOXIC BLASTEMA 2

tag: age


title: genomic DNA from 9701417115_R04C02

description: 9701417115_R04C02: Sample 287

tag: hiv

tag: agebl

tag: racecomg


title: PBMC from Stable  20.2 at T0

description: STA, Biological replicate  20 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA020.2

value: PBMC from STA020

value: STA 20 of 190

value: Replicate 2 of 2


title: AAB-N-C055-Normal-NC

tag: patient id

tag: disease status

value: Normal

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NC

value: F

value: Columbia

tag: microarray batch

value: Discovery Dataset


title: genomic DNA from 9741950050_R04C02

description: 9741950050_R04C02: Sample 286

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417093_R01C01

description: 9701417093_R01C01: Sample 285


title: PBMC from Stable  20.1 at T0

description: STA, Biological replicate  20 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA020.1

tag: tissue


title: genomic DNA from 9741950050_R06C02

description: 9741950050_R06C02: Sample 284


title: PBMC from Stable  19.2 at T0

description: STA, Biological replicate  19 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA019.2

value: PBMC from STA019

tag: individual replicate

value: STA 19 of 190

tag: techical replicate


title: AAB-HT082-AU-L

value: AU

value: L

tag: gender

tag: age

tag: registry site

value: Houston

tag: dataset


title: PBMC from Stable  18.2 at T0

description: STA, Biological replicate  18 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA018.2

value: PBMC from STA018

value: STA 18 of 190

tag: time point


title: genomic DNA from 9701417112_R01C02

description: 9701417112_R01C02: Sample 283

tag: hiv

tag: agebl

tag: racecomg

value: White


title: AAB-M058-AAP-NL

tag: patient id

tag: disease status

value: AAP

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NL

value: Minnesota

tag: microarray batch


title: NORMOXIC BLASTEMA 1

value: adult

value: regenerated (blastema) fins

tag: regeneration condition

value: normoxic (in the absence of 1mM CoCl2)

tag: harvest time point

value: after 3 days of regeneration

value: fin


title: genomic DNA from 9741950016_R04C02

description: 9741950016_R04C02: Sample 282

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Stable  18.1 at T0

description: STA, Biological replicate  18 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA018.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2


title: genomic DNA from 9407201108_R01C01

description: 9407201108_R01C01: Sample 281

tag: hiv

tag: agebl

value: Black


title: PBMC from Stable  17.1 at T0

description: STA, Biological replicate  17 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA017.1

value: PBMC from STA017

value: STA 17 of 190

tag: time point


title: AAB-C076-AAP-NL

source_name: skin biopsy

tag: patient id

tag: disease status

tag: gender

value: F

tag: age

tag: registry site

value: Columbia

tag: dataset

value: Discovery Dataset


title: PBMC from Stable  17.2 at T0

description: STA, Biological replicate  17 of 190, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA017.2

value: Replicate 2 of 2


title: PBMC from Stable  19.1 at T0

description: STA, Biological replicate  19 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA019.1

value: PBMC from STA019

value: STA 19 of 190


title: genomic DNA from 9741950076_R05C01

description: 9741950076_R05C01: Sample 280

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC from Stable  16.2 at T0

description: STA, Biological replicate  16 of 190, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA016.2

value: PBMC from STA016

value: STA 16 of 190


title: AAB-M056-AAP-NL

value: AAP

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NL

value: Minnesota

tag: microarray batch


title: AAB-M056-AAP-L

value: L


title: PBMC from Stable  15.2 at T0

description: STA, Biological replicate  15 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA015.2

tag: tissue

value: PBMC from STA015

value: STA 15 of 190


title: genomic DNA from 9407210093_R03C02

description: 9407210093_R03C02: Sample 279

source_name: whole blood

value: White

tag: nk

tag: bcell

tag: mono


title: PBMC from Stable  16.1 at T0

description: STA, Biological replicate  16 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA016.1

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Stable  15.1 at T0

description: STA, Biological replicate  15 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA015.1


title: AAB-M058-AAP-L

tag: patient id

tag: disease status

tag: gender

value: F


title: AAB-C052-AAP-NL

tag: age

tag: registry site

value: Columbia

tag: dataset


title: PBMC from Stable  14.2 at T0

description: STA, Biological replicate  14 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA014.2

value: PBMC from STA014

value: STA 14 of 190


title: genomic DNA from 9407210065_R06C02

description: 9407210065_R06C02: Sample 278

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: dmgsex

tag: gran


title: AAB-N-C042-Normal-NC

value: Normal

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NC

value: M

tag: microarray batch

value: Discovery Dataset


title: genomic DNA from 9741950050_R03C02

description: 9741950050_R03C02: Sample 277

tag: nk

tag: bcell

tag: mono


title: AAB-C052-AAP-L

value: AAP


title: genomic DNA from 9407210074_R04C01

description: 9407210074_R04C01: Sample 276

value: Black


title: AAB-N-C036-Normal-NC


title: genomic DNA from 9741950050_R04C01

description: 9741950050_R04C01: Sample 275


title: PBMC from Stable  14.1 at T0

description: STA, Biological replicate  14 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA014.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: AAB-N-C045-Normal-NC

tag: patient id

tag: disease status

tag: gender

tag: age

tag: registry site


title: AAB-N-C039-Normal-NC

tag: dataset


title: AAB-C076-AAP-L

value: L


title: AAB-M-061-AU-L

value: AU

value: Minnesota


title: PBMC from Stable  12.2 at T0

description: STA, Biological replicate  12 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA012.2

value: PBMC from STA012

value: STA 12 of 190

value: Replicate 2 of 2


title: PBMC from Stable  12.1 at T0

description: STA, Biological replicate  12 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA012.1

value: Replicate 1 of 2


title: genomic DNA from 9701417115_R02C01

description: 9701417115_R02C01: Sample 273

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC from Stable  13.2 at T0

description: STA, Biological replicate  13 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA013.2

value: PBMC from STA013

value: STA 13 of 190


title: genomic DNA from 9741950032_R01C02

description: 9741950032_R01C02: Sample 274

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9741950050_R01C01

description: 9741950050_R01C01: Sample 272


title: PBMC from Stable  13.1 at T0

description: STA, Biological replicate  13 of 190, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA013.1

tag: tissue

tag: individual replicate