title: MLL-rearranged infant ALL in vitro resistant to prednisolone 5

description:
res_5
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 12

status: Public on Oct 13 2011

type: RNA

city: Rotterdam

first: Jill

last: Spijkers-Hagelstein

address: Dr Molewaterplein 50

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia's Childrens Hospital

description:
res_12
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The CEL files represent the raw (unscaled; scaling factor = 1) gene expression data. Raw (unscaled) array data was collectively normalized using variance-stabilizing normalization (VSN), performed in the statistical environment R (version 2.10.1) using Bioconductor packages.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary infant ALL cells at diagnosis (untreated) (>90% blasts)

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

extract_protocol: Total RNA was extracted form leukemic cells using TRIzol reagent (Invitrogen) according to the manufacturer's protocol

treatment_protocol: Primary ALL samples were obtained at diagnosis (before treatment) and processed within 24 hours after sampling. All samples contained >90% leukemic blasts.

tag: disease state

value: Precursor B-cell acute lymphoblastic leukemia (ALL)

tag: cell type

tag: genotype

value: MLL-rearranged

tag: age

value: < 1 year of age

tag: prednisolone sensitivity

value: resistant


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 4

description:
res_4
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels

value: Primary infant ALL cells at diagnosis (untreated) (>90% blasts)


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 7

description:
res_7
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 14

description:
res_14
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 9

description:
res_9
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 11

description:
res_11
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 1

description:
res_1
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 13

description:
res_13
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 8

description:
res_8
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 6

description:
res_6
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 2

description:
res_2
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: MLL-rearranged infant ALL in vitro resistant to prednisolone 3

description:
res_3
Gene expression profiling data (HU133plus2.0) MLL-rearranged infant ALL cels


title: Normal Chip#7

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

country: USA

institute: Mount SinaiSchool of Medicine

description: 7_HGU133 Plus 2.0_IC_011007.CEL

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Normal

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: tissue

value: skin

tag: individual

value: Patient N-7

tag: condition

value: Normal

tag: eczema severity


title: Normal Chip#2

description: 2_HGU133 Plus 2.0_IC_011007.CEL

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

value: Patient N-2


title: Normal Chip#3

description: 3_HGU133 Plus 2.0_IC_011007.CEL

value: Patient N-3


title: Normal Chip#6

description: 6_HGU133 Plus 2.0_IC_011007.CEL

value: Patient N-6


title: Normal Chip#8

description: 8_HGU133 Plus 2.0_IC_011007.CEL

value: Patient N-8


title: TLR7 SMHC II

city: Los Angeles

first: Scott

middle: G.

last: Kitchen

state: CA

address: 615 Charles E.Young Dr. S.

institute: UCLA AIDS Institute

hyb_protocol: The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array expression arrays.

scan_protocol: The hybridized array is stained with a streptavidin phycoerythrin conjugate and scanned by the GeneChip Scanner 3000DX V.2. The amount of light emitted at 570 nm is proportional to the bound target at each location on the gene array.

data_processing: Initial levels of gene expression are reviewed by using Affymetrix software. Normalization was performed using dChip. Subsequent advanced data analysis will be performed to identify statistically, differentially expressed genes/signature potentially responsible for or associated with the physiological or pathological conditions.

source_name: monocyte, 3 hours, donor 2

label_protocol: The Total RNA (1 μg to 15 μg) is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and used as a template in the subsequent in vitro transcription (IVT) reaction.The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

growth_protocol: Cells were freshly puified

extract_protocol: Total RNA was purified using Rneasy columns (Qiagen)

treatment_protocol: Cells were treated with RPMI-1640 medium alone or with medium containing sMHC II (1 μg/ml) for three hours

value: Human peripheral blood monocytes

value: adult

tag: treatment

value: sMHC II


title: AL Chip#47

description: 6_HGU133 plus 2.0_Irma_031010.CEL

source_name: AL

value: Patient P4

value: AL


title: Normal Chip#5

description: 5_HGU133 Plus 2.0_IC_011007.CEL

value: Patient N-5


title: TLR6 SMHC II

source_name: monocyte, 3 hours, donor 1


title: TLR7 MEDIUM ONLY

value: medium only


title: TLR6 MEDIUM ONLY


title: TLR 17 MEDIUM ONLY

source_name: monocyte, 3 hours, donor 3


title: Normal Chip#4

description: 4_HGU133 Plus 2.0_IC_011007.CEL

value: Patient N-4


title: TLR17 SMHC II


title: Normal Chip#1

description: 1_HGU133 Plus 2.0_IC_011007.CEL

value: Patient N-1


title: AL Chip#45

description: 4_HGU133 plus 2.0_Irma_031010.CEL

value: Patient P3


title: AL Chip#43

description: 2_HGU133 plus 2.0_Irma_031010.CEL

value: skin

value: Patient P12


title: ANL Chip#42

description: 1_HGU133 plus 2.0_Irma_031010.CEL

source_name: ANL

value: ANL


title: ANL Chip#44

description: 3_HGU133 plus 2.0_Irma_031010.CEL


title: ANL Chip#40

description: 40_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P6


title: M.Cstr15

city: Lausanne

first: Darlene

last: Goldstein

department: IMA

country: Switzerland

institute: EPFL

description: Control groups for two drug studies. All animals injected with normal saline 30-60 minutes prior to sacrifice.

organism: Mus musculus

source_name: Mus musculus CBAxC57BL/6 strain background - wild-type


title: ANL Chip#46

description: 5_HGU133 plus 2.0_Irma_031010.CEL


title: ANL Chip#38

description: 38_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P8


title: MithSTR.16


title: MithSTR.14


title: AL Chip#35

description: 35_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P9


title: AL Chip#37

description: 37_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P2


title: M.Cstr14


title: MithSTR.15


title: AL Chip#34

description: 34_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P7


title: AL Chip#39

description: 39_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P11


title: MithSTR.11

source_name: Mus musculus CBAxC57BL/6 strain background - R6/2


title: ANL Chip#36

description: 36_HGU133 plus 2.0_Irma_030310.CEL


title: MithSTR.9


title: AL Chip#41

description: 41_HGU133 plus 2.0_Irma_030310.CEL


title: MithSTR.10


title: M.Cstr13


title: expt.1152 extraction4_array1

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: expt.1152 extraction4_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

tag: Sex

value: Male


title: seedling roots of Osabl1 under ABA treatment, biological rep 1

city: Shanghai

first: Xi

last: Yang

address: Fenglin Road, 300

country: China

description: 14-day-old seedlings of Osabl1 mutant were grown at 28±1 degree treated under 100 μM ABA, 4 hour and roots were gathered.

hyb_protocol: Affymetrix® GeneChip® Operating Software Version 1.0 was used for washing, staining, and scanning as described in the supplier’s protocol.

scan_protocol: Scanning procedures of the arrays were carried out using Affymetrix GeneChip Scanner 3000 as described in the Affymetrix technical manual.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

organism: Oryza sativa

source_name: 14-day-old seedlings roots

label_protocol: RNA was labeled for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Rice seeds were germinated in sterilized water then grew at 28±1 degree for 14 days in the greenhouse with a 14h-light/10h-dark cycle.

extract_protocol: Total RNA were extracted using TRIzol reagent (Invitrogen Life Technologies).

treatment_protocol: 14-day-old seedlings roots of Osabl1 mutant treated under 100 μM ABA, 4 hour

tag: genotype/variation

value: knockout mutant of OsABL1 (LOC_Os6g10880)


title: M.Cstr16


title: Rejection CD69- T cells

city: Seoul

first: Dong-Gyun

last: Lim

address: 245 Eulji-ro, Jung-gu

country: South Korea

institute: National Medical Center, Research Institute

description:
Rej CD69- T
CD69- T cell fraction after stimulation with donor antigen

hyb_protocol: Following fragmentation, 1.5 ug of cRNA were hybridized to the Illumina MouseWG-6 Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Array were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4). Genes were filtered to include only genes with a detection p value less than 0.05 in at least 50% of samples. Out of 45,281 probes, 16,001 were thus used for further analysis after transformation of their normalized signal intensities into log2 values.

source_name: Rejecting recipient mice

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: T cells isolated from peripheral lymphoid tissues of recipient mice were cocultured with donor T cell-depleted splenocytes.

extract_protocol: Total RNA was extracted and purified from isolated T cells using RNeasy Plus Mini Kit (Qiagen) according to the manufacturers’ protocol.

treatment_protocol: After incubation for 20-21 h, recipient CD3+CD69+ or CD3+CD69+ T cells were isolated using FACS cell sorter.

tag: strain

tag: gender

value: male

value: spleen and lymph node

value: CD69- T cell fraction

tag: recipient status

value: rejecting


title: seedling roots of WT under ABA treatment, biological rep 2

description: 14-day-old seedlings of WT were grown at 28±1 degree treated under 100 μM ABA, 4 hour and roots were gathered.

scan_protocol: Scanning procedures of the arrays were carried out using Affymetrix GeneChip Scanner 3000 as described in the Affymetrix technical manual

treatment_protocol: 14-day-old seedlings roots of WT treated under 100 μM ABA, 4 hour

value: wildtype (Oryza sativa, japonica cultivar Zhonghua 11)


title: seedling roots of Osabl1 under ABA treatment, biological rep 2

value: knockout mutant of OsABL1 (LOC_Os06g10880)


title: seedling roots of WT under ABA treatment, biological rep 1


title: AL Chip#32

description: 32_HGU133 plus 2.0_Irma_030310.CEL

value: skin

value: Patient P5

value: AL


title: ANL Chip#33

description: 33_HGU133 plus 2.0_Irma_030310.CEL

value: ANL


title: Rejection CD69+ T cells

description:
Rej CD69+ T
CD69+ T cell fraction after stimulation with donor antigen

value: CD69+ T cell fraction


title: ANL Chip#29

description: 29_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P14


title: AL Chip#30

description: 30_HGU133 plus 2.0_Irma_030310.CEL


title: ANL Chip#31

description: 31_HGU133 plus 2.0_Irma_030310.CEL


title: M.Cstr12


title: AL Chip#28

description: 28_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P1


title: M.Cstr9


title: Tolerance CD69- T cells

description:
Tol CD69- T
CD69- T cell fraction after stimulation with donor antigen

source_name: Tolerant recipient mice, d100

value: tolerant


title: M.Cstr11


title: Naïve CD69- T cells

description:
Nor CD69- T
CD69- T cell fraction after stimulation with donor antigen

source_name: Naïve mice

value: naïve


title: M.Cstr10


title: Tolerance CD69+ T cells

description:
Tol CD69+ T
CD69+ T cell fraction after stimulation with donor antigen


title: ANL Chip#27

description: 27_HGU133 plus 2.0_Irma_030310.CEL


title: Naïve CD69+ T cells

description:
Nor CD69+ T
CD69+ T cell fraction after stimulation with donor antigen


title: AL Chip#26

description: 26_HGU133 plus 2.0_Irma_030310.CEL

value: Patient P13


title: D2_epidermis_sustained_activation_biological_replicate_3

city: Cambridge

first: Kai

last: Kretzschmar

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust Centre for Stem Cell Research

country: United Kingdom

institute: University of Cambridge

description: ItgA6+ D2 sustained activation (ectopic follicles) epidermal keratinocytes

hyb_protocol: Hybridization cocktail prepared using the NugEN Cocktail PICR v1.0 protocol derived from the NuGEN FL-Ovation cDNA Biotin Module v2 user guide (FLBv2 User Guide)

scan_protocol: Affymetric GeneChip scanner 3000 running GCOS software located the PICR

data_processing: RMA normalisation (GeneSpring GX11). The expression calls were generated by java implementation (from The Paterson Institute for Cancer Research) of the MAS5.0 algorithm, as described in [Hubbel et al (2002) Bioinformatics 18, Liu et al (2002) Bioinformatics 18].

source_name: ItgA6+ sustained activated D2 epidermis from mouse 3

label_protocol: RNA amplification using the WT-Ovation Pico target prep v 1.0 protocol derived from the NuGE WT-Ovation Pico RNA Amplification system (WTO Pico UserGuide) and the NugEN FL-Ovation cDNA Biotin Module

extract_protocol: total RNA was purified from sorted cell populations using the Purelink Micro-to-Midi Total RNA Purification System Kit (Invitrogen), including an on-column Dnase treatment step

value: C57BL/6 CBA mixed background

tag: mouse

tag: sorted cell population

value: ItgA6+ sustained activated D2 epidermal keratinocytes


title: ANL Chip#25

description: 25_HGU133 plus 2.0_Irma_030310.CEL


title: D2_epidermis_sustained_activation_biological_replicate_2

source_name: ItgA6+ sustained activated D2 epidermis from mouse 2


title: D2_dermis_sustained_activation_biological_replicate_2

description: GFP+ D2 sustained activation (ectopic follicles) dermal fibroblasts

source_name: GFP+ sustained activated D2 dermis from mouse 2

value: GFP+ sustained activated D2 dermal fibroblasts


title: D2_epidermis_sustained_activation_biological_replicate_5

source_name: ItgA6+ sustained activated D2 epidermis from mouse 5


title: D2_dermis_sustained_activation_biological_replicate_3

source_name: GFP+ sustained activated D2 dermis from mouse 3


title: D2_epidermis_transient_activation_biological_replicate_4

description: ItgA6+ D2 transient activation (anagen) epidermal keratinocytes

source_name: ItgA6+ transient activated D2 epidermis from mouse 4

value: ItgA6+ transient activated D2 epidermal keratinocytes


title: Pten/Braf biological rep2

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St, LCI 501

department: Dermatology

institute: Yale School of Meicine

description: Gene expression data from uncultured mouse tumors.

hyb_protocol: Biotin-labeled cRNA fragments that were hybridized to the genechip probe array at 45°C for 16 hr.

scan_protocol: The probe arrays were scanned (Affymetrix GS3000 Scanner) to quantify the fluorescence intensity associated with each oligonucleotide probe.

data_processing: RMA expression statistic (Genepattern) http://www.broadinstitute.org/cancer/software/genepattern/

source_name: Uncultured mouse tumor tissue

label_protocol: Double-stranded cDNA was then synthesized from a T7-oligo(dT) primer followed by an in vitro transcription reaction (ENZO) and fragmentation reaction to produce biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr.

extract_protocol:
Tumors harvested at 1 cm. Tumors were macro dissected.
Total RNA was isolated with the RNAeasy Mini Kit (Qiagen) including an on-column DnaseI-digestion according to the manufacturer's protocol.

tag: cell type

value: macro dissected tumor

value: Pten/Braf

value: a mixed strain of C57BL/6, FVB, and 129


title: Pten/Braf/Bcat STA rep2

value: Pten/Braf/Bcat STA


title: D2_dermis_sustained_activation_biological_replicate_5

source_name: GFP+ sustained activated D2 dermis from mouse 5


title: Pf-5_zinc-limited_replicate 6

city: Hong Kong

first: Chee Kent

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

description: Technical replicate 3 of biological replicate 3

hyb_protocol: Microarray slides were immersed in pre-hybridization buffer (1 % BSA, 5X SSC, 0.1 % SDS, 0.45 mm-filtered) before hybridization. Slides were washed with sterile water (4x) and isopropanol (3x), spin-dried and covered with lifterslip. cDNA probes were dried using Speedvac and then resuspended in hybridization buffer (50 % formamide, 5X SSC, 0.1 % SDS, 0.45 mm-filtered). Probes were heated at 95 degrees Celcius (15 min) before applying to the slides. Hybridization was performed overnight at 42 degrees Celcius. After hybridization, slides were washed with the following steps: 2x wash buffer 1 (1X SSC, 0.2% SDS) at 42 degrees Celcius, 1x wash buffer 2 (0.1X SSC, 0.1% SDS) and 3x wash buffer 3 (0.1X SSC, 0.1% SDS).

scan_protocol: Images were scanned with Axon 4000B scanner and GenePix 4.0 software

data_processing: The microarray data was analyzed with Spotfinder (TIGR) and normalized using the LOWESS algorithm in the TIGR-MIDAS package with block mode and smoothing parameter value of 0.33

label: Alexa fluor 647

organism: Pseudomonas fluorescens

source_name: Pseudomonas fluorescens Pf-5, non-zinc treated

label_protocol: Reverse transcription of RNA samples was performed using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) with random hexamer primers. Approximately 7 µg of total RNA was used for cDNA synthesis in each reaction. cDNA samples were labeled with either Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen) according to manufacturer's instruction. Spike-in controls were made from RNA transcribed from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) with the MegaScript Kit (Ambion). Spike-in control were prepared as follow. For Alexa Fluor 555 pool, 0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.06 ng ltp6 RNA, 0.25 ng crp1 RNA, 0.95 ng nac RNA, 0.08 ng xcp2 RNA, 0.17 ng prk RNA and 0.21 ng tim RNA. For Alexa Fluor 647 pool, 0.11 ng cab RNA, 0.21 ng ltp4 RNA, 0.42 ng rca RNA, 0.63 ng rbcL RNA, 0.02 ng ltp6 RNA, 0.08 ng crp1 RNA, 0.31 ng nac RNA, 0.25 ng xcp2 RNA, 0.50 ng prk RNA and 0.63 ng tim RNA.

growth_protocol: Pseudomonas fluorescens Pf-5 was grown in M9 minimal media supplemented with 100 µM calcium chloride, 2 mM magnesium sulphate, 0.4 % glucose and 100 µM iron(III) chloride. Cultures were supplemented with 100 µg/ml streptomycin. The cultures were grown aerobically with shaking at room temperature until to about OD600= 1.1 for for both treatments

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and and treated with RNAse-free DNAse (Ambion) as per manufacturer's instruction

treatment_protocol: The zinc-replete cultures were supplemented with 800 µM zinc sulphate whereas the zinc-limited cultures were not treated with any zinc supplementation

label: Alexa fluor 555

source_name: Pseudomonas fluorescens Pf-5, zinc sulphate treated


title: Pten/Braf/Bcat STA rep1


title: D2_epidermis_transient_activation_biological_replicate_2

source_name: ItgA6+ transient activated D2 epidermis from mouse 2


title: D2_epidermis_transient_activation_biological_replicate_3

source_name: ItgA6+ transient activated D2 epidermis from mouse 3


title: Pf-5_zinc-limited_replicate 4

description: Technical replicate 1 of biological replicate 3


title: Pten/Braf biological rep1


title: Pf-5_zinc-limited_replicate 5

description: Technical replicate 2 of biological replicate 3


title: Pf-5_zinc-limited_replicate 2

description: Technical replicate 1 of biological replicate 2


title: skin_sarc_2NL

city: Radnor

first: Hongtao

last: Fan

state: PA

address: 145 King of Prussia Rd

department: RDI

institute: Centocor

hyb_protocol: Hybridization were done on Affymetrix GeneChips (U133plus2.0 cartridge arrays) for 16 hours, 48C and 55rpm, then washed on an Affymetrix FS400 instrument using the EukGE-WS2v4_450 protocol.

scan_protocol: Arrays were scanned using an Affymetrix GCS3000 7G system.

data_processing: Data was collected using GCOS (GeneChip Operating System) software.

source_name: Sarcoidosis Skin NL subj 2

label_protocol: Labeling was done using the NuGEN Encore Biotin Module (manufacturer's protocol).

extract_protocol: The amplification protocol was the NuGEN Ovation RNA Amplification System V2 (manufacturer's protocol), purified using Zymo Research DNA Clean and Concentrator-25 Kit columns (using protocol suggested by NuGEN).

tag: subject

tag: phenotype

value: Skin Non lesion


title: skin_sarc_3NL

source_name: Sarcoidosis Skin NL subj 3


title: Pf-5_zinc-limited_replicate 3

description: Technical replicate 2 of biological replicate 2


title: D2_dermis_transient_activation_biological_replicate_2

description: GFP+ D2 transient activation (anagen) dermal fibroblasts

source_name: GFP+ transient activated D2 dermis from mouse 2

value: GFP+ transient activated D2 dermal fibroblasts


title: Pf-5_zinc-limited_replicate 1

description: Biological replicate 1


title: skin_sarc_14NL

source_name: Sarcoidosis Skin NL subj 14


title: skin_sarc_10TL

source_name: Sarcoidosis Skin TL subj 10

value: Skin Lesion


title: skin_sarc_13TL

source_name: Sarcoidosis Skin TL subj 13


title: WT_epidermis_telogen_biological_replicate_4

description: ItgA6+ WT telogen epidermal keratinocytes

source_name: ItgA6+ telogen epidermis from mouse 4

value: wildtype

value: ItgA6+ telogen epidermal keratinocytes


title: WT_epidermis_telogen_biological_replicate_3

source_name: ItgA6+ telogen epidermis from mouse 3


title: D2_dermis_transient_activation_biological_replicate_3

source_name: GFP+ transient activated D2 dermis from mouse 3


title: skin_sarc_3TL

source_name: Sarcoidosis Skin TL subj 3


title: D2_dermis_transient_activation_biological_replicate_4

source_name: GFP+ transient activated D2 dermis from mouse 4


title: WT_epidermis_telogen_biological_replicate_2

source_name: ItgA6+ telogen epidermis from mouse 2


title: WT_dermis_telogen_biological_replicate_4

description: GFP+  WT telogen dermal fibroblasts

source_name: GFP+ telogen dermis from mouse 4

value: GFP+ telogen dermal fibroblasts


title: Skin_norm_20NL

source_name: normal Skin NL subj 20


title: Skin_norm_16NL

source_name: normal Skin NL subj 16


title: WT_epidermis_neonatal_biological_replicate_4

description: ItgA6+ WT neonatal epidermal keratinocytes

source_name: ItgA6+ neonatal epidermis from mouse 4

value: ItgA6+ neonatal epidermal keratinocytes


title: WT_dermis_telogen_biological_replicate_3

description: GFP+  WT telogen dermal fibroblasts

source_name: GFP+ telogen dermis from mouse 3


title: Skin_norm_19NL

source_name: normal Skin NL subj 19


title: Skin_sarc_6NL

source_name: Sarcoidosis Skin NL subj 6


title: Skin_sarc_11NL

source_name: Sarcoidosis Skin NL subj 11


title: Skin_sarc_4NL

source_name: Sarcoidosis Skin NL subj 4


title: Skin_sarc_13NL

source_name: Sarcoidosis Skin NL subj 13


title: Skin_sarc_5TL

source_name: Sarcoidosis Skin TL subj 5


title: WT_epidermis_neonatal_biological_replicate_2

source_name: ItgA6+ neonatal epidermis from mouse 2


title: Skin_sarc_8TL

source_name: Sarcoidosis Skin TL subj 8


title: Skin_norm_17NL

source_name: normal Skin NL subj 17


title: WT_dermis_neonatal_biological_replicate_1

description: GFP+ WT neonatal dermal fibroblasts

source_name: GFP+ neonatal dermis from mouse 1

value: GFP+ neonatal dermal fibroblasts


title: WT_epidermis_neonatal_biological_replicate_3

source_name: ItgA6+ neonatal epidermis from mouse 3


title: WT_dermis_neonatal_biological_replicate_3

description: GFP+ WT neonatal dermal fibroblasts

source_name: GFP+ neonatal dermis from mouse 3


title: Skin_sarc_10NL

source_name: Sarcoidosis Skin NL subj 10


title: WT_dermis_neonatal_biological_replicate_2

description: GFP+ WT neonatal dermal fibroblasts

source_name: GFP+ neonatal dermis from mouse 2


title: Skin_sarc_15TL

source_name: Sarcoidosis Skin TL subj 15


title: WT_dermis_telogen_biological_replicate_2

description: GFP+  WT telogen dermal fibroblasts

source_name: GFP+ telogen dermis from mouse 2


title: Skin_sarc_7NL

source_name: Sarcoidosis Skin NL subj 7


title: 18 month old aorta 37_old mRNA

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

institute: Amsterdam UMC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: 18 month old aorta 37_old

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted with Trizol

tag: age

value: 18 months

tag: tissue

value: aorta

tag: genetic background


title: 6 week old aorta 46_young mRNA

source_name: 6 week old aorta 46_young

value: 6 weeks


title: Skin_sarc_12TL

source_name: Sarcoidosis Skin TL subj 12


title: Skin_sarc_9TL

source_name: Sarcoidosis Skin TL subj 9


title: Skin_sarc_9NL

source_name: Sarcoidosis Skin NL subj 9


title: 18 month old aorta 38_old mRNA

source_name: 18 month old aorta 38_old


title: Pten/Braf/Bcat STA rep3

source_name: Uncultured mouse tumor tissue

extract_protocol:
Tumors harvested at 1 cm. Tumors were dissociated and FACS-enriched.
Total RNA was isolated with the RNAeasy Mini Kit (Qiagen) including an on-column DnaseI-digestion according to the manufacturer's protocol.

value: dissociated, FACS-enriched tumor


title: 6 week old aorta 45_young mRNA

source_name: 6 week old aorta 45_young


title: Skin_norm_18NL

source_name: normal Skin NL subj 18


title: 6 week old aorta 48_young mRNA

source_name: 6 week old aorta 48_young


title: 18 month old aorta 36_old mRNA

source_name: 18 month old aorta 36_old


title: Pten/Braf biological rep3


title: Skin_sarc_14TL

source_name: Sarcoidosis Skin TL subj 14


title: Skin_sarc_7TL

source_name: Sarcoidosis Skin TL subj 7


title: Early Tolerance CD69+ T cells

description:
eTol CD69+ T
CD69+ T cell fraction after stimulation with donor antigen

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina MouseRef-8 Expression Beadchip according to the protocols provided by the manufacturer.

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). Genes were filtered to include only genes with a detection p value less than 0.05 in at least 50% of samples. Out of 25,697 probes, 11,603 were thus used for further analysis after transformation of their normalized signal intensities into log2 values.

source_name: Tolerant recipient mice, d21

growth_protocol: T cells isolated from peripheral lymphoid tissues of recipient mice were cocultured with donor bone-marrow derived dendritic cells.

value: male

value: spleen and lymph node

value: CD69+ T cell fraction

value: early tolerant


title: Skin_sarc_2TL

source_name: Sarcoidosis Skin TL subj 2


title: Early Tolerance CD69- T cells

description:
eTol CD69- T
CD69- T cell fraction after stimulation with donor antigen

value: CD69- T cell fraction


title: posterior trunk expression replicate2

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

description: Gene expression data from mouse E10.5 embryonic stage posterior trunk cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with GC-RMA (Bioconductor).

source_name: Posterior trunk cells

label_protocol: 500 ng of total RNA was amplified and labeled using MessageAmp™ Premier RNA Amplification Kit (Ambion, AM1792). cRNA quality was assessed by capillary electrophoresis on an Agilent 2100 Bioanalyzer.

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

treatment_protocol: Tissue samples were isolated in PBS supplemented with 10% Fetal Calf Serum and made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Cells were takenb up in TrizolLS and stored at -80 degrees celcius.

value: posterior trunk cells


title: forebrain expression replicate2

description: Gene expression data from mouse E10.5 embryonic stage forebrain cells.

source_name: Forebrain cells

value: forebrain cells


title: Skin_sarc_4TL

source_name: Sarcoidosis Skin TL subj 4

value: Skin Lesion


title: Rejection CD69+ T cells

description:
Rej CD69+ T
CD69+ T cell fraction after stimulation with donor antigen

source_name: Rejecting recipient mice

value: rejecting


title: anterior trunk expression replicate2

description: Gene expression data from mouse E10.5 embryonic stage anterior trunk cells.

source_name: Anterior trunk cells

value: anterior trunk cells


title: Skin_sarc_1TL

source_name: Sarcoidosis Skin TL subj 1


title: forebrain expression replicate1


title: Skin_sarc_11TL

source_name: Sarcoidosis Skin TL subj 11


title: 6 week old aorta 47_young mRNA

source_name: 6 week old aorta 47_young


title: Rejection CD69- T cells

description:
Rej CD69- T
CD69- T cell fraction after stimulation with donor antigen


title: Skin_sarc_12NL

source_name: Sarcoidosis Skin NL subj 12

value: Skin Non lesion


title: 18 month old aorta 35_old mRNA

source_name: 18 month old aorta 35_old


title: Tolerance CD69+ T cells

description:
Tol CD69+ T
CD69+ T cell fraction after stimulation with donor antigen

source_name: Tolerant recipient mice, d100

value: tolerant


title: Tolerance CD69- T cells

description:
Tol CD69- T
CD69- T cell fraction after stimulation with donor antigen


title: Skin_sarc_6TL

source_name: Sarcoidosis Skin TL subj 6


title: Naïve CD69+ T cells

description:
Nor CD69+ T
CD69+ T cell fraction after stimulation with donor antigen

source_name: Naïve mice

value: naïve


title: anterior trunk expression replicate1


title: posterior trunk expression replicate1


title: Control 3

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation.

label_protocol: RNA was labelled using the TotalPrep RNA Labeling Kit (Ambion, Austin, TX).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with theQIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quantification was assessed using a Nanodrop (ND-1000) Spectrophotometer.

value: breast cancer

tag: sirna


title: PAECs treated with 5 micromolar heme rep 5

city: Atlanta

first: Tianwei

last: Yu

state: GA

address: 1518 Clifton Rd NE

department: Biostatistics

institute: Emory University

description: Gene expression data of PAECs cultured for seven days in five micromolar heme

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Gene level expression index was generated using the Affymetrix MAS 5.0 software.

source_name: cultured lung endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Endothelial cells were grown in complete medium containing fetal calf serum at 37 degrees celcius

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

treatment_protocol: Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days

value: pulmonary artery endothelial cells

tag: treatment

value: heme


title: PAECs treated with 5 micromolar heme rep 6


title: CDK4/6 silenced 3

source_name: MDA-MB-231, siRNA, CDK4/6

tag: cell line


title: Non-targeting pool siRNA 2

source_name: MDA-MB-231, siRNA, neg control

value: control


title: Naïve CD69- T cells

description:
Nor CD69- T
CD69- T cell fraction after stimulation with donor antigen

value: male


title: CDK4/6 silenced 2


title: PAECs treated with 5 micromolar heme rep 3


title: PAECs treated with 5 micromolar heme rep 1


title: Non-targeting pool siRNA 3


title: PAECs treated with 5 micromolar heme rep 2


title: PAECs treated with vehicle rep 6

description: Gene expression data of PAECs cultured for seven days in normal medium


title: CCND1 silenced 3

source_name: MDA-MB-231, siRNA, CCND1


title: PAECs treated with 5 micromolar heme rep 4


title: PAECs treated with vehicle rep 5


title: Control 2


title: CCND1 silenced 2


title: PAECs treated with vehicle rep 4


title: CCND1 silenced 1


title: PAECs treated with vehicle rep 2


title: PAECs treated with vehicle rep 1


title: PAECs treated with vehicle rep 3


title: CDK4/6 silenced 1


title: PMVECs treated with 5 micromolar heme rep 6

description: Gene expression data of PMVECs cultured for seven days in five micromolar heme

value: pulmonary microvascular endothelial cells


title: Non-targeting pool siRNA 1


title: PMVECs treated with 5 micromolar heme rep 5


title: PMVECs treated with 5 micromolar heme rep 3


title: zebrafish_WT_2.5h_2

first: Hui

address: No.100, Rd. Qinzhou

institute: Shanghai Center for Bioinformation Technology

description: experiment 2

hyb_protocol: hybridizations were carried out in Hybridization Oven 640 (Affymetrix, 800139 (220V)) using the GeneChip® Hybridization, Wash and Stain Kit, Affymetrix, P/N 900720.

scan_protocol: Chip images were scanned with GeneChip® Scanner 3000 and converted to raw data with the GCOS 1.4 software.

data_processing: The CEL-format expression data were read into the R computing environment (‘ReadAffy’ of the ‘affy’ package [6]) and normalized with the Robust Multichip Average method (‘rma’ of the ‘affy’ package).

organism: Danio rerio

source_name: 2.5-hpf wildtype zebrafish embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNAs weighted 23.3-35.0 ug (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fertilized zebrafish embryos, treated or non-treated, were allowed to develop in natural conditions and harvested at a particular time (a certain hour post fertilization) for gene expression profiling.

extract_protocol: Total RNAs were isolated from culture samples by using sing the Trizol reagent (Gibco BRL, Cleveland, OH) and further purified with the RNeasy mini kit (QIAGEN, P/N 74104) according to standard protocols

treatment_protocol: Sequence for Sb MO was designed complementary to the intron-exon junction: 5’- ACATTTGACTGTGGAGAGGAAAAAA-3’ (Gene Tools). Morpholinos were diluted to the desired concentration in nuclease free water and injected at the 1-2 cell stage.

tag: subtype

value: wildtype

tag: development hour

value: 2.5 hpf


title: PMVECs treated with 5 micromolar heme rep 2


title: zebrafish_WT_2.5h_1

description: experiment 2


title: zebrafish_WT_4h_1

description: experiment 2

source_name: 4-hpf wildtype zebrafish embryos

value: 4 hpf


title: PMVECs treated with vehicle rep 6

description: Gene expression data of PMVECs cultured for seven days in normal medium


title: zebrafish_WT_4.3h_3

description: experiment 1

source_name: 4.3-hpf wildtype zebrafish embryos

value: 4.3 hpf


title: Control 1


title: zebrafish_SB_4.3h_2

description: experiment 1

source_name: 4.3-hpf SB-treated zebrafish embryos

value: Sb morphant


title: zebrafish_WT_4h_2

description: experiment 2


title: PMVECs treated with 5 micromolar heme rep 4


title: zebrafish_WT_4.3h_2

description: experiment 1


title: PMVECs treated with vehicle rep 5


title: zebrafish_WT_4.3h_1

description: experiment 1


title: PMVECs treated with vehicle rep 3


title: zebrafish_SB_4.3h_1

description: experiment 1


title: PMVECs treated with vehicle rep 4


title: PMVECs treated with 5 micromolar heme rep 1


title: zebrafish_SB_4.3h_3

description: experiment 1


title: PMVECs treated with vehicle rep 1


title: PMVECs treated with vehicle rep2


title: Meningioma_989_Hind_50k

status: Public on Oct 12 2011

first: Stanley

middle: F

last: Nelson

address: 695 Charles E. Young Drive South, Bldg Gonda, Rm 5554

department: Human Genetics

description:
MNG_989_Hind_50k
Hybridized to 50K Hind

hyb_protocol: As per manufacturer's instructions (Affymetrix).

scan_protocol: All microarrays were scanned using the Affymetrix GeneChip 3000 scanner.  All images were manually examined to confirm that none had surface defects and exhibited proper grid alignment.

data_processing: Copy number calls were generated using the Affymetrix GTYPE CNAT ver. 3.0 algorithm using default parameters.  .CNT files were also analyzed by BioDiscovery Nexus 3.0 Professional Edition (www.BioDiscovery.com) for copy number analysis using default parameters by the Rank Segmentation algorithm.

source_name: Meningioma tumor 989

extract_protocol: DNA extraction was performed from 10-20mg of flash-frozen tumor pieces using the Gentra Puregene Tissue kit from Qiagen according to the supplied protocol.

value: meningioma tumor

tag: who grade

tag: vital status

value: Alive

tag: tts

value: M


title: Meningioma_941_Hind_50k

description:
MNG_941_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 941

label_protocol: As per manufacturer's instructions (Affymetrix).

tag: gender

value: F


title: Meningioma_822_Hind_50k

description:
MNG_822_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 822


title: Meningioma_816_Hind_50k

description:
MNG_816_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 816


title: Meningioma_977_Hind_50k

description:
MNG_977_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 977


title: Meningioma_798_Hind_50k

description:
MNG_798_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 798


title: Meningioma_789_Hind_50k

description:
MNG_789_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 789


title: Meningioma_761_Hind_50k

description:
MNG_761_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 761


title: Meningioma_908_Hind_50k

description:
MNG_908_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 908


title: Meningioma_788_Hind_50k

description:
MNG_788_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 788


title: Meningioma_760_Hind_50k

description:
MNG_760_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 760


title: Meningioma_985_Hind_50k

description:
MNG_985_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 985


title: Meningioma_776_Hind_50k

description:
MNG_776_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 776


title: Meningioma_731_Hind_50k

description:
MNG_731_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 731

value: Deceased


title: Meningioma_984_Hind_50k

description:
MNG_984_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 984


title: Meningioma_733_Hind_50k

description:
MNG_733_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 733


title: Meningioma_769_Hind_50k

description:
MNG_769_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 769


title: Meningioma_765_Hind_50k

description:
MNG_765_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 765


title: Meningioma_710_Hind_50k

description:
MNG_710_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 710


title: Meningioma_795_Hind_50k

description:
MNG_795_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 795


title: Meningioma_675_Hind_50k

description:
MNG_675_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 675


title: Meningioma_694_Hind_50k

description:
MNG_694_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 694


title: Meningioma_714_Hind_50k

description:
MNG_714_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 714


title: Meningioma_758_Hind_50k

description:
MNG_758_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 758


title: Meningioma_674_Hind_50k

description:
MNG_674_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 674


title: Meningioma_682_Hind_50k

description:
MNG_682_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 682


title: Meningioma_654_Hind_50k

description:
MNG_654_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 654


title: Meningioma_624_Hind_50k

description:
MNG_624_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 624


title: Meningioma_623_Hind_50k

description:
MNG_623_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 623


title: Meningioma_679_Hind_50k

description:
MNG_679_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 679


title: Meningioma_645_Hind_50k

description:
MNG_645_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 645


title: Meningioma_612_Hind_50k

description:
MNG_612_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 612


title: Meningioma_3720_Hind_50k

description:
MNG_3720_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3720


title: Meningioma_607_Hind_50k

description:
MNG_607_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 607


title: Meningioma_606_Hind_50k

description:
MNG_606_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 606


title: Meningioma_3650_Hind_50k

description:
MNG_3650_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3650


title: Meningioma_609_Hind_50k

description:
MNG_609_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 609


title: Meningioma_600_Hind_50k

description:
MNG_600_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 600


title: Meningioma_3685_Hind_50k

description:
MNG_3685_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3685


title: Meningioma_3644_Hind_50k

description:
MNG_3644_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3644


title: Meningioma_3619_Hind_50k

description:
MNG_3619_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3619


title: Meningioma_3456_Hind_50k

description:
MNG_3456_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3456


title: Meningioma_3300_Hind_50k

description:
MNG_3300_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3300


title: Meningioma_3655_Hind_50k

description:
MNG_3655_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3655


title: Meningioma_2891_Hind_50k

description:
MNG_2891_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2891


title: Meningioma_3069_Hind_50k

description:
MNG_3069_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3069


title: Meningioma_2889_Hind_50k

description:
MNG_2889_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2889


title: Meningioma_3489_Hind_50k

description:
MNG_3489_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3489


title: Meningioma_2952_Hind_50k

description:
MNG_2952_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2952


title: Meningioma_2950_Hind_50k

description:
MNG_2950_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2950


title: Meningioma_2756_Hind_50k

description:
MNG_2756_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2756


title: Meningioma_2827_Hind_50k

description:
MNG_2827_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2827


title: Meningioma_3375_Hind_50k

description:
MNG_3375_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3375


title: Meningioma_2507_Hind_50k

description:
MNG_2507_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2507


title: Meningioma_3255_Hind_50k

description:
MNG_3255_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3255


title: Meningioma_3096_Hind_50k

description:
MNG_3096_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3096


title: Meningioma_2364_Hind_50k

description:
MNG_2364_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2364


title: Meningioma_2407_Hind_50k

description:
MNG_2407_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2407


title: Meningioma_2469_Hind_50k

description:
MNG_2469_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2469


title: Meningioma_2366_Hind_50k

description:
MNG_2366_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2366


title: Meningioma_2354_Hind_50k

description:
MNG_2354_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2354


title: Meningioma_2078_Hind_50k

description:
MNG_2078_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2078


title: Meningioma_2077_Hind_50k

description:
MNG_2077_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2077


title: Meningioma_2276_Hind_50k

description:
MNG_2276_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2276


title: Meningioma_2055_Hind_50k

description:
MNG_2055_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2055


title: Meningioma_2316_Hind_50k

description:
MNG_2316_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2316


title: Meningioma_2076_Hind_50k

description:
MNG_2076_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2076


title: Meningioma_2281_Hind_50k

description:
MNG_2281_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2281


title: Meningioma_2232_Hind_50k

description:
MNG_2232_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2232


title: Meningioma_2042_Hind_50k

description:
MNG_2042_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2042


title: Meningioma_1937_Hind_50k

description:
MNG_1937_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1937


title: Meningioma_1916_Hind_50k

description:
MNG_1916_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1916


title: Meningioma_1892_Hind_50k

description:
MNG_1892_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1892


title: Meningioma_3651_Hind_50k

description:
MNG_3651_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 3651


title: Meningioma_1811_Hind_50k

description:
MNG_1811_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1811


title: Meningioma_1024_Hind_50k

description:
MNG_1024_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1024


title: Meningioma_1919_Hind_50k

description:
MNG_1919_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1919


title: Meningioma_941_Xba_50k

description:
MNG_941_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 941


title: Meningioma_1869_Hind_50k

description:
MNG_1869_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1869


title: Meningioma_1378_Hind_50k

description:
MNG_1378_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1378


title: Meningioma_984_Xba_50k

description:
MNG_984_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 984


title: Meningioma_1356_Hind_50k

description:
MNG_1356_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1356


title: Meningioma_1430_Hind_50k

description:
MNG_1430_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1430


title: Meningioma_977_Xba_50k

description:
MNG_977_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 977


title: Meningioma_908_Xba_50k

description:
MNG_908_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 908


title: Meningioma_1048_Hind_50k

description:
MNG_1048_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1048


title: Meningioma_985_Xba_50k

description:
MNG_985_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 985


title: Meningioma_1391_Hind_50k

description:
MNG_1391_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1391


title: Meningioma_989_Xba_50k

description:
MNG_989_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 989


title: Meningioma_2461_Hind_50k

description:
MNG_2461_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 2461


title: Meningioma_776_Xba_50k

description:
MNG_776_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 776


title: Meningioma_798_Xba_50k

description:
MNG_798_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 798


title: Meningioma_795_Xba_50k

description:
MNG_795_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 795


title: Meningioma_789_Xba_50k

description:
MNG_789_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 789


title: Meningioma_765_Xba_50k

description:
MNG_765_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 765


title: Meningioma_822_Xba_50k

description:
MNG_822_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 822


title: Meningioma_760_Xba_50k

description:
MNG_760_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 760


title: Meningioma_816_Xba_50k

description:
MNG_816_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 816


title: Meningioma_769_Xba_50k

description:
MNG_769_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 769


title: Meningioma_761_Xba_50k

description:
MNG_761_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 761


title: Meningioma_788_Xba_50k

description:
MNG_788_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 788


title: Meningioma_1702_Hind_50k

description:
MNG_1702_Hind_50k
Hybridized to 50K Hind

source_name: Meningioma tumor 1702


title: Meningioma_710_Xba_50k

description:
MNG_710_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 710


title: Meningioma_731_Xba_50k

description:
MNG_731_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 731


title: Meningioma_694_Xba_50k

description:
MNG_694_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 694


title: Meningioma_733_Xba_50k

description:
MNG_733_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 733


title: Meningioma_682_Xba_50k

description:
MNG_682_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 682


title: Meningioma_679_Xba_50k

description:
MNG_679_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 679


title: Meningioma_654_Xba_50k

description:
MNG_654_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 654


title: Meningioma_714_Xba_50k

description:
MNG_714_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 714


title: Meningioma_675_Xba_50k

description:
MNG_675_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 675


title: Meningioma_674_Xba_50k

description:
MNG_674_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 674


title: Meningioma_607_Xba_50k

description:
MNG_607_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 607


title: Meningioma_623_Xba_50k

description:
MNG_623_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 623


title: Meningioma_600_Xba_50k

description:
MNG_600_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 600


title: Meningioma_645_Xba_50k

description:
MNG_645_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 645


title: Meningioma_624_Xba_50k

description:
MNG_624_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 624


title: Meningioma_606_Xba_50k

description:
MNG_606_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 606


title: Meningioma_612_Xba_50k

description:
MNG_612_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 612


title: Meningioma_3720_Xba_50k

description:
MNG_3720_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3720


title: Meningioma_609_Xba_50k

description:
MNG_609_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 609


title: Meningioma_3655_Xba_50k

description:
MNG_3655_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3655


title: Meningioma_3650_Xba_50k

description:
MNG_3650_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3650


title: Meningioma_3651_Xba_50k

description:
MNG_3651_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3651


title: Meningioma_3644_Xba_50k

description:
MNG_3644_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3644


title: Meningioma_3489_Xba_50k

description:
MNG_3489_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3489


title: Meningioma_3619_Xba_50k

description:
MNG_3619_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3619


title: Meningioma_3375_Xba_50k

description:
MNG_3375_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3375


title: Meningioma_2952_Xba_50k

description:
MNG_2952_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2952


title: Meningioma_3069_Xba_50k

description:
MNG_3069_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3069


title: Meningioma_3456_Xba_50k

description:
MNG_3456_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3456


title: Meningioma_2756_Xba_50k

description:
MNG_2756_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2756


title: Meningioma_3300_Xba_50k

description:
MNG_3300_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3300


title: Meningioma_2950_Xba_50k

description:
MNG_2950_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2950


title: Meningioma_3255_Xba_50k

description:
MNG_3255_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3255


title: Meningioma_2889_Xba_50k

description:
MNG_2889_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2889


title: Meningioma_2891_Xba_50k

description:
MNG_2891_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2891


title: Meningioma_2469_Xba_50k

description:
MNG_2469_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2469


title: Meningioma_2281_Xba_50k

description:
MNG_2281_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2281


title: Meningioma_2276_Xba_50k

description:
MNG_2276_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2276


title: Meningioma_2316_Xba_50k

description:
MNG_2316_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2316


title: Meningioma_3096_Xba_50k

description:
MNG_3096_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3096


title: Meningioma_2364_Xba_50k

description:
MNG_2364_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2364


title: Meningioma_2354_Xba_50k

description:
MNG_2354_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2354


title: Meningioma_2461_Xba_50k

description:
MNG_2461_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2461


title: Meningioma_2407_Xba_50k

description:
MNG_2407_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2407


title: Meningioma_2507_Xba_50k

description:
MNG_2507_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2507


title: Meningioma_2078_Xba_50k

description:
MNG_2078_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2078


title: Meningioma_758_Xba_50k

description:
MNG_758_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 758


title: Meningioma_2232_Xba_50k

description:
MNG_2232_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2232


title: Meningioma_2366_Xba_50k

description:
MNG_2366_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2366


title: Meningioma_2827_Xba_50k

description:
MNG_2827_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2827


title: Meningioma_1430_Xba_50k

description:
MNG_1430_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1430


title: Meningioma_1937_Xba_50k

description:
MNG_1937_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1937


title: Meningioma_1702_Xba_50k

description:
MNG_1702_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1702


title: Meningioma_2042_Xba_50k

description:
MNG_2042_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2042


title: Meningioma_1916_Xba_50k

description:
MNG_1916_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1916


title: Meningioma_2077_Xba_50k

description:
MNG_2077_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2077


title: Meningioma_2076_Xba_50k

description:
MNG_2076_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2076


title: Meningioma_1378_Xba_50k

description:
MNG_1378_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1378


title: Meningioma_1391_Xba_50k

description:
MNG_1391_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1391


title: Meningioma_1892_Xba_50k

description:
MNG_1892_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1892


title: Meningioma_2055_Xba_50k

description:
MNG_2055_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 2055


title: Meningioma_1024_Xba_50k

description:
MNG_1024_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1024


title: Meningioma_1811_Xba_50k

description:
MNG_1811_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1811


title: Meningioma_1048_Xba_50k

description:
MNG_1048_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1048


title: Meningioma_1919_Xba_50k

description:
MNG_1919_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1919


title: Meningioma_3685_Xba_50k

description:
MNG_3685_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 3685


title: Meningioma_1356_Xba_50k

description:
MNG_1356_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1356


title: PBMC_control_AB_poly ICLC_6hrs_SR_2

city: port st-lucie

first: Ali

last: Filali

state: Florida

address: 11350 SW Village Parkway, 3rd Floor

institute: Vaccine & Gene Therapy Institute of Florida

description:
5645692009_K
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 6hrs

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Human RefSeq-8 BeadChips V3 at 58oC for 20 hrs

scan_protocol: Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using Illumina BeadStudio v3.

data_processing: Illumina probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed.Using the R software, the probe intensities were quantile-normalized followed by a log2 transformation and a batch effect subtraction using the ComBat procedure. The Y chromosome probes were filtred out.

source_name: Peripheral blood mononuclear cell (PBMCs)

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Freshly isolated PBMCs were pretreated with anti-IFNAR mAb or control-IgG and subsequently stimulated with poly IC or left unstimulated

tag: blocking

tag: stimulation

value: poly ICLC_6hrs

tag: batch

value: B


title: PBMC_control_AB_poly ICLC_13hrs_SR_2

description:
5645692009_J
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 13hrs

value: poly ICLC_13hrs


title: PBMC_control_AB_poly ICLC_6hrs_SP_2

description:
5645692009_H
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 6hrs


title: PBMC_IFNAR_AB_poly ICLC_13hrs_SR_2

description:
5645692009_D
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 13hrs


title: PBMC_IFNAR_AB_medium_SP_2

description:
5645692009_C
PBMCs collected from volunteer incubated with anti-IFNAR mAb and left non stimulated

value: medium


title: PBMC_IFNAR_AB_medium_SR_2

description:
5645692009_F
PBMCs collected from volunteer incubated with anti-IFNAR mAb and left non stimulated


title: PBMC_control_AB_medium_SP_2

description:
5645692009_I
PBMCs collected from volunteer incubated with control_IgG mAb and left non stimulated


title: PBMC_control_AB_medium_SR_2

description:
5645692009_L
PBMCs collected from volunteer incubated with control_IgG and left non stimulated


title: PBMC_control_AB_poly ICLC_13hrs_SP_2

description:
5645692009_G
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 13hrs


title: PBMC_IFNAR_AB_poly ICLC_13hrs_SP_2

description:
5645692009_A
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 13hrs


title: PBMC_IFNAR_AB_poly ICLC_6hrs_SP_2

description:
5645692009_B
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 6hrs


title: PBMC_IFNAR_AB_poly ICLC_6hrs_SR_2

description:
5645692009_E
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 6hrs


title: Meningioma_1869_Xba_50k

description:
MNG_1869_Xba_50k
Hybridized to 50K Xba

source_name: Meningioma tumor 1869


title: PBMC_control_AB_medium_SR

description:
5394951061_G
PBMCs collected from volunteer incubated with control_IgG and left non stimulated

value: A


title: PBMC_control_AB_poly ICLC_13hrs_MC

description:
5394951061_B
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 13hrs


title: Patient4_Normal_Colon

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

institute: University Medical Center Utrecht

description: Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a iScan (Illumina).

data_processing: Data processing was done using GenomeStudio (Illumina)

label: Biotin (C, G), DNP (A,T)

source_name: normal colon tissue

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Female

value: colon

value: 5FU, Leucovorin, Oxaliplatin and Bevacizumab after colon resection

tag: disease state

value: not applicable


title: PBMC_control_AB_medium_MC

description:
5394951061_A
PBMCs collected from volunteer incubated with control_IgG mAb and left non stimulated


title: PBMC_IFNAR_AB_poly ICLC_6hrs_SR

description:
5394951041_F
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 6hrs


title: PBMC_control_AB_poly ICLC_6hrs_MC

description:
5394951061_C
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 6hrs


title: PBMC_IFNAR_AB_poly ICLC_13hrs_SR

description:
5394951041_E
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 13hrs


title: PBMC_IFNAR_AB_medium_SR

description:
5394951041_G
PBMCs collected from volunteer incubated with anti-IFNAR mAb and left non stimulated


title: PBMC_IFNAR_AB_poly ICLC_6hrs_MC

description:
5394951041_C
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 6hrs


title: placebo_Day28_303

description:
5294095055_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing placebo administration

data_processing: Illumina probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed.Using the R software, the probe intensities were quantile-normalized followed by a log2 transformation and a batch effect subtraction using the ComBat procedure. The Y chromosome probes were filtred out

source_name: Blood

treatment_protocol: Blood was collected from each volunteer in PAXgene Blood RNA tubes for whole-blood RNA isolation

tag: drug administration

value: placebo

tag: route of  administration

value: subcutaneous

tag: time point

value: D


title: PBMC_control_AB_poly ICLC_6hrs_SR

description:
5394951061_F
PBMCs collected from volunteer incubated with control_IgG followed by a   stimulation with poly ICLC for 6hrs


title: Patient4_Normal_Liver

source_name: normal liver tissue

tag: tissue

value: liver


title: Patient3_Normal_Liver

value: Male

value: XELOX and Bevacizumab after colon resection


title: Patient4_Tumor_Colon

source_name: primary adenocarcinoma of the colon

value: colon tumor

value: adenocarcinoma


title: PBMC_IFNAR_AB_poly ICLC_13hrs_MC

description:
5394951041_B
PBMCs collected from volunteer incubated anti-IFNAR mAb followed by a   stimulation with poly ICLC for 13hrs


title: polyICLC_Day28_302

description:
5294095055_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration

value: polyICLC


title: PBMC_IFNAR_AB_medium_MC

description:
5394951041_A
PBMCs collected from volunteer incubated with anti-IFNAR mAb and left non stimulated


title: Patient3_Normal_Colon


title: placebo_Day14_303

description:
5294095055_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing placebo administration


title: Patient1_Normal_Colon

value: no treatment


title: polyICLC_Day28_307

description:
5294095041_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: Patient1_Tumor_Liver

source_name: liver metastasis

value: liver metastasis

value: metastasis


title: placebo_Day14_300

description:
5294095055_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing placebo administration


title: polyICLC_Day14_307

description:
5294095041_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: placebo_Day28_300

description:
5294095055_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing placebo administration


title: polyICLC_Day28_301

description:
5294095055_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: polyICLC_Day14_301

description:
5294095055_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: Patient4_Tumor_Liver

description: Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.


title: placebo_Day14_306

description:
5294095041_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing placebo administration


title: Patient1_Normal_Liver


title: polyICLC_Day28_305

description:
5294095041_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: Patient3_Tumor_Liver


title: polyICLC_Day14_304

description:
5294095041_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: placebo_Day14_311

description:
5294095033_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing placebo administration


title: polyICLC_Day14_305

description:
5294095041_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: Patient2_Normal_Colon


title: polyICLC_Day28_304

description:
5294095041_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: Patient2_Tumor_Liver


title: Patient3_Tumor_Colon


title: Patient2_Normal_Liver


title: polyICLC_Day14_302

description:
5294095055_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: Patient2_Tumor_Colon


title: Patient1_Tumor_Colon


title: polyICLC_Day28_309

description:
5294095033_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: polyICLC_12H_305

description:
5098941049_C
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing polyICLC administration

value: B


title: polyICLC_Day14_310

description:
5294095033_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: placebo_Day0_306

description:
5098941049_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing placebo administration


title: polyICLC_Day7_305

description:
5098941049_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: placebo_Day3_306

description:
5098941031_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing placebo administration


title: polyICLC_6H_305

description:
5098941049_B
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing polyICLC administration


title: PBMC_control_AB_poly ICLC_13hrs_SR

description:
5394951061_E
PBMCs collected from volunteer incubated with control_IgG  followed by a   stimulation with poly ICLC for 13hrs

value: poly ICLC_13hrs

value: A


title: polyICLC_Day14_308

description:
5294095033_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: polyICLC_Day1_305

description:
5098941049_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: placebo_Day28_311

description:
5294095033_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing placebo administration


title: polyICLC_Day28_310

description:
5294095033_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: placebo_Day7_306

description:
5098941031_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing placebo administration


title: polyICLC_Day28_308

description:
5294095033_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing polyICLC administration


title: polyICLC_Day0_305

description:
5098941049_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: polyICLC_Day3_305

description:
5098941049_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing polyICLC administration


title: polyICLC_12H_307

description:
5098941031_H
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing polyICLC administration


title: polyICLC_Day1_308

description:
5096486027_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: placebo_12H_306

description:
5098941031_B
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing placebo administration


title: polyICLC_Day0_307

description:
5098941031_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: placebo_6H_306

description:
5098941031_A
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing placebo administration


title: placebo_Day28_306

description:
5294095041_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day28 folowing placebo administration


title: placebo_Day2_306

description:
5098941031_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing placebo administration


title: polyICLC_Day7_307

description:
5096486027_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: polyICLC_Day0_308

description:
5096486027_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: placebo_Day1_306

description:
5098941031_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing placebo administration


title: polyICLC_Day3_307

description:
5096486027_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing polyICLC administration


title: polyICLC_Day2_307

description:
5096486027_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing polyICLC administration


title: polyICLC_6H_308

description:
5096486027_F
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing polyICLC administration


title: polyICLC_Day0_309

description:
5096486025_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: polyICLC_12H_309

description:
5096486025_E
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing polyICLC administration


title: polyICLC_Day2_305

description:
5098941049_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing polyICLC administration


title: placebo_Day1_311

description:
5096486016_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing placebo administration


title: polyICLC_Day1_309

description:
5096486025_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: polyICLC_Day3_309

description:
5096486025_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing polyICLC administration


title: placebo_6H_311

description:
5096486016_A
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing placebo administration


title: polyICLC_Day3_308

description:
5096486025_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing polyICLC administration


title: polyICLC_Day7_308

description:
5096486025_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: polyICLC_Day14_309

description:
5294095033_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day14 folowing polyICLC administration


title: polyICLC_Day7_309

description:
5096486025_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: polyICLC_Day1_307

description:
5096486027_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: polyICLC_6H_309

description:
5096486025_D
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing polyICLC administration


title: placebo_Day2_311

description:
5096486016_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing placebo administration


title: placebo_Day3_311

description:
5096486016_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing placebo administration


title: polyICLC_Day3_310

description:
5096486010_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing polyICLC administration


title: polyICLC_Day7_310

description:
5096486010_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: polyICLC_6H_310

description:
5096486010_B
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing polyICLC administration


title: polyICLC_Day2_310

description:
5096486010_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing polyICLC administration


title: placebo_12H_311

description:
5096486016_B
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing placebo administration


title: polyICLC_Day7_304

description:
5038737041_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: polyICLC_12H_310

description:
5096486010_C
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing polyICLC administration


title: placebo_Day0_311

description:
5096486010_H
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing placebo administration


title: polyICLC_Day3_304

description:
5038737041_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing polyICLC administration


title: polyICLC_Day1_310

description:
5096486010_D
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: polyICLC_Day0_304

description:
5038737041_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: polyICLC_Day2_304

description:
5038737041_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing polyICLC administration


title: polyICLC_Day1_304

description:
5038737041_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: placebo_Day3_300

description:
4968511055_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing placebo administration


title: polyICLC_6H_304

description:
5038737041_C
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing polyICLC administration


title: polyICLC_Day1_301

description:
4968511055_G
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: polyICLC_Day0_310

description:
5096486010_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: polyICLC_Day2_301

description:
4968511055_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing polyICLC administration


title: polyICLC_12H_304

description:
5038737041_D
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing polyICLC administration


title: placebo_6H_300

description:
4968511055_C
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing placebo administration


title: placebo_Day3_303

description:
4968473060_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day3 folowing placebo administration


title: placebo_6H_303

description:
4968473060_D
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing placebo administration


title: placebo_Day0_300

description:
4968511055_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing placebo administration


title: placebo_Day7_303

description:
4968473060_F
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing placebo administration


title: placebo_12H_300

description:
4968473060_G
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing placebo administration


title: placebo_Day1_300

description:
4968511055_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing placebo administration


title: polyICLC_6H_302

description:
4968473059_F
Blood collected from volunteer in PAXgene Blood RNA tubes at 6H folowing polyICLC administration


title: placebo_Day0_303

description:
4968473060_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing placebo administration


title: polyICLC_Day1_302

description:
4968473059_E
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing polyICLC administration


title: placebo_Day1_303

description:
4968473060_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day1 folowing placebo administration


title: polyICLC_Day2_302

description:
4968473059_C
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing polyICLC administration


title: polyICLC_12H_302

description:
4968473059_D
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing polyICLC administration


title: polyICLC_Day7_302

description:
4968473059_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day7 folowing polyICLC administration


title: placebo_Day2_303

description:
4968473060_B
Blood collected from volunteer in PAXgene Blood RNA tubes at Day2 folowing placebo administration


title: polyICLC_Day0_302

description:
4968473059_A
Blood collected from volunteer in PAXgene Blood RNA tubes at Day0 folowing polyICLC administration


title: placebo_12H_303

description:
4968473059_G
Blood collected from volunteer in PAXgene Blood RNA tubes at 12H folowing placebo administration


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 30-26°C – rep5

city: MONTPELLIER

first: Benoit

last: Bertrand

address: 911 Avenue Agropolis - BP 64501 F

department: RPB

country: France

institute: IRD - CIRAD

hyb_protocol: Prior to hybridization, excess oligonucleotide was removed from the arrays by shaking them twice1min in 0.2% SDS. Arrays were then washed 2 times in distilled water. The two labelled aRNA were added to microarray hybridization buffer version 2 (GE Healthcare) in a final concentration of 50% formamide, denaturated at 95°C for 3 min and applied to the microarrays in individual chambers of an automated slide processor (GE Healthcare). Hybridization was carried out at 37°C for 12 h. Hybridized slides were washed at 37°C successively with 1X SSC, 0.2% SDS for 10 min, twice with 0.1X SSC, 0.2% SDS for 10 min, with 0.1X SSC for 1 min and with isopropanol before air drying.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation.

data_processing: ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. A local background was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot. This background was subtracting from the foreground fluorescence intensity.

organism: Coffea arabica

source_name: Arabica cv. 'Java' at 30-26°C

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer's instructions.

growth_protocol: C. arabica and C. canephora fresh mature seeds were obtained from La Cumplida, Matagalpa, Nicaragua. C. eugenioides mature seeds were provided by Coffee Research Foundation, Kenya. The species C. arabica was represented by two accessions, namely cv. ‘Java’ derived from the wild Arabica Ethiopian pool and cv. ‘T18141’, an Arabica homozygous line derived from an interspecific hybrid between C. arabica and C. canephora, and consequently introgressed by C. canephora genes. The C. canephora species was represented by a cv. ‘Nemaya’ derived from the cross between two wild Congolese genotypes. Finally, the C. eugenioides accession seeds were collected from trees originating from the Mount Elgon forest in Kenya (1°8’ N 34°33’ E).The coffee seedlings were grown in a greenhouse with natural daylight and a constant temperature of 24°C, and watered as necessary. After 120 days, the plants were transferred to a phytotron chamber (CRYONEXT, France, model RTH 1200L).

extract_protocol: Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Hilden Germany) according to the recommendations of the manufacturer but with some slight modifications. A DNase treatment (RNase free DNase set, Qiagen) was carried out on the RNA during the extraction protocol and the total RNA was eluted in a smaller volume of 65 µl. Each RNA sample was quantified on a Nanodrop (ThermoFisher Scientific Inc., Waltham MA USA). RNA quality was confirmed on a Bioanalyser (Agilent technologies, CA, USA).

treatment_protocol: The study consisted in comparing the transcriptome of different species under two sets of growing conditions, which differed through the diurnal and nocturnal temperatures. In the two phytotron chambers, the photoperiod, humidity and luminosity were set at 12-hour days, 80-90% and 600 μE m-2s-1, respectively. The plants were subjected to a diurnal temperature of 26°C and a nocturnal temperature of 22°C in one phytotron (namely the ‘coldest’ temperature) and 30°C and 26°C respectively in a second phytotron (namely the ‘hottest’ temperature). In each phytotron chamber, from each accession, three plants were grown in a randomized complete block design. After 45 days for the ‘hottest’ temperature and 60 days for the ‘coldest’, plant size and number of newly formed leaves were similar. Then, two fully mature leaves were collected from each plant at midday (6-8 h after lights on), and then flash-frozen in nitrogen and stored at -80°C until extraction.

value: leaf

tag: cultivar

value: Java

tag: diurnal temperature

tag: nocturnal temperature

source_name: Arabica cv 'T18141' at 30-26°C


title: Arabica cv. 'T18141' vs Eugenioides at 30-26°C – rep4

source_name: Eugenioides at 30-26°C

value: Eugenioides


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 30-26°C – rep3


title: Arabica cv. 'T18141' vs Eugenioides at 30-26°C – rep2


title: Arabica cv. 'T18141' vs Eugenioides at 30-26°C – rep6


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 30-26°C – rep1


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 30-26°C – rep2


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 30-26°C – rep6


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 30-26°C – rep4


title: Arabica cv. 'T18141' vs Eugenioides at 30-26°C – rep1


title: Canephora vs Arabica cv. 'T18141' at 30-26°C – rep1

source_name: Canephora at 30-26°C

value: Canephora


title: Canephora vs Arabica cv. 'T18141' at 30-26°C – rep3


title: Canephora vs Arabica cv. 'T18141' at 30-26°C – rep5


title: Arabica cv. 'T18141' vs Eugenioides at 30-26°C – rep5


title: Arabica cv. 'T18141' vs Eugenioides at 30-26°C – rep3


title: Canephora vs Arabica cv. 'T18141' at 30-26°C – rep6


title: Canephora vs Arabica cv. 'T18141' at 30-26°C – rep4


title: Canephora vs Arabica cv. 'T18141' at 30-26°C – rep2


title: Canephora vs Eugenioides at 30-26°C – rep6


title: Canephora vs Eugenioides at 30-26°C – rep5


title: Canephora vs Eugenioides at 30-26°C – rep4


title: Canephora vs Eugenioides at 30-26°C – rep3


title: Daudi HY-2 -36 ng/ml -6 hr -AP Phenotype -repeat 1 - mAdbID:95491

city: Bethesda

first: Hana

last: Schmeisser

state: MD

address: 50 Center Drive

department: CBS

institute: NIAID

description: mAdb experiment ID: 95491

hyb_protocol: Hybridization Protocol Other: The hybridization protocol was previously published by Han et al. (Han, J., H. Lee, N. Y. Nguyen, S. L. Beaucage, and R. K. Puri. 2005. Novel multiple 5 -amino-modified primer for DNA microarrays. Genomics 86:252– 258.) After washing, arrays were dried using a Labnet Spectrafuge Mini (Labnet, Edison, NJ).

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 20 LaserPower: 3.11;; 2.68 Temperature: 22.94 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

data_processing: Calculation Method: Array data were normalized by 50th percentile normalization, and the spot intensity was calculated by subtracting the local median background from the mean foreground intensity. Array replicates were averaged across treatments, and gene expression fold values were obtained from the normalized Cy5/Cy3 ratios.

source_name: Untreated Control Sample

label_protocol:
Cy3 Sample Labeling Protocol
Other: A 5-ug portion of total RNA was labeled by using a modified Cy3 aminoallyl labeling method.

extract_protocol:
RNAeasy Kit
Other: RNA was isolated by using an RNeasy minikit (Qiagen, Stanford, CA). Cells were homogenized by using QIA shredder columns, and samples were eluted in 50 ul of RNase-free water. To ensure that there was no residual DNA contamination, samples were treated with RNase-free DNase (Qiagen) as described in the RNeasy protocol.

tag: treatment

value: blood

tag: cell line

value: Daudi cell line

tag: cell type

value: B cells

value: Burkitt's lymphoma

source_name: HY-2 -36 ng/ml -6 hr -AP Phenotype

label_protocol:
Cy5 Sample Labeling Protocol
Other: A 5-ug portion of total RNA was labeled by using a modified Cy5 aminoallyl labeling method.

treatment_protocol:
Treatment type: compound
Agent: IFN hybrid 2
Treatment dose: 36 ng/ml
Treatment time: 6 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 6 hours at an HY-2 concentration of 36 ng of HY-2/ml (displays antiproliferative (AP) phenotype).

value: HY-2 -36 ng/ml -6 hr -AP Phenotype


title: Daudi HY-2 -36 ng/ml -6 hr -AP Phenotype -repeat 2 - mAdbID:95493

description: mAdb experiment ID: 95493

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 20 LaserPower: 3.19;; 2.7 Temperature: 23.75 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Canephora vs Eugenioides at 30-26°C – rep2


title: Eugenioides vs Arabica cv. 'Java' at 30-26°C – rep5


title: Daudi HY-2 -36 ng/ml -6 hr -AP Phenotype -repeat 3 - mAdbID:95495

description: mAdb experiment ID: 95495

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 35 LaserPower: 3.21;; 2.74 Temperature: 23.88 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Eugenioides vs Arabica cv. 'Java' at 30-26°C – rep6


title: Daudi IFN-alpha2c -0.36 ng/ml -6 hr -AP Phenotype -repeat 2 - mAdbID:95492

description: mAdb experiment ID: 95492

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 20 LaserPower: 3.17;; 2.68 Temperature: 23.44 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN-alpha2c
Treatment dose: 0.36 ng/ml
Treatment time: 6 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 6 hours at an IFN concentration of 0.36 ng of IFN-alpha2c/ml (displays antiproliferative (AP) phenotype).


title: Canephora vs Eugenioides at 30-26°C – rep1


title: Eugenioides vs Arabica cv. 'Java' at 30-26°C – rep4