title: Patient M colon cancer tissue

value: Patient M

value: 79 years

value: Female


title: Patient Y  colon cancer tissue

status: Public on Dec 16 2013

type: RNA

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

country: China

institute: soochow university school of medicine

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0)(Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

molecule: total RNA

organism: Homo sapiens

source_name: colon cancer tissue

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis. Please refer to “RNA_QC.pdf”

tag: patient id

value: Patient Y

tag: age

value: 77 years

tag: gender

tag: tissue

value: colon cancer

tag: tumor stage

value: II


title: Non-spatial Aged-Impaired 8

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

country: USA

institute: Johns Hopkins Univ. School of Medicine

hyb_protocol: as per manufacture's recommendation

scan_protocol: as per manufacture's recommendation

data_processing: Using the the R/Bioconductor system data were normalized and summarized using the affy and gcRMA packages. One array was dropped as an outlier. A known batch effect was removed by subtracting the average batch deviation from the mean on an individual probe basis. An empirical low expression cutoff of 5 units was used to remove noise from the data used here, leaving 16204 of the original 31099 probe sets in the analysis.

label: biotin

organism: Rattus norvegicus

source_name: Non-spatial Aged-Impaired

label_protocol: as per manufacture's recommendation

growth_protocol: Aged rats, microdissected CA3 region of hippocampus

extract_protocol: Total RNA was extracted by homogenization in TRIzol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.

treatment_protocol: Spatial or Non-spatial task

value: CA3 Hippocampus


title: Non-spatial Aged-Impaired 5


title: Patient S colon cancer tissue

value: Patient S

value: 38 years

value: Male


title: Patient W1 colon cancer tissue

value: Patient W1

value: 73 years


title: cPTK7/726-1070

city: La Jolla

first: Vladislav

last: Golubkov

state: California

address: 10901 N. Torrey Pines Rd.

institute: Sanford-Burnham Medical Research Institute

hyb_protocol: The labeled cRNA (750 ng) was hybridized for 18 h at 58°C to the HumanHT-12 v4 Expression BeadChip. BeadChips were then developed using fluorolink streptavidin-Cy3 (GE Healthcare).

scan_protocol: Array chips were scanned using an Illumina BeadArray Reader.

data_processing: The initial data extraction and normalization were performed using the BeadArray Reader and GeneSpring GX software (Agilent).

source_name: HT1080 cells

label_protocol: Biotin-labeled cRNA samples were prepared using the Illumina RNA Amplification Kit (Ambion).

growth_protocol: Cells (1 x 10^4/ml) were plated in DMEM- 10% FBS in a 100-mm dish and grown for 72 h to produce a subconfluent culture.

extract_protocol: Total cellular RNA was extracted using a Direct-zol RNA MiniPrep kit (Zymo Research).

tag: cell line

tag: transfected with


title: Patient H colon cancer tissue

value: Patient H

value: 75 years


title: Chz

value: Chz


title: sPTK7


title: Non-spatial Aged-Impaired 3


title: cPTK7/622-1070


title: Patient Y normal colon tissue

source_name: normal colon tissue

value: normal colon


title: shPTK7


title: PTK7


title: HT1080

value: scrambled control


title: UC114-hPL-1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 114 cultivated in bag in aMEM supplemented with human platelet lysate

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr to Affymetrix Gene Chip HG_U133 Plus  2.0. GeneChips were washed, stained with SA-PE and read using an Affymetrix GeneChip fluidic station and scanner.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GS3000-7G

data_processing: Analysis of microarray data was performed using the Affymetrix Microarray Suite 5.0 and BRB Array Tools 4.2. All array experiments were normalized using RMA.

source_name: umbilical cord matrix

label_protocol: 5 μg of total RNA was used for biotinylated target synthesis according to standard protocols supplied by the manufacturer (Affymetrix).

growth_protocol: human umbilical cord tissue-derived MSCs (UCX®) were isolated using clinical grade enzymes  and cultivated in flask or bags using α-MEM basal medium with 1 g/L glucose and 2 mM glutamine supplemented with either FBS,human serum or human platelet lysate until they reached confluency

extract_protocol: Total RNA from UCX®  MSC-medium was isolated using the RNeasy Mini Kit (Qiagen) following the protocols of the manufacturer

tag: supplement

value: human platelet lysate

tag: apparatus

value: bag


title: Patient W2 normal colon tissue

value: Patient W2

value: 64 years

value: III


title: G3-FBS-2

description: Mesenchymal stromal cells of donor G3 cultivated in flask in DMEM supplemented with fetal bovine serum

source_name: bone

growth_protocol: human bone and bone marrow derived MSC were grown in DMEM supplemented with 10%FBS, umbilical cord tissue-derived MSCs (UCX®) were isolated using clinical grade enzymes  and cultivated in flask or bags using α-MEM basal medium with 1 g/L glucose and 2 mM glutamine supplemented with either FBS,human serum or human platelet lysate until they reached confluency

value: FBS

value: flask


title: UC107-FBS-2

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 107 cultivated in flask in aMEM supplemented with fetal bovine serum


title: Abeta vs control, 20% survival [S109722]

city: Cambridge

first: Giorgio

last: Favrin

address: 80 Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description:
Abeta vs control, 20% survival
ab42-20% vs 51D-20%, replicate 1

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: The raw data were filtered to remove any probes that were rejected in over 50% of samples and were quantile-normalised across all arrays using Limma. Missing values were imputed using the impute package for R

organism: Drosophila melanogaster

label_protocol: To 3 to 5 µg of total RNA, add 1 µl 500 ng/ µl of Oligo(dT)23 anchored primer (Sigma) and adjust volume to 5 µl with DEPC- water. Incubate at 65 °C for 10 min, then snap cool on ice. Add 4 µl 5x First Strand Buffer (Invitrogen), 2 µl 0.1M DTT (Invitrogen), 1 µl 10 mM dNTP mix, 0.25 µl 40 U/µl RNasin (Promega) and 0.75 µl 200 U/µl Superscript III (Invitrogen). Incubate at 46 °C for 2 hours, then at 65 °C for 15 minutes, snap cool on ice. For second strand synthesis: Add 7.5 µl Second Strand Buffer (Invitrogen), 0.75 µl 10 mM dNTP mix, 2 µl 10 U/µl DNA Polymerase I (Invitrogen), 0.1 µl 5 U/µl RnaseH (Promega), 0.5 µl 10 U/µl E. coli Ligase (NEB) adjust volume to 40 µl with DEPC-water. Incubate at 16 °C for 2 hours, then purification using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

extract_protocol: Homogenise tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle and add up to 700 µl of TRIzol. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes at 4 °C to pellet debris. Transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, shake vigorously for 15 seconds and incubate at room temperature for 2-3 minutes. Centrifuge at 13,000 rpm for 15 minutes at 4 °C. Transfer upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.7 volumes of isopropanol to precipitate the RNA. Incubate at room temperature for 5 minutes or 1 hour at -20 °C and then centrifuge at 13,000 rpm for 15 minutes at 4 °C. Discard the supernatant and wash the RNA pellet with 1 ml 70% ethanol/DEPC MilliQ water. Centrifuge at 13,000 rpm for 10 minute at 4 °C. Air-dry the pellet briefly (~ 5 minutes). Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 20 to 50 µl. The RNA will dissolve more readily if the DEPC MilliQ water is preheated to 55 °C. Verify quality of RNA on a 1 % agarose gel and quantify with a Nanodrop.

tag: condition

value: Aβ expression

tag: day

tag: survival

value: Control


title: Abeta vs control, 20% survival [S109699]

description:
Abeta vs control, 20% survival
ab42-20% vs 51D-20%, replicate 3


title: Abeta vs control, 20% survival [S109716]

description:
Abeta vs control, 20% survival
ab42-20% vs 51D-20%, replicate 2


title: UC114-HS-2

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 114 cultivated in flask in aMEM supplemented with human serum

value: human serum


title: UC107_2-FBS-2


title: UC114-hPL-2

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 114 cultivated in flask in aMEM supplemented with human platelet lysate


title: M7-FBS-2

description: Mesenchymal stromal cells of donor M7 cultivated in flask in DMEM supplemented with fetal bovine serum

source_name: bone marrow


title: UC114-HS-1

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 114 cultivated in bag in aMEM supplemented with human serum


title: UC105-FBS-2

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 105 cultivated in flask in aMEM supplemented with fetal bovine serum


title: Patient W1 normal colon tissue

value: Patient W1

value: Female

value: II


title: Patient M normal colon tissue

value: Patient M

value: 79 years


title: Patient S normal colon tissue

value: Patient S

value: 38 years

value: Male

value: normal colon


title: Patient H normal colon tissue

value: Patient H

value: 75 years


title: UC114-FBS-1

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 114 cultivated in bag in aMEM supplemented with fetal bovine serum

value: bag


title: Abeta vs control, 80% survival [S109693]

description:
Abeta vs control, 80% survival
ab42-80% vs 51D-80%, replicate4


title: Abeta vs control, 20% survival [S109721]

description:
Abeta vs control, 20% survival
ab42-20% vs 51D-20%, replicate 4


title: shRNA-Control-pSUPER gfp-neo transfected HT29 cells

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array(v.18.0)(Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

source_name: HT29 cells,stably transfected with shRNA-Control-pSUPER gfp-neo vector

tag: cell type

value: colorectal cancer

value: shRNA-Control-pSUPER gfp-neo vector

tag: genotype/variation

value: control


title: UC114-FBS-2

description: Mesenchymal stromal cells (ATMP-compliant UCX®) of donor 114 cultivated in flask in aMEM supplemented with fetal bovine serum

value: FBS

value: flask


title: Abeta vs control, 80% survival [S109696]

description:
Abeta vs control, 80% survival
ab42-80% vs 51D-80%, replicate3

value: Control

value: Aβ expression


title: shRNA-TGF-β1-pSUPER gfp-neo transfected HT29 cells

source_name: HT29 cells, stably transfected with shRNA-TGF-β1-pSUPER gfp-neo vector


title: Abeta vs control, 80% survival [S109708]

description:
Abeta vs control, 80% survival
ab42-80% vs 51D-80%, replicate2


title: shRNA-Control-pSUPER gfp-neo transfected SW620 cells

source_name: SW620 cells,stably transfected with shRNA-Control-pSUPER gfp-neo vector


title: Abeta vs control, day 20 [S109700]

description:
Abeta vs control, day 20
ab42-d20 vs 51D-d20, replicate 2


title: Articular_chondrocytes_17wks_rep1

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: The acquisition of each array image was  undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC). Subsequent raw  data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from  AGCC. A PM/MM difference model for estimating gene expression levels and a quantile  approach for data normalization were used. Thresholds for selecting significant genes were set  at a relative difference ≥ 1.5-fold for the experiment involving 5-6 week specimens and ≥ 3.0  fold for experiment involving 17 week specimens, with an absolute difference > 100 signal  intensity units. Gene expression that met all three criteria simultaneously was considered as  significantly changed. Global functional analyses, network analyses and canonical pathway  analyses were performed using Ingenuity Pathway Analysis (Ingenuity® Systems,  www.ingenuity.com).

source_name: Human fetal joint 17 wks

label_protocol: Affymetrix standard labeling kit

extract_protocol: For Condensation and Total Cells samples, LCM was used to place cells in RLT; for 17 wk samples, tissue layers were dissected off the joint surface and put directly in RLT

tag: developmental stage

value: 17 wk


title: Abeta vs control, day 20 [S109715]

description:
Abeta vs control, day 20
ab42-d20 vs 51D-d20, replicate 1


title: Abeta vs control, day 20 [S109714]

description:
Abeta vs control, day 20
ab42-d20 vs 51D-d20, replicate 3


title: shRNA-TGF-β1-pSUPER gfp-neo transfected SW620 cells

source_name: SW620 cells, stably transfected with shRNA-TGF-β1-pSUPER gfp-neo vector

value: shRNA-TGF-β1-pSUPER gfp-neo vector

value: TGF-β1-knock down


title: Abeta vs control, 80% survival [S109698]

description:
Abeta vs control, 80% survival
ab42-80% vs 51D-80%, replicate1


title: shRNA-TGF-β1-pSUPER gfp-neo transfected Lovo cells

source_name: Lovo cells, stably transfected with shRNA-TGF-β1-pSUPER gfp-neo vector

value: Lovo


title: shRNA-Control-pSUPER gfp-neo transfected Lovo cells

source_name: Lovo cells, stably transfected with shRNA-Control-pSUPER gfp-neo vector


title: Articular_chondrocytes_17wks_rep2


title: Remaining limb cells_6wks_LCM_rep5

source_name: Human fetal limb 6 wks

value: 6 wk


title: Abeta vs control, day 10 [S109713]

description:
Abeta vs control, day 10
ab42-d10 vs 51D-d10, replicate 3


title: shRNA-Control-pSUPER gfp-neo transfected CT26 cells for 48 hours

description: Sample 5

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

organism: Mus musculus

source_name: CT26 cells_shRNA-Control-pSUPER gfp-neo vector

tag: time point


title: shRNA-Control-pSUPER gfp-neo transfected CT26 cells for 72 hours

description: Sample 6


title: Abeta vs control, day 10 [S109703]

description:
Abeta vs control, day 10
ab42-d10 vs 51D-d10, replicate 1


title: Abeta vs control, day 10 [S109720]

description:
Abeta vs control, day 10
ab42-d10 vs 51D-d10, replicate 2


title: Remaining limb cells_6wks_LCM_rep6


title: Articular_chondrocytes_17wks_rep3


title: Abeta vs control, day 10 [S109704]

description:
Abeta vs control, day 10
ab42-d10 vs 51D-d10, replicate 4


title: Remaining limb cells_6wks_LCM_rep4


title: shRNA-Control-pSUPER gfp-neo transfected CT26 cells for 24 hours

description: Sample 4


title: shRNA-TGF-β1-pSUPER gfp-neo transfected CT26 cells for 48 hours

description: Sample 2

source_name: CT26 _shRNA-TGF-β1-pSUPER gfp-neo vector


title: shRNA-TGF-β1-pSUPER gfp-neo transfected CT26 cells for 24 hours

description: Sample 1


title: Abeta vs control, day 3 [S109692]

description:
Abeta vs control, day 3
ab42-d3 vs 51D-d3, replicate 4 (dye-swap)


title: Remaining limb cells_6wks_LCM_rep2


title: Chondrocyte_condensation_6wks_LCM_rep6


title: Remaining limb cells_6wks_LCM_rep1


title: Abeta vs control, day 3 [S109723]

description:
Abeta vs control, day 3
ab42-d3 vs 51D-d3, replicate 2


title: Chondrocyte_condensation_6wks_LCM_rep5


title: Remaining limb cells_6wks_LCM_rep3


title: Chondrocyte_condensation_6wks_LCM_rep2


title: Chondrocyte_condensation_6wks_LCM_rep4


title: Chondrocyte_condensation_6wks_LCM_rep3


title: Abeta vs control, day 3 [S109709]

description:
Abeta vs control, day 3
ab42-d3 vs 51D-d3, replicate 3 (dye-swap)


title: Abeta vs control, day 3 [S109705]

description:
Abeta vs control, day 3
ab42-d3 vs 51D-d3, replicate 1


title: Pex1-G844D homozygote control retina, biological replicate 3

status: Public on Dec 15 2013

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: Gene expression data of Pex1-G844D homozygote retina

hyb_protocol: Followed standard Affymetrix protocol

scan_protocol: Followed standard Affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

source_name: Retina from Pex1 G844D-homozygote

label_protocol: Used 3' IVT Express Kit from Affymetrix and followed manufacturer's instructions

growth_protocol: Mice were maintained in animal care facilities at Johns Hopkins School of Medicine.  The Johns Hopkins Animal Care and Use Program is in compliance with the Animal Welfare Act and Public Health Service policies .  The program is accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care International.

extract_protocol: Used Quick-RNA MiniPrep from the Zymo Research Corporation and followed manufacturer's instructions

tag: strain

value: Retina

tag: genotype

value: Pex1-G844D homozygote

value: 124 days

value: Female


title: Pex1-G844D heterozygote control retina, biological replicate 4

description: Gene expression data of Pex1-G844D heterozygote control retina

source_name: Retina from Pex1 G844D-heterozygote

value: Pex1-G844D heterozygote

tag: age


title: Warm treated salmon 4

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description: biological replicate 4 of 4 (warm)

hyb_protocol: Slide processing steps within the Tecan hybridisation station were conducted as follows: one 30 s slide wash step (0.014% SDS) at 23 °C with a 30 s soak time, two 30 s slide wash steps (sdH2O) at 23 °C with 30 s soak times, 3 min slide denaturation at 85 °C with agitation,1 min wash (5x SSC, 0.01% SDS, 0.2% BSA) at 43 °C with a 30 s soak time, 1 h pre-hybridization at 43 °C with medium agitation, two 1.5 min washes (water) at 43 °C with a 30 s soak time, followed by 1 minwash (8x SSC, 0.1% SDS, 4X Denhardt's) at 43 °C, sample injection at 43 °C with agitation, hybridization for 16 h at 43 °C in high viscosity mode with low frequency agitation, four 30 s wash steps, two at 43 °C (2x SSC, 0.01% SDS) followed by two at 23 °C (0.2x SSC), and slide drying at 23 °C for 2.5 min.

scan_protocol: A ScanArray Express microarray scanner (Perkin Elmer) was used to capture fluorescent images, adjusting the PMT gain for optimized visualization of each slide.

data_processing:
The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com) and spots with poor quality or no signal (b2 standard deviations from background) at both wavelengths were flagged. Raw microarray intensity data were normalized in GeneSight (version 4.1, BioDiscovery, Inc., www.biodiscovery.com) using the local intensity-dependent loess normalization in order to remove intensity-dependent dye bias (Yang et al., 2002). Flagged spots were replaced by the experimental means for each gene.
All data were log transformed (base 2) and an intensity ratio was computed by taking the differences in log transformed intensities between the sample and reference control.  These log-transformed intensity ratios were used in all further analyses. Microarray data were expressed in terms of mean normalized (background corrected) log2 ratios between each fish and the reference control.

organism: Oncorhynchus nerka

source_name: heart; adult; warm temperature challenged; exercised

label_protocol: 1 µg of total RNA was amplified using Ambion MessageAmp II-96 kit and Amplified RNA (5 ug) were reverse-transcribed  into cDNA and labelled with Alexa dyes using a SuperScript Plus Indirect Labeling Kit (Invitrogen) according to manufacturer’s instructions. Experimental samples were fluorescently tagged with Alexa 555 (green) and the reference labelled with Alexa 647 (red).

extract_protocol: Total RNA extracted using Ambion MagMax-96 for microarray following non-spin method provided by manufacturer's instructions

value: heart

tag: treatment

value: Warm treated

source_name: heart;  pooled reference sample

tag: reference

value: Pool of cold and warm treated coho salmon


title: Cold treated salmon 4

description: biological replicate 4 of 4 (cold)

source_name: heart; adult; cold temperature challenged; exercised

tag: tissue

value: Cold treated


title: shRNA-TGF-β1-pSUPER gfp-neo transfected CT26 cells for 72 hours

description: Sample 3

tag: cell line

value: colorectal cancer


title: Pex1-G844D homozygote control retina, biological replicate 1

tag: gender

value: Male


title: Pex1-G844D heterozygote control retina, biological replicate 3


title: Pex1-G844D homozygote control retina, biological replicate 4


title: Chondrocyte_condensation_6wks_LCM_rep1


title: Warm treated salmon 2

description: biological replicate 2 of 4 (warm)


title: Warm treated salmon 1

description: biological replicate 1 of 4 (warm)


title: Pex1-G844D heterozygote control retina, biological replicate 2


title: Cold treated salmon 3

description: biological replicate 3 of 4 (cold)


title: Pex1-G844D homozygote control retina, biological replicate 2


title: Warm treated salmon 3

description: biological replicate 3 of 4 (warm)


title: Cold treated salmon 2

description: biological replicate 2 of 4 (cold)


title: Cold treated salmon 1

description: biological replicate 1 of 4 (cold)


title: Pex1-G844D heterozygote control retina, biological replicate 1


title: Sample-5B-U133B Day+3

city: Phoenix

first: Yoga

last: Balagurunathan

state: AZ

address: 445 N. Fifth street

institute: TGEN

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence..This Sample-5B-U133B is Day+3.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133B. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The Cell files extracted from scanner was quantified in Affymetrix MAS5 methods implemented in Bioconductor for R (default analysis settings used)  and global scaling as normalization method.

label: biotin.

source_name: Human Keratinocytes  Differentiation.

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

growth_protocol: Primary foreskin keratinocytes were grown in serum free medium and allowed to reach confluence in order to induce differentiation.

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

treatment_protocol: Confluence-induced differentiation.

value: Primary human neonatal foreskin keratinocytes

tag: time

value: Day+3 of point of confluence


title: Sample-3B-U133B Day+1

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence..This Sample-3B-U133B is Day+1.

value: Day+1 of point of confluence


title: Sample-1B-U133B Day-2

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence..This Sample-1B-U133B is Day-2.

value: Day-2 of point of confluence


title: EiMu-NS04-32276602

city: Mississippi State

first: Attila

last: Karsi

state: MS

address: 240 Wise Center Drive

department: Department of Basic Sciences, College of Veterinary Medicine

institute: Mississippi State University

description: This sample is of Edwardsiella ictaluri 93-146 gcvP mutant treated with normal catfish serum. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the fourth of four biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Edwardsiella ictaluri 93-146

source_name: Edwardsiella ictaluri 93-146 AKMut02 treated with normal catfish serum

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Edwardsiella ictaluri 93-146 wild type strain and EiAKMut02 were streaked on Brain Heart Infusion (BHI) agar plate to grow 48 h at 30 °C. The isolated colonies were grown aerobically to mid-log phase (O.D.600nm 0.8) in BHI at 30 °C.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect bacteria reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Life Sciences and Biotechnology Institute at Mississippi State University.

treatment_protocol: The Edwardsiella ictaluri 93-146 wild type strain was incubated with normal and heat-inactivated (45 min at 45°C) specific pathogen free catfish serum for 4 hours, while the EiAKMut02 was incubated with normal serum only for 4 hours. All bacteria were harvested by centrifugation for total RNA isolation at the end of treatment.

tag: phenotype

value: virulence attenuation

tag: accession

value: normal catfish serum


title: EiWt-HS02-33123202

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with heat-inactivated catfish serum. It is the second of four biological replicates used in this experiment, each from separate cultures.

source_name: Edwardsiella ictaluri 93-146 wild type treated with heat-inactivated serum

value: wild type

value: normal

value: heat-inactivated serum


title: Sample-4B-U133B Day+2

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence..This Sample-4B-U133B is Day+2.

value: Day+2 of point of confluence


title: EiWt-HS03-32276402

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with heat-inactivated catfish serum. It is the third of four biological replicates used in this experiment, each from separate cultures.


title: Sample-2B-U133B Day0

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence..This Sample-2B-U133B is Day0.

value: Day0 of point of confluence


title: EiWt-NS03-32365702

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with normal catfish serum. It is the third of four biological replicates used in this experiment, each from separate cultures.

source_name: Edwardsiella ictaluri 93-146 wild type treated with normal catfish serum


title: EiWt-NS01-32365402

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with normal catfish serum. It is the first of four biological replicates used in this experiment, each from separate cultures.


title: EiMu-NS02-32276302

description: This sample is of Edwardsiella ictaluri 93-146 gcvP mutant treated with normal catfish serum. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the second of four biological replicates used in this experiment, each from separate cultures.


title: EiWt-NS02-32280402

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with normal catfish serum. It is the second of four biological replicates used in this experiment, each from separate cultures.


title: EiMu-NS03-32276502

description: This sample is of Edwardsiella ictaluri 93-146 gcvP mutant treated with normal catfish serum. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the third of four biological replicates used in this experiment, each from separate cultures.


title: EiWt-HS01-33123002

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with heat-inactivated catfish serum. It is the first of four biological replicates used in this experiment, each from separate cultures.


title: EiWt-HS04-32280302

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with heat-inactivated catfish serum. It is the fourth of four biological replicates used in this experiment, each from separate cultures.


title: EiMu-NS01-33123102

description: This sample is of Edwardsiella ictaluri 93-146 gcvP mutant treated with normal catfish serum. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the first of four biological replicates used in this experiment, each from separate cultures.


title: EiWt-NF01-33864502

description: This sample is of Edwardsiella ictaluri 93-146 wild type without encountering with catfish fry. It is the first of four biological replicates used in this experiment, each from separate cultures.

treatment_protocol: The Edwardsiella ictaluri 93-146 wild type strain was incubated with catfish fry or no catfish fry (pond water) at room temperature for 3 hours, while the EiAKMut02 was incubated with catfish fry at room temperature for 3 hours. The bacteria concentration in host encounter experiment was 1 x 10^7 CFU/ml water. All bacteria were harvested by centrifugation for total RNA isolation at the end of treatment.

value: incubated without catfish fry


title: EiWt-NF04-33864302

description: This sample is of Edwardsiella ictaluri 93-146 wild type without encountering with catfish fry. It is the fourth of four biological replicates used in this experiment, each from separate cultures.


title: EiWt-WF03-33864002

description: This sample is of Edwardsiella ictaluri 93-146 wild type encountered with catfish fry. It is the third of four biological replicates used in this experiment, each from separate cultures.

value: incubated with catfish fry


title: EiMu-WF02-33864102

description: This sample is of Edwardsiella ictaluri 93-146  gcvP mutant encountered with catfish fry. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the second of four biological replicates used in this experiment, each from separate cultures.

source_name: Edwardsiella ictaluri 93-146 AKMut02 encountered with catfish fry


title: EiWt-NS04-32280202

description: This sample is of wild-type Edwardsiella ictaluri 93-146 treated with normal catfish serum. It is the fourth of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 46

type: protein

first: Phillip

last: Stafford

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

description: Alexa-647 conjugated goat anti-human secondary antibody

hyb_protocol: Antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, "Physical characterization of the Immunosignaturing Effect", MCP 11(4), 2012).

scan_protocol: Scanning was done on an Agilent 'C' scanner at 10um resolution, high laser power, 70% PMT, autofocus ON, 638nm.

data_processing:
Median normalization per slide was done, and any negative values were adjusted to 0.01.
GeneSpring 7.3.1 was used to load and median-normalize raw gpr files.  Matrix of values were copied directly from GeneSpring as double-precision values.

label: direct-labeled anti-human IgG (Alexa 647)

molecule: protein

source_name: Pancreatitis

label_protocol: Alexafluor 647-labeled goat anti-human IgG heavy-chain (Rockland antibodies) secondary antibody.

value: Pancreatitis


title: Pancreatitis 47


title: Pancreatitis 48


title: Pancreatitis 45


title: Pancreatitis 44


title: EiWt-WF01-33864402

description: This sample is of Edwardsiella ictaluri 93-146 wild type encountered with catfish fry. It is the first of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 42


title: Pancreatitis 43


title: Pancreatitis 41


title: EiMu-WF01-33863802

description: This sample is of Edwardsiella ictaluri 93-146  gcvP mutant encountered with catfish fry. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the first of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 40


title: Pancreatitis 36


title: Pancreatitis 35


title: Pancreatitis 38


title: Pancreatitis 37


title: EiWt-WF02-33857302

description: This sample is of Edwardsiella ictaluri 93-146 wild type encountered with catfish fry. It is the second of four biological replicates used in this experiment, each from separate cultures.


title: EiWt-WF04-33863902

description: This sample is of Edwardsiella ictaluri 93-146 wild type encountered with catfish fry. It is the fourth of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 34


title: EiWt-NF02-33864602

description: This sample is of Edwardsiella ictaluri 93-146 wild type without encountering with catfish fry. It is the second of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 31


title: Pancreatitis 32


title: Pancreatitis 30


title: Pancreatitis 29


title: EiMu-WF03-33857602

description: This sample is of Edwardsiella ictaluri 93-146  gcvP mutant encountered with catfish fry. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the third of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 28


title: Pancreatitis 27


title: Pancreatitis 26


title: Pancreatitis 22


title: Pancreatitis 24


title: Pancreatitis 39


title: Pancreatitis 20


title: Pancreatitis 19


title: Pancreatitis 18


title: Pancreatitis 25


title: Pancreatitis 33


title: Pancreatitis 17


title: Pancreatitis 15


title: Pancreatitis 12


title: Pancreatitis 14


title: Pancreatitis 10


title: Pancreatitis 11


title: Pancreatitis 16


title: EiMu-WF04-33857402

description: This sample is of Edwardsiella ictaluri 93-146  gcvP mutant encountered with catfish fry. This is a single MAR2xT7 transposon insertion mutant of gcvP gene. It is the fourth of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatitis 8


title: Pancreatitis 6


title: Pancreatitis 5


title: Pancreatitis 4


title: Pancreatitis 23


title: Pancreatitis 21


title: Pancreatic cancer 136

source_name: Pancreatic cancer

value: Pancreatic cancer


title: Pancreatitis 1


title: Pancreatitis 2


title: Pancreatic cancer 134


title: Pancreatic cancer 133


title: Pancreatic cancer 135


title: EiWt-NF03-33857502

description: This sample is of Edwardsiella ictaluri 93-146 wild type without encountering with catfish fry. It is the third of four biological replicates used in this experiment, each from separate cultures.


title: Pancreatic cancer 131


title: Pancreatic cancer 128


title: Pancreatitis 13


title: Pancreatic cancer 129


title: Pancreatitis 9


title: Pancreatic cancer 127


title: Pancreatic cancer 130


title: Pancreatic cancer 125


title: Pancreatic cancer 123


title: Pancreatic cancer 121


title: Pancreatitis 7


title: Pancreatic cancer 122


title: Pancreatic cancer 119


title: Pancreatic cancer 120


title: Pancreatic cancer 118


title: Pancreatic cancer 117


title: Pancreatitis 3


title: Pancreatic cancer 116


title: Pancreatic cancer 114


title: Pancreatic cancer 115


title: Pancreatic cancer 113


title: Pancreatic cancer 112


title: Pancreatic cancer 111


title: Pancreatic cancer 110


title: Pancreatic cancer 109


title: Pancreatic cancer 132


title: Pancreatic cancer 106


title: Pancreatic cancer 107


title: Pancreatic cancer 104


title: Pancreatic cancer 124


title: Pancreatic cancer 126


title: Pancreatic cancer 103


title: Pancreatic cancer 105


title: Pancreatic cancer 102


title: Pancreatic cancer 99


title: Pancreatic cancer 101


title: Pancreatic cancer 98


title: Pancreatic cancer 97


title: Pancreatic cancer 96


title: Pancreatic cancer 95


title: Pancreatic cancer 91


title: Pancreatic cancer 92


title: Pancreatic cancer 93


title: Pancreatic cancer 94


title: Pancreatic cancer 89


title: Pancreatic cancer 90


title: Pancreatic cancer 88


title: Pancreatic cancer 86


title: Pancreatic cancer 85


title: Pancreatic cancer 87


title: Pancreatic cancer 84


title: Pancreatic cancer 83


title: Pancreatic cancer 82


title: Pancreatic cancer 78


title: Pancreatic cancer 81


title: Pancreatic cancer 100


title: Pancreatic cancer 75


title: Pancreatic cancer 74


title: Pancreatic cancer 79


title: Pancreatic cancer 73


title: Pancreatic cancer 77


title: Pancreatic cancer 72


title: Pancreatic cancer 76


title: Pancreatic cancer 71


title: Pancreatic cancer 68


title: Pancreatic cancer 65


title: Pancreatic cancer 63


title: Pancreatic cancer 66


title: Pancreatic cancer 67


title: Pancreatic cancer 69


title: Pancreatic cancer 64


title: Pancreatic cancer 62


title: Pancreatic cancer 59


title: Pancreatic cancer 60


title: Pancreatic cancer 61


title: Pancreatic cancer 56


title: Pancreatic cancer 55


title: Pancreatic cancer 80


title: Pancreatic cancer 57


title: Pancreatic cancer 52


title: Pancreatic cancer 49


title: Pancreatic cancer 53


title: Pancreatic cancer 54


title: Pancreatic cancer 70


title: Pancreatic cancer 47


title: Pancreatic cancer 51


title: Pancreatic cancer 44


title: Pancreatic cancer 50


title: Pancreatic cancer 48


title: Pancreatic cancer 45


title: Pancreatic cancer 43


title: Pancreatic cancer 46


title: Pancreatic cancer 38


title: Pancreatic cancer 40


title: Pancreatic cancer 42


title: Pancreatic cancer 36


title: Pancreatic cancer 41


title: Pancreatic cancer 39


title: Pancreatic cancer 37


title: Pancreatic cancer 32


title: Pancreatic cancer 33


title: Pancreatic cancer 35


title: Pancreatic cancer 31


title: Pancreatic cancer 58


title: Pancreatic cancer 34


title: Pancreatic cancer 30


title: Pancreatic cancer 28


title: Pancreatic cancer 29


title: Pancreatic cancer 26


title: Pancreatic cancer 25


title: Pancreatic cancer 24


title: Pancreatic cancer 22


title: Pancreatic cancer 27


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title: Pancreatic cancer 21


title: Pancreatic cancer 18


title: Pancreatic cancer 19


title: Pancreatic cancer 17


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title: Pancreatic cancer 15


title: Pancreatic cancer 14


title: Pancreatic cancer 12


title: Pancreatic cancer 10


title: Pancreatic cancer 9


title: Pancreatic cancer 7


title: Pancreatic cancer 6


title: Pancreatic cancer 5


title: Pancreatic cancer 3


title: Pancreatic cancer 4


title: Pancreatic cancer 1


title: Ovarian cancer 86

source_name: Ovarian cancer

value: Ovarian cancer


title: Ovarian cancer 85


title: Ovarian cancer 84


title: Ovarian cancer 82


title: Ovarian cancer 83


title: Ovarian cancer 79


title: Ovarian cancer 81


title: Ovarian cancer 78


title: Ovarian cancer 76


title: Ovarian cancer 77


title: Ovarian cancer 75


title: Ovarian cancer 74


title: Pancreatic cancer 13


title: Ovarian cancer 72


title: Ovarian cancer 71


title: Pancreatic cancer 11


title: Pancreatic cancer 8


title: Ovarian cancer 69


title: Ovarian cancer 70


title: Ovarian cancer 68


title: Ovarian cancer 66


title: Ovarian cancer 67


title: Ovarian cancer 65


title: Pancreatic cancer 2


title: Ovarian cancer 64


title: Ovarian cancer 63


title: Ovarian cancer 61


title: Ovarian cancer 60


title: Ovarian cancer 80


title: Ovarian cancer 62


title: Ovarian cancer 58


title: Ovarian cancer 57


title: Ovarian cancer 54


title: Ovarian cancer 59


title: Ovarian cancer 52


title: Ovarian cancer 56


title: Ovarian cancer 73


title: Ovarian cancer 51


title: Ovarian cancer 55


title: Ovarian cancer 48


title: Ovarian cancer 49


title: Ovarian cancer 50


title: Ovarian cancer 46


title: Ovarian cancer 45


title: Ovarian cancer 44


title: Ovarian cancer 39


title: Ovarian cancer 40


title: Ovarian cancer 38


title: Ovarian cancer 43


title: Ovarian cancer 41


title: Ovarian cancer 37


title: Ovarian cancer 35


title: Ovarian cancer 34


title: Ovarian cancer 33


title: Ovarian cancer 32


title: Ovarian cancer 53


title: Ovarian cancer 30


title: Ovarian cancer 29


title: Ovarian cancer 28


title: Ovarian cancer 31


title: Ovarian cancer 27


title: Ovarian cancer 25


title: Ovarian cancer 47


title: Ovarian cancer 26


title: Ovarian cancer 23


title: Ovarian cancer 21


title: Ovarian cancer 19


title: Ovarian cancer 18


title: Ovarian cancer 22


title: Ovarian cancer 15


title: Ovarian cancer 14


title: Ovarian cancer 42


title: Ovarian cancer 36


title: Ovarian cancer 12


title: Ovarian cancer 16


title: Ovarian cancer 10


title: Ovarian cancer 13


title: Ovarian cancer 6


title: Ovarian cancer 4


title: Ovarian cancer 2


title: Ovarian cancer 1


title: Ovarian cancer 11


title: Oligodendroglioma 48

source_name: Oligodendroglioma

value: Oligodendroglioma


title: Oligodendroglioma 45


title: Ovarian cancer 9


title: Oligodendroglioma 44


title: Ovarian cancer 20


title: Oligodendroglioma 43


title: Ovarian cancer 5


title: Ovarian cancer 8


title: Oligodendroglioma 42


title: Ovarian cancer 24


title: Pancreatic cancer 108


title: Ovarian cancer 17


title: Oligodendroglioma 47


title: Oligodendroglioma 39


title: Oligodendroglioma 40


title: Oligodendroglioma 46


title: Oligodendroglioma 41


title: Oligodendroglioma 37


title: Oligodendroglioma 38


title: Oligodendroglioma 34


title: Oligodendroglioma 36


title: Ovarian cancer 3


title: Ovarian cancer 7


title: Oligodendroglioma 33


title: Oligodendroglioma 32


title: Oligodendroglioma 30


title: Oligodendroglioma 31


title: Oligodendroglioma 29


title: Oligodendroglioma 28


title: Oligodendroglioma 27


title: Oligodendroglioma 25


title: Oligodendroglioma 24


title: Oligodendroglioma 26


title: Oligodendroglioma 23


title: Oligodendroglioma 22


title: Oligodendroglioma 18


title: Oligodendroglioma 20


title: Oligodendroglioma 19


title: Oligodendroglioma 17


title: Oligodendroglioma 15


title: Oligodendroglioma 21


title: Oligodendroglioma 16


title: Oligodendroglioma 14


title: Oligodendroglioma 13


title: Oligodendroglioma 35


title: Oligodendroglioma 11


title: Oligodendroglioma 10


title: Oligodendroglioma 9


title: Oligodendroglioma 8


title: Oligodendroglioma 12


title: Oligodendroglioma 7


title: Oligodendroglioma 5


title: Oligodendroglioma 6


title: Oligodendroglioma 1


title: Healthy normal donor 249

source_name: Healthy normal donor

value: Healthy normal donor


title: Healthy normal donor 248


title: Oligodendroglioma 4


title: Oligodendroglioma 3


title: Healthy normal donor 246


title: Healthy normal donor 241


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title: Healthy normal donor 230


title: Healthy normal donor 231


title: Healthy normal donor 229


title: Healthy normal donor 227


title: Oligodendroglioma 2


title: Healthy normal donor 225


title: Healthy normal donor 224


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title: Healthy normal donor 137


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title: Healthy normal donor 75


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title: Healthy normal donor 62


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title: Healthy normal donor 29


title: Healthy normal donor 51


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title: Healthy normal donor 31


title: Healthy normal donor 25


title: Healthy normal donor 24


title: Healthy normal donor 22


title: Healthy normal donor 26


title: Healthy normal donor 20


title: Healthy normal donor 45


title: Healthy normal donor 27


title: Healthy normal donor 23


title: Healthy normal donor 21


title: Healthy normal donor 19


title: Healthy normal donor 18


title: Healthy normal donor 15


title: Healthy normal donor 16


title: Healthy normal donor 14


title: Healthy normal donor 13


title: Healthy normal donor 12


title: Healthy normal donor 10


title: Healthy normal donor 11


title: Healthy normal donor 8


title: Healthy normal donor 6


title: Healthy normal donor 9


title: Healthy normal donor 28


title: Healthy normal donor 5


title: Healthy normal donor 4


title: Healthy normal donor 3


title: Healthy normal donor 2


title: Healthy normal donor 1


title: Mixed Oligo/Astrocytoma 97

source_name: Mixed Oligo/Astrocytoma

value: Mixed Oligo/Astrocytoma


title: Mixed Oligo/Astrocytoma 92


title: Mixed Oligo/Astrocytoma 96


title: Mixed Oligo/Astrocytoma 95


title: Mixed Oligo/Astrocytoma 91


title: Mixed Oligo/Astrocytoma 93


title: Mixed Oligo/Astrocytoma 88


title: Mixed Oligo/Astrocytoma 94


title: Mixed Oligo/Astrocytoma 87


title: Mixed Oligo/Astrocytoma 90


title: Mixed Oligo/Astrocytoma 85


title: Healthy normal donor 17


title: Mixed Oligo/Astrocytoma 82


title: Mixed Oligo/Astrocytoma 79


title: Healthy normal donor 7


title: Mixed Oligo/Astrocytoma 77


title: Mixed Oligo/Astrocytoma 76


title: Mixed Oligo/Astrocytoma 80


title: Mixed Oligo/Astrocytoma 75


title: Mixed Oligo/Astrocytoma 81


title: Mixed Oligo/Astrocytoma 74


title: Mixed Oligo/Astrocytoma 71


title: Mixed Oligo/Astrocytoma 70


title: Mixed Oligo/Astrocytoma 72


title: Mixed Oligo/Astrocytoma 69


title: Mixed Oligo/Astrocytoma 89


title: Mixed Oligo/Astrocytoma 68


title: Mixed Oligo/Astrocytoma 84


title: Mixed Oligo/Astrocytoma 67


title: Mixed Oligo/Astrocytoma 83


title: Mixed Oligo/Astrocytoma 63


title: Mixed Oligo/Astrocytoma 65


title: Mixed Oligo/Astrocytoma 62


title: Mixed Oligo/Astrocytoma 61


title: Mixed Oligo/Astrocytoma 59


title: Mixed Oligo/Astrocytoma 60


title: Mixed Oligo/Astrocytoma 66


title: Mixed Oligo/Astrocytoma 58


title: Mixed Oligo/Astrocytoma 78


title: Mixed Oligo/Astrocytoma 56


title: Mixed Oligo/Astrocytoma 57


title: Mixed Oligo/Astrocytoma 55


title: Mixed Oligo/Astrocytoma 52


title: Mixed Oligo/Astrocytoma 53


title: Mixed Oligo/Astrocytoma 54


title: Mixed Oligo/Astrocytoma 51


title: Mixed Oligo/Astrocytoma 48


title: Mixed Oligo/Astrocytoma 47


title: Mixed Oligo/Astrocytoma 50


title: Mixed Oligo/Astrocytoma 73


title: Mixed Oligo/Astrocytoma 46


title: Mixed Oligo/Astrocytoma 44


title: Mixed Oligo/Astrocytoma 86


title: Mixed Oligo/Astrocytoma 64


title: Mixed Oligo/Astrocytoma 42


title: Mixed Oligo/Astrocytoma 41


title: Mixed Oligo/Astrocytoma 40


title: Mixed Oligo/Astrocytoma 45


title: Mixed Oligo/Astrocytoma 39


title: Mixed Oligo/Astrocytoma 35


title: Mixed Oligo/Astrocytoma 34


title: Mixed Oligo/Astrocytoma 33


title: Mixed Oligo/Astrocytoma 38


title: Mixed Oligo/Astrocytoma 37


title: Mixed Oligo/Astrocytoma 43


title: Mixed Oligo/Astrocytoma 32


title: Mixed Oligo/Astrocytoma 31


title: Mixed Oligo/Astrocytoma 28


title: Mixed Oligo/Astrocytoma 36


title: Mixed Oligo/Astrocytoma 25


title: Mixed Oligo/Astrocytoma 26


title: Mixed Oligo/Astrocytoma 24


title: Mixed Oligo/Astrocytoma 29


title: Mixed Oligo/Astrocytoma 27


title: Mixed Oligo/Astrocytoma 49


title: Mixed Oligo/Astrocytoma 21


title: Mixed Oligo/Astrocytoma 23


title: Mixed Oligo/Astrocytoma 22


title: Mixed Oligo/Astrocytoma 30


title: Mixed Oligo/Astrocytoma 19


title: Mixed Oligo/Astrocytoma 20


title: Mixed Oligo/Astrocytoma 8


title: Mixed Oligo/Astrocytoma 15


title: Mixed Oligo/Astrocytoma 9


title: Mixed Oligo/Astrocytoma 17


title: Mixed Oligo/Astrocytoma 14


title: Mixed Oligo/Astrocytoma 18


title: Mixed Oligo/Astrocytoma 6


title: Mixed Oligo/Astrocytoma 7


title: Mixed Oligo/Astrocytoma 16


title: Mixed Oligo/Astrocytoma 12


title: Mixed Oligo/Astrocytoma 13


title: Mixed Oligo/Astrocytoma 4


title: Mixed Oligo/Astrocytoma 5


title: Mixed Oligo/Astrocytoma 2


title: Multiple myeloma 108

source_name: Multiple myeloma

value: Multiple myeloma


title: Multiple myeloma 110


title: Multiple myeloma 112


title: Mixed Oligo/Astrocytoma 3


title: Multiple myeloma 111


title: Multiple myeloma 104


title: Multiple myeloma 105


title: Multiple myeloma 103


title: Multiple myeloma 107


title: Multiple myeloma 109


title: Multiple myeloma 102


title: Multiple myeloma 101


title: Multiple myeloma 106


title: Mixed Oligo/Astrocytoma 1


title: Mixed Oligo/Astrocytoma 11


title: Mixed Oligo/Astrocytoma 10


title: Multiple myeloma 99


title: Multiple myeloma 97


title: Multiple myeloma 96


title: Valley Fever 142

source_name: Valley Fever

value: Valley Fever


title: Multiple myeloma 95


title: Valley Fever 140


title: Valley Fever 139


title: Valley Fever 136


title: Valley Fever 132


title: Valley Fever 138


title: Valley Fever 131


title: Valley Fever 134


title: Valley Fever 133


title: Valley Fever 127


title: Valley Fever 128


title: Valley Fever 129


title: Valley Fever 130


title: Valley Fever 126


title: Valley Fever 125


title: Valley Fever 124


title: Multiple myeloma 98


title: Multiple myeloma 100


title: Valley Fever 123


title: Valley Fever 141


title: Valley Fever 122


title: Valley Fever 120


title: Valley Fever 137


title: Valley Fever 119


title: Valley Fever 118


title: Valley Fever 117


title: Valley Fever 135


title: Valley Fever 116


title: Valley Fever 115


title: Valley Fever 114


title: Valley Fever 113


title: Valley Fever 110


title: Valley Fever 112


title: Valley Fever 109


title: Valley Fever 111


title: Valley Fever 108


title: Valley Fever 105


title: Valley Fever 104


title: Valley Fever 103


title: Valley Fever 102


title: Valley Fever 121


title: Valley Fever 101


title: Valley Fever 100


title: Valley Fever 99


title: Valley Fever 98


title: Valley Fever 96


title: Valley Fever 97


title: Valley Fever 95


title: Valley Fever 93


title: Valley Fever 91


title: Valley Fever 92


title: Valley Fever 89


title: Valley Fever 90


title: Valley Fever 87


title: Valley Fever 107


title: Valley Fever 88


title: Valley Fever 86


title: Valley Fever 106


title: Valley Fever 84


title: HCT116 shSET1 C7 #3

city: Gainesville

first: Lei

last: Zhou

state: FL

department: Molecular Genetics and Microbiology

institute: University of Florida

description: hSET1 KD

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

source_name: HCT116 hSET1 KD

growth_protocol: CRC cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (Invitrogen).

extract_protocol: 10μg RNA was reverse transcribed to cDNA using the Applied Biosystems High Capacity cDNA Reverse Transcription kit according to the manufacturer’s instructions (Applied Biosystems). cDNA products were treated with 100ng RNaseA and then purified using the Qiagen PCR purification kit according to the manufacturer’s instructions.

treatment_protocol: hSETD1A was silenced in HCT116 cells using retrovirus harboring shRNA specifically against the hSETD1A gene.

value: SET1 KD


title: Valley Fever 85


title: Valley Fever 82


title: HCT116 shSET1 C7 #2

description: hSET1 KD


title: HCT116 pSuper control #1

description: control

source_name: HCT116 control

value: Control


title: Valley Fever 81


title: Valley Fever 80


title: Valley Fever 79


title: HCT116 shSET1 C7 #1

description: hSET1 KD


title: Valley Fever 78


title: Valley Fever 77


title: Valley Fever 76


title: Valley Fever 75


title: Valley Fever 74


title: Valley Fever 94


title: Valley Fever 73


title: Valley Fever 83


title: HCT116 pSuper control #2

description: control


title: Valley Fever 72


title: Valley Fever 64


title: Valley Fever 63


title: Valley Fever 71


title: Valley Fever 69


title: Valley Fever 68


title: Valley Fever 59


title: Valley Fever 67


title: Valley Fever 60


title: Valley Fever 65


title: Valley Fever 57


title: Valley Fever 56


title: Valley Fever 62


title: Valley Fever 66


title: Valley Fever 58


title: Valley Fever 52


title: Valley Fever 55


title: Valley Fever 54


title: Valley Fever 50


title: Valley Fever 53


title: Valley Fever 49


title: Valley Fever 51


title: Valley Fever 46


title: Valley Fever 48


title: Valley Fever 47


title: Valley Fever 42


title: Valley Fever 45


title: Valley Fever 44


title: Valley Fever 43


title: Valley Fever 70


title: Valley Fever 61


title: Valley Fever 38


title: Valley Fever 36


title: Valley Fever 32


title: Valley Fever 33


title: Valley Fever 31


title: Valley Fever 25


title: Valley Fever 35


title: Valley Fever 39


title: Valley Fever 40


title: Valley Fever 26


title: Valley Fever 22


title: Valley Fever 41


title: Valley Fever 19


title: Valley Fever 34


title: Valley Fever 30


title: Valley Fever 37


title: Valley Fever 20


title: Valley Fever 21


title: Valley Fever 16


title: Valley Fever 28


title: Valley Fever 11


title: Valley Fever 27


title: Valley Fever 24


title: Valley Fever 23


title: Valley Fever 15


title: Valley Fever 29


title: Valley Fever 13


title: Valley Fever 12


title: Valley Fever 17


title: Valley Fever 14


title: Valley Fever 8


title: Valley Fever 18


title: Valley Fever 9


title: Valley Fever 5


title: Valley Fever 6


title: Valley Fever 4


title: Valley Fever 1


title: Sarcoma 18

source_name: Sarcoma

value: Sarcoma


title: Sarcoma 19


title: Valley Fever 7


title: Sarcoma 16


title: Valley Fever 2


title: Valley Fever 3


title: Sarcoma 13


title: Sarcoma 12


title: Sarcoma 15


title: Sarcoma 14


title: Sarcoma 17


title: Sarcoma 11


title: Valley Fever 10


title: Sarcoma 8


title: Sarcoma 9


title: Sarcoma 10


title: Sarcoma 7


title: Sarcoma 5


title: Sarcoma 4


title: Sarcoma 6


title: Sarcoma 3


title: Sarcoma 2


title: Pancreatitis 82


title: Pancreatitis 81


title: Sarcoma 1


title: Sarcoma 20


title: Pancreatitis 78


title: Pancreatitis 76


title: Pancreatitis 74


title: Pancreatitis 71


title: Pancreatitis 79


title: Pancreatitis 73


title: Pancreatitis 70


title: Pancreatitis 67


title: Pancreatitis 69


title: Pancreatitis 68


title: Pancreatitis 66


title: Pancreatitis 64


title: Pancreatitis 65


title: Pancreatitis 72


title: Pancreatitis 63


title: Pancreatitis 62


title: Pancreatitis 60


title: Pancreatitis 61


title: Pancreatitis 57


title: Pancreatitis 80


title: Pancreatitis 59


title: Pancreatitis 58


title: Pancreatitis 55


title: Pancreatitis 54


title: Pancreatitis 52


title: Pancreatitis 77


title: Pancreatitis 51


title: Pancreatitis 75


title: Pancreatitis 53


title: Multiple myeloma 94


title: Multiple myeloma 93


title: Multiple myeloma 92


title: Pancreatitis 50


title: Multiple myeloma 90


title: Multiple myeloma 88


title: Multiple myeloma 86


title: Multiple myeloma 87


title: Multiple myeloma 85


title: Multiple myeloma 83


title: Multiple myeloma 81


title: Multiple myeloma 82


title: Multiple myeloma 91


title: Multiple myeloma 80


title: Pancreatitis 56


title: Multiple myeloma 77


title: Multiple myeloma 78


title: Multiple myeloma 75


title: Multiple myeloma 79


title: Multiple myeloma 76


title: Multiple myeloma 71


title: Multiple myeloma 74


title: Multiple myeloma 70


title: Multiple myeloma 72


title: Multiple myeloma 67


title: Multiple myeloma 69


title: Pancreatitis 49


title: Multiple myeloma 89


title: Multiple myeloma 64


title: Multiple myeloma 60


title: Multiple myeloma 61


title: Multiple myeloma 62


title: Multiple myeloma 84


title: Multiple myeloma 59


title: Multiple myeloma 55


title: Multiple myeloma 65


title: Multiple myeloma 57


title: Multiple myeloma 58


title: Multiple myeloma 63


title: Multiple myeloma 56


title: Multiple myeloma 54


title: Multiple myeloma 53


title: Multiple myeloma 52


title: Multiple myeloma 73


title: Multiple myeloma 50


title: Multiple myeloma 49


title: Multiple myeloma 48


title: Multiple myeloma 44


title: Multiple myeloma 46


title: Multiple myeloma 47


title: Multiple myeloma 68


title: Multiple myeloma 45


title: Multiple myeloma 66


title: Multiple myeloma 43


title: Multiple myeloma 40


title: Multiple myeloma 39


title: Multiple myeloma 34


title: Multiple myeloma 31


title: Multiple myeloma 35


title: Multiple myeloma 51


title: Multiple myeloma 28


title: Multiple myeloma 41


title: Multiple myeloma 27


title: Multiple myeloma 24


title: Multiple myeloma 37


title: Multiple myeloma 38


title: Multiple myeloma 36


title: Multiple myeloma 32


title: Multiple myeloma 42


title: Multiple myeloma 30


title: Multiple myeloma 21


title: Multiple myeloma 18


title: Multiple myeloma 17


title: Multiple myeloma 29


title: Multiple myeloma 15


title: Multiple myeloma 26


title: Multiple myeloma 33


title: Multiple myeloma 25


title: Multiple myeloma 22


title: Multiple myeloma 10


title: Multiple myeloma 11


title: Multiple myeloma 23


title: Multiple myeloma 20


title: Multiple myeloma 19


title: Multiple myeloma 16


title: Multiple myeloma 6


title: Multiple myeloma 13


title: Multiple myeloma 12


title: Multiple myeloma 9


title: Multiple myeloma 3


title: Lung cancer 107

source_name: Lung cancer

value: Lung cancer


title: Multiple myeloma 8


title: Lung cancer 105


title: Lung cancer 104


title: Multiple myeloma 7


title: Lung cancer 101


title: Lung cancer 106


title: Lung cancer 103


title: Multiple myeloma 2


title: Lung cancer 96


title: Lung cancer 97


title: Lung cancer 98


title: Lung cancer 99


title: Lung cancer 94


title: Lung cancer 100


title: Multiple myeloma 5


title: Lung cancer 93


title: Lung cancer 92


title: Lung cancer 88


title: Lung cancer 90


title: Lung cancer 86


title: Multiple myeloma 1


title: Multiple myeloma 4


title: Lung cancer 89


title: Lung cancer 85


title: Multiple myeloma 14


title: Lung cancer 81


title: Lung cancer 83


title: Lung cancer 74


title: Lung cancer 80


title: Lung cancer 102


title: Lung cancer 78


title: Lung cancer 70


title: Lung cancer 68


title: Lung cancer 87


title: Lung cancer 95


title: Lung cancer 65


title: Lung cancer 77


title: Lung cancer 73


title: Lung cancer 76


title: Lung cancer 63


title: Lung cancer 62


title: Lung cancer 72


title: Lung cancer 61


title: Lung cancer 71


title: Lung cancer 69


title: Lung cancer 67


title: Lung cancer 66


title: Lung cancer 79


title: Lung cancer 84


title: Lung cancer 60


title: Lung cancer 58


title: Lung cancer 59


title: Lung cancer 64


title: Lung cancer 75


title: Lung cancer 57


title: Lung cancer 82


title: Lung cancer 51


title: Lung cancer 56


title: Lung cancer 53


title: Lung cancer 54


title: Lung cancer 49


title: Lung cancer 52


title: Lung cancer 47


title: Lung cancer 48


title: Lung cancer 45


title: Lung cancer 44


title: Lung cancer 41


title: Lung cancer 46


title: Lung cancer 40


title: Lung cancer 39


title: Lung cancer 36


title: Lung cancer 37


title: Lung cancer 35


title: Lung cancer 32


title: Lung cancer 30


title: Lung cancer 31


title: Lung cancer 29


title: Lung cancer 28


title: Lung cancer 26


title: Lung cancer 50


title: Lung cancer 27


title: Lung cancer 43


title: Lung cancer 25


title: Lung cancer 23


title: Lung cancer 24


title: Lung cancer 22


title: Lung cancer 21


title: Lung cancer 17


title: Lung cancer 20


title: Lung cancer 38


title: Lung cancer 15


title: Lung cancer 16


title: Lung cancer 14


title: Lung cancer 34


title: Lung cancer 13


title: Lung cancer 12


title: Lung cancer 11


title: Lung cancer 18


title: Lung cancer 9


title: Lung cancer 33


title: Lung cancer 10


title: Lung cancer 7


title: Lung cancer 6


title: Lung cancer 8


title: Lung cancer 4


title: Lung cancer 5


title: Lung cancer 2


title: Lung cancer 42


title: Lung cancer 1


title: Glioblastoma multiformae 26

source_name: Glioblastoma multiformae

value: Glioblastoma multiformae


title: Glioblastoma multiformae 25


title: Glioblastoma multiformae 27


title: Lung cancer 19


title: Glioblastoma multiformae 24


title: Glioblastoma multiformae 23


title: Glioblastoma multiformae 22


title: Glioblastoma multiformae 21


title: Glioblastoma multiformae 20


title: Glioblastoma multiformae 19


title: Glioblastoma multiformae 17


title: Glioblastoma multiformae 16


title: Glioblastoma multiformae 18


title: Glioblastoma multiformae 15


title: Glioblastoma multiformae 14


title: Glioblastoma multiformae 13


title: Glioblastoma multiformae 10


title: Glioblastoma multiformae 9


title: Glioblastoma multiformae 8


title: Glioblastoma multiformae 12


title: Glioblastoma multiformae 7


title: Lung cancer 3


title: Glioblastoma multiformae 6


title: Glioblastoma multiformae 5


title: Glioblastoma multiformae 3


title: Glioblastoma multiformae 1


title: Breast cancer stage IVa 41

source_name: Breast cancer stage IVa

value: Breast cancer stage IVa


title: Glioblastoma multiformae 2


title: Breast cancer stage IVa 40


title: Glioblastoma multiformae 4


title: Breast cancer stage IVa 39


title: Breast cancer stage IVa 42


title: Breast cancer stage IVa 36


title: Breast cancer stage IVa 38


title: Breast cancer stage IVa 37


title: Breast cancer stage IVa 34


title: Breast cancer stage IVa 33


title: Breast cancer stage IVa 32


title: Breast cancer stage IVa 31


title: Breast cancer stage IVa 30


title: Breast cancer stage IVa 29


title: Breast cancer stage IVa 28


title: Glioblastoma multiformae 11


title: Lung cancer 91


title: Breast cancer stage IVa 25


title: Breast cancer stage IVa 24


title: Breast cancer stage IVa 27


title: Breast cancer stage IVa 21


title: Breast cancer stage IVa 23


title: Breast cancer stage IVa 22


title: Breast cancer stage IVa 20


title: Breast cancer stage IVa 19


title: Breast cancer stage IVa 16


title: Breast cancer stage IVa 17


title: Breast cancer stage IVa 18


title: Breast cancer stage IVa 15


title: Breast cancer stage IVa 14


title: Breast cancer stage IVa 13


title: Breast cancer stage IVa 10


title: Breast cancer stage IVa 11


title: Breast cancer stage IVa 8


title: Breast cancer stage IVa 12


title: Breast cancer stage IVa 35


title: Breast cancer stage IVa 6


title: Breast cancer stage IVa 5


title: Breast cancer stage IVa 7


title: Breast cancer stage IVa 3


title: Breast cancer stage IVa 4


title: Breast cancer 141

source_name: Breast cancer

value: Breast cancer


title: Breast cancer stage IVa 2


title: Breast cancer 140


title: Breast cancer stage IVa 1


title: Breast cancer 139


title: Breast cancer 138


title: Breast cancer stage IVa 26


title: Breast cancer 135


title: Breast cancer 136


title: Breast cancer 137


title: Breast cancer 132


title: Breast cancer 133


title: Breast cancer 131


title: Breast cancer 128


title: Breast cancer 130


title: Breast cancer 129


title: Breast cancer stage IVa 9


title: Breast cancer 126


title: Breast cancer 125


title: Breast cancer 124


title: Breast cancer 122


title: Breast cancer 123


title: Breast cancer 120


title: Breast cancer 119


title: Breast cancer 118


title: Breast cancer 117


title: Breast cancer 121


title: Breast cancer 115


title: Breast cancer 113


title: Breast cancer 110


title: Breast cancer 112


title: Breast cancer 114


title: Breast cancer 116


title: Breast cancer 111


title: Breast cancer 107


title: Breast cancer 134


title: Breast cancer 109


title: Breast cancer 127


title: Breast cancer 104


title: Breast cancer 105


title: Breast cancer 103


title: Pancreatic cancer - train20

source_name: Pancreatic cancer (Site 2)


title: Breast cancer 108


title: Breast cancer 99


title: Breast cancer 102


title: Breast cancer 101


title: Pancreatic cancer - train19

source_name: Pancreatic cancer (Site 1)


title: Pancreatic cancer - train18


title: Pancreatic cancer - train17


title: Breast cancer 98


title: Pancreatic cancer - train16


title: Breast cancer 97


title: Pancreatic cancer - train15

source_name: Pancreatic cancer (Site 3)


title: Breast cancer 95


title: Pancreatic cancer - train14


title: Breast cancer 94


title: Breast cancer 93


title: Pancreatic cancer - train13


title: Breast cancer 106


title: Breast cancer 92


title: Breast cancer 91


title: Breast cancer 100


title: Pancreatic cancer - train10


title: Breast cancer 90


title: Pancreatic cancer - train11


title: Breast cancer 89


title: Pancreatic cancer - train9


title: Pancreatic cancer - train8


title: Breast cancer 87


title: Pancreatic cancer - train6


title: Pancreatic cancer - train5


title: Breast cancer 86


title: Breast cancer 88


title: Breast cancer 96


title: Pancreatic cancer - train3


title: Pancreatic cancer - train4


title: Breast cancer 83


title: Breast cancer 85


title: Pancreatic cancer - train2


title: Pancreatic cancer - train1


title: Breast cancer 82


title: Pancreatic cancer - train12


title: Breast cancer 81


title: Multiple myeloma - train20

source_name: Multiple myeloma (Site 1)


title: Breast cancer 80


title: Multiple myeloma - train19


title: Multiple myeloma - train18


title: Breast cancer 78


title: Breast cancer 79


title: Multiple myeloma - train17


title: Multiple myeloma - train16


title: Lung cancer 55


title: Pancreatic cancer - train7


title: Breast cancer 77


title: Multiple myeloma - train15


title: Multiple myeloma - train13


title: Breast cancer 84


title: Breast cancer 73


title: Multiple myeloma - train12


title: Breast cancer 72


title: Multiple myeloma - train10


title: Breast cancer 71


title: Breast cancer 70


title: Multiple myeloma - train11


title: Breast cancer 69


title: Multiple myeloma - train9


title: Multiple myeloma - train8


title: Breast cancer 68


title: Multiple myeloma - train7


title: Breast cancer 67


title: Breast cancer 66


title: Multiple myeloma - train6


title: Breast cancer 65


title: Breast cancer 64


title: Breast cancer 63


title: Multiple myeloma - train5


title: Breast cancer 76


title: Multiple myeloma - train3


title: Breast cancer 75


title: Multiple myeloma - train2


title: Multiple myeloma - train14


title: Multiple myeloma - train4


title: Multiple myeloma - train1


title: Breast cancer 61


title: Breast cancer 74


title: Breast cancer 60


title: Breast cancer 62


title: Healthy control - train19

source_name: Healthy control (Site 3)

value: Healthy control


title: Healthy control - train20


title: Healthy control - train17

source_name: Healthy control (Site 4)


title: Breast cancer 57


title: Breast cancer 59


title: Healthy control - train18

source_name: Healthy control (Site 1)


title: Breast cancer 56


title: Breast cancer 55


title: Healthy control - train16


title: Healthy control - train14

source_name: Healthy control (Site 2)


title: Healthy control - train13


title: Breast cancer 54


title: Breast cancer 53


title: Breast cancer 52


title: Healthy control - train12


title: Breast cancer 51


title: Breast cancer 50


title: Healthy control - train11


title: Healthy control - train9


title: Breast cancer 49


title: Healthy control - train8


title: Healthy control - train10


title: Healthy control - train5


title: Breast cancer 47


title: Healthy control - train6


title: Breast cancer 58


title: Breast cancer 45


title: Breast cancer 46


title: Breast cancer 43


title: Breast cancer 44


title: Healthy control - train15


title: Healthy control - train4


title: Healthy control - train2


title: Healthy control - train1


title: Breast cancer 41


title: Esophageal cancer - train20

source_name: Esophageal cancer (Adenocarcinoma only)

value: Esophageal cancer


title: Breast cancer 40


title: Breast cancer 38


title: Esophageal cancer - train18


title: Breast cancer 48


title: Breast cancer 37


title: Esophageal cancer - train17


title: Esophageal cancer - train16


title: Breast cancer 36


title: Healthy control - train7


title: Esophageal cancer - train15


title: Breast cancer 35


title: Esophageal cancer - train14


title: Healthy control - train3


title: Breast cancer 33


title: Esophageal cancer - train12


title: Breast cancer 34


title: Esophageal cancer - train13


title: Esophageal cancer - train11


title: Breast cancer 32


title: Breast cancer 31


title: Breast cancer 42


title: Esophageal cancer - train8


title: Breast cancer 29


title: Esophageal cancer - train9


title: Breast cancer 30


title: Breast cancer 28


title: Esophageal cancer - train10


title: Breast cancer 39


title: Esophageal cancer - train7


title: Breast cancer 27


title: Esophageal cancer - train19


title: Breast cancer 26


title: Esophageal cancer - train6


title: Esophageal cancer - train5


title: Breast cancer 23


title: Esophageal cancer - train2


title: Breast cancer 24


title: Esophageal cancer - train1


title: Esophageal cancer - train3


title: Esophageal cancer - train4


title: Breast cancer 22


title: Breast cancer - train19

source_name: Breast cancer (Stage IIIa site 3)


title: Breast cancer - train20

source_name: Breast cancer (Stage II site 2)


title: Breast cancer 21


title: Breast cancer 20


title: Breast cancer - train18

source_name: Breast cancer (Stage III site 1)


title: Breast cancer 18


title: Breast cancer - train17


title: Breast cancer - train15


title: Breast cancer - train14


title: Breast cancer - train16


title: Breast cancer 17


title: Breast cancer 14


title: Breast cancer - train13


title: Breast cancer 13


title: Breast cancer - train12

source_name: Breast cancer (Stage IIIa site 1)


title: Breast cancer 15


title: Breast cancer 25


title: Breast cancer 12


title: Breast cancer - train10


title: Breast cancer - train11


title: Breast cancer 11


title: Breast cancer - train9


title: Breast cancer 9


title: Breast cancer 10


title: Breast cancer 8


title: Breast cancer 19


title: Breast cancer - train8


title: Breast cancer 7


title: Breast cancer - train7


title: Breast cancer - train5


title: Breast cancer 6


title: Breast cancer 5


title: Breast cancer - train6


title: Breast cancer 4


title: Breast cancer - train3


title: Breast cancer 16


title: Breast cancer 3


title: Breast cancer - train2


title: Breast cancer 2


title: Brain cancer - train20

source_name: Brain cancer (Glioblastoma multiformae site 1)

value: Brain cancer


title: Breast cancer 1


title: Breast cancer - train1


title: Brain cancer - train19


title: Astrocytoma 165

source_name: Astrocytoma

value: Astrocytoma


title: Astrocytoma 166


title: Astrocytoma 164


title: Brain cancer - train18


title: Brain cancer - train16


title: Brain cancer - train17


title: Brain cancer - train15


title: Astrocytoma 161


title: Brain cancer - train13


title: Astrocytoma 162


title: Astrocytoma 159


title: Brain cancer - train14


title: Astrocytoma 160


title: Breast cancer - train4


title: Brain cancer - train12


title: Astrocytoma 158


title: Brain cancer - train11


title: Astrocytoma 156


title: Astrocytoma 157


title: Brain cancer - train8


title: Astrocytoma 153


title: Brain cancer - train7


title: Brain cancer - train9


title: Astrocytoma 152


title: Brain cancer - train5


title: Brain cancer - train4


title: Astrocytoma 151


title: Astrocytoma 150


title: Astrocytoma 163


title: Brain cancer - train3


title: Astrocytoma 149


title: Brain cancer - train10


title: Brain cancer - train2


title: Astrocytoma 155


title: Astrocytoma 148


title: Pancreatic cancer - test20

value: Pancreatic cancer


title: Astrocytoma 146


title: Astrocytoma 147


title: Astrocytoma 144


title: Pancreatic cancer - test17


title: Pancreatic cancer - test18


title: Pancreatic cancer - test19


title: Pancreatic cancer - test16


title: Astrocytoma 143


title: Astrocytoma 145


title: Brain cancer - train1


title: Astrocytoma 142


title: Astrocytoma 141


title: Pancreatic cancer - test15


title: Pancreatic cancer - test14


title: Astrocytoma 154


title: Astrocytoma 140


title: Pancreatic cancer - test13


title: Astrocytoma 139


title: Astrocytoma 138


title: Pancreatic cancer - test11


title: Pancreatic cancer - test10


title: Astrocytoma 137


title: Astrocytoma 136


title: Astrocytoma 135


title: Pancreatic cancer - test9


title: Pancreatic cancer - test8


title: Astrocytoma 134


title: Astrocytoma 133


title: Astrocytoma 132


title: Pancreatic cancer - test5


title: Pancreatic cancer - test7


title: Astrocytoma 131


title: Pancreatic cancer - test6


title: Pancreatic cancer - test2


title: Astrocytoma 128


title: Astrocytoma 129


title: Pancreatic cancer - test3


title: Pancreatic cancer - test4


title: Pancreatic cancer - test1


title: Multiple myeloma - test20


title: Astrocytoma 127


title: Astrocytoma 126


title: Pancreatic cancer - test12


title: Astrocytoma 125


title: Multiple myeloma - test19


title: Multiple myeloma - test18


title: Astrocytoma 124


title: Multiple myeloma - test17


title: Astrocytoma 123


title: Multiple myeloma - test16


title: Astrocytoma 121


title: Multiple myeloma - test15


title: Astrocytoma 122


title: Multiple myeloma - test14


title: Astrocytoma 120


title: Astrocytoma 130


title: Multiple myeloma - test13


title: Multiple myeloma - test11


title: Astrocytoma 117


title: Multiple myeloma - test12


title: Astrocytoma 118


title: Multiple myeloma - test10


title: Astrocytoma 116


title: Multiple myeloma - test9


title: Multiple myeloma - test8


title: Multiple myeloma - test7


title: Astrocytoma 114


title: Astrocytoma 113


title: Astrocytoma 115


title: Multiple myeloma - test6


title: Astrocytoma 112


title: Astrocytoma 111


title: Astrocytoma 110


title: Multiple myeloma - test5


title: Astrocytoma 109


title: Multiple myeloma - test2


title: Multiple myeloma - test3


title: Healthy control - test20


title: Astrocytoma 106


title: Multiple myeloma - test1


title: Healthy control - test19


title: Astrocytoma 119


title: Astrocytoma 105


title: Healthy control - test18


title: Healthy control - test16


title: Astrocytoma 102


title: Healthy control - test15


title: Astrocytoma 103


title: Astrocytoma 100


title: Healthy control - test12


title: Healthy control - test17


title: Astrocytoma 101


title: Multiple myeloma - test4


title: Astrocytoma 99


title: Astrocytoma 96


title: Astrocytoma 98


title: Astrocytoma 104


title: Healthy control - test13


title: Astrocytoma 107


title: Astrocytoma 97


title: Astrocytoma 108


title: Healthy control - test9


title: Healthy control - test8


title: Astrocytoma 95


title: Healthy control - test7


title: Healthy control - test6


title: Astrocytoma 93


title: Brain cancer - train6


title: Healthy control - test5


title: Astrocytoma 92


title: Healthy control - test10


title: Astrocytoma 91


title: Astrocytoma 90


title: Healthy control - test14


title: Healthy control - test4


title: Healthy control - test11


title: Healthy control - test2


title: Astrocytoma 88


title: Astrocytoma 89


title: Healthy control - test1


title: Astrocytoma 85


title: Esophageal cancer - test20


title: Esophageal cancer - test19


title: Astrocytoma 86


title: Astrocytoma 87


title: Astrocytoma 94


title: Esophageal cancer - test17


title: Astrocytoma 83


title: Astrocytoma 84


title: Astrocytoma 82


title: Esophageal cancer - test15


title: Esophageal cancer - test16


title: Astrocytoma 80


title: Astrocytoma 81


title: Astrocytoma 79


title: Healthy control - test3


title: Astrocytoma 78


title: Astrocytoma 77


title: Esophageal cancer - test13


title: Astrocytoma 76


title: Astrocytoma 74


title: Astrocytoma 75


title: Esophageal cancer - test12


title: Esophageal cancer - test18


title: Astrocytoma 72


title: Astrocytoma 71


title: Astrocytoma 70


title: Astrocytoma 69


title: Astrocytoma 67


title: Esophageal cancer - test10


title: Astrocytoma 68


title: Esophageal cancer - test14


title: Esophageal cancer - test8


title: Esophageal cancer - test9


title: Astrocytoma 66


title: Astrocytoma 65


title: Esophageal cancer - test7


title: Astrocytoma 64


title: Esophageal cancer - test11


title: Astrocytoma 73


title: Astrocytoma 63


title: Astrocytoma 62


title: Esophageal cancer - test6


title: Astrocytoma 61


title: Esophageal cancer - test5


title: Esophageal cancer - test4


title: Astrocytoma 59


title: Esophageal cancer - test3


title: Astrocytoma 58


title: Astrocytoma 56


title: Astrocytoma 55


title: Esophageal cancer - test2


title: dry dormant biological rep3

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

institute: University of Manitoba

description: mRNA oxidation data from dry dormant seeds, before imbibition.

hyb_protocol: Following fragmentation, labelled cRNA samples were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix Scanner 3000.

data_processing: The data were analyzed with Robust Multi-array Average methodology (RMA).

organism: Triticum aestivum

source_name: dry dormant seeds

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT Labelling Kit and the GeneChip Sample Cleanup Module

growth_protocol: Wheat plants were grown in a greenhouse at 18-22oC/14-18oC (day/night) under a 16/8 h photoperiod until harvest. Spikes were harvested at maturity.

extract_protocol: Oxidized mRNA isolation using immunostaining with 8-hydroxydeoxyguanosine (OHdG) monoclonal antibody.

treatment_protocol: One-half of the seeds were stored at -80oC to retain dormancy.To obtain AR seeds, the remaining portion of the seeds was stored at room temperature for 10 months.

value: seed

value: AC Domain

value: mature


title: dry after-ripened biological rep3

description: mRNA oxidation data from dry after-ripened seeds, before imbibition.

source_name: dry after-ripened seeds


title: dry dormant biological rep1


title: dry after-ripened biological rep1


title: Astrocytoma 54


title: Harmonic blade replicate 3

city: Mississippi state

first: Bindu

last: Nanduri

address: Box 6100 Spring Street

department: Basic Sciences

description: Abdominal incision by harmonic blade followed by sample collection by scalpel

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000-7G and the GeneChip Operating Software (GCOS)

data_processing: The data were analyzed with Affymetrix Expression Console. RMA normalization was applied to log-transformed signal intensities

label: Biotin

organism: Sus scrofa

source_name: subcutaneous fatty tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  5 µg total RNA

growth_protocol: Two female pigs weighing 40-55 kg were used

extract_protocol: Total RNA was isolated from 100 mg of tissue using RNeasy Lipid Tissue Mini Kit (Qiagen). Quality of Isolated RNA was measured using Bioanalyzer and RNA with high integrity (RIN > 8.0; 28S/18S > 2.0) and concentration (> 800 ng/μL) was used in microarray experiments

treatment_protocol: Each animal had four 4-cm midline caudal abdominal incisions created with either Electrocautery Pencil, ConMed, Utica NY or HARMONIC® Blade (HK105, Ethicon Endo-Surgery, Cincinnati OH). Each animal had two HB incisions and two ES incisions for a total of 8 incisions.Each incision was started with a scalpel blade through the skin (epidermis and dermis), and then deepened through the subcutaneous tissues down to the linea alba using either HB at power level 5 for cutting tissue and power level 3 for coagulating bleeders, or ES set at 40 Watts for cutting and Blend 2/Spray for coagulation. The linea alba was not incised. After three days, incision sites were surgically removed using a cold steel scalpel en bloc from the abdominal wall from anesthetized animals. The tissue block was sliced perpendicular to the surgically incision to create slabs 4-6 mm thick. The slab was trimmed to remove the skin from the top and muscle from the bottom of the sample. The side walls were trimmed to approximately 4 mm from the surgical incision leaving a rectangular block of subcutaneous fatty tissue. Four to six samples were taken from each incision for RNA isolation and stored in sterile DNAse-, RNAse-, protein-free Eppendorf tubes, flash frozen in liquid nitrogen, held on dry ice throughout tissue collection, and then stored at -80˚ C. Animals were then euthanized

value: subcutaneous fatty tissue


title: dry after-ripened biological rep2


title: Harmonic blade replicate 2

value: Abdominal incision by harmonic blade followed by sample collection by scalpel


title: Astrocytoma 60


title: Astrocytoma 57


title: Astrocytoma 52


title: Breast cancer - test20


title: Harmonic blade replicate 4


title: Breast cancer - test19


title: Astrocytoma 51


title: Astrocytoma 53


title: dry dormant biological rep2


title: Esophageal cancer - test1


title: Breast cancer - test18


title: Harmonic blade replicate 1


title: Astrocytoma 50


title: Astrocytoma 49


title: Electrosurgery replicate 2

description: Abdominal incision by electrosurgery followed by sample collection by scalpel


title: Breast cancer - test17


title: Electrosurgery replicate 4

value: Abdominal incision by electrosurgery followed by sample collection by scalpel


title: Electrosurgery replicate 1


title: Breast cancer - test16


title: Astrocytoma 48


title: Electrosurgery replicate 3


title: Astrocytoma 47


title: Breast cancer - test15

source_name: Breast cancer (Stage IIIa, b site 1)


title: Breast cancer - test14


title: Astrocytoma 46


title: Control replicate 4

description: Sample collection using scalpel

value: Sample collection using scalpel


title: Astrocytoma 45


title: Breast cancer - test13

source_name: Breast cancer (Stage III, site 1)


title: Astrocytoma 44


title: Control replicate 3

description: Sample collection using scalpel


title: Control replicate 1

description: Sample collection using scalpel


title: Astrocytoma 43


title: Control replicate 2

description: Sample collection using scalpel


title: Breast cancer - test11