title: OV03-01_Om_S04

description:
A594-006
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample Om_S04

value: omentum


title: Poly(allylamine hydrochloride)/lipid Au NP treated PC3 cells sample 3

status: Public on Oct 01 2014

type: RNA

city: Urbana

first: Elissa

middle: M

last: Grzincic

state: Illinois

address: A510 Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave.

department: Chemistry

country: USA

institute: University of Illinois at Urbana-Champaign

description:
Gene expression data from human prostate carcinoma exposed to poly(allylamine hydrochloride)/lipid-coated gold nanoparticles
raw data file: slide1_D.gpr

hyb_protocol: Samples were hybridized in an Agilent Hybridization Cassette according to standard protocols.

scan_protocol: Scanned on an Axon GenePix 4000B scanner; Images were quantified using Axon GenePix 6.1.

data_processing: Median foreground intensites (no background subtraction) were normalized in R (version 3.0.1) using the quantile method in limma (version 3.16.7) for a separate channel analysis . Spots with -100 flags were weighted zero before normalization.

molecule: total RNA

organism: Homo sapiens

source_name: PC3, PAHL, sample 3

label_protocol: 0.2 microgram of total RNA was labeled using the Agilent two color QuickAmp labeling kit according to the manufacturers protocol. The optional spike-in controls were not used.

growth_protocol: Standard mammalian cell culture methods

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

treatment_protocol: Cells were plated to confluency and then exposed to media containing no nanoparticles (untreated), or 20 nm gold nanoparticles surface-coated with citrate (CIT), alkanethiol/lipid (ATL, where C18SH covers the nanoparticle surface and forms a bilayer with 1:1 (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine: 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine) lipid solution), poly(allylamine hydrochloride) (PAH), or poly(allylamine hydrochloride)/lipid (PAHL, where the particle is coated with PAH first, followed by the formation of a 1:1 lipid bilayer on top of the PAH). HDF cells were treated with media containing 0.1 nM nanoparticles for 24-48 hours, and PC3 cells were treated with media containing 1 nM nanoparticles for 24-48 hours.

tag: cell type

value: human prostate carcinoma cells

tag: cell line

tag: treatment

value: 1 nM poly(allylamine hydrochloride)/lipid-coated 20 nm gold nanoparticles


title: OV03-01_Om_S03

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description:
A594-005
Hybridised to SNP 6.0 array.

hyb_protocol: Hybridisation was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

scan_protocol: Scanning was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

data_processing: Data was processed using PICNIC using the 'primary' option.

label: Biotin

molecule: genomic DNA

source_name: Ovarian cancer patient OV03-01, sample Om_S03

label_protocol: Labelling was performed by AROS Applied Biotechnology (Aarhus, Denmark) following the manufacturer's protocol.

extract_protocol: Samples were placed immediately into RNAlater at the time of collection. DNA extraction was performed using the Qiagen DNeasy Blood and Tissue Kit according to the manufacturer's instructions.

tag: study id

tag: sample id

tag: disease

value: ovarian cancer

tag: tissue

tag: timepoint

value: interval debulking surgery

tag: response to treatment

value: partial response

tag: progression-free survival (months)


title: HK_Vaccinated_Mock Challenged_3

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: This sample is collected at 25-29hrs post challenge (3 weeks post vaccination)

hyb_protocol: Equal amounts of labeled target sample cRNA (600 ng) samples were hybridized to each individual array. Microarray hybridization conditions and washing procedures were performed as described in Agilent Gene Analysis protocols (One Color Microarray-Based Gene Expression Analysis, Version 6.5).

scan_protocol: Microarray slides were scanned using Profile AgilentG3_GX_1Color and the scan data were extracted using Agilent Feature Extraction Software.

data_processing: Partek® Genomic Suite (v6.6) was used to generate the matrix table. gProcessedSignal data were quantile normalized and log2 transformed.

organism: Lates calcarifer

source_name: Head kidney, Vaccinated and Mock challenged

label_protocol: All microarray was carried out on Agilent SurePrint G3 custom gene expression 8X60K oligonucleotide array (Cat No. G4102A).Total RNA (100 ng) was reverse transcribed and labeled using Agilent Low Input Quick Amp One Color labeling kit (Cat No. 5190-2305) according to the manufacturer’s instructions. cRNA samples were labeled with cyanine 3-CTP and the amount of cyanine 3-labeled cRNA was determined using NanoDrop. Only labeled cRNA samples with cRNA yields > 0.825 µg and specific activity > 6 pmol Cy3 per µg cRNA were selected for hybridization.

extract_protocol: Total RNA was extracted from spleen and head kidney tissues using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quantity and quality was determined using spectrophotometer (NanoDrop) and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively. Only RNA samples with RIN number >8 were used for microarray analysis.

treatment_protocol: One group of juvenile seabass was vaccinated against Streptococcus iniae via peritoneal injection (from here on termed “vaccinated”) of Norvax® Strep Si (Merck Animal Health) while another group was mocked vaccinated (from here on termed “control”). Subsequently, at Day 1 and Day 7 post vaccination (dpv), fifteen seabass were sacrificed at each time point and from each group for spleen and head kidney collection. At 21 dpv, S.iniae challenge was carried out. Within the vaccinated and control groups, about 50 seabass were challenged with live pathogen via peritoneal injection (S. iniae suspended in LB broth) while 25 seabass were mock challenged.

value: Head kidney

tag: time

value: Not applicable

value: Streptococcus iniae vaccine

tag: pathogen challenge

value: Mock challenged


title: Untreated PC3 cells sample 1

description:
Gene expression data from human prostate carcinoma cells
raw data file: slide2_C.gpr

source_name: PC3, control, sample 1

value: untreated


title: Citrate Au NP treated HDF cells sample 2

description:
Gene expression data from human dermal fibroblasts exposed to citrate-capped gold nanoparticles
raw data file: slide2_A.gpr

source_name: HDF, CIT, sample 2

value: human dermal fibroblasts

value: HDF

value: 0.1 nM citrate-capped 20 nm gold nanoparticles


title: Poly(allylamine hydrochloride)/lipid Au NP treated PC3 cells sample 1

description:
Gene expression data from human prostate carcinoma exposed to poly(allylamine hydrochloride)/lipid-coated gold nanoparticles
raw data file: slide2_B.gpr

source_name: PC3, PAHL, sample 1


title: Citrate Au NP treated HDF cells sample 1

description:
Gene expression data from human dermal fibroblasts exposed to citrate-capped gold nanoparticles
raw data file: slide1_D.gpr

source_name: HDF, CIT, sample 1


title: Citrate Au NP treated PC3 cells sample 2

description:
Gene expression data from human prostate carcinoma cells exposed to citrate-capped gold nanoparticles
raw data file: slide2_A.gpr

source_name: PC3, CIT, sample 2

value: 1 nM citrate-capped 20 nm gold nanoparticles


title: HK_Vaccinated_Challenged_5

source_name: Head kidney, Vaccinated and Challenged

value: Challenged


title: OV03-04_Om_S01

description:
A594-003
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S01

value: stable disease


title: OV03-04_Om_S02

description:
A594-004
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-04, sample Om_S02

value: omentum


title: HK_Vaccinated_Mock Challenged_4


title: HK_Vaccinated_Challenged_2


title: HK_Vaccinated_Mock Challenged_5


title: HK_Vaccinated_Challenged_4


title: HK_Vaccinated_Mock Challenged_1(2)


title: Poly(allylamine hydrochloride) Au NP treated PC3 cells sample 1

description:
Gene expression data from human prostate carcinoma exposed to poly(allylamine hydrochloride)-wrapped gold nanoparticles
raw data file: slide1_C.gpr

source_name: PC3, PAH, sample 1

value: human prostate carcinoma cells

value: 1 nM poly(allylamine hydrochloride)-wrapped 20 nm gold nanoparticles


title: HK_Vaccinated_Challenged_1


title: Poly(allylamine hydrochloride) Au NP treated HDF cells sample 2

description:
Gene expression data from human dermal fibroblasts exposed to poly(allylamine hydrochloride)-wrapped gold nanoparticles
raw data file: slide2_C.gpr

source_name: HDF, PAH, sample 2

value: 0.1 nM poly(allylamine hydrochloride)-wrapped 20 nm gold nanoparticles


title: Alkanethiol/lipid Au NP treated PC3 cells sample 1

description:
Gene expression data from human prostate carcinoma cells exposed to alkanethiol/lipid-coated gold nanoparticles
raw data file: slide1_A.gpr

source_name: PC3, ATL, sample 1

value: 1 nM alkanethiol/lipid-coated 20 nm gold nanoparticles


title: HK_Unvaccinated_Mock Challenged_3

source_name: Head kidney, Unvaccinated and Mock challenged

value: Unvaccinated


title: Gastric cancer 3

city: Shanghai

first: jingyuan

last: fang

address: 145 Shandong Rd Middle

country: China

institute: Shanghai Institute of Digestive Disease

description: gastric tissue

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing:
Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 12.0 software.
Further data analysis was performed using Agilent GeneSpring GX 12.0 software. Results were provided in the Gene Expression Profiling Data.xls file and Data Analysis Folder.

source_name: Cancer 3

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling

extract_protocol: Integrity and concentration of RNA was assessed after RNA extraction and prior to sample labeling. Results were provided in the RNA_QC.pdf file

value: gastric cancer tumor


title: HK_Unvaccinated_Mock Challenged_1(2)

value: Head kidney

value: Not applicable


title: Gastric cancer 2

description: gastric tissue

source_name: Cancer 2


title: HK_Unvaccinated_Mock Challenged_4

value: Mock challenged


title: diclofenac_array_6

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 - 15 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizion (MAANOVA) was done.

organism: Folsomia candida

source_name: whole animal

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container; containing a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

value: Diclofenac

tag: concentration

value: whole animal

value: LUFA2.2 control

tag: control

value: control


title: HK_Unvaccinated_Mock Challenged_2


title: Gastric cancer 1

description: gastric tissue

source_name: Cancer 1


title: diclofenac_array_7


title: Normal 3

description: gastric tissue

source_name: Normal 3

value: normal gastric


title: diclofenac_array_4


title: Hod_High_Sulfur_Pool

first: Daiyin

last: Chao

address: 300 Fenglin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences

description: The high sulfur and selenium pool  from the F2s segregating from a HodxCol-0 cross used for eXtreme Array Mapping.

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: The signal intensity difference between the two pools for all probes were analyzed using R scripts that are available at http://ars.usda.gov/mwa/bsasnp .

label: biotin

organism: Arabidopsis thaliana

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

tag: age

value: ~6 weeks

value: Leaves

tag: genotype

tag: genetic background


title: diclofenac_array_8


title: Hod-low-Sulfur_Pool

description: The low sulfur and selenium pool  from the F2s segregating from a HodxCol-0 cross used for eXtreme Array Mapping.


title: Normal 1

description: gastric tissue

source_name: Normal 1


title: OV03-01_Om_S05

description:
A594-009
Hybridised to SNP 6.0 array.

source_name: Ovarian cancer patient OV03-01, sample Om_S05

value: ovarian cancer

value: omentum

value: interval debulking surgery

value: partial response


title: Untreated HDF cells sample 1

description:
Gene expression data from human dermal fibroblasts
raw data file: slide1_A.gpr

source_name: HDF, control, sample 1

tag: cell type

value: human dermal fibroblasts

value: HDF

value: untreated


title: HK_Unvaccinated_Challenged_8

source_name: Head kidney, Unvaccinated and Challenged

value: Head kidney

value: Unvaccinated

value: Challenged


title: HK_Unvaccinated_Challenged_7

value: Not applicable


title: diclofenac_array_5

value: Diclofenac

value: whole animal


title: HK_Unvaccinated_Challenged_9


title: diclofenac_array_3

value: LUFA2.2 control

value: control


title: IL-17A 1

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

country: Germany

institute: Rottal-Inn Kliniken KU

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing:
The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5    The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5    The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5
As test for significance the student’s t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction was applied to the complete set of p-values of all ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

source_name: monocyte-derived macrophages

label_protocol: The laboratory work was done in the Genomics and Proteomics Core Facility at the German Cancer Research Center, Heidelberg, Germany (DKFZ). Biotin-labeled cRNA samples for hybridization on Illumina Mouse Sentrix-6 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 100 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies).  Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: Human monocyte-derived macrophages were generated as described previously (Gleissner at al., Arterioscler Thromb Vasc Biol 2008)

extract_protocol: After 6 days for macrophage differentiation, RNA was isolated from macrophages using columns including a DNAse-step followed by reverse transcription (all reagents from Qiagen).

treatment_protocol: For macrophage polarization, monocyte derived macrophages were stimulated with 10ng/mL IL-17A for 18h. Unstimulated macrophages served as control. After 18h RNA was isolated from macrophages using columns including a DNAse-step followed by reverse transcription. RNA was labeled and hybridized to Illumina expression profiling for whole genome BeadChipSentrix array (kindly provided by Hudler, German Cancer Research Center). For blood withdrawal, patients gave written consent, and the study was approved by the local institutional ethics committee. To investigate the impact of IL-17A on macrophage differentiation, isolated monocytes were incubated either with 100ng/mL rhM-CSF or with 10ng/mL IL-17A or both for 6 days.

value: monocyte-derived macrophages

tag: stimulation status

value: stimulated


title: IL-17A 2


title: Control 2

value: unstimulated


title: HK_Unvaccinated_Challenged_2(2)

tag: treatment


title: Control 1


title: Normal 2

description: gastric tissue

source_name: Normal 2

value: normal gastric


title: diclofenac_array_2


title: diclofenac_array_1


title: HK_D7_Vaccinated_3(2)

source_name: Head kidney, Day 7 Vaccinated

value: Day 7 post vaccination

value: Streptococcus iniae vaccine


title: HK_D7_Vaccinated_2


title: HK_D7_Control_3

source_name: Head kidney, Day 7 Control (Unvaccinated)


title: HK_D7_Control_2


title: HK_D7_Control_1


title: HK_D1_Control_2

source_name: Head kidney, Day 1 Control (Unvaccinated)

value: Day 1 post vaccination


title: HK_D7_Vaccinated_1(2)


title: HK_D1_Vaccinated_3

source_name: Head kidney, Day 1 Vaccinated


title: HK_D1_Vaccinated_1


title: abi3-6  16 DAF Seed 3

city: Nagoya

first: Tsukaho

last: Hattori

state: Aichi Prefecture

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya Universtiy

description:
Biological replicate 3 of 3.
061122 abi3D16-3.CEL

hyb_protocol: 20 ug of labeled and fragmented cRNA was hybridized to GeneChip Arabidopsis ATH1 Genome Array using GeneChip Hybridization Oven 640 (Affymetrix). Wash and stain was performed by GeneChip Fluidics Station 450 (Affymetrix). All operations were performed with Hybridization, Stain and Wash Kit (Affymetrix) according to manufacturer's protocol (hws_kit_manual).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) controled by GCOS 1.4 (Affymetrix).

data_processing: The CEL files produced by GCOS 1.3 were analyzed using GCRMA package (ver.2.0.0) on the statistical software R.

source_name: abi3-6 mutant

label_protocol: Biotinylated cRNA were prepared from 2ug of total RNA using One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturers protocol.

growth_protocol: 16h light/8h dark, 22°C

extract_protocol: The total RNA was extracted using Concert Plant RNA Reagent (Invitrogen) and was followed by purification using RNeasy Mini Kit (Qiagen).

treatment_protocol: Developing seeds dissected from sliequs.

tag: genotype/variation

value: abi3-6 mutant

value: developing seeds dissected from sliques


title: wild-type (Col-0) 16 DAF Seed 1

description:
Biological replicate 1 of 3. Controls for abi3-6 examination.
061122 colD16-1.CEL

source_name: wild-type (Col-0)

value: wild-type (Col-0)


title: abi3-6  16 DAF Seed 1

description:
Biological replicate 1 of 3.
061122 abi3D16-1.CEL


title: HK_D1_Control_3

value: Head kidney

value: Unvaccinated


title: HK_D1_Vaccinated_2

value: Not applicable


title: wild-type (Col-0) 16 DAF Seed 3

description:
Biological replicate 3 of 3. Controls for abi3-6 examination.
061122 colD16-3.CEL


title: HK_D1_Control_1


title: wild-type (Col-0) 16 DAF Seed 2

description:
Biological replicate 2 of 3. Controls for abi3-6 examination.
061122 colD16-2.CEL


title: abi3-6  12 DAF Seed 3

description:
Biological replicate 3 of 3.
abiD12-3.CEL


title: abi3-6  16 DAF Seed 2

description:
Biological replicate 2 of 3.
061122 abi3D16-2.CEL


title: abi3-6  12 DAF Seed 2

description:
Biological replicate 2 of 3.
abiD12-2.CEL


title: SP_Vaccinated_Mock Challenged_2

description: This sample is collected at 25-29hrs post challenge (3 weeks post vaccination)

source_name: Spleen, Vaccinated and Mock challenged

value: Spleen

value: Mock challenged


title: SP_Vaccinated_Mock Challenged_3


title: abi3-6  12 DAF Seed 1

description:
Biological replicate 1 of 3.
abiD12-1.CEL


title: wild-type (Col-0) 12 DAF Seed 2-3

description:
Biological replicate 3 of 3. Controls for abi3-6 examination.
ColD12-3.CEL


title: SP_Vaccinated_Mock Challenged_4


title: SP_Vaccinated_Challenged_4

source_name: Spleen, Vaccinated and Challenged

value: Challenged


title: SP_Vaccinated_Challenged_3


title: lec2-1  12 DAF Seed 2

description:
Biological replicate 2 of 3.
lec2-12-2.CEL

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) controled by GCOS 1.3 (Affymetrix).

data_processing: The CEL files produced by GCOS 1.3 were analyzed using GCRMA package on the statistical software R.

source_name: lec2-1_12 DAF Seed

value: lec2-1 mutant


title: SP_Vaccinated_Challenged_2


title: wild-type (Col-0) 12 DAF Seed 2-2

description:
Biological replicate 2 of 3. Controls for abi3-6 examination.
ColD12-2.CEL


title: SP_Vaccinated_Challenged_1


title: lec2-1  12 DAF Seed 3

description:
Biological replicate 3 of 3.
lec2-12-3.CEL


title: lec2-1  12 DAF Seed 1

description:
Biological replicate 1 of 3.
lec2-12-1.CEL


title: SP_Unvaccinated_Mock Challenged_4

source_name: Spleen, Unvaccinated and Mock challenged


title: wild-type (Col-0) 12 DAF Seed 2-1

description:
Biological replicate 1 of 3. Controls for abi3-6 examination.
ColD12-1.CEL


title: F.pla_FG_rep2

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

description: F. placidus grown with 10 mM acetate and 100 mM Fe(III) oxide. Second biological replicate.

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, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Ferroglobus placidus

source_name: 10 mM acetate as electron donor and 100 mM Fe(III) oxide as acceptor

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

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with either 1 mM benzoate or 10 mM acetate as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85 C in the dark.

extract_protocol: Total RNA was extracted according to the HG protocol described in Holmes et al (in preparation)

treatment_protocol: Cultures (100 ml in 156 ml serum bottles) were divided into 50 ml conical tubes (Falcon), and cells were pelleted with centrifugation at 3,000 xg for 15 min. Pellets were then immediately frozen in liquid nitrogen and stored at –80 °C

tag: type of electron acceptor

value: insoluble Fe(III)-oxide

value: 10 mM acetate and 100 mM Fe(III) citrate


title: Poly(allylamine hydrochloride)/lipid Au NP treated HDF cells sample 3

description:
Gene expression data from human dermal fibroblasts exposed to poly(allylamine hydrochloride)/lipid-coated gold nanoparticles
raw data file: slide1_C.gpr

source_name: HDF, PAHL, sample 3

value: human dermal fibroblasts

tag: cell line

value: HDF

value: 0.1 nM poly(allylamine hydrochloride)/lipid-coated 20 nm gold nanoparticles


title: SP_Unvaccinated_Mock Challenged_3

tag: tissue


title: lec1-1  12 DAF Seed 2

description:
Biological replicate 2 of 3.
lec1-12-2.CEL

source_name: lec1-1_12 DAF Seed

value: lec1-1 mutant


title: SP_Unvaccinated_Mock Challenged_1


title: SP_Unvaccinated_Mock Challenged_2


title: lec1-1  12 DAF Seed 1

description:
Biological replicate 1 of 3.
lec1-12-1.CEL


title: lec1-1  12 DAF Seed 3

description:
Biological replicate 3 of 3.
lec1-12-3.CEL


title: Female CSF2 vs Control Rep. 3

city: Gainesville

first: Kyle

last: Dobbs

state: Florida

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

hyb_protocol: one Cy3 labeled DNA sample and  one Cy5 DNA sample were combined and hybridized to one area of a 2x444,000 Agilent EmbryoGene microarray slide.  635=Cy5 and 532=Cy3.

scan_protocol: Slides were scanned using a Agilent High-resolution C Scanner (Agilent Technologies, CA, USA) while features were extracted using Agilent's feature extraction software (Agilent)

data_processing: Raw data were normalized using within-array loess normalization followed by between-array quantile normalization. Normalized data were then fit to a linear model before being subjected to an empirical Bayes correction. Mean intensity of each spot on the array was transformed by log2 while p-values were determined using a moderated t-statistic (60).  Regions with an estimated absolute fold-change above 1.5 or below 0.67 and a p-value < 0.05 were considered as differentially methylated.

organism: Bos taurus

source_name: Day 15 EEM from Female CSF2 Rep. 3

label_protocol: DNA was labeled using the Universal Linkage System (ULS) by Kreatech for gene expression analysis. Microarray slides were made by Agilent and designed by EmbryoGene. ULS directly labels the aRNA through a non-enzymatic protocol which labels through the formation of a coordinate bond on the N7 position of guanine. The Cy3 and Cy5 are linked by a spacer to the ULS molecule.

growth_protocol: Fertilized embryos were grown in culture to Day 7 after fertilization and transferred into Holstein recipients. At Day 15, they were flushed from the recipient using DPBS/PVP

extract_protocol: DNA was extracted according to manufacturer's instructions using the Qiagen Allprep DNA/RNA mini kit

treatment_protocol: 10 ng/ml of CSF2 or Control (DPBS/BSA) from Day 5-7 post-insemination during in vitro culture of bovine embryos.

tag: embryo

value: Filamentous

value: whole embryo

source_name: Day 15 EEM from Female Control Rep. 3

value: control


title: wild-type (WS) 12 DAF Seed 3

description:
Biological replicate 3 of 3. Controls for lec1-1 and lec2-1 examination.
WS12-3.CEL

source_name: wild-type (WS)_12 DAF Seed

value: wild-type (WS)

value: developing seeds dissected from sliques


title: SP_Unvaccinated_Challenged_7

source_name: Spleen, Unvaccinated and Challenged

value: Unvaccinated


title: F.pla_FC_rep 1

description: F. placidus grown with 10 mM acetate and 50 mM Fe(III) citrate. First biological replicate.

source_name: 10 mM acetate as electron donor and 56 mM ferric citrate as acceptor

value: soluble Fe(III)-citrate

value: 10 mM acetate and 50 mM Fe(III) citrate


title: F.pla_FC_rep 2

description: F. placidus grown with 10 mM acetate and 50 mM Fe(III) citrate. Second biological replicate.


title: SP_Unvaccinated_Challenged_6

value: Spleen

value: Not applicable


title: wild-type (WS) 12 DAF Seed 1

description:
Biological replicate 1 of 3. Controls for lec1-1 and lec2-1 examination.
WS12-1.CEL


title: F.pla_FG_rep 1

description: F. placidus grown with 10 mM acetate and 100 mM Fe(III)-oxide. First biological replicate.


title: F.pla_phenylacetate_rep1

description: F. placidus grown with 1 mM phenylacetate. First biological replicate.

source_name: 1 mM phenylacetate as electron donor and 56 mM ferric citrate as acceptor

tag: type of electron donor

value: aromatic

value: 1 mM phenylacetate


title: lec2-1  8 DAF Seed 3

description:
Biological replicate 3 of 3.
lec2-8-3.CEL

source_name: lec2-1_8 DAF Seed

value: lec2-1 mutant


title: lec2-1  8 DAF Seed 2

description:
Biological replicate 2 of 3.
lec2-8-2.CEL


title: F.Pla_butyrate_rep2

description: F. placidus grown with 1 mM butyrate. Second biological replicate.

source_name: 1 mM butyrate as electron donor and 56 mM ferric citrate as acceptor

growth_protocol: Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with either 1 mM butyrate or 10 mM acetate as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85 C in the dark.

value: short chain fatty acid

value: 1 mM butyrate


title: Female CSF2 vs Control Rep. 2

source_name: Day 15 EEM from Female Control Rep. 2

source_name: Day 15 EEM from Female CSF2 Rep. 2


title: lec2-1  8 DAF Seed 1

description:
Biological replicate 1 of 3.
lec2-8-1.CEL


title: wild-type (WS) 12 DAF Seed 2

description:
Biological replicate 2 of 3. Controls for lec1-1 and lec2-1 examination.
WS12-2.CEL


title: SP_Unvaccinated_Challenged_2

description: This sample is collected at 25-29hrs post challenge (3 weeks post vaccination)

value: Challenged


title: SP_D7_Vaccinated_4

source_name: Spleen, Day 7 Vaccinated

value: Day 7 post vaccination

value: Streptococcus iniae vaccine


title: SP_D7_Vaccinated_3


title: F.Pla_phenylacetate_rep2

description: F. placidus grown with 1 mM phenylacetate. Second biological replicate.


title: F.Pla_butyrate_rep3

description: F. placidus grown with 1 mM butyrate. Third biological replicate.


title: SP_D7_Vaccinated_2


title: Female CSF2 vs Control Rep. 1

source_name: Day 15 EEM from Female CSF2 Rep. 1

value: Filamentous

value: whole embryo

source_name: Day 15 EEM from Female Control Rep. 1


title: F.pla_acetate_rep 3

description: F. placidus grown with 10 mM acetate. Third biological replicate.

value: short organic acid

value: 10 mM acetate


title: Male CSF2 vs Control Rep. 2

source_name: Day 15 EEM from Male Control Rep. 2

value: control

source_name: Day 15 EEM from Male CSF2 Rep. 2


title: Male CSF2 vs Control Rep. 1

source_name: Day 15 EEM from Male Control Rep. 1

source_name: Day 15 EEM from Male CSF2 Rep. 1


title: F.pla_butyrate_rep1

description: F. placidus grown with 1 mM butyrate. First biological replicate.


title: SP_D7_Control_6

source_name: Spleen, Day 7 Control (Unvaccinated)

value: Unvaccinated


title: lec1-1  8 DAF Seed 1

description:
Biological replicate 1 of 3.
lec1-8-1.CEL

source_name: lec1-1_8 DAF Seed

value: lec1-1 mutant

value: developing seeds dissected from sliques


title: lec1-1  8 DAF Seed 3

description:
Biological replicate 3 of 3.
lec1-8-3.CEL


title: lec1-1  8 DAF Seed 2

description:
Biological replicate 2 of 3.
lec1-8-2.CEL


title: wild-type (WS) 8 DAF Seed 3

description:
Biological replicate 3 of 3. Controls for lec1-1 and lec2-1 examination.
WS8-3.CEL

source_name: wild-type (WS)_8 DAF Seed

value: wild-type (WS)


title: SP_D7_Control_3

value: Spleen

value: Not applicable


title: F.pla_acetate_rep 2

description: F. placidus grown with 10 mM acetate. Second biological replicate.


title: SP_D1_Vaccinated_4

source_name: Spleen, Day 1 Vaccinated

value: Day 1 post vaccination


title: SP_D1_Vaccinated_3


title: SP_D1_Vaccinated_5


title: wild-type (WS) 8 DAF Seed 2

description:
Biological replicate 2 of 3. Controls for lec1-1 and lec2-1 examination.
WS8-2.CEL


title: SP_D7_Control_4


title: fus3-3  12 DAF Seed 3

description:
Biological replicate 3 of 3.
fus12-3.CEL

source_name: fus3-3_12 DAF Seed

value: fus3-3 mutant


title: fus3-3  12 DAF Seed 2

description:
Biological replicate 2 of 3.
fus12-2.CEL


title: F.pla_acetate_rep 1

description: F. placidus grown with 10 mM acetate. First biological replicate.

source_name: 10 mM acetate as electron donor and 56 mM ferric citrate as acceptor


title: SP_D1_Control_5

source_name: Spleen, Day 1 Control (Unvaccinated)


title: SP_D1_Control_2


title: fus3-3  12 DAF Seed 1

description:
Biological replicate 1 of 3.
fus12-1.CEL


title: SP_D1_Vaccinated_2


title: wild-type (WS) 8 DAF Seed 1

description:
Biological replicate 1 of 3. Controls for lec1-1 and lec2-1 examination.
WS8-1.CEL


title: wild-type (Col-0) 12 DAF Seed 1-3

description:
Biological replicate 3 of 3. Controls for fus3-3 examination.
Col12-3.CEL

source_name: wild-type (Col-0)_12 DAF Seed

value: wild-type (Col-0)


title: SP_Vaccinated_Mock Challenged_1

description: This sample is collected at 25-29hrs post challenge (3 weeks post vaccination)

source_name: Spleen, Vaccinated and Mock challenged

value: Mock challenged


title: SP_D1_Control_3


title: wild-type (Col-0) 12 DAF Seed 1-2

description:
Biological replicate 2 of 3. Controls for fus3-3 examination.
Col12-2.CEL


title: SP_D1_Control_1


title: wild-type (Col-0) 12 DAF Seed 1-1

description:
Biological replicate 1 of 3. Controls for fus3-3 examination.
Col12-1.CEL


title: fus3-3  8 DAF Seed 3

description:
Biological replicate 3 of 3.
fus8-3.CEL

source_name: fus3-3_8 DAF Seed


title: D9.14988_LMP

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 15060_SBT
AlternateIDRawData: D9.14988_LMP
dual-color florescent staining

hyb_protocol: Infinium HD Assay was performed using the BeadArray system according to the manufacturer's instructions (Illumina)

data_processing: Data was extracted using Illumina’s GenomeStudio v2010.3 with Genotyping module 1.8.4 software, with the default Illumina settings and Illumina HumanOmniExpress‐12v1_G_FFPE manifest cluster file

source_name: microdissected FFPE ovarian tumor

label_protocol: Infinium HD Assay was performed according to the manufacturer's instructions (Illumina)

extract_protocol: DNA was extracted from deparaffinized sections of formalin-fixed paraffin embedded (FFPE) specimens using a modified protocol of the QIAmp DNA FFPE Tissue kit (Qiagen). The Infinium HD FFPE DNA Restore Kit (Illumina) was used to repair degraded DNA samples in preparation for use with the Infinium HD Assay.

tag: patient

tag: disease state

value: LGSC

tag: component

value: Borderline


title: wild-type (Col-0) 8 DAF Seed 3

description:
Biological replicate 3 of 3. Controls for fus3-3 examination.
Col8-3.CEL

source_name: wild-type (Col-0)_8 DAF Seed


title: wild-type (Col-0) 8 DAF Seed 1

description:
Biological replicate 1 of 3. Controls for fus3-3 examination.
Col8-1.CEL


title: fus3-3  8 DAF Seed 1

description:
Biological replicate 1 of 3.
fus8-1.CEL


title: Control

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: H37Rv genomic DNA

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Gene Expression 8x15k Mycobacterium tuberculosis H37Rv Array (AMADID_020181).Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).[ Hybrdization sample H37RV Genomic DNA: The labeled sample was combined with Salmon Sperm DNA (Catlog No: 1632-011), Agilent Blocking agent (Part No: 5188-6416) and Hybridization Buffer (part No: 5188-2460) was added to it.) The labeled samples in above hybridization mix were denatured at 95oC for 3 minutes and were incubated at 37oC for 30 minutes.The samples were hybridized at 65oC for 24 hours.After hybridization, the slides were washed using Agilent wash Buffers (Agilent Technologies, Part Number 5188-5221)]

scan_protocol: Scanned using the Agilent Technologies Scanner G2505C at 5 micron resolution. Images were quantified using Agilent Feature Extraction Software

data_processing: Two color hybrdization was performed containing channel cy5 and cy3 . Channel split analysis  was performed. Only Cy3 channel data was analyzed and used for this study. Data was analyzed in GeneSpring GX software from Agilent using  Quantile Normalization.  Gene based analysis was performed. All the samples were subjected to Quantile normalization.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: The bacterial samples for Gene expression were labeled using MessageAmp II- Bacteria kit (Ambion, Cat No: 1790) as per manufacturer’s instructions. (The labeling was performed for two color  hybrdizations) [Labeling  sample H37RV Genomic DNA : 0.5ug Samples were labeled using Agilent gDNA Labeling Kit ( Part  No: 5190-0449). The labeled samples were cleaned up using Microcon columns 30 kDa (Catalog MRCF0R030).]

growth_protocol: M. tuberculosis culture was grown aerobically in Dubos medium supplemented with 0.5% BSA, 0.75% Glucose and 0.085% NaCl plus 0.1% Tween-80  (DTA medium)  till an OD595~0.1-0.2 and subsequently treated with 10 mM vitamin C for 8 hours

extract_protocol: Total M. tuberculosis RNA was extracted using Trizol based extraction protocol. [Extraction sample H37RV Genomic DNA:  Genomic DNA extraction is done using phenol/Chloroform extraction method.

treatment_protocol: Logarithmic phase culture of M. tuberculosis was diluted to an OD595~ 0.1-0.2 in DTA medium followed by addition of 10 mM of vitamin C for 8 h under shaking condition at 37C.

tag: growth condition

value: Aerobically grown

value: Control


title: AA-treated Rep 3

description: Biological replicate 3 of 3, aerobically grown OD595~0.1-0.2, 10 mM AA treated

source_name: RV V_AA

value: AA-treated


title: AA-treated Rep 1

description: Biological replicate 1 of 3, aerobically grown OD595~0.1-0.2, 10 mM AA treated

source_name: RV III_AA


title: hira-protoplast-1

first: Frederic

last: Berger

address: 1 research link, NUS

department: Chromatin & Reproduction

institute: Temasek Lifesciences Laboratory

hyb_protocol: Affymetrix 3'-IVT kit

scan_protocol: Affymetrix 3'-IVT kit

data_processing: GCRMA normalization

source_name: protoplast

label_protocol: Affymetrix 3'-IVT kit

growth_protocol: Seeds were treated at 4°C for 4 days. MS plates were placed vertically in chamber for root growth

extract_protocol: QIAGEN Rneasy Kit

treatment_protocol: Enzyme digestion

tag: genome type

value: hira

value: protoplast


title: hira-protoplast-2


title: fus3-3  8 DAF Seed 2

description:
Biological replicate 2 of 3.
fus8-2.CEL

tag: age


title: D9.14988_INV

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 15060_INV
AlternateIDRawData: D9.14988_INV
dual-color florescent staining

scan_protocol: Infinium HD Assay was performed using the BeadArray system according to the manufacturer's instructions (Illumina)

value: Invasive


title: WT-protoplast-2

value: wild type


title: Control (Untreated) Rep 2

description: Biological replicate 2 of 3, aerobically grown OD595~0.1-0.2, untreated control

source_name: Rv IV_UT

value: Control (Untreated)


title: Control (Untreated) Rep 3

description: Biological replicate 3 of 3, aerobically grown OD595~0.1-0.2, untreated control

source_name: RV V_UT


title: hira-root-1

source_name: root

value: root


title: B7.13470_INV

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65667_INV
AlternateIDRawData: B7.13470_INV
dual-color florescent staining


title: B7.13470_LMP

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65667_SBT
AlternateIDRawData: B7.13470_LMP
dual-color florescent staining


title: wild-type (Col-0) 8 DAF Seed 2

description:
Biological replicate 2 of 3. Controls for fus3-3 examination.
Col8-2.CEL

value: developing seeds dissected from sliques


title: 11.7469_LMP

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65664_SBT
AlternateIDRawData: 11.7469_LMP
dual-color florescent staining


title: WT-root-1


title: Control (Untreated) Rep 1

description: Biological replicate 1 of 3, aerobically grown OD595~0.1-0.2, untreated control

source_name: Rv III_UT


title: Tolerant T cells Experimental 1

status: Public on Sep 30 2014

city: Oxford

first: Duncan

last: Howie

state: Oxon

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: Oxford University

description: gene expression data from T cells of mice tolerant of xenograft

hyb_protocol: 5ug total RNA used for hybridisation

scan_protocol: Scanned with a GeneAtlas Scanner 3000 7G

data_processing: Affymetrix Expression Console software used follwed by Affymetrix default multichip analysis (RMA)

organism: Mus musculus

source_name: T cells from tolerant Xenograft

label_protocol: Whole target sense target labelling Assay Affymetrix

extract_protocol: Rneasy mini kit Qiagen used to extract RNA

value: T cells from tolerant Xenograft

tag: genotype

value: wildtype CD1 mice


title: Tolerant T cells Experimental 4


title: WT-protoplast-1


title: Tolerant T cells Experimental 3


title: UNTREATED 30DAY t CELL Control 1

description: gene expression data from T cells of mice rejecting xenograft

source_name: T cells from Rejecting Xenograft

value: T cells from Rejecting Xenograft


title: UNTREATED 30DAY t CELL Control 2


title: UNTREATED 30DAY t CELL Control 3


title: Paraxial tissue-mutant-rep1

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

hyb_protocol: 2ug of each labeled DNA (+water=17ul) was suspended in Agilent 2X Gene Expression hyb buffer (25ul), Agilent 10X Blocking agent (5ul), and Kreatech Kreablock (3ul).  The hybridization solutions were applied to Agilent Mouse8x60K microarrays.  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent SureScan microarray scanner to detect Cy5 fluorescence.  Gridding and analysis of images was performed using Agilent Feature Extraction v11.0.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09_red_only and Grid: 028005_D_F_20100422) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mutant embryo#1, paraxial tissue

label_protocol: cDNAs were chemically labeled with Kreatech ULS labeling kit (Kreatech Diagnostics).  Per reaction, 2.5ug of DNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled DNAs were purified with QIAquick PCR purification columns (Qiagen Sciences).  Labeled DNAs were quantitated on a Nanodrop spectrophotometer.

extract_protocol: RNA was prepared from laser captured material by following the manufacturer's instructions in the Arcturus PicoPure RNA Isolation kit from Life Technologies. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm.  Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

tag: developmental stage

value: E10.5 embryo

tag: strain

value: fl/fl; cre/o


title: WT-root-2


title: UNTREATED 30DAY t CELL Control 4

tag: cell type


title: A4.6637_INV

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65668_INV
AlternateIDRawData: A4.6637_INV
dual-color florescent staining

value: LGSC


title: Paraxial tissue-wild type-rep2

source_name: WT embryo#2, paraxial tissue


title: Paraxial tissue-mutant-rep2

source_name: Mutant embryo#2, paraxial tissue


title: Neural Tube-mutant-rep2

source_name: Mutant embryo#2, neural tube


title: Neural Tube-mutant-rep1

source_name: Mutant embryo#1, neural tube


title: Neural Tube-wild type-rep1

source_name: WT embryo#1, neural tube


title: AA-treated Rep 2

description: Biological replicate 2 of 3, aerobically grown OD595~0.1-0.2, 10 mM AA treated

source_name: RV IV_AA

tag: treatment


title: A4.6637_LMP

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65668_SBT
AlternateIDRawData: A4.6637_LMP
dual-color florescent staining

source_name: microdissected FFPE ovarian tumor

value: Borderline


title: 11.7469_INV

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65664_INV
AlternateIDRawData: 11.7469_INV
dual-color florescent staining


title: A10.5074_LMP

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65665_SBT
AlternateIDRawData: A10.5074_LMP
dual-color florescent staining


title: Tolerant T cells Expeimental 2


title: Adenocarcinomatous Smgb-Tag Submandibular Gland 3

city: Turku

first: Johannes

last: Routila

address: Tykistökatu …

department: Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalised using quantile normalisation in R, Limma

source_name: Adenocarcinoma, submandibular gland

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted using a guanidinium isothiocyanate-acid phenol procedure (TRIZOL LS Reagent, GIBCO BRL, Rockville, MD, USA), and purified on a Qiagen mini-column (Qiagen, Valencia, CA, USA).

value: Smgb-Tag

value: submandibular salivary gland

tag: tumor stage

value: adenocarcinoma


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_162

status: Public on Sep 29 2014

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

description:
sample162
hybridized to Mouse Diversity Genotype Array

hyb_protocol: Performed by The Jackson Lab

scan_protocol: Performed by The Jackson Lab

data_processing: Genotyping performed by The Jackson Lab.  PennCNV was used to determine Log R Ratio (LRR) and B Allele Frequency (BAF). MouseDivGeno 1.0.4 software was used to make SNPs calls.

source_name: Embryo

label_protocol: Performed by The Jackson Lab

growth_protocol: Mice were grown according to standard conditions

extract_protocol: DNA was extracted from adult liver or 17.5 day old embryo

tag: p53 status

value: embryo


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_154

description:
sample154
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_161

description:
sample161
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+  Female 3 months (liver)_156

description:
sample156
hybridized to Mouse Diversity Genotype Array

source_name: Liver

value: adult

tag: gender

value: Female

value: 3 months

value: liver


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_159

description:
sample159
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53-/-  Male 3 months (liver)_155

description:
sample155
hybridized to Mouse Diversity Genotype Array

value: Male

tag: tissue


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_158

description:
sample158
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_157

description:
sample157
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_160

description:
sample160
hybridized to Mouse Diversity Genotype Array


title: Adenocarcinomatous Smgb-Tag Submandibular Gland 1


title: Adenocarcinomatous Smgb-Tag Submandibular Gland 2


title: Dysplastic Smgb-Tag Submandibular Gland 3

source_name: Dysplasia, submandibular gland

value: dysplasia


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_151

description:
sample151
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_149

description:
sample149
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_152

description:
sample152
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_150

description:
sample150
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_153

description:
sample153
hybridized to Mouse Diversity Genotype Array


title: A7.5074_INV

description:
Raw data file: ILOEF-6561_FullDataTable.txt
Sample name: 65665_INV
AlternateIDRawData: A7.5074_INV
dual-color florescent staining

value: Invasive


title: Normal Smgb-Tag Submandibular Gland 2

source_name: Normal, submandibular gland

value: none (normal)


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_147

description:
sample147
hybridized to Mouse Diversity Genotype Array


title: Dysplastic Smgb-Tag Submandibular Gland 1


title: Normal Smgb-Tag Submandibular Gland 3


title: Dysplastic Smgb-Tag Submandibular Gland 2


title: Normal Smgb-Tag Submandibular Gland 1


title: 129SvSL p53+/+  Female 3 months (liver)_146

description:
sample146
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53-/-  Male 3 months (liver)_145

description:
sample145
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_148

description:
sample148
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_139

description:
sample139
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_144

description:
sample144
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53+/+  Female 3 months (liver)_137

description:
sample137
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_140

description:
sample140
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53-/-  Male 3 months (liver)_136

description:
sample136
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_134

description:
sample134
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_143

description:
sample143
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_141

description:
sample141
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_142

description:
sample142
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_133

description:
sample133
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_138

description:
sample138
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_135

description:
sample135
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_130

description:
sample130
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_132

description:
sample132
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_131

description:
sample131
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53-/-  Male 3 months (liver)_124

description:
sample124
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_129

description:
sample129
hybridized to Mouse Diversity Genotype Array


title: hira-root-2

source_name: root

value: hira

value: root


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_128

description:
sample128
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_127

description:
sample127
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_126

description:
sample126
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_122

description:
sample122
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53+/+  Female 3 months (liver)_125

description:
sample125
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_123

description:
sample123
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_121

description:
sample121
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_120

description:
sample120
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_119

description:
sample119
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_118

description:
sample118
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_113

description:
sample113
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_114

description:
sample114
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53-/-  Male 3 months (liver)_115

description:
sample115
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_117

description:
sample117
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53-/-  Female 3 months (liver)_110

description:
sample110
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53+/+  Male 3 months (liver)_111

description:
sample111
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_107

description:
sample107
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53+/+  Female 3 months (liver)_116

description:
sample116
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_112

description:
sample112
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_109

description:
sample109
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_108

description:
sample108
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_102

description:
sample102
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_106

description:
sample106
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL   p53+/- embryo (17.5 embryo)_105

description:
sample105
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53-/-  Female 3 months (liver)_103

description:
sample103
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_100

description:
sample100
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_99

description:
sample99
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_98

description:
sample98
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Female 3 months (liver)_96

description:
sample96
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53-/- Male 3 months (liver)_95

description:
sample95
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_97

description:
sample97
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_93

description:
sample93
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_101

description:
sample101
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_92

description:
sample92
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_91

description:
sample91
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_90

description:
sample90
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Female 3 months (liver)_89

description:
sample89
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/-  Male 12 months (liver)_88

description:
sample88
hybridized to Mouse Diversity Genotype Array

value: 12 months


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_87

description:
sample87
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_83

description:
sample83
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_86

description:
sample86
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_84

description:
sample84
hybridized to Mouse Diversity Genotype Array


title: C57Bl6  p53+/+  Male 3 months (liver)_104

description:
sample104
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_81

description:
sample81
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_82

description:
sample82
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_85

description:
sample85
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Female 3 months (liver)_80

description:
sample80
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/- Male 9 months (liver)_79

description:
sample79
hybridized to Mouse Diversity Genotype Array

value: 9 months


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_78

description:
sample78
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_75

description:
sample75
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_94

description:
sample94
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_77

description:
sample77
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_74

description:
sample74
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_76

description:
sample76
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_73

description:
sample73
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_68

description:
sample68
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/- Male 3 months (liver)_71

description:
sample71
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Female 3 months (liver)_72

description:
sample72
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_66

description:
sample66
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_69

description:
sample69
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_67

description:
sample67
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_65

description:
sample65
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Female 3 months (liver)_63

description:
sample63
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_64

description:
sample64
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_57

description:
sample57
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_59

description:
sample59
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/+  Male 12 months (liver)_62

description:
sample62
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_55

description:
sample55
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_54

description:
sample54
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_48

description:
sample48
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_49

description:
sample49
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Female 3 months (liver)_53

description:
sample53
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/+ Male 3 months  (liver)_46

description:
sample46
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+  Female 3 months (liver)_47

description:
sample47
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_70

description:
sample70
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_45

description:
sample45
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_58

description:
sample58
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_51

description:
sample51
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_44

description:
sample44
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_61

description:
sample61
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_40

description:
sample40
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_43

description:
sample43
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_37

description:
sample37
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53-/- Female 3 months (liver)_39

description:
sample39
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_56

description:
sample56
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_60

description:
sample60
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_42

description:
sample42
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_36

description:
sample36
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/- embryo (17.5 embryo)_41

description:
sample41
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/-  Female 12 months (liver)_35

description:
sample35
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_38

description:
sample38
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_33

description:
sample33
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/+  Male 9 months (liver)_52

description:
sample52
hybridized to Mouse Diversity Genotype Array


title: Paraxial tissue-wild type-rep1

source_name: WT embryo#1, paraxial tissue

value: E10.5 embryo

tag: genotype/variation

value: wild type


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_34

description:
sample34
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_32

description:
sample32
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/- Female 9 months (liver)_31

description:
sample31
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_30

description:
sample30
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_29

description:
sample29
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_27

description:
sample27
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_28

description:
sample28
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_25

description:
sample25
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_22

description:
sample22
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_23

description:
sample23
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_21

description:
sample21
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_18

description:
sample18
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_19

description:
sample19
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_20

description:
sample20
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_15

description:
sample15
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_16

description:
sample16
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_13

description:
sample13
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_12

description:
sample12
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_14

description:
sample14
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/+  Female 9 months (liver)_11

description:
sample11
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_9

description:
sample9
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_10

description:
sample10
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_6

description:
sample6
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_7

description:
sample7
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ORp53+/- embryo (17.5 embryo)_26

description:
sample26
hybridized to Mouse Diversity Genotype Array


title: Neural Tube-wild type-rep2

source_name: WT embryo#2, neural tube


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_5

description:
sample5
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/- Female 3 months (liver)_24

description:
sample24
hybridized to Mouse Diversity Genotype Array


title: 129SvSL p53+/+ Male 3 months (liver)_2

description:
sample2
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_3

description:
sample3
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/+ Female 3 months  (liver)_1

description:
sample1
hybridized to Mouse Diversity Genotype Array


title: C57Bl6 p53+/+  Female 12 months (liver)_17

description:
sample17
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_50

description:
sample50
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_4

description:
sample4
hybridized to Mouse Diversity Genotype Array


title: C57Bl6/129SvSL p53+/+ embryo (17.5 embryo)_8

description:
sample8
hybridized to Mouse Diversity Genotype Array


title: 20130221_NC186_NC186_12

status: Public on Aug 28 2014

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Lysates in Qiagen RTL buffer were hybridized for 12-24 hours with custom nCounter Gene Expression CodeSets.

scan_protocol: NanoString nCounter system (Nanostring; Seattle, WA) was used to digitally count transcripts in a multiplex reaction.

data_processing: The raw data is first scaled by positive spike-ins, shifted by negative spike-ins, and a negative binomial is fit using DESeq based on the scale parameter estimated from the positive spike-ins.

label: not provided

source_name: peripheral blood

growth_protocol: RosettaSep-purified CD4+ T cells were thawed and resuspended in RPMI-1640 supplemented with 10% FCS.

extract_protocol: After activation, cells were magnetically repurified with anti-CD4 Dynal beads, and lysed.

treatment_protocol: Thawed cells were activated with anti-CD3 and anti-CD28 beads, with or without IFNb (30U/ml) or with Th17 cocktail (anti-IFNg 10ng/ml, anti-IL4 10mg/ml, IL6 50ng/ml, IL23 20ng/ml, IL1b 10ng/ml, TGFb 5ng/ml).

tag: stimulation

value: Activated

tag: hours

tag: lane

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: systolic

tag: diastolic

tag: ethnicity

value: Caucasian

tag: Sex

value: F

tag: individual id


title: 20130221_NC186_NC186_11

tag: age

value: M


title: HM3 YS7_HM3_Mouse430A

status: Public on Sep 19 2014

city: New York

first: Vanessa

middle: Marie

last: Hubbard-Lucey

state: NY

address: 540 First Ave

institute: NYU School of Medicine

description: Gene expression data from mouse CD11c+ Splenic DCs

hyb_protocol: Following fragmentation and labeling, cDNA was hybridized to the GeneChip.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Affymetrix Power Tools software was used for processing and quantile normalization of fluorescence hybridization signals by the robust multichip averaging method

source_name: CD11c+ Cells

label_protocol: Cy3 cDNA were prepared according to the standard protocol from 100ng total RNA.

growth_protocol: Mice were sac'ed at 9 weeks of age at day 7 post allo-HSCT

extract_protocol: Trizol

treatment_protocol: Spleens were CD11c+ cell sorted by MACS cell sorting.

value: Spleen

tag: genetic background

tag: genotype

value: Atg16L1 hypomorphic (C57BL/6J)

value: d7 post allo-HSCT


title: 20130221_NC186_NC186_10

value: African-American


title: HM2 YS6_HM2_Mouse430A


title: WT1 4330_1_WT1_Mouse430A_2

growth_protocol: Mice were sac'ed at 8 weeks of age.

tag: cell type

value: CD11c+ Cells

value: WT (C57BL/6J)

value: 8 weeks of age


title: WT4 YS4_WT4_Mouse430A

tag: tissue


title: WT1 YS1_WT1_Mouse430A


title: WT2 YS2_WT2_Mouse430A


title: 20130221_NC186_NC186_09

value: Unstim


title: HM3 4220_6_HM3_Mouse430A_2


title: WT3 4220_3_WT3_Mouse430_2


title: WT3 YS3_WT3_Mouse430A


title: WT2 4220_2_WT2_Mouse430A_2


title: 20130221_NC186_NC186_08

value: IFNb


title: HM1 YS5_HM1_Mouse430A


title: JINB8 exosome replicate#3

status: Public on Sep 01 2014

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

description: JINB8 exosome replicate#3

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cRNAs was hybridized to The Affymetrix Human Gene 1.0 ST GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.

source_name: JINB8 Cell line

label_protocol: Per RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525) and Ambion WT Expression Kit (cat#4411973)

growth_protocol: Jurkat T cells and the corresponding CD47-deficient Jurkat mutant JinB8 were maintained at 2.0 x 105 cells per ml in RPMI 1640 medium (Life technologies) supplemented with 10% human serum AB, glutamine, penicillin, and streptomycin.  Jurkat cells were maintained for a maximum of 4 weeks for experiments.  Before exosome isolation, the cells were cultured using low human AB serum in their respective media for at least one passage.  The T cells were cultured in 75 cm3 flasks (Corning) and conditioned medium from ~40x106 cells (~100 ml) was collected. The conditioned medium was further centrifuged for 10 min at 1530×g to remove cell debris.  The supernatants were transferred to new 50 ml tubes. The supernatants were concentrated using centrifugal filter device YM-10 (Centricon). The final volume of supernatant was ~1 ml.  The concentrated supernatants  (~250 μl) from the respective cells were used to purify exosomes. The exosomes were isolated using the exoQuick kit (SBI System Biosciences) according to the manufactures instructions.  The supernatant was completely removed via centrifugation 2 times for 30 min at 1500×g. The white exosome pellet was diluted into 1 ml of ultra-pure water (~10×106 cells).   HUVEC were incubated with Jurkat and JinB8 T cell-derived exosomes using EGM2 media for 6 hours.

extract_protocol: Exosome pellets were purified from Jurkat and Jinb8 T cell conditioned medium using the Exo Quick kit TC (SBI Biosciences).  The pellets were dissolved into 100 μl of IXPBS. Total RNAs from cells or Exosomes (including small and long RNAs) was extracted using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: No treatments were performed.

value: CD47- JINB8 Cells

tag: genotype/variation

value: CD47- JINB8 exosome


title: 20130221_NC186_NC186_07

tag: stimulation


title: HM1 4220_4_HM1_Mouse430A_2


title: JINB8 exosome replicate#1

description: JINB8 exosome replicate#1


title: JK exosome replicate#2

description: JK exosome replicate#2

source_name: Jurkat cell line

value: CD47+ Jurkat cells

value: CD47+ JK exosome


title: HM2 4220_5_HM2_Mouse430A_2


title: 20130221_NC186_NC186_06

value: Activated

tag: hours


title: 20130221_NC186_NC186_05

tag: lane

value: Caucasian


title: 20130221_NC186_NC186_03

tag: height (cm)


title: 20130221_NC186_NC186_04

tag: weight (kg)


title: 20130221_NC186_NC186_01

tag: bmi

value: F


title: 20130218_NC185_NC185_12

tag: systolic

value: M


title: JK exosome replicate#1

description: JK exosome replicate#1


title: JK exosome replicate#3

description: JK exosome replicate#3


title: 20130221_NC186_NC186_02

tag: diastolic


title: 20130218_NC185_NC185_10

tag: ethnicity


title: 20130218_NC185_NC185_09

tag: Sex


title: JINB8 exosome replicate#2

description: JINB8 exosome replicate#2


title: 20130218_NC185_NC185_08

tag: individual id


title: TgSMC1_t2_rep1

status: Public on Sep 27 2014

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

description: Sample 1 and sample 4 are derived from the sample biological sample

hyb_protocol: Cy3/5 labelled DNA (input/Experiment) were precipitated with 0.1 vol of 5M NaCl and 0.9 vol Isopropanol. Using NimbleGen Hybridization Kit, manufacturer's instructions were followed for hybridization reaction

scan_protocol: Arrays were scanned at wavelengths (532=cy3, 635=Cy5) with pixel size 5μm at 100% power using Agilent's DNA Microarray Scanner using Agilent scanner software

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Toxoplasma gondii

source_name: SMC1 ChIP DNA

label_protocol: 1.2μg of Input and Experimental DNA sample were labelled with Cy3 and Cy5 dye respectively (NimbleGen Dual-Color DNA Labelling Kit) using Klenow Fragment 3->5 exo- (NEB) following manufacturer's instructions

growth_protocol: Tachyzoite parasites grown in vitro

extract_protocol: 10^9 intracellular tachyzoites in human foreskin fibroblasts were crosslinked with formaldehyde and immunoprecipitated with anti-HA Microbeads (Miltenyi Biotec; SMC1-HA line) or rabbit polyclonal anti-SMC1+Dynabeads ProteinG (Invitrogen; SMC1-HA and RHdeltaHXGPRT); all immunoprecipitated DNA samples were amplified by using Complete Whole Genome Amplification Kit (WGA2;Sigma)

tag: strain

value: RH

tag: antibody

source_name: Input Toxoplasma gondii genomic DNA


title: 20130218_NC185_NC185_07

tag: age


title: 20130218_NC185_NC185_06


title: 20130218_NC185_NC185_04


title: 20130218_NC185_NC185_05


title: 20130218_NC185_NC185_03


title: 20130218_NC185_NC185_02


title: TgSMC1_t1_rep2

description: Sample 2 and sample 5 are derived from the sample biological sample


title: TgSMC1_t2_rep3

description: Sample 3 and sample 6 are derived from the sample biological sample


title: TgSMC1_t2_rep2


title: TgSMC1_t1_rep3


title: 20130218_NC184_NC184_09


title: 20130218_NC185_NC185_01


title: 20130218_NC184_NC184_12


title: 20130218_NC185_NC185_11


title: 20130217_NC183_NC183_12


title: 20130217_NC183_NC183_11


title: 20130218_NC184_NC184_07


title: 20130218_NC184_NC184_02


title: 20130218_NC184_NC184_10


title: 20130218_NC184_NC184_04


title: 20130218_NC184_NC184_05

value: Asian


title: 20130218_NC184_NC184_03


title: 20130218_NC184_NC184_06


title: 20130217_NC183_NC183_10


title: 20130218_NC184_NC184_01

value: Asian Caucasian


title: 20130218_NC184_NC184_11


title: 20130218_NC184_NC184_08


title: 20130217_NC183_NC183_09

value: African-American


title: 20130217_NC183_NC183_03


title: 20130217_NC183_NC183_05


title: 20130217_NC183_NC183_06


title: 20130217_NC183_NC183_08


title: 20130217_NC183_NC183_02


title: 20130217_NC182_NC182_10


title: 20130217_NC182_NC182_09


title: 20130217_NC182_NC182_11


title: 20130217_NC182_NC182_12


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title: 20130217_NC181_NC181_12


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title: 20130217_NC182_NC182_01


title: 20130217_NC181_NC181_08


title: 20130217_NC181_NC181_09


title: 20130217_NC181_NC181_05


title: 20130217_NC181_NC181_06


title: TgSMC1_t1_rep1


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title: 20130217_NC183_NC183_07


title: 20130217_NC182_NC182_02


title: 20130217_NC181_NC181_04


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title: 20130211_NC147_NC147_01


title: 20130211_NC148_NC148_10


title: 20130211_NC146_NC146_11


title: 20130211_NC146_NC146_09


title: 20130211_NC146_NC146_08


title: 20130211_NC146_NC146_07


title: 20130211_NC146_NC146_05


title: 20130211_NC146_NC146_04


title: 20130211_NC145_NC145_12


title: 20130211_NC146_NC146_03


title: 20130211_NC148_NC148_03


title: 20130211_NC146_NC146_10


title: 20130211_NC146_NC146_01


title: 20130211_NC146_NC146_06


title: 20130211_NC145_NC145_10


title: 20130211_NC148_NC148_01


title: 20130211_NC145_NC145_08


title: 20130211_NC145_NC145_07


title: 20130211_NC145_NC145_09


title: 20130211_NC145_NC145_03


title: 20130211_NC145_NC145_04


title: 20130211_NC145_NC145_06


title: 20130211_NC145_NC145_05


title: 20130211_NC145_NC145_02


title: 20130211_NC144_NC144_12


title: 20130211_NC145_NC145_01


title: 20130211_NC144_NC144_06


title: 20130211_NC144_NC144_11


title: 20130211_NC144_NC144_07


title: 20130211_NC144_NC144_10