title: clam exposed for 3 days to 1000 µg IBU/l  [1000_T2_01]

treatment_protocol: digestive gland of Manila clam exposed for 3 days to 1000 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 3 days


title: clam exposed for 3 days to 1000 µg IBU/l  [1000_T2_03]

status: Public on Oct 01 2013

type: RNA

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

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

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software.

label: Cyanine 3

molecule: total RNA

organism: Ruditapes philippinarum

source_name: digestive gland of Manila clam exposed for 3 days to 1000 µg IBU/l

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

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples.

tag: time point

tag: agent

value: 1000 µg IBU/l


title: clam exposed for 3 days to 1000 µg IBU/l  [1000_T2_02]


title: clam exposed for 3 days to 1000 µg IBU/l  [1000_T2_05]


title: SCT_82_male_20O2_VitDctrl

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

hyb_protocol: GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix GeneChip® Fluidics Station 450: protocol FS450_0007 for Cartridge Arrays.

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC_3_1_1).

data_processing:
Gene Expression Console v.1.1, Affymetrix (Expression Console EC_1_1_2) using Affymetrix default analysis settings for generation of CEL files.
Data Pre-Processing (Partek Software, v.6.5: RMA (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization)); Biostatistical data analysis: R/Bioconductor.

label: biotin

organism: Homo sapiens

source_name: Isolated and in vitro cultured placental cells, syncytiotrophoblasts, male

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671).

growth_protocol: Prior to microarray analysis, 800,000 cells were seeded on 1% (v/v) gelatin-coated flasks (75 cm²) using Endothelial Basal Medium (EBM, Cambrex, Clonetics, USA) supplemented with the EGM-MV BulletKit (Clonetics). Endothelial cells were cultured for 48 h at 21% O2/5% CO2 environment at 37°C.

extract_protocol: RNA isolation with the Qiagen Mini kit according to the manufacturer.

treatment_protocol: No treatments.

tag: tissue

value: placenta

tag: cell type

value: syncytiotrophoblasts

tag: gender

value: male


title: CT_93_female_20O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, cytotrophoblasts, female

value: cytotrophoblasts

value: female


title: SCT_84m_male_20O2_VitDctrl


title: SCT_81_male_20O2_VitDctrl


title: SCT_87_female_20O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, syncytiotrophoblasts, female


title: clam exposed for 1 days to 1000 µg IBU/l  [1000_T1_05]

treatment_protocol: digestive gland of Manila clam exposed for 1 days to 1000 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 1 days


title: CT_90_male_20O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, cytotrophoblasts, male


title: CT_91_female_20O2_VitDctrl


title: clam exposed for 1 days to 1000 µg IBU/l  [1000_T1_02]

source_name: digestive gland of Manila clam exposed for 1 days to 1000 µg IBU/l


title: clam exposed for 3 days to 1000 µg IBU/l  [1000_T2_04]


title: clam exposed for 1 days to 1000 µg IBU/l  [1000_T1_01]


title: clam exposed for 1 days to 1000 µg IBU/l  [1000_T1_03]


title: clam exposed for 1 days to 1000 µg IBU/l  [1000_T1_04]


title: clam exposed for 7 days to 100 µg IBU/l  [100_T4_04]

treatment_protocol: digestive gland of Manila clam exposed for 7 days to 100 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 7 days

value: 100 µg IBU/l


title: clam exposed for 7 days to 100 µg IBU/l  [100_T4_07]

source_name: digestive gland of Manila clam exposed for 7 days to 100 µg IBU/l


title: CT_87_female_20O2_VitDctrl


title: CT_82_male_20O2_VitDctrl


title: clam exposed for 7 days to 100 µg IBU/l  [100_T4_03]


title: CT_84m_male_20O2_VitDctrl


title: clam exposed for 5 days to 100 µg IBU/l  [100_T3_05]

treatment_protocol: digestive gland of Manila clam exposed for 5 days to 100 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 5 days


title: CT_81_male_20O2_VitDctrl


title: clam exposed for 7 days to 100 µg IBU/l  [100_T4_02]


title: clam exposed for 7 days to 100 µg IBU/l  [100_T4_01]


title: CT_58_female_20O2_VitDctrl


title: CT_66_male_20O2_VitDctrl


title: NSC_ DMSO_24h_biological rep1

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from NSC SA-01 treated with DMSO (0.1 % final)

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip human Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: hESC derived-NSCs passage 14, 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: NSCs were grown in medium containing Neurobasal, D-MEM/F-12, N-2 and B-27

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

treatment_protocol: NSC were plated in 6-well polyornithine/laminin coated plates and treated 5h after plating with DMSO or X5050 during 24h.

tag: cell line

tag: treatment

value: with DMSO (0.1 % final)


title: CT_60_female_20O2_VitDctrl


title: NSC_ DMSO_24h_biological rep2


title: clam exposed for 5 days to 100 µg IBU/l  [100_T3_03]

source_name: digestive gland of Manila clam exposed for 5 days to 100 µg IBU/l


title: clam exposed for 5 days to 100 µg IBU/l  [100_T3_01]


title: NSC_ X5050_24h_biological rep1

description: Gene expression data from NSC SA-01 treated with X5050 (100 µM final)

value: with X5050 (100 µM final)


title: clam exposed for 3 days to 100 µg IBU/l  [100_T2_05]

treatment_protocol: digestive gland of Manila clam exposed for 3 days to 100 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.


title: NSC_ X5050_24h_biological rep2


title: NSC_ X5050_24h_biological rep3


title: NSC_ DMSO_24h_biological rep3


title: clam exposed for 5 days to 100 µg IBU/l  [100_T3_02]


title: clam exposed for 3 days to 100 µg IBU/l  [100_T2_03]

source_name: digestive gland of Manila clam exposed for 3 days to 100 µg IBU/l


title: clam exposed for 3 days to 100 µg IBU/l  [100_T2_01]


title: clam exposed for 3 days to 100 µg IBU/l  [100_T2_02]


title: clam exposed for 1 days to 100 µg IBU/l  [100_T1_03]

treatment_protocol: digestive gland of Manila clam exposed for 1 days to 100 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.


title: clam exposed for 1 days to 100 µg IBU/l  [100_T1_07]

source_name: digestive gland of Manila clam exposed for 1 days to 100 µg IBU/l


title: clam exposed for 1 days to 100 µg IBU/l  [100_T1_04]


title: clam exposed for 1 days to 100 µg IBU/l  [100_T1_06]


title: clam exposed for 1 days to 100 µg IBU/l  [100_T1_05]


title: control clam exposed for 7 days to ethanol  [C_T4_06]

treatment_protocol: digestive gland of Manila clam exposed for 7 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.


title: clam exposed for 3 days to 100 µg IBU/l  [100_T2_04]


title: Lower_4th_internode_35_days_after_heading_rep3

city: Nagoya

first: Ko

last: Hirano

state: Aichi

address: Furo-cho Chikusa-ku

country: Japan

institute: Nagoya University

description: Gene expression in the rice Lower 4th internode at 35 days after heading

hyb_protocol: Fragmentation and hybridization was carried out with Agilent Gene Expression Hybridization Kit. 1650 ng of labeled and fragmented cRNA was hybridized to Agilent Rice 44K custom array (G2519F) using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505B according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent).  These microarray data were subjected to variance stabilization normalization using the Bioconductor ‘vsn’ package of the R software version 2.11.1. The resulting normalized values were then transformed to log base 2. Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].

organism: Oryza sativa

label_protocol: Total RNA was extracteOne-color spike-mix was added to total RNA before labeling reaction. The Cy3-labeled cRNA was prepared from total RNA using Quick Amp Labeling Kit (Agilent Technologies) in accordance with the manufacturer's protocol. Then, labeled cRNA was purified using RNeasy mini kit (QIAGEN).d from the third or the forth internode, using RNeasy mini kit (QIAGEN).

growth_protocol: Rice (O. sativa L. ssp. japonica cv. Kinmaze) plants were grown in the field at year 2009

extract_protocol: Total RNA was extracted from the third or the forth internode, using RNeasy mini kit (QIAGEN).

treatment_protocol: no treatment

tag: subspecies

value: japonica

tag: cultivar

value: Kinmaze

value: Lower 4th internode

value: 35 days after heading


title: Upper_4th_internode_35_days_after_heading_rep2

description: Gene expression in the rice Upper 4th internode at 35 days after heading

value: Upper 4th internode


title: Upper_4th_internode_35_days_after_heading_rep3


title: Lower_4th_internode_35_days_after_heading_rep2


title: Lower_4th_internode_35_days_after_heading_rep1


title: Upper_4th_internode_13_days_after_heading_rep2

description: Gene expression in the rice Upper 4th internode at 13 days after heading

value: 13 days after heading


title: control clam exposed for 7 days to ethanol  [C_T4_04]

source_name: digestive gland of Manila clam exposed for 7 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.


title: Upper_4th_internode_13_days_after_heading_rep3


title: Middle_4th_internode_35_days_after_heading_rep3

description: Gene expression in the rice Middle 4th internode at 35 days after heading

value: Middle 4th internode


title: Middle_4th_internode_35_days_after_heading_rep2


title: control clam exposed for 7 days to ethanol  [C_T4_03]

value: ethanol added at the highest concentration (10 µl/l) used in the IBU treatment


title: control clam exposed for 7 days to ethanol  [C_T4_01]


title: Middle_4th_internode_13_days_after_heading_rep2

description: Gene expression in the rice Middle 4th internode at 13 days after heading


title: control clam exposed for 7 days to ethanol  [C_T4_02]


title: control clam exposed for 5 days to ethanol  [C_T3_04]

treatment_protocol: digestive gland of Manila clam exposed for 5 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.


title: Middle_4th_internode_13_days_after_heading_rep3


title: Upper_4th_internode_13_days_after_heading_rep1


title: Middle_4th_internode_13_days_after_heading_rep1


title: control clam exposed for 5 days to ethanol  [C_T3_06]

source_name: digestive gland of Manila clam exposed for 5 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.


title: Lower_4th_internode_13_days_after_heading_rep3

description: Gene expression in the rice Lower 4th internode at 13 days after heading


title: control clam exposed for 5 days to ethanol  [C_T3_01]


title: control clam exposed for 5 days to ethanol  [C_T3_02]


title: control clam exposed for 5 days to ethanol  [C_T3_03]


title: Lower_4th_internode_13_days_after_heading_rep1


title: Upper_4th_internode.bc.1_6_days_after_heading_rep3

description: Gene expression in the rice Upper 4th internode.bc.1 at 6 days after heading

value: Upper 4th internode.bc.1

value: 6 days after heading


title: Lower_4th_internode_13_days_after_heading_rep2


title: Upper_4th_internode.bc.1_6_days_after_heading_rep2


title: control clam exposed for 3 days to ethanol  [C_T2_05]

treatment_protocol: digestive gland of Manila clam exposed for 3 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 3 days


title: control clam exposed for 3 days to ethanol  [C_T2_02]

source_name: digestive gland of Manila clam exposed for 3 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.


title: control clam exposed for 3 days to ethanol  [C_T2_01]


title: control clam exposed for 1 days to ethanol  [C_T1_07]

treatment_protocol: digestive gland of Manila clam exposed for 1 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 1 days


title: control clam exposed for 3 days to ethanol  [C_T2_04]


title: Middle_4th_internode.bc.1._6_days_after_heading_rep2

description: Gene expression in the rice Middle 4th internode.bc.1. at 6 days after heading

value: Middle 4th internode.bc.1.


title: Middle_4th_internode.bc.1._6_days_after_heading_rep3


title: Lower_4th_internode.bc.1._6_days_after_heading_rep2

description: Gene expression in the rice Lower 4th internode.bc.1. at 6 days after heading

value: Lower 4th internode.bc.1.


title: Middle_4th_internode.bc.1._6_days_after_heading_rep1


title: Upper_4th_internode.bc.1_6_days_after_heading_rep1


title: Lower_4th_internode.bc.1._6_days_after_heading_rep1


title: control clam exposed for 1 days to ethanol  [C_T1_01]

source_name: digestive gland of Manila clam exposed for 1 days to ethanol added at the highest concentration (10 µl/l) used in the IBU treatments.


title: Middle_4th_internode_35_days_after_heading_rep1


title: clam exposed for 5 days to 100 µg IBU/l  [100_T3_06]

value: 5 days

value: 100 µg IBU/l


title: control clam exposed for 3 days to ethanol  [C_T2_03]


title: control clam exposed for 1 days to ethanol  [C_T1_04]


title: Upper_4th_internode_6_days_after_heading_rep3

description: Gene expression in the rice Upper 4th internode at 6 days after heading


title: control clam exposed for 1 days to ethanol  [C_T1_06]


title: control clam exposed for 1 days to ethanol  [C_T1_02]


title: Middle_4th_internode_6_days_after_heading_rep3

description: Gene expression in the rice Middle 4th internode at 6 days after heading


title: DRG_VEH_3

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

description: Gene expression data from rat L5 DRG after SNT

hyb_protocol: hybridized to Affymetrix Rat Gene Arrays (Rat Gene 1.0ST) on a GeneChip Fluidics Station 450.

scan_protocol: Affymetrix Gene chips scanner

data_processing: R, usual quality controls, RMA normalisation, DRG & spinal cord tissue were run in separate batches and analysed separately

organism: Rattus norvegicus

source_name: ipsilateral L5 rat DRG, day 14, veh treated

label_protocol: Ambion Whole transcript Expression Kit (Invitrogen)

extract_protocol: Frozen tissue was homogenized in 500 μL Trizol, separated into phases using chloroform and cleaned up with a Qiagen RNA microkit (74004; Qiagen, Manchester, UK) following manufacturer’s instructions.

treatment_protocol: the HDACi MS-275 was delivered i.t. via an osmotic pump (30nmol/ day)

value: injured L5 DRG


title: immunoscreening S. Enteritidis 3 (1077)

type: protein

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E.coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBST (PBS + 0.01% Tween20). Incubation with primary antibody (rabbit polyclonal to S. enterica) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBST after each incubation step. Slides were dried with nitrogen and scanned afterwards.

scan_protocol: Fluorescent array images were collected for Cy3 with a Genepix 4200A fluorescent scanner. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing: From the raw data the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities were calculated by subtraction the fluorescent intensities of the top compartment by the ones from the bottom compartment. This acknowledges the presence of unspecific interaction of the secondary antibody to the samples. Next, the contrast method was applied by calculating the contrast for each spot of the top compartment. C = [rfi(sample) - median rfi(negative reference)]/[rfi(sample) + median rfi(negative reference)]

molecule: protein

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: crude lysate Acella E.coli + recombinantly expressed proteins

extract_protocol: Fusion proteins were extracted from cultures using EasyLyse Bacterial protein extraction kit (Epicentre)

tag: strain


title: Lower_4th_internode.bc.1._6_days_after_heading_rep3

value: japonica


title: immunoscreening S. Enteritidis 3 (1970)


title: immunoscreening S. Enteritidis 4 (2500)


title: immunoscreening S. Enteritidis 4 (2502)


title: DRG_VEH_4


title: immunoscreening S. Enteritidis 3 (1075)


title: immunoscreening S. Enteritidis 2 (416929)


title: Upper_4th_internode_6_days_after_heading_rep2

value: Kinmaze


title: Middle_4th_internode_6_days_after_heading_rep2


title: immunoscreening S. Enteritidis 2 (416927)


title: immunoscreening S. Enteritidis 4 (1973)


title: DRG_VEH_2


title: Upper_4th_internode_6_days_after_heading_rep1


title: DRG_VEH_1


title: Lower_4th_internode_6_days_after_heading_rep3

description: Gene expression in the rice Lower 4th internode at 6 days after heading

value: Lower 4th internode


title: Middle_4th_internode_6_days_after_heading_rep1


title: DRG_HDACi_4

source_name: ipsilateral L5 rat DRG, day 14, HDACi treated


title: immunoscreening S. Enteritidis 2 (4169663)


title: immunoscreening S. Enteritidis 1 (4169664)


title: immunoscreening S. Enteritidis 1 (415843)


title: DRG_HDACi_3


title: DRG_HDACi_1


title: DRG_HDACi_2


title: immunoscreening S. Enteritidis 1 (415842)


title: Middle_4th_internode_1_days_before_heading_rep3

description: Gene expression in the rice Middle 4th internode at 1 days before heading

value: 1 days before heading


title: Lower_4th_internode_6_days_after_heading_rep2


title: Upper_4th_internode_1_days_before_heading_rep2

description: Gene expression in the rice Upper 4th internode at 1 days before heading

value: Upper 4th internode


title: cord_VEH_3

description: Gene expression data from rat spinal cord after SNT

source_name: dorsal ipsilateral cord, day 14, veh treated

value: dorsal ipsilateral spinal cord


title: Lower_4th_internode_6_days_after_heading_rep1


title: cord_VEH_4


title: cord_VEH_2


title: Upper_4th_internode_1_days_before_heading_rep1


title: Upper_4th_internode_1_days_before_heading_rep3


title: Atta vollenweideri Tiny Worker, pool4

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

institute: Max Planck Institute for Chemical Ecology

description: pooled from 300 animals

hyb_protocol: 1,600 ng of cyanine 3 labeled cRNA was used for each array and hybridization was carried out at 65oC for 17 hours. Slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturers instruction, using an Agilent Microarray Scanner

data_processing: Data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data output files were analyzed using the GeneSpring GX11, GeneSifter and R-based microarray analysis softwares. The data points were normalized between arrays to the median intensity and log base 2-transformation of the normalized data was performed.

organism: Atta vollenweideri

source_name: Atta vollenweideri Tiny Worker antenna, pool4

label_protocol: Agilent Technologies spike-in RNA was added to 500 ng of total RNA and labeled using a combination of the QuickAmp Amplification kit (Agilent Technologies) and the Kreatech ULS Fluorescent Labeling Kit with cyanine 3-CTP dye following the manufacturer´s instructions. Labeled amplified cRNA samples were purified using Qiagen RNeasy MinElute columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >1600 ng and the specific activity >6.0 pmol Cy3 per ug cRNA

growth_protocol: Animals were collected with all necessary permits from the Argentine Republic (Permit  Number: 23275/10), the Parques National Rio Pilcomayo and the Federal Republic of Germany. Ants (A. vollenweideri) were collected in the palm savannah of Grand Chaco, in the north of  Argentina. On two field trips in 2009 and 2010, virgin females (referred to as queens in the  following), males and workers were collected from different nests in vicinity of the field station  Rio Pilcomayo (Formosa), and transported alive to the MPI Chemical Ecology, Germany.  Antennae of sexuals and workers from the first collection (2009, C.J. Kleineidam) were pooled  for initial transcriptom sequencing, while the second collection (2010, J. Fink and S. Koch)  was kept separately for microarray studies. Since the very small workers never leave the  subterranean nest, where they care for fungus cultivation, we had to obtain them from a  laboratory colony that has been collected in Grand Chaco in 2002 (M. Bollazzi and O.  Geissler). The laboratory colony was reared in several interconnected plastic boxes (19 x 19 x  8 cm) at the University of Würzburg, and sub-colonies at the University of Konstanz at 25°C,  50-60% relative humidity and 12h/12h light/dark cycle. The workers were fed with leaf  material from Rosacea plants for fungus cultivation. Workers were collected from the feeding  site as well as from the fungus garden, and were classified as large workers in case the  measured head width was more than 1.2 mm and as tiny workers with head widths smaller  than 0.8 mm.  The numbers of collected antennae for each caste (queens, males, workers) and subcastes  (large workers and tiny workers) were adjusted to the enormous differences in body size.  Each sample consisted of approximately 300 antennae of tiny workers, 100 antennae of large  workers and 50 antennae of each of the other castes.

extract_protocol: For total RNA isolation, antennae were cut off and kept over liquid nitrogen for cooling. Subsequently they were homogenized with stainless steeal beads for 10-15 min at 50 Hz in a TissueLyser LT (Qiagen, Hilden, Germany) and RNA isolated using either Trizol as extraction reagent for large and tiny workers (Sigma Aldrich, St. Louis, MIS USA) or the innuPREP RNA Mini Kit (Analytik Jena, Jena, Germany) for the workers, queens and males samples.TotalRNA was dissolved in RNA Storage Solution (Ambion). RNA concentration was measured spectrophotometrically with a NanoDrop ND-1000 and quality of the RNA was controlled with the Agilent 2100 Bioanalyzer.

tag: Sex

value: Asexual

value: Adult antenna


title: Middle_4th_internode_1_days_before_heading_rep2

value: Middle 4th internode


title: cord_HDACi_4

source_name: dorsal ipsilateral cord, day 14, HDACi treated


title: cord_VEH_1


title: Atta vollenweideri Tiny Worker, pool2

description: pooled from 300 animals

source_name: Atta vollenweideri Tiny Worker antenna, pool2


title: Middle_4th_internode_1_days_before_heading_rep1


title: Atta vollenweideri Tiny Worker, pool3

description: pooled from 300 animals

source_name: Atta vollenweideri Tiny Worker antenna, pool3


title: Atta vollenweideri queen, pool2

description: pooled from 50 animals

source_name: Atta vollenweideri queen antenna, pool2

value: female


title: Atta vollenweideri Large Worker, pool1

description: pooled from 100 animals

source_name: Atta vollenweideri Large Worker antenna, pool1


title: Atta vollenweideri Large Worker, pool3

description: pooled from 100 animals

source_name: Atta vollenweideri Large Worker antenna, pool3


title: Atta vollenweideri queen, pool4

description: pooled from 50 animals

source_name: Atta vollenweideri queen antenna, pool4


title: Atta vollenweideri Large Worker, pool2

description: pooled from 100 animals

source_name: Atta vollenweideri Large Worker antenna, pool2


title: Lower_4th_internode_1_days_before_heading_rep2

description: Gene expression in the rice Lower 4th internode at 1 days before heading


title: cord_HDACi_3


title: Atta vollenweideri Large Worker, pool4

description: pooled from 100 animals

source_name: Atta vollenweideri Large Worker antenna, pool4


title: Atta vollenweideri queen, pool3

description: pooled from 50 animals

source_name: Atta vollenweideri queen antenna, pool3


title: Atta vollenweideri male, pool4

description: pooled from 50 animals

source_name: Atta vollenweideri male antenna, pool4

value: male


title: Atta vollenweideri queen, pool1

description: pooled from 50 animals

source_name: Atta vollenweideri queen antenna, pool1


title: Atta vollenweideri Tiny Worker, pool1

description: pooled from 300 animals

source_name: Atta vollenweideri Tiny Worker antenna, pool1


title: Lower_4th_internode_1_days_before_heading_rep3


title: Atta vollenweideri male, pool3

description: pooled from 50 animals

source_name: Atta vollenweideri male antenna, pool3


title: Upper_4th_internode_8_days_before_heading_rep2

description: Gene expression in the rice Upper 4th internode at 8 days before heading

value: 8 days before heading


title: SARSmus, HKU, Lung, 1dpi(inf), 04

city: Shinnjuku-ku

first: Naoko

last: Iwata-Yoshikawa

state: Tokyo

address: 1-23-1 Toyama

department: Pathology

institute: National institute of infectious diseases

description: Gene expression of lung in mouse immunized with UV-V at 1 day after SARS-CoV challenge

hyb_protocol: After the purification of labeled cRNA, 1.65 mg labeled samples were fragmented by the incubation with Fragmentation Buffer (Agilent) at 60°C for 30 min.  These samples were hybridized onto the Whole Mouse Genome Microarray 44k probes × 4 arrays/ slide (Agilent) at 65°C for 16 h in a rotating hyb oven at a speed of 10 rounds per min (RPM).  Microarrays slides were washed in the order of Wash Solution 1 (Agilent), Wash Solution 2 (Agilent) and acetonitrile (Wako).

scan_protocol: Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.

data_processing: The image files were analyzed by using of Feature Extraction software (Agilent) and automatically exported with flag information.

organism: Mus musculus

source_name: SARSmus, HKU, Lung, 1dpi(inf), 04

label_protocol: Three hundred nanogram of total RNA and spike-in control was amplified and labeled using Low RNA Input Linear Amplification Kit (Agilent). RNA was denatured and reverse transcribed to cDNA. cDNA was transcribed from 300 ng of total RNA using a poly-T nucleotide primer containing a T7 RNA polymerase promoter.  cRNA was subsequently synthesized and labeled with cyanine-3 (Cy3) by T7 RNA polymerase.

extract_protocol: Total RNA was purified from the samples using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. The concentrations and qualities of total RNA were measured by Spectrophotometer ND-100 (Nanodrop Technologies) and Agilent 2100 bioanalyzer (Agilent), respectively.

treatment_protocol: Mouse lungs treated with RNAlater (ABI) were stored at -80°C until use.

value: BALB/c

value: lung

value: Vaccine


title: cord_HDACi_2


title: Upper_4th_internode_8_days_before_heading_rep3


title: SARSmus, HKU, Lung, 1dpi(inf), 06

source_name: SARSmus, HKU, Lung, 1dpi(inf), 06


title: SARSmus, HKU, Lung, 1dpi(inf), 03

source_name: SARSmus, HKU, Lung, 1dpi(inf), 03


title: Lower_4th_internode_1_days_before_heading_rep1


title: cord_HDACi_1

source_name: dorsal ipsilateral cord, day 14, HDACi treated


title: 30 mins after birth neonates, DA Ecs-rep3

city: Shinjuku-ku

first: Norika

middle: Mengchia

last: Liu

address: 2-2, Wakamatsu-cho

department: Dep. Life science & Medical Bioscience

institute: Waseda University

description: Gene expression data from endothelial cells in rat neonatal ductus arteriosus

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.  Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. Transfer 80μl of hyb solution to each array, then tape holes. Hybridize 16 hours at 45° at 60rpm. Fluidics Station 450.

scan_protocol: Affymetrix, GeneChip Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: rat 30 mins after birth neonates, DA Ecs

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Rat fetuses at the 21st day of gestation (e21) and neonates 30 minutes after a delivery by cesarean section (day 0).

extract_protocol: Total RNA was extracted from the collected cells by RNeasy micro kit (QIAGEN) according to the manufacturer instructions.

treatment_protocol: Pooled tissues from the DA or the aorta were treated with collagenase-dispase enzyme mixture and reacted with FITC-conjugated anti-CD31 and APC/Cy7-conjugated anti-CD45 antibodies as cell surface markers for EC isolation using FACS.

value: vascular endothelial cells

value: ductus arteriosus

value: Wistar

tag: developmental stage

value: 30 mins after birth neonate (day0)


title: SARSmus, HKU, Lung, 1dpi(inf), 05

source_name: SARSmus, HKU, Lung, 1dpi(inf), 05


title: SARSmus, HKU, Lung, 1dpi(inf), 01

source_name: SARSmus, HKU, Lung, 1dpi(inf), 01


title: Atta vollenweideri male, pool1

description: pooled from 50 animals

source_name: Atta vollenweideri male antenna, pool1


title: SARSmus, HKU, Lung, 1dpi(inf), 02

source_name: SARSmus, HKU, Lung, 1dpi(inf), 02


title: Atta vollenweideri male, pool2

description: pooled from 50 animals

source_name: Atta vollenweideri male antenna, pool2


title: 30 mins after birth neonates, DA Ecs-rep1


title: 30 mins after birth neonates, DA Ecs-rep2


title: Middle_4th_internode_8_days_before_heading_rep1

description: Gene expression in the rice Middle 4th internode at 8 days before heading

value: japonica

value: Kinmaze


title: 30 mins after birth neonates, aorta Ecs-rep3

description: Gene expression data from endothelial cells in rat neonatal aorta

source_name: rat 30 mins after birth neonates, aorta Ecs

value: aorta


title: SARSmus,PBS, Lung, 1dpi(inf), 01-2

description: Gene expression of lung in mouse at 1 day after SARS-CoV challenge

source_name: SARSmus, PBS, Lung, 1dpi(inf), 01-2

value: Naïve


title: Upper_4th_internode_8_days_before_heading_rep1

value: Upper 4th internode


title: SARSmus,PBS, Lung, 1dpi(inf), 03

source_name: SARSmus, PBS, Lung, 1dpi(inf), 03


title: Middle_4th_internode_8_days_before_heading_rep2


title: Middle_4th_internode_8_days_before_heading_rep3


title: SARSmus,PBS, Lung, 1dpi(inf), 02

source_name: SARSmus, PBS, Lung, 1dpi(inf), 02


title: Lower_4th_internode_8_days_before_heading_rep3

description: Gene expression in the rice Lower 4th internode at 8 days before heading

value: Lower 4th internode


title: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 06

description: Gene expression of lung in mouse immunized with UV-V and TLR ligands at 1 day after SARS-CoV challenge

source_name: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 06


title: 30 mins after birth neonates, aorta Ecs-rep2


title: 30 mins after birth neonates, aorta Ecs-rep1


title: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 04

source_name: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 04


title: SARSmus,PBS, Lung, 1dpi(inf), 01

source_name: SARSmus, PBS, Lung, 1dpi(inf), 01


title: term fetuses, DA Ecs-rep2

description: Gene expression data from endothelial cells in rat fetus ductus arteriosus

source_name: rat term fetuses, DA Ecs

value: term fetus (e21)


title: term fetuses, DA Ecs-rep3


title: Lower_4th_internode_8_days_before_heading_rep1


title: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 01

source_name: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 01


title: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 02

source_name: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 02


title: term fetuses, DA Ecs-rep1


title: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 05

source_name: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 05


title: entire_4th_internode_17_days_before_heading_rep3

description: Gene expression in the rice entire 4th internode at 17 days before heading

value: entire 4th internode

value: 17 days before heading


title: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 03

source_name: SARSmus, UV-V+TLR, Lung, 1dpi(inf), 03


title: SARSmus, UV-V, Lung, 1dpi(inf), 03

source_name: SARSmus, UV-V, Lung, 1dpi(inf), 03


title: SARSmus, UV-V, Lung, 1dpi(inf), 04

source_name: SARSmus, UV-V, Lung, 1dpi(inf), 04


title: Lower_4th_internode_8_days_before_heading_rep2

value: 8 days before heading


title: SARSmus, UV-V, Lung, 1dpi(inf), 06

source_name: SARSmus, UV-V, Lung, 1dpi(inf), 06

value: BALB/c


title: SARSmus, UV-V, Lung, 1dpi(inf), 05

source_name: SARSmus, UV-V, Lung, 1dpi(inf), 05

value: lung


title: term fetuses, aorta Ecs-rep2

description: Gene expression data from endothelial cells in rat fetus aorta

source_name: rat term fetuses, aorta Ecs


title: entire_3rd_internode_17_days_before_heading_rep1

description: Gene expression in the rice entire 3rd internode at 17 days before heading

value: entire 3rd internode


title: SARSmus, UV-V, Lung, 1dpi(inf), 01

source_name: SARSmus, UV-V, Lung, 1dpi(inf), 01

value: Vaccine


title: entire_4th_internode_17_days_before_heading_rep2


title: entire_4th_internode_17_days_before_heading_rep1


title: entire_3rd_internode_17_days_before_heading_rep2


title: term fetuses, aorta Ecs-rep3

value: vascular endothelial cells


title: entire_3rd_internode_17_days_before_heading_rep3


title: SARSmus, UV-V, Lung, 1dpi(inf), 02

source_name: SARSmus, UV-V, Lung, 1dpi(inf), 02


title: 4F EDHB 72h

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

institute: Max Delbrueck Center for Molecular Medicine

description:
SAMPLE 46
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadStudio software version 3

source_name: foreskin

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion  (RNase-free DNase Set, Quiagen) has been applied on the columns during  isolation.

value: Foreskin fibroblasts transduced with the four factors and treated with EDHB

tag: age

value: Passage 3

value: fetal foreskin fibroblasts


title: 4F EDHB 48h

description:
SAMPLE 45
replicate 1


title: HIF1-KD

description:
SAMPLE 47
replicate 1

value: Foreskin fibroblasts knocked down for HIF1A


title: SCR-KD

description:
SAMPLE 48
replicate 1

value: Foreskin fibroblasts knocked down for a scrambled sequence


title: E16 cruciate ligament replicate 3

city: Boston

first: Dorothy

middle: E

last: Pazin

state: MA

address: 188 Longwood Ave. REB513

department: Developmental Biology

country: USA

institute: Harvard School of Dental Medicine

hyb_protocol: Standard Illumina hybridization protocol using 750ng labeled product

scan_protocol: Standard Illumina scanning protocol using Illumina iScan scanner

data_processing: The data were normalised using quantile normalisation in Illumina GenomeStudio

source_name: E16 mouse hindlimb

label_protocol: Biotinylated cRNA were prepared with the Nugen Encore BiotinIL Module kist for Illumina arrays

extract_protocol: RNA was extracted and Dnase I treated using the Arcturus Picopure RNA isolation kit. RNA amplificaiton was performed using the Ovation Pico SL WTA System V2 (Nugen)

value: cruciate ligament


title: 4F EDHB 24h

description:
SAMPLE 44
replicate 1


title: E16 articular cartilage replicate 3

value: articular cartilage


title: EDHB 72h

description:
SAMPLE 43
replicate 1

value: Foreskin fibroblasts treated with EDHB


title: EDHB 48h

description:
SAMPLE 42
replicate 1


title: E16 cruciate ligament replicate 2


title: E16 cruciate ligament replicate 1


title: term fetuses, aorta Ecs-rep1

value: aorta

value: Wistar

value: term fetus (e21)


title: sample 30: chest normal tissue

city: Stanford

first: Ming

last: Zheng

state: CA

address: Room L212, Lane Bldg

institute: Stanford University

data_processing: The data were normalised using quantile normalisation in R 2.15, 2012-06-22, windows 64-bit version.

label_protocol: Standard Illumina label protocol

extract_protocol: Ambion microRNA extraction Kit

tag: source

value: chest


title: sample 29: chest normal tissue


title: sample 31: chest normal tissue


title: EDHB 24h

description:
SAMPLE 41
replicate 1


title: E16 articular cartilage replicate 2


title: E16 meniscus replicate 3

value: meniscus


title: sample 28: chest normal tissue


title: sample 27: chest normal tissue


title: sample 26: chest normal tissue


title: sample 25: chest tumor tissue


title: sample 24: chest tumor tissue


title: 4F 72h_rep2

description:
SAMPLE 40
replicate 2

value: Foreskin fibroblasts transduced with the four reprogramming factors


title: sample 18: chest tumor tissue


title: sample 23: non-chest tumor tissue


title: sample 22: chest tumor tissue


title: sample 21: non-chest tumor tissue


title: 4F 48h_rep2

description:
SAMPLE 38
replicate 2


title: E16 meniscus replicate 1


title: E16 meniscus replicate 2


title: skin_αβ_detc_2

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

country: Australia

institute: University of Melbourne

description:
αβ-DETC from naive TCRδ-/- mice.
Derived from TCRδ-/- mice (which is on a C57/BL6 background).
skin_ab_detc

hyb_protocol: Performed using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

scan_protocol: Performed using GeneChip Scanner 7G (Affymetrix), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

data_processing: The following analyses were conducted in R. CEL files were normalised with background correction using RMA, quantile normalization, probe-specific background correction using MAS, and summarization using the median polish algorithm.

label: Biotin

source_name: TCRδ-/- skin, naïve

label_protocol: Performed using Encore Biotin module (Nugen), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

extract_protocol: Skin and spleen were processed as described in (Gebhardt T, et al. 2011 Nature 14:216-219). Gut and lungs were processed as described in (Masopust D, et al. 2006 J Immunology 176:2079-2083) and (Wakim L, et al. 2013 Nature Immunology 14:238-246), respectively. Briefly, skin were digested with dispase (Roche) and DNase (Sigma), followed by mechanical separation of epidermis and dermis. The epidermal sheets were then incubated in trypsin/EDTA (SAFC Biosciences) before making into cell suspensions. Spleens were disrupted by passage through wire meshes. Lungs were digested with collagenase type 3 (Worthington) and DNAse (Sigma). Gut pieces (without the lamina propria) were incubated with dithioerythritol in HBSS/HEPES bicarbonate.

value: Skin

value: αβ-dendritic epidermal T cells (DETC)

tag: infection

value: naïve

tag: time

value: control


title: 4F 24h_rep1

description:
SAMPLE 35
replicate 1

value: Passage 3


title: skin_αβ_detc_3


title: E16 articular cartilage replicate 1


title: sample 19: chest tumor tissue


title: Line 41 [AFC-iPSCs]_rep2

description:
SAMPLE 30
replicate 2

source_name: reprogramming, iPSCs from AFCs

value: Line 41

value: Passage 19

value: iPSCs from AFCs


title: skin_αβ_detc_1


title: 4F 24h_rep2

description:
SAMPLE 36
replicate 2

value: fetal foreskin fibroblasts


title: sample 20: chest tumor tissue


title: 4F 72h_rep1

description:
SAMPLE 39
replicate 1


title: sample 16: non-chest tumor tissue


title: sample 17: chest tumor tissue


title: 4F 48h_rep1

description:
SAMPLE 37
replicate 1


title: Line 41 [AFC-iPSCs]_rep1

description:
SAMPLE 29
replicate 1


title: sample 14: non-chest tumor tissue


title: sample 13: non-chest tumor tissue


title: sample 15: non-chest tumor tissue


title: sample 12: non-chest tumor tissue


title: sample 11: non-chest tumor tissue


title: skin_trm_3

description:
memory gB-T CD8+. CD103+ T cells isolated from the skin of C57/BL6 mice on day 30 p.i. with HSV KOS.
skin_trm

source_name: C57/BL6 skin, HSV, 30 days p.i.

value: memory gB-T CD8+. CD103+ T cells

value: HSV, 30 days p.i.

value: 30 days p.i.


title: sample 10: non-chest tumor tissue


title: Line 4 [AFC-iPSCs]

description:
SAMPLE 25
replicate 1

value: Line 4

value: Passage 21


title: Line 6 [AFC-iPSCs]

description:
SAMPLE 27
replicate 1

value: Line 6


title: skin_trm_2


title: OiPS16 [NFH2-iPSCs]_rep2

description:
SAMPLE 24
replicate 2

source_name: reprogramming, iPSCs from NFH2 fibroblasts

value: Passage 15

value: iPSCs from NFH2 fibroblasts


title: spleen_tem_3

description:
memory CD62L low CD8+ T cells from the spleen of mice of day 30 p.i. with HSV KOS.
spleen_tem

source_name: C57/BL6 spleen, HSV, 30 days p.i.

value: Spleen

value: memory CD62L low CD8+ T cells


title: sample 09: chest tumor tissue

value: chest


title: sample 08: non-chest tumor tissue


title: skin_trm_1

value: Skin


title: Line 10 [AFC-iPSCs]

description:
SAMPLE 28
replicate 1

value: Line 10


title: spleen_tcm_2

description:
memory CD62L high CD8+ T cells from the spleen of mice on day 30 p.i. with HSV KOS.
spleen_tcm

value: memory CD62L high CD8+ T cells


title: sample 07: chest tumor tissue


title: sample 06: chest tumor tissue


title: spleen_tem_2


title: spleen_tem_1


title: spleen_tcm_1


title: OiPS8 [NFH2-iPSCs]_rep2

description:
SAMPLE 22
replicate 2


title: spleen_tcm_3


title: Line 5 [AFC-iPSCs]

description:
SAMPLE 26
replicate 1

value: Line 5


title: OiPS16 [NFH2-iPSCs]_rep1

description:
SAMPLE 23
replicate 1


title: lung_trm_3

description:
memory gB-T CD8+ T cells from the lung of mice on day 30 p.i. with influenza WSN.
lung_trm

source_name: C57/BL6 lung, Flu WSN, 30 days p.i.

value: Lung

value: memory gB-T CD8+ T cells

value: Flu WSN, 30 days p.i.


title: spleen_naive_1

description:
naive gB-T CD8+ T cells from the spleen of naive gB-T transgenic mice.
spleen_naive

source_name: C57/BL6 spleen, naïve

value: naive gB-T CD8+ T cells

value: naïve

value: control


title: OiPS8 [NFH2-iPSCs]_rep1

description:
SAMPLE 21
replicate 1


title: lung_trm_2

value: 30 days p.i.


title: OiPS6 [NFH2-iPSCs]_rep2

description:
SAMPLE 20
replicate 2


title: sample 05: non-chest tumor tissue


title: spleen_naive_3


title: sample 02: non-chest tumor tissue


title: OiPS6 [NFH2-iPSCs]_rep1

description:
SAMPLE 19
replicate 1


title: sample 04: chest tumor tissue


title: sample 03: chest tumor tissue


title: iB5_b [BJ-iPSCs]

description:
SAMPLE 12
replicate 2

source_name: reprogramming, iPSCs from BJ fibroblasts

value: iPSCs from BJ fibroblasts


title: OiPS3 [NFH2-iPSCs]_rep2

description:
SAMPLE 18
replicate 2

value: Passage 15


title: OiPS3 [NFH2-iPSCs]_rep1

description:
SAMPLE 17
replicate 1

value: iPSCs from NFH2 fibroblasts


title: iB5_a [BJ-iPSCs]

description:
SAMPLE 11
replicate 1


title: iB4_b [BJ-iPSCs]

description:
SAMPLE 10
replicate 2


title: iB4_a [BJ-iPSCs]

description:
SAMPLE 9
replicate 1


title: gut_trm_2

description:
memory P14 CD8+ T cells isolated from gut of mice on day 60 p.i. with LCMV Armstrong.
gut_trm

source_name: C57/BL6 gut, LCMV, 60 days p.i.

value: Gut

value: memory P14 CD8+ T cells

value: LCMV, 60 days p.i.

value: 60 days p.i.


title: sample 01: chest tumor tissue

value: chest


title: skin_γδ_detc_1

description:
γδ-DETC isolated from the skin of C57/BL6 mice on day 30 p.i. with HSV KOS.
skin_gb_detc

value: Skin

value: γδ-dendritic epidermal T cells (DETC)

value: HSV, 30 days p.i.


title: gut_trm_3


title: NFH2_b

description:
SAMPLE 6
replicate 2

source_name: derma

value: 84 year old woman, passage 4

value: dermal fibroblasts


title: NFH2_a

description:
SAMPLE 5
replicate 1


title: skin_γδ_detc_2


title: AFCs_rep2

description:
SAMPLE 8
replicate 2

source_name: amniotic fluid

value: AFCs

value: Gestation, passage 17

value: amniotic fluid


title: gut_trm_1


title: spleen_naive_2

value: Spleen

value: naive gB-T CD8+ T cells

value: naïve

value: control


title: Embryonic ventral forebrain sample 2

city: Cincinnati

first: Masato

last: Nakafuku

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Embryonic ventral forebrain sample 2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were analyzed using Silicon Genetics GeneSpring Software GX7.3.1.

source_name: wild type E14.5 ventral forebrain

label_protocol: Samples were enzymatically fragmented and biotinylated using the Terminal Labeling Kit (Affymetrix)

growth_protocol: Secondary neurospheres derived from adult and embryonic brains and spinal cord

extract_protocol: RNeasy mini kit (QIAGEN) was used for isolation and purification of total RNAs. The concentration of RNA was measured using RNA Assay Nanoprep Chip 6000 and Bioanalyzer (Agilent). To compare the expression profiles across the samples, Affymetrix GeneChip Mouse Genome 430 2.0 Array Platform.

treatment_protocol: Not applicable

value: embryo (E14.5)

value: ventral forebrain


title: lung_trm_1

value: Lung

value: memory gB-T CD8+ T cells

value: Flu WSN, 30 days p.i.

value: 30 days p.i.


title: AFCs_rep1

description:
SAMPLE 7
replicate 1

value: Gestation, passage 6


title: E3 - Batch 0 - Repl 1

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

description: Gene expression data from ES cells

hyb_protocol: Following fragmentation, approx. 1.85ug of biotin-cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS3000.

data_processing: RMA normalisation implemented in Bioconductor's oligo package

source_name: M.musculus ES cells

label_protocol: Biotinylated cDNA were prepared according to the recommended protocol from approx 500ng total RNA, using Ambion's WT Expression Labelling kit and the WT Terminal Labelling kit (Affymetrix)

growth_protocol: ES cells were cultured as embryoid bodies (EBs) in serum-free conditions. On day 2 of the culture, the EBs were induced with retinoic acid and Smoothened agonist to form caudal/spinal and ventral neural tissue. On day 5 of the culture, EBs were dissociated, and ES cell-derived motor neurons isolated by magnetic cell sorting (MACS) for the motor neuron-specific surface reporter transgenes CD2 or CD14.

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

treatment_protocol: The MACS-enriched motor neurons were induced with doxycycline to express one or two candidate phrenic neuron determinant gene(s) and cultured on matrigel-coated permanox-slides for 30 hours. In some experiments with Notch-intracellular domain genes, the transgene was only induced for the last 10 hours of the culture.

value: ES cells

tag: induced gene

value: E3 parental induced

tag: processing


title: skin_γδ_detc_3

value: Skin

value: γδ-dendritic epidermal T cells (DETC)

value: HSV, 30 days p.i.


title: Embryonic ventral forebrain sample 1

description: Embryonic ventral forebrain sample 1


title: E3 - Batch 0 - Repl 2

description: Gene expression data from ES cells


title: Embryonic dorsal forebrain sample 2

description: Embryonic dorsal forebrain sample 2

source_name: wild type E14.5 dorsal forebrain

value: dorsal forebrain


title: Pou3f1;Lhx3 - Batch 7 - Repl 4

description: Gene expression data from ES cells induced with Pou3f1;Lhx3

source_name: M.musculus ES cells induced with Pou3f1;Lhx3


title: Embryonic dorsal forebrain sample 1

description: Embryonic dorsal forebrain sample 1


title: Adult subventricular zone sample 3

description: Adult subventricular zone sample 3

source_name: wild type adult brain subventricular zone

value: adult

value: brain subventricular zone


title: Roots from Ca. L. asiaticus infected plant 6, biological rep2

city: Lake Alfred

first: Valente

last: Aritua

state: Florida

address: 700 Experiment Staion Road

department: Plant Pathology

institute: University of Florida

description:
Valencia sweet orange
Gene expression data from roots of 3 year old plants infected with Ca. L. asiaticus

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

scan_protocol: GeneChips were scanned using Affymetrics Model 3000 7G scanner according to the manufacture's recommended protocols.

data_processing:
Raw data collected using Microarray Suite version 5.0 (MAS 5.0). Statistical tests were performed using the BioConductor statistical software, Version 2.5.
Normalsied log2 fold change (stems from Ca. L. asiaticus infected plants/healthy, roots from Ca. L. asiaticus infected plants/healthy); False discovery rate; P-values; MAS5.0 signal intensity

organism: Citrus sinensis

source_name: Citrus roots from Ca. L. asiaticus infected plants 16 months after innoculation

label_protocol: Four micrograms of total RNA was used to generate biotinylated cRNA using one-cycle target labelling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated from freshly obtained stems and roots using RNeasy Plant Mini kit and treated with DNase (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Valencia sweet orange (C. sinensis) plants were graft inoculated with budwood from Ca. L. asiaticus-infected citrus plants

value: lateral roots branching off taproots

value: 3 year old plants graft innoculated with Ca. L. asiaticus

value: Candidatus Liberibacter asiaticus


title: Embryonic spinal cord sample

description: Embryonic spinal cord sample

source_name: wild type E14.5 spinal cord

value: embryo (E14.5)

value: spinal cord


title: Roots from Ca. L. asiaticus infected plant 8, biological rep3


title: Adult subventricular zone sample 2

description: Adult subventricular zone sample 2


title: NERT (10) - Batch 7 - Repl 2

description: Gene expression data from ES cells induced with NERT (10)

source_name: M.musculus ES cells induced with NERT (10)

value: NERT (10)


title: NERT (30) - Batch 7 - Repl 2

description: Gene expression data from ES cells induced with NERT (30)

source_name: M.musculus ES cells induced with NERT (30)

value: NERT (30)


title: Adult striatum sample 3

description: Adult striatum sample 3

source_name: wild type adult brain striatum

value: brain striatum


title: Roots from Ca. L. asiaticus infected plant 5, biological rep1


title: YFP - Batch 7 - Repl 2

description: Gene expression data from ES cells induced with YFP

source_name: M.musculus ES cells induced with YFP

value: YFP


title: Roots from healthy plant 3, biological rep2

description:
Valencia sweet orange
Gene expression data from roots of healthy 3 year old plants

source_name: Citrus roots from non-infected plants

value: 3 year old plants


title: Pou3f1;Lhx3 - Batch 7 - Repl 3

value: ES cells


title: Roots from healthy plant 4, biological rep3


title: Adult subventricular zone sample 1

description: Adult subventricular zone sample 1


title: Roots from healthy plant 2, biological rep1


title: Stem from Ca. L. asiaticus infected plant 8, biological rep3

description:
Valencia sweet orange
Gene expression data from stems of 3 year old plants infected with Ca. L. asiaticus

source_name: Citrus stems from Ca. L. asiaticus infected plants  16 months after innoculation

value: young stem tissues and bark peels with phloem


title: Stem from Ca. L. asiaticus infected plant 6, biological rep2


title: Adult neocortex sample 3

description: Adult neocortex sample 3

source_name: wild type adult brain neocortex

value: brain neocortex


title: Adult striatum sample 1

description: Adult striatum sample 1


title: Adult striatum sample 2

description: Adult striatum sample 2


title: NERT (30) - Batch 7 - Repl 1


title: Stem from Ca. L. asiaticus infected plant 5, biological rep1


title: YFP - Batch 7 - Repl 1


title: NERT (10) - Batch 7 - Repl 1


title: Stem from healthy plant 4, biological rep3

description:
Valencia sweet orange
Gene expression data from stems of healthy 3 year old plants

source_name: Citrus stems from non-infected plants


title: Adult neocortex sample 2

description: Adult neocortex sample 2


title: Adult neocortex sample 1

description: Adult neocortex sample 1


title: Flag;Pou3f1 - Batch 6 - Repl 1

description: Gene expression data from ES cells induced with Flag;Pou3f1

source_name: M.musculus ES cells induced with Flag;Pou3f1


title: Flag;Pou3f1 - Batch 6 - Repl 2


title: Stem from healthy plant 3, biological rep2


title: Pou3f1;Hoxc6 - Batch 6 - Repl 2

description: Gene expression data from ES cells induced with Pou3f1;Hoxc6

source_name: M.musculus ES cells induced with Pou3f1;Hoxc6


title: mg060509_m430_2_116

city: Rotterdam

first: Andreas

last: Kremer

address: Dr. Molewaterplein 50

department: Bioinformatics

country: Netherlands

institute: Erasmus MC

description: Sample 116

hyb_protocol: Following fragmentation, 15 mg of cRNA were hybridized for 16 hours at 45C on GeneChip  Mouse Genome 430 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: Affymetrix protocol using Gene Chip Scanner 3000, GCOS software

data_processing: Data processing MAS5 with global scaling to target value 100, followed by setting all values lower than 30 at 30, and then log2 transformation

source_name: intestinal tumor, Lin-P1P2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 nanogram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix MOE430 plus2.0 microarray platform using the Two-cycle Labelling kit according to manufacturer’s instruction.

growth_protocol: Cells are directly isolated from fresh tumor & had no culture step.

extract_protocol: total RNA was isolated from 104 sorted cells by RNAeasy Micro kit (QIAGEN) and quality controlled by RNA 6000 Pico and Nano LabChip kits (Agilent Technologies).

treatment_protocol: Tumors were harvested from Apc1638N/+ and Apc1638N/+/KRASV12G mice aged 6 to 8 months. Tumors from individual animals were pooled, minced with a razor blade, and suspended into 10 ml digestion medium (RPMI, EGF 5 ng ml-1, Hydrocortisone 50 ng ml-1, Insulin/Transferrin) supplemented with 10% foetal calf serum and containing 4 mg ml-1 collagenase A (#11088793001, Roche), 0.1 mg ml-1  Dispase II (#165859, Roche) and 50 mg ml-1 DNaseI (#DN-25, Sigma). Digestions were conducted for 2 h at 370C, 5% CO2. The final cell suspension was filtrated through a 70-mm cell strainer (BD) and stained with antibodies.

tag: background

tag: genotype

tag: tissue type

value: intestinal adeno tumor


title: YFP - Batch 6 - Repl 2

tag: cell type


title: Stem from healthy plant 2, biological rep1

tag: tissue


title: Pou3f1;Hoxc6 - Batch 6 - Repl 1


title: mg060509_m430_2_117

description: Sample 117

source_name: intestinal tumor, Lin-P3


title: mg060509_m430_2_106

description: Sample 106

source_name: intestinal tumor, Lin-


title: Pou3f1;Hoxa5 - Batch 6 - Repl 2

description: Gene expression data from ES cells induced with Pou3f1;Hoxa5

source_name: M.musculus ES cells induced with Pou3f1;Hoxa5


title: mg060509_m430_2_115

description: Sample 115


title: Pou3f1;Hoxa5 - Batch 6 - Repl 3


title: E3 - Batch 6 - Repl 0

description: Gene expression data from ES cells induced with E3

source_name: M.musculus ES cells induced with E3

value: E3 parental


title: Leaves from Ca. L. asiaticus infected plant 5, biological rep2

description:
Valencia sweet orange
Gene expression data in leaves  infected with Ca. L. asiaticus

data_processing:
Raw data collected using Microarray Suite version 5.0 (MAS 5.0). Statistical tests were performed using the BioConductor statistical software, Version 2.5.
Normalsied log2 fold change (leaves from Ca. L. asiaticus infected plants/healthy); False discovery rate; detection P-values; MAS5.0 signal intensity

source_name: Citrus leaves from Ca. L. asiaticus infected plants, 8 months after innoculation

extract_protocol: Total RNA was isolated from freshly obtained leaf tissues using RNeasy Plant Mini kit and treated with DNase (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: old symptomatic leaves

value: ~2 year old plants graft innoculated with Ca. L. asiaticus


title: Pou3f1 - Batch 6 - Repl 1

description: Gene expression data from ES cells induced with Pou3f1

source_name: M.musculus ES cells induced with Pou3f1


title: Leaves from healthy plant 2, biological rep2

description:
Valencia sweet orange
Gene expression data in leaves from healthy  plants

source_name: Citrus leaves from non-infected plants

value: old symptomless leaves

value: ~2 year old plants


title: Pou3f1 - Batch 6 - Repl 2


title: Leaves from healthy plant 3, biological rep3


title: Leaves from healthy plant 1, biological rep1


title: Leaves from Ca. L. asiaticus infected  plant 6, biological rep3

value: Candidatus Liberibacter asiaticus


title: Zic1 - Batch 6 - Repl 1

description: Gene expression data from ES cells induced with Zic1

source_name: M.musculus ES cells induced with Zic1


title: Pou3f1;Lhx3 (DN) - Batch 6 - Repl 2

description: Gene expression data from ES cells induced with Pou3f1;Lhx3 (DN)

source_name: M.musculus ES cells induced with Pou3f1;Lhx3 (DN)


title: mg060509_m430_2_93

description: Sample 93

value: intestinal adenocarcinoma tumor


title: Lhx3 - Batch 6 - Repl 1

description: Gene expression data from ES cells induced with Lhx3

source_name: M.musculus ES cells induced with Lhx3


title: mg060509_m430_2_98

description: Sample 98


title: mg060509_m430_2_102

description: Sample 102


title: Leaves from Ca. L. asiaticus infected plant 4, biological rep1


title: mg060509_m430_2_108

description: Sample 108


title: mg060509_m430_2_97

description: Sample 97


title: mg060509_m430_2_92

description: Sample 92


title: mg060509_m430_2_91

description: Sample 91


title: mg060509_m430_2_107

description: Sample 107


title: Pou3f1;Lhx3 (DN) - Batch 6 - Repl 1


title: mg060509_m430_2_80

description: Sample 80


title: mg060509_m430_2_84

description: Sample 84


title: Pou3f1;Hoxa1 - Batch 6 - Repl 1

description: Gene expression data from ES cells induced with Pou3f1;Hoxa1

source_name: M.musculus ES cells induced with Pou3f1;Hoxa1


title: YFP - Batch 6 - Repl 1

source_name: M.musculus ES cells induced with YFP


title: mg060509_m430_2_79

description: Sample 79


title: Lhx3 - Batch 5 - Repl 2


title: Hoxc6 - Batch 5 - Repl 1

description: Gene expression data from ES cells induced with Hoxc6

source_name: M.musculus ES cells induced with Hoxc6


title: Zic1 - Batch 5 - Repl 2


title: 14 hrs poly IC IFNAR-/- DC 1

city: New York

first: Paula

last: Longhi

address: 1230 York Av

institute: The Rockefeller University

description:
SAMPLE 34
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with GeneSpring.

source_name: splenic CD11chi, IFNAR/-, poly IC, 14hr

label_protocol: ~200 ng of total RNA was used to prepare biotin-labeled RNA using MessageAmp™ Premier RNA Amplification Kit.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit.

tag: strain/background

value: IFNAR/-

value: splenic CD11chi CD3- DX5- B220- dendritic cells

tag: treatment

value: poly IC

tag: treatment duration


title: Pou3f1;Hoxa1 - Batch 5 - Repl 2

tag: strain


title: 14 hrs poly IC IFNAR-/- DC 3

description:
SAMPLE 36
Replicate 3


title: 14 hrs poly IC WT DC 4

description:
SAMPLE 31
Replicate 4

source_name: splenic CD11chi, wild-type, poly IC, 14hr

value: wild-type


title: 14 hrs poly IC IFNAR-/- DC 2

description:
SAMPLE 35
Replicate 2


title: 14 hrs poly IC WT DC 6

description:
SAMPLE 33
Replicate 6


title: 14 hrs poly IC WT DC 3

description:
SAMPLE 30
Replicate 3


title: mg060509_m430_2_60

description: Sample 60


title: mg060509_m430_2_34

description: Sample 34


title: mg060509_m430_2_57

description: Sample 57


title: H4 - Batch 5 - Repl 0

description: Gene expression data from ES cells induced with H4

source_name: M.musculus ES cells induced with H4

value: H4 parental


title: mg060509_m430_2_32

description: Sample 32


title: 14 hrs poly IC WT DC 5

description:
SAMPLE 32
Replicate 5


title: 14 hrs poly IC WT DC 2

description:
SAMPLE 29
Replicate 2


title: Hoxc6 - Batch 5 - Repl 2


title: mg060509_m430_2_46

description: Sample 46


title: mg060509_m430_2_52

description: Sample 52


title: mg060509_m430_2_48

description: Sample 48

source_name: intestinal tumor, Lin-P1P2


title: mg060509_m430_2_53

description: Sample 53


title: Hoxa5 - Batch 5 - Repl 1

description: Gene expression data from ES cells induced with Hoxa5

source_name: M.musculus ES cells induced with Hoxa5


title: Arid5b - Batch 4 - Repl 1

description: Gene expression data from ES cells induced with Arid5b

source_name: M.musculus ES cells induced with Arid5b


title: Hey1 - Batch 4 - Repl 2

description: Gene expression data from ES cells induced with Hey1

source_name: M.musculus ES cells induced with Hey1


title: Molly-Insect day 3.3

city: Lincoln

first: Chitvan

last: Khajuria

state: NE

address: 103 Entomology Hall

institute: University of Nebraska-Lincoln

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Mayetiola destructor

source_name: Larvae reared in Molly plants

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Twenty germinated wheat seeds were planted in 10-cm-diameter pots filled with PRO-MIX ‘BX’ potting mix (Hummert Inc., Earth City, MO) in a growth chamber programmed at 20:18°C (L:D) with a photoperiod of 14:10 (L:D) h.  When wheat seedlings reached the 1.5 leaf stage (stage 11 on Zadoks scales) [35], the plants were infested with 0.5 Hessian fly females per plant on average by confining the insects in a screened cage.

extract_protocol: Total RNA was extracted using a miRNA isolation kit (miRNeasy kit, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Larvae were collected one and three days after egg hatch from susceptible Newton and resistant Molly plants

value: whole Ist instar larvae

value: Larvae reared in Molly plants

value: 3 d


title: Molly-Insect day 3.2


title: Notch1 ICD (10) - Batch 4 - Repl 2

description: Gene expression data from ES cells induced with Notch1 ICD (10)

source_name: M.musculus ES cells induced with Notch1 ICD (10)

value: ES cells

value: Notch1 ICD (10)


title: 14 hrs poly IC WT DC 1

description:
SAMPLE 28
Replicate 1


title: Pou3f1 - Batch 4 - Repl 1

source_name: M.musculus ES cells induced with Pou3f1


title: 4 hrs poly IC IFNAR-/- DC 3

description:
SAMPLE 25
Replicate 3

source_name: splenic CD11chi, IFNAR/-, poly IC, 4hr


title: Molly-Insect day 3.1


title: Newton-Insect day 3.3

source_name: Larvae reared in Newton plants

value: Larvae reared in Newton plants


title: 4 hrs poly IC IFNAR-/- DC 1

description:
SAMPLE 23
Replicate 1


title: 4 hrs poly IC IFNAR-/- DC 4

description:
SAMPLE 26
Replicate 4


title: H4 - Batch 4 - Repl 0


title: Pou3f1 - Batch 4 - Repl 2


title: 4 hrs poly IC IFNAR-/- DC 2

description:
SAMPLE 24
Replicate 2


title: mg060509_m430_2_30

description: Sample 30


title: Newton-Insect day 3.1


title: Newton-Insect day 3.2


title: Molly-Insect day 1.3

value: 1 d


title: Notch1 ICD (10) - Batch 4 - Repl 1


title: 4 hrs poly IC PRR-/- DC 5

description:
SAMPLE 22
Replicate 5

source_name: splenic CD11chi, PRR-/-, poly IC, 4hr

value: PRR-/-


title: 4 hrs poly IC IFNAR-/- DC 5

description:
SAMPLE 27
Replicate 5


title: 4 hrs poly IC PRR-/- DC 3

description:
SAMPLE 20
Replicate 3


title: Hoxa5 - Batch 4 - Repl 2


title: Chd5 - Batch 4 - Repl 2

description: Gene expression data from ES cells induced with Chd5

source_name: M.musculus ES cells induced with Chd5


title: 4 hrs poly IC PRR-/- DC 1

description:
SAMPLE 18
Replicate 1


title: 4 hrs poly IC PRR-/- DC 2

description:
SAMPLE 19
Replicate 2


title: Tox - Batch 3 - Repl 2

description: Gene expression data from ES cells induced with Tox

source_name: M.musculus ES cells induced with Tox

value: Tox


title: Btbd3 - Batch 3 - Repl 1

description: Gene expression data from ES cells induced with Btbd3

source_name: M.musculus ES cells induced with Btbd3


title: Tox - Batch 3 - Repl 1


title: Molly-Insect day 1.2


title: Molly-Insect day 1.1


title: 4 hrs poly IC PRR-/- DC 4

description:
SAMPLE 21
Replicate 4


title: Newton-Insect day 1.3


title: 4 hrs poly IC WT DC 8

description:
SAMPLE 17
Replicate 8

source_name: splenic CD11chi, wild-type, poly IC, 4hr


title: Arid5b - Batch 3 - Repl 1


title: Vwc2 - Batch 3 - Repl 1

description: Gene expression data from ES cells induced with Vwc2

source_name: M.musculus ES cells induced with Vwc2


title: 4 hrs poly IC WT DC 6

description:
SAMPLE 15
Replicate 6


title: Lhx3 (DN) - Batch 3 - Repl 2

description: Gene expression data from ES cells induced with Lhx3 (DN)

source_name: M.musculus ES cells induced with Lhx3 (DN)


title: Notch1 ICD (30) - Batch 3 - Repl 2

description: Gene expression data from ES cells induced with Notch1 ICD (30)

source_name: M.musculus ES cells induced with Notch1 ICD (30)

value: Notch1 ICD (30)


title: 4 hrs poly IC WT DC 5

description:
SAMPLE 14
Replicate 5


title: 4 hrs poly IC WT DC 4

description:
SAMPLE 13
Replicate 4


title: 4 hrs poly IC WT DC 3

description:
SAMPLE 12
Replicate 3


title: Newton-Insect day 1.2


title: 4 hrs poly IC WT DC 2

description:
SAMPLE 11
Replicate 2


title: 4 hrs poly IC WT DC 7

description:
SAMPLE 16
Replicate 7


title: Unstimulated DC 8

description:
SAMPLE 8
Replicate 8

source_name: splenic CD11chi, unstimulated


title: 4 hrs poly IC WT DC 1

description:
SAMPLE 10
Replicate 1


title: Vwc2 - Batch 3 - Repl 2


title: Btbd3 - Batch 3 - Repl 2


title: Unstimulated DC 9

description:
SAMPLE 9
Replicate 9


title: YFP - Batch 3 - Repl 1

description: Gene expression data from ES cells induced with YFP

source_name: M.musculus ES cells induced with YFP

value: YFP


title: Unstimulated DC 7

description:
SAMPLE 7
Replicate 7


title: Lhx3 (DN) - Batch 3 - Repl 1


title: Unstimulated DC 6

description:
SAMPLE 6
Replicate 6


title: Notch1 ICD (30) - Batch 3 - Repl 1


title: Unstimulated DC 5

description:
SAMPLE 5
Replicate 5


title: YFP - Batch 3 - Repl 2


title: Klf6 - Batch 3 - Repl 2

description: Gene expression data from ES cells induced with Klf6

source_name: M.musculus ES cells induced with Klf6


title: Klf6 - Batch 2 - Repl 2


title: Chd5 - Batch 3 - Repl 1


title: Unstimulated DC 4

description:
SAMPLE 4
Replicate 4


title: Newton-Insect day 1.1


title: Klf5 - Batch 2 - Repl 8

description: Gene expression data from ES cells induced with Klf5

source_name: M.musculus ES cells induced with Klf5


title: Unstimulated DC 3

description:
SAMPLE 3
Replicate 3


title: Unstimulated DC 2

description:
SAMPLE 2
Replicate 2


title: Zbtb7c - Batch 2 - Repl 2

description: Gene expression data from ES cells induced with Zbtb7c

source_name: M.musculus ES cells induced with Zbtb7c


title: Sfmbt2 - Batch 2 - Repl 2

description: Gene expression data from ES cells induced with Sfmbt2

source_name: M.musculus ES cells induced with Sfmbt2


title: Unstimulated DC 1

description:
SAMPLE 1
Replicate 1


title: Hoxa1 - Batch 2 - Repl 8

description: Gene expression data from ES cells induced with Hoxa1

source_name: M.musculus ES cells induced with Hoxa1


title: Zbtb7c - Batch 2 - Repl 1


title: Pou3f1 - Batch 2 - Repl 2

description: Gene expression data from ES cells induced with Pou3f1

source_name: M.musculus ES cells induced with Pou3f1


title: adult hepatocyte parental control [AH_CRTL2]

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

description:
Control sample
SAMPLE 60

data_processing: Data was processed by means of Genome Studio v2011 from illumina, Inc.

label_protocol: Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

value: adult hepatocyte parental control


title: Pou3f1 - Batch 1 - Repl 6


title: adult hepatocyte parental control [AH_CRTL4]

description:
Control sample
SAMPLE 62


title: H2122-LKB1KD_rep3

city: Columbus

first: David

last: Carbone

state: Ohio

address: 460 West 12th Avenue; 488 BRT

department: Internal Medicine

institute: Ohio State University

description: H2122 cells stably expressing pBABE LKB1 K78I

hyb_protocol: 5.5ug of fragmented, biotinylated cDNA were hybridized for 16 hours to a HT Human Gene 1.1 ST PM16 array plate utilizing the GeneTitan instrument.

scan_protocol: HT Human Gene 1.1 ST chips were scanned using scanned on the Affymetrix Gene Titan AGCC v. 3.2.3

data_processing: CEL files were analyzed on Affymetrix Expression Console v. 1.1 using a RMA normalization algorithm producing log base 2 results.

source_name: Lung cancer cell line H2122 with empty vector pBABE

label_protocol: Ambion WT Expression reactions for all samples were started using 130ng of total RNA. Resulting cRNA products from the overnight IVT reactions were cleaned with Ambion-WT bead cleanup kit. 10.5ug cRNA was used for cDNA synthesis. Resulting cDNA was cleaned with Ambion-WT bead cleanup kit. 5.5ug of cDNA was used for biotin labeling reactions.

growth_protocol: Cell lines were grown in RPMI1640 containing 5% fetal bovine serum, without antibiotics. Cells were harvested during logarithmic growth.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Isolated RNA was bioanalyzed using Agilent to determine 260/280 ratio, RNA concentration, and RIN.

treatment_protocol: Cell lines were stably transduced with pBABE retroviral constructs expressing wild-type LKB1 (LKB1-WT), or controls of empty pBABE (pBABE) or kinase dead mutant LKB1 (LKB1-K78I). Selection for cell lines with stable expression of these constructs was achieved by culturing cells in growth media containing 1.0 micrograms/milliliter puromycin for two weeks.

tag: disease state

value: Non-small cell lung cancer

tag: cell line

tag: gene transduction

value: pBABE LKB1 K78I


title: hepatoblast parental control [HB_CRTL2]

description:
Control sample
SAMPLE 56

value: hepatoblast parental control


title: H2122-LKB1_rep2

description: H2122 cells stably expressing pBABE LKB1 wild-type

source_name: Lung cancer cell line H2122 with wild-type LKB1

value: pBABE LKB1 wild-type


title: H2122-LKB1_rep3

source_name: Lung cancer cell line H2122 with LKB1 K78I


title: H2122-pBABE_rep2

description: H2122 cells stably expressing pBABE empty vector

value: pBABE empty vector


title: YFP - Batch 2 - Repl 2


title: H2122-LKB1KD_rep1


title: H2122-LKB1KD_rep2


title: adult hepatocyte parental control [AH_CRTL3]

description:
Control sample
SAMPLE 61


title: hepatoblast parental control [HB_CRTL3]

description:
Control sample
SAMPLE 57


title: hepatoblast parental control [HB_CRTL4]

description:
Control sample
SAMPLE 58


title: Hey1 - Batch 2 - Repl 1

description: Gene expression data from ES cells induced with Hey1

source_name: M.musculus ES cells induced with Hey1


title: Sfmbt2 - Batch 1 - Repl 5


title: H4 - Batch 2 - Repl 0

description: Gene expression data from ES cells induced with H4

source_name: M.musculus ES cells induced with H4

value: H4 parental


title: H2122-pBABE_rep1


title: H2122-LKB1_rep1


title: adult hepatocyte parental control [AH_CRTL1]

description:
Control sample
SAMPLE 59


title: YFP - Batch 1 - Repl 1


title: hepatoblast parental control [HB_CRTL1]

description:
Control sample
SAMPLE 55


title: oval cell parental control [HPC_CRTL4]

description:
Control sample
SAMPLE 54

value: oval cell parental control


title: oval cell parental control [HPC_CRTL3]

description:
Control sample
SAMPLE 53


title: Hoxa1 - Batch 1 - Repl 6


title: oval cell parental control [HPC_CRTL1]

description:
Control sample
SAMPLE 51


title: adult hepatocyte derived tumor [AH20]

description:
Tumor
SAMPLE 50

value: adult hepatocyte derived tumor


title: Klf5 - Batch 1 - Repl 7

value: ES cells


title: A549-pBABE_rep2

description: A549 cells stably expressing pBABE empty vector

source_name: Lung cancer cell line A549 with empty vector pBABE


title: A549-LKB1KD_rep2

description: A549 cells stably expressing pBABE LKB1 K78I

source_name: Lung cancer cell line A549 with LKB1 K78I


title: A549-LKB1KD_rep3


title: A549-LKB1_rep2

description: A549 cells stably expressing pBABE LKB1 wild-type

source_name: Lung cancer cell line A549 with wild-type LKB1


title: adult hepatocyte derived tumor [AH19]

description:
Tumor
SAMPLE 49


title: A549-pBABE_rep1


title: adult hepatocyte derived tumor [AH15]

description:
Tumor
SAMPLE 45


title: A549-pBABE_rep3


title: adult hepatocyte derived tumor [AH13]

description:
Tumor
SAMPLE 43


title: oval cell parental control [HPC_CRTL2]

description:
Control sample
SAMPLE 52


title: adult hepatocyte derived tumor [AH18]

description:
Tumor
SAMPLE 48


title: adult hepatocyte derived tumor [AH17]

description:
Tumor
SAMPLE 47


title: A549-LKB1_rep1


title: adult hepatocyte derived tumor [AH12]

description:
Tumor
SAMPLE 42


title: A549-LKB1_rep3


title: adult hepatocyte derived tumor [AH9]

description:
Tumor
SAMPLE 39


title: adult hepatocyte derived tumor [AH11]

description:
Tumor
SAMPLE 41


title: adult hepatocyte derived tumor [AH16]

description:
Tumor
SAMPLE 46


title: adult hepatocyte derived tumor [AH14]

description:
Tumor
SAMPLE 44


title: adult hepatocyte derived tumor [AH10]

description:
Tumor
SAMPLE 40


title: A549-LKB1KD_rep1


title: adult hepatocyte derived tumor [AH8]

description:
Tumor
SAMPLE 38


title: adult hepatocyte derived tumor [AH6]

description:
Tumor
SAMPLE 36


title: adult hepatocyte derived tumor [AH5]

description:
Tumor
SAMPLE 35


title: adult hepatocyte derived tumor [AH7]

description:
Tumor
SAMPLE 37


title: adult hepatocyte derived tumor [AH2]

description:
Tumor
SAMPLE 32


title: Hypo 8hours IFN

city: Austin

first: Chris

last: Sullivan

state: TX

address: 2506 Speedway

institute: University of Texas-Austin

description: SAMPLE J

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

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: Dicer Hypomorph

value: 8 hours IFN


title: Hypo 24hours IFN

description: SAMPLE L

value: 24 hours IFN


title: adult hepatocyte derived tumor [AH3]

description:
Tumor
SAMPLE 33


title: wild type 8 hours IFN

description: SAMPLE F

value: wild type


title: adult hepatocyte derived tumor [AH4]

description:
Tumor
SAMPLE 34


title: hepatoblast derived tumor [HB18]

description:
Tumor
SAMPLE 28

value: hepatoblast derived tumor


title: hepatoblast derived tumor [HB20]

description:
Tumor
SAMPLE 30


title: MKN45_mutYAP1_2

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a gene expression data matrix based on unique gene, the Sample Gene Profile option of Illumina BeadStudio software was used.

source_name: MKN45, YAP-S127A vector

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations were determined using a spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

value: gastric cancer cells

value: YAP-S127A vector


title: Hypo 3hours control

description: SAMPLE H

value: 3 hours control


title: hepatoblast derived tumor [HB19]

description:
Tumor
SAMPLE 29


title: hepatoblast derived tumor [HB15]

description:
Tumor
SAMPLE 25


title: MKN45_mutYAP1_1


title: adult hepatocyte derived tumor [AH1]

description:
Tumor
SAMPLE 31


title: hepatoblast derived tumor [HB17]

description:
Tumor
SAMPLE 27


title: Hypo 24hours control

description: SAMPLE I

value: 24 hours control


title: hepatoblast derived tumor [HB16]

description:
Tumor
SAMPLE 26


title: wild type 3hours IFN

description: SAMPLE B

value: 3 hours IFN


title: Hypo 3hours IFN

description: SAMPLE K


title: MKN45_mutYAP1_3


title: wild type 8hours control

description: SAMPLE E

value: 8 hours control


title: wild type 24hours control

description: SAMPLE C


title: MKN45_VEC_2

source_name: MKN45, control vector

value: control vector


title: wild type 24hours IFN

description: SAMPLE D


title: wild type 3hours control

description: SAMPLE A


title: K14-Cre;Tgfbr2 fl/fl Mutant Posterior Palate 6

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: Whole genome transcriptome profile of murine posterior palatal tissue, collected at E15.5, from mutant mice with a conditional inactivation of Tgfbr2 in epithelial cells.

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: Samples were processed by RMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray.

source_name: E15.5 K14-Cre;Tgfbr2 fl/fl Conditional Knockout Mutant Mouse Model

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used

extract_protocol: Embryo was harvested at embryonic day 15.5 of development. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from anterior or posterior palatal tissue, from either mutant or control mice as designated.

treatment_protocol: Mice were maintained under standard IACUC protocols.

value: K14-Cre;Tgfbr2 fl/fl

value: Posterior Palate

tag: age

tag: gender

value: Not determined


title: Hypo 8hours control

description: SAMPLE G


title: MKN45_VEC_1


title: K14-Cre;Tgfbr2 fl/fl Mutant Posterior Palate 5


title: hepatoblast derived tumor [HB12]

description:
Tumor
SAMPLE 22


title: hepatoblast derived tumor [HB13]

description:
Tumor
SAMPLE 23


title: MKN45_CON_2

source_name: MKN45, mock

value: mock


title: hepatoblast derived tumor [HB9]

description:
Tumor
SAMPLE 19


title: K14-Cre;Tgfbr2 fl/fl Mutant Posterior Palate 2


title: hepatoblast derived tumor [HB11]

description:
Tumor
SAMPLE 21


title: K14-Cre;Tgfbr2 fl/fl Mutant Posterior Palate 4


title: K14-Cre;Tgfbr2 fl/fl Mutant Posterior Palate 3


title: MKN45_CON_1


title: DEXA shPTEN rep1

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

data_processing: Data was transformed to log2 scale and quantile normalized. MATLAB and MATLAB Bioinformatics Toolbox was used for data processing.

source_name: shPTEN DND41 cell lines treated with DEXA

label_protocol: 500 ng of RNA from each sample was amplified and biotinylated using the Illumina® TotalPrep™ RNA Amplification Kit.

extract_protocol: RNA isolation from treated DND41 cell line samples was performed in triplicate using the RNeasy micro kit (Qiagen) according to manufacturer's protocol

treatment_protocol: DND41 human cell line infected with shPTEN or shLUC, and treated with 1µM Dexamethasone or DMSO for 24h in triplicate.

tag: infection

value: shPTEN

tag: agent

value: Dexamethasone


title: hepatoblast derived tumor [HB10]

description:
Tumor
SAMPLE 20


title: hepatoblast derived tumor [HB7]

description:
Tumor
SAMPLE 17


title: K14-Cre;Tgfbr2 fl/fl Mutant Posterior Palate 1


title: NahG-Rywal_6dpi_PVY_plant2

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: biological replicate 2 of 4

hyb_protocol: Hybridization mixture was set up using Gene Expression Hybridization Kit (Agilent) and applied to the microarray. The hybridization at 65°C for 17 h was followed by washing according to the manufacturer’s protocol.

scan_protocol: Dried microarrays were scanned with LS200 Array Scanner (Tecan Group Ltd., Switzerland) at 160 gain laser power and two times oversampling at 633 nm, taking care not to saturate any spots. The scanned images were analysed and data were extracted with ArrayPro (Media Cybernetics, Inc., MD).

data_processing: Data was analyzed in R environment with limma package. Quantile normalization was used, background was not substacted.

organism: Solanum tuberosum

source_name: NahG-Rywal, whole PVY-inoculated leaf, 6 dpi

label_protocol: 1 μg of RNA was spiked with 500 ng of One–Color Spike–Mix (Agilent) and amplified and labelled with Cy–5 using MessageAmp II aRNA Amplification Kit (Ambion), both according to manufacturers' protocols.

growth_protocol: Potato plants were grown in pots (ø 15 cm) in growth chambers under controlled conditions of light (5,000 Lx), temperature (22°C – day, 18°C – night) and photoperiod (16 h – day, 8 h – night).

extract_protocol: Total RNA was extracted from leaves  using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The isolation was followed with DNase (Invitrogen, Carlsbad, CA) treatment using 0.4 U of DNase per 1 μg of RNA. Finally, RNA was purified with RNeasy MinElute Cleanup Kit (Qiagen). All RNA samples were checked for quality with Bioanalyzer (Agilent), and RNA concentration was measured using NanoDrop spectrophotometer (Thermo Fisher Scientific Inc., DE).

treatment_protocol: PVY or mock- infection was performed on 4–week–old potato plants from in vitro cultures grown in soil. Selected leaves were dusted with carborundum powder and rubbed with a cloth dipped in a sap prepared from leaves of previously PVY–infected tobacco. After 10 min, the leaves were washed liberally with water. As a mock control, water was used instead of the sap.

value: NahG-Rywal

value: PVY-inoculation

tag: time

value: 6 dpi


title: NahG-Rywal_6dpi_PVY_plant4

description: biological replicate 4 of 4

tag: genotype


title: DEXA shPTEN rep3


title: hepatoblast derived tumor [HB8]

description:
Tumor
SAMPLE 18

value: hepatoblast derived tumor


title: Tgfbr2 fl/fl Control Posterior Palate 4

description: Whole genome transcriptome profile of murine posterior palatal tissue, collected at E15.5, from control mice.

source_name: E15.5 Tgfbr2 Wildtype Mouse Model

value: Tgfbr2 fl/fl


title: DEXA shPTEN rep2


title: MKN45_CON_3

value: gastric cancer cells


title: hepatoblast derived tumor [HB14]

description:
Tumor
SAMPLE 24


title: NahG-Rywal_6dpi_PVY_plant1

description: biological replicate 1 of 4


title: DMSO shPTEN rep3

source_name: shPTEN DND41 cell lines treated with DMSO

value: control


title: Tgfbr2 fl/fl Control Posterior Palate 5


title: NahG-Rywal_6dpi_PVY_plant3

description: biological replicate 3 of 4


title: DMSO shPTEN rep2


title: MKN45_VEC_3


title: hepatoblast derived tumor [HB6]

description:
Tumor
SAMPLE 16


title: Tgfbr2 fl/fl Control Posterior Palate 6


title: Tgfbr2 fl/fl Control Posterior Palate 2


title: Tgfbr2 fl/fl Control Posterior Palate 3


title: hepatoblast derived tumor [HB4]

description:
Tumor
SAMPLE 14


title: hepatoblast derived tumor [HB5]

description:
Tumor
SAMPLE 15


title: NahG-Rywal_6dpi_mock_plant3

description: biological replicate 3 of 4

source_name: NahG-Rywal, whole mock-inoculated leaf, 6 dpi

value: mock-inoculation


title: DEXA shLUC rep3

source_name: shLUC DND41 cell lines treated with DEXA

value: shLUC


title: NahG-Rywal_6dpi_mock_plant4

description: biological replicate 4 of 4


title: DMSO shPTEN rep1


title: NahG-Rywal_6dpi_mock_plant2

description: biological replicate 2 of 4


title: DEXA shLUC rep2


title: hepatoblast derived tumor [HB1]

description:
Tumor
SAMPLE 11


title: Tgfbr2 fl/fl Control Anterior Palate 5

description: Whole genome transcriptome profile of murine anterior palatal tissue, collected at E15.5, from control mice.

value: Anterior Palate


title: DEXA shLUC rep1


title: hepatc progenitor cell derived tumor [HPC10]

description:
Tumor
SAMPLE 10

value: hepatc progenitor cell derived tumor


title: Tgfbr2 fl/fl Control Posterior Palate 1


title: DMSO shLUC rep3

source_name: shLUC DND41 cell lines treated with DMSO


title: NahG-Rywal_3dpi_PVY_plant4

description: biological replicate 4 of 4

source_name: NahG-Rywal, whole PVY-inoculated leaf, 3 dpi

value: 3 dpi


title: Tgfbr2 fl/fl Control Anterior Palate 4


title: hepatoblast derived tumor [HB2]

description:
Tumor
SAMPLE 12


title: Tgfbr2 fl/fl Control Anterior Palate 2


title: hepatoblast derived tumor [HB3]

description:
Tumor
SAMPLE 13


title: hepatc progenitor cell derived tumor [HPC9]

description:
Tumor
SAMPLE 9


title: NahG-Rywal_6dpi_mock_plant1

description: biological replicate 1 of 4


title: Tgfbr2 fl/fl Control Anterior Palate 6


title: hepatc progenitor cell derived tumor [HPC8]

description:
Tumor
SAMPLE 8


title: Tgfbr2 fl/fl Control Anterior Palate 3


title: NahG-Rywal_3dpi_PVY_plant2

description: biological replicate 2 of 4


title: DMSO shLUC rep1


title: DMSO shLUC rep2


title: hepatc progenitor cell derived tumor [HPC6]

description:
Tumor
SAMPLE 6


title: NahG-Rywal_3dpi_PVY_plant3

description: biological replicate 3 of 4


title: NahG-Rywal_3dpi_PVY_plant1

description: biological replicate 1 of 4