title: Grafted drought tolerant grapevine rootstock (110R) under drought stress (DS) _rep2

description:
110R_DS_grafted_2
Vitis berlandieri X Vitis rupestris
Gene expression data from drought treated roots of grafted-drought tolerant grapevine rootstock (110R).

value: grafted drought tolerant

value: two-year-old grafted and rooted cuttings


title: Patient 4 primary tumour

status: Public on Dec 31 2017

type: genomic

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: minfi 1.18.1, SWAN Normalisation

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE primary tumour tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Promega ReliaPrep™ FFPE gDNA Miniprep System.

tag: tissue type (primary=0, recurrent=1, recurrent2=2)

tag: gender

value: M

tag: age

tag: survival (months)

tag: time to relapse (months)

tag: survival (months

tag: includepaired (0=no, 1=yes)

tag: replicate array (0=no, 1=yes)

tag: treatment prior to second surgery

value: Stupp concurrent and standard adjuvant


title: Patient 3 recurrent tumour

value: Stupp concurrent and 4 cycles adjuvant


title: Grafted drought tolerant grapevine rootstock (110R) under well watered period (WWP) _rep2

type: RNA

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

description:
110R_WWP_grafted_2
Vitis berlandieri X Vitis rupestris
Gene expression data from well watered roots of grafted-drought tolerant grapevine rootstock (110R).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Vitis vinifera (grape) Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

molecule: total RNA

organism: Vitis cinerea var. helleri x Vitis rupestris

source_name: roots grown under well watered control condition at 90-100% field capacity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Drought tolerant 110R rootstock were firstly grafted with sultana seedless. After callusing and rooting, grafted and non-grafted plants were grown for two years in 20 L pots filled with soil (clay loam (pH 6.4) with 0.0062 dS/m EC, 1.9% organic carbon content) perlite mixture (4:1). All the experiments were carried out in semi-controlled greenhouse.

extract_protocol: Roots collected from control and drought treated plants were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al. (2007).

treatment_protocol: Drought treatment applied to plants by completely withholding irrigation from the pots. Sampling was done when the soil water content of the pots decreased to 5-10% at the end of drought treatment. Control condition was created by well irrigation of the replicates at the field capacity.

tag: tissue

value: root

tag: genotype/variation

tag: treatment

value: well watered


title: Patient 14 recurrent tumour rep 1


title: Patient 18 primary tumour

value: F


title: Patient 3 primary tumour


title: Grafted drought tolerant grapevine rootstock (110R) under drought stress (DS)_rep1

description:
110R_DS_grafted_1
Vitis berlandieri X Vitis rupestris
Gene expression data from drought treated roots of grafted-drought tolerant grapevine rootstock (110R).

source_name: drought treated roots at 5-10% field capacity

value: drought


title: Non-grafted drought tolerant grapevine rootstock (110R) under well watered period (WWP) _rep1

description:
110R_WWP_non-grafted_1
Vitis berlandieri X Vitis rupestris
Gene expression data from well watered roots of nongrafted-drought tolerant grapevine rootstock (110R).

value: non-grafted drought tolerant

value: two-year-old non-grafted and rooted cuttings


title: Grafted drought tolerant grapevine rootstock (110R) under well watered period (WWP) _rep1

description:
110R_WWP_grafted_1
Vitis berlandieri X Vitis rupestris
Gene expression data from well watered roots of grafted-drought tolerant grapevine rootstock (110R).


title: Patient 1 primary tumour


title: Patient 11 primary tumour

value: Stupp concurrent only


title: 177Lu_Z97-70_xenograft_10_MBq_#2 [mouse]

city: Boston

first: Johan

last: Spetz

state: MA

address: HSPH2, Room 229, 655 Huntington Ave.

department: JBL Center for Radiation Sciences

country: USA

institute: Harvard School of Public Health

scan_protocol: Standard Illumina iScan N240 scanning protocol Direct Hyb

data_processing: The data were normalized using quantile normalization with BASE

label: biotin

organism: Mus musculus

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

tag: host strain

value: Balb/c

tag: xenograft tissue

tag: injected with

tag: injected activity

value: 10 MBq

tag: time point


title: Patient 9 recurrent tumour

tag: tissue type (primary=0, recurrent=1, recurrent2=2)

value: Stupp concurrent and adjuvant AVAglio (+/-bev)


title: Patient 14 primary tumour

tag: gender


title: Patient 12 recurrent tumour rep 1

tag: age


title: 177Lu_Z97-70_xenograft_10_MBq_#3 [mouse]


title: Patient 9 primary tumour rep 1

tag: survival (months)


title: Patient 10 primary tumour

tag: time to relapse (months)

value: Stupp concurrent and 2 cycles adjuvant AVAglio (+/-bev)


title: Patient 3 primary tumour rep 1

tag: survival (months


title: 177Lu_Z97-Control_xenograft_0_MBq_#1 [mouse]

value: 0 MBq


title: 177Lu_Z97-23_xenograft_10_MBq_#2 [mouse]


title: 177Lu_Z97-Control_xenograft_0_MBq_#2 [mouse]


title: affected member 31

city: Tianjin

first: Liu

last: Chang

address: 94 Weijin Road

department: College of Life Science

country: China

institute: Nankai University

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
31p-7

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix 7G Scanner

data_processing: The genotype calls of each individual were determined by the Birdseed version 1 genotype calling algorithm, embedded in the software Affymetrix Genotyping Console 2.0 (Affymetrix). Genotype Call (SNP call): AA, AB, BB

source_name: affected member of a FNMTC family

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) according to the manufactures’ instructions. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: peripheral blood

tag: disease status

value: Familial nonmedullary thyroid cancer (FNMTC)

value: male


title: Patient 11 recurrent tumour

value: M

tag: includepaired (0=no, 1=yes)

tag: replicate array (0=no, 1=yes)


title: Patient 2 recurrent tumour

tag: treatment prior to second surgery


title: 177Lu_Z97-23_xenograft_10_MBq_#3 [mouse]


title: normal member 36

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
36n-9

source_name: normal member of a FNMTC family

tag: tissue

value: healthy


title: Patient 3 recurrent tumour rep 1

value: Stupp concurrent and 4 cycles adjuvant


title: Patient 1 recurrent tumour


title: 177Lu_Z97-70_xenograft_10_MBq_#1 [mouse]


title: 177Lu_BDT-Control_xenograft_0_MBq_#2 [mouse]

source_name: 177Lu GOT1-Control xenograft_0 MBq


title: 177Lu_BDT-24_xenograft_7_MBq_#1 [mouse]

source_name: 177Lu GOT1-24h xenograft_7 MBq

value: 7 MBq


title: 177Lu_Z97-23_xenograft_10_MBq_#1 [mouse]


title: 177Lu_Z97-0.5_xenograft_10_MBq_#1 [mouse]


title: normal member 33

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
33n-4

value: female


title: Non-grafted drought tolerant grapevine rootstock (110R) under drought stress (DS) _rep2

description:
110R_DS_non-grafted_2
Vitis berlandieri X Vitis rupestris
Gene expression data from drought treated roots of nongrafted-drought tolerant grapevine rootstock (110R).

value: root

tag: genotype/variation

tag: treatment

value: drought


title: affected member 32

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
32p-8


title: affected member 22

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
22p-2


title: 177Lu_Z97-0.5_xenograft_10_MBq_#2 [mouse]

tag: host strain

tag: xenograft tissue


title: normal member 26

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
26n-3


title: affected member 24

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
24p-11


title: 177Lu_BDT-Control_xenograft_0_MBq_#1 [mouse]

tag: injected with

tag: injected activity


title: normal member 21

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
21n-10


title: affected member 12

description:
Hybridized to Affymetrix Genome-Wide Human SNP Array 6.0
12p-1


title: Landrace 35 Re-watered Replicate 3

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

hyb_protocol: Equal quantities (up to 100 pmol) of dye coupled cDNA were combined and to this, 11 µl 10X Agilent Blocking buffer and 2.2 µl 25X Agilent Fragmentation buffer were added. Samples were incubated at 60°C for 30 minutes. Agilent 2X GE hybridisation buffer (55 µl) was added to samples before 100 µl of the mix was carefully pipetted onto the centre of a gasket slide, over which the microarray slide was placed, and secured in the chamber with a clamp assembly. Slides were rotated at 10 rpm and maintained at 65°C overnight (17 hours). Following separation from the cover gasket slide, the microarray was washed with Agilent Wash buffers 1 and 2 as per manufacturer’s instructions. Microarray slides were spin-dried for 15 s and scanned immediately.

scan_protocol: Slides were scanned on a Genepix 4000B scanner. Images were quantified using the Genepix 6.1 Software (version 6.1.0.4).

data_processing: LIMMA in R was used to perform background subtraction (using the normexp function with an offset of 50), as well as robust-spline and aquantile normalization.

organism: Sorghum bicolor

source_name: LR35 Control

label_protocol:
Equal amounts (5 µg each) of three RNA samples from individual plants were pooled and first strand cDNA was synthesized using 9 µg of pooled RNA with 1.5 µl oligo (dT) (2 µg/µl) and 6 µl Random primer stock (0.5 µg/µl). After incubation for 10 min at 70°C, the following components were added: 2.25 µl Superscript® III reverse transcriptase (400 U), 15 µl 5X SST buffer, 7.5 µl 10X aa-dUTP mix, 7.5 µl 100mM DTT and 1.5 µl Ribolock RNase Inhibitor. Samples were incubated at 25°C for 5 min, followed by 42°C overnight (~19 hours). To each reaction, 15 µl 0.5 M EDTA and 15 µl 1 N NaOH was added, and incubated for 10 min at 65°C. Reactions were cleaned with the Macherey-Nagel Nucleospin Gel and PCR Clean-up kit as per manufacturer’s instructions.
Each cDNA treatment and its corresponding control sample were dye labelled with either Cy3 or Cy5 reactive dye. The appropriate dye (2.5 µl) was added to 2.5 µl cDNA sample and 5 µl 0.2 M Na2CO3 buffer (pH 9.0), then incubated in the dark for 2 hours. A dye swap of one of the three pooled replicates per treatment was included. The Qiagen PCR Purification kit was used to clean reactions.

growth_protocol: Sorghum plants were grown in pots under controlled conditions to a 30-60 cm stalk height.

extract_protocol: Total RNA was extracted from ground, frozen leaf material using the QIAzol Lysis Reagent and Qiagen RNeasy kits. Powdered leaf material (~50 mg) was combined with 1 ml QIAzol reagent in a 2 ml micro-centrifuge tube, vortexed and incubated for 5 min at ambient temperature (24-28oC). Chloroform (0.2 ml) was added; tubes were vigorously shaken for 15 sec and incubated for 3 min at ambient temperature. Samples were centrifuged at 12 000 g for 10 min at 4°C. The upper aqueous phase was combined with an equal volume of 70% ethanol, gently mixed, then transferred onto RNeasy columns and centrifuged at 8000 g for 15 s. Thereafter, total RNA was purified as per manufacturer’s instructions. An on-column DNase I digestion was included using 27 Kunitz units for 15 min. RNA was eluted with nuclease-free water.

treatment_protocol: For Mild stress plants water was withheld for four days. Rewatered plants were withheld from water for seven days, followed by re-watering and leaf harvesting after five hours. For Severe stress plants water was withheld for six days.

value: Leaf material

tag: strain

value: South African Landrace 35

source_name: LR35 Re-watered


title: HB3_48hr_2 (gene-level)

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 100 Galvin Life Science Building

department: Biological Science

institute: University of Notre Dame

description: Gene expression of synchronized untreated cultures , 48 hours post invasion, biological replicate 2

hyb_protocol: 5.33ug of labeled sample was suspended in 3.3uL of 3.75X Denhardt's Solution and mixed with 4.7uL of Nimblegen's hybridization mastermix (2X hybe buffer, component A, and Alignment Oligo). 6.0uL of each sample was loaded onto the array and hybrizided for 17 hours in on the Nimblegen hybridization station in mix mode B.

scan_protocol: Microarrays were scanned with the Nimblegen scanner at 2.0uM resolution. Autogain for each sample area determined the specific laser intensity setting for each sample.

data_processing: Image data was processed using Nimblescan to align images and generate .pair files. Robust multiarray averaging was done simultaneously for all the samples used for this project. Probes below the backgound signal and lower than the 5% false discovery rate were removed from further analysis. Probes were then averaged by gene.

organism: Plasmodium falciparum

source_name: O+ blood culture of HB3 parasites, 48 hours post invasion

label_protocol: 300ng of RNA was used as starting material for cDNA synthesis using Sigma WTA2 kit. Then 1ug of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: Parasite cultures were grown in replicates at 37C and 5% hematocrit in O+ human erythrocytes using RPMI 1640 supplemented with 0.5% Albumax I, 0.25% sodium bicarbonate, and 0.01mg/mL genatmicin under an atmosphere of 90% nitrogen, 5% oxygen, and 5% carbon dioxide.

extract_protocol: Total RNA was extracted from 20mLs of culture using TriZol reagent.

treatment_protocol: Cultures were synchronized using 5% sorbitol prior to collection of specific time points.

tag: time

value: 48 hours post invasion

tag: host cell type

value: human erythrocyte


title: HB3_36hr_2 (gene-level)

description: Gene expression of synchronized untreated cultures , 36 hours post invasion, biological replicate 2

source_name: O+ blood culture of HB3 parasites, 36 hours post invasion

value: 36 hours post invasion


title: HB3_48hr_1 (gene-level)

description: Gene expression of synchronized untreated cultures , 48 hours post invasion, biological replicate 1


title: Landrace 35 Re-watered Replicate 1


title: Landrace 35 Re-watered Replicate 2


title: HB3_24hr_1_rep2 (gene-level)

description: Gene expression of synchronized untreated cultures , 24 hours post invasion, biological replicate 1, technical replicate 2

source_name: O+ blood culture of HB3 parasites, 24 hours post invasion

value: 24 hours post invasion


title: 177Lu_BDT-24_xenograft_7_MBq_#2 [mouse]

value: Balb/c

tag: time point


title: Landrace 35 Mild Stress Replicate 3

source_name: LR35 Mild stress


title: HB3_36hr_1 (gene-level)

description: Gene expression of synchronized untreated cultures , 36 hours post invasion, biological replicate 1


title: Landrace 35 Severe Stress Replicate 2

source_name: LR35 Severe stress


title: Landrace 35 Severe Stress Replicate 1


title: Landrace 35 Severe Stress Replicate 3


title: Landrace 35 Mild Stress Replicate 2


title: Landrace 6 Severe Stress Replicate 3

source_name: LR6 Severe stress

value: South African Landrace 6

source_name: LR6 Control


title: HB3_24hr_1_rep1 (gene-level)

description: Gene expression of synchronized untreated cultures , 24 hours post invasion, biological replicate 1, technical replicate 1


title: HB3_24hr_2_rep1 (gene-level)

description: Gene expression of synchronized untreated cultures , 24 hours post invasion, biological replicate 2, technical replicate 1


title: HB3_12hr_2 (gene-level)

description: Gene expression of synchronized untreated cultures , 12 hours post invasion, biological replicate 2

source_name: O+ blood culture of HB3 parasites, 12 hours post invasion

value: 12 hours post invasion


title: HB3_24hr_2_rep2 (gene-level)

description: Gene expression of synchronized untreated cultures , 24 hours post invasion, biological replicate 2, technical replicate 2


title: Landrace 6 Severe Stress Replicate 1


title: Landrace 35 Mild Stress Replicate 1


title: Landrace 6 Re-watered Replicate 3

source_name: LR6 Re-watered


title: Landrace 6 Severe Stress Replicate 2


title: Landrace 6 Re-watered Replicate 2


title: Landrace 6 Mild Stress Replicate 3

source_name: LR6 Mild stress


title: Landrace 6 Re-watered Replicate 1


title: HB3_36hr_B (gene-level)

description: Gene expression of synchronized untreated cultures , 36 hours post invasion, biological replicate B


title: HB3_12hr_1 (gene-level)

description: Gene expression of synchronized untreated cultures , 12 hours post invasion, biological replicate 1


title: Landrace 6 Mild Stress Replicate 2


title: HB3_36hr_A (gene-level)

description: Gene expression of synchronized untreated cultures , 36 hours post invasion, biological replicate A


title: HB3_12hr_C (gene-level)

description: Gene expression of synchronized untreated cultures 12 hours post invasion, biological replicate C


title: HB3-48h (gene-level)

description:
2 biological replicates: HB3-1-48h , HB3-2-48h
Raw data files:
2015-07-29_256178610013_HB3-1-48h_532_635_converted_GE1_Dec2014_MTF_EXP_1_4.txt
2015-07-29_256178610013_HB3-2-48h_532_635_converted_GE1_Dec2014_MTF_EXP_2_4.txt

hyb_protocol: 2.5ug of labeled cDNA was mixed with Agilent 10X Blocking Agent and 2X Hi-RPM Hybridization Buffer as directed by standard Agilent protocols to bring total volume of sample to 50.0uL. A total of 40uL was loaded into the gasket slides and hybridized to the Agilent Array.

scan_protocol: Microarrays were scanned with the Nimblegen scanner at 2.0uM resolution. Autogain for the entire array was set based on laser intensity for plex 1-1.

data_processing: Image file was processed using Agilent Feature Extraction. Samples were robust multiarray averaged simultaneously with all samples used in this study. Probes below background and those not meeting a 5% false discovery rate were removed before further analysis. Signal intensities for probes were then averaged by exon and by gene.


title: HB3-36h (gene-level)

description:
2 biological replicates: HB3-1-36h , HB3-2-36h
Raw data files:
2015-07-29_256178610013_HB3-1-36h_532_635_converted_GE1_Dec2014_MTF_EXP_1_3.txt
2015-07-29_256178610013_HB3-2-36h_532_635_converted_GE1_Dec2014_MTF_EXP_2_3.txt


title: HB3_12hr_A (gene-level)

description: Gene expression of synchronized untreated culture 12 hours post invasion, biological replicate A


title: HB3-24h (gene-level)

description:
2 biological replicates: HB3-1-24h , HB3-2-24h
Raw data files:
2015-07-29_256178610013_HB3-1-24h_532_635_converted_GE1_Dec2014_MTF_EXP_1_2.txt
2015-07-29_256178610013_HB3-2-24h_532_635_converted_GE1_Dec2014_MTF_EXP_2_2.txt


title: Young basidiocarp-30 days

city: Irapuato

first: Claudia

middle: Geraldine

last: Leon-Ramirez

state: Guanajuato

address: Km. 9.6 Lib. Nte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Cinvestav Unidad Irapuato

description: Ustilago maydis diploid strain Uid1 (a1b1Δpan/a2b2Δodc::HygR) (Ruiz-Herrera et al., 1999) growth at pH7 for one month

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

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

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

organism: Mycosarcoma maydis

label_protocol: Synthesis and labeling of cDNA were performed by Roche  NimbleGen Inc.

growth_protocol: U. maydis diploid strain Uid1 (a1b1Δpan/a2b2Δodc::HygR) was recovered from minimal medium (MM; Holliday, 1974) pH 7 and inoculated into 500 ml MM adjusted to pH 7.  Incubation under shaking conditions of 150 rpm at 28 ºC for 18 h.

extract_protocol: RNA was isolated from three independent cell cultures (biological replicates) using the Trizol method (Invitrogen, Carlsband, CA, USA) following the manucfactures´s instructions and purified with QIAGEN columns. RNA concentrations were messured by absorbance at 260 nm with Nanodrop (Termo Scientific, Waltham, MA, USA), and its integrity was observed by electrophoresis in denaturing agarose gels.

treatment_protocol: Basidiocarps were induced according to Cabrera et al. 2012, 25 l 105 cells/mL of a diploid strain Uid1 (a1b1Δpan/a2b2Δodc::HygR) (Ruiz-Herrera et al., 1999) was cultured on PCD2  medium (Murashige and Skoog medium, supplemented with Dicamba 2 mg/L, adenine 40 mg/L, pH 5.6, gelrite 3 g/L) and separated for 1 cm of 50 mg of maize embryogenic calli inbred line H99. Incubated in light conditions with 50 moles/m2/sec and 25ºC of temperature.

value: Diploid strain Uid1

tag: phenotype

value: Basidiocarp

tag: growth condition

value: mm pH7

value: 30 days


title: Mature basidiocarp-120 days

description: Ustilago maydis diploid strain Uid1 (a1b1Δpan/a2b2Δodc::HygR) (Ruiz-Herrera et al., 1999) growth at pH7 for four months

value: 120 days


title: Landrace 6 Mild Stress Replicate 1


title: Landrace 5 Severe Stress Replicate 3

source_name: LR5 Control

value: South African Landrace 5

source_name: LR5 Severe stress


title: Diploid yeast-like 18h

description: Ustilago maydis diploid strain Uid1 (a1b1Δpan/a2b2Δodc::HygR) (Ruiz-Herrera et al., 1999) growth at pH7 18h

value: Yeast


title: Landrace 5 Severe Stress Replicate 2


title: Landrace 5 Re-watered Replicate 2

source_name: LR5 Re-watered


title: Landrace 5 Re-watered Replicate 1


title: HB3-12h (gene-level)

description:
2 biological replicates: HB3-1-12h , HB3-2-12h
Raw data files:
2015-07-29_256178610013_HB3-1-12h_532_635_converted_GE1_Dec2014_MTF_EXP_1_1.txt
2015-07-29_256178610013_HB3-2-12h_532_635_converted_GE1_Dec2014_MTF_EXP_2_1.txt


title: Landrace 5 Severe Stress Replicate 1


title: Landrace 5 Re-watered Replicate 3


title: Landrace 5 Mild Stress Replicate 2

source_name: LR5 Mild stress


title: BrdU + CXCL12_rep1

status: Public on Dec 30 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description:
Cells treated with 100 uM BrdU and 200 ng/ml of CXCL12 for 48 hours
BS 48_4_R1

hyb_protocol: 600 ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent designed Human Gene expression Microarray 8x60K (AMADID No: 027114) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

source_name: BrdU + CXCL12, ATCC HeLa cell line

label_protocol: Samples for Gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). 500 ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: HeLa cells cultured in DMEM media containing 10% FBS

extract_protocol: RNA extraction was performed using the Qiagen RNA isolation kit as per manufacturer’s protocol. The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).

treatment_protocol: Control, 100μM BrdU, CXCL12 200ng/ml, CXCL12 200ng/ml+100μM BrdU for 48 hours

tag: cell line

value: HeLa

value: BrdU and CXCL12


title: Landrace 5 Mild Stress Replicate 1

value: Leaf material


title: Landrace 5 Mild Stress Replicate 3


title: OE-N6

city: Guiyang

first: Xiaozhen

last: Huang

state: Guizhou

address: South campus of Guizhou University, Huaxi, Guiyang

institute: Guizhou University

description: Gene expression data from 2-week-old seedlings of the OE-N6

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis ATH1 Genome  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard Genesystem Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

source_name: Transgenic plant overexpressing NHRGP (OE-N6) plants

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

growth_protocol: seedlings of the wild-type and OE-N6 grown on 1/2 MS medium containing 2% sucrose at 22˚C under a 16-h light/8-h dark photoperiod at 100 μmol m–2 s–1.

extract_protocol: Total RNAs were extracted using the Plant RNA Prep Kit (Qiagen, Hilden, Germany)

value: whole plant

tag: cultivar

tag: genotype

tag: age

value: 2-week-old seedlings


title: Control + CXCL12_rep1

description:
Cells treated with 200 ng/ ml of CXCL12 for 48 hours
CS 48_3_R1

source_name: Control + CXCL12, ATCC HeLa cell line


title: Control + CXCL12_rep2

description:
Cells treated with 200 ng/ ml of CXCL12 for 48 hours
CS 48_3_R2


title: Columbia-0

description: Gene expression data from 2-week-old seedlings of the wild-type(col)

source_name: Arabidopsis wild-type (Columbia-0:Col )

tag: tissue

value: wildtype


title: BrdU + CXCL12_rep2

description:
Cells treated with 100 uM BrdU and 200 ng/ml of CXCL12 for 48 hours
BS 48_4_R2


title: BrdU_rep2

description:
Cells treated with 100 uM BrdU for 48 hours
Brdu 48_2_R2

source_name: BrdU, ATCC HeLa cell line

value: BrdU


title: BrdU_rep1

description:
Cells treated with 100 uM BrdU for 48 hours
Brdu 48_2_R1


title: Control_rep1

description:
Control untreated cells for 48 hours
Control 48_1_R1

source_name: Control, ATCC HeLa cell line

value: control


title: Control_rep2

description:
Control untreated cells for 48 hours
Control 48_1_R2


title: skin SMA+ [028005]

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

description: SAMPLE 1

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent G2595C Scanner

data_processing: Genespring 14.5, Normalization: Shift to 75 percentile

source_name: skin

label_protocol: Agilent low-Input QuickAmp Labeling Kit

extract_protocol: Trizol for RNA isolation

tag: cell type

value: fibroblast-like cells


title: skin SMA+ [026655], 2

description: SAMPLE 6


title: wound SMA+++ [028005]

description: SAMPLE 2

source_name: wound

value: myofibroblast


title: wound SMA+++ [026655], 2

description: SAMPLE 5


title: skin SMA+ [026655], 1

description: SAMPLE 4


title: wound SMA+++ [026655], 1

description: SAMPLE 3


title: H2009 shKRAS_low Q

city: Palo Alto

first: E.

middle: Alejandro

last: Sweet-Cordero

state: CA

address: 265 Campus Drive

department: Pediatrics

institute: Stanford University

description:
Cells expressed KRAS hairpin
100896670057__H

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using the R lumi package

source_name: NSCLC cell line

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

growth_protocol: Cells were cultured in DMEM supplemented with 5% serum and penicillin/streptomycin at 37degrees C with 5%CO2.

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.

treatment_protocol: Cells stably expressing doxycycline-inducible shGFP or shKRAS were cultured for 3 days with 1ug/mL doxycycline in 0.5mM glutamine where indicated prior to RNA extraction.

value: NSCLC

tag: shRNA

value: shKRAS

tag: q concentration

value: 0.5mM Q


title: Moyo-S_Dengue_Serotype3_infected_18hr_post_feeding_batch 2

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

description: Sample 21

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

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

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

organism: Aedes aegypti

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

growth_protocol:
Moyo-S females were orally fed with defribinated sheep blood that was either contaminated or not conatminated with different serotypes of dengue virus (DENV-1 Hawaii, DENV-2 JAM1409, DENV-3 YUC97 and DENV-4 H-241).
Moyo-R females were orally fed with defribinated sheep blood that was either contaminated or not conatminated with different serotypes of dengue virus (DENV-1 Hawaii, DENV-2 JAM1409, DENV-3 YUC97 and DENV-4 H-241).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

value: Moyo-S

tag: Sex

value: female

tag: genotype/variation

value: wild-type

tag: phenotype (for dengue virus)

value: Susceptible

tag: infected with

value: 18hr post feeding


title: Moyo-R_Dengue_Serotype3_infected_18hr_post_feeding_batch 2

description: Sample 23

tag: strain

value: Moyo-R

value: Refractory


title: H358 shKRAS_low Q

description:
Cells expressed KRAS hairpin
100896670057__F

scan_protocol: Standard Illumina hybridization protocol


title: Moyo-R_Dengue_Serotype4_infected_3hr_post_feeding_batch 2

description: Sample 20

value: 3hr post feeding


title: H2009 shGFP_low Q

description:
Cells expressed control hairpin
100896670057__G

value: shGFP


title: Moyo-R_Dengue_Serotype4_infected_18hr_post_feeding_batch 2

description: Sample 24


title: A549 shKRAS_low Q

description:
Cells expressed KRAS hairpin
100896670057__D


title: H358 shGFP_low Q

description:
Cells expressed control hairpin
100896670057__E


title: H460 shKRAS_low Q

description:
Cells expressed KRAS hairpin
100896670057__C


title: Moyo-S_Dengue_Serotype3_infected_3hr_post_feeding_batch 2

description: Sample 17


title: Moyo-S_Dengue_Serotype4_infected_18hr_post_feeding_batch 2

description: Sample 22

value: none (uninfected control)


title: Moyo-S_Uninfected_control_18hr_post_feeding_batch 2

description: Sample 15


title: Moyo-S_Dengue_Serotype4_infected_3hr_post_feeding_batch 2

description: Sample 18


title: Moyo-R_Dengue_Serotype3_infected_3hr_post_feeding_batch 2

description: Sample 19


title: H460 shGFP_low Q

description:
Cells expressed control hairpin
100896670057__A


title: A549 shGFP_low Q

description:
Cells expressed control hairpin
100896670057__B


title: Moyo-R_Uninfected_control_18hr_post_feeding_batch 2

description: Sample 16


title: Moyo-R_Uninfected_control_3hr_post_feeding_batch 2

description: Sample 14


title: W3_A2B(Cy3)_R2

description:
US90403632_252665510202_S01_GE2_107_Sep09_1_2
Week 3

hyb_protocol: 825ng each of cy3 and Cy5 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner

data_processing: Images Analysis using Agilent Feature Extraction Software Version 11.5 to obtain raw data. Probe intensities generated from feature extraction raw data were split based on channel type and analysis was performed.

source_name: Brain

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0444). Five hundred nanograms each of the  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP and Cy5 CTP was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol.

value: Week 3


title: W40_A2B(Cy5)_R4

description:
US90403632_252665510202_S01_GE2_107_Sep09_1_2
Week 40

value: Week 40


title: H2009 shGFP_high Q

description:
Cells expressed control hairpin
8508853067_G

treatment_protocol: Cells stably expressing doxycycline-inducible shGFP or shKRAS were cultured for 3 days with 1ug/mL doxycycline in 4mM Q where indicated prior to RNA extraction.

value: 4mM Q


title: Moyo-S_Uninfected_control_3hr_post_feeding_batch 2

description: Sample 13


title: W40_A2B(Cy5)_R2

description:
US90403632_252665510203_S01_GE2_107_Sep09_1_2
Week 40


title: Moyo-R_Dengue_Serotype2_infected_18hr_post_feeding_batch 1

description: Sample 12


title: W12_A1B(Cy3)_R1

description:
US90403632_252665510203_S01_GE2_107_Sep09_1_1
Week 12

value: Week 12


title: W40_A1B(Cy5)_R3

description:
US90403632_252665510202_S01_GE2_107_Sep09_1_1
Week 40


title: W12_A2B(Cy3)_R2

description:
US90403632_252665510203_S01_GE2_107_Sep09_1_2
Week 12


title: H358 shKRAS_high Q

description:
Cells expressed KRAS hairpin
8508853067_F

value: NSCLC


title: H2009 shKRAS_high Q

description:
Cells expressed KRAS hairpin
8508853067_H

value: shKRAS


title: Moyo-R_Dengue_Serotype1_infected_18hr_post_feeding_batch 1

description: Sample 11


title: Moyo-S_Dengue_Serotype1_infected_18hr_post_feeding_batch 1

description: Sample 8


title: W40_A1B(Cy5)_R1

description:
US90403632_252665510203_S01_GE2_107_Sep09_1_1
Week 40


title: H460 shGFP_high Q

description:
Cells expressed control hairpin
8508853067_A


title: H460 shKRAS_high Q

description:
Cells expressed KRAS hairpin
8508853067_B


title: A549 shKRAS_high Q

description:
Cells expressed KRAS hairpin
8508853067_D


title: Moyo-S_Dengue_Serotype2_infected_18hr_post_feeding_batch 1

description: Sample 9


title: A549 shGFP_high Q

description:
Cells expressed control hairpin
8508853067_C


title: H358 shGFP_high Q

description:
Cells expressed control hairpin
8508853067_E


title: Moyo-S_Uninfected_control_18hr_post_feeding_batch 1

description: Sample 7


title: Moyo-R_Dengue_Serotype2_infected_3hr_post_feeding_batch 1

description: Sample 6


title: H1792 4mM Q

description:
Cells grown under high glutamine conditions (4mM)
200319680035_K

treatment_protocol: Cells were grown with 4mM or 0.5mM glutamine.


title: A549 0.5mM Q

description:
Cells grown under low glutamine conditions (0.5mM)
200319680035_J


title: Moyo-R_Uninfected_control_18hr_post_feeding_batch 1

description: Sample 10


title: H1792 0.5mM Q

description:
Cells grown under low glutamine conditions (0.5mM)
200319680035_L


title: Moyo-R_Dengue_Serotype1_infected_3hr_post_feeding_batch 1

description: Sample 5


title: Moyo-S_Dengue_Serotype2_infected_3hr_post_feeding_batch 1

description: Sample 3


title: Moyo-R_Uninfected_control_3hr_post_feeding_batch 1

description: Sample 4


title: Moyo-S_Dengue_Serotype1_infected_3hr_post_feeding_batch 1

description: Sample 2


title: H358 0.5mM Q

description:
Cells grown under low glutamine conditions (0.5mM)
200319680035_D


title: H2009 4mM Q

description:
Cells grown under high glutamine conditions (4mM)
200319680035_E


title: H2009 0.5mM Q

description:
Cells grown under low glutamine conditions (0.5mM)
200319680035_F


title: HUVECs_VEGF_treatment_0min_rep1.

status: Public on Dec 29 2017

city: Seoul

first: YUJIN

last: KWON

address: 50 Yonsei-fo, Seodaemun-gu

country: South Korea

institute: YONSEI UNIVERSITY

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: HUVECs, VEGF treatment, 0min.

growth_protocol: Primary human umbilical vein endothelial cells (HUVECs) were isolated from human placental microvessels according to previous methods and maintained in M199 supplemented with 20% fetal bovine serum, 1% penicillin/streptomycin, 10 µg/mL bFGF and 2500 units/mL heparin.

extract_protocol: RNA was extracted from HUVECs using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA).

treatment_protocol: HUVECs were treated with recombinant HMGB-1 at 1 µg/mL and recombinant VEGF at 50 ng/mL for 20 minutes, 45 minutes, 2 hours, 6 hours, or 12 hours.


title: HUVECs_VEGF treatment_45min_rep1.

source_name: HUVECs, VEGF treatment, 45min.

value: Primary human umbilical vein endothelial cells (HUVECs)


title: H358 4mM Q

description:
Cells grown under high glutamine conditions (4mM)
200319680035_C


title: HUVECs_VEGF treatment_2h_rep2.

source_name: HUVECs, VEGF treatment, 2h.


title: HUVECs_VEGF treatment_45min_rep2.


title: HUVECs_HMGB-1 treatment_45min_rep2.

source_name: HUVECs, HMGB-1 treatment, 45min.


title: HUVECs_HMGB-1 treatment_12h_rep1.

source_name: HUVECs, HMGB-1 treatment, 12h.


title: HUVECs_HMGB-1 treatment_45min_rep1.


title: HUVECs_HMGB-1 treatment_6h_rep1.

source_name: HUVECs, HMGB-1 treatment, 6h.


title: HUVECs_VEGF treatment_12h_rep1.

source_name: HUVECs, VEGF treatment, 12h.


title: HUVECs_HMGB-1 treatment_6h_rep2.


title: HUVECs_HMGB-1 treatment_0min_rep2.

source_name: HUVECs, HMGB-1 treatment, 0min.


title: Moyo-S_Uninfected_control_3hr_post_feeding_batch 1

description: Sample 1

value: Moyo-S


title: HUVECs_VEGF treatment_6h_rep2.

source_name: HUVECs, VEGF treatment, 6h.


title: HUVECs_HMGB-1 treatment_12h_rep2.


title: HUVECs_VEGF treatment_2h_rep1.


title: HUVECs_HMGB-1 treatment_20min_rep2.

source_name: HUVECs, HMGB-1 treatment, 20min.


title: HUVECs_HMGB-1 treatment_2h_rep2.

source_name: HUVECs, HMGB-1 treatment, 2h.


title: HUVECs_VEGF treatment_12h_rep2.


title: HUVECs_HMGB-1 treatment_0min_rep1.


title: HUVECs_VEGF treatment_20min_rep1.

source_name: HUVECs, VEGF treatment, 20min.


title: HUVECs_HMGB-1 treatment_20min_rep1.


title: HUVECs_VEGF_treatment_0min_rep2.


title: HUVECs_VEGF treatment_6h_rep1.


title: HUVECs_HMGB-1 treatment_2h_rep1.


title: HUVECs_VEGF treatment_20min_rep2.


title: A549 4mM Q

description:
Cells grown under high glutamine conditions (4mM)
200319680035_I


title: atg1Δ rep3

type: SRA

city: Madison

first: David

last: Eide

state: WI

address: 1415 Linden Drive

department: Nutrional Sciences

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
Sequencing reads were adapter- and quality-trimmed to Q20 using the Skewer trimming program
Alignment of sequence reads, clone sequences and assembly contigs was performed with BWA-MEM.
Quality reads were subsequently aligned to the annotated reference genome using the STAR aligner
Quality reads were subsequently aligned to the annotated reference genome using the STAR aligner (Dobin et al. 2013). Quantification of expression for each gene was calculated by RSEM (Li and Dewey 2011). The expected read counts from RSEM were filtered for low/empty values, requiring at least 1 CPM in at least three samples. Differential gene expression analysis was performed using EdgeR (Robinson et al. 2010).
Genome_build: S288C 2010
Supplementary_files_format_and_content: Spreadsheets containing differential and quantitative gene expression data

organism: Saccharomyces cerevisiae

source_name: yeast cell pellet

growth_protocol: Yeast were pre-grown in zinc-replete medium and then washed 3X and shifted to fresh zinc-limiting medium for 8 hours. All growth was performed in liquid culture at 30 degrees

extract_protocol:
Yeast cultures were collected after 8 hours of zinc deficiency and mixed with 1/8 volume of 95% ethanol, 5% phenol, pelleted, and frozen in liquid nitrogen for storage at -80 degrees. RNA was prepared using hot phenol. mRNA was purified from 1 ug total RNA using poly-T oligo-attached magnetic beads.
Each RNA library was generated following the Illumina TruSeq RNA Sample Preparation v2 (Rev. E) Guide using the Illumina TruSeq RNA Sample Preparation Kit.

tag: nutrtient status

value: zinc-deficient


title: WT rep4

value: wild type


title: atg41Δ rep4


title: atg1Δ rep4


title: atg41Δ rep2


title: atg41Δ rep3


title: WT rep3


title: iNKT 4h after Transwell-separated co-culture with aGC-loaded NHBE epithelial cells, biological rep3

first: Kambez

last: Hajipouran Benam

address: Center for Life Science Boston, 3 Blackfan Circle

institute: Wyss Insstitute, Harvard Medical School

hyb_protocol: Following fragmentation, cDNA molecules were labeled with biotin using uracil DNA glycosylase (UDG), and then hybridized for 16 hr at 45C on Human Whole Transcript (WT) 1.0 Sense Target (ST) Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Fluorescent images on GeneChips were captured using gene Array scanner 3000 and GCOS 1.2 software (Affymetrix).

data_processing: The flourescent data were initially analyzed with GeneChip Operating Software. Then in R, data were normalised using RMA algorithm and scripts were written to plot data in 3D. Gene-set enrichment analysis (GSEA) - http://www.broadinstitute.org/gsea/index.jsp, and Database for Annotation, Visualization and Integrated Discovery (DAVID) - http://david.abcc.ncifcrf.gov/, were also used for data analysis.

source_name: iNKT cells seprated by a transwell insert in co-culture system with glycolipid-loaded airway epithelial cells

label_protocol: Biotinylated cDNA (generated from cRNA, and after fragmentation) were prepared according to the standard Affymetrix protocol from 100-300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix; http://media.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

growth_protocol: Human iNKT cells were grown in RPMI-1640 medium supplemented with 10% human serum and 1% Penicillin/Streptomycin at 37C.

extract_protocol: Total RNA extraction with Rneasy Mini Kit was performed according to the manufacturer's instructions.

treatment_protocol: Human iNKT cells (non-adherent) were carefully aspirated from NHBE (adherent) epithelial cells after 4h co-culture, or used at 0h as untouched cells. Total RNA was isolated by RNeasy Mini Kit (Qiagen).

value: Invariant Natural Killer T lymphocytes


title: atg1Δ rep2


title: iNKT 4h after Transwell-separated co-culture with aGC-loaded NHBE epithelial cells, biological rep1


title: atg41Δ rep1


title: W3_A1B(Cy3)_R1

description:
US90403632_252665510202_S01_GE2_107_Sep09_1_1
Week 3

value: female


title: iNKT 4h after Direct co-culture with aGC-loaded NHBE epithelial cells, biological rep2

source_name: iNKT cells activated by direct contact with glycolipid-loaded airway epithelial cells


title: atg1Δ rep1


title: iNKT at T0, biological rep3

source_name: Untouched iNKT cells


title: iNKT at T0, biological rep1


title: iNKT 4h after Direct co-culture with aGC-loaded NHBE epithelial cells, biological rep1


title: iNKT at T0, biological rep2


title: iNKT 4h after Transwell-separated co-culture with aGC-loaded NHBE epithelial cells, biological rep2


title: iNKT 4h after Direct co-culture with aGC-loaded NHBE epithelial cells, biological rep3


title: WT rep1


title: umbilical cord Wharton's jelly-derived stem cell, explant isolation, passage 3 (repl 5)

status: Public on Dec 28 2017

city: Diepenbeek

first: Raf

last: Donders

address: Agoralaan Building C

department: Biomedical Research Institute

country: Belgium

institute: Hasselt University

hyb_protocol: Following fragmentation and labeling, cDNA was hybridized for 16 hr at 45°C on the human Gene 1.0 ST Array in a GenChip hybridization oven 645. Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.

data_processing: Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.

source_name: term umbilical cord tissue, blood free

label_protocol: cDNA was prepared from 100ng of total RNA according to the Ambion WT expression kit protocol. Subsequently, the cDNA was fragmented and labeled using the Affymetrix GeneChip WT terminal labeling and hybridization kit, according to the manufacturer's instructions.

growth_protocol: All stem cells were grown as monolayer cultures in plastic culture flasks. Cells were harvested and pelleted at 300xg.

extract_protocol: Total RNA was prepared using the Ambion MagMAX-96 for microarrays kit (Applied Biosystems), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer and Agilent BioAnalyzer.

treatment_protocol: The cell pellets were resuspended in TRI reagent (Ambion MagMAX-96 kit), snap frozen with liquid nitrogen and stored at -80°C until RNA extraction.

value: term umbilical cord tissue, blood free

tag: medium

value: KO-DMEM/F12, 2mM L-glut, 10% FBS

tag: detachment

value: Accutase, 5 minutes


title: WT rep2


title: Ly-6C+ CD4 TN_rep2

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (CEL files) and metrics for Quality Controls. CEL files were then normalized and processed to signal intensities using the RMA algorithm from the Bioconductor library and the cdf file EntrezGene V19 from BrainArray.

source_name: Naïve Ly-6C+ CD4+ T cells

label_protocol: 5 ng of total RNA is reverse transcribed following the Ovation Pico WTA System V2 (Nugen). After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (QIAGEN) according to manufacturer's manual.

treatment_protocol: CD4 T cells from peripheral and mesenteric lymph nodes of C57BL/6 Foxp3-GFP mice were purified by using Dynabeads Untouched Mouse CD4 Cells Kit (Invitrogen). Then, Ly-6C- and Ly-6C+ CD4 TN cells were flow-cytometry sorted as CD4+ CD8α- TCRβ+ GFP- CD25- CD44-/lo cells using a FACS-ARIA3 flow cytometer.

value: 6-8 weeks

value: C57BL/6 Foxp3-GFP

value: Peripheral and mesenteric Lymph Nodes

value: CD4+ T cells

tag: cell marker


title: Ly-6C+ CD4 TN_rep1


title: Ly-6C- CD4 TN_rep2

source_name: Naïve Ly-6C- CD4+ T cells


title: Ly-6C- CD4 TN_rep1


title: bone marrow-derived mononuclear cell, passage 3 (repl 5)

source_name: bone marrow-derived mononuclear cells

value: bone marrow-derived mononuclear cells

value: Lonza Poietics MSCGM™

value: 0.05% trypsin/EDTA, 3-5 minutes, fresh medium inactivation


title: Ly-6C+ CD4 TN_rep3


title: multipotent adult progenitor cell (repl 2)

source_name: long term cultures of bone marrow mononuclear cells

value: Chemically defined medium


title: umbilical cord Wharton's jelly-derived stem cell, explant isolation, passage 3 (repl 2)


title: multipotent adult progenitor cell (repl 1)

value: long term cultures of bone marrow mononuclear cells


title: Ly-6C- CD4 TN_rep3


title: multipotent adult progenitor cell (repl 3)


title: umbilical cord Wharton's jelly-derived stem cell, explant isolation, passage 3 (repl 4)


title: umbilical cord Wharton's jelly-derived stem cell, explant isolation, passage 3 (repl 1)


title: bone marrow-derived mononuclear cell, passage 3 (repl 2)


title: multipotent adult progenitor cell (repl 5)


title: bone marrow-derived mononuclear cell, passage 3 (repl 4)


title: MCLFVB 2352

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

source_name: mammary gland

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Animals used: p38a-lox, MMTV-Cre vs MMTV-Cre (9 weeks-old) and p38a-lox, MMTV-Cre, MMTV-PyMT vs MMTV-Cre, MMYV-PyMT (6 weeks-old)

extract_protocol: Cells were sorted on  TRIzol® Plus RNA Purification Kit (Life Technologies).Total RNA was extracted using RNAeasy Micro Kit (Quiagen).

treatment_protocol: Luminal population of the mammary gland purified by FACs from p38a-lox, MMTV-Cre vs MMTV-Cre (9 weeks-old) and p38a-lox, MMTV-Cre, MMTV-PyMT vs MMTV-Cre, MMYV-PyMT (6 weeks-old) mice

value: luminal population of the mammary gland


title: bone marrow-derived mononuclear cell, passage 3 (repl 1)


title: multipotent adult progenitor cell (repl 4)


title: bone marrow-derived mononuclear cell, passage 3 (repl 3)


title: MCLFVB2310


title: non-Diabetic Foot Skin 03

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

hyb_protocol: Hybridization was done using the GeneChip® Hybridization Wash and Stain Kit

scan_protocol: Chips were scanned with a GeneChip scanner 3000 (Affymetrix)

data_processing: The data were analyzed with Affymetrix transcriptome analysis software using Affymetrix default analysis settings and global scaling as normalization method.  The signficance value was set at an FDR of 0.05 and the fold change cut-off was filtered for 2 or more (calculated from DFU/FS)

source_name: foot skin

label_protocol: fragmentation and labeling were done using the GeneChip® WT PLUS Reagent Kit following affymetrix protocols

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

value: foot skin

tag: disease state

value: non-diabetic


title: MCLFVB2286


title: MCLFVB2056


title: MCLFVB1999


title: MCLFVB 1989


title: MCLFVB 2035


title: non-Diabetic Foot Skin 02


title: MCLFVB 1985


title: umbilical cord Wharton's jelly-derived stem cell, explant isolation, passage 3 (repl 3)


title: non-Diabetic Foot Skin 01


title: Diabetic Foot Skin 03

value: diabetic


title: A01 lymphocyte

city: Shanghai

first: Ronggui

last: Hu

state: Shanghai

address: Room 405, New Biochemistry Building, 320 Yue-yang Road, Shanghai, China

institute: Institute of Biochemsitry and Cell Biology

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad BeadChip microarray (Illumina)

hyb_protocol: Standard Illumina protocol for Human660W-Quad Beadchip

label: C-Bio and A-DNP

source_name: blood lymphocyte

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

tag: gender

value: Male

tag: disease

value: ASD


title: A02 lymphocyte

scan_protocol: Standard Illumina protocol for Human660W-Quad Beadchip

data_processing: Genomic DNA extracted from blood was genotyped using Human660W-Quad BeadChip microarray (Illumina)


title: A03 lymphocyte

label_protocol: Standard Illumina protocol for Human660W-Quad Beadchip


title: nkx_ctl_3

status: Public on Dec 27 2017

city: New York

first: Daylon

last: James

state: NY

address: 515 East 71st Street

institute: Weill Cornell Medicine

data_processing:
Samples were aligned to the human GRCh38 reference assembly using STAR alginer and subsequently genes were counted in htseq
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file inluding fitted counts

source_name: human pluripotent stem cells

growth_protocol: hPSCs were differentiated in conditions that promote cardiovascular specification and the populations in question were isolated by FACS at day 7 of differentiation

extract_protocol:
Total RNA was isolated form cells using the Arcturus picoPure RNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent stem cell-derived cardiac and endothelial cells

tag: passages

tag: parent line

value: Mel-1 NkxeGFP/w

tag: expression

value: NKX2.5 alone


title: 31_ctl_2

tag: cell type

value: endothelial markers.


title: MCLFVB 1937

tag: tissue

tag: genotype


title: Diabetic Foot Ulcer 24

source_name: foot ulcer

value: foot ulcer


title: nkx-31_ctl_3

value: NKX2.5 and endothelial markers


title: 31_ctl_3


title: Diabetic Foot Skin 01


title: 31_ctl_1


title: Diabetic Foot Ulcer 15


title: nkx_ctl_1


title: MCLFVB 2243


title: MCLFVB 2309


title: nkx-31_ctl_2


title: nkx-31_ctl_1


title: MCLFVB 2318

value: MMTV-Cre


title: nkx_ctl_2


title: MCLFVB 1935


title: Diabetic Foot Ulcer 31


title: MCLFVB 2302


title: Diabetic Foot Ulcer 07


title: MCLFVB 1987


title: MCLFVB 1895


title: Diabetic Foot Ulcer 27


title: Diabetic Foot Skin 02


title: FGK3_tcells

city: New Haven

first: Curtis

middle: J

last: Perry

address: 1 Gilbert st.

institute: Yale University

description:
Sample 8
CD40

data_processing:
aligned using STAR to the GRCm38 (mm10) reference genome
mappable data were counted using HTSeq
imported into R for differential expression analysis using the DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including normalized read counts for each sample

source_name: melanoma

growth_protocol: BrafCA; Tyr::CreER; Ptenlox4-5  mice have been previously described(Dankort et al., 2009b). Local tumor induction was performed as previously described(Ho et al., 2014). Age-matched mice that were housed in the same room of the same facility were used for each experiment. Mice were randomized to mouse size and litter, and treated mice were co-housed with controls whenever possible. The investigators were not blinded to mouse allocation. Group size was chosen based on constraints of age-matched litters.

extract_protocol:
Tumors for flow cytometry and RNAseq were minced in Hank’s Balanced Salt Solution with 0.5mg/ml collagenase IV and 200 mg/L DNase, digested in a 37C incubator for 30 minutes and filtered to remove debris. Tumors for Single Cell Barcode Chip or intracellular cytokine stain were minced in complete RPMI with 5% serum, 0.5mg/ml collagenase IV and 200 mg/L DNase, digested in a 37C incubator for 30 minutes and filtered to remove debris. The filtrate was incubated with ACK lysis buffer (Invitrogen) for 4 minutes, washed and re-suspended in complete RPMI. For RNAseq, single-cell suspension was purified of dead cells with Lymphoprep (Stem Cell) per protocol. For RNAseq, at least three tumors were pooled for each sample collected in triplicate, with further characterization of phenotype by flow cytometry of each independent tumor. Total RNA was purified with the use of QIAzol and RNeasy Mini kit (QIAGEN), in which an on-column DNase treatment was included. Purified RNA was submitted to the Yale Center for Genomic Analysis where it was subjected to mRNA isolation and library preparation.
Non-strand specific libraries were generated from 50ng total RNA using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit.  Libraries were pooled, six samples per lane, and sequenced on an Illumina HiSeq 2500 (75-bp paired end reads), and aligned using STAR to the GRCm38 (mm10) reference genome. A count-based differential expression protocol was adapted for this analysis(Anders et al., 2013); mappable data were counted using HTSeq, and imported into R for differential expression analysis using the DESeq2.To find differentially regulated sets of genes for signature generation, a 1.5-Log2 fold-change difference between samples and p-adjusted (Holm-Sidak) ≤ 0.01 was used.

treatment_protocol: 30 days after tumor induction, when tumors were measurable but total volume less than 100 mm3, BrafCA; Tyr::CreER; Ptenlox4-5  mice received normal or CSF1Ri PLX6134 chow (600mg PLX6134/kg, generously provided by Plexxikon) for 30 days or until tumors reached endpoint ( 2 cm3 as pre-specified in each experiment). In various experiments, mice also received either control vehicle (PBS) or CD40 agonistic antibody (FGK4.5 10mg/kg every three days i.p.)  for a total of ten treatments or until pre-specified tumor endpoint,

value: BrafCA; Tyr::CreER; Ptenlox4-5

value: tumor associated macrophages

value: wild type


title: P+F1_tcells

description:
Sample 9
CSF1Ri+CD40


title: CTL3_Tcells

description:
Sample 3
Control


title: PLX6_Tcells

description:
Sample 5
CSF1Ri


title: FGK1_tcells

description:
Sample 6
CD40


title: P+F3_tcells

description:
Sample 10
CSF1Ri+CD40


title: Diabetic Foot Ulcer 14


title: PLX_tcells

description:
Sample 4
CSF1Ri


title: CTL1_Tcells

description:
Sample 1
Control


title: CTL2_Tcells

description:
Sample 2
Control


title: Test Group 4

city: La Jolla

first: Aime

last: Lopez Aguilar

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: The Scripps Research Institute

description:
Fucosylated
M4

data_processing:
CT values were exported to an Excel file to create a table of CT values. This table was then uploaded on to the data analysis web portal at http://www.qiagen.com/geneglobe. Samples were assigned to controls and test groups. CT values were normalized with an arithmetic mean of houskeeping genes B2m, Gapdh and Hsp90ab1 included in the array.
Geneglobe software does not make normalized values available only final fold-change. Fold-change values for fucosylated/untreated organoids.

label: SYBR Green

source_name: Lgr5-EGFP-IRES-CreER reporter mice, fucosylated, Lgr5+ mouse stem cells

label_protocol: RNA was reverse transcribed and amplified with a RT2 PreAMP kit (Qiagen)

growth_protocol: Crypt isolation and organoid preparation were prepared using standard protocols. Organoids were maintained in crypt culture medium (Advanced DMEM/F12, 2 mM GlutaMax, 10 mM Hepes, 1X PenStrep, 1X N2, 1X B27, 1 uM N-acetylcysteine, 50ng/ml EGF, 100 ng/ml Noggin, 1 ug/ml R-spondin). EGF, Noggin and R- spondin were replenished every 2 days, and the full media was changed every 4 days.

extract_protocol: RNA was isolated using QIAShredder columns and a RNA Ready Micro kit (Qiagen) according to manufacturer's instructions

treatment_protocol: Treated organoids were fucosylated daily for 30 mins using H. pylory 1,3 Fucosyltransferase and GDP-Fucose

value: Lgr5+ mouse stem cells

tag: treatment

value: fucosylation


title: Test Group 3

description:
Fucosylated
M3


title: Test Group 6

description:
Fucosylated
M6


title: Control Group 2

description:
Untreated
M2-C

source_name: Lgr5-EGFP-IRES-CreER reporter mice, untreated, Lgr5+ mouse stem cells

value: control


title: Control Group 3

description:
Untreated
M3-C


title: Control Group 5

description:
Untreated
M5-C


title: Control Group 6

description:
Untreated
M6-C


title: Control Group 4

description:
Untreated
M4-C


title: Test Group 2

description:
Fucosylated
M2


title: Control_3

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human HT PrimeView Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data were analyzed using GeneSpring GX v12.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Gene expression data from Retinoblastoma cell line (Y79) Untreated

growth_protocol: Retinoblastoma cell (Y79) cultured using RPMI cell culture media

extract_protocol: RNA isolation by per the protocol prescribed in the kit

treatment_protocol: Y97 cells were treated with Gold nanoparticles (GNPs) and GNPs-HDM2 (Human Double Minute 2) peptide conjugate

tag: cell line

value: Retinoblastoma cell line


title: GNPs-HDM2_1

source_name: Gene expression data from Retinoblastoma(Y97) cells treated with GNPs-HDM2 (Human Double Minute 2) peptide conjugate


title: Control_1


title: GNPs-HDM2_2


title: GNPs_3

source_name: Gene expression data from Retinoblastoma(Y97) cells treated with Gold nanoparticles (GNPs)


title: GNPs-HDM2_3


title: Control_2


title: GNPs_2


title: GNPs_1


title: Test Group 1

description:
Fucosylated
M1


title: Test Group 5

description:
Fucosylated
M5


title: osvil2 4 mm panicle rep 2

status: Public on Dec 26 2017

first: liang

last: wanqi

address: 800 Dongchuan Road

department: Department of Bioscience and Biotechnology,School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

description: processed data file: All_Fragments.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Tophat mapping to reference genome.
Count counting.
Genome_build: Oryza sativa tigr7 (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/)
Supplementary_files_format_and_content: All_Fragments.txt: Tab-delimited text file contains raw counts for each sample.

organism: Oryza sativa Japonica Group

source_name: inflorescence

growth_protocol: Plants were grown in the paddy field under natural condition.

extract_protocol:
Panicles in the lengths of 2 mm and 4 mm were obtained from WT and osvil2 mutant plants. Total RNAs were isolated using RNeasy Plant Mini Kit (Qiagen, Cat. No. 74904). Double-stranded cDNAs were synthesized with random hexamers and ligated to adaptors.
The library was pair-end sequenced using the PE90 strategy on an Illumina HiSeq™ 2000.

tag: cultivar

value: Dongjin

tag: genotype/variation

value: Panicle

tag: panicle length

value: 4 mm


title: osvil2 4 mm panicle rep 3

description: processed data file: All_Fragments.txt


title: osvil2 2 mm panicle rep 1

description: processed data file: All_Fragments.txt

value: 2 mm


title: osvil2 2 mm panicle rep 2

description: processed data file: All_Fragments.txt


title: WT 4 mm panicle rep 2

description: processed data file: All_Fragments.txt


title: WT 2 mm panicle rep 1

description: processed data file: All_Fragments.txt


title: Control Group 1

description:
Untreated
M1-C


title: osvil2 4 mm panicle rep 1

description: processed data file: All_Fragments.txt


title: WT 2 mm panicle rep 2

description: processed data file: All_Fragments.txt


title: WT 4 mm panicle rep 1

description: processed data file: All_Fragments.txt


title: WT 4 mm panicle rep 3

description: processed data file: All_Fragments.txt


title: osvil2 2 mm panicle rep 3

description: processed data file: All_Fragments.txt


title: tumor cell line 11 _gammaD12

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

institute: Medizinische Hochschule Hannover

description:
tumor cell line 11
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome -U74v2 Arrays covering approximately 12,000 full-length mouse gene transcripts and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same. Microarray chips were analyzed by the GCOS (GeneChip Operating Software) from Affymetrix with the default settings except that the target signal was set to 250 and used to generate a microarray quality control and data report. First, we have evaluated and compared multiple data from each tumor cell line using statistical analysis with the Affymetrix Data Mining Tool (DMT). Since significant differences observed between the tumor cell lines we prepared additionally two replicates from tumor cell lines with most differences such as A2C12, cRaf_cMyc, A2B1, B3, gammaA7 and gammaB8 and conducted further data analysis. CEL files exported from GCOS were uploaded into ArrayTrack software (National Center for Toxicological Research, U.S. FDA, Jefferson, AR, USA (NCTR/FDA)).

source_name: mouse lung carcinoma cell line was isolated from lung tumors of double c-myc and c-raf transgenic mice

label_protocol: Total RNA (5µg) was used to generate biotin-labeled cRNA (10 µg) by means of GeneChip® One-Cycle cDNA Synthesis Kit and GeneChip® IVT Labeling Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a Bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

growth_protocol: Each cell line was passaged weekly and maintained in culture for up to 50 passages.  Eleven transformed mouse cell lines from lung tumor of double c-Myc and c-Raf transgenic mice were used for this project (A2B1, A2C12, B3, βD5, βD10, c-Myc_c-Raf, γA3, γA7, γB8, γD1, γD12).  The tumor cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM, PAA, Pashing, Austria) supplemented with 10% fetal calf serum (FCS, FHG, Pashing, Austria), 2mM L-Glutamin, 100units/ml streptomycin and 100µg/ml penicillin in a humidified atmosphere at 37ºC containing 5% CO2 to maintain the medium pH at a value of 7,4.  Alveolar epithelial cells (AECs) were used as control.

extract_protocol: RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MidiKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: tumor cell line 11 (gammaD12)

value: lung cancer


title: tumor cell line 8 _gammaA7_replicate 2

description:
tumor cell line 8
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 8 (gammaA7)


title: tumor cell line 10 _gammaD1

description:
tumor cell line 10
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 10 (gammaD1)


title: tumor cell line 9 _gammaB8_replicate 2

description:
tumor cell line 9
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 9 (gammaA8)


title: tumor cell line 6 _cRAF_cMYC_replicate 2

description:
tumor cell line 6
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 6 (cRAF_cMYC)


title: tumor cell line 6 _cRAF_cMYC_replicate 1


title: tumor cell line 8 _gammaA7


title: tumor cell line 9 _gammaB8


title: tumor cell line 7 _gammaA3

description:
tumor cell line 7
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 7 (gammaA3)


title: tumor cell line 8 _gammaA7_replicate 1


title: tumor cell line 6 _cRAF_cMYC


title: tumor cell line 5 _betaD10

description:
tumor cell line 5
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 5 (betaD10)


title: tumor cell line 9 _gammaB8_replicate 1


title: tumor cell line 3 _B3

description:
tumor cell line 3
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 3 (B3)


title: tumor cell line 4 _betaD5

description:
tumor cell line 4
Isolation of control and tumor cells: Alveolar epithelial type II cells and tumor cells were isolated as originally described by Richards et al. (1987) [129], with the following modifications: Briefly, 8-month-old transgenic mice were anesthetized by intraperitoneal injection of Ketamin® (100 mg/kg) and Rompun® (10 mg/kg). After tracheotomy the trachea was cannulated with a bulb head cannula. Following midline incision and removal of the rib cage, a Luer cannula was inserted via the vena cava cranialis into the right atrium. The pulmonary circulation was perfused with ice cold PBS using a peristaltic pump at a flow rate of 4 ml/min. The perfusate was removed by incision of the left atrium, and perfusion with the buffer was continued for 2–3 min until the lungs were completely free of blood. The lungs were explanted, placed in a 50 ml Falcon tube containing 30 ml ice cold PBS and transferred to a sterile flow cabinet. The lungs were then lavaged four times with 6 ml PBS, and subsequently 6 ml Trypsin–EDTA solution (0.25%) was instilled into the trachea. The lungs were incubated with trypsin at 37 °C for a total of 45 min. Every 15 min, 4 ml trypsin solution was pumped via the tracheal cannula.The trachea and main bronchi were removed, and the parenchymal lung tissue was dissected into 1- to 2-mm pieces in a petri dish containing 10 ml ice cold PBS with Ca2+. The lung tissue suspension was incubated for 10 min with 10 ml DNase solution at a concentration of 250 μg/ml DNase and then filtered through a nylon mesh (100 and 60 μm pore size). The alveolar type II pneumocytes were prepared by discontinuous percoll gradient centrifugation (heavy density 1.089 and low density 1.040). Following centrifugation for 30 min at 250g and 4 °C, the cell fraction at the interface between the heavy and low-density gradient was removed and mixed with DNase solution containing 50 μg/ml DNase. The cell suspension was again centrifuged at 140g at 4 °C for 6 min. The resulting cell pellet was then resuspended in DMEM supplemented with 10% FCS or 5% rat serum and incubated in a 25 cm2 tissue culture flask at 37 °C for 60 min. The non-adherent cells were removed and plated on collagen-coated 12-well plates. Approximately 2 × 106 cells were seeded per cm2 in 1 ml culture medium.

value: tumor cell line 4 (betaD5)


title: tumor cell line 3 _B3_replicate 1


title: tumor cell line 3 _B3_replicate 2


title: VP gene expression profile in gastric cancer cells [DMSO_2_MKN45]

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

institute: ChuangAng University

description: control

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing: GenomeStudio was used for data processing and quantile normalization method was used.

source_name: gastric cancer cell

label_protocol: Extracted RNA was amplified and labeled with Amplification kit (AMIL1791; Ambion)

growth_protocol: The cells were grown in RPMI1640 media.

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Cells were treated with DMSO or VP for 36 hrs.

tag: agent

value: DMSO


title: VP gene expression profile in gastric cancer cells [DMSO_1_MKN45]

description: control


title: VP gene expression profile in gastric cancer cells [VP_3_AGS]

description: VP treatment in gastric cancer cell

value: AGS

value: Verteporfin


title: VP gene expression profile in gastric cancer cells [VP_1_AGS]

description: VP treatment in gastric cancer cell


title: VP gene expression profile in gastric cancer cells [VP_3_MKN45]

description: VP treatment in gastric cancer cell


title: VP gene expression profile in gastric cancer cells [VP_2_MKN45]

description: VP treatment in gastric cancer cell


title: VP gene expression profile in gastric cancer cells [VP_1_MKN45]

description: VP treatment in gastric cancer cell


title: VP gene expression profile in gastric cancer cells [DMSO_3_MKN45]

description: control