title: AGILENT_HUMAN_ AR NO TX 17

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP+ 2

status: Public on Jun 20 2017

type: RNA

city: Aguascalientes

first: Noe

last: Macias-Segura

state: Aguascalientes

address: Av. Universidad #940 ciudad universitaria cp20131

department: Physiology

country: Mexico

institute: Universidad Autonoma de Aguascalientes

description: Gene expression from human whole blood

hyb_protocol: Hybridization protocol was carried out following the supliers instruction from the one-color low input RNA labeling kit (Agilent)

scan_protocol: Inmediately after wash step the microarrays were scaned in the Agilent G4900DA SureScan Microarray Scanner equipment (Agilent) following the supliers intructions and the default parameters.

data_processing: The median intensity values from the microarray images were obtained using the Feature extraction software (Agilent) version 11.5.1.1 following the supliers instructions and default parameters using the protocol GE1_1105 and grid 026652_D_F_20140228.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood, relative ACPA postive

label_protocol: Total RNA exracted from samples was labeled with Cy3 under suplier instructions folowing the protocol of one sample low input RNA labeling kit (Agilent), and purified with QIAmp mini-columns (QIAGEN). Dye incorporation and RNA yield were measured by Nanodrop 1000 (Thermo scientific)

extract_protocol: Total RNA was extracted and proceced in QIAmp RNA mini-columns according the suplier intructions (QIAGEN, 2014) and the integrity was measured with the RNA 6000 nano kit in a Bioanalyzer 2100 (Agylent technologies)

treatment_protocol: Whole blood from al the subject was obtained in EDTA colection tubes and 1ml of RNA later was added to preserve the RNA.

tag: tissue

value: whole blood

tag: gender

value: Female

tag: age

tag: clinical stage

value: Relative in preclinical autoimmune stage


title: Mouse HILPDA WT BF3

city: Columbus

first: Ioanna

last: Papandreou

state: OH

department: Radiation Oncology

country: USA

institute: The Ohio State University Comprehensive Cancer Center

description:
WT3 BF
RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing:
Raw data were processed with the SST-RMA algorithm in Expression Console  (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with Transcritome Analysis Console (Affymetrix).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

organism: Mus

source_name: HILPDA WT_brown fat

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

growth_protocol: Brown adipose tissues were collected by dissecting the butterfly of interscapular brown fat.

extract_protocol: RNA was isolated from BAT with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. A reverse transcription PCR was performed with SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase (Invitrogen) according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: wild type

tag: Sex

value: female

value: brown adipose tissue


title: Resistant clone C#3, biological rep1

city: Salamanca

first: Sara

last: García-Alonso

state: Salamanca

address: Campus Miguel de Unamuno s/n

country: Spain

institute: Centro de Investigación del Cáncer

description: Gene expression data from T-DM1 resistant clone, C#3, derived from BT474 cell line

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST 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: Data were processed using the RMA algorithm implemented in the Affimetrix Expression Console (version 1.4.1; Affymetrix). Differentially expressed genes were identified using Transcriptome Analysis Console (TAC version 3.0; Affymetrix).

source_name: Breast cancer cell line

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: Cell lines were cultured at 37°C in a humidified atmosphere in the presence of 5% CO2 and 95% air. Cells were grown in Dulbecco´s Modified Eagle´s Medium (DMEM) supplemented with 10% FBS, 100 mU/mL penicillin and 100 µg/mL streptomycin.

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

treatment_protocol: T-DM1 resistant clones were derived from parental cells by prolonged exposure to T-DM1 following an initial dose-response study of T-DM1 (0.1 nM - 100 nM) over 5 days. Resistant BT474 T-DM1R cell lines were obtained by single-cell cloning and continuously cultured in the presence of 5 nM T-DM1 for 3 months. Clones were routinely tested for resistance.

tag: drug resistance

value: T-DM1 resistant clone

tag: cell line


title: Mouse HILPDA WT BF1

description:
WT1 BF
RMA expression value derived from Expression Console software; core-exon analysis


title: AGILENT_HUMAN_CONTROL CCP+ 1

description: Gene expression from human whole blood


title: Spleen, day 1, mock-infected, replicate 1

city: Riverside

first: Juliet

last: Morrison

state: CA

address: 900 University Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

description:
Mock_24h_Sp_1
251486840584_1_3
Gene expression from spleen, day 1 post mock infection.

hyb_protocol: Microarray slide hybridization for each biological replicate was performed using the Mouse Whole Genome Microarray 4x44K Kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting and raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1).

data_processing:
Extracted raw data was partitioned into liver and spleen samples and separately background corrected using the “norm-exp” method with an offset of 1 and quantile normalized using the limma package in the R environment.
Filtering: The arrays were background corrected using Limma's 'normexp' correction. They were then quantile normalized and batch corrected across plates with ComBat. Probes were filtered for low intensity requiring at least two samples with intensity above a threshold set at the 5% quantile for intensity. This resulted in 32,986 probes retained for the liver samples, and 29,608 probes retained for the spleen samples. Probes were mean-summarized by gene to give the results mentioned below.
DEmatrix-2and2k-spleen.txt includes Log2 Fold Changes (Log2FC) in the 'Coef' columns.

organism: Mus musculus

source_name: Spleen, mock-infected, day 1

label_protocol: Probe labeling for each biological replicate was performed using the Mouse Whole Genome Microarray 4x44K Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted from tissues homogenized in Trizol (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Mice were infected with 1x10e6 plaque-forming units (pfu) of DENV2 strain Eden2 by i.p. injection in 100μL of PBS. Drug-treated animals were given 0.6mg per mouse per day of ketotifen (Sigma) or an equivalent volume of saline by i.p. injection. The first dose was administered 1h after infection, with daily drug injections thereafter at 24h intervals.

tag: strain/background

value: Spleen

tag: treatment

value: mock-infected

tag: time

value: day 1


title: AGILENT_HUMAN_CONTROL CCP- 9

description: Gene expression from human whole blood

source_name: Peripheral blood, relative ACPA negative

value: Healthy relatives


title: Spleen, day 1, mock-infected, replicate 3

description:
Mock_24h_Sp_3
251486840585_1_1
Gene expression from spleen, day 1 post mock infection.


title: CNE2-RRM2-c2orf48-PMSCV

city: Guangzhou

first: Tianliang

last: Xia

address: Dongfeng Road East 651

country: China

institute: Sun Yat-sen University Cancer Center

description: Gene expression data of CNE2-RC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 10 min at 45°C on GeneChip Drosophila Genome Array

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000

data_processing: We applied a two class unpaired method available through the Significant Analysis of Microarray software (SAM) to identify significantly differentially expressed genes between vector and over-expression samples.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: CNE2 cell line cultured in RPMI-1640 medium (Gibco, USA) with 10% fetal bovine serum (Gibco, USA) as described in our lab

extract_protocol: Total RNA from different cell lines and human tissues was extracted using Trizol reagent (Invitrogen, Carlsbad, CA). RNA concentrations and quantities were determined using a NanoDrop spectrophotometer (ND-1000, Thermo Scientific, USA).

treatment_protocol: The CNE2 NPC cell lines were infected with retroviral particles containing human chimeric gene RRM2-c2orf48 to form stable transfected cell lines. The empty vector was used as a negative control. The cells were selected and maintained in puromycin (1 μg/ml).

value: nasopharyngeal carcinoma cell line


title: Spleen, day 1, DENV2 and ketotifen, replicate 2

description:
DENV2K_24h_Sp_2
251486840586_1_3
Gene expression from spleen, day 1 post DENV2 infection and ketotifen treatment.

source_name: Spleen, DENV2 and ketotifen, day 1

value: DENV2 infection and ketotifen


title: Mouse HILPDA WT BF4

description:
WT4 BF
RMA expression value derived from Expression Console software; core-exon analysis


title: Mouse HILPDA KO BF4

description:
HILPDA KO4 BF
RMA expression value derived from Expression Console software; core-exon analysis

source_name: HILPDA KO_brown fat

value: HILPDA KO


title: Spleen, day 3, DENV2, replicate 3

description:
DENV2_72h_Sp_3
251486840581_1_4
Gene expression from spleen, day 3 post DENV2 infection.

source_name: Spleen, DENV2, day 3

value: DENV2 infection

value: day 3


title: Mouse HILPDA KO BF3

description:
HILPDA KO3 BF
RMA expression value derived from Expression Console software; core-exon analysis


title: Mouse HILPDA WT BF2

description:
WT2 BF
RMA expression value derived from Expression Console software; core-exon analysis


title: CNE2-PMSCV

description: Gene expression data of CNE2-VC


title: Spleen, day 1, DENV2, replicate 2

description:
DENV2_24h_Sp_2
251486840587_1_3
Gene expression from spleen, day 1 post DENV2 infection.

source_name: Spleen, DENV2, day 1


title: Spleen, day 3, DENV2 and ketotifen, replicate 3

description:
DENV2K_72h_Sp_3
251486840572_1_3
Gene expression from spleen, day 3 post DENV2 infection and ketotifen treatment.

source_name: Spleen, DENV2 and ketotifen, day 3


title: Spleen, day 3, mock-infected, replicate 2

description:
Mock_72h_Sp_2
251486840580_1_4
Gene expression from spleen, day 3 post mock infection.

source_name: Spleen, mock-infected, day 3


title: Spleen, day 3, mock-infected, replicate 1

description:
Mock_72h_Sp_1
251486840574_1_1
Gene expression from spleen, day 3 post mock infection.


title: Spleen, day 1, mock-infected, replicate 2

description:
Mock_24h_Sp_2
251486840570_1_1
Gene expression from spleen, day 1 post mock infection.


title: Spleen, day 3, DENV2 and ketotifen, replicate 2

description:
DENV2K_72h_Sp_2
251486840579_1_4
Gene expression from spleen, day 3 post DENV2 infection and ketotifen treatment.


title: Spleen, day 1, DENV2 and ketotifen, replicate 3

description:
DENV2K_24h_Sp_3
251486840569_1_3
Gene expression from spleen, day 1 post DENV2 infection and ketotifen treatment.


title: Spleen, day 1, DENV2 and ketotifen, replicate 1

description:
DENV2K_24h_Sp_1
251486840567_1_4
Gene expression from spleen, day 1 post DENV2 infection and ketotifen treatment.


title: Spleen, day 3, DENV2 and ketotifen, replicate 1

description:
DENV2K_72h_Sp_1
251486840569_1_4
Gene expression from spleen, day 3 post DENV2 infection and ketotifen treatment.


title: Spleen, day 1, DENV2, replicate 1

description:
DENV2_24h_Sp_1
251486840577_1_1
Gene expression from spleen, day 1 post DENV2 infection.


title: Mouse HILPDA KO BF1

description:
HILPDA KO1 BF
RMA expression value derived from Expression Console software; core-exon analysis


title: Spleen, day 3, DENV2, replicate 1

description:
DENV2_72h_Sp_1
251486840573_1_3
Gene expression from spleen, day 3 post DENV2 infection.


title: Spleen, day 3, DENV2, replicate 2

description:
DENV2_72h_Sp_2
251486840577_1_2
Gene expression from spleen, day 3 post DENV2 infection.


title: Mouse HILPDA KO BF2

description:
HILPDA KO2 BF
RMA expression value derived from Expression Console software; core-exon analysis


title: Spleen, day 1, DENV2, replicate 3

description:
DENV2_24h_Sp_3
251486840571_1_4
Gene expression from spleen, day 1 post DENV2 infection.


title: Liver, day 3, DENV2, replicate 2

description:
DENV2_72h_Li_2
251486840586_1_4
Gene expression from liver, day 3 post DENV2 infection.

data_processing:
Extracted raw data was partitioned into liver and spleen samples and separately background corrected using the “norm-exp” method with an offset of 1 and quantile normalized using the limma package in the R environment.
Filtering: The arrays were background corrected using Limma's 'normexp' correction. They were then quantile normalized and batch corrected across plates with ComBat. Probes were filtered for low intensity requiring at least two samples with intensity above a threshold set at the 5% quantile for intensity. This resulted in 32,986 probes retained for the liver samples, and 29,608 probes retained for the spleen samples. Probes were mean-summarized by gene to give the results mentioned below.
DEmatrix-2and2k-liver.txt includes Log2 Fold Changes (Log2FC) in the 'Coef' columns.

source_name: Liver, DENV2, day 3

value: Liver


title: Liver, day 1, DENV2, replicate 1

description:
DENV2_24h_Li_1
251486840584_1_1
Gene expression from liver, day 1 post DENV2 infection.

source_name: Liver, DENV2, day 1


title: Liver, day 1, mock-infected, replicate 3

description:
Mock_24h_Li_3
251486840580_1_2
Gene expression from liver, day 1 post mock infection.

source_name: Liver, mock-infected, day 1


title: Liver, day 1, mock-infected, replicate 1

description:
Mock_24h_Li_1
251486840581_1_2
Gene expression from liver, day 1 post mock infection.


title: Liver, day 3, DENV2 and ketotifen, replicate 3

description:
DENV2K_72h_Li_3
251486840581_1_3
Gene expression from liver, day 3 post DENV2 infection and ketotifen treatment.

source_name: Liver, DENV2 and ketotifen, day 3


title: Liver, day 1, mock-infected, replicate 2

description:
Mock_24h_Li_2
251486840577_1_3
Gene expression from liver, day 1 post mock infection.


title: Liver, day 3, mock-infected, replicate 2

description:
Mock_72h_Li_2
251486840581_1_1
Gene expression from liver, day 3 post mock infection.

source_name: Liver, mock-infected, day 3


title: Liver, day 1, DENV2, replicate 5

description:
DENV2_24h_Li_5
251486840572_1_1
Gene expression from liver, day 1 post DENV2 infection.


title: Liver, day 1, DENV2 and ketotifen, replicate 5

description:
DENV2K_24h_Li_5
251486840579_1_3
Gene expression from liver, day 1 post DENV2 infection and ketotifen treatment.

source_name: Liver, DENV2 and ketotifen, day 1


title: S2 circRNA

city: Shanghai

first: lv

last: qi

address: Xincun Road 389

institute: Tongji Hospital affiliated to Tongji university

description: circRNA expression data from matched non-tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 8 samples have flags in P or M (“All Targets Value”) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: matched non-tumor tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: CCRCC and matched non-tumor skin tissues

treatment_protocol: Tissues from CCRCC surgury were immersed overnight in RNAlater at 4 ℃ and preserved at -80 ℃.

value: matched non-tumor tissue

value: 51 years old


title: Liver, day 1, DENV2 and ketotifen, replicate 3

description:
DENV2K_24h_Li_3
251486840584_1_2
Gene expression from liver, day 1 post DENV2 infection and ketotifen treatment.


title: Spleen, day 3, mock-infected, replicate 3

description:
Mock_72h_Sp_3
251486840567_1_3
Gene expression from spleen, day 3 post mock infection.


title: Liver, day 3, DENV2 and ketotifen, replicate 1

description:
DENV2K_72h_Li_1
251486840572_1_2
Gene expression from liver, day 3 post DENV2 infection and ketotifen treatment.


title: Liver, day 3, mock-infected, replicate 1

description:
Mock_72h_Li_1
251486840571_1_1
Gene expression from liver, day 3 post mock infection.


title: S8 circRNA

value: male

value: 70 years old


title: Liver, day 3, DENV2, replicate 3

description:
DENV2_72h_Li_3
251486840569_1_1
Gene expression from liver, day 3 post DENV2 infection.


title: Liver, day 1, DENV2 and ketotifen, replicate 4

description:
DENV2K_24h_Li_4
251486840574_1_3
Gene expression from liver, day 1 post DENV2 infection and ketotifen treatment.


title: Liver, day 3, mock-infected, replicate 3

description:
Mock_72h_Li_3
251486840570_1_4
Gene expression from liver, day 3 post mock infection.


title: S6 circRNA

value: 49 years old


title: S4 circRNA

value: female

value: 65 years old


title: S5 circRNA

description: circRNA expression data from CCRCC patients (CCRCC) tissue

source_name: renal clear cell carcinoma(CCRCC) tumor tissue

value: renal clear cell carcinoma (CCRCC) tumor tissue


title: Liver, day 3, DENV2 and ketotifen, replicate 2

description:
DENV2K_72h_Li_2
251486840570_1_3
Gene expression from liver, day 3 post DENV2 infection and ketotifen treatment.


title: S3 circRNA


title: S1 circRNA


title: Liver, day 3, DENV2, replicate 1

description:
DENV2_72h_Li_1
251486840570_1_2
Gene expression from liver, day 3 post DENV2 infection.


title: Liver, day 1, DENV2, replicate 4

description:
DENV2_24h_Li_4
251486840580_1_1
Gene expression from liver, day 1 post DENV2 infection.


title: S7 circRNA


title: Wt Mtb treated 1XAG 12 hrs 3

city: New York

first: SAURABH

last: MISHRA

state: New York

address: 1300 York Ave, Box 62, New York

department: Microbiology and Immunology

institute: Weill Cornell Medicine

description: Gene expression of Mtb early log phase cultures in 7H9-ADS medium

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040).  The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into the hybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µm using Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and data transformation was done to median of all samples using GeneSpring Gx V 12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis H37Rv

source_name: Wt Mtb H37Rv, 1XAG Treated, 12hrs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mtb H37Rv was grown till early log phase of ~0.4.

extract_protocol: Gene expression from Treated cultures were fixed using Guanidine thiocyanate, pelleted and total RNA was isolated using FastRNA PRO blue kit (according to manufacturer's instructions). RNA was purified using Qiagen RNeasy plus kit according to manufacturer's instructions. DNAse treatment was done using Ambion TURBO DNA-free kit according to manufacturer's instructions. RNA quality was measured using Agilent Bioanalyzer.

treatment_protocol: Early log phase culture cells were taken. Mtb H37Rv was treated with 10 or 50 µg/ml of Amoxicillin and 8 µg/ml of Clavulanate in 7H9-ADS medium for 6 or 12 hrs.

value: wildtype

tag: growth phase

value: early log

value: 1X AG (Amoxicillin and Clavulanate), 12h


title: Wt Mtb treated 5XAG 12 hrs 1

source_name: Wt Mtb H37Rv, 5XAG Treated, 12hrs

value: 5X AG (Amoxicillin and Clavulanate), 12h


title: Wt Mtb treated 5XAG 12 hrs 2


title: Col0_3MB_flg22_rep2

city: Beloit

first: Amy

middle: Graham

last: Briggs

state: WI

address: 700 College St.

department: Biology

institute: Beloit College

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB) and the MAMP flg22. It is the second of three biological replicates.

hyb_protocol: Hybridization was performed by the Gene Expression Center, Madison, WI USA, following Nimblegen's 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: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0 wild-type, 10 day old whole seedlings

label_protocol: Labeling was performed by the Gene Expression Center, Madison, WI USA, following Nimblegen's standard operating protocol. See www.nimblegen.com.

growth_protocol: Each biological replicate included 48, 10 day-old Arabidopsis thaliana seedlings pooled for each treatment. Col-0 seedlings were pre-treated for 2 hours with either 60% DMSO, 250mM 3AB (dissolved in 60% DMSO), or 250mM 3MB (dissolved in 60% DMSO). Col-0 seedlings were then treated for one hour with either ddH2O or 1uM flg22, or 1uM elf18, and parg1 seedlings were treated for one hour with either ddH2O or 1uM elf18.

extract_protocol: Total RNA was extracted using Rneasy Mini Kit (Qiagen), and DNA was removed by DNase digestion with the RNase-free DNase Set (Qiagen) RNA quality and concentration was determined using an Agilent 2100 bioanalyzer at the Gene Expression Center at University of Wisconsin-Madison Biotechnology Center, Madison, WI, USA).

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: accession

value: CS[ ]

value: whole seedling


title: Wt Mtb treated 5XAG 12 hrs 3


title: Wt Mtb treated 1XAG 12 hrs 1


title: Col0_3AB_flg22_rep1

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-amino benzamide (3AB) and the MAMP flg22. It is the first of three biological replicates.


title: Wt Mtb treated 5XAG 6 hrs 2

source_name: Wt Mtb H37Rv, 5XAG Treated, 6hrs

value: 5X AG (Amoxicillin and Clavulanate), 6h


title: Wt Mtb treated 5XAG 6 hrs 3


title: Col0_DMSO_H2O_rep2

description: This sample is of wild-type Arabidopsis thaliana, untreated. It is the second of three biological replicates.


title: Wt Mtb treated 1XAG 6 hrs 1

source_name: Wt Mtb H37Rv, 1XAG Treated, 6hrs

value: 1X AG (Amoxicillin and Clavulanate), 6h


title: Wt Mtb treated 1XAG 6 hrs 2


title: Wt Mtb treated 5XAG 6 hrs 1


title: Wt Mtb treated 1XAG 12 hrs 2


title: Wt Mtb untreated 3_2

source_name: Wt Mtb H37Rv, Untreated


title: Wt Mtb treated 1XAG 6 hrs 3


title: Wt Mtb untreated 2_2


title: Col0_3AB_H2O_rep1

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-amino benzamide (3AB). It is the first of three biological replicates.


title: Col0_DMSO_flg22_rep2

description: This sample is of wild-type Arabidopsis thaliana, treated with the MAMP flg22. It is the second of three biological replicates.


title: Col0_3MB_H2O_rep1

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB). It is the first of three biological replicates.


title: Col0_DMSO_H2O_rep1

description: This sample is of wild-type Arabidopsis thaliana, untreated. It is the first of three biological replicates.


title: Col0_3AB_flg22_rep2

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-amino benzamide (3AB) and the MAMP flg22. It is the second of three biological replicates.


title: Wt Mtb untreated 4_2


title: Col0_DMSO_flg22_rep3

description: This sample is of wild-type Arabidopsis thaliana, treated with the MAMP flg22. It is the third of three biological replicates.


title: parg1_H2O_rep1

description: This sample is of Arabidopsis thaliana SALK_116088 TDNA insertion knockout of the parg1 gene, untreated. It is the first of three biological replicates.

source_name: Arabidopsis thaliana Col-0 parg1-2, 10 day old whole seedlings

value: TDNA insertion knockout parg1-2 (SALK_116088)

value: long free-running circadian period; excessive MAMP-induced phenylpropanoid deposition; excessive MAMP-induced seedling growth inhibition; mitomycin-C sensitivity; accelerated Botrytis cinerea infection symptoms;


title: Col0_3AB_H2O_rep2

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-amino benzamide (3AB). It is the second of three biological replicates.


title: Col0_DMSO_elf18_rep3

description: This sample is of wild-type Arabidopsis thaliana, treated with the MAMP elf18. It is the third of three biological replicates.


title: parg1_H2O_rep3

description: This sample is of Arabidopsis thaliana SALK_116088 TDNA insertion knockout of the parg1 gene, untreated. It is the third of three biological replicates.


title: Wt Mtb untreated 1_2


title: 151245B_326C

status: Public on Jun 19 2017

city: Fuzhou

first: Lie

last: Wang

address: Xierhuan Road

institute: Fuzhou general Hospital

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: gastric cancer (GC)

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: tissue type

value: gastric cancer (GC)


title: 151245B_313N

source_name: non-gastric cancer (non-GC)

value: non-gastric cancer (non-GC)


title: 151245A_292N


title: 151245B_313C


title: 151245A_287N


title: AGILENT_HUMAN_CONTROL CCP+ 4

description: Gene expression from human whole blood

source_name: Peripheral blood, relative ACPA postive

tag: tissue

value: whole blood

value: Female

value: Relative in preclinical autoimmune stage


title: 151245A_292C


title: 151245A_286C


title: Col0_DMSO_elf18_rep2

description: This sample is of wild-type Arabidopsis thaliana, treated with the MAMP elf18. It is the second of three biological replicates.


title: 151245A_287C


title: 151245A_286N


title: parg1_elf18_rep2

description: This sample is of Arabidopsis thaliana SALK_116088 TDNA insertion knockout of the parg1 gene, treated with the MAMP elf18. It is the second of three biological replicates.


title: Col0_3MB_H2O_rep2

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB). It is the second of three biological replicates.


title: Col0_DMSO_elf18_rep1

description: This sample is of wild-type Arabidopsis thaliana, treated with the MAMP elf18. It is the first of three biological replicates.


title: Col0_3AB_H2O_rep3

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-amino benzamide (3AB). It is the third of three biological replicates.


title: 151245B_326N


title: parg1_H2O_rep2

description: This sample is of Arabidopsis thaliana SALK_116088 TDNA insertion knockout of the parg1 gene, untreated. It is the second of three biological replicates.


title: parg1_elf18_rep1

description: This sample is of Arabidopsis thaliana SALK_116088 TDNA insertion knockout of the parg1 gene, treated with the MAMP elf18. It is the first of three biological replicates.


title: parg1_elf18_rep3

description: This sample is of Arabidopsis thaliana SALK_116088 TDNA insertion knockout of the parg1 gene, treated with the MAMP elf18. It is the third of three biological replicates.


title: Col0_DMSO_flg22_rep1

description: This sample is of wild-type Arabidopsis thaliana, treated with the MAMP flg22. It is the first of three biological replicates.


title: Col0_3AB_flg22_rep3

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-amino benzamide (3AB) and the MAMP flg22. It is the third of three biological replicates.


title: Col0_3MB_flg22_rep1

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB) and the MAMP flg22. It is the first of three biological replicates.


title: Col0_3MB_H2O_rep3

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB). It is the third of three biological replicates.


title: Col0_DMSO_H2O_rep3

description: This sample is of wild-type Arabidopsis thaliana, untreated. It is the third of three biological replicates.


title: Col0_3MB_flg22_rep3

description: This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB) and the MAMP flg22. It is the third of three biological replicates.


title: Lung_TB-infected_2

status: Public on Jun 17 2017

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: gene expression data

hyb_protocol: Hybridization to Affymetrix Mouse Gene ST 1.0 microarrays was performed at 45oC for 16 hours at 60 rpm in the Affymetrix rotisserie hybridization oven.  The signal amplification protocol for washing and staining of eukaryotic targets was performed in an automated fluidics station (Affymetrix FS450) using Affymetrix protocol FS450_0007.

scan_protocol: The arrays were scanned in the GCS3000 laser scanner with autoloader and 3G upgrade (Affymetrix). Quality assessment of hybridizations and scans was performed with Expression Console software (Affymetrix).

data_processing: The data were analyzed with Partek Genomics Suite version 6.0 using default import and analysis settings for Affymetrix microarrays (RMA algorithm for background correction, quantile normalization, and median polish summarization of probes). ANOVA , with linear contrasts, was performed to generate p-values and fold changes. Infected samples were normalized to uninfected controls.

source_name: C57BL/6 mouse lung

label_protocol: Biotinylated ss-cDNA were prepared using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay kit, according to the manufacturer’s recommended protocol, from 100 nanograms of total RNA.

extract_protocol: Trizol Reagent (Life Technologies) and the RNeasy Mini kit (Qiagen) were used for extraction and purification of RNA from frozen lung tissue. Following elution of purified RNA from the columns with Nuclease-free water, quantitation was performed using a NanoDrop spectrophotometer, and quality assessment determined by RNA Nano LabChip analysis on an Agilent BioAnalyzer 2100.

tag: strain

value: lung

value: TB

tag: infection status

value: Infected with Mycobacterium tuberculosis


title: Lung_TB+Filaria-infected_8

description: gene expression data

value: TB+Filaria

value: Infected with Brugia malayi and Mycobacterium tuberculosis


title: Lung_TB+Filaria-infected_5

description: gene expression data


title: Lung_TB+Filaria-infected_6

description: gene expression data


title: Lung_Filaria-infected_6

description: gene expression data

value: Filaria

value: Infected with Brugia malayi


title: Lung_TB-infected_5

description: gene expression data


title: Lung_Filaria-infected_7

description: gene expression data


title: Lung_TB-infected_4

description: gene expression data


title: Lung_Filaria-infected_5

description: gene expression data


title: Lung_Filaria-infected_2

description: gene expression data


title: Lung_TB+Filaria-infected_1

description: gene expression data


title: Lung_TB+Filaria-infected_4

description: gene expression data


title: Lung_TB+Filaria-infected_2

description: gene expression data


title: Lung_Filaria-infected_3

description: gene expression data


title: Lung_Non-infected_3

description: gene expression data

value: Control

value: uninfected


title: Lung_Filaria-infected_4

description: gene expression data


title: Lung_Non-infected_2

description: gene expression data


title: Lung_Non-infected_4

description: gene expression data


title: Lung_TB-infected_1

description: gene expression data


title: Lung_TB-infected_3

description: gene expression data


title: Lung_TB+Filaria-infected_7

description: gene expression data


title: Lung_TB+Filaria-infected_3

description: gene expression data


title: Lung_Filaria-infected_1

description: gene expression data


title: Lung_Non-infected_1

description: gene expression data


title: ERaUtcKO E2 24h-1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
gene expression after E2, 24h treatment
Esr1f/f;PgrCre+ mouse on C57B6

hyb_protocol: Five and one half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

source_name: ovariectomized ERaUtcKO uterus, E2 treated for 24h, replicate 1

label_protocol: Three hundred nanograms (300 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

extract_protocol: RNA was isolated using Trizol reagent (Thermo Scientific). RNA was further purified using Qiagen RNAeasy RNA clean-up protocol with DNAse treatment

treatment_protocol: Ovariectomized  mice were injected intraperitoneally with vehicle (100 ul saline) , E2 (250 ng in 100 ul saline) or IGF1 (50 ug in 100 ul PBS), or had an osmotic pump (Alza 100 3D; 3 day) containg IGF1 (0.5 mg/ml 0.1N acetic acid) inserted intraperitoneally. Uterine tissue was collected after 2 hours or 24 hours, frozen in liquid nitrogen and crushed

value: uterus


title: ERaUtcKO E2 2h-3

description:
gene expression after E2, 2h treatment
Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized ERaUtcKO uterus, E2 treated for 2h, replicate 3


title: ERaUtcKO E2 24h-2

source_name: ovariectomized ERaUtcKO uterus, E2 treated for 24h, replicate 2


title: ERaUtcKO E2 2h-2

source_name: ovariectomized ERaUtcKO uterus, E2 treated for 2h, replicate 2


title: ERaUtcKO E2 24h-3

source_name: ovariectomized ERaUtcKO uterus, E2 treated for 24h, replicate 3


title: ERaUtcKO E2 2h-1

source_name: ovariectomized ERaUtcKO uterus, E2 treated for 2h, replicate 1


title: 12h_mlo2612_rep1

city: Aachen

first: Hannah

last: Kuhn

address: Worringerweg 1

department: Institute for Biology I

country: Germany

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized to the ATH1 gene chip for 16 h, as recommended by the supplier (Gene expression analysis manual; Affymetrix).

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

data_processing: Raw data files were processed in Bioconductor/R using packages Affy and limmaGUI. Background correction and quantile normalization were performed using the Guanine Cytosine Robust Multi-Array Analysis (GCRMA) function.

source_name: mlo2 mlo6 mlo12 plants 12 h after G. orontii inoculation

label_protocol: Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labeling with the IVT labeling kit (GeneChip One-cycle target labeling and control reagents; Affymetrix).

growth_protocol: Plants were soil grown for 4 weeks under controlled conditions with a 10/14 h light/dark cycle at 23°C and 65 % relative humidity.

extract_protocol: RNA was extracted with 1 ml Trizol (Invitrogen, Karlsruhe, Germany) per 100 mg leaf material according to the manufacturer’s instructions.  In this case, further purification of the isolated RNA was performed using mini columns from  the RNeasy Plant Kit as suggested by the manufacturers (QIAGEN, Hilden, Germany).

treatment_protocol: Plants were inoculated with G. orontii spores via leaf-to-leaf transfer from fully infected hypersusceptible A. thaliana eds1 mutants. Rosette leaves were sampled prior or 8 and 12 hours after inoculation.

value: A. thaliana Col-0 mlo2 mlo6 mlo18

value: Rosette leaf

tag: age

value: 12 h after G. orontii inoculation


title: 8h_mlo2612_rep3

source_name: mlo2 mlo6 mlo12 plants 8 h after G. orontii inoculation

value: A. thaliana Col-0 mlo2 mlo6 mlo17

value: 8 h after G. orontii inoculation


title: WT (ERaUtcKO) E2 2h-1

description:
gene expression after E2, 2h treatment
WT littermate of Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, E2 treated for 2h, replicate 1

value: WT littermate of Esr1f/f;PgrCre+


title: 0h_mlo2612_rep2

source_name: mlo2 mlo6 mlo12 plants prior to G. orontii inoculation

value: A. thaliana Col-0 mlo2 mlo6 mlo13

value: prior inoculation (0 h)


title: 12h_mlo2612_rep2

value: A. thaliana Col-0 mlo2 mlo6 mlo19


title: 8h_mlo2612_rep1

value: A. thaliana Col-0 mlo2 mlo6 mlo15


title: WT (ERaUtcKO) IGF1 24h-2

description:
gene expression after IGF1, 24h treatment
WT littermate of Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized WT (ERaUtcKO littermate) uterus,IGF1treated for 24h, replicate 2


title: 8h_mlo2612_rep2

value: A. thaliana Col-0 mlo2 mlo6 mlo16


title: WT (ERaUtcKO) E2 2h-3

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, E2 treated for 2h, replicate 3


title: ERaUtcKO IGF1 2h-3

description:
gene expression after IGF1, 2h treatment
Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized ERaUtcKO uterus,IGF1 treated for 2h, replicate 3


title: 12h_mlo2612_rep3

value: A. thaliana Col-0 mlo2 mlo6 mlo20


title: ERaUtcKO V-3

description:
gene expression after V, 24h treatment
Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized ERaUtcKO uterus, vehicle treated for 24h, replicate 3


title: WT (ERaUtcKO) IGF1 24h-3

source_name: ovariectomized WT (ERaUtcKO littermate) uterus,IGF1treated for 24h, replicate 3


title: WT (ERaUtcKO) E2 24h-3

description:
gene expression after E2, 24h treatment
WT littermate of Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, E2 treated for 24h, replicate 3


title: 0h_mlo2612_rep3

value: A. thaliana Col-0 mlo2 mlo6 mlo14


title: WT (ERaUtcKO) E2 24h-2

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, E2 treated for 24h, replicate 2


title: 12h_Col-0_rep3

source_name: Col-0 plants 12 h after G. orontii inoculation

value: A. thaliana Col-0 wt


title: ERaUtcKO IGF1 2h-2

source_name: ovariectomized ERaUtcKO uterus,IGF1 treated for 2h, replicate 2


title: WT (ERaUtcKO) E2 2h-2

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, E2 treated for 2h, replicate 2


title: WT (ERaUtcKO) E2 24h-1

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, E2 treated for 24h, replicate 1


title: ERaUtcKO IGF1 2h-1

source_name: ovariectomized ERaUtcKO uterus,IGF1 treated for 2h, replicate 1


title: ERaUtcKO IGF1 24h-1

description:
gene expression after IGF1, 24h treatment
Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized ERaUtcKO uterus,IGF1 treated for 24h, replicate 1


title: ERaUtcKO IGF1 24h-3

source_name: ovariectomized ERaUtcKO uterus,IGF1 treated for 24h, replicate 3


title: ERaUtcKO V-1

source_name: ovariectomized ERaUtcKO uterus, vehicle treated for 24h, replicate 1


title: WT (ERaUtcKO) IGF1 2h-2

description:
gene expression after IGF1, 2h treatment
WT littermate of Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized WT (ERaUtcKO littermate) uterus,IGF1treated for 2h, replicate 2


title: ERaUtcKO IGF1 24h-2

source_name: ovariectomized ERaUtcKO uterus,IGF1 treated for 24h, replicate 2


title: ERaUtcKO V-2

source_name: ovariectomized ERaUtcKO uterus, vehicle treated for 24h, replicate 2


title: WT (ERaUtcKO) IGF1 2h-1

source_name: ovariectomized WT (ERaUtcKO littermate) uterus,IGF1treated for 2h, replicate 1


title: WT (ERaUtcKO) IGF1 24h-1

source_name: ovariectomized WT (ERaUtcKO littermate) uterus,IGF1treated for 24h, replicate 1


title: 12h_Col-0_rep2


title: 8h_Col-0_rep3

source_name: Col-0 plants 8 h after G. orontii inoculation


title: 8h_Col-0_rep2


title: 12h_Col-0_rep1


title: 0h_Col-0_rep3

source_name: Col-0 plants prior to G. orontii inoculation


title: WT (ERaUtcKO) V-2

description:
gene expression after V, 24h treatment
WT littermate of Esr1f/f;PgrCre+ mouse on C57B6

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, vehicle treated for 24h, replicate 2


title: 0h_Col-0_rep1


title: 8h_Col-0_rep1


title: E9-5_Heart_KO_rep1

city: liverpool

first: Iain

middle: M

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

country: United Kingdom

institute: Liverpool John Moores University

description: gene-level analysis

hyb_protocol: Mouse Exon 1.0 ST whole transcript array genechip (Affymetrix).

scan_protocol: Affymetrix GeneChip Microarray System at UCL Genomics Institute of Child Health

data_processing: CHP data generated using Expression Console (Affymetrix). RMA algorithm. Gene core profiles.

label: Biotin

source_name: Heart

label_protocol: WT Expression kit (Ambion); genechip terminal labelling and hydrolyzing kit (Affymetrix, Santa Clara USA)

extract_protocol: Whole heart containing blood removed. Each sample is a pool of 4-6 hearts. RNA prepared using RNA Mini kit (Qiagen)

value: Mesp1Cre/+; Hic2 FL/FL

value: heart


title: E9-5_Heart_KO_rep3

description: gene-level analysis


title: E9-5_Heart_WT_rep3

description: gene-level analysis

value: Mesp1+/+; Hic2 FL/FL


title: E9-5_Heart_KO_rep2

description: gene-level analysis


title: Ex3aERKO IGF1 2h-2

description:
gene expression after IGF1, 2h treatment
Ex3aERKO (Esr1-null) mouse on C57B6

source_name: ovariectomized Ex3aERKO uterus, IGF1 treated for 2h, replicate 2

value: Ex3aERKO (Esr1-null)

value: uterus


title: 0h_Col-0_rep2

value: Rosette leaf


title: E9-5_Heart_WT_rep2

description: gene-level analysis


title: WT (ERaUtcKO) V-1

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, vehicle treated for 24h, replicate 1


title: WT (ERaUtcKO) V-3

source_name: ovariectomized WT (ERaUtcKO littermate) uterus, vehicle treated for 24h, replicate 3


title: Ex3aERKO IGF1 24h-1

description:
gene expression after IGF1, 24h treatment
Ex3aERKO (Esr1-null) mouse on C57B6

source_name: ovariectomized Ex3aERKO uterus, IGF1 treated for 24h, replicate 1


title: Ex3aERKO E2 2h-1

description:
gene expression after E2, 2h treatment
Ex3aERKO (Esr1-null) mouse on C57B6

source_name: ovariectomized Ex3aERKO uterus, E2 treated for 2h, replicate 1


title: Ex3aERKO IGF1 24h-3

source_name: ovariectomized Ex3aERKO uterus, IGF1 treated for 24h, replicate 3


title: Ex3aERKO E2 2h-3

source_name: ovariectomized Ex3aERKO uterus, E2 treated for 2h, replicate 3


title: Ex3aERKO V-3

description:
gene expression after V, 24h treatment
Ex3aERKO (Esr1-null) mouse on C57B6

source_name: ovariectomized Ex3aERKO uterus,vehicle treated for 24h, replicate 3


title: Ex3aERKO E2 24h-1

description:
gene expression after E2, 24h treatment
Ex3aERKO (Esr1-null) mouse on C57B6

source_name: ovariectomized Ex3aERKO uterus, E2 treated for 24h, replicate 1


title: E9-5_Heart_WT_rep1

description: gene-level analysis


title: 0h_mlo2612_rep1

source_name: mlo2 mlo6 mlo12 plants prior to G. orontii inoculation

value: A. thaliana Col-0 mlo2 mlo6 mlo12


title: Ex3aERKO V-2

source_name: ovariectomized Ex3aERKO uterus,vehicle treated for 24h, replicate 2


title: Ex3aERKO IGF1 24h-2

source_name: ovariectomized Ex3aERKO uterus, IGF1 treated for 24h, replicate 2


title: Ex3aERKO IGF1 2h-1

source_name: ovariectomized Ex3aERKO uterus, IGF1 treated for 2h, replicate 1


title: Ex3aERKO E2 24h-3

source_name: ovariectomized Ex3aERKO uterus, E2 treated for 24h, replicate 3


title: WT (Ex3aERKO) IGF1 24h-2

description:
gene expression after IGF1, 24h treatment
WT littermate of Ex3aERKO (Esr1-null) mouse on C57Bl6

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, IGF1 treated for 24h, replicate 2

value: wildtype


title: WT (Ex3aERKO) E2 24h-3

description:
gene expression after E2, 24h treatment
WT littermate of Ex3aERKO (Esr1-null) mouse on C57Bl6

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, E2 treated for 24h, replicate 3


title: WT (Ex3aERKO) IGF1 2h-3

description:
gene expression after IGF1, 2h treatment
WT littermate of Ex3aERKO (Esr1-null) mouse on C57Bl6

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, IGF1 treated for 2h, replicate 3


title: WT (Ex3aERKO) E2 24h-2

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, E2 treated for 24h, replicate 2


title: WT (Ex3aERKO) IGF1 24h-3

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, IGF1 treated for 24h, replicate 3


title: WT (Ex3aERKO) IGF1 24h-1

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, IGF1 treated for 24h, replicate 1


title: WT (Ex3aERKO) V-3

description:
gene expression after V, 24h treatment
WT littermate of Ex3aERKO (Esr1-null) mouse on C57Bl6

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, vehicle treated for 24h, replicate 3


title: WT (Ex3aERKO) E2 2h-2

description:
gene expression after E2, 2h treatment
WT littermate of Ex3aERKO (Esr1-null) mouse on C57Bl6

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, E2 treated for 2h, replicate 2


title: WT (Ex3aERKO) E2 2h-3

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, E2 treated for 2h, replicate 3


title: THP-1_GNP + LL37

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

description: THP-1 cells, originated from peripheral blood monocyte of an 1 year old human infant, purchased from NCCS, India

hyb_protocol: 825 ng each of test and reference Cy dye  labeled RNA was mixed together and was fragmented using Agilent fragmentation kit in the presence of blocking reagent for 30 minutes in 60 degree celsius. Equal volume of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture to stop the reaction. 100 μl of the mixture was added to each of the chamber of the hybridization gasket and the array slide was sandwitched over it. The hybridization reaction was done for 17 hours in 65 degree celsius with moist condition in a hybridization oven.

scan_protocol: Scanned on an Agilent G2505C scanner using Agilent Scan control (version 8.3.1.1). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: THP-1 cells treated with a mixture of GNP and LL37 (Spiked) for 6 hours  vs reference

label_protocol: 500 ng of total RNA were primed with 1.2 µl (3rd dilution) of  T7 promoter primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of MMLV Rtase. The c-DNA was then transcribed by T7 RNA Polymerase in the presence of NTPs and labeled with Cy3-CTP (For Rererence) and Cy5-CTP (For test).

growth_protocol: Cells were grown in RPMI-1640 medium (Himedia, India) supplemented with 10% heat inactivated fetal bovine serum (Himedia, India) (without any antibiotic) in 75 cm2 tissue culture flasks (BD Biosciences, USA) at 37 degree Celcius in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA extracted using Qiagen RNEasy mini kit following manufacturer's instructions

source_name: pooled whole RNA from all the test groups and untreated group (Reference)


title: WT (Ex3aERKO) IGF1 2h-1

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, IGF1 treated for 2h, replicate 1


title: WT IGF1 24h-2

description:
gene expression after IGF1, 24h treatment
C57Bl6 from Charles River Inc, Raleigh NC

source_name: ovariectomized WT uterus, IGF1 treated for 24h, replicate 2


title: THP-1_CNT + LL37

source_name: THP-1 cells treated with a mixture of CNT and LL37 (Spiked) for 6 hours  vs reference


title: WT (Ex3aERKO) E2 2h-1

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, E2 treated for 2h, replicate 1


title: THP-1_LL37(20 ug)

source_name: THP-1 cells treated with LL37 (20 μg/ml) for 6 hours  vs reference


title: WT IGF1 24h-3

source_name: ovariectomized WT uterus, IGF1 treated for 24h, replicate 3

value: C57Bl6 from Charles River Inc, Raleigh NC


title: WT IGF1 2h-2

description:
gene expression after IGF1, 2h treatment
C57Bl6 from Charles River Inc, Raleigh NC

source_name: ovariectomized WT uterus, IGF1 treated for 2h, replicate 2


title: WT IGF1 2h-1

source_name: ovariectomized WT uterus, IGF1 treated for 2h, replicate 1


title: WT IGF1 24h-1

source_name: ovariectomized WT uterus, IGF1 treated for 24h, replicate 1


title: WT E2 24h-3

description:
gene expression after E2, 24h treatment
C57Bl6 from Charles River Inc, Raleigh NC

source_name: ovariectomized WT uterus, E2 treated for 24h, replicate 3


title: THP-1_GNP-LL37

source_name: THP-1 cells treated with GNP-LL37 conjugate for 6 hours  vs reference


title: THP-1_CNT-LL37 + GNP-LL37

source_name: THP-1 cells treated with a mixture of CNT-LL37 and GNP-LL37 conjugate for 6 hours  vs reference


title: THP-1_LL37(0.02 ug)

source_name: THP-1 cells treated with LL37 (0.02 μg/ml) for 6 hours  vs reference


title: WT E2 24h-2

source_name: ovariectomized WT uterus, E2 treated for 24h, replicate 2


title: WT (Ex3aERKO) V-2

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, vehicle treated for 24h, replicate 2


title: THP-1_CNT-LL37

source_name: THP-1 cells treated with CNT-LL37 conjugate for 6 hours  vs reference


title: WT E2 24h-1

source_name: ovariectomized WT uterus, E2 treated for 24h, replicate 1


title: PFC_PND28 mice glyphosate-treated

status: Public on Jun 16 2017

city: HangZhou City

first: Hua

last: Ji

state: Zhejiang

address: No.481 Bingwen road

department: Department of Basic Medicine

institute: Hangzhou medical college

description:
Experimental animals were male offspring produced by ICR mice (SLAC, Shanghai, China).
pooled total RNA sample taken from 8 Glyphosate treated PND 28 male mice offsprings' PFC (the glyphosate treated group), the pregnant mice were provided with 0.38% glyphosate in drinking water (1% Roundup  ), equivalent to 50 mg of glyphosate/kg/day.

hyb_protocol: The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min; Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA); Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Axon GenePix 4000B microarray scanner

data_processing: Data were processed using Median Normalization Method to obtain “Normalized Data”. Then the statistical significance of differentially expressed miRNA was analyzed by T-test.   Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

source_name: brain

label_protocol: Samples were enzymatically fragmented and biotinylated using the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon)

growth_protocol: Mouse PFC dissected from PND28 mouse brain

extract_protocol: The pregnant ICR mice were randomly allocated in two groups, each group consisting of 8 pregnant mice (Slac, China ). Each group were used for the miRNA microarray assay. In the control group, pregnant mice were provided with purified water. In the glyphosate treated group, pregnant mice were provided with 0.38% glyphosate in drinking water (1% Roundup®), equivalent to 50 mg of glyphosate/kg/day.

treatment_protocol: not applicable

tag: gender

value: male

value: ICR

value: 4 weeks old

value: prefrontal cortex


title: WT E2 2h-3

description:
gene expression after E2, 2h treatment
C57Bl6 from Charles River Inc, Raleigh NC

source_name: ovariectomized WT uterus, E2 treated for 2h, replicate 3

tag: genotype/variation


title: WT V-3

description:
gene expression after V, 24h treatment
C57Bl6 from Charles River Inc, Raleigh NC

source_name: ovariectomized WT uterus, vehicle treated for 24h, replicate 3


title: WT V-2

source_name: ovariectomized WT uterus, vehicle treated for 24h, replicate 2


title: WT E2 2h-2

source_name: ovariectomized WT uterus, E2 treated for 2h, replicate 2


title: WT V-1

source_name: ovariectomized WT uterus, vehicle treated for 24h, replicate 1


title: PFC_PND28 mice control

description:
Experimental animals were male offspring produced by ICR mice (SLAC, Shanghai, China).
pooled total RNA sample taken from 8 control postnatal day (PND) 28 male mice offsprings' prefrontal cortex (PFC) (the control group), the pregnant mice were provided with purified water.


title: LPS.12h.2

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

hyb_protocol: Biotinylated cRNA was hybridized to an Affymetrix Mouse Exon 1.0 ST GeneChip using standard protocols and reagents from Affymetrix.

scan_protocol: Imaging was performed with the Affymetrix GeneChip Scanner 3000.

data_processing: Data were processed using Affymetrix power tools. Brain Array (v. 18.0) custom CDFs were used for probe mapping (apt-probeset-summarize -a rma-sketch --pgf-file ../LibraryFiles/BrainArray/MoEx10stv1_Mm_ENTREZG_18.0.0.pgf --clf-file ../LibraryFiles/MoEx-1_0-st-v1.r2.clf --use-disk false -o outENTREZv18.0-LPS --cel-files celFilesLPS.txt).

source_name: LPS stimulated - 12h mouse 2

label_protocol: Sample mRNA was amplified and labeled with the Affymetrix One-Cycle Eukaryotic Target Labeling Assay protocol and reagents.

growth_protocol: Bone marrow cells collected from femurs were plated on non-tissue culture-treated plastic in complete RPMI medium [RPMI 1640 (Invitrogen) containing L-glutamine, supplemented with 10% (v/v) FBS (Invitrogen, cat #10437), 100 IU/mL penicillin and 100 Î¼g/mL streptomycin (all from Cellgro)] plus 50 ng/mL recombinant human macrophage colony-stimulating factor (rhM-CSF, Chiron) (hereafter, BMDM medium). On day four, the medium was replaced, and on day six, adherent cells were lifted in PBS + 1 mM EDTA, counted, pelleted, resuspended in BMDM medium, and plated into six-well tissue culture plates.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent 2100 Bioanalyzer.

treatment_protocol: On day seven, for samples intended for LPS stimulation, LPS (List Biological Labs) was introduced into the culture medium, at 10 ng/mL. Cells were then incubated for 1, 4 or 12 hours.

value: female

value: 8-12 weeks

tag: cell type

value: Bone marrow-derived macrophages

tag: stimulus

value: LPS

tag: stimulus concentration

value: 10 ng/mL

tag: stimulus duration


title: WT E2 2h-1

source_name: ovariectomized WT uterus, E2 treated for 2h, replicate 1


title: LPS.12h.1

source_name: LPS stimulated - 12h mouse 1


title: LPS.4h.2

source_name: LPS stimulated - 4h mouse 2

value: 4 h


title: LPS.1h.2

source_name: LPS stimulated - 1h mouse 2

value: 1 h


title: LPS.12h.3

source_name: LPS stimulated - 12h mouse 3


title: LPS.4h.3

source_name: LPS stimulated - 4h mouse 3


title: LPS.1h.1

source_name: LPS stimulated - 1h mouse 1


title: LPS.1h.3

source_name: LPS stimulated - 1h mouse 3


title: Unstim.2

source_name: Unstimulated Mouse 2


title: Unstim.3

source_name: Unstimulated Mouse 3


title: LPS.4h.1

source_name: LPS stimulated - 4h mouse 1


title: 4'-OH-2,5-DCB 1

status: Public on Jun 15 2017

city: Philadelphia

first: Benoit

last: Van Aken

state: PA

address: 1947 N. 12th Street

department: CEE

institute: Temple University

description: Gene expression data from plants exposed to 5 mg/L 4'-OH-2,5-DCB

hyb_protocol: 100 ng RNA was used as input, 15 microg cRNA was used in the 2nd cycle, and 3.5 microg ss-cDNA was hybridized on the GeneChip Arabidopsis Genome ATH1 Array using Hybridization Oven 645. GeneChips were washed  and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Thermo Fisher GeneChip Scanner GCS3000-7G.

data_processing:
.CEL files were converted into .chp files using the Affymetrix Expression Console and expression levels were calculated using the Affymetrix Transcription Analysis Console.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Plants exposed to 5 mg/L 4'-OH-2,5-DCB

label_protocol: Biotinylated cRNA was prepared using the GeneChip® WT PLUS Reagent Kit according to the standard Affymetrix protocol.

growth_protocol: A. thaliana plantlets were grown for 21 days in Magenta boxes containing 0.5-strength MS nutrient solution with 0.3% sucrose and 0.7% phytoagar (pH 7.2). Plantlets were incubated at 25ºC under white (cool) fluorescent light (0.4 W ft-2) with a 16-h light/8-h dark photoperiod.

treatment_protocol: Plantlets were exposed to 2,5-DCB (50 mg L-1) and 4'-OH-2,5-DCB (5 mg L-1) supplemented in the nutrient solution. Control plantlets were grown in the presence of the solvent carrier only (acetone).

value: whole plant

value: 21 days

tag: exposed to


title: CHIP504LYF

type: genomic

city: changsha

first: xiong

last: bo

address: xiangya road

institute: xiangya

description: Hybridized to cyto 750K

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (AGCC). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Chromosome Analysis Suite(CHAS 3.1) softwares.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease state

value: Comorbid familial non-obstructive azoospermia (NOA) and congenital cataract (CC)

value: peripheral blood


title: Unstim.1

source_name: Unstimulated Mouse 1


title: 4'-OH-2,5-DCB 3


title: 4'-OH-2,5-DCB 2


title: 2,5-DCB 2

description: Gene expression data from plants exposed to 50 mg/L 2,5-DCB

source_name: Plants exposed to 50 mg/L 2,5-DCB


title: 2,5-DCB 1


title: Control 1

description: Gene expression data from control, non-exposed plants

source_name: Control, non-exposed plants

value: solven carrier only; control


title: 2,5-DCB 3


title: Control 3


title: Control 2


title: Liver_backcross_breast cancer [282Bx]

status: Public on Jun 14 2017

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Grade of aging and breast cancer susceptibility

hyb_protocol: cRNA was hybridized to Mpuse Gene 2.0 ST Array (Affymetrix)

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Normalization of microarray signal data across chips were performed with the Robust Multichip Analysis (RMA) algorithm in the Affymetrix Expression Console v. 1.4.1

source_name: Liver_backcross_breast cancer

label_protocol: 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix)

extract_protocol: Total RNA was extracted from purified cell populations using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

value: liver

tag: genetic background

value: C57xFVB backcross

tag: comorbidity

value: breast cancer

tag: transgene

value: MMTV-Neu (protooncogene)


title: Liver_backcross_breast cancer [261Bx]


title: Liver_backcross_breast cancer [200Bx]


title: Liver_backcross_breast cancer [292Bx]


title: Liver_backcross_breast cancer [179Bx]


title: Liver_backcross_breast cancer [257Bx]


title: Liver_backcross_breast cancer [235Bx]


title: Liver_backcross_breast cancer [231Bx]


title: Liver_backcross_breast cancer [289Bx]


title: Liver_backcross_breast cancer [267Bx]


title: Liver_backcross_breast cancer [229Bx]


title: Liver_backcross_breast cancer [265Bx]


title: WT (Ex3aERKO) E2 24h-1

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, E2 treated for 24h, replicate 1

value: wildtype

value: uterus


title: Liver_backcross_breast cancer [223Bx]

value: female


title: Liver_backcross_breast cancer [161Bx]


title: Liver_backcross_breast cancer [270Bx]


title: Liver_backcross_breast cancer [290Bx]


title: Liver_backcross_breast cancer [170Bx]


title: Liver_backcross_breast cancer [301Bx]


title: Liver_backcross_breast cancer [284Bx]


title: Liver_backcross_breast cancer [187Bx]


title: Liver_backcross_breast cancer [165Bx]


title: Liver_backcross_breast cancer [258Bx]


title: Liver_backcross_breast cancer [195Bx]


title: Liver_backcross_breast cancer [253Bx]


title: Liver_backcross_breast cancer [232Bx]


title: Liver_backcross_breast cancer [171Bx]


title: THP-1_CNT + GNP + LL37

source_name: THP-1 cells treated with a mixture of CNT, GNP, and LL37 (Spiked) for 6 hours  vs reference

tag: cell line

source_name: pooled whole RNA from all the test groups and untreated group (Reference)


title: Liver_backcross_breast cancer [142Bx]


title: WT (Ex3aERKO) IGF1 2h-2

source_name: ovariectomized WT (Ex3aERKO littermate) uterus, IGF1 treated for 2h, replicate 2


title: Liver_backcross_breast cancer [149Bx]


title: Liver_backcross_breast cancer [128Bx]


title: Liver_backcross_breast cancer [109Bx]


title: Liver_backcross_breast cancer [84Bx]


title: Liver_backcross_breast cancer [117Bx]


title: Liver_backcross_breast cancer [24Bx]


title: Liver_backcross_breast cancer [113Bx]


title: Liver_backcross_breast cancer [123Bx]


title: Liver_backcross_breast cancer [91Bx]


title: Liver_backcross_breast cancer [64Bx]


title: Liver_backcross_breast cancer [87Bx]


title: Liver_backcross_breast cancer [10Bx]


title: Liver_backcross_breast cancer [114Bx]


title: Liver_backcross_breast cancer [73Bx]


title: Liver_backcross_breast cancer [40Bx]


title: Liver_backcross_breast cancer [7Bx]


title: Liver_backcross_breast cancer [137Bx]


title: Liver_backcross_breast cancer [96Bx]


title: Liver_backcross_breast cancer [89Bx]


title: Liver_backcross_breast cancer [101Bx]


title: Liver_backcross_breast cancer [60Bx]


title: Liver_backcross_breast cancer [79Bx]


title: coculture1.2

city: Nanjing

first: Pingping

last: Shen

state: Jiangsu

address: 163 Xianlin Road

institute: Nanjing University

description: gene expression data from cells

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating software using Affymetrix default analysis settings and global scaling as normalization method. The microarray analysis was conducted by Gminix (Shanghai, China).

source_name: THP-1 macrophages co-cultured with MCF-7

label_protocol: 3' IVT Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All THP-1 cells were obatined from China Center for Type Culture collection. Standard media were used with 1% penicillin-streptomycin and 10% FBS.

treatment_protocol: THP-1 cells and MCF-1 cells were cocultured in RPMI1640 medium supplemented with 10% FBS and 1% antibiotics. 50 uM YVAD was used to treated cells for 48 hours.

value: macrophage cells


title: Ctrl2.1

description: gene expression data from cells

source_name: THP-1 macrophages


title: YVAD2.3

description: gene expression data from cells

source_name: THP-1 macrophages co-cultured with MCF-7 in presence of YVAD


title: coculture2.2

description: gene expression data from cells


title: Ctrl3.1

description: gene expression data from cells


title: coculture3.2

description: gene expression data from cells


title: YVAD3.3

description: gene expression data from cells


title: YVAD1.3

description: gene expression data from cells


title: Ctrl1.1

description: gene expression data from cells


title: 24 hr following FFSS rep3

city: Kansas City

first: Tarak

last: Srivastava

state: MO

address: 2401 Gillham Road

department: Pediatric Nephrology

institute: Children's Mercy Hospital

description: 24 hr following fluid flow shear stress

hyb_protocol: Two performance controls were incorporated into each array run: (i) Target amplification and labeling control by addition of polyadenylated transcript controls from Bacillus subtilis using the Poly-A Control kit (900433 Affymetrix). The poly-A controls were added to total RNA and served as a control for the RNA amplification and biotin labeling procedure, and (ii) GeneChip hybridization was controlled by the addition 3' Amplification Reagent Hybridization Controls (900454 Affymetrix). The Hybridization controls were composed of biotin labeled E. coli transcripts (bioB, bioC, bioD, cre) which were spiked into the hybridization cocktail with increasing concentrations. The hybridization spike controls served to control the hybridization procedure.

scan_protocol: standard Affymetrix protocol

data_processing: The data were normalized using Robust Multichip Average algorithm which consisted of three steps: a background adjustment, quantile normalization, log-2 transformation and final summarization. Analysis of array data was performed on Partek Gemomics Suite (http://www.partek.com/pgs). Two way ANOVA with group and replicate effects were fitted to the model, and the confounding effects of replication were adjusted by the ANOVA model.

source_name: Mouse Podocyte Cell Line

growth_protocol: Conditionally immortalized mouse podocyte line with thermosensitive tsA58 mutant T-antigen was used in these studies. Podocytes were propagated in RPMI 1640 with L-glutamine supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 0.1 mg/ml streptomycin (Invitrogen, Carlsbad, CA) under permissive conditions (33ºC with 10 units/ml of γ-interferon (Cell Sciences, Norwood, MA)). Cells were transferred to non-permissive conditions (37ºC without γ-interferon) to induce differentiation. Three glass slides (25 x 75 x1 mm, Fisher Scientific, Pittsburg, PA) were maintained in one culture dish containing 12 ml of culture medium. The medium was changed 24 hours prior to the application of FFSS. Differentiated podocytes were used for FFSS experiments on day 14.

extract_protocol: Podocytes following application of FFSS were processed using the Trizol / Phaselock protocol. Total RNA fraction was purified by RNA Clean-Up protocol using the RNeasy mini kit (74104 Qiagen). RNA bound on the RNeasy column was DNase treated using the RNase free DNase set (79254 Qiagen), eluted and  quantitated using Nanodrop-1000 spectrophotometer. Aliquots were run on an Agilent 2100 Bioanalyzer using the RNA6000 LabChip Nano kit ver II for quality assessment and quantification of RNA. The Affymetrix GeneChip® Mouse Exon 1.0 ST Array with over 4.5 million unique 25-mer oligonucleotides constituting ~1.2 million probe sets, with ~4 probes/ exon and ~40 probes/ gene was used. In gene-level expression analysis, multiple probes on different exons were summarized into a single gene-level expression data point.

treatment_protocol: FFSS was applied to differentiated podocytes using a FlexCell Streamer Gold apparatus (Flexcell International, Hillsborough, NC) as described earlier [83]. FFSS was applied at 2 dynes/cm2 (or 75 ml/min) for 2 hours at 37°C with 5% CO2. A set of podocytes (untreated control group) were placed in the same hood and incubator but were not exposed to FFSS. A 3-way stop-cock was attached to collect 1.5 ml aliquots of the medium at 0, 30 and 120 minutes during application of FFSS. Collected medium was used for cAMP measurement. Following FFSS treatment, podocytes on slides were returned to the original medium for recovery up to 24 hours in the incubator at 37°C under 5% CO2 humidified atmosphere. Samples obtained prior to exposing cells to FFSS, at the end of FFSS treatment, and following FFSS at 2hr and 24hr  treatment were termed pre-FFSS (or Control), End-FFSS, Post-2hr and Post-24hr, respectively. Pre-FFSS (Control), End and Post-FFSS 2h/24h cells were harvested for analysis. In addition, podocytes were treated with PGE2 without application of FFSS, and harvested at 0, 2, 5, 15, 60 and 120 minutes.

tag: sample type

value: Cell line from Immortomouse

tag: timepoint

value: 24 hr following fluid flow shear stress


title: 24 hr following FFSS rep2

description: 24 hr following fluid flow shear stress

label_protocol: Two performance controls were incorporated into each array run: (i) Target amplification and labeling control by addition of polyadenylated transcript controls from Bacillus subtilis using the Poly-A Control kit (900433 Affymetrix). The poly-A controls were added to total RNA and served as a control for the RNA amplification and biotin labeling procedure, and (ii) GeneChip hybridization was controlled by the addition 3' Amplification Reagent Hybridization Controls (900454 Affymetrix). The Hybridization controls were composed of biotin labeled E. coli transcripts (bioB, bioC, bioD, cre) which were spiked into the hybridization cocktail with increasing concentrations. The hybridization spike controls served to control the hybridization procedure.


title: 2 hr following FFSS rep1

description: 2 hr following fluid flow shear stress

value: 2 hr following fluid flow shear stress


title: 24 hr following FFSS rep1

description: 24 hr following fluid flow shear stress


title: End of FFSS rep3

description: End of fluid flow shear stress

value: End of fluid flow shear stress


title: 2 hr following FFSS rep2

description: 2 hr following fluid flow shear stress


title: Control rep1

description: Control untreated cells

value: Control untreated cells


title: Control rep2

description: Control untreated cells


title: 5_72_37.6 pM GGF2

status: Public on Jun 13 2017

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description: human hepatocyte RNA

hyb_protocol: Labeled cRNA (15 μg) was fragmented and prepared for hybridization.

scan_protocol: The Affymetrix HT HG-U133+ PM peg arrays were used with the Affymetrix Gene Titan system. Gene Titan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg arrays.

data_processing: Affymetrix CEL files were normalized using Robust Multi-array Average (RMA) method with a log base 2 (log2) transformation (Irizarry et al., 2003). Two (2) samples (Donor 4: 6 h: 0.376 pM GGF2 and Donor 5: 24 h: 0.1% GGF2 Buffer) failed QC and were omitted from analysis. Principal component analysis (PCA) was used to evaluate the overall performance of the arrays and identify outliers. One group of samples, Donor 1: 6 h clustered together and were > 3 SD away from the mean suggesting that these samples may also be aberrant and were therefore also omitted from analysis. A filtering step was performed to remove control probe sets, probe sets without mRNA annotation, and low expression probe sets. Gene expression differences were identified using ANOVA models with linear contrasts.

source_name: primary human hepatocytes_donor 5

label_protocol: Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix) according to manufacturer’s instructions.

growth_protocol: Hepatocytes were cultured in a sandwich configuration using previously described methods (LeCluyse et al., 2005)

extract_protocol: Cells were lysed using RLT buffer (Qiagen) mixed with Trizol (Life Technologies) at a 1:1 ratio (200 µl total) and isolated using either an RNeasy total RNA isolation kit or the QIAcube automated system (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Treatment was initiated 24 h after seeding. Four (4) treatment regimens were used for each donor including 3 different time points of continuous exposure (6, 24, and 72 h; media replaced every 24 h) plus a 24 h continuous exposure with a 48 h recovery (media changed to remove compound at 24 h; media replaced every 24 h). Hepatocytes were exposed to 5 different concentrations of GGF2 plus a GGF2 vehicle control (0.1% GGF2 formulation buffer).

tag: donor (#)

tag: donor (id)

tag: time (h)

tag: treatment

value: 37.6 pM GGF2


title: 2 hr following FFSS rep3

description: 2 hr following fluid flow shear stress


title: 5_72_0.1% GGF2 Buffer

description: human hepatocyte RNA

value: 0.1% GGF2 Buffer


title: 5_72_3760 pM GGF2

description: human hepatocyte RNA

value: 3760 pM GGF2


title: End of FFSS rep1

description: End of fluid flow shear stress


title: End of FFSS rep2

description: End of fluid flow shear stress


title: 5_72_0.376 pM GGF2

description: human hepatocyte RNA


title: Control rep3

description: Control untreated cells


title: 5_24+48R_3760 pM GGF2

description: human hepatocyte RNA


title: 5_72_376 pM GGF2

description: human hepatocyte RNA

value: 376 pM GGF2


title: 5_72_3.76 pM GGF2

description: human hepatocyte RNA

value: 3.76 pM GGF2


title: 5_24_3760 pM GGF2

description: human hepatocyte RNA


title: HT29_1

city: Tokyo

first: Hiroyuki

last: Seimiya

address: 3-8-31 Ariake, Koto-ku

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: Human Colon Cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The cell line was cultured in vitro until 80-90% confluency and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: no treatment

value: Human Colon Cancer


title: 5_24+48R_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 5_6_376 pM GGF2

description: human hepatocyte RNA


title: 5_24_376 pM GGF2

description: human hepatocyte RNA


title: 5_24_3.76 pM GGF2

description: human hepatocyte RNA


title: 5_24_37.6 pM GGF2

description: human hepatocyte RNA


title: Liver_backcross_breast cancer [126Bx]

city: Salamanca

tag: tissue

value: liver

value: C57xFVB backcross

value: breast cancer

tag: gender


title: 5_24_0.376 pM GGF2

description: human hepatocyte RNA


title: 5_6_3.76 pM GGF2

description: human hepatocyte RNA


title: 5_6_37.6 pM GGF2

description: human hepatocyte RNA


title: 5_6_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 5_6_3760 pM GGF2

description: human hepatocyte RNA


title: 4_72_376 pM GGF2

description: human hepatocyte RNA

source_name: primary human hepatocytes_donor 4


title: 4_72_3.76 pM GGF2

description: human hepatocyte RNA


title: 4_24_376 pM GGF2

description: human hepatocyte RNA


title: 5_6_0.376 pM GGF2

description: human hepatocyte RNA


title: 4_24_37.6 pM GGF2

description: human hepatocyte RNA


title: 4_72_3760 pM GGF2

description: human hepatocyte RNA


title: 4_24_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 4_72_37.6 pM GGF2

description: human hepatocyte RNA


title: 4_72_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 4_72_0.376 pM GGF2

description: human hepatocyte RNA


title: 4_6_376 pM GGF2

description: human hepatocyte RNA


title: 3_72_376 pM GGF2

description: human hepatocyte RNA

source_name: primary human hepatocytes_donor 3


title: 3_72_3760 pM GGF2

description: human hepatocyte RNA


title: 4_24+48R_3760 pM GGF2

description: human hepatocyte RNA


title: 4_24+48R_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 4_6_3760 pM GGF2

description: human hepatocyte RNA


title: 4_24_3.76 pM GGF2

description: human hepatocyte RNA


title: 4_6_37.6 pM GGF2

description: human hepatocyte RNA


title: 3_72_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 4_24_0.376 pM GGF2

description: human hepatocyte RNA


title: 3_72_37.6 pM GGF2

description: human hepatocyte RNA


title: 4_24_3760 pM GGF2

description: human hepatocyte RNA


title: 4_6_3.76 pM GGF2

description: human hepatocyte RNA


title: 3_72_3.76 pM GGF2

description: human hepatocyte RNA


title: 3_72_0.376 pM GGF2

description: human hepatocyte RNA


title: 3_24+48R_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 3_24+48R_3760 pM GGF2

description: human hepatocyte RNA


title: 4_6_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 3_24_376 pM GGF2

description: human hepatocyte RNA


title: 3_24_0.376 pM GGF2

description: human hepatocyte RNA


title: 3_24_37.6 pM GGF2

description: human hepatocyte RNA


title: 3_24_3760 pM GGF2

description: human hepatocyte RNA


title: 3_6_37.6 pM GGF2

description: human hepatocyte RNA


title: 2_72_3760 pM GGF2

description: human hepatocyte RNA

source_name: primary human hepatocytes_donor 2


title: 3_6_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 2_24+48R_3760 pM GGF2

description: human hepatocyte RNA


title: 3_6_0.376 pM GGF2

description: human hepatocyte RNA


title: 3_6_3.76 pM GGF2

description: human hepatocyte RNA


title: 2_6_3760 pM GGF2

description: human hepatocyte RNA


title: 2_72_0.376 pM GGF2

description: human hepatocyte RNA


title: 2_24_376 pM GGF2

description: human hepatocyte RNA


title: 2_6_376 pM GGF2

description: human hepatocyte RNA


title: 3_6_376 pM GGF2

description: human hepatocyte RNA


title: 2_72_3.76 pM GGF2

description: human hepatocyte RNA


title: 2_72_376 pM GGF2

description: human hepatocyte RNA


title: 2_72_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 2_24_37.6 pM GGF2

description: human hepatocyte RNA


title: 2_24_3.76 pM GGF2

description: human hepatocyte RNA


title: 2_24_0.376 pM GGF2

description: human hepatocyte RNA


title: 2_24_3760 pM GGF2

description: human hepatocyte RNA


title: 2_24_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 2_24+48R_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 2_72_37.6 pM GGF2

description: human hepatocyte RNA


title: 2_6_0.376 pM GGF2

description: human hepatocyte RNA


title: 3_24_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 3_6_3760 pM GGF2

description: human hepatocyte RNA


title: 1_72_376 pM GGF2

description: human hepatocyte RNA

source_name: primary human hepatocytes_donor 1


title: 2_6_37.6 pM GGF2

description: human hepatocyte RNA


title: 2_6_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 3_24_3.76 pM GGF2

description: human hepatocyte RNA


title: 2_6_3.76 pM GGF2

description: human hepatocyte RNA


title: 1_72_0.376 pM GGF2

description: human hepatocyte RNA


title: 1_72_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 1_24_376 pM GGF2

description: human hepatocyte RNA


title: 1_24+48R_0.1% GGF2 Buffer

description: human hepatocyte RNA


title: 1_24+48R_3760 pM GGF2

description: human hepatocyte RNA


title: Organoids 1 CC

city: Glasgow

first: Patrizia

last: Cammareri

address: Garscube Estate

institute: CRUK Beatson Institute

description: organoid generated from crypts

hyb_protocol: Samples were hybridized according to affymetrix protocol.

scan_protocol: Scanner provided by the Paterson Institue Manchester (UK).

data_processing:
The data were pre-processed using affy package in R language, version 2.15.0.
Background correction, quantile normalization, and probe summarisation were performed using the Robust Multi-array Analysis algorithm. Normalized data were analysed using the Limma package48.

source_name: Organoid from small intestine

label_protocol: Samples were labelled according to affymetrix protocol.

growth_protocol: Cells were plated in 24-well plates in Advanced DMEM/F12 supplemented with penicillin/streptomycin,  HEPES,  Glutamine, N2, B27, EGF and Noggin.

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

treatment_protocol: Cell pellets were used for RNA extractions.

tag: cells

value: Organoids

tag: origin

value: crypts

tag: genotype

value: VillinCreER Apcfl/fl KrasG12D


title: Organoids 2 SFV

description: organoid generated from villi

value: villi


title: 1_72_37.6 pM GGF2

description: human hepatocyte RNA


title: 1_72_3760 pM GGF2

description: human hepatocyte RNA


title: Organoids 1 SFV

description: organoid generated from villi


title: fbs1 knockout, biological rep1

city: Tacoma

first: Bryan

last: Thines

state: Washington

address: 1500 North Warner Street

institute: University of Puget Sound

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45oC on the Arabidopsis ATH1 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with R/Bioconductor and normalized using RMA.  The trimmed mean target intensity of each array was set to 100.

source_name: fbs1 knockout seedlings_12 days old_10oC cold for 7days

label_protocol: Biotinylated cRNA were prepared using the 3' IVT PLUS Reagent Kit according to standard Affymetrix protocols from 250 ng total RNA

growth_protocol: Seeds were surface-sterilized in 50% bleach containing 0.01% Tween-20 and stratified for five days in 0.1% agarose in the dark at 4oC.  Seeds were then sown onto sterile Whatman filter paper (Whatman, www.whatman.com) and placed on square plates containing 50 mL of MS medium at pH 5.8 with 0.8% type I micropropagation agar (Caisson Laboratories, www.caissonlabs.com).  All seedlings were grown in Percival CU-30L2 growth chambers (Percival Scientific, www.percival-scientific.com), set to either constant 24oC or 10oC and identical long-day conditions (16 hr light:8 hr darkness) with cool white light at 100 μmol/m2/s.

extract_protocol: Total RNA was isolated with the Qiagen RNeasy Kit and contaminating genomic DNA digested on column with the Qiagen RNase-free DNase Set according to the manufacturer’s protocol (Qiagen, www.qiagen.com/us/).

treatment_protocol: For chilling treatments, seedlings were grown for five days at 24oC before being transferred at dawn of the sixth day to 10oC and grown for seven additional days.

tag: accession background

tag: genotype/variation

value: fbs1-1 mutant

value: 12 day-old seedlings

tag: treated at

value: 10oC cold for 7 days


title: Allograft 1 SFV

description: Gene expression data from allograft tumour

source_name: Subcutaneous tumour

growth_protocol: For transplantation experiments, 50 spheroids were suspended in 100 μL of Matrigel and injected subcutaneously into a single flank of  female athymic (CD-1) nude mice.Tumours were harvested at the end-point (15mm or ulceration).

extract_protocol: Total RNA was isolated by Qiagen RNeasy Mini Kit according to the manufacturer's protocol.

treatment_protocol: RNAlater (Sigma) at -20C.

value: tumour

tag: strain

tag: end point

value: (15 mm or ulceration)


title: 1_24_0.376 pM GGF2

description: human hepatocyte RNA


title: Organoids 2 CC

description: organoid generated from crypts


title: Allograft 1 CC

growth_protocol: For transplantation experiments, 50 spheroids were suspended in 100 μL of Matrigel  and injected subcutaneously into a single flank of  female athymic (CD-1) nude mice.Tumours were harvested at the end-point (15mm or ulceration).


title: Allograft 3 CC

value: VillinCrER Apc fl/fl KrasG12D


title: 1_24_37.6 pM GGF2

description: human hepatocyte RNA

value: 37.6 pM GGF2


title: 1_24_3.76 pM GGF2

description: human hepatocyte RNA


title: wild type, biological rep3

source_name: WT seedlings_12 days old_10oC cold for 7days

value: wild type


title: Allograft 3 SFV

growth_protocol: For transplantation experiments, 50 spheroids were suspended in 100 μL of Matrigel  and injected subcutaneously into a single flank of female athymic (CD-1) nude mice.Tumours were harvested at the end-point (15mm or ulceration).


title: fbs1 knockout, biological rep2


title: Organoids 3 SFV

description: organoid generated from villi


title: Allograft 2 SFV


title: Organoids 3 CC

description: organoid generated from crypts


title: fbs1 knockout, biological rep3


title: 1_72_3.76 pM GGF2

description: human hepatocyte RNA

value: 3.76 pM GGF2


title: 1_24_3760 pM GGF2

description: human hepatocyte RNA

value: 3760 pM GGF2


title: 1_24_0.1% GGF2 Buffer

description: human hepatocyte RNA

value: 0.1% GGF2 Buffer


title: Senescent BJ cells transfected with siCtrl, biological repeat 2

city: Rehovot

first: Valery

last: Krizhanovsky

address: Herzel 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Expression data of damage-induced senescent human fibroblasts (BJ cells)

hyb_protocol: cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip PrimeView, Human Gene Expression Array, according to standard manufacturer protocols.

scan_protocol: Hybridized chips were stained, washed, and scanned with the Affymetrix GeneChip 3000 7G Plus scanner and converted to cell intensity files by Affymetrix Expression Console SoftwareTM.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.  Transcriptome analysis (processing of raw data, clustering, and creation of correlation matrices) was carried out with Partek Genomics Suite 6.6 (http://www.partek.com/). The raw probe intensities were adjusted according to the numbers of G and C bases in the probe sequence before any probe correction. Preprocessing was performed with the Robust Microarray Averaging algorithm (Irizarry, Hobbs et al., 2003). Genes expressed below background levels (log 1.5 intensity of 6.9) in all examined conditions were excluded from further analyses.

source_name: Human senescent primary fibroblasts BJs after transfection with sictrl

growth_protocol: Human  BJ fibroblasts were maintained in DMEM supplemented with 2 mM L-glutamine, 100 units/ml of penicillin, 100 µg/ml of streptomycin, and 10% fetal bovine serum (FBS). DNA damage-induced senescence (DIS) was introduced by treatment with etoposide (E1383, Sigma-Aldrich) at a concentration of  50 µM for 48 h.

extract_protocol: Total RNA was extracted from growing and damage-induced senescenct (DIS) BJ cells transfected with siRNA against p21, or with control siRNA, using an RNeasy Mini Kit (QIAGEN). RNA purity was assessed with an ND-1000 NanoDrop Spectrophotometer (Peqlab Biotechnologie) and BioAnalyzer 2100 system (Agilent Technologies).

treatment_protocol: BJ growing and etoposide treated cells (DIS) were plated in 12-well plates. Cells were transfected with ON-TARGETplus SMARTpool small interfering RNA (siRNA) targeting p21 (L-002000-00-0005) or a control, with Non-Targeting siRNA Pool (D-001810-10-20), using DharmaFECT formulation 1 reagent (T-2001-03) according to the instructions of the manufacturer (Thermo Fisher Scientific). After 3 days, total RNA was extracted.

value: human skin fibroblasts

value: BJ cell line

tag: age

value: senescent

tag: transfection

value: siCtrl


title: Adjacent nontumor (Gastric tissue)

city: JiNan

first: zhang

last: yan

state: shandong

address: Culture west road

department: Department of pharmacology

institute: Shandong University

description: Fresh tissue of adjacent nontumor (Gastric tissue)

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Adjacent nontumor (Gastric tissue)

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: Fresh tisuues of adjacent nontumor(Gastirc tissue) and low-differentiated adenocarcinoma(Gastric Cancer)

value: Adjacent nontumor (Gastric tissue)

value: male


title: Senescent BJ cells transfected with sip21, biological repeat 2

description: Expression data of damage-induced senescent human fibroblasts (BJ cells), after p21 knockdown

source_name: Human senescent primary fibroblasts BJs after transfection with sip21

label_protocol: cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip PrimeView, Human Gene Expression Array, according to standard manufacturer protocols.


title: Low-differentiated adenocarcinoma (Gastric Cancer)

description: Fresh tissue of low-differentiated adenocarcinoma (Gastric Cancer)


title: Senescent BJ cells transfected with sip21, biological repeat 3


title: Senescent BJ cells transfected with siCtrl, biological repeat 3


title: wild type, biological rep2


title: Growing Bj cells transfected with sip21, biological repeat 3

description: Expression data of growing human fibroblasts (BJ cells) after p21 knockdown

source_name: Human primary fibroblasts BJs after transfection with sip21

value: primary


title: Growing BJ cells transfected with siCtrl, biological repeat 3

description: Expression data of growing human fibroblasts (BJ cells)

source_name: Human primary fibroblasts BJs after transfection with siCtrl


title: Tery_mixture_ctrl

status: Public on Jun 11 2017

city: Xiamen

first: Tuo

last: Shi

state: Fujian

address: No. 1 South Xiang'an Rd.

institute: Xiamen University

description:
Sample 28
This sample is Trichodesmium erythraeum IMS101 total RNA from all the samples mixed at equimolar scale and used as a control in the experiment.
GenBank Accession NC_008312

hyb_protocol: Hybridization was performed following the standard operating protocol of Roche NimbleGen, Inc., Madison, WI, USA. See www.nimblegen.com.

scan_protocol: Scanning was performed following the standard operating protocol of Roche NimbleGen, Inc., Madison, WI, USA. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to Robust Multi-Array Average (RMA) analysis (Irizarry et al., 2003, Biostatistics 4: 249-264), quantile normalization (Bolstad et al., 2003, Bioinformatics 19: 185-193), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichodesmium erythraeum IMS101

label_protocol: Reverse transcription of the total RNA and labeling of cDNA were performed following the standard operating protocol of Roche NimbleGen, Inc., Madison, WI, USA. See www.nimblegen.com.

growth_protocol:
Axenic cultures of Trichodesmium erythraeum IMS101 were maintained at 26 ℃ on a 12h:12h light/dark cycle at 50 μmol quanta m-2 s-1 in YBCII media (Chen et al., 1996, Journal of Phycology 32: 916-923) supplemented with 2.8 μM ferric ammonium citrate. The light was set on at 7:00 and off at 19:00 o′clock. Samples were taken on a 3-hr interval starting at the onset of the light period until the end of the dark period for a total of 24 hr.
At designated time, 200 ml each of triplicate cultures (replicates from different flasks) was filtered onto a 5 μm pore-size 47 mm diameter polycarbonate membrane filter. The filters were immediately frozen in liquid nitrogen and stored at -80 ℃ until processing.

extract_protocol: Total RNA was extracted using the Ambion RiboPure Bacteria kit (Life Technologies, Carlsbad, CA, USA), followed by in-solution DNase digestion with the RNase-Free DNase set and on-column cleanup with the RNeasy MiniElute kit (Qiagen, Valencia, CA, USA). RNA quality and concentration was determined by analysis with a NanoDrop 1000 spectrophotometer (Thermo Scienctific, Waltham, MA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) at the UCSC Microbial Environmental Genomics Applications: Modeling, Experimentation and Remote Sensing (MEGAMER) facility (University of California, Santa Cruz, CA, USA).

tag: light/dark cycle

value: mixed

tag: hours into light (l) /dark (d) period


title: Growing Bj cells transfected with sip21, biological repeat 2


title: Senescent BJ cells transfected with siCtrl, biological repeat 1


title: Growing Bj cells transfected with siCtrl, biological repeat 2


title: wild type, biological rep1

value: 12 day-old seedlings

value: 10oC cold for 7 days


title: Allograft 2 CC

value: tumour

value: crypts

value: VillinCreER Apcfl/fl KrasG12D

value: (15 mm or ulceration)