title: Her2+ER+.TB148

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

hyb_protocol: Hyb on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3.

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina BeadStudio v.3.0 software was used to export expression levels and detect p-values for each probe of each sample. Quality control of each array was performed using median Spearman correlation computed against all other arrays. Arrays whose median correlation differed from the global correlation by more than 8 absolute deviations were marked as outliers and not used for further analysis, resulting in the removal of one TNBC sample, TB147. The remaining 19 arrays were then quantile-normalized between each other and filtered to remove non-informative probes (probes with a detection p-value>0.05 in all samples). Between-batch normalization was performed using Distance Weighted Discrimination (DWD) approach using 4 samples replicated in the 2 microarray batches. Average expression between replicates was used for data analysis.

source_name: Cancer associated fibroblasts derived from breast cancer

label_protocol: Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit(Cat #AMIL1791)

extract_protocol: The tissues were stored in ice cold medium DMEM/F12 supplemented with 10% fetal bovine serum (FBS), penicillin and streptomycin.  The fresh tumor tissue was kept on ice at 4oC until ready for processing within 6 hours from the excision time.  If the tumor tissue weighed less than 0.5 gram, the tissue was mechanically dissociated by mincing with scalpel and scissors to 1-2 mm3 in a 10 cm tissue culture plate. Fibroblast growth medium (DMEM supplemented with 10% FBS penicillin and streptomycin) was then added.  After several days, outgrowth of spindle shaped cells was observed.  Tissue debris and non-adherent cells were removed and medium changed between day 2 - 4.   For tissues weighing more than 0.5 gram, the tissue was minced as described above and then enzymatically dissociated in tissue digestion buffer containing collagenase I (Worthington), hyaluronidase (Sigma), Collagenase IV (Worthington) at 1 mg/ml of each enzyme in DMEM/F12 medium in a volume of 1:5 ratio of tumor to buffer (wt/vol) on a gyrating platform at 37o C for 30 min.  The digestion was quenched by addition of fibroblast growth medium and filtered through a 70   m cell strainer.  Cells were pelleted at 1500 rpm for 10 min. Tissue debris and non-adherent cells were removed during medium change between day 2 or 4.   By 10     14 days, near confluent adherent spindle shaped cells were harvested using 0.25% trypsin in versene, washed and replated in fresh fibroblast growth medium.  Medium was changed every 4     7 days.  CAFs from early passages (passage 2 - 3) were harvested and the cell pellet was stored in RNA later (Applied Biosystems) at -80oC until RNA was isolated. RNA purification was carried out using TRI Reagent   (Molecular Research Center) according to manufacturer   s recommendations.  RNA quality was determined using the Bioanalyzer (Agilent). Only samples with 28S/16S ratios >0.75 were used for further studies. Equal amounts (400ng) of total RNA was amplified as recommended by Illumina and hybridized to the HumanHT-12 v4 human whole genome bead arrays.

value: breast cancer associated fibroblasts (cfa)

tag: class

tag: batch

tag: set

value: testing

tag: replicates

value: no


title: DobermPinscher-BI_20908

status: Public on Dec 20 2013

type: genomic

city: Cambridge

first: Hyun Ji

last: Noh

state: MA

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

country: USA

institute: Broad Institute

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® Operating Software.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from blood using the Puregene DNA purification Kit (Gentra Systems) protocol.

tag: phenotype

value: compulsive disorder


title: DobermPinscher-BI_20911_rep

value: control


title: DobermPinscher-BI_20907


title: DobermPinscher-BI_20906


title: DobermPinscher-BI_20904_rep


title: DobermPinscher-BI_20905


title: Her2+.TB129

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: patient id


title: DobermPinscher-BI_20903_rep


title: 293T_H1.2sh_rep2

city: Los Angeles

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

description:
H1.2sh-2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were processed/normalized and analyzed by the Array Pipe software.

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

extract_protocol: Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.

tag: cell line

value: 293T embryonic kidney cells (derived from 293 cells but stably express the SV40 T antigen)

tag: genotype/variation

value: H1.2 depletion


title: TNBC.TB164

value: TNBC


title: TNBC.TB160

value: training


title: ER+.TB165

value: ER+


title: DobermPinscher-BI_20903


title: DobermPinscher-BI_20900


title: DobermPinscher-BI_20901


title: DobermPinscher-BI_20899


title: Her2+.TB122

value: yes


title: ER+.TB163


title: DobermPinscher-BI_20898


title: 293T_Cul4Ash_rep1

description:
Cul4Ash-1
replicate 1

value: Cul4A depletion


title: TNBC.TB162


title: DobermPinscher-BI_20904


title: Her2+.TB117

data_processing: Illumina BeadStudio v.3.0 software was used to export expression levels and detect p-values for each probe of each sample. Quality control of each array was performed using median Spearman correlation computed against all other arrays. Arrays whose median correlation differed from the global correlation by more than 8 absolute deviations were marked as outliers and not used for further analysis, resulting in the removal of one TNBC sample, TB147.  The remaining 19 arrays were then quantile-normalized between each other and filtered to remove non-informative probes (probes with a detection p-value>0.05 in all samples). Between-batch normalization was performed using Distance Weighted Discrimination (DWD) approach using 4 samples replicated in the 2 microarray batches.  Average expression between replicates was used for data analysis.


title: ER+.TB130


title: Her2+.TB76


title: DobermPinscher-BI_20897


title: DobermPinscher-BI_20896_rep


title: ER+.TB120


title: DobermPinscher-BI_20896


title: 293T_NCsh_rep1

description:
NCsh-1
replicate 1


title: DobermPinscher-BI_20902


title: DobermPinscher-BI_20895


title: DobermPinscher-BI_20895_rep


title: DobermPinscher-BI_20894


title: DobermPinscher-BI_20893_rep


title: ER+.TB98


title: Her2+.TB136


title: DobermPinscher-BI_20891


title: DobermPinscher-BI_20891_rep


title: ER+.TB75


title: DobermPinscher-BI_20890_rep


title: DobermPinscher-BI_20890


title: DobermPinscher-BI_20887_rep


title: DobermPinscher-BI_20889_rep


title: DobermPinscher-BI_20887


title: DobermPinscher-BI_20889


title: DobermPinscher-BI_20886


title: TNBC.TB134


title: DobermPinscher-BI_20885_rep


title: DobermPinscher-BI_20885


title: DobermPinscher-BI_20886_rep


title: DobermPinscher-BI_20884


title: ER+.TB71


title: TNBC.TB123


title: DobermPinscher-BI_20894_rep


title: DobermPinscher-BI_20880


title: DobermPinscher-BI_20893


title: DobermPinscher-BI_20878


title: DobermPinscher-BI_20879


title: DobermPinscher-BI_20881


title: DobermPinscher-BI_20874


title: DobermPinscher-BI_20875


title: DobermPinscher-BI_20869


title: DobermPinscher-BI_20870


title: DobermPinscher-BI_20868


title: DobermPinscher-BI_20871


title: DobermPinscher-BI_20883


title: DobermPinscher-BI_20862


title: DobermPinscher-BI_20861


title: DobermPinscher-BI_20860


title: DobermPinscher-BI_20865


title: DobermPinscher-BI_20867


title: DobermPinscher-BI_20866


title: DobermPinscher-BI_20857


title: TNBC.TB125


title: DobermPinscher-BI_20882


title: DobermPinscher-BI_20856_rep


title: DobermPinscher-BI_20852_rep


title: DobermPinscher-BI_20877


title: DobermPinscher-BI_20856


title: DobermPinscher-BI_20850


title: DobermPinscher-BI_20849


title: DobermPinscher-BI_20851


title: DobermPinscher-BI_20872


title: DobermPinscher-BI_20852


title: DobermPinscher-BI_20848


title: DobermPinscher-BI_20847


title: DobermPinscher-BI_20873


title: DobermPinscher-BI_20843


title: DobermPinscher-BI_20844


title: DobermPinscher-BI_20863


title: DobermPinscher-BI_20845


title: DobermPinscher-BI_20842


title: DobermPinscher-BI_20841


title: DobermPinscher-BI_20858


title: DobermPinscher-BI_20837


title: DobermPinscher-BI_20836


title: DobermPinscher-BI_20840


title: DobermPinscher-BI_20854


title: DobermPinscher-BI_20833


title: DobermPinscher-BI_20838


title: DobermPinscher-BI_20832


title: DobermPinscher-BI_20830


title: DobermPinscher-BI_20834


title: DobermPinscher-BI_20828


title: DobermPinscher-BI_20824


title: DobermPinscher-BI_20827


title: DobermPinscher-BI_20826


title: DobermPinscher-BI_20823


title: DobermPinscher-BI_20846


title: DobermPinscher-BI_20825


title: DobermPinscher-BI_20821


title: DobermPinscher-BI_20822


title: DobermPinscher-BI_20819


title: DobermPinscher-BI_20831


title: DobermPinscher-BI_20817


title: DobermPinscher-BI_20818


title: DobermPinscher-BI_20816


title: DobermPinscher-BI_20815


title: DobermPinscher-BI_20813


title: DobermPinscher-BI_20820


title: DobermPinscher-BI_20829


title: DobermPinscher-BI_20814


title: DobermPinscher-BI_20807


title: DobermPinscher-BI_20812


title: DobermPinscher-BI_20809


title: DobermPinscher-BI_20806


title: DobermPinscher-BI_20811


title: DobermPinscher-BI_20805


title: DobermPinscher-BI_20808


title: DobermPinscher-BI_20804


title: DobermPinscher-BI_15260


title: DobermPinscher-BI_20803


title: DobermPinscher-BI_20802


title: DobermPinscher-BI_15259


title: DobermPinscher-BI_15233


title: DobermPinscher-BI_15246


title: DobermPinscher-BI_15237


title: DNOP_3

city: RTP

first: Charles

last: Wood

state: NC

address: 109 TW Alexander Drive

institute: US EPA

description:
EC-555
#46.AVG_Signal-DNOP_3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina Genome Studio

organism: Mus musculus

source_name: mouse liver

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

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

tag: strain

tag: gender

value: male

tag: age

value: 28 days old

tag: agent

value: DNOP

value: liver


title: DNOP_4

description:
EC-554
#45.AVG_Signal-DNOP_4
replicate 4


title: DEHP_4

description:
EC-283
#23.AVG_Signal-DEHP_4
replicate 4

value: DEHP


title: cont_3

description:
EC-16
#6.AVG_Signal-cont_3
replicate 3


title: DEHP_2

description:
EC-284
#24.AVG_Signal-DEHP_2
replicate 2


title: IPI-2I infected with ST, 4 hpi, rep1

city: Malaga

first: Rocio

last: Bautista

address: Edificio de Bioinnovación, C/ Severo Ochoa, 34

country: Spain

institute: Plataforma Andaluza de Bioinformatica, Universidad de Malaga

description:
IPI_ST_t4_1
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 4h with ST.

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

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

data_processing: The data were pre-processed using the robust multi-array analysis (RMA) included in the affy library Bioconductor package (v. 2.5) using R version 2.7.0.

organism: Sus scrofa

source_name: epithelial cell line from ileum, S. typhimurium infection, 4 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Epithelial cells were seeded into 6-well tissue culture plates and grown to confluence in 5% CO2 at 37ºC.

extract_protocol: RNA extraction was done using the Rneasy Mini Kit according to manufacturer instructions.

treatment_protocol: Monolayers were infected for 1 h with Salmonella typhimurium (MOI 1:10) or incubated with media alone (control cells). Extracellular bacteria were removed, and cultures were further incubated during 2 and 4 h. in the presence of 50 µg/ml of the non-cell-permeant antibiotic gentamicin to kill remaining extracellular bacteria.

tag: cell type

value: adult ileum epithelial

tag: infection

value: Salmonella typhimurium

tag: infection time

value: 4 hr


title: DNOP_5

description:
EC-556
#47.AVG_Signal-DNOP_5
replicate 5


title: IPI-2I cell line non_infected, rep3b

description:
IPI_ST_t0_3
Gene expression data from IPI-2I cell line, not infected, derived from the ileum of an adult.

source_name: epithelial cell line from ileum, not infected

value: uninfected

value: 0 hr


title: DEHP_5

description:
EC-285
#25.AVG_Signal-DEHP_5
replicate 5


title: cont_5

description:
EC-17
#7.AVG_Signal-cont_5
replicate 5

value: control


title: cont_6

description:
EC-18
#8.AVG_Signal-cont_6
replicate 6


title: IPI-2I cell line non_infected, rep2b

description:
IPI_ST_t0_2
Gene expression data from IPI-2I cell line, not infected, derived from the ileum of an adult.


title: DEHP_3

description:
EC-286
#26.AVG_Signal-DEHP_3
replicate 3


title: cont_4

description:
EC-15
#5.AVG_Signal-cont_4
replicate 4


title: DEHP_1

description:
EC-287
#27.AVG_Signal-DEHP_1
replicate 1


title: cont_1

description:
EC-13
#3.AVG_Signal-cont_1
replicate 1


title: IPI-2I infected with ST, 4 hpi, rep2

description:
IPI_ST_t4_2
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 4h with ST.


title: IPI-2I infected with ST, 4 hpi, rep3

description:
IPI_ST_t4_3
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 4h with ST.


title: cont_2

description:
EC-14
#4.AVG_Signal-cont_2
replicate 2


title: cecum_CRA+Lajo_4

city: San Francisco

first: Susan

last: Lynch

state: CA

address: 513 Parnassus Ave

department: GI

institute: UCSF

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk115

hyb_protocol: Hybridization solution contained 100 mM MES (N-morpholinoethanesulfonic acid), 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20, pH 6.6 (referred to as 1X MES). In addition, the solution contained 0.1 mg of herring sperm DNA (Promega)/ml, 0.5 mg of acetylated bovine serum albumin (BSA; Invitrogen)/ml, and 50 pM control oligonucleotide B2 (Affymetrix). Hybridization was carried out at 45°C for 16 h with mixing on a rotary mixer at 60 rpm. Following hybridization, the sample solution was removed and the array was washed and stained in a GeneChip Fluidics Station (Affymetrix). In brief, to enhance the signals, 10 ug of streptavidin (Vector Laboratories)/ml and 2 mg of BSA/ml in 1X MES were used as the first staining solution. After the streptavidin solution was removed, an antibody mix was added as the second stain, containing 0.1 mg of goat immunoglobulin G (Sigma-Aldrich)/ml, 5 ug of biotinylated anti-streptavidin antibody (Vector Laboratories)/ml, and 2 mg of BSA/ml in 1X MES. Nucleic acid was fluorescently labeled by incubation with 10 ug of streptavidin R-phycoerythrin conjugate (Molecular Probes)/ml and 2 mg of BSA/ml in 1X MES.

scan_protocol: The arrays were scanned at 570 nm with a resolution of 3 um with a GeneChip Scanner 3000 (GCS 3000; Affymetrix).

data_processing: Fluorescence intensities were normalized to spike-in control oligonucleotides provided by SecondGenome, Inc. (San Bruno, CA, USA) using the proprietary PhyCA processing technique developed by SecondGenome, Inc, which utilizes aggregate measures (“r scores”) that incorporate mismatch probe fluorescence intensity as well as distribution of total chip fluorescence. Quartile r score cutoffs were chosen based on r scores retrieved for control probes spiked-in at known concentrations, as recorded from all Phylochip microarrays of the current study, and were as follows: rQ1 > .30, rQ2 > .65, rQ3 > .88.

source_name: BALB/c_gavaged with L. johnsonii prior to CRA-challenge

label_protocol: DNA was resuspended in 96 ul of 30 mM MOPS (morpholinepropanesulfonic acid, pH 7.5), and 4 ul of a 50 mM polyethylene oxide-iodoacetyl biotin (Pierce Chemical) solution was added to introduce the biotin label. The reaction mixture was incubated at 37°C for 1 h, and the labeled DNA was subsequently ethanol precipitated and washed twice with 70% ethanol to remove unreacted biotin compounds.

extract_protocol: Murine ceca were transferred to Lysis Matrix B (MP Biomedicals, OH) tubes containing 600ul RLT buffer (Qiagen, CA). Samples were subjected to 30 seconds of bead beating at 5.5 m/second, followed by centrifugation for one minute at 2000 rpm. Supernatant was transferred to the AllPrep DNA (Qiagen, CA) spin column and nucleic acid purification was carried out according to the manufacturer's instructions. Nucleic acid concentrations were determined using a NanoDrop spectophotometer (Thermo Scientific, MA).

tag: gavaged with

value: L. johnsonii, CRA challenged

value: cecum


title: cecum_control_A4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk114

source_name: BALB/c_gavaged with sterile saline

value: sterile saline, no allergen


title: DNOP_2

description:
EC-557
#48.AVG_Signal-DNOP_2
replicate 2


title: cecum_Lajo_4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk113

source_name: BALB/c_gavaged with L. johnsonii

value: L. johnsonii, no allergen


title: IPI-2I infected with ST, 2 hpi, rep1

description:
IPI_ST_t2_1
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 2h with ST.

source_name: epithelial cell line from ileum, S. typhimurium infection, 2 hr

value: 2 hr


title: IPI-2I infected with ST, 2 hpi, rep2

description:
IPI_ST_t2_2
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 2h with ST.


title: DNOP_1

description:
EC-553
#44.AVG_Signal-DNOP_1
replicate 1


title: cecum_CRA+Lajo_3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk111

value: BALB/c


title: cecum_Lajo_3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk110


title: IPI-2I infected with ST, 2 hpi, rep3

description:
IPI_ST_t2_3
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 2h with ST.


title: cecum_control_A3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk108


title: IPI-2I infected with SC, 4 hpi, rep2

description:
IPI_SC_t4_2
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 4h with SC.

source_name: epithelial cell line from ileum, S. choleraesuis infection, 4 hr

treatment_protocol: Monolayers were infected for 1 h with Salmonella choleraesuis (MOI 1:10) or incubated with media alone (control cells). Extracellular bacteria were removed, and cultures were further incubated during 2 and 4 h in the presence of 50 µg/ml of the non-cell-permeant antibiotic gentamicin to kill remaining extracellular bacteria.

value: Salmonella choleraesuis


title: cecum_control_A2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk107


title: cecum_control_A1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk106


title: cecum_CRA+Lajo_2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk104


title: cecum_Lajo_2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk109


title: cecum_CRA_4

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk112

source_name: BALB/c_challenged with CRA

tag: challenged with

value: cockroach allergen (CRA)


title: IPI-2I cell line non_infected, rep1b

description:
IPI_ST_t0_1
Gene expression data from IPI-2I cell line, not infected, derived from the ileum of an adult.


title: IPI-2I infected with SC, 4 hpi, rep1

description:
IPI_SC_t4_1
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 4h with SC.


title: IPI-2I infected with SC, 4 hpi, rep3

description:
IPI_SC_t4_3
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 4h with SC.


title: IPI-2I infected with SC, 2 hpi, rep1

description:
IPI_SC_t2_1
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 2h with SC.

source_name: epithelial cell line from ileum, S. choleraesuis infection, 2 hr


title: IPI-2I cell line non_infected, rep3

description:
IPI_SC_t0_3
Gene expression data from IPI-2I cell line, not infected, derived from the ileum of an adult.


title: cecum_CRA_1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk102


title: cecum_Lajo_1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk103


title: cecum_CRA+Lajo_1

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk105


title: IPI-2I infected with SC, 2 hpi, rep2

description:
IPI_SC_t2_2
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 2h with SC.


title: IPEC-J2 infected with ST, 4 hpi, rep3

description:
IPEC_ST_t4_3
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 4h with ST.

source_name: epithelial cell line from jejunum, S. typhimurium infection, 4 hr

value: neonatal jejunum epithelial


title: cecum_CRA_3

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk101


title: cecum_CRA_2

description:
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.
Luk100

source_name: BALB/c_challenged with cockroach allergen (CRA)


title: IPI-2I infected with SC, 2 hpi, rep3

description:
IPI_SC_t2_3
Gene expression data from IPI-2I cell line, derived from the ileum of an adult, infected for 2h with SC.


title: IPI-2I cell line non_infected, rep1

description:
IPI_SC_t0_1
Gene expression data from IPI-2I cell line, not infected, derived from the ileum of an adult.


title: IPI-2I cell line non_infected, rep2

description:
IPI_SC_t0_2
Gene expression data from IPI-2I cell line, not infected, derived from the ileum of an adult.


title: IPEC-J2 infected with ST, 2 hpi, rep3

description:
IPEC_ST_t2_3
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 2h with ST.

source_name: epithelial cell line from jejunum, S. typhimurium infection, 2 hr


title: IPEC-J2 infected with ST, 4 hpi, rep2

description:
IPEC_ST_t4_2
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 4h with ST.


title: IPEC-J2 infected with ST, 2 hpi, rep2

description:
IPEC_ST_t2_2
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 2h with ST.


title: IPEC-J2 infected with ST, 2 hpi, rep1

description:
IPEC_ST_t2_1
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 2h with ST.


title: cecum_petDust_4

description:
Luk127
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

hyb_protocol: Hybridization solution contained 100 mM MES (N-morpholinoethanesulfonic acid), 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20, pH 6.6 (referred to as 1Ã— MES). In addition, the solution contained 0.1 mg of herring sperm DNA (Promega)/ml, 0.5 mg of acetylated bovine serum albumin (BSA; Invitrogen)/ml, and 50 pM control oligonucleotide B2 (Affymetrix). Hybridization was carried out at 45°C for 16 h with mixing on a rotary mixer at 60 rpm. Following hybridization, the sample solution was removed and the array was washed and stained in a GeneChip Fluidics Station (Affymetrix). In brief, to enhance the signals, 10 ug of streptavidin (Vector Laboratories)/ml and 2 mg of BSA/ml in 1Ã— MES were used as the first staining solution. After the streptavidin solution was removed, an antibody mix was added as the second stain, containing 0.1 mg of goat immunoglobulin G (Sigma-Aldrich)/ml, 5 ug of biotinylated anti-streptavidin antibody (Vector Laboratories)/ml, and 2 mg of BSA/ml in 1Ã— MES. Nucleic acid was fluorescently labeled by incubation with 10 ug of streptavidin R-phycoerythrin conjugate (Molecular Probes)/ml and 2 mg of BSA/ml in 1Ã— MES.

source_name: BALB/c_pet house dust suspension

value: pet house dust suspended in sterile saline


title: cecum_control_B3

description:
Luk128r
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

source_name: BALB/c_sterile saline

value: sterile saline


title: cecum_petDust_5

description:
Luk125
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: cecum_nopetDust_2

description:
Luk126
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

source_name: BALB/c_no pet house dust suspension

value: no pet house dust suspended in sterile saline


title: U87DK -rep1

city: La Jolla

first: Frank

middle: B

last: Furnari

address: 9500 Gilman Dr.

institute: Ludwig Institute for Cancer Research

hyb_protocol: Liu C-G, Calin GA, Volinia S and Croce CM. MicroRNA expression profiling using microarrays. Nature Protocols, 3(4):563-578, 2008

data_processing: Quantiles normalization was used

label_protocol: biotin end-labeled random-octamer oligonucleotide primers

extract_protocol: Trizol

treatment_protocol: 48 hrs serum starvation plus or minus EGF

value: cell line overexpressing  dead kinase ΔEGFR


title: U87WT -rep3

scan_protocol: Liu C-G, Calin GA, Volinia S and Croce CM. MicroRNA expression profiling using microarrays. Nature Protocols, 3(4):563-578, 2008

value: cell line overexpressing wild type EGFR


title: cecum_petDust_1

description:
Luk124
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: RBM10 sh3

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

description: Additional analysis data in VALCARCEL_RBM10-sh_vs_plko.xls

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Affymetrix HJAY dataset analysis was performed by GenoSplice technology (www.genosplice.com). Raw data was processed using Expression Console to get the RMA intensities values of Affymetrix HJAY probesets. Additional analysis included the follwing. Data were normalized using quantile normalization. Background corrections were made with antigenomic probes and probes were selected according to their %GC, cross-hybridization status and potential overlap with repeat region as previously described [PMID:23321315, PMID:23284676]. Only probes targeting exons and exon-exon junctions annotated from FAST DB® transcripts (release fastdb_2012_2) were selected [PMID:16052034,PMID:17547750]. Only probes with a DABG Pvalue ≤ 0.05 in at least half of the arrays were considered for statistical analysis [PMID:23321315, PMID:23284676]. Only genes expressed in at least one compared condition were analyzed. To be considered to be expressed, the DABG Pvalue had to be ≤ 0.05 for at least half of the gene probes. We performed an unpaired Student’s t-test to compare gene intensities between two experimental conditions. Genes were considered significantly regulated when fold-change was ≥1.5 and Pvalue 0.05 (unadjusted P-value). Analysis at the splicing level was first performed taking into account only exon probes (EXON analysis) in order to potentially detect new alternative events that could be differentially regulated (i.e., without taking into account exon-exon junction probes). Analysis at the splicing level was also performed by taking into account exon-exon junction probes (SPLICING PATTERN analysis) using the FAST DB® splicing patterns annotation (i.e., for each gene, all possible splicing patterns were defined and analyzed. All types of alternative events can be analyzed: Alternative first exons, alternative terminal exons, cassette exon, mutually exclusive exons, alternative 5’ donor splice site, alternative 3’ acceptor splice sites and intron retention). EXON and SPLICING PATTERN analyses were performed using unpaired Student's t-test on the splicing-index as previously described [PMID:23321315, PMID:23284676]. Results were considered statistically significant for unadjusted P-values ≤ 0.05 and fold-changes ≥ 2.0 for EXON analysis and for unadjusted P-values ≤ 0.05 and fold-changes ≥ 1.5 for SPLICING PATTERN analysis. Gene Ontology (GO), KEGG and REACTOME analyses of differentially regulated genes were performed using DAVID [PMID:19131956].

source_name: HeLa cell, RBM10 kd

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

growth_protocol: HeLa cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol: RNA from three biological replicates of sh-RBM infected HeLa cells was purified using Rneasy mini kit (Qiagen).

treatment_protocol: Knockdowns of RBM5, RBM6 or RBM10 in Hela cells were performed by lentiviral infections using the pLKO.1 carrier vector for specific shRNA (Sigma Aldrich).

tag: shRNA sequence

value: HeLa

tag: treatment

value: RBM10 kd


title: IPEC-J2 infected with ST, 4 hpi, rep1

description:
IPEC_ST_t4_1
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 4h with ST.

value: Salmonella typhimurium

value: 4 hr


title: U87WT -rep2


title: cecum_control_B2

description:
Luk123
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: cecum


title: IPEC-J2 cell line non_infected, rep1b

description:
IPEC_ST_t0_1
Gene expression data from IPEC-J2 cell line, not infected, derived from neonatal jejunal epithelia.

source_name: epithelial cell line from jejunum, not infected

value: uninfected

value: 0 hr


title: IPEC-J2 cell line non_infected, rep2b

description:
IPEC_ST_t0_2
Gene expression data from IPEC-J2 cell line, not infected, derived from neonatal jejunal epithelia.


title: IPEC-J2 cell line non_infected, rep3b

description:
IPEC_ST_t0_3
Gene expression data from IPEC-J2 cell line, not infected, derived from neonatal jejunal epithelia.


title: U87 -rep3

value: cell line


title: U87WT -rep1


title: RBM10 sh2


title: cecum_nopetDust_4

description:
Luk122
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: BALB/c


title: cecum_petDust_2

description:
Luk120
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: cecum_nopetDust_1

description:
Luk121
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: U87 -rep1


title: RBM10 sh1


title: RBM6 sh2

description: Additional analysis data in VALCARCEL_RBM6-sh_vs_plko.xls

source_name: HeLa cell, RBM6 kd

value: RBM6 kd


title: U373 WT + EGF -rep3

source_name: U373 WT + EGF

value: U373 WT + EGF

value: cell line overexpressing wild type EGFR stimulated EGF for 1hr


title: RBM6 sh1


title: RBM6 sh3


title: cecum_control_B1

description:
Luk118
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: IPEC-J2 infected with SC, 4 hpi, rep3

description:
IPEC_SC_t4_3
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 4h with SC.

source_name: epithelial cell line from jejunum, S. choleraesuis infection, 4 hr

value: neonatal jejunum epithelial

value: Salmonella choleraesuis


title: U87 -rep2


title: cecum_nopetDust_3

description:
Luk119
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: no pet house dust suspended in sterile saline


title: IPEC-J2 infected with SC, 4 hpi, rep2

description:
IPEC_SC_t4_2
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 4h with SC.


title: RBM5 sh3

description: Additional analysis data in VALCARCEL_RBM5-sh_vs_plko.xls

source_name: HeLa cell, RBM5 kd

value: RBM5 kd


title: IPEC-J2 infected with SC, 2 hpi, rep3

description:
IPEC_SC_t2_3
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 2h with SC.

source_name: epithelial cell line from jejunum, S. choleraesuis infection, 2 hr

value: 2 hr


title: U373 WT + EGF -rep2


title: U373 WT + EGF-rep1


title: cecum_nopetDust_5

description:
Luk117
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.


title: cecum_petDust_3

description:
Luk116
16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

value: pet house dust suspended in sterile saline


title: IPEC-J2 infected with SC, 4 hpi, rep1

description:
IPEC_SC_t4_1
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 4h with SC.


title: housedust_dogDust_Luk129

description: 16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

organism: dust metagenome

source_name: housedust collected from homes with dog

tag: environmental

value: housedust


title: U373 Δ -rep3

value: cell line overexpressing  ΔEGFR


title: IPEC-J2 cell line non_infected, rep3

description:
IPEC_SC_t0_3
Gene expression data from IPEC-J2 cell line, not infected, derived from neonatal jejunal epithelia.


title: RBM5 sh2

value: HeLa


title: housedust_catDust_DA20

source_name: housedust collected from homes with cat


title: housedust_catDust_DA9


title: U373 Δ -rep2


title: IPEC-J2 infected with SC, 2 hpi, rep2

description:
IPEC_SC_t2_2
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 2h with SC.


title: U373 DK -rep3

source_name: U373 DK

value: U373 DK

value: cell line overexpressing  dead kinase ΔEGFR


title: U373 Δ -rep1


title: housedust_nopetDust_DA18

source_name: housedust collected from homes with no pets


title: IPEC-J2 infected with SC, 2 hpi, rep1

description:
IPEC_SC_t2_1
Gene expression data from IPEC-J2 cell line, derived from neonatal jejunal epithelia, infected for 2h with SC.


title: RBM5 sh1


title: housedust_dogDust_DA8


title: housedust_nopetDust_DA16


title: Control 3

source_name: HeLa cell, control

value: control


title: IPEC-J2 cell line non_infected, rep2

description:
IPEC_SC_t0_2
Gene expression data from IPEC-J2 cell line, not infected, derived from neonatal jejunal epithelia.

value: uninfected

value: 0 hr


title: 200 nm SiO2 worms 1.5 hr incubation 100 ug/ml nSiO2_W1.5

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

hyb_protocol: Agilent two-color GE hyb/wash protocol

scan_protocol: Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802

data_processing: Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted

source_name: HAEC nSiO2 worm

label_protocol: Agilent two-color LRILAK labeling protocol

growth_protocol: All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Media 200 with supplements and allowed to grow until >80% confluent changing media daily.

extract_protocol: Total RNA was collected using Qiagen RNeasy Mini kits.

treatment_protocol:
The media was removed and replaced with 2 ml of new media and then treated with the nanomaterials for 24 hrs or 4 hrs (the final 4 of the 24 hr time window) prior to RNA collection. Multiple experiments were carried out in parallel and the best RNA samples by RQI (all samples had RQI's > 7) were selected for microarray analysis. Six control samples were processed and were combined to phenotypically anchor the the expressioin data as the Cy3 channel control sample.
For the SiO2 spheres, two doses were used for the 4 hr samples - 100 ug/ml and ~73 ug/ml to determine if we observed a difference in gene expression due to the surface area of the silica nanoconstructs - the ~73 ug/ml dose has the same surface area as the 100 ug/ml silica worms.

tag: time

value: 1.5 hr incubation

tag: dose

value: 100 ug/ml

value: Primary human aortic endothial cells

value: 200 nm SiO2 worms

source_name: HAEC untreated control

value: media control


title: U373 WT -rep3

source_name: U373 WT

value: U373 WT

value: cell line overexpressing wild type EGFR


title: U373 DK -rep1


title: U373 DK -rep2


title: G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24c

source_name: HAEC G4-NH2 dendrimer

value: 24 hr incubation

value: G4-NH2 PAMAM


title: G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4c

value: 4 hr incubation


title: Control 2


title: housedust_nopetDust_DA14

value: housedust


title: housedust_dogDust_DA6


title: Control 1

value: HeLa


title: IPEC-J2 cell line non_infected, rep1

description:
IPEC_SC_t0_1
Gene expression data from IPEC-J2 cell line, not infected, derived from neonatal jejunal epithelia.

value: neonatal jejunum epithelial


title: G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4b


title: G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24b


title: housedust_dogDust_DA5


title: U373 -rep1

value: cell line


title: U373 -rep2


title: housedust_catDust_DA12


title: U373 WT-rep1


title: U373 -rep3


title: housedust_catDust_DA10


title: housedust_dogDust_DA7


title: LN229 -rep3


title: LN229 -rep2


title: G4-NH2 PAMAM 24 hr incubation 0.5 uM G4N_24a


title: G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24a

source_name: HAEC G3.5-COOH dendrimer

value: G3.5-COOH PAMAM


title: U178 -rep3


title: LN229 -rep1


title: U178 -rep2


title: G4-NH2 PAMAM 4 hr incubation 0.5 uM G4N_4a


title: G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24b


title: G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4b


title: U87 WT + EGF-rep3

source_name: U87 WT + EGF

value: U87 WT + EGF

value: cell line overexpressing wild type EGFR stimulated EGF for 1hr


title: U87 WT + EGF-rep2


title: housedust_dogDust_DA3


title: 200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24c

source_name: HAEC nSiO2 sphere

value: 200 nm SiO2 spheres


title: U87 WT + EGF-rep1


title: G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4c


title: G3.5-COOH PAMAM 24 hr incubation 0.5 uM G3.5C_24c


title: 200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4c


title: U87 Δ -rep3

source_name: U87 Δ

value: U87 Δ

value: cell line overexpressing  ΔEGFR


title: U87 Δ -rep2


title: 200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24b

value: Primary human aortic endothial cells


title: G3.5-COOH PAMAM 4 hr incubation 0.5 uM G3.5C_4a

value: media control


title: 200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4a


title: 200 nm SiO2 spheres 24 hr incubation 73.38 ug/ml nSiO2_Ss24a


title: housedust_catDust_DA13


title: U87 Δ -rep1


title: 200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24c

value: 100 ug/ml

value: 200 nm SiO2 worms


title: 200 nm SiO2 spheres 4 hr incubation 73.38 ug/ml nSiO2_Ss4b


title: U87DK -rep3

value: cell line overexpressing  dead kinase ΔEGFR


title: U178 -rep1


title: genomic DNA from cultured melanoma cells [WM852]

city: Boston

first: Byungwoo

last: Ryu

state: MA - Massachusetts

address: 609 Albany Street

department: Dermatology

institute: Boston University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Melanoma 8

label_protocol: Standard Illumina Protocol

growth_protocol: Cutaneous melanocytes were short-term cultured in melanocyte growth medium 254 supplemented with human melanocyte growth supplements (HMGS, Life Technologies). Melanoma cells were cultured in medium 254 supplemented with PMA-free HMSG-2 (Life Technologies) and 2% FBS.

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: Melanoma cells derived from metastatic lesion

tag: pathologic stages

value: Metastatic


title: 200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4a

value: 4 hr incubation


title: 200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4c


title: U87DK -rep2

tag: cell line


title: genomic DNA from cultured melanoma cells [1205Lu]

source_name: Melanoma 10


title: genomic DNA from cultured melanoma cells [WM983A]

source_name: Melanoma 6

value: Melanoma cells derived from primary lesion

value: VGP-like


title: 200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24b

value: 24 hr incubation


title: ecfG2

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

description: Rhizobium etli CFN42 ecfG2 mutant grown in stationary phase

hyb_protocol: Samples were labeled, hybridized and scanned by Nimblegen

data_processing: Data preprocessing was done by performing a nonlinear intensity dependent rescaling on non-background corrected data. To this end, a loess fit normalization with a span of 25% was performed for each array compared against an artificial reference array, consisting of the median intensity values of each probe across all arrays. To ensure that the artificial reference itself was not altered by this rescaling, the artificial reference expression levels were chosen for the average log intensity in the loess fit (instead of the mean expression levels of the respective array and the artificial reference). A robust median-polish procedure was used to combine measurements from multiple probes into a single value. Results are linked as supplementary files.

organism: Rhizobium etli CFN 42

source_name: ecfG2 mutant grown in stationary phase

growth_protocol: R. etli cells were grown at 30°C in TY medium, while monitoring the optical density (OD) of the culture. Samples were taken at OD595 = 0.85, representing stationary phase.

extract_protocol: Total RNA was isolated using a previously optimized protocol (Vercruysse et al., 2010). In short, the RNA content of 50 ml bacterial culture in early stationary phase, grown in rich medium without treatment was stabilized using a phenol:ethanol (5:95) solution. Cells were flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using the TRIzol Plus RNA Purification System (Invitrogen). DNA contamination was removed by 2 treatments with 2 µl TURBO DNase (Ambion) and afterwards verified by PCR (30 cycles). To increase yields, RNA was precipitated. RNA integrity was analyzed using Experion RNA StdSens Chips (Bio-Rad), RNA quantity and purity were assessed using a NanoDrop ND-1000. Double-stranded cDNA was synthesized using random decamers (Ambion) and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s protocol.

tag: genotype


title: ecfG1ecfG2

description: Rhizobium etli CFN42 ecfG1 and ecfG2 double mutant grown in stationary phase

scan_protocol: Samples were labeled, hybridized and scanned by Nimblegen

value: delta-ecfG1 delta-ecfG2


title: genomic DNA from cultured melanoma cells [WM983B]

source_name: Melanoma 9


title: 200 nm SiO2 worms 24 hr incubation 100 ug/ml nSiO2_W24a


title: genomic DNA from cultured melanoma cells [WM278]

source_name: Melanoma 5


title: 200 nm SiO2 spheres 4 hr incubation 100 ug/ml nSiO2_S4b


title: WT

description: Rhizobium etli CFN42 wild-type grown in stationary phase

source_name: wild-type grown in stationary phase

label_protocol: Samples were labeled, hybridized and scanned by Nimblegen

value: wild-type


title: genomic DNA from cultured melanoma cells [WM902B]

source_name: Melanoma 4


title: ecfG1

description: Rhizobium etli CFN42 ecfG1 mutant grown in stationary phase

source_name: ecfG1 mutant grown in stationary phase


title: genomic DNA from cultured melanoma cells [WM793]

source_name: Melanoma 7


title: genomic DNA from cultured melanoma cells [WM1552C]

source_name: Melanoma 3

value: RGP-like


title: 200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4a

source_name: HAEC nSiO2 worm

source_name: HAEC untreated control


title: genomic DNA from cultured melanoma cells [Sbcl2]

source_name: Melanoma 2


title: 200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4c


title: 200 nm SiO2 worms 4 hr incubation 100 ug/ml nSiO2_W4b


title: genomic DNA from cultured human primay melanocytes [HPM1]

source_name: HPM culture 1

value: Melanocytes isolated from lightly pigmented adult skin

value: Normal


title: osteoblasts_PP1

city: L'Aquila

first: Barbara

last: Peruzzi

address: Via Vetoio

country: Italy

institute: University of L'Aquila

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

scan_protocol: GeneChips were scanned using thevAffymetrix GeneChip scanner 3,000 at 570 nm

data_processing: The data were analyzed with Affymetrix Microarray Suite 5.0 software. using Affymetrix default analysis settings and global scaling as normalization method.

source_name: osteoblasts_2uM PP1_24hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (AffymetrixR Technical Manual (701021 rev 1) for GeneChipR Expression Analysis).

growth_protocol: Primary osteoblasts grew in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 4 mM L-glutamine, 5 IU/ml penicillin and 5 µg/ml streptomycin

extract_protocol: Total RNA was extracted from cultured cells using the standard Trizol procedure

treatment_protocol: Primary osteoblasts were starved for 24 hours using DMEM medium supplemented with 0,25% of Bovine Serum Albumin (BSA), 4 mM L-glutamine, 5 IU/ml penicillin and 5 µg/ml streptomycin and then treated with 2 microM  PP1 (c-Src inhibitor) for 24 hours.

tag: strain

value: 7 days

value: Calvarial bones

value: mouse primary osteoblasts


title: genomic DNA from cultured human melanoma cells [HPM2]

source_name: HPM culture 2


title: genomic DNA from cultured melanoma cells [WM35]

source_name: Melanoma 1


title: RCAP_42°C_6h_2

status: Public on Dec 19 2013

city: Ankara

first: Muazzez

last: Gurgan

address: Üniversiteler Mahallesi

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

hyb_protocol: Labeled samples were hybridized with Rhodobacter capsulatus TR_RCH2a520699F array (Affymetrix) at 50°C  for 17 hours, washed and stained at GeneChip Fluidics Station 450 at the METU Central Laboratory, Ankara, Turkey.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000 which was operated by GCOS according to instructions of the manufacturer (Affymetrix).

data_processing: CHP files from the scanned arrays were generated by GCOS and analyzed by using GeneSpring GX 11 software (Agilent Technologies, Santa Clara, CA).

organism: Rhodobacter capsulatus

source_name: Bacterial cell

label_protocol: The fragmented cDNA was biotynilated with the GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: 1.5x109 bacterial cells from cultures of optimum condition and stress applications were collected via centrifugation.

extract_protocol: Total RNA isolation was performed by using Trizol Reagent (Invitrogen).

treatment_protocol: The cell pellets were frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: 6 h


title: RCAP_42°C_2h_2

value: 2 h


title: RCAP_42°C_2h_1


title: RCAP_4°C_6h_1

value: 4 C


title: osteoblasts_DMSO

treatment_protocol: Primary osteoblasts were starved for 24 hours using DMEM medium supplemented with 0,25% of Bovine Serum Albumin (BSA), 4 mM L-glutamine, 5 IU/ml penicillin and 5 µg/ml streptomycin and then treated with vehicle (DMSO) for 24 hours.

tag: age


title: RCAP_4°C_6h_2


title: RCAP_42°C_6h_1


title: RCAP_4°C_2h_2


title: RCAP_4°C_2h_1


title: RCAP_30°C_0h_2

value: 0 h


title: RCAP_30°C_0h_1


title: Cytokine condition, 72h, replicate 1

city: Brussels

first: Miguel

last: Lopes

address: Campus de la Plaine Boulevard du Triomphe

department: Computer Science Department

institute: Universite Libre de Bruxelles

hyb_protocol: standard Affymetrix protocol

scan_protocol: The output of microarray experiments (Affymetrix Ragene10stv1) were stored in DAT files, processed by Affymetrix software to perform background subtraction and saved as .CEL files, containing intensity values for the probes in the chip.

data_processing: The pre-processing of the .CEL files was done using Custom Chip Definition (CDF) files, based on ENTREZ gene Ids (platform Ragene10stv1). The R package simpleaffy was used to read the data.

organism: Rattus norvegicus

source_name: INS1 cell lines

label_protocol: standard Affymetrix protocol

extract_protocol: Following the different periods of cytokine exposure, RNA was prepared from 500-1000 islets/group using the Phenol-Chaosolv method (ULTRASPEC RNA isolation system from Biotecx).

treatment_protocol: INS-1E cells (1.3*10^6 cells/condition) were exposed to recombinant human IL-1 (10 units/ml) plus recombinant murine IFN-g (100 units/ml)

value: IFN-beta and IFN-gamma


title: Cytokine condition, 8h, replicate 2


title: Cytokine condition, 8h, replicate 1


title: Cytokine condition, 60h, replicate 2


title: Cytokine condition, 6h, replicate 1


title: Cytokine condition, 60h, replicate 1


title: Cytokine condition, 4h, replicate 2


title: Cytokine condition, 72h, replicate 2


title: Cytokine condition, 6h, replicate 2


title: Cytokine condition, 48h, replicate 1


title: Cytokine condition, 4h, replicate 1


title: Cytokine condition, 36h, replicate 2


title: Cytokine condition, 48h, replicate 2


title: Control condition, 8h, replicate 1

value: control


title: Cytokine condition, 2h, replicate 1


title: Cytokine condition, 1h, replicate 2


title: Cytokine condition, 1h, replicate 1


title: Cytokine condition, 36h, replicate 1


title: Cytokine condition, 2h, replicate 2


title: Cytokine condition, 24h, replicate 2


title: Cytokine condition, 12h, replicate 1


title: Control condition, 6h, replicate 1


title: Control condition, 48h, replicate 1


title: Control condition, 4h, replicate 1


title: Cytokine condition, 12h, replicate 2


title: Control condition, 72h, replicate 1


title: Cytokine condition, 0h, replicate 1


title: Control condition, 36h, replicate 1


title: U373 WT -rep2

source_name: U373 WT

value: U373 WT

value: cell line overexpressing wild type EGFR


title: Cytokine condition, 24h, replicate 1


title: Cytokine condition, 10h, replicate 1


title: Control condition, 24h, replicate 1


title: Control condition, 0h, replicate 2


title: Control condition, 60h, replicate 1


title: Cytokine condition, 0h, replicate 2


title: Control condition, 10h, replicate 1


title: Control condition, 2h, replicate 1


title: Control condition, 12h, replicate 1


title: Control condition, 0h, replicate 1


title: Cytokine condition, time 60h, replicate 3

scan_protocol: The output of microarray experiments (Affymetrix Human Genome U133 Plus 2.0 array) were stored in DAT files, processed by Affymetrix software to perform background subtraction and saved as .CEL files, containing intensity values for the probes in the chip.

data_processing: The pre-processing of the .CEL files was done using Custom Chip Definition (CDF) files, based on ENTREZ gene Ids (platform hgu133plus2). The R package simpleaffy was used to read the data.

source_name: human islet beta cells

growth_protocol: The human pancreatic islets were isolated from the pancreas of brain dead organ donors using collagenase digestion and Biocoll gradient centrifugation. After isolation the islets were pre-cultured free floating in Sterilin dishes in RPMI 1640 medium containing 5.6 mM glucose, 10% FCS and 2 mM Lglutamine for 3-5 days.

treatment_protocol: Following the initial culture period, islets were cultured for the indicated time points (1, 2, 4, 8, 12, 24, 36, 48, 60, 72, 84, 96, 108, 120,132, 144 and 168 hours.) at 5.6 mM glucose RPMI-1640 containing 10% FCS and recombinant human IL-1β (25 units/ml) (PeproTech, London, U.K.) and IFN-γ (1,000 units/ml) (PeproTech) before being retrieved for RNA extraction and array analysis. The culture media were changed on days 2 and 5.

value: human islet beta cells


title: Control condition, 1h, replicate 2


title: Control condition, 1h, replicate 1


title: Cytokine condition, time 96h, replicate 3


title: Cytokine condition, time 24h, replicate 3


title: Cytokine condition, time 8h, replicate 3


title: Cytokine condition, time 48h, replicate 3


title: Cytokine condition, time 132h, replicate 3


title: Cytokine condition, time 2h, replicate 3


title: Cytokine condition, time 36h, replicate 3


title: Control condition, time 8h, replicate 3


title: Cytokine condition, time 0h, replicate 3


title: Cytokine condition, time 84h, replicate 3


title: Cytokine condition, time 72h, replicate 3


title: Control condition, time 96h, replicate 3


title: Control condition, time 84h, replicate 3


title: Cytokine condition, time 108h, replicate 3


title: Cytokine condition, time 4h, replicate 3


title: Control condition, time 48h, replicate 3


title: Cytokine condition, time 12h, replicate 3


title: Control condition, time 4h, replicate 3


title: Cytokine condition, time 120h, replicate 3


title: Control condition, time 60h, replicate 3


title: Control condition, time 120h, replicate 3


title: Control condition, time 72h, replicate 3


title: Control condition, time 36h, replicate 3


title: Control condition, time 132h, replicate 3


title: Cytokine condition, time 8h, replicate 2


title: Control condition, time 12h, replicate 3


title: Control condition, time 108h, replicate 3


title: Cytokine condition, time 96h, replicate 2


title: Control condition, time 2h, replicate 3


title: Control condition, time 0h, replicate 3


title: Cytokine condition, time 84h, replicate 2


title: Cytokine condition, time 36h, replicate 2


title: Cytokine condition, time 60h, replicate 2


title: Cytokine condition, time 24h, replicate 2


title: Cytokine condition, time 2h, replicate 2


title: Cytokine condition, time 12h, replicate 2


title: Cytokine condition, time 4h, replicate 2


title: Control condition, time 24h, replicate 3


title: Cytokine condition, time 132h, replicate 2


title: Cytokine condition, time 120h, replicate 2


title: Cytokine condition, time 108h, replicate 2


title: Cytokine condition, time 144h, replicate 2


title: Cytokine condition, time 1h, replicate 2


title: Cytokine condition, time 0h, replicate 2


title: Control condition, time 84h, replicate 2


title: Cytokine condition, time 48h, replicate 2


title: Control condition, time 8h, replicate 2


title: Control condition, time 4h, replicate 2


title: Control condition, time 60h, replicate 2


title: Control condition, time 48h, replicate 2


title: Control condition, time 24h, replicate 2


title: Cytokine condition, time 72h, replicate 2


title: Control condition, time 72h, replicate 2


title: Control condition, time 144h, replicate 2


title: Control condition, time 168h, replicate 2


title: Cytokine condition, time 96h, replicate 1


title: Control condition, time 132h, replicate 2


title: Cytokine condition, time 84h, replicate 1


title: Control condition, time 36h, replicate 2


title: Control condition, time 1h, replicate 2


title: Cytokine condition, time 72h, replicate 1


title: Cytokine condition, time 48h, replicate 1


title: Control condition, time 12h, replicate 2


title: Cytokine condition, time 168h, replicate 2


title: Control condition, time 2h, replicate 2


title: Control condition, time 0h, replicate 2


title: Cytokine condition, time 24h, replicate 1


title: Cytokine condition, time 2h, replicate 1


title: Cytokine condition, time 12h, replicate 1


title: Control condition, time 96h, replicate 2


title: Cytokine condition, time 04h, replicate 1


title: Control condition, time 108h, replicate 2


title: Cytokine condition, time 36h, replicate 1


title: Control condition, time 96h, replicate 1


title: Control condition, time 84h, replicate 1


title: Control condition, time 60h, replicate 1


title: Control condition, time 120h, replicate 2


title: Cytokine condition, time 60h, replicate 1


title: Control condition, time 72h, replicate 1


title: Control condition, time 2h, replicate 1


title: Cytokine condition, time 1h, replicate 1


title: Control condition, time 4h, replicate 1


title: Control condition, time 24h, replicate 1


title: Control condition, time 1h, replicate 1


title: Control condition, time 12h, replicate 1


title: Control condition, time 36h, replicate 1


title: Control condition, time 0h, replicate 1


title: Control condition, time 48h, replicate 1


title: Control condition, time 8h, replicate 1


title: Validation R0441_13904228

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

country: France

institute: INRA

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Detection of the fluorescence signals was made with a laser scanner (GenePix 4000A from Axon Instruments, CA) keeping a constant PMT gain fro each channel. The images were analysed with GenePixTM Pro 6.0 software (Axon instruments, Inc., Union City, CA).

data_processing: All microarray analysis, including pre-processing, normalization and statistical analysis was carried out using Bioconductor packages in R programming language (version 2.14). The centring was preformed by “Lowes fitness”to take into account the intensity dependence of the fluorescence bias.

source_name: CD4CD8, TCR, IgG,IL10, IL2, IFN, phagocytosis

label_protocol: 5 µg ofRNA from both blood and reference samples were reverse transcribed to cDNAand fluorescent-labelled by Cy3 and Cy5, respectively, using the ChipShotTM Direct Labeling System (Promega, Charbonnieres, France). The CyDye-labelled cDNA were purified usingChipShotTMMembrane Clean-Up System (Promega, USA), and 750 ng each of Cy3-labeled and Cy5-labeled cDNA targets were combined for slide hybridization with a freshly prepared solution of 1% BSA, 2 x SSC, 0.1% SDS over 30 min at 50°C. After automatic washing according to manufacturer’sinstructions, the slides were hybridized for 17h at 60ºC.

extract_protocol: Total RNA extracted using PAXgene blood RNA Kid (Qiagen, France) following manufacturer's instructions

tag: animal

value: peripheral blood

tag: sample type

value: validation

source_name: reference

tag: reference

value: pooling of total RNAs from different porcine tissues


title: Validation R0413_13904467

tag: cell type


title: Validation R0266_13904227


title: Validation R0355_13904466


title: Validation R0245_13904221


title: Validation R0180_13904472


title: Validation R0078_13904464


title: Validation 14120390


title: Validation 14120403


title: Validation R0028_13904461


title: Validation R0303_13904460


title: Validation R0036_13904465


title: Validation R0316_13904229


title: Validation 14120378


title: Validation 13904483

description:
13904483
alternative to:
GSM1098903


title: Validation 13904482

description:
13904482
alternative to:
GSM1098902


title: Validation R0282_13904225


title: Validation 13904477


title: Validation R0196_13904224


title: Validation 13904484

description:
13904484
alternative to:
GSM1098904


title: Validation 14120399


title: Validation 13904476

description:
13904476
alternative to:
GSM1098914


title: Validation 13904220

description:
13904220
alternative to:
GSM1098908


title: Validation 13903821


title: Validation 13904485

description:
13904485
alternative to:
GSM1098905


title: Validation 13904474

description:
13904474
alternative to:
GSM1098912


title: Validation 13891302

description:
13891302
alternative to:
GSM1098927


title: Validation 13904473

description:
13904473
alternative to:
GSM1098911


title: Validation 13904475

description:
13904475
alternative to:
GSM1098913


title: Validation 13904219

description:
13904219
alternative to:
GSM1098909


title: Validation 13904218

description:
13904218
alternative to:
GSM1098910


title: Validation 13903819

description:
13903819
alternative to:
GSM1098907


title: Validation 13890855

description:
13890855
alternative to:
GSM1098919


title: Validation 13890859

description:
13890859
alternative to:
GSM1098931


title: Validation 13890850


title: Validation 13890861

description:
13890861
alternative to:
GSM1098930


title: Validation 13903818

description:
13903818
alternative to:
GSM1098906


title: Validation 13890856

description:
13890856
alternative to:
GSM1098926


title: Validation 13890714

description:
13890714
alternative to:
GSM1098921


title: Validation 13890853

description:
13890853
alternative to:
GSM1098925


title: Validation 13890851

description:
13890851
alternative to:
GSM1098915


title: Validation 13891301

description:
13891301
alternative to:
GSM1098928


title: Validation 13890858

description:
13890858
alternative to:
GSM1098916


title: Validation 13890854


title: Validation 13890588

description:
13890588
alternative to:
GSM1098823


title: Validation 13890713

description:
13890713
alternative to:
GSM1098920


title: Validation 13890590


title: Validation 13890857


title: Validation 13890710

description:
13890710
alternative to:
GSM1098929


title: Validation 13890849

description:
13890849
alternative to:
GSM1098917


title: Validation 13890596

description:
13890596
alternative to:
GSM1098824


title: Validation 13890595

description:
13890595
alternative to:
GSM1098821


title: Validation 13890585

description:
13890585
alternative to:
GSM1098831


title: Validation 13890584


title: Validation 13890580

description:
13890580
alternative to:
GSM1098829


title: Validation 13890592

description:
13890592
alternative to:
GSM1098822


title: Validation 13832966

description:
13832966
alternative to:
GSM1098840


title: Validation 13890578

description:
13890578
alternative to:
GSM1098828


title: Validation 13832611

description:
13832611
alternative to:
GSM1098838


title: Validation 13832609

description:
13832609
alternative to:
GSM1098836


title: Validation 13832610

description:
13832610
alternative to:
GSM1098837


title: Validation 13832613

description:
13832613
alternative to:
GSM1098848


title: Validation 13890581

description:
13890581
alternative to:
GSM1098827


title: Validation 13832769

description:
13832769
alternative to:
GSM1098940


title: Validation 13832604

description:
13832604
alternative to:
GSM1098853


title: Validation 13832612

description:
13832612
alternative to:
GSM1098839


title: Validation 13832605

description:
13832605
alternative to:
GSM1098854


title: Validation 13832608

description:
13832608
alternative to:
GSM1098846


title: Validation 13832586

description:
13832586
alternative to:
GSM1098826


title: Validation 13832600

description:
13832600
alternative to:
GSM1098852


title: Validation 13832606

description:
13832606
alternative to:
GSM1098845


title: Phag_High_13832768

tag: group

value: High

value: test


title: Validation 13890583

description:
13890583
alternative to:
GSM1098830


title: Validation 13832602

description:
13832602
alternative to:
GSM1098844


title: Phag_High_13832765


title: Phag_High_13832764


title: Phag_High_13832763


title: Phag_High_13832766


title: Validation 13832597

description:
13832597
alternative to:
GSM1098851


title: Phag_High_13832762


title: Phag_High_13832771


title: Control (stably transfected with scramble) Replicate2

city: Omaha

first: Sushil

last: Kumar

state: NE

address: 985870 Nebraska Medical Center, DRC1

institute: UNMC

description: The biological replicate CD18/HPAF control (N2) compared to the CD18/HPAF cells after the stable knockdown of NCOA3 (S2)

hyb_protocol: The hybridization was performed overnight using Ambion Hybridization buffer 2 at 42 0C using Human array from Phalanx Biotech.

scan_protocol: Scanned on Axon GenePix 4000b scanner

data_processing: LOWEES normalization using BRB-Array Tools version 3.1

source_name: CD18/HPAF pancreatic cancer cell line, comparison of the gene expression between control (N2) cell line

label_protocol: 1 μg of total RNA was used for the labeling reaction using Amino Allyl MessageAmp II kit from Ambion (as per the manufacturer’s instructions).

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin G and streptomycin in a humidified atmosphere of 5% CO2 at 37°C

extract_protocol: Total RNA was isolated using RNeasy Kit from Qiagen  with on column DNase1 digestion.

treatment_protocol: Stably transfected cells (scrambled and NCOA3 KD constructs) were grown for 48h

source_name: CD18/HPAF pancreatic cancer cell lines after NCOA3 knock down (S2)


title: Control (stably transfected with scramble) Replicate1

description: The biological replicate CD18/HPAF control (N1) compared to the CD18/HPAF cells after the stable knockdown of NCOA3 (S1)

source_name: CD18/HPAF pancreatic cancer cell line, comparison of the gene expression between control (N1) cell line

source_name: CD18/HPAF pancreatic cancer cell lines after NCOA3 knock down (S1)


title: VvMYBA1 in W115 rep.2

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

institute: University of Verona

description: MYBA1 2

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as the following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST wash solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software, and a quantile normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the SAM analysis (T-MEV 4.3)

organism: Petunia x hybrida

source_name: VvMYBA1 overexpression in W115

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions

growth_protocol: Petunia hybrida plants were grown in soil under normal greenhouse conditions.

extract_protocol: Total RNA was isolated using Trizol reagent (Life Technologies, Cleveland, OH) according to the manufacturer instructions.

treatment_protocol: Stable genetic transformation

tag: transgene name

tag: developemental stage

value: petal stage 5-6


title: Phag_High_13832759


title: Phag_Low_13832767

value: Low


title: VvMYBA1 in W115 rep.3

description: MYBA1 3


title: Control (stably transfected with scramble) Replicate3

description: The biological replicate CD18/HPAF control (N3) compared to the CD18/HPAF cells after the stable knockdown of NCOA3 (S3)

source_name: CD18/HPAF pancreatic cancer cell line, comparison of the gene expression between control (N3) cell line

source_name: CD18/HPAF pancreatic cancer cell lines after NCOA3 knock down (S3)


title: Phag_High_13832761


title: Phag_Low_13832780


title: Phag_Low_13832769


title: Phag_Low_13832776


title: VvMYB5b in W115 rep.3

description: MYB5b 3

source_name: VvMYB5b overexpression in W115


title: Phag_Low_13832777


title: Phag_Low_13832779


title: VvMYB5b in W115 rep.2

description: MYB5b 2


title: Phag_Low_13832775


title: VvMYBA1 in W115 rep.1

description: MYBA1 1


title: Phag_Low_13832770


title: VvMYB5b in W115 rep.1

description: MYB5b 1


title: W115 petal rep.2

description: W115 2

source_name: W115 wild type petal

value: none (wild type)


title: VvMYB5a in W115 rep.3

description: MYB5a 3

source_name: VvMYB5a overexpression in W115


title: VvMYB5a in W115 rep.2

description: MYB5a 2


title: Phag_Low_13832772


title: TNF_High_13890835


title: W115 petal rep.3

description: W115 3


title: TNF_High_13891302


title: TNF_Low_13890716


title: TNF_High_13890861


title: W115 petal rep.1

description: W115 1


title: TNF_High_13890853


title: TNF_High_13890859


title: TNF_Low_13891303


title: VvMYB5a in W115 rep.1

description: MYB5a 1


title: TNF_High_13890856


title: TNF_Low_13890713


title: TNF_High_13891301


title: Phag_Low_13832774


title: TNF_Low_13890849


title: TNF_High_13890710


title: TNF_Low_13890715


title: TNF_Low_13890851


title: TNF_Low_13890855


title: IFN_High_13904476


title: TNF_Low_13890858


title: Phag_Low_13832773


title: IFN_High_13904218


title: IFN_High_13904220


title: IFN_High_13904219


title: IFN_High_13904473


title: IFN_Low_13903818


title: IFN_High_13904475


title: IFN_High_13904474


title: IL10_High_13890696


title: IL10_High_13890705


title: IFN_Low_13904482


title: IL10_High_13890708


title: IFN_Low_13904484


title: IFN_Low_13904478


title: IFN_Low_13903819


title: IFN_Low_13904479


title: IL10_High_13890700


title: IFN_Low_13904483


title: IFN_Low_13890577


title: IL10_High_13890697


title: IFN_Low_13904481


title: IL10_High_13891295


title: IL10_High_13890698


title: IFN_Low_13904480


title: IL10_High_13890699


title: IL10_Low_13890702


title: IL10_Low_13890703


title: IL10_Low_13891294


title: IL10_Low_13891299


title: IL10_Low_13890706


title: IL10_Low_13890709


title: IL10_Low_13890701


title: IL10_Low_13890704


title: IL10_Low_13891297


title: IL10_Low_13890707


title: IFN_Low_13904485


title: IL10_High_13891300


title: IL-2_High_13832534


title: IL-2_High_13832533


title: IL-2_High_13832529


title: IL-2_High_13832531


title: IL-2_High_13832526


title: IL-2_High_13832579


title: IL-2_High_13832535


title: IL2_Low_13832549


title: IL2_Low_13832547


title: IL-2_High_13832532


title: IL-2_High_13832528


title: IL2_Low_13832546


title: TNF_Low_13890714


title: IL-2_High_13832527


title: IL2_Low_13832541


title: IL2_Low_13832542


title: IgG_High_13832605


title: IL2_Low_13832544


title: IL2_Low_13832540


title: IgG_High_13832604


title: IL2_Low_13832537


title: IgG_High_13832600


title: IL2_Low_13832545


title: IL2_Low_13832539


title: IgG_High_13832593


title: IgG_High_13832597


title: IL2_Low_13832543


title: sample collected from patient 7D at 3 months after transplantation

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: For all samples a total of 750 ng of labeled cRNA was hybridized at 58°C for 16 hours to the Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) and subsequently washed.

scan_protocol: Fluorescence signals of the hybridized IlLumina Microarrays were detected using BeadStation 500 instrument (Illumina Inc). The raw data were extracted with the BeadStudio Data Analysis Software (Illumina).

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3, imported into R and normalized using the quantile method in the Lumi package. Please note that only the probes (23,719 ID_REFs) that were expressed in the biopsy renal allograft samples are chosen for data normalization.

source_name: deteriorated renal graft function_3 months

label_protocol: RNA was amplified and biotinylated  for hybridization using Ambion® Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer´s instructions. For all samples 200 ng of total RNA was used for amplification. Yields of labeled cRNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The small portion (2mm) of the  the renal graft biopsy was immediately placed in RNA later (Ambion Corporation, Austin, TX), snap frozen and stored at -80 °C until RNA extraction. RNA was isolated from renal biopsies using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany).Quality and integrity of PAXgene RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring absorbance at 260 nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Comparison of patients with stable and deteriorated renal graft function (defined as as the increase in serum creatinine level of more than 25% of its value at 3 months) during 2 years afte transplantation by analyzing RNA profiles at the time of   border line changes diagnosis  in early (≤2 months) or protocolar (3 months) renal graft  biopsies.

tag: patient id

tag: time after transplantation

value: 3 months

tag: deterioration of graft function within 2 years after transplantation

value: yes

value: renal graft biopsy


title: IgG_High_13832607


title: IgG_High_13832968


title: IgG_High_13832595


title: IgG_High_13832613


title: sample collected from patient 6D at 3 months after transplantation


title: IgG_Low_13832606


title: sample collected from patient 1D at 3 months after transplantation


title: sample collected from patient 5D at 3 months after transplantation


title: sample collected from patient 2D at 3 months after transplantation


title: IL10_High_13891293


title: sample collected from patient 3D at 3 months after transplantation


title: IgG_High_13832608


title: sample collected from patient 4D at 3 months after transplantation


title: IgG_Low_13832599


title: IgG_Low_13832596


title: sample collected from patient 7C at 3 months after transplantation

source_name: stable renal graft function_3 months

value: no


title: sample collected from patient 6C at 3 months after transplantation


title: IgG_Low_13832611


title: IgG_Low_13832602


title: IgG_Low_13832598


title: IgG_Low_13832610


title: IgG_Low_13832966


title: sample collected from patient 4C at 3 months after transplantation


title: IgG_Low_13832612


title: IgG_Low_13832609


title: sample collected from patient 2C at 3 months after transplantation


title: sample collected from patient 5C at 3 months after transplantation


title: TCR_High_13890594


title: TCR_High_13890589


title: sample collected from patient 6B ≤2 months after transplantation

source_name: deteriorated renal graft function_≤2 months

value: ≤2 months


title: sample collected from patient 3C at 3 months after transplantation


title: sample collected from patient 8C at 3 months after transplantation


title: sample collected from patient 1C at 3 months after transplantation


title: sample collected from patient 7B ≤2 months after transplantation


title: TCR_High_13890586


title: sample collected from patient 3B ≤2 months after transplantation


title: TCR_High_13890585


title: TCR_High_13890591


title: sample collected from patient 5B ≤2 months after transplantation


title: sample collected from patient 4B ≤2 months after transplantation


title: TCR_High_13890583


title: TCR_High_13890578


title: TCR_Low_13832586


title: sample collected from patient 5A ≤2 months after transplantation

source_name: stable renal graft function_≤2 months


title: sample collected from patient 2A ≤2 months after transplantation


title: sample collected from patient 6A ≤2 months after transplantation


title: sample collected from patient 1B ≤2 months after transplantation


title: TCR_Low_13890597


title: TCR_High_13890581


title: sample collected from patient 3A ≤2 months after transplantation


title: TCR_High_13890580


title: 20ObA

city: Irvine

first: Kristin

middle: Lynn

last: Eckel-Mahan

address: 360 Sprague Hall

department: Biological Chemistry

institute: UCI

description: ZT20, high fat diet #1

hyb_protocol: Following the recommended procedure, 2 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Mouse Gene 1.0 ST array (Affymetrix, 901171).  The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3.to produce .CEL intensity files.

data_processing: These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). (Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

label: TdT

source_name: ZT20_high fat diet

label_protocol: The fragmented single-stranded DNA is  labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin

growth_protocol: Animals housed in 12-hr L/D cycle. Animals fed adlibitum.

extract_protocol: Liver chunks were homogenized in Trizol. Target Preparation/Processing for GeneChip® Analysis Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix Genechip® Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, Inc., Santa Clara, CA)  In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNAs were quantified (Nanodrop) with a portion of the recovered total RNA adjust to a final concentration of 100ng/ul.  All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250ng/well) onto a RNA 6000 Nano LabChip that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the Ambion® WT Expression  Kit (Life Technologies, Carlsbad, CA) and random hexamers tagged with a T7 promoter sequence.  The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase.  10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 70 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip® WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

treatment_protocol: Livers were quickly rinsed in PBS and then rapidly  frozen in liquid nitrogen. All samples stored at -80 until RNA preparation.

tag: strain info

value: JAX stock #000664

tag: diet

value: high fat diet

tag: harvest timepoint

tag: age (at sacrifice)

value: 16 wks

value: liver


title: TCR_Low_13890598

tag: tissue

value: peripheral blood


title: TCR_Low_13890596


title: sample collected from patient 1A ≤2 months after transplantation


title: sample collected from patient 4A ≤2 months after transplantation


title: 20ObC

description: ZT20, high fat diet #3

tag: strain


title: TCR_Low_13890592


title: sample collected from patient 2B ≤2 months after transplantation


title: TCR_Low_13890588


title: 20NWC

description: ZT20, normal chow #3

source_name: ZT20_normal chow

value: normal chow


title: CD4CD8_Low_14120401

source_name: reference

value: pooling of total RNAs from different porcine tissues


title: CD4CD8_High_14120379

value: High


title: 16ObB

description: ZT16, high fat diet #2

source_name: ZT16_high fat diet


title: CD4CD8_Low_14120386

value: test


title: CD4CD8_High_14120395


title: TCR_Low_13890595


title: CD4CD8_High_14120383


title: 16ObC

description: ZT16, high fat diet #3


title: 20ObB

description: ZT20, high fat diet #2


title: 20NWA

description: ZT20, normal chow #1


title: CD4CD8_Low_14120400


title: CD4CD8_Low_14120384


title: 16NWC

description: ZT16, normal chow #3

source_name: ZT16_normal chow


title: 16NWB

description: ZT16, normal chow #2


title: 20NWB

description: ZT20, normal chow #2


title: 16NWA

description: ZT16, normal chow #1


title: 12ObA

description: ZT12, high fat diet #1

source_name: ZT12_high fat diet


title: 16ObA

description: ZT16, high fat diet #1


title: CD4CD8_Low_14120381


title: 12ObB

description: ZT12, high fat diet #2


title: 8ObB

description: ZT8, high fat diet #2

source_name: ZT8_high fat diet


title: 8ObC

description: ZT8, high fat diet #3


title: TCR_Low_13832587


title: 12NWC

description: ZT12, normal chow #3

source_name: ZT12_normal chow


title: 12NWB

description: ZT12, normal chow #2


title: 8NWC

description: ZT8, normal chow #3

source_name: ZT8_normal chow


title: 8ObA

description: ZT8, high fat diet #1


title: 4ObC

description: ZT4, high fat diet #3

source_name: ZT4_high fat diet


title: 12ObC

description: ZT12, high fat diet #3


title: 4ObA

description: ZT4, high fat diet #1


title: 8NWB

description: ZT8, normal chow #2


title: 12NWA

description: ZT12, normal chow #1


title: 0ObB

description: ZT0, high fat diet #2

source_name: ZT0_high fat diet


title: 4NWC

description: ZT4, normal chow #3

source_name: ZT4_normal chow


title: 4NWA

description: ZT4, normal chow #1


title: 0ObC

description: ZT0, high fat diet #3


title: 0ObA

description: ZT0, high fat diet #1


title: 4NWB

description: ZT4, normal chow #2


title: 0NWB

description: ZT0, normal chow #2

source_name: ZT0_normal chow


title: 8NWA

description: ZT8, normal chow #1


title: 4ObB

description: ZT4, high fat diet #2


title: 0NWC

description: ZT0, normal chow #3


title: hIPod dediff. 3

city: Los Angeles

first: Stefano

last: Da Sacco

address: 4650 Sunset Blvd MS#35

institute: Children's Hospital Los Angeles

description:
Expanded at 33C in RPMI-1640, 10% FBS, 1% Pen/Strep, 1X ITS
AB061-HuGene-1_0-st-v1-01-1 (C3)

hyb_protocol: Labeled samples were hybridized to Affymetrix Human Gene 1.0 ST arrays

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

data_processing: Array data were imported into Partek genomic Suite 6.6 (Partek Incorporated) and quantile normalized using robust multichip averaging (RMA). Following normalization, log2 expression signals from probe sets were summarized in a data table

source_name: hIPod de-differentiated

label_protocol: RNA was labeled using Ambion WT Expression Kit (Life Technologies) and cDNA produced.

extract_protocol: Extraction of RNA was performed using Qiagen mRNAeasy kit following manufacturer standard protocol

tag: cell line

value: hIPod

tag: growth condition

value: human immortalized podocyte cell line


title: hIPod rediff. 3

description:
Re-differentiated at 37C with VRADD media
AB062-HuGene-1_0-st-v1-01-1 (D3)

source_name: hIPod re-differentiated


title: hIPod dediff. 2

description:
Expanded at 33C in RPMI-1640, 10% FBS, 1% Pen/Strep, 1X ITS
AB059-HuGene-1_0-st-v1-01-1 (C2)


title: hIPod rediff. 1

description:
Re-differentiated at 37C with VRADD media
AA336-HuGene-1_0-st-v1-01-1 (D)


title: hIPod dediff. 1

description:
Expanded at 33C in RPMI-1640, 10% FBS, 1% Pen/Strep, 1X ITS
AA335-HuGene-1_0-st-v1-01-1 (C)


title: control 1

city: Chicago

first: Amy

middle: L

last: Kenter

state: IL

address: 835 South Wolcott E825

department: Microbiology/Immunology

institute: University of Ilinois at Chicago College of Medicine

description: gene expression from CH12 cell line activated for 24 hours with IgA inducers

hyb_protocol: Affymetrix hybridization at 45 C for 18 hrs and wash FS450_0007 protocol

scan_protocol: Affymetrix GeneChip 7G scanner

data_processing: RMA

source_name: control

label_protocol: Affymetrix WT labeling protocol

growth_protocol: CH12.F3 cell line grown in RPMI supplemented with 6%FCS, Glutamine, beta-mercapto, and pen-strep

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. polyA RNA purified using a Qiagen RNeasy MiniElute Clean-up kit

treatment_protocol: Cells were treated with CD40L (25% vol/vol), TGFb (0.2 ng/ml), and IL4, (5ng/ml) for 24 hours to induce IgA switching

tag: treatment

value: control


title: Mbd4 KO 1

source_name: Mbd4 KO

value: Mbd4 KO


title: control 2


title: Mbd4 KO -2


title: hAKPC-P diff. 2

description:
Differentiated with VRADD Media
AB064-HuGene-1_0-st-v1-01-1 (B4)

source_name: hAKPC-P differentiated

value: hAKPC-P

value: Differentiated with VRADD Media

value: human amniotic fluid


title: hIPod rediff. 2

description:
Re-differentiated at 37C with VRADD media
AB060-HuGene-1_0-st-v1-01-1 (D2)


title: hAKPC-P und. 3

description:
Expanded in Chang's media
AE272-HuGene-1_0-st-v1-01-1 (A7)

source_name: hAKPC-P undifferentiated

value: Expanded in Chang's media


title: hAKPC-P diff. 1

description:
Differentiated with VRADD Media
AA334-HuGene-1_0-st-v1-01-1 (B)


title: hAKPC-P und. 1

description:
Expanded in Chang's media
AA333-HuGene-1_0-st-v1-01-1 (A)


title: hAKPC-P diff. 3

description:
Differentiated with VRADD Media
AB065-HuGene-1_0-st-v1-01-1 (B5)


title: 0NWA

description: ZT0, normal chow #1

value: JAX stock #000664


title: VezoM40

city: Cambridge

first: Luca

last: Pagani

state: UK

address: Henry Wellcome Building, Fitzwilliam Street

department: Biological Anthropology

country: United Kingdom

institute: University of Cambridge

description:
200
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: Blood

label_protocol: Followed Illumina standard protocol

extract_protocol: Extraction of genomic DNA from saliva was performed using standard extraction protocols.

tag: gender

value: F

value: Blood

tag: population

value: Vezo

tag: region

value: Madagascar


title: VezoM42

description:
202
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: M


title: VezoM27

description:
197
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: hAKPC-P und. 2

description:
Expanded in Chang's media
AB227-HuGene-1_0-st-v1-01-1 (A6)


title: VezoM30

description:
198
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM17

description:
192
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM19

description:
193
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM41

description:
201
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM33B

description:
199
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM25

description:
195
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM24

description:
194
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: VezoM51

description:
203
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: THP-1_4h_200µg/mL_of_empty_ENP_rep3

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

description: Gene expression in THP-1 cells after 4 h in presence of empty ENP exposure (200 µg/mL)

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA (specific activity > 10 pmol Cy3 / µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent), and immediately dried by brief immersion in acetonitrile.

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

source_name: THP-1, 4 h, 200 µg/mL of empty ENP, replicate 3

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: THP-1 human monocyte cell line is derived from a blood sample of a one-year old child suffering from acute monocytic leukemia and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in RPMI 1640 medium (GIBCO, Invitrogen, Cergy Pontoise, France) supplemented with 10 % of heat-inactivated fetal bovine serum (Eurobio, Les Ullis, France), as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma, Saint Quentin Fallavier, France). Cells were incubated at 37°C to an atmosphere composed of 95 % air, 5 % CO2 and diluted by half every 3 days.

extract_protocol: The quality of the RNA extracted by TRIzol® Reagent (Invitrogen, La Jolla, CA) was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 9, Agilent 2100 Bioanalyser, Santa Clara, CA, USA).

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 200 µg / mL of empty polymeric Eudragit® RL nanoparticles (empty ENP; 50 µg/mL) for 4 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany).

value: peripheral blood

value: male

tag: age

tag: time

value: 4 h

value: 200 µg/mL of empty ENP


title: THP-1_4h_200µg/mL_of_empty_ENP_rep1

source_name: THP-1, 4 h, 200 µg/mL of empty ENP, replicate 1


title: THP-1_4h_200µg/mL_of_empty_ENP_rep2

source_name: THP-1, 4 h, 200 µg/mL of empty ENP, replicate 2


title: THP-1_24h_50µg/mL_of_GSNO_loaded_ENP_rep3

description: Gene expression in THP-1 cells after 24 h in presence of GSNO-loaded ENP exposure (50 µg/mL)

source_name: THP-1, 24 h, 50 µg/mL of GSNO-loaded ENP, replicate 3

treatment_protocol: THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 50 µg / mL of S-Nitrosoglutathione-loaded polymeric Eudragit® RL nanoparticles (GSNO-loaded ENP; 50 µg/mL) for 24 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany). GSNO [CAS number: 57564-91-7] was synthesized by Dr F. Aldeek and Prof. R. Schneider in LRGP UPR-CNRS 3349 laboratories (Lorraine University, France).

value: 50 µg/mL of GSNO-loaded ENP


title: VezoM26

description:
196
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).


title: HS983a cells at passage 5

city: Stockholm

first: Sergey

last: Rodin

address: Scheelesvag 2, Plan 4:B1

country: Sweden

institute: Karolinska institute

description: HS983a p5

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/G

data_processing:
The array image was acquired using Affymetrix GeneChip®Command Console 3.1. The CEL files were analyzed using Affymetrix Genotyping Console version 4.1.4.840. Copy Number/LOH analysis was performed according to the Genotyping Console manual, using a set of 75 healthy individuals as a reference (75_samples_ref.REF).
CNCHP files containing information on the observed copy number of genomic segments. One REF file produced by the Batch Sample Mode of copy number analysis in the Affymetrix Genotyping Console.

source_name: human ES cells line HS983a

label_protocol: According to Affymetrics instructions

growth_protocol: Human Es cells were grown on laminin-521

extract_protocol: DNA was extracted using Qiagen DNA Mini Kit

tag: cell type

value: human ES cells

tag: passage

value: passage 5


title: THP-1_24h_50µg/mL_of_GSNO_loaded_ENP_rep4

source_name: THP-1, 24 h, 50 µg/mL of GSNO-loaded ENP, replicate 4


title: HS975 cells at passage 35

description: HS975 p35

source_name: human ES cells line HS975

value: passage 35


title: HS983a cells at passage 15

description: HS983a p15

value: passage 15


title: HS975 cells at passage 6

description: HS975 p6

value: passage 6


title: THP-1_24h_50µg/mL_of_GSNO_loaded_ENP_rep2

source_name: THP-1, 24 h, 50 µg/mL of GSNO-loaded ENP, replicate 2


title: HS980 cells at passage 6

description: HS980 p6

source_name: human ES cells line HS980


title: HS181 just transfered from feeders

description: HS181 p0

source_name: human ES cells line HS181

value: just transfered from feeders


title: HS916 cells at passage 17

description: HS916 p17

source_name: human ES cells line HS916

value: passage 17


title: THP-1_24h_50µg/mL_of_GSNO_loaded_ENP_rep1

source_name: THP-1, 24 h, 50 µg/mL of GSNO-loaded ENP, replicate 1


title: HS980 cells at passage 31

description: HS980 p31

value: passage 31


title: HS181 at passage 19 on laminin-521 after the transfer

description: HS181 p19


title: VezoM15

description:
191
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Blood


title: VezoM14

description:
190
Genomic DNA extracted from blood was genotyped using OmniExpress 720K Bead Chip (Illumina).

value: Vezo