title: DSS Liver

city: Tokyo

first: Kato

last: Hisanori

address: 1-1-1 Yayoi, Bunkyo-ku,

institute: The University of Tokyo

hyb_protocol: Purified mRNA samples (15 µg) were used to prepare fragmented biotinylated cRNA for hybridization. The DNA microarray (Mouse Genome 430 2.0 Array GeneChip) was hybridized with a mixture of fluorescence-labeled DNA at 45 °C for 16 h, and then was washed and stained using GeneChip Fluidics Station 400 (Affymetrix).

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

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

source_name: Liver from mice in DSS group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA .

growth_protocol: Seven-week-old male C57BL6/J mice obtained from Charles River Japan (Tokyo ) were housed individually in animal cages in a room with controlled temperature (23±2°C), humidity (50±10%), and lighting (lights on from 08:00 to 20:00). After 3 days of acclimatization, the mice were divided into three groups (n=7) with equal mean body weights: (1) mice given a basal diet and normal drinking water for the course of the entire experiment (CON group), (2) mice given the basal diet and normal drinking water for 1 week, after which colitis was induced by administering 1.5% (w/v) DSS (DSS molecular weight, 40 KDa; MP Biomedicals, Irvine, CA, USA) drinking water (DSS group); and (3) mice given a 2% PAR-supplemented basal diet and normal drinking water for 1 week, after which colitis was induced by administering 1.5% DSS drinking water (DSSPAR group) for 9 days.

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

treatment_protocol:
Mice fed on basal diet throughout the entire experiment. Mice drank normal drinking water for the 1st 7 days of the experiment after which 1.5% DSS in drinking water was administred for 10 days.
At the time of sacrifice, the mice were deeply anaesthetized with sodium pentobarbital followed by bleeding from the carotid artery. Excised colon tissue and liver tissue were snap-frozen in liquid nitrogen and stored at −80°C until further analysis.

tag: strain background

value: male

value: 7 weeks

tag: mice group

value: dextran sodium sulphate (DSS)-induced colitis

value: Liver


title: DSSPAR Colon

status: Public on Jan 24 2014

type: RNA

country: Japan

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Colon from mice in DSSPAR group

treatment_protocol:
Mice fed on 2% Parsley supplemented diet throughout the entire experiment. Mice drank normal drinking water for the 1st 7 days of the experiment after which 1.5% DSS in drinking water was administred for 9 days.
At the time of sacrifice, the mice were deeply anaesthetized with sodium pentobarbital followed by bleeding from the carotid artery. Excised colon tissue and liver tissue were snap-frozen in liquid nitrogen and stored at −80°C until further analysis.

tag: gender

tag: age

value: DSS with PAR supplementation

tag: tissue

value: Colon


title: MCF-10A shPTEN replicate 3 [Set 2]

city: Houston

first: Chun-Jen

middle: Curtis

last: Lin

state: Texas

address: 7345 Fannin Street

department: Systems Biology

country: USA

institute: University of Texas MD Anderson Cancer Center

description: PTEN 23

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data is not normalized

label: Biotin

organism: Homo sapiens

source_name: MCF-10A shPTEN

label_protocol: Biotinylated cRNA were prepared with illumina TotalPrep RNA Amplification Kit

growth_protocol: All cell were cultured in MCF-10A medium

extract_protocol: total RNA was extracted with ambion mirVara miRNA isolation kit.

treatment_protocol: shRNA stable knockdown

tag: cell line

tag: cell type

value: mammary epithelial cells

tag: transfected with

value: shPTEN


title: MCF-10A shPTEN replicate 2 [Set 2]

description: PTEN 22


title: MCF-10A shATM-3 replicate 3 [set 5]

data_processing: The data were log2 transformed and normalized using quantile normalization with BRB array tool (developed by Biomertric Research Branch of Division of Cancer Treatment and Diagnosis of National Cancer Institute)


title: MCF-10A shATM-3 replicate 1 [set 5]


title: MCF-10A shATM-3 replicate 2 [set 5]


title: CON Colon

source_name: Colon from mice in CON group

treatment_protocol:
Mice fed on basal diet and drinking water throughout the entire experiment
At the time of sacrifice, the mice were deeply anaesthetized with sodium pentobarbital followed by bleeding from the carotid artery. Excised colon tissue and liver tissue were snap-frozen in liquid nitrogen and stored at −80°C until further analysis.

value: control group


title: CON Liver

source_name: Liver from mice in CON group


title: DSSPAR Liver

source_name: Liver from mice in DSSPAR group

treatment_protocol:
GMice fed on 2% Parsley supplemented diet throughout the entire experiment. Mice drank normal drinking water for the 1st 7 days of the experiment after which 1.5% DSS in drinking water was administred for 9 days.
At the time of sacrifice, the mice were deeply anaesthetized with sodium pentobarbital followed by bleeding from the carotid artery. Excised colon tissue and liver tissue were snap-frozen in liquid nitrogen and stored at −80°C until further analysis.


title: MCF-10A shPTEN replicate 1 [Set 2]

description: PTEN 21


title: MCF-10A shATM-1 replicate 3 [set 5]


title: DSS Colon

source_name: Colon from mice in DSS group


title: MCF-10A shATM-1 replicate 2 [set 5]


title: WM3523cln6 cells 10 days after transduction with lentiviral library (day 10)

type: genomic

city: Leipzig

first: Manfred

last: Kunz

address: Philipp-Rosenthal-Str. 23

department: Department of Dermatology

country: Germany

institute: University of Leipzig

description: shRNA levels from WM3523cln6 cells transduced with the lentiviral library at day 10

hyb_protocol: 10 ug of biotin-labelled cDNA were hybridized for 16 hr at 450C on a HG-U133APlus2.0 array. Gene microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were loaded into an AffyBatch object and preprocessed using MAS for background correction and RMA for normalization. No summarization step was performed. Using the index information in the files infos_probes_*.txt file (column indices.int) probes were annotated with custom siRNA identifiers and corresponding Ensembl transcript identifiers. Low expressed probes and probes not mapping to an Ensembl ID were removed from further analyses. Low expression was estimated as the 90% quantile of the expression of the background probes and probes had to have an expression greater than this threshold is more than 50% of the arrays to be kept. Gene annotation for shRNAs was performed using GeneNet siRNA Library Data analysis Software Version 2.6 (SBI System Biosciences). All analyses were performed using the software package R version 2.9.0.

molecule: genomic DNA

label_protocol: PCR amplification of integrated shRNAs was performed as nested PCR according to the GeneNet Lentiviral siRNA Library Protocol (cat.#SI206B-1), using a biotinylated nested forward primer in the second round. Lambda exonuclease treatment was performed to remove second non-biotinylated strand.

growth_protocol: Different melanoma cell lines were grown in DMEM Medium supplemented with L-Glutamin and Pen/Strep.

extract_protocol: Genomic DNA (with integrated shRNAs) was extracted using the DNeasy Blood and Tissue Kit from QIAGEN according to the manufacturers specifications.

treatment_protocol: Different melanoma cell lines were transduced with a commercially available lentiviral shRNA library covering all human genes including ESTs (more than 200.000 siRNAs) in a pooled approach and grown for 10 days under puromycin selection. Control cells of respective cell lines were transduced with the lentiviral library and frozen immediately after shRNA integration (termed day 0). The GeneNet Lentiviral siRNA Library from SBI System Biosciences was used (ca.#SI206B-1).

tag: original source

value: skin

value: melanoma


title: Control biological replicate 3

city: Sutton

first: Emma

middle: Marie

last: Smith

address: 15 Cotswold Road

department: Haemato-Oncology

country: United Kingdom

institute: Institute of Cancer Research

hyb_protocol: Affymetrix Fluidics Station Protocol: Hybridization-EukGE-WS2v5_450, 15ug of fragmented cRNA were hybridised to U133 Plus 2.0 arrays using the standard Affymetrix conditions for 16 hours at 45C.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G/4 color early acces scanner and processed using GCOS 1.4.0.

data_processing: The data were analyzed with dChip (April 2007 build) using default analysis settings for normalization and summarization methods.

source_name: H929 myeloma cell line

label_protocol: 100 ng of RNA was used in the Affymetrix 2-cycle IVT reaction and cRNA was labelled with biointylated rUTP during the second IVT reaction as per Affymetrix protocol.

growth_protocol: H929 human myeloma cell line was maintained in RPMI-1640 with 10% FBS and pen/strep.

extract_protocol: Rneasy Miniprep kit (Qiagen)

value: myeloma cell line

tag: drug treatment

value: Untreated cells


title: SK-Mel-5 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from SK-Mel 5 cells transduced with the lentiviral library at day 10

tag: other

value: derived from metastatic axilliary node, 24 years, female


title: MCF-10A shControl replicate 3 [set 5]

value: shControl


title: Control biological replicate 1


title: MCF-10A shControl replicate 3 [Set 2]

description: Control 3

source_name: MCF-10A shControl


title: MCF-10A shControl replicate 2 [Set 2]

description: Control 2


title: Control biological replicate 2


title: SK-Mel-29 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from SK-Mel 29 cells transduced with the lentiviral library at day 10

value: metastasis


title: Chr3996 biological replicate 2

value: CHR3996 250 nanomolar 24 hours


title: MCF-10A shControl replicate 2 [set 5]


title: Chr3996 biological replicate 3


title: MCF-10A shATM-1 replicate 1 [set 5]


title: MCF-10A shControl replicate 4 [Set 2]

description: Control 4


title: Chr3996 biological replicate 1


title: dsmc5ARA(3).gpr

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description: Biological replicate 3 of 3. Dye swap 2

hyb_protocol: For hybridization, yeast tRNA and salmon testes DNA were added to labeled cDNA along with a formamide hybridization buffer. Samples were applied to slides, and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

scan_protocol: Arrays were scanned on a Axon instruments GenePix 4000B scanner.  Images were processed using GenePix Pro software (version 4.1)  and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

data_processing: Data normalization between and within array using LOWESS in R Statistical Programming (v.11.1)/Bioconductor (v.1.6).

organism: Limosilactobacillus reuteri

source_name: DSM 17938_wild type

label_protocol: 2 ug of total RNA were primed with 2.5 ug of random hexamers (Qiagen) at 70 degrees Celsius for 10 minutes. Reverse transcription was then carried out using Superscript III (Invitrogen) with 500 uM each dATP, dCTP, and dGTP, 300 uM dTTP, and 200 uM aminoallyl dUTP. After reverse transcription, RNA was removed by hydrolysis and cDNA was cleaned. cDNA was then labeled using CyDye Post-labeling reactive dye packs (Amersham).

growth_protocol: Bacterial cells were grown for 24h in MRS at 37C in anaerobic conditions

extract_protocol: At the specified times, 5 ml of bacterial were collected and mixed with an equal part of ice-cold methanol. Cell pellets were centrifuged, washed, and resuspended in 0.25 units/ul mutanolysin. After incubation at 37 degrees Celsius for 20 minutes, total RNA was collected according to the manufacturer's instructions with the Qiagen RNeasy Kit.

tag: strain

tag: genotype/variation

value: wild type

source_name: pocR mutant

value: pocR mutant


title: dsmc5ARA(2).gpr

description: Biological replicate 2 of 3. Dye swap 2


title: SK-Mel-28 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from SK-Mel-28 cells transduced with the lentiviral library at day 10

value: metastasis, 51 years, male


title: MCF-10A wild type replicate 3 [set 5]

source_name: MCF-10A_wild type

value: none (mock control)


title: MCF-10A shControl replicate 1 [Set 2]

description: Control 1


title: dsmc3ARA(2).gpr

description: Biological replicate 2 of 3. Dye swap 1


title: MCF-10A shControl replicate 1 [set 5]


title: Chr2797 biological replicate 1

value: CHR2797 1 micromolar 24 hours


title: dsmc5ARA(1).gpr

description: Biological replicate 1 of 3. Dye swap 2


title: SK-Mel-147 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from SK-Mel-147 cells transduced with the lentiviral library at day 10


title: SK-Mel-103 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from SK-Mel-103 cells transduced with the lentiviral library at day 10


title: MCF-10A wild type replicate 2 [set 5]


title: dsmc3ARA(1).gpr

description: Biological replicate 1 of 3. Dye swap 1


title: U2OS shCHK1-4 replicate 2 [set 4]

description: U2OS shCHK1-4_2

growth_protocol: All U2OS cell were cultured in McCOY 5A medium with 10% FBS

value: human osteosarcoma cells


title: Chr2797 biological replicate 3


title: Combination biological replicate 2

value: CHR2797 1 micromolar + CHR3996 250 nanomolar 24 hours


title: Chr2797 biological replicate 2


title: U2OS shCHK1-4 replicate 1 [set 4]

description: U2OS shCHK1-4_1


title: A375 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from A375 cells transduced with the lentiviral library at day 10

value: 54 years, female


title: WM3523cln6 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from WM3523cln6 cells transduced with the lentiviral library at day 0


title: dsmc3ARA(3).gpr

description: Biological replicate 3 of 3. Dye swap 1


title: SK-Mel-19 cells 10 days after transduction with lentiviral library (day 10)

description: shRNA levels from SK-Mel-19 cells transduced with the lentiviral library at day 10


title: Combination biological replicate 3


title: SK-Mel-5 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from SK-Mel 5 cells transduced with the lentiviral library at day 0


title: MCF-10A shBrit1 replicate 3 [Set 1]

description: Brit1 2C

source_name: MCF-10A shBrit1

value: mammary epithelial cells


title: Combination biological replicate 1


title: SK-Mel-29 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from SK-Mel 29 cells transduced with the lentiviral library at day 0

value: skin


title: U2OS shCHK1-4 replicate 3 [set 4]

description: U2OS shCHK1-4_3


title: SK-Mel-28 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from SK-Mel 28 cells transduced with the lentiviral library at day 0

value: melanoma


title: U2OS shCHK1-3 replicate 2 [set 4]

description: U2OS shCHK1-3_2


title: MCF-10A shBrit1 replicate 4 [Set 1]

description: Brit1 2D


title: MCF-10A shBrit1 replicate 2 [Set 1]

description: Brit1 2B


title: U2OS shCHK1-3 replicate 1 [set 4]

description: U2OS shCHK1-3_1


title: MCF-10A shBrit1 replicate 1 [Set 1]

description: Brit1 2A2


title: MCF-10A wild type replicate 1 [set 5]


title: U2OS shControl replicate 3 [set 4]

description: U2OS shCtrl_3


title: U2OS shCHK1-3 replicate 3 [set 4]

description: U2OS shCHK1-3_3


title: Gill_AW_96h_rep3

city: Shanghai

first: Zongli

last: Yao

address: No.300 Jungong Road

country: China

institute: East China Sea Fisheries Research Institute

description: Gene expression in gill of medaka exposed to AW for 96h

hyb_protocol: Labeled cRNA was was prepared for fragmentation adding 11 μl 10× Blocking Agent and 2.2 μl of 25× Fragmentation Buffer, heated at 60°C for 30 min, and finally diluted by addition with 55 μl 2× GE Hybridization buffer. A volume of 100 µl of hybridization solution was then dispensed in the gasket slide and assembled to the microarray slide (each slide containing four arrays). Slides were incubated for 17 h at 65°C in a Agilent Hybridization Oven, subsequently removed from the hybridization chamber, quickly submerged in GE Wash Buffer 1 to disassembly the slides and then washed in GE Wash Buffer 1 for approximately 1 minute followed by one additional wash in pre-warmed (37°C) GE Wash Buffer 2.

scan_protocol: The arrays were scanned on a Agilent G2565BA DNA microarray scanner, at a resolution of 5 µm, modifying default settings to scan the same slide twice at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryzias latipes

source_name: Gill, AW, 96h, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from 50~100 mg gills using Trizol (Invitrogen, Burlington, ON, Canada) isolation reagent following the manufacturer’s instructions. Total RNA concentration and quality were determined spectrophotometrically (Bioanalyzer2100, Angilent, British), with purity assessed (A260/A280 was ≥1.8; rRNA Ratio [28S/18S] values > 0.9; RNA integrity number RIN(Schroeder 2006) values > 8.0). Total RNA was treated with RQ1 RNase-free DNase (Promega). RNA samples were stored at -80˚C following isolation.

tag: condition

value: high carbonate alkalinity water

value: Gill


title: A375 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from A375 cells transduced with the lentiviral library at day 0


title: U2OS shControl replicate 2 [set 4]

description: U2OS shCtrl_2


title: SK-Mel-19 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from SK-Mel-19 cells transduced with the lentiviral library at day 0


title: U2OS shControl replicate 1 [set 4]

description: U2OS shCtrl_1


title: Gill_AW_96h_rep2

source_name: Gill, AW, 96h, replicate 2


title: Gill_FW_96h_rep2

description: Gene expression in gill of medaka exposed to FW for 96h

source_name: Gill, FW, 96h, replicate 2

value: freshwater


title: Gill_AW_96h_rep1

source_name: Gill, AW, 96h, replicate 1


title: Gill_FW_96h_rep1

source_name: Gill, FW, 96h, replicate 1


title: SK-Mel-147 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from SK-Mel-147 cells transduced with the lentiviral library at day 0


title: MCF-10A shControl replicate 3 [Set 1]

value: shControl


title: MCF-10A shControl replicate 1 [Set 1]


title: MCF-10A shControl replicate 2 [Set 1]


title: MAVS-/- MEFs, 8hpi with Type Imaf1KO Toxoplasma, biological rep1

status: Public on Jan 23 2014

city: Stanford

first: John

last: Boothroyd

state: CA

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on the Mouse Genome 430 2.0 Array

scan_protocol: GeneChips were scanned using the Affymetrix gene scanner 7G

data_processing: RMA for Affymetrix data

source_name: MAVS-/- MEFs_8hpi_Type Imaf1KO Toxoplasma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from .5 ug total RNA (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: 4.5e5 MEFs (genotype as indicated) were in a 6 well plate. 4 h after plating, infected with Toxoplasma parasites (strain as indicated) at an MOI of 5

treatment_protocol: 8 hpi supernatant was removed and replaced with 1 ml of TriZol

value: 129/Sv (Z.J. Chen, U.T. Southwestern)

value: MAVS-/-

value: MEFs

tag: multiplicity of infection

tag: infected with

value: Type Imaf1KO Toxoplasma

tag: time point

value: 8h post infection


title: WT MEFs 8hpi with Type II Toxoplasma, biological rep2

source_name: WT MEFs 8hpi_Type II Toxoplasma

tag: strain background

value: 129/SvEv (ATCC CRL-2991)

value: wild type

value: Type II Toxoplasma


title: MAVS-/- MEFs, 8hpi with Type Imaf1KO Toxoplasma, biological rep2


title: WT MEFs 8hpi with Type II:MAF1 Toxoplasma, biological rep1

source_name: WT MEFs 8hpi_Type II:MAF1 Toxoplasma

value: Type II:MAF1 Toxoplasma


title: MPC-coated scaffold replicate-2

city: Kobe

first: Tomo

last: EHASHI

address: 1-1 Rokkodai, Nada

institute: Kobe University

description:
Experimental replicate 2 of 2. RNA from infiltrated host cells into implanted scaffold selected by laser microdissection.
Sample name: MPC-2
In the each .gpr file, Block 1 corresponds to sample COL-1, Block 2 to MPC-1, Block 3 to  COL-2, Block 4 to MPC-2.
A total of three gpr files were submitted, each gpr representing a different gain (high, medium, low).

hyb_protocol: Labelled samples were mixed with hybridization buffer (Agilent GE Hybridization Kit) and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Scanned on an GenePix 4000B scanner.

data_processing:
Images were quantified using GenePix Pro Software (ver. 4.1). Three profiles (gain changed) were combined and processed by LOWESS.Reproducible values were obtained from two hybridization.
Three profiles (gain changed) were combined and processed by LOWESS.

source_name: infiltrated host cells into implanted PMB-coated scaffold

label_protocol: 825 ng of total RNA were amplified and labelled with Cy5 or Cy3 using Ambion Amino Ally MessageAmp II aRNA Amplification Kit.

growth_protocol: Mice were maintained in conditioned circumstance at 25oC

extract_protocol: Implanted scaffolds were excised with dorsal skin, embedded in OTC compound, and cryosectioned. Scaffolds and thin surrounding tissues were cut out by laser microdissection. Total RNA extracted using Isogen following manufacturer's instructions

treatment_protocol: Porous scaffolds which were un-coated or coated with collagen or PMB were implanted subcutaneously for 7 days in mice dorsal area.

value: male

tag: implanted period

value: 7 days

tag: implanted scaffold

value: PMB-coated scaffold

value: infiltrated host cells

source_name: infiltrated host cells into implanted non coat scaffold (reference)

value: non coat scaffold


title: WT MEFs 8hpi with Type II Toxoplasma, biological rep1


title: WT MEFs 8hpi with Type Imaf1KO Toxoplasma, biological rep1

source_name: WT MEFs 8hpi_Type Imaf1KO Toxoplasma


title: MPC-coated scaffold replicate-1

description:
Experimental replicate 1 of 2. RNA from infiltrated host cells into implanted scaffold selected by laser microdissection.
Sample name: MPC-1
In the each .gpr file, Block 1 corresponds to sample COL-1, Block 2 to MPC-1, Block 3 to  COL-2, Block 4 to MPC-2.
A total of three gpr files were submitted, each gpr representing a different gain (high, medium, low).

tag: gender

tag: age


title: WT MEFs 8hpi with Type Imaf1KO Toxoplasma, biological rep2


title: WT MEFs 8hpi with Type I Toxoplasma, biological rep2

description: WT MEFs_Type I_2

source_name: WT MEFs 8hpi_Type I Toxoplasma

value: Type I Toxoplasma


title: MAVS-/- MEFs, 8hpi with Type I Toxoplasma, biological rep1

description: MAVSKO_Type I_1

source_name: MAVS-/- MEFs_8hpi_Type I Toxoplasma


title: WT MEFs 8hpi with Type I Toxoplasma, biological rep1

description: WT MEFs_Type I_1


title: collagen-coated scaffold replicate-1

description:
Experimental replicate 1 of 2. RNA from infiltrated host cells into implanted scaffold selected by laser microdissection.
Sample name: COL-1
In the each .gpr file, Block 1 corresponds to sample COL-1, Block 2 to MPC-1, Block 3 to  COL-2, Block 4 to MPC-2.
A total of three gpr files were submitted, each gpr representing a different gain (high, medium, low).

source_name: infiltrated host cells into implanted collagen-coated scaffold

value: collagen-coated scaffold


title: B73 stem tissue biological replicate 2

city: beijing

first: qiuxue

last: zhang

address: 12 Zhong Guan Cun South Street, Haidian District

institute: biotechnology research institute  ,Chinese Academy of Agricultural Sciences

description: Gene expression data from untreated maize stem

hyb_protocol: Following fragmentation, cRNA were hybridized. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: Raw data were normalized by MAS 5.0 algorithm

organism: Zea mays

source_name: Zea mays big trumpet period stem tissue

label_protocol: total RNA were labeled with the GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA) following manufacturer’s instructions

growth_protocol: All experimental materials were  sowed and nursed with normal agricultural practice.

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

treatment_protocol: No

tag: tissue

value: stem

tag: genotype


title: MAVS-/- MEFs, 8hpi with Type I Toxoplasma, biological rep2

description: MAVSKO_Type I_2

value: 129/Sv (Z.J. Chen, U.T. Southwestern)

tag: cell type


title: B73 stem tip tissue biological replicate 2

description: Gene expression data from untreated maize stem tip

source_name: Zea mays big trumpet period stem tip tissue

value: stem tip


title: B73 stem tip tissue biological replicate 1


title: B73 stem tissue biological replicate 3


title: collagen-coated scaffold replicate-2

description:
Experimental replicate 2 of 2. RNA from infiltrated host cells into implanted scaffold selected by laser microdissection.
Sample name: COL-2
In the each .gpr file, Block 1 corresponds to sample COL-1, Block 2 to MPC-1, Block 3 to  COL-2, Block 4 to MPC-2.
A total of three gpr files were submitted, each gpr representing a different gain (high, medium, low).


title: B73 stem tip tissue biological replicate 3


title: B73 stem tissue biological replicate 1


title: B73 root tissue biological replicate 2

description: Gene expression data from untreated maize root

source_name: Zea mays big trumpet period root tissue

value: root


title: B73 silk tissue biological replicate 1

description: Gene expression data from untreated maize silk

source_name: Zea mays before pollination silk tissue

value: silk


title: B73 root tissue biological replicate 3


title: B73 root tissue biological replicate 1


title: B73 silk tissue biological replicate 3


title: B73 silk tissue biological replicate 2


title: B73 ear tissue biological replicate 1

description: Gene expression data from untreated maize ear

source_name: Zea mays before pollination ear tissue

value: ear


title: B73 leaf tissue biological replicate 1

description: Gene expression data from untreated maize leaf

source_name: Zea mays big trumpet period leaf tissue

value: leaf


title: B73 leaf tissue biological replicate 2


title: B73 ear tissue biological replicate 2


title: B73 ear tissue biological replicate 3


title: B73 20DAP embryo tissue biological replicate 2

description: Gene expression data from untreated maize 20DAP embryo

source_name: Zea mays 20 day after pollination embryo tissue

tag: Stage

value: 20 day after pollination embryo


title: B73 25DAP embryo tissue biological replicate 1

description: Gene expression data from untreated maize 25DAP embryo

source_name: Zea mays 25 day after pollination embryo tissue

value: 25 day after pollination embryo


title: B73 25DAP embryo tissue biological replicate 2


title: B73 leaf tissue biological replicate 3


title: B73 25DAP endosperm tissue biological replicate 2

description: Gene expression data from untreated maize 25DAP endosperm

source_name: Zea mays 25 day after pollination endosperm tissue

value: 25 day after pollination endosperm


title: B73 25DAP endosperm tissue biological replicate 1


title: B73 25DAP embryo tissue biological replicate 3


title: B73 20DAP endosperm tissue biological replicate 2

description: Gene expression data from untreated maize 20DAP endosperm

source_name: Zea mays 20 day after pollination endosperm tissue

value: 20 day after pollination endosperm


title: B73 20DAP embryo tissue biological replicate 1


title: B73 15DAP endosperm tissue biological replicate 3

description: Gene expression data from untreated maize 15DAP endosperm

source_name: Zea mays 15 day after pollination endosperm tissue

value: 15 day after pollination endosperm


title: B73 20DAP endosperm tissue biological replicate 1


title: B73 15DAP endosperm tissue biological replicate 2


title: B73 25DAP endosperm tissue biological replicate 3


title: B73 15DAP embryo tissue biological replicate 1

description: Gene expression data from untreated maize 15DAP embryo

source_name: Zea mays 15 day after pollination embryo tissue

value: 15 day after pollination embryo


title: B73 20DAP endosperm tissue biological replicate 3


title: B73 20DAP embryo tissue biological replicate 3


title: B73 15DAP embryo tissue biological replicate 2


title: B73 15DAP embryo tissue biological replicate 3


title: SK-Mel-103 cells immediately after transduction with lentiviral library (day 0)

description: shRNA levels from SK-Mel-103 cells transduced with the lentiviral library at day 0

tag: cell line

tag: original source

value: skin

value: melanoma

value: metastasis


title: B73 10DAP endosperm tissue biological replicate 3

description: Gene expression data from untreated maize 10DAP endosperm

source_name: Zea mays 10 day after pollination endosperm tissue

value: 10 day after pollination endosperm


title: WT MEFs 8hpi with Type II:MAF1 Toxoplasma, biological rep2

source_name: WT MEFs 8hpi_Type II:MAF1 Toxoplasma

value: 129/SvEv (ATCC CRL-2991)

value: wild type

value: MEFs

value: Type II:MAF1 Toxoplasma

value: 8h post infection


title: B73 10DAP endosperm tissue biological replicate 2


title: B73 15DAP endosperm tissue biological replicate 1


title: Control SW480 cells transfected with an empty vector, replicate 4

city: Lodz

first: Magdalena

last: Nowakowska

address: Zeligowskiego 7/9

department: Department of Molecular Cancerogenesis

country: Poland

institute: Medical University of Lodz

hyb_protocol: Before pre-hybridization microarrays were pre-heated at 60˚C for 10 min., followed by 99% ethanol wash. Residual ethanol was removed by thorough rinse in deionized water. Hybridization was carried out in a humidity chamber filled with 2X SSPE buffer at 42°C for 16 – 18 h. Post-hybridization washings comprised 1 X SSPE / 0.03% SDS for 2 min. at 42°C, then in 1 X SSPE for 2 min. RT, and  0.1 X SSPE, RT.

scan_protocol: Microarray scanning was done by means of ProScanArray (Perkin Elmer, USA).

data_processing:
Preliminary analysis using ScanArrayExpress software (Perkin Elmer, USA). Further analysis procedures were carried out on freeware TM4 software suite, which is provided by The Institute for Genomic Research on http://www.tm4.org/ site. Normalization and transformation was performed using MIDAS (v2.22). Data from dye-swap experiments were merged, lowess normalized with a smoothing parameter of 0.33  and then standard deviation regularized. Pairs of flip-dye data were then subjected to a flip-dye consistency check.
Statystical analysys were performed in MeV software (v.4.6.1; MultiExperiment Viewer, TM4 software suite)

source_name: colon cancer cell line

label_protocol: Labeling with Cy3 and Cy5 was performed according to the ULS™ Labelling Kit manufacturer's instructions (Kreatech Diagnostics, Netherlands)

growth_protocol: SW480 cells, derived from a human colorectal adenoracinoma were grown in RPMI-1640 medium (Gibco) supplemented with 2 mM L-glutamine (Gibco), 0.1 mM NEAA (Gibco), 10% heat inactivated FBS (Gibco), 0.05 mg/ml penicillin (Gibco), 0.05 mg/ml streptomycin (Gibco) and 0.1 mg/ml neomycin (Gibco) in a humified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated using TRIzol reagent (Life Technologies). The cDNA synthesis was performed from 10 µg of total RNA  using ImProm RT-IITM reverse transcriptase (Promega)

treatment_protocol: The WWOX gene cDNA was introduced into SW480 cells by a retroviral transfection. The pLNCX2 retroviral vector with cloned WWOX was produced in the PT67 packaging line. Target cells were grown to 30% confluence and infected with the viruses (approximately 1E+06 CFU/ml) suspended in culture medium with Polybrene as vehicle (8 μg/ml, Sigma Aldrich). After 24 h, medium was replaced, and stable transfectants were selected with 400 μg/ml G418 (Sigma Aldrich) in seven doses, added every 48 hours. Pool of stable transfectants was used for a microarray study of global gene expression and biological experiments. Transfection efficiency was confirmed by real-time RT-PCR and Western Blot.

tag: treatment

value: control empty vector transfection

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: Universal Human Reference RNA composed of total RNA from 10 human cell lines


title: Control SW480 cells transfected with an empty vector, replicate 3


title: SW480 stably transfected with retroviral vector carying WWOX cDNA, replicate 1

value: WWOX transfection


title: B73 10DAP endosperm tissue biological replicate 1


title: HT29 stably transfected with retroviral vector carying WWOX cDNA, replicate 4

growth_protocol: HT29 cells, derived from a human colorectal adenoracinoma were grown in Mc Coy's medium (Gibco) supplemented with 2 mM L-glutamine (Gibco), 0.1 mM NEAA (Gibco), 10% heat inactivated FBS (Gibco), 0.05 mg/ml penicillin (Gibco), 0.05 mg/ml streptomycin (Gibco) and 0.1 mg/ml neomycin (Gibco) in a humified atmosphere containing 5% CO2 at 37°C.

treatment_protocol: The WWOX gene cDNA was introduced into HT29 cells by a retroviral transfection. The pLNCX2 retroviral vector with cloned WWOX was produced in the PT67 packaging line. Target cells were grown to 30% confluence and infected with the viruses (approximately 1E+06 CFU/ml) suspended in culture medium with Polybrene as vehicle (8 μg/ml, Sigma Aldrich). After 24 h, medium was replaced, and stable transfectants were selected with 400 μg/ml G418 (Sigma Aldrich) in seven doses, added every 48 hours. Pool of stable transfectants was used for a microarray study of global gene expression and biological experiments. Transfection efficiency was confirmed by real-time RT-PCR and Western Blot.


title: SW480 stably transfected with retroviral vector carying WWOX cDNA, replicate 3


title: B73 10DAP embryo tissue biological replicate 3

description: Gene expression data from untreated maize 10DAP embryo

source_name: Zea mays 10 day after pollination embryo tissue

value: 10 day after pollination embryo


title: SW480 stably transfected with retroviral vector carying WWOX cDNA, replicate 2


title: Control SW480 cells transfected with an empty vector, replicate 2


title: Control SW480 cells transfected with an empty vector, replicate 1


title: HT29 stably transfected with retroviral vector carying WWOX cDNA, replicate 3


title: HT29 stably transfected with retroviral vector carying WWOX cDNA, replicate 2


title: Control HT29 cells transfected with an empty vector, replicate 4


title: HT29 stably transfected with retroviral vector carying WWOX cDNA, replicate 1


title: B73 10DAP embryo tissue biological replicate 1


title: B73 10DAP embryo tissue biological replicate 2


title: Control HT29 cells transfected with an empty vector, replicate 1


title: Control HT29 cells transfected with an empty vector, replicate 3


title: SW480 stably transfected with retroviral vector carying WWOX cDNA, replicate 4


title: Control HT29 cells transfected with an empty vector, replicate 2


title: MCF7 YB1 IP B

city: Auckland

first: Cherie

last: Blenkiron

address: Private bag 92019

department: Surgery

country: New Zealand

institute: University of Auckland

hyb_protocol: biotinylated RNA was hybridized to GeneChip miRNA V1.0 arrays at 480C, 60rpm for 16 hours. GeneChips were washed and stained in the Affy Fluidics station 450.

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

data_processing: Affymetrix .CEL files were analysed using the statistical programming language R using the Bioconductor packages affy, affyPLM and limma. The data was preprocessed using RMA.

source_name: MCF7 breast cancer cells, immunoprecipitated with YB-1

label_protocol: 8ul RNA was direct labelled using the Flashtag HSR kit as standard

growth_protocol: Cell grown in RPMI-1640 with 5% FCS at 37oC

extract_protocol: Extracted with TRIzol and purelink mini RNA kit using the protocol for total RNA

treatment_protocol: untreated

value: YB1 IP


title: Gill_FW_96h_rep3

description: Gene expression in gill of medaka exposed to FW for 96h

source_name: Gill, FW, 96h, replicate 3

tag: condition

value: freshwater

value: Gill


title: MDA input

source_name: MDA-MB-435S breast cancer cells, input lysate

value: input


title: MDA YB1 IP A

source_name: MDA-MB-435S breast cancer cells, immunoprecipitated with YB-1


title: MCF7 YB1 IP A


title: MCF7 YB1 IP C


title: MCF7 input

source_name: MCF7 breast cancer cells, input lysate


title: MDA YB1 IP B


title: MDA CTRL 2

hyb_protocol: biotinylated RNA was hybridised to GeneChip miRNA V1.0 arrays at 480C, 60rpm for 16 hours. GeneChips were washed and stained in the Affy Fluidics station 450.

source_name: MDA-MB-435S breast cancer cells treated with siCtrl

treatment_protocol: Treated with Stealth 5nM siRNA using lipofectamine RNAiMax for 24 hours

value: si-Control

tag: genotype/variation

value: control


title: MDA CTRL 3


title: MCF7 CTRL C

source_name: MCF7 breast cancer cells treated with si-Ctrl


title: MCF7 YB1 B

source_name: MCF7 breast cancer cells treated with siYB-1

value: YB-1 KD


title: MDA CTRL1


title: MCF7 CTRL B


title: MDA YB1 A

source_name: MDA-MB-435S breast cancer cells treated with siYB-1


title: MDA YB1 B


title: MCF7 CTRL A


title: MCF7 YB1 A


title: MDA YB1 C


title: MCF7 YB1 C


title: MDA YB1 IP C


title: SM014_nsp16_d7_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

value: lung

tag: infection


title: SM014_nsp16_d4_4


title: SM014_nsp16_d4_1


title: SM014_nsp16_d7_1


title: SM014_nsp16_d7_2


title: SM014_nsp16_d4_3


title: SM014_nsp16_d2_4


title: SM014_mock_d7_1

value: mock


title: SM014_mock_d4_3


title: SM014_mock_d2_3


title: SM014_nsp16_d1_3


title: SM014_mock_d2_1


title: SM014_nsp16_d1_4


title: SM014_mock_d2_2


title: SM014_mock_d4_1


title: SM014_mock_d7_3


title: SM014_mock_d4_2


title: SM014_nsp16_d2_1


title: SM014_nsp16_d1_2


title: SM014_mock_d1_3


title: SM014_nsp16_d2_2


title: ctl_S52 vs. 1D_S52

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: S52 non-inoculated susceptible leaves vs. S52 inoculated susceptible leaves in the soybean leaves(1D)

hyb_protocol: After checking labeling efficiency, each 750 ng of cyanine 3-labeled and cyanine 5-labeled cRNA targets were mixed and the fragmentation of cRNA was performed by adding 10x blocking agent and 25x fragmentation buffer and incubating at 60 °C for 30 min. The fragmented cRNA was resuspended with 2x hybridization buffer and directly pipetted onto soybean microarray placed in Hybridization Chamber (Agilent Technologies). The arrays hybridized at 65 °C for 16 h using Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray scanner and the data quantification was performed using Agilent Feature Extraction software.

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring GX 7.3 (Agilent Technology). Genes were filtered with removing flag-out genes in each experiment. Intensity-dependent normalization (LOWESS) was performed, where the ratio was reduced to the residual of the Lowess fit of the intensity vs. ratio curve.

organism: Glycine max

source_name: S52 non-inoculated susceptible leaves

label_protocol: For non-inoculated (Cy3) and inoculated (resistant or susceptible) (Cy5) soybean RNAs, the synthesis of target cRNA and hybridization were performed using Agilent’s Low RNA Input Linear Amplification Kit PLUS (Agilent Technology) according to the manufacturer’s instructions.

growth_protocol: We developed two sets of near-isogenic line (NIL) by selecting heterozygous F5 plants among pedigree breeding lines from the cross Saturn  SS97225 (Lee x Seunheuk). F5 pedigree lines were grown in 2006 and inoculated with Xag strain 8ra. Seed from F5 plants that were heterozygous for the disease resistance was harvested and F5:6 pedigree lines were grown in 2007. About 40 F6 plants from each segregating F5:6 lines were inoculated with the strain 8ra. F6 lines that were homozygous for the disease resistance were selected and harvested as F6:7 pedigree lines. About 40 F7 plant from each F6:7 lines were inoculated with the strain 8ra and homozygous for the disease resistance. Thus a NIL set consisted of F5 derived families homozygous phenotype for the disease resistance.

extract_protocol: Ten leaves, non-inoculated (control sample) and inoculated resistant or susceptible leaves at two time points, 1-day and 10-day (test groups, 2-condition  2-time), for total RNA isolation were homogenized using liquid nitrogen with a mortar and pestle. Total RNA and genomic DNA from homogenized sample were extracted using TRIZOL reagent (GibcoBRL, Rockville, MD, USA) according to the protocol of the manufacturer. Total RNA was treated with the RNase-free DNase I (Promega, Madison, WI, USA) to reduce DNA contamination. Total RNA concentration and purity were determined spectrophotometrically by the absorbance ratio at 260:280 nm 1.8 or more. The integrity of total RNA samples was also ascertained by appearance of distinct 28S and 18S bands of ribosomal RNA using Bioanalyzer 2100 system (Agilent Technology, Santa Clara, CA, USA).

treatment_protocol: In the green house experiment, individual plant was inoculated with the strain 8ra Xag. The inoculum was prepared by culturing in PDA (potato dextrose agar) medium. Bacterial cells on the culture plates were sterile distilled water and adjusted to optical density 0.3~0.5 (108 colony forming units (cfu) per milliliter) at 600 nm in UV/Visible spectrophotometer. Inoculations were conducted on recently expanded second trifoliate leaves of 20- to 25-day-old plants. Surface of the leaves were sprayed with inoculum suspensions until water-soaking appearance. For better development of disease symptoms after inoculation, green house condition was held at 28 °C and 100% relative humidity by spraying water and by covering another polypropylene vinyl to protect infected soybean plants from direct sunlight.

value: non-inoculated susceptible leaves

tag: inoculum

source_name: S52 inoculated susceptible leaves

value: inoculated susceptible leaves

value: X. axonopodis pv. Glycines


title: ctl_R47 vs. 10D_R47

description: R47 non-inoculated resistant leaves vs. R47 inoculated resistant leaves in the soybean leaves(10D)

source_name: R47 non-inoculated resistant leaves

value: non-inoculated resistant leaves

source_name: R47 inoculated resistant leaves

value: inoculated resistant leaves


title: SM014_MA15_d7_4


title: ctl_S52 vs. 10D_S52

description: S52 non-inoculated susceptible leaves vs. S52 inoculated susceptible leaves in the soybean leaves(10D)


title: SM014_mock_d1_2


title: ctl_S51 vs. 1D_S51

description: S51 non-inoculated susceptible leaves vs. S51 inoculated susceptible leaves in the soybean leaves(1D)

source_name: S51 non-inoculated susceptible leaves

source_name: S51 inoculated susceptible leaves


title: ctl_R49 vs. 10D_R49

description: R49 non-inoculated resistant leaves vs. R49 inoculated resistant leaves in the soybean leaves(10D)

source_name: R49 non-inoculated resistant leaves

source_name: R49 inoculated resistant leaves


title: ctl_S50 vs. 1D_S50

description: S50 non-inoculated susceptible leaves vs. S50 inoculated susceptible leaves in the soybean leaves(1D)

source_name: S50 non-inoculated susceptible leaves

source_name: S50 inoculated susceptible leaves


title: ctl_R46 vs. 10D_R46

description: R46 non-inoculated resistant leaves vs. R46 inoculated resistant leaves in the soybean leaves(10D)

source_name: R46 non-inoculated resistant leaves

source_name: R46 inoculated resistant leaves


title: SM014_mock_d7_2


title: ctl_S50 vs. 10D_S50

description: S50 non-inoculated susceptible leaves vs. S50 inoculated susceptible leaves in the soybean leaves(10D)


title: ctl_S51 vs. 10D_S51

description: S51 non-inoculated susceptible leaves vs. S51 inoculated susceptible leaves in the soybean leaves(10D)


title: ctl_R47 vs. 1D_R47

description: R47 non-inoculated resistant leaves vs. R47 inoculated resistant leaves in the soybean leaves(1D)


title: ctl_R49 vs. 1D_R49

description: R49 non-inoculated resistant leaves vs. R49 inoculated resistant leaves in the soybean leaves(1D)


title: SM014_MA15_d4_3


title: SM014_MA15_d4_1


title: SM014_MA15_d2_1


title: SM014_MA15_d2_4


title: SM014_MA15_d4_2


title: SM014_MA15_d2_2


title: SM014_MA15_d1_1


title: SM012_10^5 MA15_d7_3

value: Lung


title: SM012_10^5 MA15_d7_2


title: SM012_mock_d1_1


title: SM014_MA15_d1_3


title: SM014_MA15_d2_3


title: SM012_mock_d2_3


title: SM014_MA15_d1_4


title: SM012_mock_d2_4


title: SM012_mock_d4_1


title: SM014_MA15_d7_1


title: SM014_MA15_d1_2


title: SM012_mock_d7_3


title: SM012_mock_d4_2


title: SM012_mock_d2_2


title: SM012_mock_d4_3


title: SM012_mock_d7_1


title: SM014_MA15_d7_2


title: SM014_MA15_d4_4


title: SM012_mock_d1_5


title: SM012_10^5 MA15_d7_1


title: SM012_10^5 MA15_d4_2


title: ctl_R46 vs. 1D_R46

description: R46 non-inoculated resistant leaves vs. R46 inoculated resistant leaves in the soybean leaves(1D)


title: RNA_rdp1_1

city: Huddinge

first: Agata

last: Smialowska

address: Halsovagen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: Total RNA from rdp1Δ cells, replicate 1

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR at the Affymetrix Core Facility at Novum (apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix Core Facility at Novum (apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL files were analysed using Affymetrix Tiling Array Software (TAS) software v.1.1, with scaling and quantile normalisation. Strand specific gene expression values were calculated using Podbat (Sadeghi et al, 2011)
wt.bar; dcr1_vs_wt_f_signal.bar; dcr1_vs_wt_r_signal.bar; rdp1_vs_wt_f_signal.bar; rdp1_vs_wt_r_signal.bar
BAR files of strand specific gene expression values; log2 of mutant to wt ratio

organism: Schizosaccharomyces pombe 972h-

source_name: RNA from rdp1Δ S. pombe, actinomycin D

label_protocol: RNA was treated according to the Affymetrix total RNA labeling protocol (www.affymetrix.com).

growth_protocol: Yeast cultures were grown in YES media at 30°C.

extract_protocol: Total RNA was extracted by phenol:chloroform following mechanical cell disruption. RNA was precipitated by ethanol, resuspended in water, and the integrity was assessed using Bioanalizer.

treatment_protocol: Liquid yeast cultures were grown in YES media at 30°C until mid-logarithmic phase.


title: RNA_rdp1_3

description: Total RNA from rdp1Δ cells, replicate 3


title: SM012_10^5 MA15_d1_3


title: SM012_10^5 MA15_d2_3


title: SM012_10^5 MA15_d4_3


title: exp2_Scr

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

description: Gene expression data from MLL-AF9 AML cells with JMJD1C knock down

hyb_protocol: standard Agilent procedure

scan_protocol: standard Agilent procedure

data_processing:
All the data processing including background correction (backgroundCorrect with parameters: method=normexp;offset=50), normalization (normalizeBetweenArrays with parameters: method=quantile), filtering (a probe must be expressed in at least two samples of one group above the 95% quantile value of the negative controls), statistical analysis and plotting was done in R using the 'limma' package.  The annotation for the SurePrint G3 Mouse GE 8x60K microarray was downloaded from https://www.genomics.agilent.com
normexp' background corrected, 'quantile' normalized and log2-transformed signal

source_name: mouse AML (MLL-AF9 transformed bone marrow cells)

label_protocol: standard Agilent procedure

growth_protocol: MLL-AF9 mouse primary AML cells were grown in RPMI 1640 with 20% heat inactivated FBS and 20% X-63 cell conditioned media or IL-3. Cells were transduced with retrovirus using RetroNectin®-bound Virus (RBV) infection method according to manufacturer’s protocol (Takara)  and FACS sorted after 48h.

extract_protocol: RNA was purified using RNeasy Plus RNA kit (Qiagen) and reverse transcribed using TaqMan Reverse Transcription Reagents (Applied Biosystems).

tag: secondary leukemia

value: MLL-AF9 transformed bone marrow cells


title: NCI-H1666 infected and MK2206 treated-rep1

city: Helsinki

first: Denis

last: Kainov

address: Tukholmankatu 8

department: Institute for Molecular Medicine Finland

country: Finland

institute: Helsinki University

description: NCI-H1666 A/Helsinki/P14/2009-infected MK2206-treated

data_processing: The data were processed using Limma and Beadarray R packages from Bioconductor suite. The raw data was exported from GenomeStudio and log2 transformed prior to quantile normalization. We applied IlluminaHumanv3.db annotation data freely available from Bioconductor in order to map Illumina probes to known genes and annotate the probes. To rank the genes in order of evidence for differential expression we computed moderated t-statistics and log-odds of differential expression by Empirical Bayes estimator.

source_name: Human non-small cell lung cancer line NCI-H1666

label_protocol: Illumina TotalPrep 96 RNA Amplification Kit was used to amplify and label the RNA

extract_protocol: RNA was isolated using RNAeasy plus mini kit (Qiagen)

value: non-small cell lung cancer


title: NCI-H1666 MK2206 treated-rep2

description: NCI-H1666 mock-infected MK2206-treated


title: NCI-H1666-rep2

description: NCI-H1666 mock-infected non-treated


title: SM012_10^5 MA15_d2_5


title: SM012_10^5 MA15_d4_1


title: SM012_10^5 MA15_d2_1


title: RNA_rdp1_2

description: Total RNA from rdp1Δ cells, replicate 2


title: NCI-H1666 infected-rep1

description: NCI-H1666 A/Helsinki/P14/2009-infected non-treated


title: NCI-H1666 MK2206 treated-rep1

description: NCI-H1666 mock-infected MK2206-treated


title: NCI-H1666 infected-rep2


title: NCI-H1666 infected and MK2206 treated-rep2


title: SM014_nsp16_d7_4


title: exp3_Scr

value: mouse AML (MLL-AF9 transformed bone marrow cells)


title: SM012_10^5 MA15_d1_2


title: SM012_mock_d1_4


title: SM012_10^5 MA15_d1_4


title: NCI-H1666-rep1

description: NCI-H1666 mock-infected non-treated


title: RNA_dcr1_2

description: Total RNA from dcr1Δ cells, replicate 2

source_name: RNA from dcr1Δ S. pombe, actinomycin D


title: SM014_nsp16_d2_3


title: RNA_dcr1_3

description: Total RNA from dcr1Δ cells, replicate 3


title: exp3_868

value: JMJD1C depletion


title: RNA_wt_3

description: Total RNA from WT cells, replicate 3

source_name: RNA from wt S. pombe, actinomycin D

value: wildtype


title: RNA_dcr1_1

description: Total RNA from dcr1Δ cells, replicate 1


title: RNA_wt_1

description: Total RNA from WT cells, replicate 1


title: RNA_wt_2

description: Total RNA from WT cells, replicate 2


title: exp1_Scr


title: SM012_10^5 dORF6_d7_2


title: exp2_868


title: SM012_10^5 dORF6_d2_3


title: exp1_868


title: SM012_10^5 dORF6_d4_2


title: SM012_10^5 dORF6_d7_3


title: SM012_10^5 dORF6_d2_4


title: strain 45957

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: strain comparison

hyb_protocol: Labelled gDNA was re-suspended in the universal hybridization buffer of the Pronto kit (Promega, United States), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, slides were washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices©, USA).

data_processing: Raw median intensity data were imported into R version 2.13.1 for statistical analysis using the LIMMA package version 2.15.15 as available from BioConductor. Raw data were backgroundcorrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. Analysis of previously characterized C. metallidurans CH34 derivatives (loss of either pMOL28 or pMOL30, IS1071-mediated loss of growth on CO2 and H2) allowed us to validate and optimize the trade-off between the number of false-positives and false-negatives. In the final analyses, a cut-off of 20-fold change in hybridization intensity compared to the background was used.

organism: Cupriavidus metallidurans CH34

source_name: strain CH34

label_protocol: gDNA was labeled with the BioPrime® Array CGH Genomic Labeling System (Invitrogen, Merelbeke, Belgium).

growth_protocol: C. metallidurans strains were routinely cultured at 30°C in Tris salt mineral medium (MM284) supplemented with 0.2% (wt/vol) gluconate.

extract_protocol: Genomic DNA (gDNA) was prepared using the QIAamp DNA mini kit (Qiagen, Venlo, The Netherlands) and 4 µg of gDNA was fragmented to 50 to 150 bp by partial digestion with Sau3AI (Fermentas, St. Leon-Rot, Germany).

treatment_protocol: No treatment was applied. Only extraction of genomic DNA.

tag: strain

organism: Cupriavidus metallidurans

source_name: strain 45957


title: C57Bl/6J PN0 Male 6, cortex and hippocampus

city: Los Angeles

first: Christopher

last: Armoskus

department: Biological Sciences

institute: California State University - Long Beach

description: male 6

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were normalized by quantile normalization and log2 transformed

source_name: C57Bl/6J PN0 Male

label_protocol: Biotin-labeled

growth_protocol: Standard chow, 12:12 light:dark cycle.

extract_protocol: Qiagen RNeasy® Lipid Tissue Mini Kit protocol

treatment_protocol: No treatment

tag: Sex

value: male

value: cortex and hippocampus

tag: genetic background


title: C57Bl/6J PN0 Male 5, cortex and hippocampus

description: male 5

tag: age


title: SM012_10^5 dORF6_d1_3

tag: tissue


title: SM012_10^5 dORF6_d1_5


title: SM012_10^5 dORF6_d1_1


title: C57Bl/6J PN0 Male 7, cortex and hippocampus

description: male 7


title: INTOV11 siCHKA a

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: Ovarian carcinoma cell line transiently transfected with specified siRNA pool

data_processing: Primary data were extracted using BeadArray. Data were further processed and quantile normalised using BeadStudio software

source_name: INTOV11 cell line, transfected with CHKA-specific siRNA

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.

treatment_protocol: cells were transiently transfected for 7h with indicated siRNApool and then relapsed for 72h before RNA extraction and gene expression analysis

tag: knockdown

value: CHKA


title: SM012_10^5 dORF6_d4_3


title: SM012_10^5 dORF6_d2_1


title: INTOV11 ctrl b

source_name: INTOV11  cell line, transfected with unrelated siRNA

value: control


title: strain NA4

description: strain comparison

source_name: strain NA4


title: strain 43015

description: strain comparison

source_name: strain 43015


title: SM012_10^5 dORF6_d7_1


title: SM012_10^5 dORF6_d4_1


title: C57Bl/6J PN0 Male 8, cortex and hippocampus

description: male 8


title: C57Bl/6J PN0 Male 9, cortex and hippocampus

description: male 9


title: INTOV11 siCHKA c


title: INTOV11 siCHKA b


title: SKOV3 siCHKA c

source_name: SKOV3  cell line, transfected with CHKA-specific siRNA


title: INTOV11 ctrl c


title: INTOV11 ctrl a

source_name: INTOV11 cell line, transfected with unrelated siRNA


title: strain NA2

description: strain comparison

source_name: strain NA2


title: strain SV661

description: strain comparison

source_name: strain SV661


title: strain NE12

description: strain comparison

source_name: strain NE12


title: strain NA1

description: strain comparison

source_name: strain NA1


title: C57Bl/6J PN0 Male 3, cortex and hippocampus

description: male 3


title: strain 31A

description: strain comparison

source_name: strain 31A


title: C57Bl/6J PN0 Male 4, cortex and hippocampus

description: male 4


title: strain AS39

description: strain comparison

source_name: strain AS39


title: strain AS167

description: strain comparison

source_name: strain AS167


title: strain AS168

description: strain comparison

source_name: strain AS168


title: strain CH42

description: strain comparison

source_name: strain CH34

source_name: strain CH42


title: strain KT21

description: strain comparison

source_name: strain KT21


title: Hep3B cells, biological rep2

city: Guangzhou

first: Yuan

last: Lin

state: Guangdong

address: No.74, Zhongshan 2nd Rd.

institute: Sun Yat-sen University

description:
Gene expression data from Hep3B cells.
Hep3B_2

hyb_protocol: The bio-tagged cRNA were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix. The fragmented cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 Array. Hybridization was performed at 45℃ with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4.

source_name: Hep3B cells, normally cultured

label_protocol: An aliquot of 2 µg of total RNA was used to synthesize double-stranded cDNA, then produce biotin-tagged cRNA using the MessageAmpTM II aRNA Amplification Kit

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions.

tag: resistance of cells against alphavirus

value: susceptible


title: Control Vs db-cAMP treated cells Replicate 2

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

description: Biological replicate 2 of 3.

hyb_protocol: Cy labeled cDNAs and hybridization buffer (10X SSC, 50% Formamide and 0.2% SDS containing 40µg PolyA, 8µg yeast tRNA and 10µg human COT-1 DNA) were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequentially with buffers containing decreasing concentrations of SSC and SDS.

scan_protocol: Scanned on a GenePix 4000A microarray scanner (Axon Instruments). Images were quantified using GenePix Pro 4.0 software (Axon Instruments).

data_processing: Normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Mycobacterium tuberculosis

source_name: Total RNA from butyric acid treated cells

label_protocol: 5 µg of total RNA were primed with 6 µg of random hexamer primer at 70°C for 10 min, then reversed transcribed at 37°C for 1 h in the presence of 1µl BD PowerScript™ Reverse Transcriptase (BD Biosciences), and 1x dNTP mix (Atlas Glass Fluorescent Labeling Kit, BD Biosciences), followed by coupling with monoreactive Cy dyes (GE Healthcare) according to manufacturer's instructions.

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

treatment_protocol: Cells treated with 20mM butyric acid for 2hr at 37°C

value: 20mM butyric acid for 2hr at 37°C

source_name: Total RNA from db-cAMP treated cells

treatment_protocol: Cells treated with 20mM db-cAMP for 2hr at 37°C

value: 20mM db-cAMP for 2hr at 37°C


title: Control Vs db-cAMP treated cells Replicate 3

description: Biological replicate 3 of 3.


title: C57Bl/6J PN0 Female 2, cortex and hippocampus

description: female 2

hyb_protocol: Standard Illumina hybridization protocol

source_name: C57Bl/6J PN0 Female

value: female


title: C57Bl/6J PN0 Male 2, cortex and hippocampus

description: male 2

source_name: C57Bl/6J PN0 Male


title: L-02 cells, biological rep1

description:
Gene expression data from L-02 cells.
L-02_1

source_name: L-02 cells, normally cultured

value: resistant


title: C57Bl/6J PN0 Female 8, cortex and hippocampus

description: female 8


title: C57Bl/6J PN0 Female 4, cortex and hippocampus

description: female 4


title: C57Bl/6J PN0 Male 1, cortex and hippocampus

description: male 1


title: C57Bl/6J PN0 Female 7, cortex and hippocampus

description: female 7


title: SKOV3 ctrl c

scan_protocol: Standard Illumina scanning protocol

source_name: SKOV3  cell line, unrelated siRNA


title: Hep3B cells, biological rep1

description:
Gene expression data from Hep3B cells.
Hep3B_1


title: C57Bl/6J PN0 Female 6, cortex and hippocampus

description: female 6


title: C57Bl/6J PN0 Female 5, cortex and hippocampus

description: female 5


title: L-02 cells, biological rep2

description:
Gene expression data from L-02 cells.
L-02_2


title: SKOV3 siCHKA a

source_name: SKOV3  cell line, transfected with CHKA-specific siRNA


title: C57Bl/6J PN0 Female 3, cortex and hippocampus

description: female 3


title: SKOV3 siCHKA b


title: SKOV3 ctrl b

source_name: SKOV3 cell line, unrelated siRNA


title: SKOV3 ctrl a

source_name: SKOV3 cell line, transfected with unrelated siRNA


title: C57Bl/6J PN0 Female 1, cortex and hippocampus

description: female 1


title: Control Vs db-cAMP treated cells Replicate 1

description: Biological replicate 1 of 3.


title: strain KT02

description: strain comparison

source_name: strain KT02


title: strain KT01

description: strain comparison

source_name: strain KT01


title: NIL(hwi1)-15d-1 sample 19

status: Public on Jan 22 2014

city: Yangzhou

first: Chen

last: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

institute: Yangzhou University

description: Gene expression data from basal nodes at 15d

hyb_protocol: standard Affymetrix procedures.

scan_protocol: GeneChips were scanned using the Gene array Scanner3000.

organism: Oryza sativa

source_name: NIL(hwi1) 15 days after shift into 30 °C ondition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Plants were incubated in Yoshida’s culture solution in a growth chamber set with a 10 h dark/14 h light cycle at 50% humidity.

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

treatment_protocol: At the first 20 days after gemination, NIL(hwi1) and NIL(Hwi1) were grown at 20 °C. Then plants were transferred into 30 °C condition.

value: basal nodes

tag: genotype

tag: time


title: NIL(Hwi1)-15d-2 sample 23

source_name: NIL(Hwi1) 15 days after shift into 30 °C ondition


title: prostate of AR3 transgenic mouse 2

city: Baltimore

first: Hegang

state: MD

address: 660 West Redwood Street

institute: University of Maryland School of Medicine

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 200?l of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using dChip software. The probe intensities were normalized by invariant set nonlinear normalization method and gene level expression were calculated by model based expression index from dChip.

source_name: prostate from AR3 transgenic mouse 2

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

growth_protocol: Prostates from 4-week-old AR3Tg or wild-type mice

extract_protocol: Prostates were dissected from AR3Tg or wild-type mice. Total RNA including miRNAs was isolated from cells or tissues by using RNeasy mini kit (QIAGEN), and then RNA was treated with RQ1 RNase-Free DNase (Promega) according to the manufacturer’s instructions.

value: prostate

value: 4 weeks

value: AR3 transgenic


title: NIL(hwi1)-7d-3 sample 15

description: Gene expression data from basal nodes at 7d

source_name: NIL(hwi1) 7 days after shift into 30 °C ondition


title: NIL(Hwi1)-3d-1 sample 10

description: Gene expression data from basal nodes at 3d

source_name: NIL(Hwi1) 3 days after shift into 30 °C ondition


title: NIL(hwi1)-15d-3 sample 21


title: NIL(Hwi1)-7d-3 sample 18

source_name: NIL(Hwi1) 7 days after shift into 30 °C ondition


title: NIL(hwi1)-3d-1 sample 7

source_name: NIL(hwi1) 3 days after shift into 30 °C ondition


title: NIL(Hwi1)-15d-1 sample 22


title: prostate of AR3 transgenic mouse 1

source_name: prostate from AR3 transgenic mouse 1


title: NIL(Hwi1)-7d-1 sample 16


title: prostate of AR3 transgenic mouse 3

source_name: prostate from AR3 transgenic mouse 3


title: NIL(hwi1)-7d-2 sample 14


title: NIL(Hwi1)-0d-1 sample 4

description: Gene expression data from basal nodes at 0d

source_name: 20-day-old 20 °C-grown NIL(Hwi1) plants


title: NIL(Hwi1)-15d-3 sample 24


title: prostate of wild-type mouse 3

source_name: prostate from wild-type mouse 3

value: wild-type


title: NIL(hwi1)-0d-2 sample 2

source_name: 20-day-old 20 °C-grown NIL(hwi1) plants


title: NIL(hwi1)-7d-1 sample 13


title: NIL(Hwi1)-3d-2 sample 11


title: prostate of wild-type mouse 2

source_name: prostate from wild-type mouse 2


title: NIL(hwi1)-0d-1 sample 1


title: NIL(Hwi1)-7d-2 sample 17


title: NIL(Hwi1)-0d-2 sample 5


title: NIL(Hwi1)-3d-3 sample 12


title: NIL(hwi1)-3d-2 sample 8


title: NIL(hwi1)-0d-3 sample 3


title: NIL(hwi1)-15d-2 sample 20


title: NIL(hwi1)-3d-3 sample 9


title: NIL(Hwi1)-0d-3 sample 6


title: prostate of wild-type mouse 1

source_name: prostate from wild-type mouse 1


title: NK_IL15_invivo_CD11b_ko2

city: Rehovot

first: Joseph

last: Lotem

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing protocol is FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G.

data_processing: Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization.

source_name: spleen

label_protocol: cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit.

growth_protocol: Mouse splenic NK cells freshly isolated from mice injected twice, 2 days apart, with IL15/Ra complexes.

extract_protocol: Total RNA was isolated using the RNeasy micro kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: NK cells were enriched by negative selection using NK cell isolation kit (R&D) and FACS sorted into three NKp46+ subpopulations including immature CD27+CD11b- (CD27), mature CD27+CD11b+ (DP) and mature CD27-CD11b+ (CD11b) NK cells.

tag: cell type

value: CD11b NK cells

value: 6 weeks

value: Runx3 -/-

value: male or female

value: ICR


title: NK_IL15_invivo_DP_ko3

value: DP NK cells


title: NK_IL15_invivo_CD11b_ko1


title: NK_IL15_invivo_DP_wt1

value: Runx3 +/+


title: NK_IL15_invivo_DP_ko2


title: NK_IL15_invivo_CD27_ko3

value: CD27 NK cells


title: NK_IL15_invivo_CD11b_wt2


title: NK_IL15_invivo_CD27_wt2


title: NK_IL15_invivo_CD11b_wt3


title: NK_IL15_invivo_DP_ko1


title: NK_IL15_invivo_CD27_ko2


title: iMPC-Heps in vitro, biological rep1

city: San Francisco

first: Saiyong

last: Zhu

address: 1650 Owens Street, GICD, 4P

institute: Gladstone Institute

description: Gene expression data.

hyb_protocol: The labeled cDNA was hybridized to Human GeneChipR Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: The signal intensity fluorescent images produced during Affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner.

data_processing:
The data were converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).
RMA normalized values reported on a log2 scale. (Average normalized expression is typically ~7.0.) Only average values log2 intensity greater than 3.0 were included.

source_name: human iMPC-Heps in vitro

label_protocol: The NuGEN Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation and biotin-labeling.

growth_protocol: In vitro iMPC-Heps and iPSC-Heps underwent complete hepatic differentiation protocol at 37°C. In vitro aHeps were freshly isolated. In vivo samples were dissected around 9 months after transplantation.

extract_protocol: RNA was extracted and purified using the Arcturus Pico Pure RNA Isolation Kit (AB Biosystems).

treatment_protocol: All in vitro samples were washed with Phosphate Buffered Saline and treated with Arcturus Extraction Buffer for RNA extraction. All in vivo samples were isolated from Laser Capture Microscopy (Zeiss) dissectants and were also treated with Arcturus Extraction Buffer for RNA extraction.

value: hepatocyte-like cells in culture


title: NK_IL15_invivo_CD27_wt1


title: aHeps in vivo, biological rep3

description: Gene expression data.

source_name: human adult hepatocytes in vivo

value: hepatocytes from repopulated mouse livers by aheps


title: aHeps in vivo, biological rep1

description: Gene expression data.


title: NK_IL15_invivo_DP_wt3


title: iMPC-Heps in vivo, biological rep1

description: Gene expression data.

source_name: iMPC-Heps in vivo

value: hepatocytes from mouse livers repopulated by iMPC-heps


title: iPSC-Heps in vitro, biological rep1

description: Gene expression data.

source_name: human iPSC-Heps in vitro


title: aHeps in vitro, biological rep2

description: Gene expression data.

source_name: human adult hepatocytes freshly isolated/in vitro

value: hepatocytes in culture


title: iMPC-Heps in vitro, biological rep2

description: Gene expression data.


title: NK_IL15_invivo_CD11b_wt1


title: aHeps in vitro, biological rep1

description: Gene expression data.


title: NK_IL15_invivo_DP_wt2


title: iMPC-Heps in vivo, biological rep2

description: Gene expression data.


title: NK_IL15_invivo_CD11b_ko3


title: iPSC-Heps in vitro, biological rep2

description: Gene expression data.


title: NK_IL15_invivo_CD27_wt3


title: NK_IL15_invivo_CD27_ko1


title: aHeps in vivo, biological rep2

description: Gene expression data.


title: Non tumor NT_BS_241

city: Modena

first: Erica

last: Villa

address: Via del Pozzo 71

institute: University of Modena and Reggio Emilia

description: Gene expression of non tumor liver tissue

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (44K, Design ID 014850) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software was used to read out and process the microarray image files.

source_name: Biopsy of cirrhotic non-malignant  tissue

label_protocol: Cyanine-3 (Cy3) Cy3-labeled cRNA was prepared from 0.5 ug RNA using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) or  the Agilent Quick Amp Labeling Kit (Agilent Technologies)  following the manufacturer’s protocol.  Yields of cRNA and the dye-incorporation rate were  measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Total RNA was isolated from non tumor (NT) and tumor (T) liver tissues using Trizol (Invitrogen Corp., Carlsbad, California, USA) protocol. Quality and quantity of the RNA samples was checked on an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and ND-1000 Spectrophotometer (NanoDrop Technologies), respectively.

tag: tissue type

value: Liver

tag: gender

value: male

tag: amplification and labeling kit

value: Agilent Quick Amp Labeling Kit

tag: scanner update

tag: feature extraction software update


title: Non tumor NT_BY_255

value: Biopsy of cirrhotic non-malignant  tissue

value: female


title: Non tumor NT_BX_253


title: Non tumor NT_BU_247


title: Non tumor NT_BW_251


title: Non tumor NT_BR_239


title: Non tumor NT_BP_226


title: Non tumor NT_BT_243


title: Non tumor NT_BH_206


title: Non tumor NT_BV_249


title: Non tumor NT_BN_222


title: Non tumor NT_BM_208


title: Non tumor NT_BL_218


title: Non tumor NT_BO_224


title: Non tumor NT_BJ_214


title: Non tumor NT_BE_192


title: Non tumor NT_BF_198


title: Non tumor NT_BG_202


title: Subject C058 [mRNA]

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: normalized mRNA expression data from cord blood (log2 transformed)

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix Human Gene 2.0 ST Array

scan_protocol: Microarrays were scanned using Affymetrix Microarray Scanner

data_processing: Data were normalized by robust multi-chip averaging using Partek® Genomics SuiteTM software (version 6.5)

source_name: Cord blood from newborn, subject C058

label_protocol: Labeled cRNA were prepared with biotin according to the standard Affymetrix protocol

extract_protocol: This cohort includes residents from Gómez Palacio, located in the state of Durango in the Lagunera region of Northern Mexico. A total of 200 pregnant women residing in Gómez Palacio, State of Durango, Mexico, were recruited at the General Hospital of Gómez Palacio to participate in the BEAR prospective pregnancy cohort. The present study focuses on mRNA expression profiles and utilizes 38 samples obtained from mother-newborn pairs selected from the larger cohort (n=200). Cord blood samples were collected from the newborns immediately after infant delivery. Blood samples were collected using PreAnalytix PaxGene RNA tubes and extracted using the PAXgene RNA Kit, per standard protocol (Qiagen, Valencia, CA). Isolated RNA used for microarray analysis were amplified and labeled using the NuGEN Ovation Pico WTA System V2 and Encore Biotin Module, respectively (NuGEN, San Carlos, CA). RNA isolated from 38 cord blood samples were labeled and hybridized to the Human Gene 2.0 ST Array

tag: mother's age (years)

tag: smoking status

value: Nonsmoker

tag: gestational age (weeks)

tag: newborn weight (grams)

tag: newborn sex

value: Cord blood from newborn

tag: total urinary arsenic (specific gravity adjusted) (ug/l)

tag: arsenic in drinking water (ug/l)


title: Subject C074 [mRNA]

source_name: Cord blood from newborn, subject C074

tag: tissue


title: Non tumor NT_BK_216


title: Non tumor NT_BI_210


title: Subject C071 [mRNA]

source_name: Cord blood from newborn, subject C071


title: Non tumor NT_BC_184


title: Non tumor NT_BB_182


title: Non tumor NT_BA_180


title: Non tumor NT_BD_190


title: Non tumor NT_BQ_232


title: Subject C026 [mRNA]

source_name: Cord blood from newborn, subject C026


title: Subject C003 [mRNA]

source_name: Cord blood from newborn, subject C003


title: Non tumor NT_AZ_178


title: Subject C024 [mRNA]

source_name: Cord blood from newborn, subject C024


title: Subject C120 [mRNA]

source_name: Cord blood from newborn, subject C120


title: Subject C133 [mRNA]

source_name: Cord blood from newborn, subject C133


title: Non tumor NT_AY_172


title: Non tumor NT_AV_166


title: Subject C116 [mRNA]

source_name: Cord blood from newborn, subject C116


title: Subject C059 [mRNA]

source_name: Cord blood from newborn, subject C059


title: Non tumor NT_AS_152


title: Subject C007 [mRNA]

source_name: Cord blood from newborn, subject C007


title: Non tumor NT_AW_168


title: Subject C062 [mRNA]

source_name: Cord blood from newborn, subject C062


title: Subject C067 [mRNA]

source_name: Cord blood from newborn, subject C067


title: Subject C117 [mRNA]

source_name: Cord blood from newborn, subject C117


title: Subject C104 [mRNA]

source_name: Cord blood from newborn, subject C104


title: Non tumor NT_AR_151

value: Agilent Low RNA Input Linear Amp Kit


title: Non tumor NT_AP_145


title: Non tumor NT_AQ_149


title: Non tumor NT_AN_130


title: Non tumor NT_AO_137


title: Subject C079 [mRNA]

source_name: Cord blood from newborn, subject C079


title: Subject C134 [mRNA]

source_name: Cord blood from newborn, subject C134


title: Non tumor NT_AU_162

source_name: Biopsy of cirrhotic non-malignant  tissue


title: Non tumor NT_AT_158


title: Subject C129 [mRNA]

source_name: Cord blood from newborn, subject C129


title: Non tumor NT_AX_170


title: Subject C132 [mRNA]

source_name: Cord blood from newborn, subject C132


title: Non tumor_rep1 NT_AL_126r


title: Subject C124 [mRNA]

source_name: Cord blood from newborn, subject C124


title: Non tumor NT_AK_116


title: Non tumor NT_AL_126


title: Subject C111 [mRNA]

source_name: Cord blood from newborn, subject C111


title: Subject C123 [mRNA]

source_name: Cord blood from newborn, subject C123


title: Non tumor NT_AJ_114


title: Subject C139 [mRNA]

source_name: Cord blood from newborn, subject C139


title: Non tumor NT_AI_112


title: Subject C151 [mRNA]

source_name: Cord blood from newborn, subject C151


title: Subject C085 [mRNA]

source_name: Cord blood from newborn, subject C085


title: Non tumor NT_AM_128


title: Non tumor NT_AF_103


title: Non tumor NT_AC_093


title: Subject C029 [mRNA]

source_name: Cord blood from newborn, subject C029


title: Non tumor NT_AH_108


title: Non tumor NT_AE_097


title: Subject C194 [mRNA]

source_name: Cord blood from newborn, subject C194


title: Non tumor NT_AG_106


title: Subject C086 [mRNA]

source_name: Cord blood from newborn, subject C086

value: Smoker


title: Subject C027 [mRNA]

source_name: Cord blood from newborn, subject C027


title: Non tumor NT_AB_090


title: Subject C113 [mRNA]

source_name: Cord blood from newborn, subject C113


title: Subject C075 [mRNA]

source_name: Cord blood from newborn, subject C075


title: Non tumor NT_AD_095


title: Subject C081 [mRNA]

source_name: Cord blood from newborn, subject C081


title: Non tumor_rep1 NT_AG_106r


title: Non tumor NT_Z_079


title: Non tumor NT_AA_088


title: Subject C094 [mRNA]

source_name: Cord blood from newborn, subject C094


title: Subject C092 [mRNA]

source_name: Cord blood from newborn, subject C092


title: Subject C115 [mRNA]

source_name: Cord blood from newborn, subject C115


title: RA-8, Naive, Treg, MTX Ad

city: Groningen

first: Bart-Jan

last: Kroesen

address: Hanzeplein 1

department: Department of Laboratory Medicine

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

description: SAMPLE 32

hyb_protocol: Hybridization was performed following the Agilent protocols

scan_protocol: Slides were scanned immediately after washing on the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol, using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Array images were analyzed using Agilent feature extraction software (v10.7.3.1) and GeneSpring GX, version 12.5 (Agilent). TXT files for each array were preprocessed using default settings, as follows: threshold raw signals to 1.0, followed by 95 percentile shift normalization.  miRNAs detected or compromised, as assigned by the Agilent Feature Extraction software, in at least 16 out of 32 samples (50%), and miRNAs with an expression value above -3.5 in at least 24 out of the samples (75%) were used in the subsequent analyses. Control probes were excluded from the analysis.

source_name: RA_Naive_Treg_MTX Ad

label_protocol: Approximately 100 ng of total RNA was Cy3 labeled using miRNA Complete Labeling and Hyb Kit (Agilent) following the manufacturer's protocols

growth_protocol: Cells were not cultured

extract_protocol: Total cellular RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands), following manufacturer’s instruction, with additional chloroform extraction, and triple washing step with RPE buffer. RNA concentrations were quantified using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and RNA quality was assessed using the Experion HighSens RNA analysis Kit (Bio-Rad, Hercules, California, USA). RNA with the RNA quality Indicator value (RQI) above 8.8 was used for downstream applications.

treatment_protocol: Cells were not treated

tag: donor

value: RA patient (RA-8)

tag: treatment

value: methotrexate + anti-TNF-α

tag: geneder

tag: age (yrs)

value: peripheral blood

value: CD4+ T lymphocyte (CD3+CD8-)

tag: phenotype

value: naive (CD45RO-)

tag: subset

value: T regulatory (CD25+)


title: RA-8, Memory, Treg, MTX Ad

description: SAMPLE 30

source_name: RA_Memory_Treg_MTX Ad

tag: cell type

value: memory (CD45RO+)


title: RA-8, Naive, Tconv, MTX Ad

description: SAMPLE 31

source_name: RA_Naive_Tconv_MTX Ad

value: T conventional (CD25-)


title: RA-8, Memory, Tconv, MTX Ad

description: SAMPLE 29

source_name: RA_Memory_Tconv_MTX Ad


title: RA-28, Memory, Treg, MTX Ad

description: SAMPLE 26

value: RA patient (RA-28)


title: RA-28, Naive, Treg, MTX Ad

description: SAMPLE 28


title: RA-27, Naive, Treg, New RA

description: SAMPLE 24

source_name: RA_Naive_Treg_New RA

value: RA patient (RA-27)

value: before treatment

value: male


title: RA-28, Naive, Tconv, MTX Ad

description: SAMPLE 27

value: female


title: RA-28, Memory, Tconv, MTX Ad

description: SAMPLE 25


title: Non tumor NT_W_068

source_name: Biopsy of cirrhotic non-malignant  tissue

tag: tissue type

value: Liver

tag: gender

tag: amplification and labeling kit

tag: scanner update


title: RA-27, Naive, Tconv, New RA

description: SAMPLE 23

source_name: RA_Naive_Tconv_New RA


title: Subject C221 [mRNA]

source_name: Cord blood from newborn, subject C221

tag: mother's age (years)

tag: smoking status

value: Nonsmoker

tag: gestational age (weeks)

value: Cord blood from newborn


title: Subject C095 [mRNA]

source_name: Cord blood from newborn, subject C095

tag: newborn weight (grams)

tag: newborn sex

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: Non tumor NT_V_064

value: Biopsy of cirrhotic non-malignant  tissue

tag: tissue

value: Agilent Low RNA Input Linear Amp Kit

tag: feature extraction software update


title: Non tumor NT_Y_077


title: Non tumor NT_X_072


title: Non tumor NT_R_054


title: Non tumor NT_U_044


title: Non tumor NT_M_034


title: Non tumor NT_T_058


title: Non tumor NT_N_040


title: Non tumor NT_P_048


title: Non tumor NT_Q_052


title: Non tumor NT_O_046


title: RA-27, Memory, Treg, New RA

description: SAMPLE 22

source_name: RA_Memory_Treg_New RA

tag: donor

tag: treatment

tag: geneder


title: Non tumor NT_L_028


title: Non tumor NT_S_056


title: Subject C128 [mRNA]

source_name: Cord blood from newborn, subject C128

tag: arsenic in drinking water (ug/l)


title: Non tumor_rep1 NT_O_046r

value: Agilent Quick Amp Labeling Kit


title: RA-22, Naive, Treg, 3 MTX

description: SAMPLE 20

source_name: RA_Naive_Treg_3 MTX

value: RA patient (RA-22)

value: methotrexate treatment

tag: age (yrs)

value: peripheral blood

tag: cell type

tag: phenotype

tag: subset


title: RA-22, Memory, Treg, 3 MTX

description: SAMPLE 18

source_name: RA_Memory_Treg_3 MTX

value: CD4+ T lymphocyte (CD3+CD8-)

value: T regulatory (CD25+)


title: RA-22, Naive, Tconv, 3 MTX

description: SAMPLE 19

source_name: RA_Naive_Tconv_3 MTX

value: naive (CD45RO-)

value: T conventional (CD25-)


title: RA-15, Naive, Treg, 3 MTX

description: SAMPLE 16

value: RA patient (RA-15)


title: RA-15, Naive, Tconv, 3 MTX

description: SAMPLE 15


title: RA-27, Memory, Tconv, New RA

description: SAMPLE 21

source_name: RA_Memory_Tconv_New RA

value: RA patient (RA-27)

value: before treatment

value: memory (CD45RO+)


title: RA-15, Memory, Tconv, 3 MTX

description: SAMPLE 13

source_name: RA_Memory_Tconv_3 MTX

value: male


title: RA-10, Memory, Treg, New RA

description: SAMPLE 10

value: RA patient (RA-10)


title: RA-10, Naive, Tconv, New RA

description: SAMPLE 11


title: RA-10, Naive, Treg, New RA

description: SAMPLE 12


title: RA-22, Memory, Tconv, 3 MTX

description: SAMPLE 17

value: female


title: Non tumor NT_G_018

tag: tissue type

value: Biopsy of cirrhotic non-malignant  tissue

value: Liver

tag: gender

tag: amplification and labeling kit

tag: scanner update


title: Non tumor NT_E_010

value: Agilent Low RNA Input Linear Amp Kit


title: Non tumor NT_I_022


title: Non tumor NT_K_026


title: Non tumor NT_D_008


title: Non tumor NT_H_020


title: RA-10, Memory, Tconv, New RA

description: SAMPLE 9


title: Non tumor NT_J_024


title: RA-15, Memory, Treg, 3 MTX

description: SAMPLE 14


title: Non tumor NT_B_004


title: Non tumor NT_C_006


title: Non tumor NT_A_002


title: HC-6b, Naive, Treg, Healthy control

description: SAMPLE 8

source_name: HC_Naive_Treg_Healthy control

value: healthy control (HC-6b)


title: HC-6b, Naive, Tconv, Healthy control

description: SAMPLE 7

source_name: HC_Naive_Tconv_Healthy control


title: Tumor T_BX_254

description: Gene expression of tumor liver tissue

source_name: Biopsy of tumor tissue

value: Biopsy of tumor tissue

tag: doubling time (days)

tag: survival time(months)

value: Agilent Quick Amp Labeling Kit


title: HC-6b, Memory, Tconv, Healthy control

description: SAMPLE 5

source_name: HC_Memory_Tconv_Healthy control

value: peripheral blood

value: CD4+ T lymphocyte (CD3+CD8-)


title: Tumor T_BV_250

description: Gene expression of tumor liver tissue


title: Tumor T_BW_252

description: Gene expression of tumor liver tissue


title: HC-6b, Memory, Treg, Healthy control

description: SAMPLE 6

source_name: HC_Memory_Treg_Healthy control

value: T regulatory (CD25+)


title: Non tumor NT_F_012


title: Tumor T_BT_244

description: Gene expression of tumor liver tissue


title: Tumor T_BU_248

description: Gene expression of tumor liver tissue


title: HC-2, Naive, Treg, Healthy control

description: SAMPLE 4

value: healthy control (HC-2)

value: naive (CD45RO-)


title: Tumor T_BS_242

description: Gene expression of tumor liver tissue


title: HC-2, Memory, Treg, Healthy control

description: SAMPLE 2


title: HC-2, Naive, Tconv, Healthy control

description: SAMPLE 3

value: T conventional (CD25-)


title: HC-2, Memory, Tconv, Healthy control

description: SAMPLE 1


title: Tumor T_BP_227

description: Gene expression of tumor liver tissue


title: Tumor T_BY_256

description: Gene expression of tumor liver tissue


title: Tumor T_BR_240

description: Gene expression of tumor liver tissue


title: Tumor T_BQ_233

description: Gene expression of tumor liver tissue


title: Tumor T_BN_223

description: Gene expression of tumor liver tissue


title: Tumor T_BL_238

description: Gene expression of tumor liver tissue


title: Tumor T_BK_217

description: Gene expression of tumor liver tissue


title: Tumor T_BO_225

description: Gene expression of tumor liver tissue


title: Tumor T_BJ_215

description: Gene expression of tumor liver tissue


title: Tumor T_BI_211

description: Gene expression of tumor liver tissue


title: Tumor T_BH_207

description: Gene expression of tumor liver tissue


title: Tumor T_BM_221

description: Gene expression of tumor liver tissue


title: Tumor T_BF_199

description: Gene expression of tumor liver tissue


title: DMSO vehicle biological replicate 6

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

institute: LACDR

description: Gene expression data of Primary mouse hepatocytes isolated from 8-10 weeks old male C57BL/6 mice

hyb_protocol: hybridized to the Affymetrix Mouse Genome 430 2.0 GeneChip arrays, according to the manufacturer’s instructions.

scan_protocol: After hybridization the array chips were washed and stained with a Genechip Fluidics Station 450 and scanned using the Affymetrix gene chip scanner 3000.

data_processing: Affymetrix CEL files were each checked on quality, including RNA degradation control, correlation and clustering. All quality checks were within acceptable limits, according to Affymetrix standards. After quality control the files were normalized with the Multichip Average (RMA) procedure (Irizarry et al., 2003), using the custom chip description files (CDFs) as described by de Leeuw et al. (2008). Of the hybrid probe-set definitions included in the custom annotation, only the 16,331 probe sets selected according to Dai et al. (2005) and the 4,648 Affymetrix probe sets corresponding to an Entrez Gene ID were used for further analysis, giving a total of 20,979 probe sets. Principal Component Analysis (PCA) was used to rule out effects of the experimental variables. For detecting significantly regulated genes, the microarray analysis of variance (MAANOVA) package in R was used (R version 2.9.2, www.r-project.org). For the analyses on significantly regulated genes per compound between treated and control samples, an F1-test was used. Gene-specific P-values were corrected with a Benjamini- Hochberg false discovery rate (FDR) with a cut-off at 0.05 (Benjamini and Hochberg, 1995).

source_name: 10 weeks old male C57BL/6

label_protocol: Labeled RNA was prepared using the Affymetrix gene chip 3’IVT express kit

growth_protocol: Primary mouse hepatocytes were isolated from 8-10 weeks old male C57BL/6 mice by a modified two-step collagenase perfusion technique (collagenase type IV, Sigma-Aldrich, Zwijndrecht, The Netherlands), as described by van Kesteren et al. (2011). In short, hepatocytes suspensions with at least 80% viability were seeded onto plates coated with collagen gel and after attachment overlayed with a second layer of collagen gel, to form a sandwich configuration. Cells were kept in serum-free medium and the culture medium was changed daily until exposures were performed.

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and purified using a RNeasy mini kit (Qiagen), both according to the manufacturer’s protocol.

treatment_protocol: Forty-six hours after isolation, hepatocytes were exposed to either 300 µM DCF or the solvent DMSO.

value: control

value: Primary mouse hepatocytes

tag: genetic background

tag: age

value: 10 weeks


title: DMSO vehicle biological replicate 5

value: male


title: Tumor T_BG_203

description: Gene expression of tumor liver tissue

tag: tissue

value: female

tag: feature extraction software update


title: Tumor T_BB_183

description: Gene expression of tumor liver tissue


title: DMSO vehicle biological replicate 1

tag: treatment


title: DMSO vehicle biological replicate 4


title: Tumor T_BD_191

description: Gene expression of tumor liver tissue


title: Tumor T_BE_193

description: Gene expression of tumor liver tissue


title: Tumor T_BA_181

description: Gene expression of tumor liver tissue


title: Tumor T_BC_185

description: Gene expression of tumor liver tissue


title: 300 µM DCF  biological replicate 2

value: diclofenac


title: 300 µM DCF  biological replicate 3


title: 300 µM DCF  biological replicate 4


title: Tumor T_AW_169

description: Gene expression of tumor liver tissue

value: Liver


title: Tumor T_AY_173

description: Gene expression of tumor liver tissue


title: 300 µM DCF  biological replicate 1


title: DMSO vehicle biological replicate 2


title: Tumor T_AZ_179

description: Gene expression of tumor liver tissue


title: DMSO vehicle biological replicate 3


title: Tumor T_AX_171

description: Gene expression of tumor liver tissue


title: Tumor T_AV_167

description: Gene expression of tumor liver tissue