title: V/SVZ_3

description: manually dissected E16 V/SVZ tissue

source_name: manually dissected E16 V/SVZ tissue

value: V/SVZ


title: V/SVZ_1

status: Public on Jan 01 2016

type: RNA

city: Tokyo

first: Itsuki

last: Ajioka

address: 1-5-45 Yushima, Bunkyo-ku

department: Center for Brain Integration Research

country: Japan

institute: Tokyo Medical and Dental University

description: manually dissected E16 V/SVZ tissue

hyb_protocol: The amplified cRNA (1.5 µg) was hybridized on Agilent Whole mouse Genome Array (4 × 44K) ver 2.0 for 17 hours.

scan_protocol: The Chips were scanned on a Agilent DNA Microarray Scanner using Feature Extraction software ver 10.7.1.1 (Agilent).

data_processing:
Normalized by pergentile shift (75%) and baseline to median of all samples; GeneSpring software ver 11.5.
Entities were filtered based on their signal intensity value (20-100%), and then the standard deviation (< 0.1). Filtered data linked as supplementary file on Series record.

molecule: total RNA

organism: Mus musculus

label_protocol: Total RNA was amplified following One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), ver 6.0.

extract_protocol: 100 ng of the total RNA was purified by RNeasy Micro (QIAGEN)

tag: strain

value: ICR

tag: developmental stage

tag: tissue


title: V/SVZ_2

description: manually dissected E16 V/SVZ tissue


title: Blood-0.0Gy-1hr-rep3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Louisville

description: Leukocytes treated with 0.0 Gy radiation, measured 1 hr post-exposure.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45oC to Affymetrix® Human gene 1.0 ST v1 arrays according to the GeneChip® WT Terminal Labeling and Hybridization User Manual from Affymetrix®.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix) and the GeneChip® Command Console® software version 3.1 (Affymetrix®).

data_processing:
All data analysis was performed in R using bioconductor packages.  CEL files were preprocessed and normalized using robust multichip averaging (RMA) within the oligo package.  Differential expression was performed using Limma.
annotation file: HuGene-1_0-st-v1.na34.1.hg19.transcript.csv

label: biotin

organism: Homo sapiens

source_name: blood, isolated leukocytes, 0.0 Gy radiation, 1hr post-exposure

label_protocol: Biotinylated cDNA were prepared according to the standard protocol for Affymetrix® GeneChip® WT Expression protocol (Affymetrix® Inc., Santa Clara, CA) (Ambion WT Expression kit followed by GeneChip® WT Terminal Labeling and Hybridization kit) from 100 ng total RNA.

growth_protocol: Whole blood was drawn from four (4) volunteers using a Safety Winged IV blood draw set (Exel International, St. Petersburg, FL) in 7-ml lavender topped Ethylenediaminetetraacetic acid (EDTA) anticoagulant-containing vacutainers.  Blood samples were aliquoted and kept at room temperature throughout the radiation and white blood cell (WBC) isolation process.

extract_protocol: Approximately 30 minutes after completion of the radiation cycle, red blood cells (RBC) were lysed by adding 15ml of NH4Cl red blood cell (RBC) lysis buffer for each ml of whole blood (1:15 v/v dilution) in order to isolate leukocytes.  The tubes were agitated 5 minutes on a rocker platform and centrifuged for 5 minutes at 1,500 RPM at room temperature.  Cells were suspended in 10 ml of phosphate-buffered saline (PBS) and centrifuged again twice for 5 minutes at 1,500 RPM.  White blood cells (WBC) were suspended in 2 ml PBS, equivalent to the initial volume of the whole blood.  WBC were centrifuged 5 min at 1,500 RPM.  Supernatant was discarded and cell pellets were suspended in 600µl RLT lysis buffer (Qiagen, Venlo, The Netherlands) and tubes were vortexed vigorously and stored at -70oC until RNA purification. Purification of total RNA was performed using the RNAeasy Mini Kit (Qiagen).  Optional on-column DNase digestion was performed to eliminate genomic DNA contamination.  Total RNA was eluted in 60 µl of RNase-free water. The quantity analysis of the total RNA was performed with a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE).  The quality of the total RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, Santa Clara, CA).

treatment_protocol: Whole blood samples were radiated at the Kentucky Lion Eye Center using a Gammacell 1000 Elite (Cs-137) (Best Theratronics Ltd., Ottawa, Canada) for 0 seconds (control – 0.0 Gy exposure), 3 seconds (0.30 Gy exposure), 16 seconds (1.5 Gy exposure), or 32 seconds (3.0 Gy exposure).

tag: volunteer

tag: radiation dose

tag: time

value: 1 hr

value: blood, isolated leukocytes


title: genomic DNA from peripheral blood 19

type: genomic

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

description: normal peripheral blood control

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood 19

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using Gentra Puregene Blood Kit according to standard instructions

tag: disease state

value: control


title: genomic DNA from peripheral blood 21

description: peripheral blood given by child born SGA

source_name: peripheral blood 21

value: SGA


title: Blood-0.0Gy-1hr-rep2


title: genomic DNA from peripheral blood 20

source_name: peripheral blood 20


title: genomic DNA from peripheral blood 22

source_name: peripheral blood 22


title: Control 1067

city: San Diego

first: YING

last: DING

state: CA

address: 10777 Science Center Dr.

department: Computational Biology

institute: Pfizer

description: Gene expression data from human postmotem brain region AMY

hyb_protocol: standard Affymetrix protocol

scan_protocol: Microarrays were scanned and summarized by manufacturers’ defaults

data_processing: Data from Affymetrix arrays were processed by robust multi-array (RMA) method

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

extract_protocol: unknown

tag: Sex

value: M

tag: pair

tag: disease status

value: Control


title: shDr3

city: Duarte

first: Krist

last: Azizian

address: 1500 E. Duarte Rd.

department: Molecular and Cellular Biology

institute: Beckman Research Institute of City of Hope

description: Gene expression data

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.0.

label: Biotin

source_name: mutant primary CD34+ HSPCs

label_protocol: WT Target Labeling Assay was performed using 100ng of total RNA accorind to Affymetrix's 100 ng Total RNA Labeling Protocol.

growth_protocol: Cells were cultured in serum-free medium containing growth factors SCF, FLT3-L, TPO, IL-3 and IL-6.

extract_protocol: RNA was extracted with the RNeasy kit (Qiagen)

treatment_protocol: RNA was prepared from cell lines growing in above-mentioned growth protocol conditions.

tag: cell type

value: Drosha-deficient primary CD34+ HSPCs


title: Control subject C13

city: Hasselt

first: An

middle: M

last: Voets

address: Martelarenlaan 42

department: BIOMED

country: Belgium

institute: Hasselt University

description: Gene expression data of muscle from control subject C13

hyb_protocol: A mixture of cDNA and added hybridization controls was hybridized on Affymetrix HG-U133 Plus 2.0 chips, followed by staining and washing steps in the Affymetrix GeneChip fluidics station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with R, a free software program for statistical computing and graphics. Normal linear regression models were used to asses significantly differentially expressed genes between patients and controls.

source_name: skeletal muscle control subject

label_protocol: 150ng muscle RNA was reverse transcribed into cDNA and amplified in a two-round amplification according to the manufacturer's protocol (Affymetrix)

extract_protocol: Total RNA was isolated using the TRIzol reagent and purified with the Rneasy clean-up kit (Qiagen)

treatment_protocol: After biopsy, the muscle samples were immediately frozen in liquid nitrogen.

tag: gender

value: male

tag: age

tag: age group

value: young

value: skeletal muscle


title: Control subject C16

description: Gene expression data of muscle from control subject C16


title: V/SVZ_4

description: manually dissected E16 V/SVZ tissue


title: EV2

description: Gene expression data

source_name: primary CD34+ HSPCs

value: unaltered primary CD34+ HSPCs


title: Control subject C15

description: Gene expression data of muscle from control subject C15

value: female


title: Blood-0.0Gy-1hr-rep1


title: genomic DNA from peripheral blood 16

description: normal peripheral blood control

source_name: peripheral blood 16


title: EV1

description: Gene expression data


title: Control subject C14

description: Gene expression data of muscle from control subject C14


title: Control subject C12

description: Gene expression data of muscle from control subject C12


title: EV3

description: Gene expression data


title: Control subject C8

description: Gene expression data of muscle from control subject C8

value: old


title: Control subject C11

description: Gene expression data of muscle from control subject C11


title: Mixture, biological rep3

city: Paris

first: Lawrence

last: Aggerbeck

address: 45 rue des Saints Peres

country: France

institute: INSERM UMR S-747

description: Gene expression data from HepaRG cells treated with the mixture of TCDD and endosulfan for 30 hours.

hyb_protocol: ssDNA targets were hybridized onto high-density microarrays (Affymetrix Human Genome 1.0 ST GeneChip array) according to the Affymetrix Eukaryotic Target manual.The microarrays were then washed and stained using the Affymetrix fluidics station 450/250 and Genechip Operating Software.

scan_protocol: The microarrays were scanned with an Affymetrix GeneArray scanner.

data_processing: The datasets obtained were processed and normalized using the plier program in R.

label_protocol: ssDNA (sense single stranded DNA) was synthetized using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay kit, according to the manufacturer’s protocol. ssDNA samples were then fragmented according to the Affymetrix protocol. The purified ssDNA was quantified and its quality was assessed with a Bioanalyzer. Subsequent labeling of the samples was performed by synthesis of Biotin-labeled ssDNA using the GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: HepaRG were differentiated as described previously except that 1.5% DMSO was used for cell differentiation (Aninat et al. 2006).

extract_protocol: RNA from HepaRG cells (one well from a six-well plate) was prepared using the RNeasy mini kit from Qiagen (France) as described previously (Bui et al. 2009) except that a DNase I step was included in the protocol. For the microarray studies, the quality of the RNA (RIN value) was assessed with a Bionalyzer (Agilent Technologies).

treatment_protocol: DMSO was removed from the medium for twenty-four hours before treating the cells for 30 hours with 25nM TCDD, 10μM alphaendosulfan, the mixture of the two pollutants or the vehicle (0.15% DMSO).

value: HepaRG cells


title: shDr2

description: Gene expression data


title: Control subject C9

description: Gene expression data of muscle from control subject C9

value: middle


title: genomic DNA from peripheral blood 14

description: normal peripheral blood control

source_name: peripheral blood 14


title: shDr1

description: Gene expression data


title: genomic DNA from peripheral blood 17

description: normal peripheral blood control

source_name: peripheral blood 17


title: genomic DNA from peripheral blood 15

description: normal peripheral blood control

source_name: peripheral blood 15


title: Mixture, biological rep2

source_name: HepaRG cells treated with the mixture of TCDD and endosulfan for 30 hours


title: Endo, biological rep2

description: Gene expression data from HepaRG cells treated with10uM endosulfan for 30 hours.

source_name: HepaRG cells treated with 10uM endosulfan for 30 hours


title: Zebrafish_96h_AgNO3_20ppb_treatment_rep3

city: Daejeon

first: Jinjong

last: Bong

address: Daehak-ro

country: South Korea

institute: NEXBIO

description: Gene expression after 36hr in AgNO3-treated zebrafish

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Gene Expression Microarrays (G2519F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then air-dried by slowly removing the slide rack minimizing droplets on the slides.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026437_D_F20130127) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: Zebrafish, 96hour, AgNO3, 20ppb, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The zebrafish larvae (72hpf) was exposed to AgNPs (1 mg/l, 50 and 150nm), PVP (0.1 mg/l, AgNPs coated substance), and AgNO3 (20ug/l, positive control) for 96hr.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole body


title: genomic DNA from peripheral blood 13

description: normal peripheral blood control

source_name: peripheral blood 13


title: Endo, biological rep3


title: genomic DNA from peripheral blood 12

description: normal peripheral blood control

source_name: peripheral blood 12


title: Mixture, biological rep1


title: Endo, biological rep1


title: genomic DNA from peripheral blood 11

description: normal peripheral blood control

source_name: peripheral blood 11


title: Zebrafish_96h_AgNO3_20ppb_treatment_rep2

source_name: Zebrafish, 96hour, AgNO3, 20ppb, replicate 2


title: Control subject C7

description: Gene expression data of muscle from control subject C7


title: Zebrafish_96h_Ag150nm treatment_rep2

description: Gene expression after 36hr in Ag150nm-treated zebrafish

source_name: Zebrafish, 96hour, Ag150nm, replicate 2


title: Control subject C5

description: Gene expression data of muscle from control subject C5


title: Zebrafish_96h_AgNO3_20ppb_treatment_rep1

source_name: Zebrafish, 96hour, AgNO3, 20ppb, replicate 1


title: Control subject C4

description: Gene expression data of muscle from control subject C4


title: TCDD, biological rep3

description: Gene expression data from HepaRG cells treated with25nM TCDD for 30 hours.

source_name: HepaRG cells treated with 25nM TCDD for 30 hours


title: Zebrafish_96h_Ag150nm treatment_rep3

source_name: Zebrafish, 96hour, Ag150nm, replicate 3


title: genomic DNA from peripheral blood 8

description: normal peripheral blood control

source_name: peripheral blood 8


title: genomic DNA from peripheral blood 9

description: normal peripheral blood control

source_name: peripheral blood 9


title: Control subject C3

description: Gene expression data of muscle from control subject C3

source_name: skeletal muscle control subject


title: POLG1 patient P509

description: Gene expression data from muscle of patient P509

source_name: skeletal muscle POLG1 patient


title: genomic DNA from peripheral blood 7

description: normal peripheral blood control

source_name: peripheral blood 7


title: genomic DNA from peripheral blood 10

description: normal peripheral blood control

source_name: peripheral blood 10


title: Zebrafish_96h_Ag150nm treatment_rep1

source_name: Zebrafish, 96hour, Ag150nm, replicate 1


title: TCDD, biological rep2


title: POLG1 patient P477

description: Gene expression data from muscle of patient P477


title: Zebrafish_96h_Ag50nm treatment_rep3

description: Gene expression after 36hr in Ag50nm-treated zebrafish

source_name: Zebrafish, 96hour, Ag50nm, replicate 3


title: DMSO, biological rep2

description: Gene expression data from HepaRG cells treated with 0.15% DMSO for 30 hours.

source_name: HepaRG cells treated with 0.15%DMSA for 30 hours


title: TCDD, biological rep1


title: Left atria-PAF-Rep3

city: La Coruña

first: Mario

last: Torrado

state: La Coruña

address: Campus de Oza, Edificio El Fortin

department: Institute of Health Sciences

country: Spain

institute: University of La Coruña

description:
FA6-EXP
microRNA Expression Profiling using LC Sciences Pig miRNA Array (MRA-1013, version miRPig_20, based on Sanger miRBase Release 20) including 322 unique probes (9 repeats each) og pig mature miRNAs

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

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

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between 'control' and 'test' sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Sus scrofa

source_name: left atria-PAF

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 1 µg total RNA samples, which were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Neonatal piglets were maintained in a conventional Nurtinger nursery system

extract_protocol: Purification of total RNA, including small RNAs, from left atria was performed using miRNeasy Mini kit (Qiagen) including the on-column Dnase digestion with RNase-free DNase.

treatment_protocol: Deep-frozen cardiac-tissue samples were directly homogenized in QIAzol lysis reagent (Qiagen) using a high-speed rotor-stator homogenizer (Ultra-Turrax T8), as described in the Qiagen Manual

tag: piglet group

value: PAF group

value: Left atria


title: POLG1 patient P423

description: Gene expression data from muscle of patient P423


title: Zebrafish_96h_Ag50nm treatment_rep1

source_name: Zebrafish, 96hour, Ag50nm, replicate 1


title: Zebrafish_96h_Ag50nm treatment_rep2

source_name: Zebrafish, 96hour, Ag50nm, replicate 2


title: POLG1 patient P38

description: Gene expression data from muscle of patient P38


title: Zebrafish_96h_pvp treatment_rep3

description: Gene expression after 36hr in pvp-treated zebrafish

source_name: Zebrafish, 96hour, pvp, replicate 3


title: genomic DNA from peripheral blood 3

description: normal peripheral blood control

source_name: peripheral blood 3


title: DMSO, biological rep3


title: genomic DNA from peripheral blood 5

description: normal peripheral blood control

source_name: peripheral blood 5


title: genomic DNA from peripheral blood 2

description: normal peripheral blood control

source_name: peripheral blood 2


title: POLG1 patient P194

description: Gene expression data from muscle of patient P194


title: genomic DNA from peripheral blood 4

description: normal peripheral blood control

source_name: peripheral blood 4


title: Left atria-PAF-Rep2

description:
FA5-EXP
microRNA Expression Profiling using LC Sciences Pig miRNA Array (MRA-1013, version miRPig_20, based on Sanger miRBase Release 20) including 322 unique probes (9 repeats each) og pig mature miRNAs


title: Zebrafish_96h_pvp treatment_rep2

source_name: Zebrafish, 96hour, pvp, replicate 2


title: genomic DNA from peripheral blood 6

description: normal peripheral blood control

source_name: peripheral blood 6


title: Zebrafish_96h_pvp treatment_rep1

source_name: Zebrafish, 96hour, pvp, replicate 1


title: POLG1 patient P54

description: Gene expression data from muscle of patient P54

source_name: skeletal muscle POLG1 patient


title: Left atria-PAF-Rep1

description:
FA3-EXP
microRNA Expression Profiling using LC Sciences Pig miRNA Array (MRA-1013, version miRPig_20, based on Sanger miRBase Release 20) including 322 unique probes (9 repeats each) og pig mature miRNAs


title: genomic DNA from peripheral blood 18

description: normal peripheral blood control

source_name: peripheral blood 18


title: Leiomyosarcoma tumor - ST275 (expression)

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: Tumor sampls were obtained from the tissues bank at the Laboratory of Oncology Research of the Rizzoli Orthopaedic Institute, Bologna, Italy

hyb_protocol: Hybridization, washing and scanning were performed according to the manufacturer's directions

data_processing: Expression data were normalized by the VST-RSN method using the lumi R package available at Bioconductor

source_name: Leiomyosarcoma tumor

label_protocol: Biotinylated cRNA was prepared using Ambion TotalPrep RNA Amplification Kit starting with 200 ng total RNA

growth_protocol: Commercially available osteosarcoma cell lines were grown according to the supplier’s recommendations.

extract_protocol: Total RNA  was extracted using Trizol and chloroform. Purification was performed on RNAeasy columns according to manufacturer’s instructions

tag: Sample type

value: Leiomyosarcoma tumor


title: DMSO, biological rep1


title: Left atria-Control-Rep3

description:
FA8-CON
microRNA Expression Profiling using LC Sciences Pig miRNA Array (MRA-1013, version miRPig_20, based on Sanger miRBase Release 20) including 322 unique probes (9 repeats each) og pig mature miRNAs

source_name: left atria-Control

value: sham-control group


title: Leiomyosarcoma tumor - ST312 (expression)

scan_protocol: Hybridization, washing and scanning were performed according to the manufacturer's directions


title: Left atria-Control-Rep2

description:
FA4-CON
microRNA Expression Profiling using LC Sciences Pig miRNA Array (MRA-1013, version miRPig_20, based on Sanger miRBase Release 20) including 322 unique probes (9 repeats each) og pig mature miRNAs


title: Zebrafish_96h_Control_rep2

description: Gene expression after 36hr in non-treated zebrafish

source_name: Zebrafish, 96hour, no treatment, replicate 2


title: Leiomyosarcoma tumor - ST89 (expression)


title: Leiomyosarcoma tumor - ST284 (expression)


title: Zebrafish_96h_Control_rep3

source_name: Zebrafish, 96hour, no treatment, replicate 3


title: Zebrafish_96h_Control_rep1

source_name: Zebrafish, 96hour, no treatment, replicate 1


title: E-PZ-1-iPS-like-4 in induction medium PSA day 5

city: Stanford

first: Hongjuan

last: Zhao

address: 300 Pasteur Dr

department: Urology

institute: Stanford

description:
Sample name: PSA day 5 treated
normal iPS cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450K Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

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

treatment_protocol: For prostate sphere differentiation: E-PZ-iPS-like cells cultured on Matrigel were digested with collagenase type IV (Invitrogen) and transferred to ultra-low attachment plates (Corning Life Sciences, Tewksbury, MA) for suspension culture for 8 days in DMEM/F12 (1:1) medium supplemented with 5 ng/ml bFGF (PeproTech), 10 ng/ml LIF (Santa Cruz Biotechnology Inc.), and 5% knockout FBS (Invitrogen).  For basal epithelial cell differentiation, E-PZ-iPS-like spheres were then cultured in Complete PFMR-4A medium [29] for 3 days.  To induce expression of androgen receptor (AR), E-PZ-iPS-like spheres were further cultured in Complete PFMR-4A medium with 10 nM R1881 for 3 days.  To induce expression of prostate-specific antigen (PSA), E-PZ-iPS-like spheres were co-cultured with rat urogenital sinus (UGS) isolated from E17 rat embryos as previously described [31] in Complete PFMR-4A medium with 10 nM R1881 for 5 days.

value: Male

tag: cell line

value: induced pluripotent stem cells derived from prostate epithelial cells

value: normal

tag: protocol

value: induction medium PSA

value: day 5


title: Left atria-Control-Rep1

description:
FA2-CON
microRNA Expression Profiling using LC Sciences Pig miRNA Array (MRA-1013, version miRPig_20, based on Sanger miRBase Release 20) including 322 unique probes (9 repeats each) og pig mature miRNAs


title: Leiomyosarcoma tumor - ST64 (expression)


title: Leiomyosarcoma tumor - ST62 (expression)


title: E-PZ-1-iPS-like-4 in control medium PSA day 5

description:
Sample name: PSA day 5 control
normal iPS cells

value: control medium PSA


title: E-PZ-1-iPS-like-4 in induction medium PSA day 3

description:
Sample name: PSA day 3 treated
normal iPS cells

value: day 3


title: KO3

city: Suita

first: Hiroyasu

last: Kidoya

state: Osaka

address: 3-1 Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka university

description: Gene expression of skin endothelial cells in APJ deficent mouse 3.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner 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: The image files were analyzed by using of Feature Extraction software (Agilent) and quantile-normalized.

source_name: Endothelial cells from KO3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp WT Labeling 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-2000 Spectrophotometer.

growth_protocol: FACS sort only, no treatment afterwards

extract_protocol: Total RNA isolated with RNeasy Plus Mini Kit (QIAGEN, 74134).

treatment_protocol: FACS sort only, no treatment afterwards

tag: strain

tag: genotype/variation

value: APJ KO

value: Endotheila cells


title: Mulberry-5

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

description: gene expression data from liver of mouse fed a high-cholesterol diet with mulberry leaf extract

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized for 17 hr at 65C on a Whole Mouse Genome Microarray 4x44K (Agilent).

scan_protocol: Microarrays were scanned using a DNA Microarray Scanner (Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction 10.1.1.1 (Agilent Technologies) to obtain background subtracted and spatially detrended Processed signal intensities. Signal intensities of same gene symbol were averaged using statistical language R (http://www.r-project.org/) and non-redundant gene list was obtained. The non-redundant data were normalized with quantile normalization (Bolstad et al., Bioinformatics, 2003;19:185–193) using R.

label_protocol: Cy3-labeled cRNA were prepared from 500 ng total RNA according to the standard Agilent protocol.

extract_protocol: RNAiso extraction (Takara Bio) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice fed a high-cholesterol diet were orally administrated mulberry leaf extract as drinking water. After 4 weeks, mice were anesthetized and killed by exsanguination. Parts of liver of each mice was taken and immediately immersed in RNAlater (Applied Biosystems).

value: male

tag: treatment

tag: tissue

value: liver


title: KO2

description: Gene expression of skin endothelial cells in APJ deficent mouse 2.

source_name: Endothelial cells from KO2


title: genomic DNA from peripheral blood 1

description: normal peripheral blood control

source_name: peripheral blood 1

value: control


title: Mulberry-4

source_name: liver of mouse fed a high-cholesterol diet with mulberry leaf extract


title: Leiomyosarcoma tumor - ST13 (expression)


title: Leiomyosarcoma tumor - ST16 (expression)


title: KO1

description: Gene expression of skin endothelial cells in APJ deficent mouse 1.

source_name: Endothelial cells from KO1


title: E-PZ-1-iPS-like-4 in control medium PSA day 3

description:
Sample name: PSA day 3 control
normal iPS cells

tag: time


title: Osteosarcoma tumor - 24949 (expression)

source_name: Osteosarcoma tumor


title: E-PZ-1-iPS-like-4 in induction medium PSA day 1

description:
Sample name: PSA day 1 treated
normal iPS cells

tag: disease state

value: day 1


title: Mulberry-3

value: fed a high-cholesterol diet with mulberry leaf extract


title: Mulberry-1


title: WT3

description: Gene expression of skin endothelial cells in wild type mouse3.

source_name: Endothelial cells from WT3

value: wildtype


title: 4310479163_F

city: New Lambton Heights

first: Katie

last: Baines

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

description: SAMPLE 50

hyb_protocol: 750ng reverse-transcribed cRNA was hybridized to the Illumina Sentrix HumanRef-8 Version 2 Expression BeadChip, which measured the expression of 20590 genes.

scan_protocol: BeadChips were scanned using the Illumina Bead Station and data was captured using VeadScan 3.5.11.

data_processing: Sample and gene profiling results were included in the analysis if the sample was of suitable purity (OD 260/280 ratio between 1.7-2.1) and was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (correlation coefficients and priciple component analysis plots)

source_name: induced sputum

label_protocol: 500ng wxtracted RNA was reverse-transcribed into cRNA and labeled with biotin-uridine-5'-triphosphate by using the Illumina TotalPrep RNA Amplication Kit.

extract_protocol: RNA was extracted from induced sputum using the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quatitation was performed using the Quanti-iT RiboGreen RNA Quantitation Assay Kit (Molecular Probes Inc, Invitrogen, Eugene, OR, USA).

tag: bmi

tag: smoking pack-years


title: Osteosarcoma tumor - 25517 (expression)

value: osteosarcoma tumor


title: Control-5

description: gene expression data from liver of mouse fed a high-cholesterol diet without mulberry leaf extract


title: WT2

description: Gene expression of skin endothelial cells in wild type mouse2.

source_name: Endothelial cells from WT2


title: 4310479156_C

description: SAMPLE 48

value: Female

tag: systemic inflammation group


title: WT1

description: Gene expression of skin endothelial cells in wild type mouse1.

source_name: Endothelial cells from WT1

tag: cell type


title: E-PZ-1-iPS-like-4 in control medium PSA day 1

description:
Sample name: PSA day 1 control
normal iPS cells

tag: gender

value: Male


title: Mulberry-2


title: 4310479173_A

description: SAMPLE 49

tag: age


title: Control-4

source_name: liver of mouse fed a high-cholesterol diet without mulberry leaf extract


title: C_2

city: Jerusalem

first: Jussi

last: Leinonen

address: Kiryat Hadassah p.o.b 12000

department: Cardiovascular Research Center, Heart Institute

country: Israel

institute: Hadassah-Hebrew University Medical Center

description:
8th passage derivates from c-kit+/CD45+ cells
C

hyb_protocol: The Cy3 labeled cRNA was hybridized to the 8 X 60K Agilent Whole Mouse Genome Oligo Microarray V2 (design 028005 Agilent Technologies, USA) for 17 hours at 65°C in an Agilent DNA-Microarray Hybridization Oven.

scan_protocol: The Microarray was scanned using the Agilent High-Resolution Microarray Scanner.

data_processing: Data was extracted from the resulting images using the Feature Extraction 10.7 software.

source_name: Cell culture, replicate 2

label_protocol: 200 ng of total RNA for each sample was amplified and labeled with a fluorescent dye (Cy3 ) using the Low RNA Input Linear Amplification & Labeling kit (Agilent ).

growth_protocol: Adult (8-12 weeks old) C57BL/6 mice were deeply anesthetized with isoflurane and left atrial appendages were removed. The explants were then digested three times (5min) with trypsin & collagenase D. Strong enzyme digestion was performed with trypsin 0.25% and collagenase D 0.1% and alternatively, weak enzyme digestion with trypsin 0.05% and collagenase D 0.1%. After digestion the explants were placed on 24 –well plates (tissue culture treated) in culture medium (CEM: Isocove’s modified Dulbecco’s Medium with 25mM HEPES, supplemented with 10% FBS (fetal bovine serum), 1% L-glutamine, 1% penicillin-streptomycin & 0.1mM 2 -mercaptoethanol).

extract_protocol: Total RNA of cultured cells was extracted with High Pure RNA isolation kit (Roche) according to the manufacturer’s instructions. RNA -sample quality and integrity was tested with Bioanalyzer 2100 (Agilent Technologies). RNA from control tissue samples was isolated using Tri-reagent.

value: 8-12 week old mice

value: heart left atrial appendage


title: B_2

description:
Primary cells (c-kit+/CD45+ sorted) from left atrial appendage tissue culture
B
B samples were treated with weak enzyme digestion.


title: E-PZ-1-iPS-like-4 in control medium AR day 3

description:
Sample name: AR day 3 control
normal iPS cells

value: induced pluripotent stem cells derived from prostate epithelial cells

value: normal

value: control medium AR


title: Control-3

value: fed a high-cholesterol diet without mulberry leaf extract


title: 4147931034_H

description: SAMPLE 47


title: 4147931029_F

description: SAMPLE 45


title: E-PZ-1-iPS-like-4 in induction medium AR day 1

description:
Sample name: AR day 1 treated
normal iPS cells

value: induction medium AR


title: E-PZ-1-iPS-like-4 in induction medium AR day 3

description:
Sample name: AR day 3 treated
normal iPS cells

value: day 3


title: E-PZ-1-iPS-like-4 in control medium AR day 1

description:
Sample name: AR day 1 control
normal iPS cells


title: 4135447179_F

description: SAMPLE 46


title: A_2

description:
Primary cells (c-kit+/CD45- sorted) from left atrial appendage tissue culture
A
A samples were treated with strong enzyme digestion.


title: A_1

source_name: Cell culture, replicate 1


title: C_1


title: Control-2

value: male


title: 4135447160_D

description: SAMPLE 44


title: MDM non infected basal, rep2

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description: human monocyte derived macrophages Control sample HIV-

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® human Gene 1.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix)

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

data_processing: the data were RMA normalized

source_name: human monocyte derived macrophages from healthy donor

label_protocol: After purification according to Nugen protocol, 2.5 ug of single strand DNA is used for fragmentation and biotin labelling using Encore Biotin Module (Nugen)

growth_protocol: monocytes were isolated from blood of healthy donors and grown for 11 days in the presence of 10 ng/ml of rhGM-CSF

extract_protocol: RNA was extracted using RNeasy® Plus mini kit (Qiagen)

treatment_protocol: in vitro differentiated macrophages were infected with HIV-1 ADA (HIV+) or not (HIV-) for 8 days and then incubated or not (contrôle) with IgG-opsonized particles (FcR) or with Salmonella typhimurium 4/74 (4 74)

value: monocyte derived macrophages


title: MDM HIV-infected, Salmonella stimulated, rep1

description: human monocyte derived macrophages 474 sample HIV+


title: B_1


title: MDM non infected, Salmonella stimulated, rep1

description: human monocyte derived macrophages 474 sample HIV-


title: 4310479168_H

description: SAMPLE 41


title: MDM HIV-infected basal, rep2

description: human monocyte derived macrophages Control sample HIV+


title: 4135447160_C

description: SAMPLE 43


title: Control_1

description:
Left ventricular wall biopsy
Control

source_name: Heart tissue, replicate 1

value: 12 week old mouse

value: heart left ventrical wall


title: Control_2

description:
Left ventricular wall biopsy
Control

source_name: Heart tissue, replicate 2


title: MDM HIV-infected, FcR stimulated, rep1

description: human monocyte derived macrophages FcR sample HIV+


title: 4310479156_G

description: SAMPLE 37


title: MDM non infected, FcR stimulated, rep2

description: human monocyte derived macrophages FcR sample HIV-


title: 4135447160_B

description: SAMPLE 42


title: MDM HIV-infected basal, rep1


title: 4310479166_A

description: SAMPLE 39


title: 4310479166_E

description: SAMPLE 40


title: MDM non infected, FcR stimulated, rep1


title: 4310479156_E

description: SAMPLE 36


title: 4310479163_B

description: SAMPLE 38


title: MDM HIV-infected, Salmonella stimulated, rep3


title: 4135447178_A

description: SAMPLE 35


title: 4135447179_D

description: SAMPLE 32


title: MDM non infected, FcR stimulated, rep3


title: 4135447194_G

description: SAMPLE 34


title: Control-1

description: gene expression data from liver of mouse fed a high-cholesterol diet without mulberry leaf extract

value: liver


title: 4147931029_C

description: SAMPLE 29


title: 4147931029_D

description: SAMPLE 30


title: MDM HIV-infected, FcR stimulated, rep3


title: MDM non infected basal, rep3


title: 4135447179_H

description: SAMPLE 33


title: MDM non infected basal, rep1


title: 4135447160_H

description: SAMPLE 25


title: 4135447179_B

description: SAMPLE 31


title: MDM non infected, Salmonella stimulated, rep2


title: 4147931008_B

description: SAMPLE 26


title: PRL2010 cultivated on kefir as unique carbon source II

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Transcription hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Transcription Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent's standard procedures.

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner.

data_processing:
Signal intensities for each spot and data extraction were carried out using Mapix 5.5 software (Innopsys, Carbonne, France). Data were analyzed for the final version using the median of the values of each ORF. In addition "TMev" software (http://www.tm4.org/mev/documentation/mev.html) has been used for statistical analysis. In particular, an adjustment of the data that has been applied consisting by a median center samples/column, followed by LIMMA software (Linear Models for Microarray data).
Only B. bifidum PRL2010 genes were analyzed (resulting in a subset of  8130 ID_REFs out of a possible 36186).

organism: Bifidobacterium bifidum

source_name: PRL2010_kefir grains_12h.

label_protocol: Reverse transcription and amplification of 500 ng of total RNA was performed with ImProm-IITM Reverse Transcriptase (Promega, Madison, USA) according to the manufacturer’s instructions. 5 µg of RNA was then labelled with ULS Labelling kit with Cy5 or Cy3 (Kreatech, The Netherlands). For the purpose of the tiling array, samples containing kefir/kefiran cDNA was labelled with Cy5, while control samples (MRS) were labelled with Cy3.

growth_protocol: B. bifidum PRL2010 was grown anaerobically in  kefir grains and incubated at 37°C.

extract_protocol: For RNA extraction, cell pellets/tissue materials were resuspended in 1 ml of QUIAZOL (Qiagen, UK) and placed in a tube containing 0.8 g of glass beads (diameter, 106 μm; Sigma). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation.

tag: cultivated on

value: kefir grains for 12h

source_name: PRL2010_MRS (control)

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.

value: MRS (control)


title: PRL2010 cultivated on kefiran as unique carbon source I

source_name: PRL2010_MRS plus kefiran_12h

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) with 2% of kefiran supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C.

value: MRS plus kefiran for 12h


title: 4310479156_F

description: SAMPLE 23

value: Male


title: PRL2010 cultivated on kefiran as unique carbon source II


title: PRL2010 cultivated on kefir as unique carbon source I


title: 4147931008_C

description: SAMPLE 27


title: MDM HIV-infected basal, rep3


title: 4147931029_A

description: SAMPLE 28

value: Female


title: Head kidney_PTU_day7_rep4

city: Madrid

first: José María

last: Navas

state: Madrid

address: Crta de la Coruña Km 7.5

department: Environment

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

organism: Oncorhynchus mykiss

source_name: Head kidney of 2 rainbow trout

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Juvenile rainbow trout of 50 g  were selected from the stock population reared at the Centre for Fish and Wildlife Health, University of Bern, Switzerland. The fish were distributed into six glass aquaria, each with a volume of 200 L (ten fish per aquarium). They were kept under ﬂow-through conditions (0.5 L/min) in air-saturated tap water (total hardness (CaCO3): 2.13 ppm; chlorine dioxide: <0.01 mg/l) and at a water temperature of 15 ± 1ºC under a natural light-dark photoperiod.

extract_protocol: RNA was extracted using the RNAeasyPlus kit (Qiagen, Hilden, Germany).

treatment_protocol: Juvenile rainbow trout  were orally exposed to T3 (20 µg/g fish feed) or PTU (5000 µg/g fish feed) for 7  consecutive days.

tag: development stage

value: Juvenile

tag: agent

value: PTU (5000 µg/g fish feed)


title: 4135447160_A

description: SAMPLE 24


title: MDM HIV-infected, Salmonella stimulated, rep2


title: 4147931034_D

description: SAMPLE 21


title: Head kidney_PTU_day7_rep3


title: Head kidney_PTU_day7_rep1


title: 4135447179_A

description: SAMPLE 20


title: 4135447194_H

description: SAMPLE 22


title: MDM non infected, Salmonella stimulated, rep3


title: 4147931029_B

description: SAMPLE 18


title: DTS in the presence elemental sulfur, replicate 2

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

description: Technical replicate 2 of 2. DTS grown in the presence of elemental sulfur at 85˚C

hyb_protocol: The labeled cDNA was dissolved in hybridization buffer (30 µl) containing 6×SSC (1×SSC is 0.1 M NaCl, 0.015 M sodium citrate), 0.2% Sodium lauryl sulfate, 5×Denhard's solution (Sigma-Aldrich), and 0.1 mg/ml denatured salmon sperm DNA. Hybridization was perfomed under a coverslip (Spaced cover glass XL, Takara bio) in a humidity chamber at 65˚C for 15 h. After hybridiztion, the microarray plates were washed four times with 2×SSC and 0.2% SDS at 55˚C for 5 min, rinsed in 0.05×SSC, and dried by centrifugation.

scan_protocol: The intensities of the Cy3 and Cy5 dyes were measured by using an Affymetrix 428 array scanner (Affymetrix)

data_processing: The microarray image analysis was processed by ImaGene 5.5 software (Biodiscovery) using a local background correction. For normalization of data, global intensity normalization was performed.

organism: Thermococcus kodakarensis

label_protocol: 10 µg of total RNA was annealed with random hexamers, and reverse transcription was performed in solutions containing CyDye-labeled dUTP (GE Healthcare). RNA was subsequently degraded with RNase H, and the labeled cDNA was purified by using a QiaQuick PCR purification kit (Qiagen).

growth_protocol: KU216 and DTS strains were individually cultivated at 85°C in the rich media supplemented with elemental sulfur. Cells were harvested in the mid-logarithmic phase.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen).

treatment_protocol: The grown cells were freezed at -80˚C prior to RNA extraction.

tag: genotype

value: ∆tk1086, ∆pyrF

tag: growth condition

value: The cells were grown in ASW-YT media supplemented with elemental sulfur at 85˚C for mid-logarithmic phase

value: ∆pyrF


title: Head kidney_PTU_day7_rep2


title: DTS in the presence elemental sulfur, replicate 1

description: Technical replicate 1 of 2. DTS grown in the presence of elemental sulfur at 85˚C


title: Head kidney_T3_day7_rep3

value: T3 (20 µg/g fish feed)


title: Head kidney_T3_day7_rep2


title: 4310479167_D

description: SAMPLE 16


title: 4310479173_F

description: SAMPLE 14


title: 4147931008_E

description: SAMPLE 17


title: 4310479173_C

description: SAMPLE 12


title: Head kidney_control__day7_rep1


title: Head kidney_T3_day7_rep4


title: Head kidney_control__day7_rep2


title: 4310479168_D

description: SAMPLE 15


title: Head kidney_control__day7_rep3


title: Head kidney_T3_day7_rep1


title: 4147931029_H

description: SAMPLE 19


title: 4147931034_E

description: SAMPLE 8


title: Head kidney_control__day7_rep4


title: 4147931034_C

description: SAMPLE 7


title: 4135447194_D

description: SAMPLE 10


title: 4135447178_F

description: SAMPLE 11


title: 4147931034_G

description: SAMPLE 9


title: 4310479173_D

description: SAMPLE 13


title: 120 min after fluoride introduced

city: Changsha

first: Liyuan

last: Ma

address: 932 S. Lushan Rd.

country: China

institute: Central South University

description: RNA from control samples were compared to the experimental samples taken at 10, 30, 60, 120 and 240 min after fluoride added.

hyb_protocol: Labelled cDNA were concentrated 30-45 min by concentrator (Eppendorf Inc., Hamburg, Germany) at45℃ and hybridised using the TECAN HS4800 Pro system (TECAN，US).  Arrays then hybridised by the following steps,Step 1: 0.l× SSC, 0.1% SDS washed, 23℃, 1 min; Step 2: 1× SSC, 0.1% SDS washed, 37℃, 1 min; Step 3: 5× SSC, 0.1% SDS, 0.1% BSA washed, 42℃, 1 min; Step 4: prehybridization, 42℃, 45 min; Step 5:5× SSC, 0.1% SDS, 0.1% BSA washed, 42℃, 1 min; Step 6: 1× SSC, 0.1% SDS washed, 42℃, 1 min; Step 7: sample injection, 55℃; Step 8: Hybridization, 45℃, 10 h, agitation; Step 9: 1× SSC, 0.1% SDS washed, 42℃, 10 sec; Step 10: 1× SSC, 0.1% SDS washed, 37℃, 10 sec; Step 11: 0.l× SSC, 0.1% SDS washed, 23℃, 20 sec; Step 11: 0.1× SSC washed, 23℃, 10 sec.

scan_protocol: Arrays scanned by a GenePix Personal 4100A scanner (AXON instruments, Inc, USA) and then was converted to digital signals by Genepix Pro 6.1 software.

data_processing: A grid of individual circles defining the location of each DNA spot on the array was superimposed on the image to designate each fluorescent spot to be quantified. The mean signal intensity was determined for each spot. The local background signal was subtracted automatically from the hybridization signal of each separate spot also computed for each spot to discriminate true signals from noise. The SNR ratio was also calculated based on the following formula: SNR=(signal intensity – background)/standard deviation of background, in which the background measurement refers to the local spot background intensity and the standard deviation of background was calculated across all pixels measured by the ImaGene software. The SNRs from four replicate data sets were then averaged to represent the SNR for a particular probe. A commonly accepted criterion for the minimum signal (threshold) that can be accurately quantified is SNR > 2. Spots that appeared to be lower than the threshold value were removed from the data set.

organism: Acidithiobacillus ferrooxidans ATCC 23270

source_name: Continuous cultured experimental samples after 120 min fluoride introduced

label_protocol: The pure RNA was converted to cDNA with random primers following the manufacturer’s protocol for the ImProm-II™ Reverse Transcription System (Promega Corporation, Madison, USA), and purified with the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany).The cDNA of samples with/without fluoride treatment were labeled using Cy3-/Cy5-dUTP fluorescent dyes

growth_protocol: Control group was set up without fluoride. Experimental group were treated by adding 476 mM sodium fluoride solution to the basal medium, with the final fluoride concentration 4.8 mM,  when cells grown to the mid-log phase (40 hours) .

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, USA) and RNeasy mini kit (Qiagen, Valencia, USA). RNA quality was assessed by Bioanalyzer (Agilent, USA) and spectrophotometer (Nanodrop Technologies).

treatment_protocol: The strain A. ferrooxidans ATCC 23270 was cultured in 9K basal medium (initial pH 2.0) added with FeSO4•7H2O (44.7 g/L) or S0 (10 g/L) as energy substrate. The 9K basal medium contained the following components: (NH4)2SO4, 3.0 g/L; MgSO4•7H2O, 0.5 g/L; K2HPO4, 0.5 g/L; KCl, 0.1 g/L, Ca(NO3)2, 0.01 g/L. The inoculum density of A. ferrooxidans was 5.6×105 cells/mL. It was cultivated aerobically at 30 °C in a rotary platform at 170 rpm.

tag: strain

source_name: Continuous cultured control samples at 120 min without fluoride introduced


title: 4135447179_E

description: SAMPLE 5


title: 240 min after fluoride introduced

source_name: Continuous cultured experimental samples after 240 min fluoride introduced

source_name: Continuous cultured control samples at 240 min without fluoride introduced


title: ESF3, biological rep3

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

country: India

institute: CSIR-National Environmental Engineering Research Institute

description: gene expression profiling of SHSY5Y cells exposed to Endosulfan

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

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

data_processing: The data were analyzed with Expression Console  using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: SHSY5Y Cell Line

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

growth_protocol: SHSY5Y cells grown in MEM:F12 (1:1) media cointaning 10 % Fetal bovin serum

extract_protocol: Total RNA prepared using Rneasy mini kit

treatment_protocol: Treated with  3 μM of endosulfan (1/5of LC50) for 24hrs.

tag: cell line

value: Neuroblastoma cell line SHSY5Y

value: Endosulfan


title: 4147931034_A

description: SAMPLE 6

source_name: induced sputum


title: S3-H230

status: Public on Dec 25 2015

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Genotyped using Illumina Genotyping BeadChips

source_name: Human breast cancer

label_protocol: Standard Illumina protocol

extract_protocol: The DNA from human breast cancer samples was isolated using the Qiagen DNeasy kit/protocol.

tag: ChIP

value: Illumina Human610-Quad v1.0 BeadChip

value: Breast cancer

tag: age, years

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Pre-Menopausal

tag: histology

value: Infiltrating Ductal Carcinoma

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

tag: pr

tag: triple negative

value: TN

tag: tumor size

tag: metastases

value: No mets


title: 60 min after fluoride introduced

source_name: Continuous cultured experimental samples after 30 min fluoride introduced

source_name: Continuous cultured control samples at 60 min without fluoride introduced


title: C3, biological rep3

description: gene expression profiling of SHSY5Y cells exposed to control

tag: agent

value: control


title: 30 min after fluoride introduced

source_name: Continuous cultured control samples at 30 min without fluoride introduced


title: S3-H229

tag: tissue

tag: gender

value: Female

tag: tumor grade

value: Poorly Differentiated


title: S3-H226

tag: ChIP

value: Post-Menopausal

value: Moderately Differentiated

tag: positive nodes


title: S3-H228

tag: age, years


title: S3-H227


title: ESF2, biological rep2

tag: cell line


title: S3-H225

tag: race

tag: body mass index

tag: menopausal status


title: 4147931008_H

description: SAMPLE 3

tag: bmi

tag: systemic inflammation group

tag: smoking pack-years

tag: age


title: S3-H224

tag: histology

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple negative

tag: tumor size


title: C2, biological rep2

tag: agent


title: S3-H222

tag: ChIP

tag: tissue

tag: age, years

tag: gender

tag: tumor grade

tag: positive nodes

tag: metastases


title: 10 min after fluoride introduced

source_name: Continuous cultured experimental samples after 10 min fluoride introduced

tag: strain

source_name: Continuous cultured control samples at 10 min without fluoride introduced


title: C1, biological rep1

tag: cell line


title: S3-H219

tag: race

tag: menopausal status

tag: histology


title: 4147931008_A

description: SAMPLE 2

value: Male

tag: bmi

tag: smoking pack-years

tag: age


title: genes expression in esophageal squamous cell carcinoma  KYSE150  cells transfected with empty vector

city: Shantou

first: Guo-Qing

last: Lv

state: Guangdong

address: Xinling road

institute: Department of Biochemistry and Molecular Biology

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

data_processing: All probe signals were normalized log2 ratio, then RMA analysyis: background correction on the PM values, quantile normalization across all the chips in the experiment, Log2 transformation, median polish summarization.

source_name: esophageal squamous cell carcinoma

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

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

tag: treatment

value: empty vector


title: S3-H218

tag: body mass index

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr

tag: triple negative

tag: tumor size


title: S3-H217

tag: ChIP

tag: tissue

tag: age, years

tag: gender

value: Asian

tag: tumor grade

tag: positive nodes

tag: metastases


title: ESF1, biological rep1

tag: cell line

value: Neuroblastoma cell line SHSY5Y

tag: agent

value: Endosulfan


title: S3-H216

value: Illumina Human610-Quad v1.0 BeadChip

value: Breast cancer

tag: race

value: Caucasian

tag: menopausal status

tag: histology

value: any size with direct extension


title: 4135447179_C

description: SAMPLE 4

tag: bmi

tag: systemic inflammation group

tag: smoking pack-years

tag: age


title: S3-H215

value: Pre-Menopausal

value: Infiltrating Ductal Carcinoma

tag: ajcc stage (7th edition, 2010)

tag: set

value: Discovery TN

tag: er

value: Negative

tag: pr

tag: triple negative

tag: tumor size


title: S3-H221

tag: ChIP

tag: tissue

tag: age, years

tag: gender

value: Female

tag: body mass index

value: TN

tag: tumor grade

tag: positive nodes

value: No mets


title: genes expression in esophageal squamous cell carcinoma  KYSE150  cells transfected with LOXL2 wildtype

tag: treatment

value: LOXL2 wildtype overexpression

tag: cell line


title: S3-H214

tag: race

tag: histology

value: Poorly Differentiated

tag: metastases


title: S3-H213

tag: menopausal status

value: Post-Menopausal

tag: ajcc stage (7th edition, 2010)

tag: set


title: genes expression in esophageal squamous cell carcinoma  KYSE150  cells transfected with LOXL2 △e13

value: LOXL2 △e13 overexpression


title: S3-H210

value: Menopausal

tag: er

tag: pr

tag: triple negative

value: Moderately Differentiated


title: S3-H211

tag: ChIP

value: Illumina Human610-Quad v1.0 BeadChip

tag: tissue

tag: tumor size


title: S3-H207

value: Breast cancer

tag: age, years

tag: gender

tag: body mass index


title: S3-H206

value: Caucasian

tag: positive nodes


title: S3-H220

value: Carcinoma of the breast

tag: tumor grade


title: S3-H201

tag: race


title: S3-H205

value: Pre-Menopausal

tag: histology


title: S3-H202

value: Infiltrating Ductal Carcinoma

tag: metastases


title: S3-H209

tag: menopausal status

value: Discovery TN


title: S3-H204

tag: ajcc stage (7th edition, 2010)

value: Negative


title: S3-H203

value: Female

tag: set


title: S3-H200

tag: er

value: TN


title: S3-H199

tag: pr

value: No mets


title: S3-H198

tag: triple negative


title: S3-H197

tag: ChIP


title: S3-H212

tag: tissue


title: 4135447160_F

description: SAMPLE 1

value: Male

tag: bmi

tag: systemic inflammation group

tag: smoking pack-years

tag: age


title: S3-H196

tag: age, years

tag: gender

tag: body mass index

tag: tumor size


title: S3-H194

tag: race

tag: histology

tag: tumor grade

tag: positive nodes

tag: metastases


title: S3-H191

tag: menopausal status

tag: ajcc stage (7th edition, 2010)

tag: set

tag: er

tag: pr


title: S3-H193

tag: ChIP

tag: tissue

tag: triple negative

value: Poorly Differentiated


title: S3-H187

tag: age, years

value: Post-Menopausal


title: S3-H208

tag: gender


title: S3-H189

tag: body mass index


title: S3-H188

value: Asian/Pacific Islander

tag: tumor size


title: S3-H190

tag: race


title: S3-H185

tag: histology


title: S3-H182

tag: tumor grade


title: S3-H181

tag: positive nodes


title: S3-H180

tag: metastases


title: S3-H179

tag: menopausal status


title: S3-H178

tag: ajcc stage (7th edition, 2010)


title: S3-H175

tag: set


title: S3-H174

tag: er


title: S3-H173

tag: pr


title: S3-H172

tag: ChIP


title: S3-H171

tag: tissue


title: S3-H170

tag: triple negative


title: S3-H168

tag: age, years


title: S3-H184

tag: gender

value: any size with direct extension


title: S3-H167

tag: body mass index


title: S3-H165

tag: tumor size


title: S3-H166

tag: race


title: S3-H164

tag: histology


title: S3-H186

tag: tumor grade


title: S3-H163

tag: positive nodes


title: S3-H159

value: Moderately Differentiated

tag: metastases


title: S3-H162

value: Illumina Human610-Quad v1.0 BeadChip

tag: menopausal status


title: MDM HIV-infected, FcR stimulated, rep2

source_name: human monocyte derived macrophages from healthy donor

tag: cell type

value: monocyte derived macrophages


title: S3-H161

value: Breast cancer

tag: ajcc stage (7th edition, 2010)

tag: set


title: S3-H160

tag: er

tag: pr


title: S3-H177

tag: ChIP

tag: tissue

value: Caucasian


title: S3-H183

tag: age, years

tag: triple negative


title: S3-H155

tag: gender

tag: body mass index


title: S3-H154

tag: race

value: Invasive carcinoma of the breast

tag: tumor size


title: S3-H152

tag: histology

value: Infiltrating Ductal Carcinoma

tag: tumor grade


title: S3-H157

value: Pre-Menopausal

value: Discovery TN

tag: positive nodes

tag: metastases


title: S3-H150

value: Female

tag: menopausal status

value: Negative

value: Mets fo


title: S3-H153

tag: ajcc stage (7th edition, 2010)

value: TN


title: S3-H149

tag: set

value: Poorly Differentiated


title: S3-H176

value: Post-Menopausal

tag: er

value: No mets


title: S3-H158

tag: pr


title: S3-H148

tag: ChIP


title: S3-H147

tag: tissue


title: S3-H146

tag: age, years

value: Well Differentiated


title: S3-H143

tag: triple negative

value: Moderately Differentiated


title: S3-H156

value: Illumina Human610-Quad v1.0 BeadChip

tag: gender


title: S3-H97C

value: Illumina Human660W-Quad v1.0 BeadChip

tag: body mass index

value: Validation TN


title: S3-H144

value: Breast cancer

tag: race

value: Caucasian


title: S3-H134

value: Infiltrating Ductal Carcinoma

tag: tumor size


title: S3-H96C

tag: histology


title: S3-H94C

value: Menopausal

tag: tumor grade


title: S3-H145

value: Discovery TN

tag: positive nodes


title: S3-H129

value: Female

value: Pre-Menopausal

value: TXNXMX


title: S3-H120

value: Negative

value: TN

tag: metastases


title: S3-H111

tag: menopausal status


title: S2-H91B

tag: ajcc stage (7th edition, 2010)


title: S3-H133

tag: set

value: any size with direct extension


title: S2-H84

tag: er

value: No mets


title: S3-H151

value: Post-Menopausal

tag: pr


title: S2-H90

tag: ChIP


title: S2-H82

tag: tissue


title: S2-H80

tag: age, years


title: S1-H9

tag: triple negative

value: Poorly Differentiated


title: S1-H8

tag: gender


title: S2-H83

tag: body mass index


title: S1-H73

tag: race


title: S1-H71

value: Well Differentiated

tag: tumor size


title: S1-H7

value: Illumina Human660W-Quad v1.0 BeadChip

tag: histology


title: S1-H69

value: Validation TN

tag: tumor grade


title: S1-H68

value: Breast cancer


title: S1-H67

value: Caucasian


title: S1-H66

value: Infiltrating Ductal Carcinoma

tag: positive nodes


title: S1-H60

value: Moderately Differentiated

tag: metastases


title: S1-H65

tag: menopausal status

value: Menopausal


title: S1-H58B

value: Female

tag: ajcc stage (7th edition, 2010)


title: S2-H81

value: Pre-Menopausal

tag: set


title: S1-H6

tag: er


title: S1-H53

tag: pr


title: S2-H79

tag: ChIP


title: S1-H50

tag: tissue


title: S1-H49


title: S1-H47


title: S1-H51

tag: age, years


title: S1-H48

tag: triple negative


title: S2-H78

tag: gender


title: S1-H52

tag: body mass index

value: Medullary Carcinoma


title: S1-H72B

tag: race

value: Negative


title: S1-H59

value: TN

tag: tumor size


title: S1-H46

tag: histology


title: S1-H45


title: S1-H41


title: S1-H44

tag: tumor grade


title: S1-H38

tag: positive nodes


title: S1-H36


title: S1-H40


title: S1-H43

value: Infiltrating Lobular Carcinoma

tag: metastases


title: S1-H3B

tag: menopausal status

value: No mets


title: S1-H61

tag: ajcc stage (7th edition, 2010)


title: S1-H29

value: Post-Menopausal

tag: set


title: S1-H28

tag: er

value: Poorly Differentiated


title: S1-H35B

tag: pr


title: S1-H27

tag: ChIP

value: Pre-menopausal


title: S1-H14

value: Illumina Human660W-Quad v1.0 BeadChip

tag: tissue


title: S1-H10

value: Validation TN


title: S1-H19

value: Breast cancer

tag: age, years


title: S1-H20B

value: Caucasian

tag: triple negative


title: HEK293-CT.R2

status: Public on Dec 11 2015

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

institute: INRAE - University PARIS SACLAY

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized wiht GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) as described by the manufacturer.

scan_protocol: Microarrays was scanned with the Affymetrix GeneChip Scanner 7G and the FS450_0007 protocol , as recommended in the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)

data_processing: data were normalized with RMA, analysed with LPE with three FDR methods; the zreal value is indicated in the matrix

source_name: HEK293-CT cells

label_protocol: RNA was amplified with GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix) and biotin labeld with GeneChip® WT Terminal Labeling Kit (Affymetrix) according to the manufacturer's

growth_protocol: Cells were grown at 37°C, in a humidified 10% CO2 incubator, in Dulbecco's modified Eagle's medium with GlutaMAX (Gibco) supplied with 10%FBS (Gibco) and 200 ug/ml Hygromycin B (10687-010-Invitrogen).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), from three biological replicates, according to was performed according to the manufacturer's instructions.

treatment_protocol: HEK-BAHD1 were generated by integration of a single copy of the BAHD1 cDNA under the control of the human cytomegalovirus (CMV) immediate-early enhancer/promoter in the HEK293 genome. In the isogenic control line (HEK293-CT), the β-galactosidase DNA sequence was inserted in place of BAHD1, albeit out-of-frame to avoid translation into protein.

tag: treatment

value: control

tag: cell line


title: SilX-BAHD1.R2

description: Gene expression data

scan_protocol: Affymetrix Human Gene 1.0 ST Array was scanned with the Affymetrix GeneChip Scanner 7G and the FS450_0007 protocol , as recommended in the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)

data_processing: Data were normalized with RMA

source_name: SilX-BAHD1 cells

growth_protocol: Cells were grown at 37°C, in a humidified 10% CO2 incubator, in Dulbecco's modified Eagle's medium with GlutaMAX (Gibco) supplied with 10%FBS (Gibco) and 70 ug/ml Hygromycin B (10687-010-Invitrogen).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), from three biological replicates, according to the manufacturer's instructions.  RNA was treated with DNase I to remove residual DNA and then cleaned with DNase Inactivation Reagent (Ambion® Inc.) RNA was quality checked an then store at -80°C.

treatment_protocol: We established a BAHD1 gene-specific knockdown cell line using the SilenciX® siRNA delivery system (Tebu-bio). This technology is based on EBV-replication, and ensures chromosome-like replication of an episome stably expressing either a shRNA against BAHD1 (silXBAHD1) or a control shRNA (silX-CT).

tag: genotype/variation

value: BAHD1 knockdown


title: SilX-CT.R2

description: Gene expression data

source_name: SilX-CT cells


title: ACHN with Kindlin-2 knockdown

status: Public on Dec 16 2015

city: Beijing

first: Huiying

last: He

address: 38# Xueyuan Road, Haidian District

institute: Peking University Health Science Center

description:
E_(HuGene-1_0-st-v1)
Gene expression data from ACHN Kindlin-2-depleting cells.

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method (Expression Console 1.4.1). The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: human clear cell renal cell carcinoma cells, Kindlin-2 knockdown

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

growth_protocol: The transfected ACHN cells were cultured in minimum essential medium (MEM) with 10% FBS with 400 µg/ml G418.

treatment_protocol: ACHN cells were transfected with control shRNA and Kindlin-2 shRNA, and the cells were collected for further total RNA extraction.

value: ACHN

tag: cell type

value: clear cell renal cell carcinoma cell line

tag: shRNA


title: Distal_Intestine_24CM_Tank18_Fish2

status: Public on Nov 13 2015

city: St. John's

first: Tyler

last: Brown

state: Newfoundland

address: 1 Marine Lab Road

department: Biology

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299) as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray was scanned at 5 µm resolution and 90% of laser power using a ScanArray Gx Plus scanner and ScanArray Express software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using ImaGene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 log ratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Log ratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 2 * SD) for each channel on each array. Log ratio data for a particular spot was also removed if the spot was flagged in ImaGene.

organism: Salmo salar

source_name: Distal Intestine, 24% CM diet week 16, individual fish

label_protocol: Nine individual fish, each from the 24CM and 0CM control diet groups, were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified liver total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quality and quantity of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

growth_protocol: Six hundred fish were randomly distributed into twelve 500L tanks (50 fish per tank) with flow-through water supply at a rate of 12 L min-1 (temperature: 14°C, dissolved oxygen: 10 mgL-1) and all fish were kept on a photoperiod of 12 hours light and 12 hours dark. Fish were fed a commercial diet (Nutra Transfer NP, 3 mm, Skretting Canada, St. Andrews, NB, Canada) during a 1 week acclimation period. Once the fish were acclimated, they were gradually moved onto the control diet over a period of 3 days. Initial sampling was done 1 week after the experimental fish were completely weaned from the commercial diet. Subsequently, fish were weaned onto their assigned experimental diet over another period of 3 days. Fish were fed the experimental diets to apparent satiety twice daily in triplicate tanks over a period of 16 weeks.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions.

treatment_protocol: Fish were fed either a control control diet with 34.9% FM; or a camelina meal (CM)-containing diet with partial replacement of FM with 8% CM; 16% CM or 24% CM.

value: Distal Intestine

tag: life stage

value: Juvenile

tag: diet

value: 24% Camelina meal for 16 wks

source_name: Distal Intestine, Pooled Control from tissues involved in the microarray experiment, week 16

tag: sample type

value: pooled reference


title: HEK-BAHD1.R2

description: Gene expression data

source_name: HEK-BAHD1 cells

value: over-expressing the BAHD1 gene


title: SilX-CT.R1

description: Gene expression data


title: HEK293-CT.R1

description: Gene expression data


title: SilX-BAHD1.R1

description: Gene expression data


title: SilX-CT.R3

description: Gene expression data


title: HEK293-CT.R3

description: Gene expression data


title: Distal_Intestine_24CM_Tank11_Fish3


title: HEK-BAHD1.R3

description: Gene expression data


title: Distal_Intestine_24CM_Tank6_Fish2


title: Distal_Intestine_24CM_Tank11_Fish2


title: HEK-BAHD1.R1

description: Gene expression data


title: Distal_Intestine_24CM_Tank18_Fish3


title: Distal_Intestine_24CM_Tank11_Fish1


title: Distal_Intestine_24CM_Tank6_Fish3


title: ACHN control cells

description:
NC_(HuGene-1_0-st-v1)
Gene expression data from ACHN control cells.

source_name: human clear cell renal cell carcinoma cells, control


title: Distal_Intestine_24CM_Tank18_Fish1


title: Distal_Intestine_0CM_Tank52_Fish1

source_name: Distal Intestine, 0% CM diet week 16, individual fish

value: 0% Camelina meal for 16 wks


title: SilX-BAHD1.R3

description: Gene expression data


title: Distal_Intestine_0CM_Tank52_Fish3


title: Distal_Intestine_0CM_Tank51_Fish3


title: Distal_Intestine_0CM_Tank51_Fish2


title: Distal_Intestine_24CM_Tank6_Fish1


title: Distal_Intestine_0CM_Tank51_Fish1


title: Distal_Intestine_0CM_Tank52_Fish2


title: Distal_Intestine_0CM_Tank13_Fish1


title: Distal_Intestine_0CM_Tank13_Fish2


title: Distal_Intestine_0CM_Tank13_Fish3


title: Mouse_Muscle_Dysf w ACVR2B/Fc_2

status: Public on Sep 04 2015

city: Baltimore

first: Yun-Sil

last: Lee

state: Maryland

address: 725 North Wolfe Street, PCTB 803

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: 10 weeks_quadriceps muscle

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: None, surgical biopsy

extract_protocol: Quadriceps muscle (100 mg) was homogenized in TRIzol Reagent (Life Technologies), and RNA was isolated from the supernatant with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. All samples were treated with RNase-free DNase set (Qiagen) to remove trace amounts of genomic DNA.

treatment_protocol: Male C57BL/6 (wt) and Dysf-/- mice beginning at 6 weeks of age were given four weekly Intraperitoneal injections of ACVR2B/Fc (10 mg kg-1, i.e., 200 ug per injection)

value: quadriceps muscle

value: Dysf-/-

tag: gender

value: male


title: Mouse_Muscle_F66_2


title: Mouse_Muscle_Dysf_2


title: Mouse_Muscle_WT_2

value: WT


title: Mouse_Muscle_F66_Dysf_2


title: Mouse_Muscle_F66_1


title: Mouse_Muscle_Dysf_3


title: Mouse_Muscle_WT w ACVR2B/Fc_2


title: R0052-SLP-only treatment of HT-29 cells_4

status: Public on Aug 25 2015

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

institute: Lallemand Health Solutions Inc.

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50oC for 18h on the whole human gene expression microarrays version 2 Agilent microaray (GE 4x44K; GPL10332).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with ImaGene® microarray analysis software.

data_processing:
Global LOWESS normalization was conducted with ImaGene® microarray analysis software. Statistical analysis (T-test) was performed with Multi-Experiment Viewer (MeV, version 4.2).

The Sample supplementary .txt file includes the quantified normalized data before data analysis (e.g., log2 fold and T-test analysis). The Sample data table includes the raw log2fold changes before statistical analysis using T-test from MeV.

source_name: Control Rep 4

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript III (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Burlington, ON, Canada) following manufacturer's protocol and with PhaseLock tubes (5 Prime, Gaithersburg, MD) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, Germantown, MD). Quality was assessed by Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). RIN over 9.0 were considered good quality RNA for reverse transcription.

treatment_protocol: HT-29 cells were incubated for 3 h with with either the single strains (R0033, R0052 or R0071), probiotic combination (PC), R0052-SLP (38µg/ml) alone or in combination with poly (I:C) at 10 µg/mL at a MOI of 100:1.

value: Colonic adenocarcinoma cells

value: unchallenged HT-29 cells

source_name: PC-only Rep 4

value: 3h incubation of HT-29 cells with R0052-SLP 38ug/ml


title: Mouse_Muscle_Dysf w ACVR2B/Fc_3


title: Mouse_Muscle_F66_Dysf_3


title: R0052-SLP-only treatment of HT-29 cells_2

source_name: SLP-only Rep 2

source_name: Control Rep 2


title: R0052-SLP-only treatment of HT-29 cells_3

source_name: Control Rep 3

source_name: PC-only Rep 3


title: Mouse_Muscle_WT_3


title: Mouse_Muscle_WT w ACVR2B/Fc_1


title: Mouse_Muscle_F66_3


title: Mouse_Muscle_WT_1


title: Mouse_Muscle_WT w ACVR2B/Fc_3


title: Mouse_Muscle_F66_Dysf_1


title: R0071+poly (I:C) treatment of HT-29 cells_3

description: R0071+poly (I:C)

value: 3h incubation of HT-29 cells with R0071 (MOI 100:1) + poly IC


title: S2-H89

source_name: Human breast cancer

value: Illumina Human660W-Quad v1.0 BeadChip

value: Breast cancer

value: Female

tag: race

value: Caucasian

tag: body mass index

tag: menopausal status

value: Post-Menopausal

tag: histology

value: Infiltrating Ductal Carcinoma

tag: ajcc stage (7th edition, 2010)

value: Validation TN

value: Negative

value: TN

tag: tumor grade

value: Poorly Differentiated

tag: tumor size

tag: positive nodes

tag: metastases

value: No mets


title: Mouse_Muscle_Dysf_1

tag: tissue

value: quadriceps muscle

tag: treatment

value: Dysf-/-

value: male


title: R0071+poly (I:C) treatment of HT-29 cells_4

description: R0071+poly (I:C)

tag: cell line

tag: cell type

value: Colonic adenocarcinoma cells

value: unchallenged HT-29 cells


title: R0071+poly (I:C) treatment of HT-29 cells_1

description: R0071+poly (I:C)

source_name: R0071+IC Rep 1

value: 3h incubation of HT-29 cells with R0071 (MOI 100:1) + poly IC

source_name: Control Rep 1


title: R0052-SLP-only treatment of HT-29 cells_1

source_name: SLP-only Rep 1

value: 3h incubation of HT-29 cells with R0052-SLP 38ug/ml


title: R0071+poly (I:C) treatment of HT-29 cells_2

description: R0071+poly (I:C)

source_name: R0071+IC Rep 2


title: R0052+poly (I:C) treatment of HT-29 cells_2

description: R0052+poly (I:C)

source_name: R0052+IC Rep 2

value: 3h incubation of HT-29 cells with R0052 (MOI 100:1) + poly IC


title: R0052+poly (I:C) treatment of HT-29 cells_4

description: R0052+poly (I:C)


title: R0052+poly (I:C) treatment of HT-29 cells_1

description: R0052+poly (I:C)

source_name: R0052+IC Rep 1


title: R0033+poly (I:C) treatment of HT-29 cells_4

description: R0033+poly (I:C)

value: 3h incubation of HT-29 cells with R0033 (MOI 100:1) + poly IC


title: R0052+poly (I:C) treatment of HT-29 cells_3

description: R0052+poly (I:C)


title: R0033+poly (I:C) treatment of HT-29 cells_3

description: R0033+poly (I:C)


title: FH8-RA

status: Public on Jul 22 2015

city: Leiden

first: Cathelijne

middle: W

last: van den Berg

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description:
Chip 2
Sample 16

hyb_protocol: Per sample, 750 ng of the obtained biotinylated ss-cDNA samples was hybridized onto the Illumina HumanHT-12 v4 microarray chips according to the Illumina Manual “Direct Hybridization Assay Guide”.

scan_protocol: Scanning was performed on the Illumina iScan. Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with default settings (no background subtraction and no normalization).

data_processing: The raw files were processed with the lumi R package (Du et al. 2008). Probes with the present count 0 were discarded. The raw intensity values of the microarray data were normalized by variance stabilizing normalization using the vsn R package (Huber et al., 2002) and subsequently normalized by the common references (chip 1-AH-pool replicate 1 and chip 2-AH-pool replicate 1).  Normalized data were summarized at the gene level. When a gene had more than one microarray probe, the one with the highest variance across the samples was used for subsequent analysis. Genes were binned into 30 bins by the intensity and the t-test applied to each bin. The processed data file "normalized_data.txt" contains log2 normalized intensities.

source_name: heart right atrium

label_protocol: Biotinylated ss-cDNA was prepared using the NuGEN Ovation PicoSL WTA v2 System according to the manufacturer’s specifications with an input of approximately 50 ng total RNA.

extract_protocol: Total RNA was extracted from the samples. The quality and integrity of the RNA samples was confirmed using Lab-on-Chip RNA 6000 Nano and RNA 6000 Pico (both Agilent) on the Agilent 2100 Bioanalyzer.

value: female

tag: age

value: 20+ weeks

value: fetal heart

tag: heart compartment

value: right atrium


title: Ref-pool

description:
Chip 2
Sample 20

source_name: Universal Human Reference RNA

value: mix


title: AH-pool_1

description:
Chip 1
replicate 1
Sample 17

source_name: Human Normal Heart Donor Pool

value: heart


title: AH-pool_3

description:
Chip 2
replicate 1
Sample 19


title: AH-pool_2

description:
Chip 2
replicate 2
Sample 18


title: R0052-SLP+poly (I:C) treatment of HT-29 cells_2

description: R0052-SLP+poly (I:C)

source_name: R0052-SLP Rep 2


title: FH8-RV

description:
Chip 2
Sample 15

source_name: heart right ventricle

value: right ventricle


title: R0033+poly (I:C) treatment of HT-29 cells_2

description: R0033+poly (I:C)

source_name: R0033+IC Rep 2


title: PC-only treatment of HT-29 cells_3

description: PC-only (PC-only = ProbioKid-only)

value: 3h incubation of HT-29 cells with PC-only (MOI 100:1)


title: PC-only treatment of HT-29 cells_2

description: PC-only (PC-only = ProbioKid-only)

source_name: ProbioKid Rep 2


title: PC-only treatment of HT-29 cells_4

description: PC-only (PC-only = ProbioKid-only)

source_name: Control Rep 4

source_name: PC-only Rep 4


title: R0033+poly (I:C) treatment of HT-29 cells_1

description: R0033+poly (I:C)

source_name: R0033+IC Rep 1


title: R0052-SLP+poly (I:C) treatment of HT-29 cells_1

description: R0052-SLP+poly (I:C)

source_name: R0052-SLP Rep 1


title: R0052-SLP+poly (I:C) treatment of HT-29 cells_4

description: R0052-SLP+poly (I:C)


title: PK+ poly IC treatment of HT-29 cells_4

description: PC = probiotic combination (R0033, R0052, R0071) = PK

source_name: PC + poly IC Rep 4

value: 3h incubation of HT-29 cells with PC (MOI 100:1) + poly IC


title: PC-only treatment of HT-29 cells_1

description: PC-only (PC-only = ProbioKid-only)

source_name: ProbioKid Rep 1

source_name: Control Rep 1


title: PK+ poly IC treatment of HT-29 cells_2

source_name: PK+IC Rep 2

source_name: Control Rep 2


title: PK+ poly IC treatment of HT-29 cells_1

source_name: PK+IC Rep 1


title: FH7-V

description:
Chip 1
Sample 12

source_name: heart ventricle

value: 20 weeks

value: ventricle


title: FH5-RA

description:
Chip 2
Sample 10

source_name: heart right atrium

value: male

value: 15 weeks


title: FH8-LV

description:
Chip 1
Sample 13

source_name: heart left ventricle

value: left ventricle


title: FH6-V

description:
Chip 1
Sample 11

value: 15 weeks, 3 days


title: FH8-LA

description:
Chip 2
Sample 14

source_name: heart left atrium

value: left atrium


title: R0052-SLP+poly (I:C) treatment of HT-29 cells_3

description: R0052-SLP+poly (I:C)

source_name: Control Rep 3

value: Colonic adenocarcinoma cells

value: unchallenged HT-29 cells

source_name: PC-only Rep 3

value: 3h incubation of HT-29 cells with R0052-SLP 38ug/ml


title: FH5-LV

description:
Chip 2
Sample 9

value: fetal heart


title: FH5-RV

description:
Chip 2
Sample 8

source_name: heart right ventricle


title: FH4-V

description:
Chip 1
Sample 6

value: female

value: 10 weeks, 5 days


title: FH3-A

description:
Chip 2
Sample 5

source_name: heart atrium

value: 7 weeks, 4 days

value: atrium


title: FH2-A

description:
Chip 2
Sample 3


title: FH5-LA

description:
Chip 2
Sample 7


title: FH2-V

description:
Chip 1
Sample 2


title: FH1-V

description:
Chip 1
Sample 1

value: 7 weeks, 2 days


title: PK+ poly IC treatment of HT-29 cells_3

source_name: PC + poly IC Rep 3

value: 3h incubation of HT-29 cells with PC (MOI 100:1) + poly IC


title: CTL_AN08161_ba41-42-22_8.1

status: Public on Dec 09 2014

type: SRA

city: Los Angeles

first: Neelroop

last: Parikshak

state: California

address: 695 Charles E. Young Dr. South

institute: UCLA

description: Total RNA (rRNA depleted)

library_source: transcriptomic

data_processing:
Aligned to the Human reference genome assembly GRCh37.73 using Tophat2 {v2.0.9, Trapnell:2012gg} as follows:  tophat -o outputfolder -g 10 -p 8 -r 99 --no-novel-juncs -G GRCh37.73.gtf hg19bowtieindex pairedread1.fastq pairedread2.fastq  Aligned reads were sorted and reads mapped to different chromosomes were removed from the BAM file using samtools v0.1.19.
Quantification of gene expression levels with HTSeq (v.0.6.1) with a union exon model as follows:  python -m HTSeq.scripts.count --stranded=no --mode=union --type=exon --quiet inputfile.sam --GTF GRCh37.73.gtf >> outputfolder
Calculated FPKM values from count level data as follows: datFPM <- sweep(log2(datExpr + 1), 2, log2(apply(datExpr,2,sum)/10^6))  keep <- apply(datFPM>1,1,sum)>(0.80*ncol(datFPM)) ## Keep those with > 1 FPM in 80% of samples                                         datExpr <- datFPM[keep,]. Adjusted expression values were calculated by running the following linear model: lm.out <- lm(thisExpr ~ diagnosis + age + sex + RIN + brainbank + seqStatPC1 + seqStatPC2); where seqStatPC1 and seqStatPC2 are calculated from the first two principal components from the 15 sequencing quality metrics. Followed by: thisExpr.reg <- coef[1] + coef[2]*regvars[,"diagnosis"] + lm.out$residuals; where coef[1] and coef[2] are the intercept and the coefficient corresponding to diagnosis, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: Count-level data generated by HTSeq; adjusted FPKM values generated in R as described in the data processing step

source_name: Post-mortem brain tissue

extract_protocol:
Approximately 100mg of tissue across the cortical region of interest was isolated from each sample for up to two RNA extractions using the miRNeasy kit (Qiagen). The best RNA extraction based on RIN was used for RNA-seq.
Ribosomal RNA was depleted from 2ug total RNA with the Ribo-Zero Gold kit (Epicentre). Remaining RNA was then size selected with AMPure XP beads (Beckman Coulter) and resuspended in 8.5 ul of Illumina resuspension buffer and an additional 8.5 ul of 2x EPF buffer. Subsequent steps followed the Illumina TruSeq protocol (starting at page 84 of the sample prep v2 guide, no changes). After this protocol was followed, libraries were quantified with the Quant-iT PicoGreen assay (Life Technologies) and validated on an Agilent 2200 TapeStation system. Libraries were pooled to multiplex 24 samples per lane using Illumina barcodes, and each pool was sequenced six times on a HiSeq2000/2500 instrument using high output mode with standard chemistry and protocols for 50bp paired end reads. Most libraries were sequenced across two sequencing cores at UCLA. Read quality was similar across both core facilities, and reads across six lanes for each sample were pooled after demultiplexing (with Casava v1.8) for downstream analysis.

tag: brainid

tag: regionid

tag: diagnosis

value: CTL

tag: Sex

value: F

tag: rin

tag: brainbank

value: ATP

tag: pmi

tag: primarycauseofdeath

value: Multisystem Failure


title: CTL_UMB5079_ba41-42-22_7.9

description: Total RNA (rRNA depleted)

value: M

value: NICHD

value: Drowning

tag: secondarycauseofdeath

value: Alcohol intoxication


title: CTL_AN17425_ba41-42-22_7.9

description: Total RNA (rRNA depleted)

value: Heart Attack

value: Heart Disease


title: FH3-V

description:
Chip 1
Sample 4

tag: gender

value: male

value: fetal heart

value: ventricle


title: PSI-less/Scp-less, Biological replicate 1 of 3

status: Public on Mar 30 2015

city: Sydney

first: Miguel

middle: A

last: Hernández-Prieto

address: Macleay Building A12

department: School of life and environmental sciences

institute: University of Sydney

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing: The scanned images were analyzed with Agilent's Feature Extraction program version 10.5.1.1 (Protocol: GE1_105_Dec08). gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized in R using the bioconductor package OLIN.

organism: Synechocystis sp. PCC 6803

source_name: Photosystem I less strain grown under low light and 10 mM glucose

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Synechocystis 6803 PSI-less and PSI-less/ScpABCDE- mutants were cultivated at 30°C at a light intensity of 4–5 μmol photons m–2 s–1 in BG-11 growth medium (Rippka et al 1979) supplemented with 10 mM glucose.

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959).

tag: strain

value: Photosystem I-less

source_name: Photosystem I-less/ScpABCDE-less strain grown under low light and 10 mM glucose

value: Photosystem I-less/ScpABCDE-less


title: PSI-less/Scp-less, Biological replicate 2 of 3