title: AF blood 3

city: Shanghai

first: Yingjia

last: Xu

address: No.241, Huaihai west Road,

institute: Shanghai Chest Hospital

description:
Sample name: 236046
lncRNA and mRNA expression

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k 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 scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: AF blood 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: Blood from every subject were snap-frozen in liquid nitrogen immediately after resection and stored at -80 °C until use.

tag: disease state

value: AF

value: blood

value: Female


title: ER_siNS_24h_b3

status: Public on Jan 01 2016

type: RNA

city: Los Angeles

first: Dai-Ying

last: Wu

state: CA

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

country: USA

institute: University of Southern California

description: rep 3

hyb_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

data_processing: Bead summarized data was output from GenomeStudio. This data were normalized using neqc with limma (3.14.4) in R (2.15.3)

label: biotin

molecule: total RNA

organism: Homo sapiens

growth_protocol: A clonal line of U2OS cells that stably express wild-type rat ER were plated in 6-well dishes with medium supplemented with 5% fetal bovine serum.

extract_protocol: Total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using electrophoresis on an Agilent Bioanalyzer using the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 5 ug of high quality total RNA was submitted to the Southern California Genotyping Consortium at the University of California, Los Angeles.

treatment_protocol: On the next day the cells were transfected with 60 pmol of siRNA per well using Lipofectamine RNAiMAX (Invitrogen) using manufacturer’s protocol. After 2 days (24hr time point), or 3 days (2 hr and 4 hr timepoints) cells were treated with Dex for the indicated times. All treatment groups were harvested at the same time.

tag: time point

tag: transfection

value: siNS


title: ER_siNS_24h_b4

description: rep 4

scan_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.


title: normal blood 2

country: China

description:
Sample name: 235879
lncRNA and mRNA expression

source_name: normal blood 2

value: normal

tag: tissue

tag: gender

tag: age


title: AF blood 1

description:
Sample name: 153531
lncRNA and mRNA expression

source_name: AF blood 1


title: DOG6_SL_B2

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: The Affymetrix GeneTitan automatic work flow was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

label_protocol: Nugen protocol

growth_protocol: For the transcriptome analyses NILDOG1, NILDOG3 and NILDOG6 were grown in a randomized complete block design with three replicates for each environmental condition. Each replicate consisted of a bulk of four plants. The precise growth conditions used were described by (He et al., 2014 Journal of Experimental Botany).

extract_protocol: The polysome associated RNA is isolated from the polysome region of a linear sucrose gradient and total RNA is isolated from the raw extraction buffer  purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from freshly harvested, dry seeds of three biological replicates of each treatment

tag: genetic background

value: near isogenic line of DELAY OF GEMRMINATION 6 (DOG6)

tag: plant stage

value: freshly harvested dry seed

tag: growth condition

value: standard light (SL)


title: DOG6_SL_B3


title: ER_siHic5_2_4h_b2

description: rep 2

label_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.


title: AF blood 2

description:
Sample name: 235778
lncRNA and mRNA expression

source_name: AF blood 2

value: Male


title: normal blood 3

description:
Sample name: 235993
lncRNA and mRNA expression

source_name: normal blood 3


title: ER_siHic5_2_4h_b3

description: rep 3


title: normal blood 1

description:
Sample name: 235830
lncRNA and mRNA expression

source_name: normal blood 1


title: DOG6_SL_B1


title: DOG3_SL_B3

value: near isogenic line of DELAY OF GEMRMINATION 3 (DOG3)


title: ER_siHic5_2_4h_b1

description: rep 1


title: ER_siNS_4h_b3

description: rep 3


title: ER_siHic5_2_0h_b2

description: rep 2


title: ER_siNS_24h_b1

description: rep 1


title: DOG3_SL_B2


title: ER_siNS_0h_b3

description: rep 3


title: DOG3_SL_B1


title: ER_siNS_4h_b4

description: rep 4


title: ER_siNS_4h_b2

description: rep 2


title: Normal mammary gland tissue

city: Tottori

first: Tomohiro

last: Osaki

state: Tottori

address: 4-101 Koyamachominami

department: Faculty of Agriculture

country: Japan

institute: Tottori University

hyb_protocol: We followed protocol of manual that is FlashTagTM Biotin HSR RNA Labeling Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (RMA) were used Affymetrix® Expression Console™ Software.

organism: Canis lupus familiaris

source_name: Normal mammary gland tissue

growth_protocol: For clonal experiments, we serially diluted cell suspensions and plated them onto 96-well plates. We marked wells containing one single cell after microscopic confirmation. A colony was then sub-cultured from each marked well into a 12-well plate. Cloning was repeated two times. Cell lines were maintained in continuous culture over 60 passages, and we designated the established cell line as SNP cells.

extract_protocol: miRNeasy® Mini Kit was used.

treatment_protocol: Establishment of the cell line.The tumor cells were prepared under aseptic conditions for cell culture. The cells were cultured in 35-mm diameter petri dishes (Nunc, Ltd., Roskilde, Denmark) in RPMI 1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% heat-inactivated fetal bovine serum (Nichirei Biosciences Inc., Tokyo, Japan) and PSN (5 mg/ml penicillin, 5 mg/ml streptomycin, and 10 mg/ml neomycin) solution (Invitrogen), then incubated in 5% CO2 at 37 °C. The cells were subcultured by washing with phosphate-buffered saline. Then, the cells were harvested from near-confluent cultures by brief exposure to a solution containing 0.25% trypsin and 1 mmol/l tetrasodium ethylenediaminetetraacetic acid solution with phenol red (Invitrogen). Trypsinization was stopped using RPMI 1640 containing 10% fetal bovine serum. Trypsinized cells were transferred to a new petri dish.

value: female

value: normal mammary gland tissue


title: DOG1_SL_B3

value: near isogenic line of DELAY OF GEMRMINATION 1 (DOG1)


title: ER_siHic5_2_24h_b1

description: rep 1


title: DOG6_LL_B3

value: low light (LL)


title: SNP cells

source_name: Canine mammary gland tumor

label_protocol: We followed protocol of manual that is FlashTagTM Biotin HSR RNA Labeling Kit User Manual.

value: tumor cells in the pleural effusion


title: male breast cancer 172

type: genomic

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if flagged during image-analysis. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

molecule: genomic DNA

source_name: male breast cancer

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: DNA was extracted from fresh frozen tissue using a modification of a back-extraction protocol from the organic phase of the Qiagen Lipid mini RNA kit (Qiagen, Valencia, CA) as follows: 1 M Tris-buffer containing 4 M Guanidine Thiocyanate and 50 mM Sodium Citrate, followed by glycogen precipitation.

tag: size

tag: nhg

value: II

value: negative

tag: er

value: positive

source_name: normal genomic DNA from Promega

tag: sample type

value: reference


title: BCG::B412_4

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
6898350077_L
BCG::B412

hyb_protocol: Hybridization (Illumina), washing, and staining were performed as per manufacturer instructions.

scan_protocol: Arrays were scanned on Illumina BeadStation 500.

data_processing: Probe average intensity signal was calculated with BeadStudio without background correction. Raw data were analyzed with Bioconductor using the one ChannelGUI package. Average probe intensities were log2-transformed and normalized by the lowess method.

source_name: BCG not expressing RD1 region

label_protocol: Labelling was done with the Illumina TotalPrep™ RNA Amplification Kit (Life Technologies) as indicated by the manufacturer.

growth_protocol: DCs were generated by culturing CD14+ monocytes with 50 ng/ml GM-CSF and 1000 U/ml IL-4 (R&D Systems) for 5 days at 0.5 x 10^6 cells/ml in RPMI 1640 (Lonza), supplemented with 2 mM L-glutamine and 15% Fetal Bovine Serum (FBS) (Lonza). At day 5, the cells were tested for their differentiation status by evaluating CD1a expression (>90% CD1a+) and lack of CD14 (>95% CD14-). Before infection, the medium was replaced with RPMI without antibiotics and supplemented with 2 mM L-glutamine and 15% FBS. Cytokine deprivation did not affect DC survival rate, which was >90%.

extract_protocol: RNAs were extracted with the mirVana Isolation Kit (Ambion, Life Technologies) according to the manufacturer's instructions. Quantification and assessment of RNA integrity were inspected by Bioanalyzer analysis (Agilent Technologies).

treatment_protocol: DC cultures were infected with a multiplicity of infection (MOI) of 1 bacteria/cell for 8h.

value: healthy donor

tag: cell type

value: dendritic cells (DC)

tag: infection

value: BCG not complemented with RD1 region

tag: donor


title: DOG6_LL_B2

value: near isogenic line of DELAY OF GEMRMINATION 6 (DOG6)


title: BCG::RD1_4

description:
6898350077_K
BCG::RD1

source_name: DC infected with attenuated Mycobacterium bovis Bacillus Calmette-Guerin (BCG) expressing RD1 region

value: BCG complemented with RD1 region


title: DOG1_SL_B2

value: freshly harvested dry seed

value: standard light (SL)


title: MtbdelRD1::RD1_4

description:
6898350077_I
MtbdelRD1::RD1

source_name: Mtb expressing RD1 region

value: MtbdelRD1 complemented with RD1 region


title: Male rWT TCDD 1000 μg/kg rep1

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: Sample name: WT553

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada.

data_processing: Each genotype was processed separately. Raw array data (CEL files) were loaded into the R statistical environment (v3.1.2) using the affy package (v1.44.0) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. 3 rWT samples were identified as outliers; these were removed and remaining samples re-processed. An updated Probe-to-Entrez Gene ID map, mogene11stv1mmentrezgcdf (v19.0.0), was used for annotation.

organism: Mus musculus

source_name: liver, male rWT, TCDD treated, 1000 μg/kg

growth_protocol: Animals were housed in Macrolon cages with pelleted Altromin 1314 feed and tap water available ab libitum. The housing environment was maintained at 21°C with 50 ± 10% relative humidity and artificial illumination on a 12/12 hour light/dark cycle. Animals were housed individually to avoid aggressive behavior.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated by oral gavage with a single bolus of either one dosage of TCDD (125, 250, 500, or 1000 μg/kg) dissolved in corn oil vehicle or corn oil alone (10mL/kg).

tag: strain/background

tag: genotype/variation

value: rWT

tag: Sex

value: male

value: 12-15 weeks

value: liver

tag: treatment

value: 1000 ug/kg TCDD

tag: exposure time

value: 96 hours


title: Male rWT TCDD 500 μg/kg rep4

description: Sample name: WT625

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada.

source_name: liver, male rWT, TCDD treated, 500 μg/kg

tag: tissue

value: 500 ug/kg TCDD


title: Male rWT TCDD 1000 μg/kg rep2

description: Sample name: WT597

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada.

tag: age


title: DOG6_LL_B1

tag: genetic background

value: low light (LL)


title: DOG1_SL_B1

value: near isogenic line of DELAY OF GEMRMINATION 1 (DOG1)

tag: plant stage


title: Mtb4

description:
6898350077_H
Mtb

source_name: DC infected with Mycobacterium tuberculosis (Mtb)

tag: disease state

value: healthy donor

value: Mtb


title: DOG3_LL_B1

value: near isogenic line of DELAY OF GEMRMINATION 3 (DOG3)

tag: growth condition


title: Male rWT TCDD 500 μg/kg rep3

description: Sample name: WT596


title: DOG3_LL_B3


title: BCG::RD1_3

description:
6898350077_E
BCG::RD1

value: dendritic cells (DC)


title: BCG::B412_3

description:
6898350077_F
BCG::B412

value: BCG not complemented with RD1 region


title: DOG3_LL_B2

value: freshly harvested dry seed


title: Male rWT TCDD 500 μg/kg rep2

description: Sample name: WT563


title: Male rWT TCDD 500 μg/kg rep1

description: Sample name: WT552


title: Male rWT TCDD 250 μg/kg rep3

description: Sample name: WT600

source_name: liver, male rWT, TCDD treated, 250 μg/kg

value: 250 ug/kg TCDD


title: Male rWT TCDD 250 μg/kg rep1

description: Sample name: WT551


title: DOG6_N0_B3

value: near isogenic line of DELAY OF GEMRMINATION 6 (DOG6)

value: low nitrate (N0)


title: MtbdelRD1::RD1_3

description:
6898350077_C
MtbdelRD1::RD1

value: MtbdelRD1 complemented with RD1 region


title: Male rWT TCDD 125 μg/kg rep3

description: Sample name: WT599

source_name: liver, male rWT, TCDD treated, 125 μg/kg

value: rWT

value: male

value: 12-15 weeks

value: 125 ug/kg TCDD


title: Male rWT TCDD 250 μg/kg rep2

description: Sample name: WT562

value: liver

value: 96 hours


title: BCG::B412_2

description:
6898350079_L
BCG::B412


title: Ctrl3

description:
6898350077_A
Ctrl

source_name: dendritic cells (DC)


title: DOG1_LL_B1

value: near isogenic line of DELAY OF GEMRMINATION 1 (DOG1)

value: low light (LL)


title: DOG1_LL_B3


title: DOG3_N0_B2


title: DOG3_N0_B3


title: Mtb3

description:
6898350077_B
Mtb

value: healthy donor

value: Mtb


title: DOG1_LL_B2


title: DOG6_N0_B1


title: MtbdelRD1::B412_3

description:
6898350077_D
MtbdelRD1::B412

source_name: Mtb not expressing RD1 region

value: dendritic cells (DC)

value: MtbdelRD1 not complemented with RD1 region


title: Male rWT TCDD 125 μg/kg rep1

description: Sample name: WT543


title: DOG1_N0_B3

value: freshly harvested dry seed


title: Male rWT CornOil rep5

description: Sample name: WT642

source_name: liver, male rWT, corn oil treated

value: corn oil vehicle


title: DOG6_N0_B2

value: near isogenic line of DELAY OF GEMRMINATION 6 (DOG6)


title: BCG::RD1_2

description:
6898350079_K
BCG::RD1

value: BCG complemented with RD1 region


title: Mtb2

description:
6898350079_H
Mtb


title: Male rWT TCDD 125 μg/kg rep2

description: Sample name: WT564


title: MtbdelRD1::B412_2

description:
6898350079_J
MtbdelRD1::B412


title: Male rWT CornOil rep3

description: Sample name: WT612


title: Male rWT CornOil rep4

description: Sample name: WT636


title: Ctrl2

description:
6898350079_G
Ctrl


title: MtbdelRD1::RD1_2

description:
6898350079_I
MtbdelRD1::RD1

value: MtbdelRD1 complemented with RD1 region


title: BCG::B412_1

description:
6898350079_F
BCG::B412

value: BCG not complemented with RD1 region


title: DOG1_N0_B2

value: low nitrate (N0)


title: DOG1_N0_B1


title: Male rWT CornOil rep1

description: Sample name: WT528

value: rWT

value: male

value: 12-15 weeks


title: Male rWT CornOil rep2

description: Sample name: WT595

value: liver

value: 96 hours


title: Male INS TCDD 1000 μg/kg rep5

description: Sample name: S434

source_name: liver, male INS, TCDD treated, 1000 μg/kg

value: INS

value: 1000 ug/kg TCDD


title: Male INS TCDD 1000 μg/kg rep3

description: Sample name: S418


title: MtbdelRD1::B412_1

description:
6898350079_D
MtbdelRD1::B412

value: healthy donor


title: DOG6_20°C_B3


title: DOG3_20°C_B3

value: near isogenic line of DELAY OF GEMRMINATION 3 (DOG3)


title: Male INS TCDD 1000 μg/kg rep1

description: Sample name: S373


title: MtbdelRD1::RD1_1

description:
6898350079_C
MtbdelRD1::RD1

value: dendritic cells (DC)


title: BCG::RD1_1

description:
6898350079_E
BCG::RD1


title: DOG6_20°C_B2

value: freshly harvested dry seed


title: Male INS TCDD 1000 μg/kg rep2

description: Sample name: S402


title: Male INS TCDD 1000 μg/kg rep4

description: Sample name: S426


title: Mtb1

description:
6898350079_B
Mtb

value: Mtb


title: DOG3_20°C_B2


title: DOG6_20°C_B1

value: near isogenic line of DELAY OF GEMRMINATION 6 (DOG6)


title: Male INS TCDD 500 μg/kg rep4

description: Sample name: S419

source_name: liver, male INS, TCDD treated, 500 μg/kg

value: 500 ug/kg TCDD


title: Ctrl1

description:
6898350079_A
Ctrl


title: Male INS TCDD 500 μg/kg rep3

description: Sample name: S416


title: DOG1_20°C_B3

value: near isogenic line of DELAY OF GEMRMINATION 1 (DOG1)


title: DOG1_20°C_B2


title: 48h100_3

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

description:
keratinocyte_100 µM genistein_48h_rep3
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio software package (gene expression module version 1.9.0).

source_name: keratinocytes

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrepAmp Kit for Illumina arrays

growth_protocol: Keratinocytes were cultured from cryo-preserved cells in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% antibiotic/antimycotic solution at 37 oC in a humidified atmosphere of 5% CO2. 10E5 cells were seeded in 6-well plates and grown to a confluence of approximately 80 %.

extract_protocol: Total RNA was extracted from cells using the High Pure RNA Isolation Kit in accordance with the prescribed protocol, quantified with Quant iT RiboGreen Assay Kit

treatment_protocol: The medium was replaced by fresh medium non-supplemented, containing dimethyl sulfooxide (DMSO) added to a final concentration of 0.05%, or genistein at 30, 60 and 100 µM concentrations, with 0.05% DMSO. The experimental treatment was carried out for 24 h and 48 h period.

tag: cell line

value: HaCaT

value: human immortalized keratinocyte


title: Male INS TCDD 500 μg/kg rep1

description: Sample name: S390


title: 48hK_3

description:
keratinocyte_K_0.05%DMSO_48h_rep3
replicate 3


title: DOG1_20°C_B1


title: DOG3_20°C_B1


title: 24hK_3

description:
keratinocyte_K_0.05%DMSO_24h_rep3
replicate 3


title: Male INS TCDD 250 μg/kg rep3

description: Sample name: S415

source_name: liver, male INS, TCDD treated, 250 μg/kg

value: 250 ug/kg TCDD


title: 24h100_3

description:
keratinocyte_100 µM genistein_24h_rep3
replicate 3


title: Male INS TCDD 500 μg/kg rep2

description: Sample name: S408

value: male


title: 48h30_3

description:
keratinocyte_30 µM genistein_48h_rep3
replicate 3


title: 48h60_3

description:
keratinocyte_60 µM genistein_48h_rep3
replicate 3


title: Male INS TCDD 250 μg/kg rep4

description: Sample name: S433

value: 12-15 weeks


title: DOG6_15°C_B2


title: DOG3_15°C_B3


title: 24h60_3

description:
keratinocyte_60 µM genistein_24h_rep3
replicate 3


title: DOG6_15°C_B1


title: Male INS TCDD 250 μg/kg rep1

description: Sample name: S389

value: liver


title: Male INS TCDD 125 μg/kg rep4

description: Sample name: S425

source_name: liver, male INS, TCDD treated, 125 μg/kg

value: 125 ug/kg TCDD

value: 96 hours


title: 24h30_3

description:
keratinocyte_30 µM genistein_24h_rep3
replicate 3


title: Male INS TCDD 125 μg/kg rep3

description: Sample name: S414

value: INS


title: DOG3_15°C_B1


title: DOG6_15°C_B3


title: Male INS TCDD 250 μg/kg rep2

description: Sample name: S411


title: 48hK_2

description:
keratinocyte_K_0.05%DMSO_48h_rep2
replicate 2


title: DOG3_15°C_B2


title: Male INS TCDD 125 μg/kg rep2

description: Sample name: S396


title: Ctrl4

description:
6898350077_G
Ctrl

value: healthy donor


title: DOG1_15°C_B2


title: MtbdelRD1::B412_4

description:
6898350077_J
MtbdelRD1::B412

value: MtbdelRD1 not complemented with RD1 region


title: DOG1_15°C_B3


title: Male INS CornOil rep4

description: Sample name: S417

source_name: liver, male INS, corn oil treated

value: corn oil vehicle


title: 48h100_2

description:
keratinocyte_100 µM genistein_48h_rep2
replicate 2


title: Male INS TCDD 125 μg/kg rep1

description: Sample name: S380


title: Male INS CornOil rep3

description: Sample name: S410


title: 48h60_2

description:
keratinocyte_60 µM genistein_48h_rep2
replicate 2


title: DOG1_15°C_B1

value: freshly harvested dry seed


title: 48h30_2

description:
keratinocyte_30 µM genistein_48h_rep2
replicate 2


title: Male INS CornOil rep2

description: Sample name: S385


title: Dressler_019_3391_TG_HFD

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

department: Pathology

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on [Array], and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515).

scan_protocol: Array plates were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Data were analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Dressler 019 3391 TG HFD

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Mice were 2-3 months old and were kept on a normal or high fat diet for 4 weeks prior to tissue harvesting.

extract_protocol: RNA was isolated from whole liver tissue using the RNA easy mini kit from Qiagen


title: 24h60_2

description:
keratinocyte_60 µM genistein_24h_rep2
replicate 2


title: 24h100_2

description:
keratinocyte_100 µM genistein_24h_rep2
replicate 2


title: 24hK_2

description:
keratinocyte_K_0.05%DMSO_24h_rep2
replicate 2


title: Dressler_018_3387_TG_HFD

source_name: Dressler 018 3387 TG HFD


title: 48hK_1

description:
keratinocyte_K_0.05%DMSO_48h_rep1
replicate 1


title: Male INS CornOil rep5

description: Sample name: S447


title: Dressler_017_3331_TG_HFD

source_name: Dressler 017 3331 TG HFD


title: Male DEL TCDD 1000 μg/kg rep3

description: Sample name: D292

source_name: liver, male DEL, TCDD treated, 1000 μg/kg

value: DEL

value: 1000 ug/kg TCDD


title: Dressler_015_3226_KO_HFD

source_name: Dressler 015 3226 KO HFD


title: Male DEL TCDD 1000 μg/kg rep4

description: Sample name: D315


title: Male INS CornOil rep1

description: Sample name: S372


title: 48h100_1

description:
keratinocyte_100 µM genistein_48h_rep1
replicate 1


title: Dressler_016_3329_TG_HFD

source_name: Dressler 016 3329 TG HFD


title: 48h60_1

description:
keratinocyte_60 µM genistein_48h_rep1
replicate 1


title: Male DEL TCDD 1000 μg/kg rep2

description: Sample name: D284


title: 24h30_2

description:
keratinocyte_30 µM genistein_24h_rep2
replicate 2


title: Dressler_013_3224_KO_HFD

source_name: Dressler 013 3224 KO HFD


title: Dressler_014_3225_KO_HFD

source_name: Dressler 014 3225 KO HFD


title: Male DEL TCDD 1000 μg/kg rep1

description: Sample name: D275


title: 24hK_1

description:
keratinocyte_K_0.05%DMSO_24h_rep1
replicate 1


title: 48h30_1

description:
keratinocyte_30 µM genistein_48h_rep1
replicate 1


title: Male DEL TCDD 500 μg/kg rep4

description: Sample name: D307

source_name: liver, male DEL, TCDD treated, 500 μg/kg

value: 500 ug/kg TCDD


title: Male DEL TCDD 500 μg/kg rep3

description: Sample name: D300


title: Dressler_012_3277_WT_HFD

source_name: Dressler 012 3277 WT HFD


title: 24h60_1

description:
keratinocyte_60 µM genistein_24h_rep1
replicate 1


title: 24h100_1

description:
keratinocyte_100 µM genistein_24h_rep1
replicate 1


title: Dressler_011_3276_WT_HFD

source_name: Dressler 011 3276 WT HFD


title: 24h30_1

description:
keratinocyte_30 µM genistein_24h_rep1
replicate 1


title: Dressler_010_3275_WT_HFD

source_name: Dressler 010 3275 WT HFD


title: Male DEL TCDD 500 μg/kg rep2

description: Sample name: D285


title: Male DEL TCDD 250 μg/kg rep4

description: Sample name: D305

source_name: liver, male DEL, TCDD treated, 250 μg/kg


title: Dressler_007_58_TG_ND

source_name: Dressler 007 58 TG ND


title: Male DEL TCDD 500 μg/kg rep1

description: Sample name: D274


title: Dressler_008_59_TG_ND

source_name: Dressler 008 59 TG ND


title: SUP-HD1_2C

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

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

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

value: Hodgkin Lymphoma

tag: drug concentration

value: 10 µM

tag: time exposure


title: SUP-HD1_2B

tag: cell type


title: Male DEL TCDD 250 μg/kg rep1

description: Sample name: D276


title: Dressler_004_06_KO_ND

source_name: Dressler 004 06 KO ND


title: Dressler_005_07_KO_ND

source_name: Dressler 005 07 KO ND


title: Dressler_009_93_TG_ND

source_name: Dressler 009 93 TG ND


title: SUP-HD1_1C

value: CTRL


title: Male DEL TCDD 125 μg/kg rep4

description: Sample name: D316

source_name: liver, male DEL, TCDD treated, 125 μg/kg


title: Male DEL TCDD 125 μg/kg rep2

description: Sample name: D283


title: Male DEL TCDD 125 μg/kg rep3

description: Sample name: D293


title: Dressler_003_65_WT_ND

source_name: Dressler 003 65 WT ND


title: KM-H2_2C


title: SUP-HD1_1B


title: Male DEL TCDD 250 μg/kg rep3

description: Sample name: D301

value: 250 ug/kg TCDD


title: Dressler_001_63_WT_ND

source_name: Dressler 001 63 WT ND


title: SUP-HD1_2A


title: Dressler_006_08_KO_ND

source_name: Dressler 006 08 KO ND


title: Dressler_002_64_WT_ND

source_name: Dressler 002 64 WT ND


title: SUP-HD1_1A


title: KM-H2_1C


title: Male DEL TCDD 125 μg/kg rep1

description: Sample name: D271

value: male


title: Male DEL TCDD 250 μg/kg rep2

description: Sample name: D295

value: 12-15 weeks


title: KM-H2_1B


title: KM-H2_2B


title: Male DEL CornOil rep5

description: Sample name: D317

source_name: liver, male DEL, corn oil treated

value: liver


title: KM-H2_2A


title: Male DEL CornOil rep3

description: Sample name: D302


title: L-428_1B


title: L-428_2B


title: Male DEL CornOil rep4

description: Sample name: D304


title: Male DEL CornOil rep1

description: Sample name: D270


title: Male DEL CornOil rep2

description: Sample name: D280


title: KM-H2_1A


title: L-428_2C


title: L-428_1C


title: L-428_2A


title: L-540_2C


title: L-540_1C


title: L-428_1A


title: L-540_2A


title: L-540_2B


title: L-540_1B


title: L-540_1A


title: Umbilical cord tissue - control mother - replicate 5

city: Turku

first: Anna

last: Koskinen

address: Kiinamllynkatu 10

department: Research centre of Applied and Preventive Cardiovascular Medicine (CAPC)

country: Finland

institute: University of Turku

description: replicate 5

data_processing: The data were normalised using quantile normalisation with limma package in R (v.2.15)/Bioconductor (v.2.10) tool

source_name: Umbilical cord_control

extract_protocol: Total RNA was isolated from umbilical cord by using TissueLyser (Qiagen, Hilden, Germany) followed by purification using RNeasy mini kit and RNase-free DNase I (Qiagen, Hilden, Germany). The concentration and the quality were measured by spectrophotometry (NanoDrop ND-2000, Thermo Fisher Scientific, Wilmington, USA) and automated electrophoresis system (Bioanalyzer, Agilent Technologies, CA, USA).

tag: sample group

value: healthy pregnancies (control)

value: Umbilical cord


title: Umbilical cord tissue - control mother - replicate 6

description: replicate 6


title: Umbilical cord tissue - control mother - replicate 4

description: replicate 4


title: CD8+ T cell clone 4.1 stimulation 2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the hybridization oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.

data_processing: Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 11.5.1.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package 43 of Bioconductor 44.

label: Lowinput Quick Amp Labeling Kit

source_name: Cerebrospinal fluid infiltrating cells

label_protocol: Microarrays were done using the "Low RNA Input linear Amplification Kit Plus, One Color" protocol (Cat. N°: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol. Global gene expression analysis was applied using the Agilent SurePrint G3 Human GE v2 8x60K Kit, P/N G4851B, (Agilent Microarray Design ID 039494. 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: TCCs from CSF-infiltrating T cells sorted after staining with specific TCR Vβ-familes, were established by seeding in 96-well U-botton microtiter plates 0.3 T cells cells/well with 2 x 105 non-autologous, irradiated PBMC, 2.5 µg/ml of PHA-L (Sigma) and IL-2 at the same medium used to expand CSF cells. Additional IL-2 was added every 3-4 days and after two weeks cells were pooled and analyzed, cryopreserved or restimulated.

extract_protocol: RNA extraction, including a DNAse treatment step, was performed with RNeasy Micro (QIAGEN, Hilden, Germany) following manufacturer’s instructions.

treatment_protocol: 1 x 106 T cells were stimulated with 1 µg/ml of surface-coated anti-CD3 (OKT3, Ortho Biotech Products, Raritan, NJ) and 10-7 M PMA (SIGMA) for 24h.

tag: gender

value: Female

value: 36 years old

value: CD8+ T simulating


title: Umbilical cord tissue - control mother - replicate 3

description: replicate 3


title: CD8+ T cell clone 4.1 stimulation 1


title: Umbilical cord tissue - control mother - replicate 2

description: replicate 2


title: Genomic DNA from SM4XBYC_T

city: London

first: Andrew

last: Feber

address: Division of Surgery & Interventional Science, Charles Bell House, 43-45 Foley Street

institute: University College London

description:
primary NA
9370847111

hyb_protocol: Illumina HumMeth 450K protocol

scan_protocol: Illumina HumMeth 450K protocol

data_processing: The ChAmp pipeline (Bioconductor). Normalisation with BMIQ and batch correction with ComBat as part of the ChAmp pipeline.

label: Cy5 and Cy3

source_name: primary

label_protocol: Illumina HumMeth 450K protocol

extract_protocol: DNA was extracted using the Qiagen QIAamp DNA mini kit

tag: lesion

value: primary

tag: sample site

tag: primary site

value: small intestine

tag: grade

tag: source tissue type

value: FFPE


title: Umbilical cord tissue - diabetic mother - replicate 6

description: replicate 6

source_name: Umbilical cord_DM

value: maternal diabetes (DM)

tag: tissue


title: CD8+ T cell clone 17.2 stimulation 1

tag: age


title: CD4+ T cell clone 21.1 stimulation 1

value: CD4+ T simulating


title: Genomic DNA from SM4XBYB_T

description:
metastasis NA
9370847109

source_name: metastasis

value: metastasis


title: Umbilical cord tissue - diabetic mother - replicate 5

description: replicate 5


title: Umbilical cord tissue - control mother - replicate 1

description: replicate 1


title: CD4+ T cell clone 21.1 stimulation 2


title: Genomic DNA from SM4XBYD_T

description:
metastasis NA
9370847143


title: CD4+ T cell clone 17.1 stimulation 1


title: Genomic DNA from SM4XBY6_T

description:
metastasis NA
9370847111


title: Umbilical cord tissue - diabetic mother - replicate 4

description: replicate 4


title: CD4+ T cell clone 17.1 stimulation 2


title: stimulated circulating memory CD4+ T cells

source_name: Peripheral blood mononuclear cells

value: CD4+ T circulating


title: Umbilical cord tissue - diabetic mother - replicate 3

description: replicate 3


title: Δpgm vs. Δpgm ΔypeIR rep6

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: The strain Δpgm is the Y.pestis CO92 pigmentation-negative mutant.

hyb_protocol: Corresponding equal amounts (1.5 µg) of Alexa 555- or Alexa 647-labelled cDNA targets were mixed and dried using a Thermo Scientific Savant DNA SpeedVac Concentrator. Targets were suspended in 60 µl hybridization buffer (40% formamide, 5x SSC, 0.1% SDS, 0.6 µg/µl Salmon Sperm DNA), incubated at 95°C for 5 min, centrifuged (10,000 x g, 4 min), and kept at room temperature until placed in a hybridization chamber. Hybridization lasted for 16 h at 42°C and washed in a series of wash buffers (2x saline-sodium citrate (SSC) - 0.1% SDS; 0.1x SSC – 0.1% SDS, and 0.1x SSC) and dried by centrifugation at 1500 x g for 30 s.

scan_protocol: Arrays scanned on a ProScanArray HT scanner (Perkin Elmer, Wellesley, MA) three times with varying photomultiplier tube gain and laser power settings.

data_processing: Data acquisition, normalization and data analysis have been described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

organism: Yersinia pestis

source_name: Δpgm ΔypeIR

label_protocol: Target generation and labeling were performed as described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

growth_protocol: An overnight culture was diluted 1:100 and grown for 9 h at 37°C in BHI broth at which time an optical density 600 nm of 1.0 is reached.

extract_protocol: Cells were pelleted and immediately resuspended in 1 ml of Trizol (Ambion) and were then frozen. RNA was extracted from frozen cell pellets using the Trizol reagent protocol. The RNA was treated with DNase I (Ambion) at 37°C for 30 min to remove contaminating genomic DNA. The RNA was purified and concentrated by Microcon Ultracel/YM 30.

treatment_protocol: Microarray studies were performed by comparing strains Δpgm and Δpgm ΔypeIR  grown at a mid logarithmic phase.

tag: genotype/variation

value: ΔPgm

tag: strain

source_name: Δpgm

value: Δpgm


title: Genomic DNA from SM4XBY9_T

description:
primary small intestine
9370847143


title: Umbilical cord tissue - diabetic mother - replicate 2

description: replicate 2


title: Genomic DNA from SM4XBY8_T

description:
primary small intestine
9370847109


title: Genomic DNA from SM4XBY4_T

description:
primary NA
9370847143

value: FF


title: Genomic DNA from SM4XBY7_T

description:
metastasis NA
9370847144


title: Genomic DNA from SM4XBXY_T

description:
primary small intestine
9370847111


title: Δpgm vs. Δpgm ΔypeIR rep4


title: Genomic DNA from SM4XBYA_T

description:
primary small intestine
9370847144


title: Δpgm vs. Δpgm ΔypeIR rep3

value: ΔypeIR ΔyspIR AHL-null mutant

value: Δpgm ΔypeIR


title: Δpgm vs. Δpgm ΔypeIR rep2


title: Δpgm vs. Δpgm ΔypeIR rep5


title: Genomic DNA from SM4XBY1_T

description:
primary colon
9370847143

value: colon


title: TSG derived from patient tumor

city: Stanford

first: Hongjuan

last: Zhao

address: 300 Pasteur Dr

department: Urology

institute: Stanford

description: A coring device (Alabama Research and Development, Mundford, AL) was used to procure aseptic, 8-mm diameter cores from fresh RCC tissues.  These cores were submerged in ice-cold HEPES-buffered saline and cut into slices of 300-um in thickness using a Krumdieck tissue slicer (Alabama Research and Development).  Serially numbered slices were then labeled by core of origin and submerged in ice-cold HEPES-buffered saline prior to implantation.Male and female RAG2-/-γC-/- mice between 6- and 8-weeks of age from our breeding colony were used.  Subrenal capsular  implantation of tissue slices was performed and TSGs were harvested one month after implantation.

hyb_protocol: Standard Illumina beadarray hybrydization protocol for gene expression profiling (carried out in Stanford Functional Genomics Facility).

scan_protocol: Standard Illumina beadarray scan protocol for gene expression profiling (carried out in Stanford Functional Genomics Facility).

data_processing: BeadStudio/GenomeStudio software (Illumina) was used to generate signal intensity values from the scans. For normalization, the software was used to subtract background and scale average signal intensity for each sample to the global average signal intensity for all samples.

source_name: TSG harvested from subrenal implantation in mice

label_protocol: Standard Illumina beadarray probe synthesis for gene expression profiling (carried out in Stanford Functional Genomics Facility).

extract_protocol: Total RNA was extracted using an AllPrep DNA/RNA/Protein Mini Kit from Qiagen according to manufacturer's instructions.


title: parent tumor

description: Fresh RCC tissues were obtained from patients undergoing radical or partial nephrectomy from 9/2011 to 5/2012 at Stanford under an Institutional Review Board- approved protocol.  Frozen sections were utilized to histologically confirm the diagnosis of RCC.  Specimens with gross tissue necrosis, primarily cystic structure, or size smaller than 2-cm were excluded.

source_name: tumor tissue from nephrectomy

growth_protocol: A coring device (Alabama Research and Development, Mundford, AL) was used to procure aseptic, 8-mm diameter cores from fresh RCC tissues.  These cores were submerged in ice-cold HEPES-buffered saline and cut into slices of 300-um in thickness using a Krumdieck tissue slicer (Alabama Research and Development).  Serially numbered slices were then labeled by core of origin and submerged in ice-cold HEPES-buffered saline prior to implantation.Male and female RAG2-/-γC-/- mice between 6- and 8-weeks of age from our breeding colony were used.  Subrenal capsular implantation of tissue slices was performed and TSGs were harvested one month after implantation.

value: tumor tissue from nephrectomy

value: male

tag: furhman grade

value: II


title: CD8+ T cell clone 17.2 stimulation 2

value: Female

value: 36 years old

value: CD8+ T simulating


title: cultured cells derived from patient tumor

description: A coring device (Alabama Research and Development, Mundford, AL) was used to procure aseptic, 8-mm diameter cores from fresh RCC tissues.  These cores were submerged in ice-cold HEPES-buffered saline and cut into slices of 300-um in thickness using a Krumdieck tissue slicer (Alabama Research and Development).  Serially numbered slices were then labeled by core of origin and submerged in ice-cold HEPES-buffered saline prior to implantation.Male and female RAG2-/-γC-/- mice between 6- and 8-weeks of age from our breeding colony were used.  Subrenal capsular implantation of tissue slices was performed and TSGs were harvested one month after implantation.

source_name: culutred cells harvested from culture dishes

value: cultured cells harvested from culture dishes


title: Δpgm vs. Δpgm ΔypeIR rep1


title: SJG15 miR-203 overexpressing cells, 15_203_3

first: Nathan

last: Benaich

address: Great Maze Pond

department: Centre for Stem Cells and Regenerative Medicine

institute: King's College London

description: Primary, early passage squamous cell carcinoma cell line from tongue SCC.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was log base 2 quantile normalised after artifact removal using the BASH and HULK algorithms in the R beadarray package.

label: Biotin

source_name: SJG15 human cell line, miR-203

label_protocol: Standard Illumina labeling protocol.

extract_protocol: Total RNA was extracted using a miRNeasy Mini Kit (Qiagen) and RNA quality was analyzed using a Bioanalyzer 2100 (Agilent) and RNA Nano Chip. RIN values were all above 9.3.

treatment_protocol: Total RNA (including small RNAs) was isolated from cultured cells stably infected in biological duplicate with either a scrambled control hairpin or miR-203. Samples were harvested in technical duplicate.

tag: stable infection

tag: batch infection

tag: technical replicate


title: 37°C vs. 30°C rep6

description: The Δpgm strain R88 is the Y.pestis CO92 pigmentation-negative mutant.

hyb_protocol: Microarray hybridization and post washes were performed using a Lucidea Slidepro Hybridization Station (GE Healthcare). Corresponding equal amounts (1.5 µg) of Cy3- or Cy5-labelled cDNA targets were mixed and dried using a Thermo Scientific Savant DNA SpeedVac Concentrator (Waltham, MA). Targets were suspended in 225 μl Long Oligo hybridization solution (Corning, Inc., Corning, NY), incubated at 95°C for 5 min, centrifuged (10,000 x g, 4 min), and kept at room temperature until injected into the hybridization station. Hybridization lasted for 16 hours at 42°C and washed in a series of wash buffers (2x saline-sodium citrate (SSC), 0.1% SDS; 1x SSC, and 0.1x SSC) by the hybridization station and dried by centrifugation at 1500 x g for 30 secs.

data_processing: Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102 [PMID 19473256]).

label_protocol: Target generation and labeling were performed as described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102 [PMID 19473256]).

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C or 37°C in HIB until an optical density 600 nm of 1.0 is reached.

extract_protocol: Cells were pelleted and immediately resuspended in 0.5 ml of RNA Protect Reagent (Qiagen, Valencia, CA). RNA was extracted from frozen cell pellets using the RNeasy Mini kit (Qiagen). The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 30 min to remove the genomic DNA. The RNA was purified and concentrated by Microcon Ultracel/YM 30(Millipore, Billerica, MA).

treatment_protocol: The strain R88 was grown at two different growth temperatures (30°C and 37°C).

value: Δpgm strain R88

tag: temperature


title: SJG15 miR-203 overexpressing cells, 15_203_4

tag: cell line


title: Genomic DNA from SM4XBXU_T

description:
primary small intestine
9370847143

value: primary

value: small intestine

value: F


title: 37°C vs. 30°C rep4


title: Genomic DNA from SM4XBXV_T

description:
primary small intestine
9370847143


title: Genomic DNA from SM4XBXO_T

description:
metastasis lymph node
9370847109

value: metastasis

value: lymph node


title: SJG15 control cells, 15_EV_4

source_name: SJG15 human cell line, control

value: scrambled control hairpin


title: Genomic DNA from SM4XBXP_T

description:
primary gastric
9370847111

value: gastric

value: FF


title: Genomic DNA from SM4XBXJ_T

description:
primary small intestine
9370847144

value: FFPE


title: 37°C vs. 30°C rep2


title: Genomic DNA from SM4XBXQ_T

description:
primary small intestine
9370847144


title: 37°C vs. 30°C rep5


title: 37°C vs. 30°C rep3


title: Genomic DNA from SM4XBXN_T

description:
primary gastric
9370847109


title: SJG15 control cells, 15_EV_3


title: 37°C vs. 30°C rep1


title: Genomic DNA from SM4XBXM_T

description:
metastasis soft tissue
9370847144

value: soft tissue


title: Genomic DNA from SM4XBXI_T

description:
metastasis liver
9370847143

value: liver


title: SJG15 control cells, 15_EV_2


title: Genomic DNA from SM4XBXT_T

description:
primary small intestine
9370847144


title: SCC13 miR-203 overexpressing cells, 13_203_4

description: Established squamous cell carcinoma cell line from facial SCC.

source_name: SCC13 human cell line, miR-203


title: Genomic DNA from SM4XBXR_T

description:
primary gastric
9370847144


title: AHLs treated vs. control rep6

description: The strain Δpgm is pigmentation-negative mutant. The AHLs is the two AHL signals added in treatment.The control is the cells grown and treated under the same conditions without added in signals.

source_name: AHLs treated

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C in HIB broth.

treatment_protocol: The overnight wild type cultures were washed twice with PBS buffer to remove the endogenous quorum sensing signals, the cells were diluted 1:100 in fresh culture medium, and then the cells were incubated for 2 hours at 30°C. Purified signals were then added to the cultures at the following concentrations: AHLs (5 μM N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone). The control consisted of cells grown and treated under the same conditions without added signals. After 4 hours of induction, all of the cultures were centrifuged.

value: Δpgm

tag: treatment

value: AHL signal

source_name: control


title: AHLs treated vs. control rep2


title: AHLs treated vs. control rep5


title: SCC13 miR-203 overexpressing cells, 13_203_2


title: AHLs treated vs. control rep4


title: Genomic DNA from SM2QX4X_T

description:
primary colon
9266441100

value: colon

tag: gender


title: Genomic DNA from SM2QX52_T

description:
metastasis soft tissue
9374342055

tag: lesion

value: M


title: SJG15 miR-203 overexpressing cells, 15_203_1


title: Genomic DNA from SM2QX4U_T

description:
metastasis node
9266441100

tag: sample site

value: node


title: SJG15 miR-203 overexpressing cells, 15_203_2


title: Umbilical cord tissue - diabetic mother - replicate 1

description: replicate 1

tag: sample group

value: maternal diabetes (DM)

value: Umbilical cord


title: Genomic DNA from SM2QX4L_T

description:
metastasis liver
9374342055

tag: primary site

value: small intestine

tag: grade


title: AHLs treated vs. control rep3


title: Genomic DNA from SM2QX4K_T

description:
metastasis liver
9266441100

tag: source tissue type


title: SCC13 control cells, 13_EV_3

source_name: SCC13 human cell line, control


title: SCC13 miR-203 overexpressing cells, 13_203_3


title: SCC13 miR-203 overexpressing cells, 13_203_1


title: AHLs treated vs. control rep1


title: SCC13 control cells, 13_EV_4


title: SJG15 control cells, 15_EV_1


title: Genomic DNA from SM2QX4R_T

description:
primary gastric
9266441100

value: primary

tag: age


title: Genomic DNA from SM2QX53_T

description:
metastasis liver
9266441100

value: metastasis

value: F


title: Genomic DNA from SM2QX4J_T

description:
primary small intestine
9374342114


title: AI-2 treated vs. control rep5

description: The strain Δpgm is pigmentation-negative mutant. The AI-2 treated is AI-2 added in treatment.The control is the cells grown and treated under the same conditions without added in signals.

treatment_protocol: The overnight wild type cultures were washed twice with PBS buffer to remove the endogenous quorum sensing signals, the cells were diluted 1:100 in fresh culture medium, and then the cells were incubated for 2 hours at 30°C. Purified signal was then added to the cultures at the following concentrations: AI-2 (500 nM final concentration). The control consisted of cells grown and treated under the same conditions without added signals. After 4 hours of induction, all of the cultures were centrifuged.

tag: genotype/variation

source_name: AI-2 treated


title: AI-2 treated vs. control rep4

tag: strain


title: SCC13 control cells, 13_EV_2

value: scrambled control hairpin


title: AI-2 treated vs. control rep6


title: SCC13 control cells, 13_EV_1


title: AI-2 treated vs. control rep3


title: Genomic DNA from SM2QX4I_N

description:
normal liver
9374342114

source_name: normal

value: normal


title: Genomic DNA from SM2QX4E_T

description:
metastasis liver
9374342114

value: FF


title: AI-2 treated vs. control rep2


title: Genomic DNA from SM2Q4G_T

description:
primary small intestine
9374342114

source_name: primary


title: AHLs vs. control rep6

description: The strain Pgm- is pigmentation-negative mutant. The AHLs is the two AHL signals added in treatment.The control is the cells grown and treated under the same conditions without added three signals.

data_processing:
Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Madsen ML, Nettleton D, Thacker EL, Minion FC. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology 152:937-944 [PMID 16549658]) excluding slide region and slide-by-region interaction effects. Intensity = mu + trt + dye + slide
Images were quantified using the softWorRx Tracker analysis software package (Applied Precision). Spot-specific mean signals were corrected for local background by subtracting spot-specific median background intensities. The natural logarithms of the background-corrected signals from a single scan were adjusted by an additive constant so that all scans of the same array-by-dye combination would have a common median. The median of these adjusted-log-background-corrected signals across multiple scans was then computed for each spot to obtain one value for each combination of spot, array and dye channel. These data for the two dye channels on any given array were normalized using locally weighted scatterplot smoother (LOWESS) normalization to adjust for intensity-dependent dye bias (Dudoit et al., 2000Down; Yang et al., 2002Down). Following LOWESS adjustment, the data from each channel were adjusted by an additive constant so that the median for any combination of array and dye would be the same for all array-by-dye combinations. The normalized values for triplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples.
A separate mixed linear model analysis was conducted for each probe sequence using the normalized data (Wolfinger et al., 2001Down). Each mixed model included fixed effects for treatment (iron depletion versus control), slide region (upper versus lower) and dye (Alexa 555 versus 647) as well as random effects for slide and slide-by-region interaction. A t-test for differential expression across treatments was conducted for each probe as part of our mixed linear model analyses. The P-values from these t-tests were converted to q-values using the method of Storey & Tibshirani (2003)Down. These q-values can be used to obtain approximate control of the false discovery rate at a specified value. For example, declaring probes with q-values less than or equal to 0·05 to be differentially expressed produces a list of significant results for which the false discovery rate is estimated to be approximately 5 %. Along with q-values, estimates of fold change were computed for each probe by taking the inverse natural log of the mean treatment difference estimated as part of our mixed linear model analyses.

source_name: AHLs

growth_protocol: An overnight culture was diluted 1:100 and grown at 37°C in BHI broth.

treatment_protocol: The overnight wild type cultures were washed twice with PBS buffer to remove the endogenous quorum sensing signals, the cells were diluted 1:100 in fresh culture medium, and then the cells were incubated for 2 hours at 37°C. Purified signals were then added to the cultures at the following concentrations: AHLs (5 μM N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone). The control consisted of cells grown and treated under the same conditions without added signals. After 4 hours of induction, all of the cultures were centrifuged.

tag: variant

value: Pgm-


title: Genomic DNA from SM2QX4A_N

description:
normal NA
9374342114


title: AI-2 treated vs. control rep1


title: parent tumor of case 10

growth_protocol: A coring device (Alabama Research and Development, Mundford, AL) was used to procure aseptic, 8-mm diameter cores from fresh RCC tissues.  These cores were submerged in ice-cold HEPES-buffered saline and cut into slices of 300-um in thickness using a Krumdieck tissue slicer (Alabama Research and Development).  Serially numbered slices were then labeled by core of origin and submerged in ice-cold HEPES-buffered saline prior to implantation.Male and female RAG2-/-γC-/- mice between 6- and 8-weeks of age from our breeding colony were used.  Subrenal capsular  implantation of tissue slices was performed and TSGs were harvested one month after implantation.

value: female

tag: furhman grade

value: II

tag: tissue

value: tumor tissue from nephrectomy

tag: origin

value: case 10


title: AHLs vs. control rep4


title: parent tumor of case 1

value: III

value: case 1


title: AHLs vs. control rep5


title: AHLs vs. control rep3


title: Genomic DNA from SM2QX4F_N

description:
normal small intestine
9374342114

value: M


title: AHLs vs. control rep2


title: Genomic DNA from SM2QX4H_T

description:
metastasis liver
9374342114

source_name: metastasis

value: liver


title: parent tumor of case 9

value: male

value: case 9


title: TSG derived from case 1

value: TSG harvested from subrenal implantation in mice


title: Genomic DNA from SM2QX4C_N

description:
normal liver
9266441100


title: AHLs vs. control rep1


title: Genomic DNA from SM2QX49_T

description:
metastasis liver
9374342055

value: metastasis

value: small intestine


title: Genomic DNA from SM2QX4D_T

description:
metastasis liver
9266441100

value: F


title: TSG derived from case 9


title: TSG derived from case 10


title: cholesterol rep 4 vs. glycerol rep 4

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

description: Biological replicate 4 of 4.

hyb_protocol: Each pair of differentially labeled probes was resuspended in 60 ml of hybridization buffer (500 ml formamide, 250 ml 206 SSC, 5 ml 10% SDS, 245 ml ultrapure water) and hybridized to the microarray slide overnight in a 42C water bath. Slides were then washed in increasingly stringent wash conditions (3 times 5 min 16SSC 0.1% SDS, 3 times 5 min 0.16 SSC 0.1% SDS, 3 times 5 min 0.16 SSC and a final dip in 0.22 mm-filtered MQ water).

scan_protocol: Arrays were scanned in a Genepix 4000A scanner Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Spots quantified with TIGR Spotfinder. The data was then processed in TIGR MIDAS. Two color tiff images of the microarrays were visually inspected for defects and obvious spatial biases. Prior to normalization pin-tip (block) intensity box plots were used to detect slides exhibiting spatial and/or pin biases, with post-normalization intensity box plots and MA plots used to assess the effectiveness of normalization in correcting these biases. RI plots were also used to identify outlier slides and for assessing the effectiveness of the normalization process, and Z-score histograms were used to look for slides with abnormal intensity distributions. Slides that did not pass the quality control process were rejected, and repeat hybridizations were performed. Post normalization (Total Intensity and LOWESS) the in-slide replicate spots were averaged before expression ratios were calculated. The results from 4 biological replicates including two dye swaps were then subjected to a t-test without false discovery correction in TIGR MeV software.

organism: Mycolicibacterium smegmatis MC2 155

label_protocol: Labeling was performed using protocols SOP# M007 from The Institute of Genomic Research (TIGR)

extract_protocol: Total RNA was extracted using TRIZOL® reagent (Invitrogen) according to the manufacturer’s instructions. Cell lysis was achieved by three cycles of bead beating in a Mini-Beadbeater (Biospec) at 5,000 r.p.m. for 30 seconds. DNA was removed from the RNA preparation by treatment with 2 U RNase-free DNase using the TURBO DNA-free kit (Ambion), according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop ND-1000 spectrophotometer and the quality of RNA checked on a 1.2 % agarose gel.

tag: condition

value: M. smegmatis grown cholesterol-limited chemostat

value: M. smegmatis grown glycerol-limited chemostat


title: Genomic DNA from SM2QX47_T

description:
metastasis liver
9374342055

value: FF


title: Saturated fat diet 4

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA express was used to generate the RMA file

source_name: Xenograft

label_protocol: Affymetrix standard protocol

growth_protocol: LAPC-4 prostate cancer xenografts in SCID mice consuming one of four treatment diets.  Animals euthanized when tumors reach 1000 mm^3.

extract_protocol: Excised xenograft purified by Trizol Protocol

treatment_protocol: Excised xenograft immediately flash frozen to -80C

value: Xenograft

tag: diet

value: Saturated fat


title: glycerol rep 1 vs. cholesterol rep 1

description: Biological replicate 1 of 4.


title: Saturated fat diet 5


title: Saturated fat diet 6


title: cholesterol rep 2 vs. glycerol rep 2

description: Biological replicate 2 of 4.


title: Saturated fat diet 3


title: Genomic DNA from SM2QX4V_T

description:
primary colon
9266441100

value: primary

value: colon


title: Saturated fat diet 2


title: Saturated fat diet 1


title: Genomic DNA from SM2QX48_N

description:
normal liver
9374342055

value: normal


title: Genomic DNA from SM2QX46_T

description:
primary small intestine
9374342055


title: Genomic DNA from S0303430B8_N

description:
normal small intestine
7973219126

value: FFPE


title: Genomic DNA from SM2QX45_N

description:
normal small intestine
9266441100

value: M


title: Genomic DNA from S088069A10_T

description:
primary small intestine
7990895058


title: Olive oil diet 6

value: Olive oil


title: glycerol rep 3 vs. cholesterol rep 3

description: Biological replicate 3 of 4.


title: Olive oil diet 5


title: NCI-HPN-M2K colon p59 Transformed

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

state: MD

address: 50 South Drive

department: Genetics Branch

institute: NCI

description: male

hyb_protocol: The differentially labeled targets sample and reference DNA  were combined with Agilent 10X Blocking Agent, Agilent 2X Hybridization Buffer,  and Cot-1 DNA , denatured at 95°C for 3 min and preannealed for 30 min at 37°C according to the Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol. The denatured probe was applied to the Agilent Mouse Genome CGH 244K Microarray Kit according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using an Agilent Scanner System. Images were quantified using Agilent Feature Extraction Software (version 8.1.1).

data_processing: Rank Segmentation algorithm of Nexus Copy Number 6 was used to analyze aCGH data. Significance Threshold: 5E-6; Max Contiguous Probe Spacing: 3000; Min number of probes per segment: 10; Systematic correction: linear correction with correction file provided by Nexus.

source_name: mouse colon epithelial cells

label_protocol: 7ug of digested DNA was prepared for labeling with the BioPrime Array Genomic Labeling Kit using Cy3 -dUTP for the test DNA and Cy5-dUTP for the reference DNAas described in Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol.

growth_protocol: The epithelial cells were grown in DMEM/F12 media supplemented with low fetal bovine serum (2-5%).The cells were fed every 10 days to promote in vitro cellular transformation (Padilla Nash et al., 2012).

extract_protocol: DNA was extracted from the murine epithelial cells and the mouse C57BL/6 liver cells (normal reference DNA) using protocols described in http://www.riedlab.nci.nih.gov/protocols.

tag: Stage

value: male

source_name: Male Mouse DNA

value: mouse liver cells


title: Genomic DNA from S0303430B13_T

description:
primary small intestine
7973219126

tag: gender


title: Olive oil diet 4


title: Olive oil diet 3


title: Olive oil diet 2


title: NCI-HPN-M2C colon p48 Transformed

description: male


title: NCI-HPN-M1Kcolon p59 Transformed

description: male


title: Olive oil diet 1


title: Fish oil diet 6

value: Fish oil


title: NCI-HPN-F4K Colon p56 Transformed

description: female

value: female


title: Fish oil diet 4


title: Fish oil diet 5


title: Fish oil diet 2


title: Fish oil diet 3


title: NCI-HPN-F2K Colon p65 Transformed

description: female


title: NCI-HPN-F1K Colon p51 Transformed

description: female


title: Genomic DNA from PH1015539A03691_T

description:
primary small intestine
7973219155

tag: lesion

value: small intestine


title: NCI-HPN-F3K Colon p58 Transformed

description: female


title: Genomic DNA from PH1015539A03692_N

description:
normal small intestine
7973219155

tag: sample site


title: Corn oil diet 6

value: Corn oil


title: Genomic DNA from S088069A2_N

description:
normal small intestine
7990895058

value: F


title: Genomic DNA from H112177A2_N

description:
normal appendix
9247377041

value: appendix


title: Genomic DNA from CDNT125b_T

description:
cell line cell line
9370847109

source_name: cell line

value: cell line


title: Fish oil diet 1

value: Xenograft


title: Corn oil diet 4


title: Genomic DNA from H112177A4_N

description:
normal appendix
7990895058


title: Corn oil diet 3


title: Corn oil diet 2


title: Genomic DNA from H112177A2_T

description:
primary appendix
9247377041


title: Corn oil diet 5


title: Corn oil diet 1


title: Genomic DNA from M02316052_T

description:
primary small intestine
9370847111


title: Genomic DNA from CDNT125a_T

description:
cell line cell line
9370847144


title: Genomic DNA from H06195487_T

description:
primary colon
9247377041


title: Genomic DNA from B052175A23082_N

description:
normal small intestine
7973219155


title: P-Fe-2

city: New Delhi

first: Vandna

last: Rai

state: Delhi

address: Pusa campus

department: Genomics

country: India

institute: NRCPB

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

scan_protocol: standard Affymetrix protocol

data_processing: Expression console ver1.1

organism: Oryza sativa Indica Group

source_name: O. sativa roots root

label_protocol: standard Affymetrix protocol

growth_protocol: Samples were grown in hydroponic conditions for 10days

extract_protocol: Seedlings were grown in P+, P-, Fe- and P-Fe- conditions and total RNA was isolated using SpectrumTM Plant Total RNA kit as described (Sigma, USA)

treatment_protocol: 5days young seedlings were grown in different nutrient conditions

value: root

tag: treatment

value: Phophorus and Fe deficiency


title: P-Fe-1


title: Genomic DNA from 972181IVB_N

description:
normal liver
7973219126

value: liver

tag: primary site


title: treatment resistant prostate cancer - stem cells - sample 3

city: Tampere

first: Antti

last: Ylipää

address: Korkeakoulunkatu 1

institute: Tampere University of Technology

description: 43 Y01411 SC

hyb_protocol: Standard Agilent protocol for microRNA array

scan_protocol: Agilent Technologies Scanner G2505B US22502675, Feature Extractor v.10.7.1.1

data_processing: The data was quantile normalized using Matlab version 8.0.0.783 (R2012b).

source_name: treatment resistant prostate cancer_stem cells

label_protocol: Standard Agilent protocol

growth_protocol: Primary prostate epithelial cells were grown in stem cell media and passaged twice.

extract_protocol: Described in Collins et al., 2005 Cancer Research

treatment_protocol: No treatment

value: treatment resistant prostate cancer

tag: cell type

value: stem cells


title: treatment resistant prostate cancer - transit amplifying cells - sample 3

description: 43 Y01411 TA

source_name: treatment resistant prostate cancer_transit amplifying cells

value: transit amplifying cells


title: P-2

value: Phophorus deficiency


title: 1#A_H3K27me3_replicate2

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

country: France

institute: UMR7216-Epigenetics and stem cell

hyb_protocol: Hybridisation was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

scan_protocol: Scanning was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

data_processing: Reproducibility and quality control of the data were assessed using the “R” software combined with an algorithm especially developed for ChIP-on-Chip data analysis of histone modifications (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=43). Briefly, the global hybridisation patterns across each array were controlled by MA-plotting of all the probe signals on the array and by calculating the Pearson correlation coefficients between pairs of replicates (all the coefficients were > 0.8). The two replicates showing the highest Pearson correlation coefficient were used for further analysis. We applied a Lowess normalisation to each dataset and the “SAM” algorithms to determined statistically enriched probe (Tusher et al., PNAS, 2001). A VSN (variance stabilization) normalisation of each array was also performed independently, then a SAM algorithm and a lfdr > 0,2 (local false discovery rate probability test) to determine the significance of enrichment of each probel were applied (data not included in this submission but available upon request).

source_name: Revertant female TS cells H3K27me3 ChIP DNA rep2

label_protocol: Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).

tag: genotype

value: XHprt-/XWT

value: Trophoblast Stem cells isolated from E3.5 blastocysts

tag: chip antibody

value: none, input DNA

source_name: input DNA from revertant female TS cells H3K27me3 ChIP DNA rep4

value: H3K27me3 (Millipore#17-622)


title: Genomic DNA from 972181IVB_T

description:
metastasis liver
7973219126

value: metastasis

value: small intestine

tag: grade

tag: source tissue type

value: FFPE

tag: age


title: Fe-1

value: Fe deficiency


title: Fe-2


title: Genomic DNA from B052175A23081_T

description:
metastasis small intestine
7973219155

value: M


title: Genomic DNA from 929097G_N

description:
normal small intestine
9374342114

value: normal


title: Genomic DNA from 9572A6308_T

description:
primary small intestine
7990895026

value: primary


title: F3_H3K27me3_replicate2

tag: strain

source_name: input DNA from wildtype female TS cells H3K27me3 ChIP DNA rep2


title: Genomic DNA from 952583C_T

description:
primary small intestine
7990895026


title: Genomic DNA from 9613888IIIF_T

description:
primary small intestine
7973219096

value: F


title: Genomic DNA from 929097H_T

description:
primary small intestine
7973219096


title: F3_H3K27me3_replicate1

source_name: input DNA from wildtype female TS cells H3K27me3 ChIP DNA rep1


title: treatment resistant prostate cancer - committed basal cells - sample 3

description: 43 Y01411 CB

source_name: treatment resistant prostate cancer_committed basal cells

tag: tissue

value: committed basal cells


title: 1#A_H3K27me3_replicate1

source_name: Revertant female TS cells H3K27me3 ChIP DNA rep1

source_name: input DNA from revertant female TS cells H3K27me3 ChIP DNA rep3


title: F2_H3K27me3_replicate1

value: XHprt-/Y

source_name: input DNA from wildtype male TS cells H3K27me3 ChIP DNA rep1


title: F2_H3K27me3_replicate2

source_name: input DNA from wildtype male TS cells H3K27me3 ChIP DNA rep2


title: Genomic DNA from 929097J_N

description:
normal small intestine
7973219096

source_name: normal


title: Genomic DNA from 9913069VIC_T

description:
metastasis liver
7973219126

source_name: metastasis

value: liver


title: Genomic DNA from 9913069VIC_N

description:
normal liver
7973219126


title: Genomic DNA from 80852_T

description:
metastasis liver
9370847111

value: FF


title: Genomic DNA from 811068A5_T

description:
primary small intestine
9370847109

source_name: primary


title: Genomic DNA from 3945D05_T

description:
primary small intestine
9247377041


title: treatment resistant prostate cancer - stem cells - sample 2

description: 42 Y01810 SC

value: treatment resistant prostate cancer

value: stem cells


title: treatment resistant prostate cancer - committed basal cells - sample 2

description: 42 Y01810 CB


title: P+2

value: root

value: control


title: P-1

value: Phophorus deficiency


title: treatment resistant prostate cancer - stem cells - sample 1

description: 41 Y08909 SC


title: treatment resistant prostate cancer - transit amplifying cells - sample 2

description: 42 Y01810 TA

value: transit amplifying cells


title: Genomic DNA from 192971C308_T

description:
primary small intestine
7973219155

value: small intestine


title: ZE-24

city: Guangzhou

first: Jingxin

last: Zhang

state: Guangdong

institute: Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R.China

description: blast-susceptible rice line Zhonger-Ruanzhan inoculated with blast pathogen after 24h

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affy Rice GeneChip  with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Oryza sativa

source_name: blast-treated blast-susceptible rice line Zhonger-Ruanzhan

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: H4 and Zhonger-Ruanzhan were grown on sterilized soil in growth chambers with 13 h light/day and 11 h dark/night, 28.5°C during the day and 25°C during the night, and 85% relative humidity.

extract_protocol: Total RNA of leaf in different treatment was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: At trefoil stage, the plants were sprayed by rice blast isolate GD0193 suspension with 5×104 spores per ml or untreated separately.

tag: cultivar

value: indica

value: trefoil stage

value: leaf

value: blast-susceptible rice line Zhonger-0


title: H4-24

address: Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences

description: blast-resistant rice line H4 inoculated with blast pathogen after 24h

source_name: blast-treated blast-resistant rice line  H4

value: mutant H4-0


title: P+1

source_name: O. sativa roots root


title: treatment resistant prostate cancer - transit amplifying cells - sample 1

description: 41 Y08909 TA


title: CTL ovary replication4

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

hyb_protocol: Four independent hybridization were performed for DHT and CTL  sample groups. Array hybridization was done by mixing  the recommended amounts of  fragmented and labelled cRNA, control oligonucleotide B2 (3 nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix , DMSO and RNAse free water.The hybridization mix was heated to 99°C for 5 min followed by heating at  45°C for 5 min. Following this the samples were hybridized to the GeneChip® Rat Genome Array (Affymetrix, CA, USA) for 16 h at 45°C.

scan_protocol: The arrays  were scanned  using affymetrix®GeneChip™3000 slide scanner (Affymetrix, CA, USA).

data_processing: Data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) .  Differentially expressed genes were identified  using linear model for microarray data analysis (LIMMA).  For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

organism: Rattus norvegicus

source_name: Ovarian samples derived from control rat groups (CTL4)

label_protocol: The  amplified RNA samples  of DHT and CTL groups were  biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual

extract_protocol:
[RNA isolation] Total RNA was isolated from 3 independent DHT and CTL rat ovaries using miRNeasy mini kit (Qiagen, Hilden, Germany).
[RNA Amplification ] RNA amplification was performed using GeneChip®3’ IVT Express Kit according to the guidelines described in GeneChip®3’ IVT Express Kit user manual [(P/N 702646 Rev. 8) (Affymetrix Inc)].   RNA amplification was done from  3 biological replicates and the fourth replicate was generated by pooling equal amount of RNA from  three biological replicates of DHT or  CTL groups.

value: Sprague-Dawley

tag: agent

value: ovary


title: ZE-0

description: untreated blast-susceptible rice line Zhonger-Ruanzhan

source_name: mock-treated blast-susceptible rice line Zhonger-Ruanzhan

value: untreated


title: Genomic DNA from 72652_T

description:
metastasis small intestine
9370847111

value: metastasis

value: F


title: Genomic DNA from 5623834_T

description:
primary small intestine
7990895026

value: primary

value: FFPE


title: Genomic DNA from 186353_T

description:
primary small intestine
9370847109

value: FF

value: M


title: prostate cancer - stem cells - sample 5

description: 35 H06711 LB SC

source_name: prostate cancer_stem cells

value: prostate cancer

value: stem cells


title: Genomic DNA from 8175834_T

description:
primary small intestine
7973219155

value: small intestine


title: prostate cancer - committed basal cells - sample 5

description: 35 H06711 LB CB

source_name: prostate cancer_committed basal cells

value: committed basal cells


title: prostate cancer - transit amplifying cells - sample 5

description: 35 H06711 LB TA

source_name: prostate cancer_transit amplifying cells

value: transit amplifying cells


title: prostate cancer - stem cells - sample 4

description: 34 Y03311 SC


title: CTL ovary replication2

source_name: Ovarian samples derived from control rat groups (CTL2)

value: control


title: prostate cancer - committed basal cells - sample 4

description: 34 Y03311 CB


title: prostate cancer - transit amplifying cells - sample 4

description: 34 Y03311 TA


title: Genomic DNA from 12A5867A5_N

description:
normal small intestine
7990895058

value: normal


title: H4-0

description: untreated blast-resistant rice line H4

source_name: mock-treated blast-resistant rice line H4

value: indica

value: trefoil stage

value: leaf

value: Blast-resistant rice line H4


title: CTL ovary replication3

source_name: Ovarian samples derived from control rat groups (CTL3)

value: Sprague-Dawley

value: ovary


title: CTL ovary replication1

source_name: Ovarian samples derived from control rat groups (CTL1)


title: prostate cancer - transit amplifying cells - sample 3

description: 33 H06611 LB TA


title: DHT treated ovary replication3

source_name: Ovarian samples derived from rat ovaries treated with DHT (DHT3)

value: DHT


title: treatment resistant prostate cancer - committed basal cells - sample 1

description: 41 Y08909 CB

source_name: treatment resistant prostate cancer_committed basal cells

value: treatment resistant prostate cancer


title: DHT treated ovary replication4

source_name: Ovarian samples derived from rat ovaries treated with DHT (DHT4)


title: DHT treated ovary replication2

source_name: Ovarian samples derived from rat ovaries treated with DHT (DHT2)


title: prostate cancer - stem cells - sample 3

description: 33 H06611 LB SC


title: Osteosarcoma tumor - 25491 (HD aCGH)

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

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

hyb_protocol: Reference and experimental samples DNA were co-hybridized on the custom made high density array chips containing 34,966 probes. The interested region was 1.5 Mb. The average spatial resolution between the probes was 200bp. The hybridization was carried out for 40h at 65°C.

scan_protocol: After washing, the slides were scanned on a laser-based microarray scanner (Agilent) using a resolution of 5 μm

data_processing: aCGH data were extracted (not normalized) using the default procedure in Agilent's Feature Extraction Software and visualized using Agilent CGH Analytics 3.4.27 software

source_name: Osteosarcoma tumor

label_protocol: 3 μg of digested DNAs from samples and references were differentially labeled with dUTP-Cy5 and dUTP-Cy3 respectively in a random primer reaction

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

extract_protocol: Genomic DNA was isolated using a standard proteinase K digestion followed by phenol/chloroform/isoamyl alcohol extraction, precipitated with 3M sodium acetate (pH 5.2) and 100% ethanol. The pellet was washed with 70% ethanol and resuspended in TE.

tag: Sample type

value: osteosarcoma tumor

source_name: genomic DNA from Promega

value: DNA reference


title: Genomic DNA from 12A5867A1_N

description:
normal small intestine
7990895058

source_name: normal

value: FFPE

value: M


title: Genomic DNA from 119541C3_T

description:
metastasis mes_omentum
7973219119

source_name: metastasis

value: metastasis

value: small intestine

value: F


title: prostate cancer - committed basal cells - sample 3

description: 33 H06611 LB CB

value: prostate cancer

value: committed basal cells


title: prostate cancer - committed basal cells - sample 2

description: 32 H04811 LB CB


title: prostate cancer - transit amplifying cells - sample 2

description: 32 H04811 LB TA

value: transit amplifying cells


title: Genomic DNA from 119541C22_T

description:
metastasis mes_omentum
7973219119


title: Genomic DNA from 1229081A_N

description:
normal small intestine
9374342055

value: normal


title: prostate cancer - stem cells - sample 2

description: 32 H04811 LB SC

value: stem cells


title: Genomic DNA from 11C11786B13_T

description:
primary small intestine
9374342055

source_name: primary

value: primary


title: Osteosarcoma tumor - 25517 (HD aCGH)


title: Osteosarcoma tumor - 22164 (HD aCGH)


title: Genomic DNA from 12A5867A6_T

description:
primary small intestine
7990895058


title: Genomic DNA from 1229081KT2_T

description:
primary small intestine
9374342055


title: Genomic DNA from 119541C21_N

description:
normal mes_omentum
7973219096


title: Genomic DNA from 1186316308A_T

description:
primary small intestine
7990895026


title: prostate cancer - committed basal cells - sample 1

description: 31 H05411 RA CB


title: Genomic DNA from 119541C1_T

description:
metastasis mes_omentum
7973219119


title: Osteosarcoma tumor - 24949 (HD aCGH)


title: Genomic DNA from 11197A42_T

description:
metastasis liver
7973219096

value: liver


title: Genomic DNA from 11197A2_T

description:
metastasis liver
7973219096


title: prostate cancer - stem cells - sample 1

description: 31 H05411 RA SC


title: DHT treated ovary replication1

source_name: Ovarian samples derived from rat ovaries treated with DHT (DHT1)

value: Sprague-Dawley

value: ovary


title: benign prostatic hyperplasia - transit amplifying cells - sample 5

description: 25 Y07611 TA

source_name: benign prostatic hyperplasia_transit amplifying cells

value: benign prostatic hyperplasia


title: Genomic DNA from 1111775D2_T

description:
metastasis mes_omentum
7973219119


title: Genomic DNA from 11197A41_N

description:
normal liver
7973219096


title: benign prostatic hyperplasia - stem cells - sample 5

description: 25 Y07611 SC

source_name: benign prostatic hyperplasia_stem cells


title: Osteosarcoma tumor - 25384 (HD aCGH)

value: osteosarcoma tumor


title: Osteosarcoma cell line - HOS (HD aCGH)

source_name: Osteosarcoma cell line

value: cell line

value: DNA reference


title: Genomic DNA from 116106G69_T

description:
primary small intestine
7990895026

value: FFPE


title: benign prostatic hyperplasia - committed basal cells - sample 4

description: 24 Y02411 rCB

source_name: benign prostatic hyperplasia_committed basal cells


title: Genomic DNA from 11000181O_N

description:
normal small intestine
9374342055


title: Osteosarcoma cell line - 143B (HD aCGH)


title: Osteosarcoma tumor - 25044 (HD aCGH)


title: benign prostatic hyperplasia - stem cells - sample 4

description: 24 Y02411 rSC


title: Osteosarcoma cell line - MG63 (HD aCGH)


title: benign prostatic hyperplasia - committed basal cells - sample 5

description: 25 Y07611 CB


title: benign prostatic hyperplasia - transit amplifying cells - sample 4

description: 24 Y02411 TA


title: Osteosarcoma cell line - G292 (HD aCGH)


title: Osteosarcoma tumor - 20490 (HD aCGH)


title: prostate cancer - transit amplifying cells - sample 1

description: 31 H05411 RA TA

source_name: prostate cancer_transit amplifying cells


title: Osteosarcoma tumor - 22900 (HD aCGH)


title: Osteosarcoma cell line - CAL72 (HD aCGH)


title: benign prostatic hyperplasia - committed basal cells - sample 3

description: 23 Y02611 rCB


title: benign prostatic hyperplasia - transit amplifying cells - sample 2

description: 22 Y03411 TA


title: Osteosarcoma cell line - HUO3N1 (HD aCGH)


title: benign prostatic hyperplasia - stem cells - sample 3

description: 23 Y02611 SC


title: benign prostatic hyperplasia - stem cells - sample 2

description: 22 Y03411 r SC


title: Δpgm vs. Δpgm ΔypeIR rep6

description: The strain Δpgm is the Y.pestis CO92 pigmentation-negative mutant R88. The Δpgm ΔypeIR ΔyspIR is R114 strain.

source_name: Δpgm ΔypeIR

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C in HIB broth until an optical density 600 nm of 1.0 is reached.

treatment_protocol: Microarray studies were performed by comparing strains R88 and R109 grown at a mid logarithmic phase.

tag: genotype/variation

value: Δpgm ΔypeIR

source_name: Δpgm

value: Δpgm


title: Osteosarcoma cell line - NY (HD aCGH)


title: Δpgm vs. Δpgm ΔypeIR rep5


title: Genomic DNA from 111197A1_T

description:
metastasis liver
7973219096

value: metastasis

value: small intestine

tag: gender

value: F


title: Genomic DNA from 1111775A2_T

description:
primary small intestine
7973219119

tag: lesion

value: M


title: Genomic DNA from 1015089A3_N

description:
normal small intestine
7973219155

value: normal

tag: sample site


title: benign prostatic hyperplasia - committed basal cells - sample 2

description: 22 Y03411 CB

value: committed basal cells


title: Genomic DNA from 11000181J_T

description:
primary small intestine
9374342055

value: primary


title: Osteosarcoma cell line - HUO9 (HD aCGH)


title: Δpgm vs. Δpgm ΔypeIR rep3


title: Δpgm vs. Δpgm ΔypeIR rep4


title: benign prostatic hyperplasia - transit amplifying cells - sample 3

description: 23 Y02611 TA

value: transit amplifying cells


title: Genomic DNA from 1015089A3_T

description:
primary small intestine
7973219155


title: Genomic DNA from 10105121C_T

description:
primary small intestine
7990895058


title: benign prostatic hyperplasia - stem cells - sample 1

description: 21 Y03111 SC

value: stem cells


title: Genomic DNA from 10D22894A169_T

description:
metastasis liver
7990895026

value: liver


title: Δpgm vs. Δpgm ΔypeIR rep2


title: benign prostatic hyperplasia - transit amplifying cells - sample 1

description: 21 Y03111 TA

value: benign prostatic hyperplasia


title: Genomic DNA from 1013495A17_T

description:
primary small intestine
7990895026

value: <2% (mitoses 2/10hpf)


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep6

growth_protocol: An overnight culture was diluted 1:100 and grown at 37°C in HIB broth until an optical density 600 nm of 1.0 is reached.

treatment_protocol: Microarray studies were performed by comparing strains R88 and R114 grown at a mid logarithmic phase.

source_name: Δpgm ΔypeIR ΔyspIR

value: Δpgm ΔypeIR ΔyspIR


title: normal prostate analogue - transit amplifying cells - sample 1

description: 1 PrEC rTA

source_name: normal prostate analogue_transit amplifying cells

value: normal prostate analogue


title: benign prostatic hyperplasia - committed basal cells - sample 1

description: 21 Y03111 CB


title: Genomic DNA from 09A44A6_T

description:
primary small intestine
9247377041

value: FFPE


title: normal prostate analogue - stem cells - sample 1

description: 1 PrEC SC

source_name: normal prostate analogue_stem cells


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep4


title: Genomic DNA from 1111775A14_N

description:
normal small intestine
7973219119


title: Δpgm vs. Δpgm ΔypeIR rep1

value: Δpgm ΔypeIR


title: normal prostate analogue - committed basal cells - sample 1

description: 1 PrEC CB

source_name: normal prostate analogue_committed basal cells


title: Genomic DNA from 10H002719A7_T

description:
primary colon
9266441100

value: colon


title: Genomic DNA from 08S016176A2_N

description:
normal small intestine
9370847144


title: BMCs_CD45 Neg_Day 10 [D]

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

description:
Sample D
Gene expression of Niche cell (CD45 Neg) on day 10

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array (AMADID: 26986) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies)

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

source_name: BMCs_CD45 Neg_Day 10

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop

growth_protocol: BMCs were freshly isolated and sorted for LSK cells on day 0 and day 10 post transplantation in the stress mouse model created.

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit as per the manufacturer’s instructions.

treatment_protocol: In A-D samples, thirty thousand Lin-Sca-1+c-kit+ (LSK) of CD45.2 mouse Bone Marrow (BM) cells was transplanted in each mouse (CD45.1) through lateral tail vein injection. After 10 days of transplantation, mice was sacrificed and BM stromal cells (CD45.1-) and LSK were sorted using a customized FACS AriaIII (BD Biosciences, San Jose, CA). Healthy mice respective phenotypes were used as control (Day 0).

value: bone marrow

value: 7 week

tag: treatment

value: 30,000 LSK cells transplantation into recipient mice

tag: stress

value: recipient mice exposed to 700 CGy radiation

value: Stromal cells (CD45-)

tag: time

value: sorted from BMCs isolated on Day 10 (post-transplantation)


title: Genomic DNA from 0918157B6264_T

description:
primary small intestine
7973219119

value: primary

value: small intestine

tag: primary site

value: F


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep1

value: Δpgm


title: BMCs_CD45 Neg_Day 0 [C]

description:
Sample C
Gene expression of Niche cell (CD45 Neg) on day 0
Sample C is the control of Sample D.

source_name: BMCs_CD45 Neg_Day 0

value: control

tag: cell type

value: sorted from BMCs isolated on Day 0 (before transplantation)


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep3

value: Δpgm ΔypeIR ΔyspIR


title: Genomic DNA from 073098E2_T

description:
metastasis mes_omentum
9370847143

value: metastasis

tag: grade


title: Δpgm vs. Δpgm ΔyspI at 30C rep5

description: The strain Δpgm is the Y.pestis CO92 pigmentation-negative mutant R88.

treatment_protocol: Microarray studies were performed by comparing strains R88 and Δpgm ΔyspI grown at a mid logarithmic phase.

source_name: Δpgm ΔyspI

value: Δpgm ΔyspI


title: Aerobic-xylose cy3-1

city: Daejeon

first: Oh Cheol

last: Kim

address: Gwahakro 125

country: South Korea

institute: KRIBB

description: The transcriptomes of Hansenula polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions

hyb_protocol: The fluorescent-labeled cDNA was concentrated under a vacuum and resuspended in 15 µl of preheated hybridization buffer (25% formamide, 5x SSC, 0.1% SDS). The pairs of Cys3 and Cys5-labeled samples were mixed and applied to a post-processing H. polymorpha microarray chip.

scan_protocol: After incubation in the dark at 42°C for 16 – 18 h, the slide was washed, dried, and scanned for Cy5(635 nm) and Cy3(532 nm) signals using a GenePix4000B scanner (Axon Instruments)

data_processing:
Spot identification and fluorescent signal quantitation were conducted using GenePix Pro v6.0 software, where any flagged, not found, saturated, or bad signal spot was automatically and manually eliminated.
Data processing and normalization were performed with the Arraynorm program. This data has the Matrix worksheet in your submission contains the normalized data that was generated by the Arraynorm software.

organism: Ogataea angusta

source_name: Aerobic-xylose cy3

label_protocol: 30 µg total RNA of each samples was used for first-strand cDNA synthesis using SuperScript III reverse transcriptase (Invitrogen, USA) with the oligo dT primer. The cDNA labeling was performed using an Aminoallyl post-DNA labeling kit (GeneChem, Korea) following the manufacturer’s protocol with some modifications.

extract_protocol: To grow the cells aerobically, 500 ml Erlenmeyer flasks containing 50 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and incubated at 37°C while shaking at 180 rpm in an orbital shaker. For microaerobic growth, 250 ml Erlenmeyer flasks containing 100 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and were incubated at 37°C while shaking at 100 rpm in an orbital shaker. Cell growth was monitored by determining the optical density (OD600) with a SHIMADZU UV-2550 Spectrophotometer. The total RNA was extracted by a hot phenol method followed by purification using an RNeasy column kit (Qiagen)

source_name: Aerobic-glucose cy5


title: Aerobic-xylose cy3-2


title: Δpgm vs. Δpgm ΔyspI at 30C rep6


title: Δpgm vs. Δpgm ΔyspI at 30C rep4


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep2


title: BMCs_HSC (LSK)_Day 10 [B]

description:
Sample B
Gene expression of HSC on day 10

source_name: BMCs_HSC (LSK)_Day 10

value: HSC (LSK cells)


title: Δpgm vs. Δpgm ΔyspI at 30C rep3


title: Aerobic-xylose cy5-2

source_name: Aerobic-xylose cy5

source_name: Aerobic-glucose cy3


title: BMCs_HSC (LSK)_Day 0 [A]

description:
Sample A
Gene expression in HSC on day 0
Sample A is the control of Sample B.

source_name: BMCs_HSC (LSK)_Day 0


title: Genomic DNA from 068279A3_T

description:
primary small intestine
9370847109

data_processing: The ChAmp pipeline (Bioconductor). Normalisation with BMIQ and batch correction with ComBat as part of the ChAmp pipeline.

source_name: primary

tag: source tissue type

value: FFPE


title: Δpgm vs. Δpgm ΔyspI at 30C rep2

data_processing: Data acquisition, normalization and data analysis have been described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).


title: Aerobic-xylose cy5-1