title: Ex_10d_control_labE_rep2

description:
LabE_Ex_C2
Gene expression profiling after 10-day exposure.


title: epith-SW-C35

status: Public on Jan 26 2015

type: RNA

city: Corvallis

first: Natalia

last: Shulzhenko

state: Oregon

address: 700 SW 30th St, 105 Dryden Hall

country: USA

institute: Oregon State University

hyb_protocol: individual samples labeled with Cy5 were co-hybridized with a common reference RNA labeled with Cy3 using MAUI hybridization system as described by Schaupp et al. 2005; PMID: 15679093

scan_protocol: Images were scanned by GenePix4000B Scanner (Axon Instruments/Molecular Devices).

data_processing: After subtraction of local background, signal intensity values were filtered to remove those lower than 100 in both channels and normalized using lowess smoother in BRB Array Tools. Probes present in >50% of arrays were considered for statistical analyses.

molecule: total RNA

organism: Mus musculus

source_name: villous epith

label_protocol: RNA was amplified and labeled using Aminoallyl RNA Amplification and Labeling System (NuGEN Technologies) following manufacturer’s protocol. Cy5-labeled samples were co-hybridized to Agilent microarrays with Cy3-labeled common reference RNA from control mouse intestine.

growth_protocol: Protocol suggested by Leica Microsystems for preparing samples for laser microdissection was generally followed. Specifically, immediately after harvesting, 1-2 cm of terminal ileum were embedded in OCT media and frozen at -80oC. Sections of 12 um were obtained using a cryostat at -18oC and placed on polyethylene naphthalate (PEN) coated slides (Leica).

extract_protocol: Dissected cells were directly harvested into RNA lysis buffer of RNAeasy Micro kit (Qiagen) and the instructions for RNA isolation were followed.

treatment_protocol: For microdissection, the slides were fixed in ethanol 70% (30 sec), washed in sterile water (10 dips), stained with hematoxylin (20 sec), washed again in water, fixed sequentially in ethanol 70%, 95% and 100% (1 min each). After a short air drying, the slides were positioned under the microscope of LMD6000 system (Leica) for microdissection.

tag: mouse strain

value: Swiss Webster

tag: tissue

value: villous epith

source_name: ileum

tag: sample description

value: pooled reference 1

value: ileum


title: crypt-C43

source_name: crypt

value: crypt


title: epith-SW-C3


title: WB_10d_cyfluthrin_labF_rep5

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description:
LabF_WB_Cyf5
Gene expression profiling after 10-day exposure.

hyb_protocol: Cy3-labeled cRNA (specific activity averaged between 7 and 18 pmol Cy3/ug cRNA among the labs) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto Agilent-042708 custom-designed Eohaustorius estuarius arrays (8x15K format), except in lab C which used Agilent-029660 arrays (4x44K format), for 15-20 hours at 65°C in a rotating hybridization oven.

scan_protocol: Slides were scanned using Agilent Microarray Scanners using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (for 8x15K format - protocol GE1-v5_10 and Grid: 042708_D_F_20120821) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw signal intensity data were log2 transformed and quantile normalized using GeneSpring software v12. For each lab, the two array datasets (Ex and WB) were normalized separately.

organism: Eohaustorius estuarius

source_name: whole body, 10d, LabF, cyfluthrin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Low Input Quick Amp labeling kit (Agilent). Cy3 dye incorporation and cRNA yield were measured with a NanoDrop spectrophotometer.

extract_protocol: Total RNA was extracted and purified using RNeasy columns (Qiagen), except for one lab that used RNSTAT-60 (Tel-Test) for RNA extraction. RNA was quantified using a NanoDrop spectrophotometer.

treatment_protocol: Eohaustorius estuarius were exposed to cyfluthrin-spiked sediment (nominal concentration 1.6 μg/kg) or solvent-spiked sediment (control) for 10 days according to standard procedures (USEPA 1994).

tag: sample type

value: Whole Body (WB)

tag: laboratory

value: F

value: whole body

tag: treatment

value: cyfluthrin

tag: treatment duration

value: 10 days


title: epith-C43


title: WB_10d_cyfluthrin_labF_rep6

description:
LabF_WB_Cyf6
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labE_rep1

description:
LabE_Ex_C1
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabE, control

value: RNA Extract (Ex)

value: E

value: solvent control


title: crypt-SW-C35


title: epith-C23


title: WB_10d_cyfluthrin_labF_rep3

description:
LabF_WB_Cyf3
Gene expression profiling after 10-day exposure.


title: crypt-SW-C3


title: WB_10d_cyfluthrin_labF_rep1

description:
LabF_WB_Cyf1
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labF_rep4

description:
LabF_WB_Cyf4
Gene expression profiling after 10-day exposure.


title: crypt-C16


title: ileum_5dNF_SW-GF5

label_protocol: 20 ug of total RNA were directly fluorescently labeled in a reverse transcription reaction using Cy3-dUTP or Cy5-dUTP (GE Healthcare) and Oligo(dT)12-18 Primer and SuperScript II reverse transcriptase

growth_protocol: 2 cm of full-thickness terminal ileum of small intestine was used

extract_protocol: tissues were homogenized in RLT buffer from Qiagen RNAeasy KIT. Total RNA were isolated according to the standard protocol

treatment_protocol: mice with different types of microbiota. Antibiotics were administered in drinking water for 4-5 weeks in the following concentrations: ampicillin (1 g/L), vancomycin (0.5 g/L), neomycin trisulfate (1 g/L), metronidazole (1 g/L). Colonizations of germfree mice were performed using stool samples of control or antibiotics-treated mice.

tag: Sex

value: M

tag: microbiota status

tag: microbiota status explanation

value: colonized 5 days with normal microbiota


title: WB_10d_cyfluthrin_labF_rep2

description:
LabF_WB_Cyf2
Gene expression profiling after 10-day exposure.


title: epith-SW-C1


title: crypt-C23


title: WB_10d_cyfluthrin_labF_rep8

description:
LabF_WB_Cyf8
Gene expression profiling after 10-day exposure.


title: crypt-SW-C1


title: WB_10d_control_labF_rep7

description:
LabF_WB_C7
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabF, control


title: WB_10d_control_labF_rep6

description:
LabF_WB_C6
Gene expression profiling after 10-day exposure.


title: ileum_GF_SW-GF3

value: GF

value: germfree


title: WB_10d_control_labF_rep8

description:
LabF_WB_C8
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labF_rep5

description:
LabF_WB_C5
Gene expression profiling after 10-day exposure.


title: ileum_GF_SW-GF2

value: Swiss Webster


title: CD43+/41+/235+ progenitors generated from T21/GATA1s iPSC line, biological rep1

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: Gene expression data from CD43+/41+/235+ progenitors generated from T21/GATA1s iPSCs

hyb_protocol: cRNA was hybridized according to the Affymetrix GeneChip Technical Manual.

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

data_processing: The raw intensity values from CEL files were processed using RMA method implemented by the Bioconductor R oligo package. RMA processing resulted in 33,297 probesets, that were then mapped to 19,392 RefSeq genes. In cases where several probesets mapped to one RefSeq gene the expression values were averaged to obtain one value per gene.

label: biotin

organism: Homo sapiens

source_name: CD43+/41+/235+ progenitors isolated from hematopoietic differentiation of human iPSCs

label_protocol: Biotinylated cRNA was prepared according to manufacturer instructions for the NuGEN WT-Ovation Pico RNA kt .

growth_protocol: For hematopoietic differentiation, embryoid bodies were generated by culturing small aggregates of feeder-depleted iPSCs in 6 well low-cluster plates in StemPro-34 (Invitrogen) media supplemented with glutamine, ascorbic acid, transferrin, monothioglycerol, and with the following cytokines: bone morphogenic protein 4 (BMP4) 25 ng/ml and vascular endothelial growth factor (VEGF) 50 ng/ml on days 0-2; BMP4 25 ng/ml, VEGF 50 ng/ml, stem cell factor (SCF) 50 ng/ml, thrombopoietin (TPO) 50 ng/ml, Flt3 ligand (FLT3) 50 ng/ml, and fibroblast growth factor (bFGF) 20 ng/ml on days 2-4; VEGF 50 ng/ml, SCF 50 ng/ml, TPO 50 ng/ml, FLT3 50 ng/ml, and bFGF 20 ng/ml on days 4-8.

extract_protocol: Total RNA was extracted with the Qiagen miRneasy kit per manufacturer's instructions.

treatment_protocol: Embryoid bodies were dissociated to single cells by a 1 hour incubation with 0.2% Collagenase B containing 20% serum followed by a 2 minute incubation with trypsin (0.05% trypsin-EDTA) at 37ºC. After enzymatic treatment, 1 ml serum was added and the embryoid bodies were disaggregated to single cells by multiple passages through a 20-gauge needle. Cells were stained with anti-human CD41 and CD235, and flow cytometrically sorted for the double positive population to extract RNA.

tag: cell type

value: hematopoietic cell

tag: genotype/variation


title: epith-C16

value: villous epith

value: pooled reference 1


title: WB_10d_control_labF_rep3

description:
LabF_WB_C3
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labF_rep7

description:
LabF_Ex_Cyf7
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabF, cyfluthrin


title: WB_10d_control_labF_rep1

description:
LabF_WB_C1
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labF_rep8

description:
LabF_Ex_Cyf8
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labF_rep2

description:
LabF_WB_C2
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labF_rep4

description:
LabF_WB_C4
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labF_rep2

description:
LabF_Ex_Cyf2
Gene expression profiling after 10-day exposure.


title: ileum_no-AB_SW-C44

value: no-AB

value: no antibiotics control

value: ileum


title: ileum_no-AB_SW-C5


title: Ex_10d_cyfluthrin_labF_rep3

description:
LabF_Ex_Cyf3
Gene expression profiling after 10-day exposure.

value: F

value: whole body


title: ileum_no-AB_SW-C48


title: Ex_10d_cyfluthrin_labF_rep6

description:
LabF_Ex_Cyf6
Gene expression profiling after 10-day exposure.

value: cyfluthrin

value: 10 days


title: ileum_GF_SW-GF4


title: Ex_10d_cyfluthrin_labF_rep1

description:
LabF_Ex_Cyf1
Gene expression profiling after 10-day exposure.

value: RNA Extract (Ex)


title: ileum_7dNF_SW-C32

value: colonized 7 days with  normal microbiota


title: ileum_7dNF_SW-C33


title: ileum_7dNF_SW-C34


title: Ex_10d_control_labF_rep8

description:
LabF_Ex_C8
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabF, control

value: solvent control


title: Ex_10d_cyfluthrin_labF_rep4

description:
LabF_Ex_Cyf4
Gene expression profiling after 10-day exposure.


title: ileum_7dNF_SW-C31

value: M


title: ileum_GF_SW-GF1

value: GF


title: Ex_10d_cyfluthrin_labF_rep5

description:
LabF_Ex_Cyf5
Gene expression profiling after 10-day exposure.


title: ileum_no-AB_SW-C49


title: Ex_10d_control_labF_rep5

description:
LabF_Ex_C5
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labF_rep4

description:
LabF_Ex_C4
Gene expression profiling after 10-day exposure.


title: ileum_no-AB_SW-C3


title: ileum_7dFAB_SW-C28

value: colonized 7 days with AB-microbiota


title: ileum_7dFAB_SW-C29

value: Swiss Webster


title: Ex_10d_control_labF_rep6

description:
LabF_Ex_C6
Gene expression profiling after 10-day exposure.


title: ileum_7dFAB_SW-C30


title: Ex_10d_control_labF_rep7

description:
LabF_Ex_C7
Gene expression profiling after 10-day exposure.


title: ileum_3dFAB_SW-C22

value: colonized 3 days with AB-microbiota


title: Ex_10d_control_labF_rep3

description:
LabF_Ex_C3
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labE_rep8

description:
LabE_WB_Cyf8b
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabE, cyfluthrin

value: Whole Body (WB)

value: E


title: ileum_3dNF_SW-C26

value: colonized 3 days with normal microbiota

value: pooled reference 1


title: WB_10d_cyfluthrin_labE_rep7

description:
LabE_WB_Cyf8a
Gene expression profiling after 10-day exposure.


title: ileum_3dNF_SW-C25

value: ileum


title: Ex_10d_control_labF_rep1

description:
LabF_Ex_C1
Gene expression profiling after 10-day exposure.

value: F


title: Ex_10d_control_labF_rep2

description:
LabF_Ex_C2
Gene expression profiling after 10-day exposure.

value: whole body


title: ileum_3dNF_SW-C23


title: ileum_3dNF_SW-C24


title: ileum_7dFAB_SW-C27


title: ileum_no-AB_SW-C4

value: no-AB

value: no antibiotics control


title: ileum_3dFAB_SW-C21


title: WB_10d_cyfluthrin_labE_rep6

description:
LabE_WB_Cyf6
Gene expression profiling after 10-day exposure.

value: cyfluthrin

value: 10 days


title: WB_10d_cyfluthrin_labE_rep4

description:
LabE_WB_Cyf4
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labE_rep5

description:
LabE_WB_C4
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabE, control

value: solvent control


title: WB_10d_control_labE_rep6

description:
LabE_WB_C5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labE_rep5

description:
LabE_WB_Cyf5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labE_rep1

description:
LabE_WB_Cyf1
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labE_rep4

description:
LabE_WB_C3b
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labE_rep3

description:
LabE_WB_Cyf3
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labE_rep1

description:
LabE_WB_C1
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labE_rep2

description:
LabE_WB_C2
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labE_rep3

description:
LabE_WB_C3a
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labD_rep8

description:
LabD_WB_Cyf8
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabD, cyfluthrin

value: D


title: WB_10d_cyfluthrin_labE_rep2

description:
LabE_WB_Cyf2
Gene expression profiling after 10-day exposure.


title: ileum_GF-AB_GF29

value: M

value: GF-AB

value: germfree treated with antibiotics


title: ileum_3dFAB_SW-C19

value: Swiss Webster

value: colonized 3 days with AB-microbiota


title: ileum_3dFAB_SW-C20


title: ileum_GF-AB_GF27


title: ileum_AB_SW-C16

value: AB

value: antibiotic-treated


title: ileum_GF-AB_GF26

value: pooled reference 1


title: ileum_AB_SW-C15

value: ileum


title: ileum_GF-AB_GF25

value: F


title: ileum_no-AB_SW-C2


title: WB_10d_cyfluthrin_labD_rep6

description:
LabD_WB_Cyf6
Gene expression profiling after 10-day exposure.

value: Whole Body (WB)

value: whole body


title: ileum_AB_SW-C14


title: ileum_AB_SW-C17


title: ileum_GF-AB_GF24


title: ileum_GF-AB_GF22


title: WB_10d_cyfluthrin_labD_rep5

description:
LabD_WB_Cyf5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labD_rep7

description:
LabD_WB_Cyf7
Gene expression profiling after 10-day exposure.


title: ileum_GF-AB_GF23


title: WB_10d_control_labD_rep7

description:
LabD_WB_C7
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabD, control


title: WB_10d_cyfluthrin_labD_rep1

description:
LabD_WB_Cyf1
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labD_rep5

description:
LabD_WB_C5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labD_rep3

description:
LabD_WB_Cyf3
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labD_rep2

description:
LabD_WB_Cyf2
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labD_rep4

description:
LabD_WB_Cyf4
Gene expression profiling after 10-day exposure.


title: ileum_GF_GF12

value: GF

value: germfree


title: ileum_GF_GF16


title: ileum_GF_GF11


title: ileum_no-AB_C48

value: no-AB

value: no antibiotics control


title: ileum_AB_C45


title: ileum_AB_C47


title: ileum_no-AB_C46


title: WB_10d_control_labD_rep4

description:
LabD_WB_C4
Gene expression profiling after 10-day exposure.

value: D

value: solvent control

value: 10 days


title: WB_10d_control_labD_rep2

description:
LabD_WB_C2
Gene expression profiling after 10-day exposure.


title: ileum_7dNF_C42

value: colonized 7 days with  normal microbiota


title: ileum_GF_GF15

value: M


title: ileum_no-AB_C44


title: ileum_7dNF_C41


title: WB_10d_control_labD_rep3

description:
LabD_WB_C3
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labD_rep6

description:
LabD_WB_C6
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labD_rep8

description:
LabD_WB_C8
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labD_rep4

description:
LabD_Ex_Cyf4
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabD, cyfluthrin

value: RNA Extract (Ex)

value: cyfluthrin


title: Ex_10d_cyfluthrin_labD_rep7

description:
LabD_Ex_Cyf7
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labD_rep6

description:
LabD_Ex_Cyf6
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labD_rep5

description:
LabD_Ex_Cyf5
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labD_rep1

description:
LabD_WB_C1
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labD_rep8

description:
LabD_Ex_Cyf8
Gene expression profiling after 10-day exposure.


title: ileum_7dFAB_C38

value: colonized 7 days with AB-microbiota


title: ileum_7dNF_C40

value: pooled reference 1


title: ileum_7dFAB_C39

value: ileum


title: Ex_10d_cyfluthrin_labD_rep2

description:
LabD_Ex_Cyf2
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labD_rep1

description:
LabD_Ex_Cyf1
Gene expression profiling after 10-day exposure.


title: ileum_3dNF_C34

value: colonized 3 days with normal microbiota


title: ileum_3dNF_C35


title: ileum_3dFAB_C33

value: F

value: colonized 3 days with AB-microbiota


title: Ex_10d_control_labD_rep6

description:
LabD_Ex_C6
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabD, control

value: whole body


title: Ex_10d_control_labD_rep5

description:
LabD_Ex_C5
Gene expression profiling after 10-day exposure.


title: ileum_3dFAB_C30


title: ileum_7dFAB_C37


title: ileum_AB_C28

value: AB

value: antibiotic-treated


title: Ex_10d_control_labD_rep8

description:
LabD_Ex_C8
Gene expression profiling after 10-day exposure.


title: ileum_3dFAB_C32


title: ileum_3dNF_C36


title: Ex_10d_control_labD_rep7

description:
LabD_Ex_C7
Gene expression profiling after 10-day exposure.


title: ileum_AB_C26


title: ileum_3dFAB_C31


title: Ex_10d_cyfluthrin_labD_rep3

description:
LabD_Ex_Cyf3
Gene expression profiling after 10-day exposure.


title: ileum_GF-AB_GF28

value: GF-AB

value: germfree treated with antibiotics


title: Ex_10d_control_labD_rep1

description:
LabD_Ex_C1
Gene expression profiling after 10-day exposure.

value: D

value: solvent control


title: ileum_AB_C27


title: Ex_10d_control_labD_rep2

description:
LabD_Ex_C2
Gene expression profiling after 10-day exposure.

value: 10 days


title: Ex_10d_control_labD_rep3

description:
LabD_Ex_C3
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labD_rep4

description:
LabD_Ex_C4
Gene expression profiling after 10-day exposure.


title: ileum_no-AB_C18

value: M

value: no-AB

value: no antibiotics control


title: ileum_no-AB_C13


title: ileum_no-AB_C19


title: ileum_AB_C25


title: WB_10d_cyfluthrin_labB_rep6

description:
LabB_WB_Cyf6
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabB, cyfluthrin

value: Whole Body (WB)

value: B

value: cyfluthrin


title: WB_10d_cyfluthrin_labB_rep7

description:
LabB_WB_Cyf7
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labB_rep8

description:
LabB_WB_Cyf8
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labB_rep4

description:
LabB_WB_Cyf4
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labB_rep3

description:
LabB_WB_Cyf3
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labB_rep5

description:
LabB_WB_Cyf5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labB_rep1

description:
LabB_WB_Cyf1
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labB_rep2

description:
LabB_WB_Cyf2
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labB_rep4

description:
LabB_WB_C4
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabB, control


title: WB_10d_control_labB_rep5

description:
LabB_WB_C5
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labB_rep2

description:
LabB_WB_C2
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labB_rep3

description:
LabB_WB_C3
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labB_rep1

description:
LabB_WB_C1
Gene expression profiling after 10-day exposure.


title: ileum_no-AB_4782

value: ileum

value: pooled reference 1


title: WB_10d_control_labB_rep6

description:
LabB_WB_C6
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labB_rep8

description:
LabB_WB_C8
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labB_rep7

description:
LabB_WB_C7
Gene expression profiling after 10-day exposure.


title: ileum_no-AB_C12

value: F


title: Ex_10d_cyfluthrin_labB_rep8

description:
LabB_Ex_Cyf8
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabB, cyfluthrin

value: RNA Extract (Ex)

value: whole body


title: Ex_10d_cyfluthrin_labB_rep3

description:
LabB_Ex_Cyf3
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labB_rep7

description:
LabB_Ex_Cyf7
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labB_rep4

description:
LabB_Ex_Cyf4
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labB_rep5

description:
LabB_Ex_Cyf5
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labB_rep2

description:
LabB_Ex_Cyf2
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep8

description:
LabB_Ex_C8
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabB, control


title: Ex_10d_cyfluthrin_labB_rep6

description:
LabB_Ex_Cyf6
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep7

description:
LabB_Ex_C7
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep4

description:
LabB_Ex_C4
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep6

description:
LabB_Ex_C6
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep8

description:
LabA_WB_Cyf8
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabA, cyfluthrin

value: A


title: Ex_10d_control_labB_rep2

description:
LabB_Ex_C2
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep3

description:
LabB_Ex_C3
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep2

description:
LabA_WB_Cyf2
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep5

description:
LabB_Ex_C5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep4

description:
LabA_WB_Cyf4
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep6

description:
LabA_WB_C6
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabA, control


title: WB_10d_cyfluthrin_labA_rep6

description:
LabA_WB_Cyf6
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep3

description:
LabA_WB_Cyf3
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep5

description:
LabA_WB_C5
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep5

description:
LabA_WB_Cyf5
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep4

description:
LabA_WB_C4
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep7

description:
LabA_WB_C7
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep1

description:
LabA_WB_Cyf1
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep3

description:
LabA_WB_C3
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep8

description:
LabA_WB_C8
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep6

description:
LabA_Ex_Cyf6
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabA, cyfluthrin


title: WB_10d_control_labA_rep2

description:
LabA_WB_C2
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep7

description:
LabA_Ex_Cyf7
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep8

description:
LabA_Ex_Cyf8
Gene expression profiling after 10-day exposure.


title: WB_10d_cyfluthrin_labA_rep7

description:
LabA_WB_Cyf7
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labB_rep1

description:
LabB_Ex_C1
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep4

description:
LabA_Ex_Cyf4
Gene expression profiling after 10-day exposure.


title: WB_10d_control_labA_rep1

description:
LabA_WB_C1
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep5

description:
LabA_Ex_Cyf5
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep3

description:
LabA_Ex_Cyf3
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep2

description:
LabA_Ex_Cyf2
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labA_rep1

description:
LabA_Ex_Cyf1
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep5

description:
LabA_Ex_C5
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabA, control


title: Ex_10d_control_labA_rep6

description:
LabA_Ex_C6
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep2

description:
LabA_Ex_C2
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep3

description:
LabA_Ex_C3
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep8

description:
LabA_Ex_C8
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep1

description:
LabA_Ex_C1
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep7

description:
LabA_Ex_C7
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labA_rep4

description:
LabA_Ex_C4
Gene expression profiling after 10-day exposure.


title: Endometrial inter-site_pregnant sows_day 24_rep2

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

country: China

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description:
Gene expression on day 24 of gestation
D24b-002

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The raw gene expression data were extracted from Agilent Feature Extraction Software (Version 10.7) and imported into Agilent GeneSpring GX software (version 11.0) for further analysis.

organism: Sus scrofa

source_name: Endometrial inter-site, gestation day 24

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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: Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA according to the manufacturer’s instructions.

treatment_protocol: The sows of pregnant group were inseminated twice, 12 and 24 h after heat detection. The sows of non-pregnant group were treated with inactivate sperms from the same boar. Nine pregnant sows were slaughtered by electrical on day 13, day 18 and day 24 after insemination (the pregnant group, three sows every period). The non-pregnant sows were slaughtered on day 13 after inseminated (n=3).

value: Endometrial inter-site

tag: developmental stage

value: pregnant

tag: time

value: day 24

tag: breed

value: Large White


title: Endometrial inter-site_pregnant sows_day 18_rep1

description:
Gene expression on day 18 of gestation
D18b-001

source_name: Endometrial inter-site, gestation day 18

value: day 18


title: Endometrial inter-site_pregnant sows_day 24_rep3

description:
Gene expression on day 24 of gestation
D24b-003


title: Endometrial attachment site_pregnant sows_day 24_rep3

description:
Gene expression on day 24 of gestation
D24a-003

source_name: Endometrial attachment site, gestation day 24

value: Endometrial attachment site


title: Endometrial attachment site_pregnant sows_day 24_rep1

description:
Gene expression on day 24 of gestation
D24a-001


title: Endometrial attachment site_pregnant sows_day 24_rep2

description:
Gene expression on day 24 of gestation
D24a-002


title: Endometrial inter-site_pregnant sows_day 24_rep1

description:
Gene expression on day 24 of gestation
D24b-001


title: Endometrial inter-site_pregnant sows_day 18_rep2

description:
Gene expression on day 18 of gestation
D18b-002


title: Endometrial inter-site_pregnant sows_day 18_rep3

description:
Gene expression on day 18 of gestation
D18b-003


title: Endometrial attachment site_pregnant sows_day 18_rep3

description:
Gene expression on day 18 of gestation
D18a-003

source_name: Endometrial attachment site, gestation day 18


title: Endometrial attachment site_pregnant sows_day 18_rep2

description:
Gene expression on day 18 of gestation
D18a-002


title: Endometrial attachment site_pregnant sows_day 18_rep1

description:
Gene expression on day 18 of gestation
D18a-001


title: 457_W0_A07.CEL

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix Expression Console version 1.1. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 100.. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median

source_name: Abdominal subcutaneous adipose tissue

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNA was extracted using the miRNeasy mini kit (cat.no 217004, Qiagen). RNA samples were treated with RNase-free DNase (cat.no 79254, Qiagen).

treatment_protocol: Patients had been fasting over night. An abdominal subcutaneous adipose tissue needle biopsy was obtained under local anesthesia. The biopsy was rapidly rinsed in saline and snap frozen in liqued nitrogen.

value: White adipose tissue

tag: genotype

value: Female

tag: age

tag: study group


title: 457_W24_A07.CEL

tag: tissue


title: Endometrial attachment site_pregnant sows_day 13_rep2

description:
Gene expression on day 13 of gestation
D13a-002

source_name: Endometrial attachment site, gestation day 13

value: day 13


title: 445_W24_C07.CEL


title: Endometrial attachment site_pregnant sows_day 13_rep1

description:
Gene expression on day 13 of gestation
D13a-001


title: 449_W24_A05.CEL


title: Endometrium of non-pregnant sows_rep3

description:
Gene expression during corresponding cylic controls
NP-003

source_name: endometrium of non-pregnant sows

value: endometrium

value: non-pregnant


title: 452_W24_G07.CEL


title: Endometrial inter-site_pregnant sows_day 13_rep1

description:
Gene expression on day 13 of gestation
D13b-001

source_name: Endometrial inter-site, gestation day 13


title: Endometrial inter-site_pregnant sows_day 13_rep3

description:
Gene expression on day 13 of gestation
D13b-003


title: 449_W0_C07.CEL


title: Endometrial inter-site_pregnant sows_day 13_rep2

description:
Gene expression on day 13 of gestation
D13b-002


title: 452_W0_A05.CEL


title: Endometrium of non-pregnant sows_rep2

description:
Gene expression during corresponding cylic controls
NP-002


title: Endometrium of non-pregnant sows_rep1

description:
Gene expression during corresponding cylic controls
NP-001


title: 445_W0_A09.CEL


title: 443_W24_B05.CEL

value: Male


title: 437_W0_G05.CEL


title: 437_W24_B05.CEL


title: Ex_10d_cyfluthrin_labB_rep1

description:
LabB_Ex_Cyf1
Gene expression profiling after 10-day exposure.

value: B

value: cyfluthrin

value: 10 days


title: Endometrial attachment site_pregnant sows_day 13_rep3

description:
Gene expression on day 13 of gestation
D13a-003


title: 443_W0_E05.CEL


title: 435_W24_D05.CEL


title: 429_W0_H09.CEL


title: 428_W0_G09.CEL


title: 426_W24_C09.CEL


title: 429_W24_D07.CEL


title: 435_W0_F07.CEL


title: 426_W0_H05.CEL


title: 425_W24_D05.CEL


title: 428_W24_B07.CEL


title: 425_W0_A09.CEL


title: 424_W0_B09.CEL


title: 424_W24_B09.CEL


title: 418_W24_D09.CEL


title: 420_W0_C09.CEL


title: 415_W0_C05.CEL


title: 420_W24_D07.CEL


title: 415_W24_H07.CEL


title: 416_W0_F09.CEL


title: 402_W24_B07.CEL


title: 418_W0_E09.CEL


title: 416_W24_F05.CEL


title: 247_W24_D07.CEL


title: 250_W24_E09.CEL


title: 249_W0_G05.CEL


title: 247_W0_C05.CEL


title: 250_W0_H05.CEL


title: 403W24_C05.CEL


title: 246_W0_E07_3.CEL


title: 402_W0_E07.CEL


title: 249_W24_G07.CEL


title: 244_W0_D09.CEL


title: 244_W24_H09.CEL


title: 243_W24_A05.CEL


title: 403_W0_D09.CEL


title: 240_W24_C05.CEL


title: 238_W24_E07.CEL


title: 222_W24_E05.CEL


title: 238_W0_G09.CEL


title: 229_W0_F07.CEL


title: 220_W0_A05.CEL


title: 232_W0_A09.CEL


title: 229_W24_F05.CEL


title: 228_W24_D05.CEL


title: 240_W0_G05.CEL


title: 228_W0_H07.CEL


title: 232_W24_C09.CEL


title: 0.5 hr release 1

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

description: Tiling array 0.5 hr release

hyb_protocol: 15 ug of the labelled cDNA was hybridized to each array, and hybridization was performed on 3 separate arrays (3 technical replicates).

scan_protocol: The arrays were scanned on a Molecular Devices GenePix Axon 4400A at 2.5 uM resolution.

data_processing: The scanned array data was converted into pair and gff files using the NimbleScan software package. Probe intensities across technical replicates were quantile normalised and a three-probe sliding window together with the Hodges-Lehmann estimator of location were used to smooth the data and collapse the replicates into one set per sample  Background subtraction was performed using the top 2% of random probes.  Possible single probe introns were recovered by performing bacground subtraction on pre-smoothened data and setting final probe intensities to zero if their pre-smoothened median across replicates is zero.

organism: Oikopleura dioica

source_name: cDNA from 0.5 hr after release whole animals

label_protocol: For each sample, cDNA was labeled and amplified using the Roche NimbleGen gene expression protocol (http://www.nimblegen.com/products/lit/05434505001_NG_Expression_UGuide_v6p0.pdf).

growth_protocol: Animals released from day 7 of growth arrest by dilution to normal culture density and sampled in a half hour window centred on 30 minutes after dilution.

extract_protocol: Animals were anesthetized in cold ethyl 3-aminobenzoate methanesulfonate salt (MS-222) and collected by centrifigation. Total RNA was extracted from whole animals or isolated animal tissues using the Qiagen RNeasy kit. RNA quality control was performed using an Agilent 2100 Bio-analyzer.Double stranded cDNA was generated according to the Roche NimbleGen gene expression protocol (http://www.nimblegen.com/products/lit/05434505001_NG_Expression_UGuide_v6p0.pdf), using the Life technologies/Invitrogen Superscript double stranded cDNA synthesis kit.

value: Day 7 growth arrest recovery

tag: gender

value: Mixed


title: 216_W24_D07.CEL


title: 220_W24_H05.CEL


title: 4 hr release 1

description: Tiling array 4 hr release

source_name: cDNA from 4 hr after release whole animals

growth_protocol: Animals released from day 7 of growth arrest by dilution to normal culture density and sampled in a half hour window centred on 4 hrs after dilution.


title: 0.5 hr release 2

description: Tiling array 0.5 hr release


title: 222_W0_F07.CEL


title: 1.5 hr release 1

description: Tiling array 1.5 hr release

source_name: cDNA from 1.5 hr after release whole animals

growth_protocol: Animals released from day 7 of growth arrest by dilution to normal culture density and sampled in a half hour window centred on 1.5 hours after dilution.


title: 215_W24_F09.CEL


title: 1.5 hr release 2

description: Tiling array 1.5 hr release


title: Stasis 2

description: Tiling array stasis release

source_name: cDNA from stasis whole animals

growth_protocol: Animals cultured in dense conditions to induce growth arrest and sampled at day 7

value: Day 7 stasis


title: Stasis 1

description: Tiling array stasis

value: Day 7 growth arrested


title: 212_W24_A07.CEL


title: 215_W0_E05.CEL


title: 4 hr release 2

description: Tiling array 4 hr release


title: 210_W24_B07.CEL


title: 159_W18_G05.CEL


title: 216_W0_G07.CEL


title: 210_W0_B07.CEL


title: 204_W24_B09.CEL


title: Ex_10d_control_labC_rep6

description:
LabC_Ex_C6
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabC, control

tag: sample type

value: RNA Extract (Ex)

value: C

value: whole body

value: solvent control


title: 205_W24_D05.CEL

value: White adipose tissue


title: 207_W0_B05.CEL

value: Female


title: 205_W0_C07.CEL


title: 212_W0_H07.CEL


title: Ex_10d_control_labC_rep7

description:
LabC_Ex_C7
Gene expression profiling after 10-day exposure.

tag: laboratory


title: 204_W0_F05.CEL


title: 159_W0_B07.CEL


title: 157_W18_D05.CEL


title: 207_W24_B05.CEL


title: Ex_10d_control_labC_rep8

description:
LabC_Ex_C8
Gene expression profiling after 10-day exposure.

tag: treatment


title: 157_W0_A09.CEL


title: 246_W24_A07.CEL


title: Ex_10d_control_labC_rep5

description:
LabC_Ex_C5
Gene expression profiling after 10-day exposure.

tag: treatment duration


title: Ex_10d_control_labC_rep4

description:
LabC_Ex_C4
Gene expression profiling after 10-day exposure.


title: 156_W18_H09.CEL


title: Ex_10d_control_labC_rep3

description:
LabC_Ex_C3
Gene expression profiling after 10-day exposure.


title: 156_W0_F07.CEL


title: Ex_10d_control_labC_rep1

description:
LabC_Ex_C1
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labC_rep2

description:
LabC_Ex_C2
Gene expression profiling after 10-day exposure.


title: 154_W18_D07.CEL


title: 150_W18_B05.CEL


title: 154_W0_G09.CEL


title: Ex_10d_cyfluthrin_labC_rep7

description:
LabC_Ex_Cyf7
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabC, cyfluthrin


title: 151_W0_G05.CEL


title: Ex_10d_cyfluthrin_labC_rep4

description:
LabC_Ex_Cyf4
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labC_rep6

description:
LabC_Ex_Cyf6
Gene expression profiling after 10-day exposure.


title: 151_W18_E07.CEL


title: Ex_10d_cyfluthrin_labC_rep1

description:
LabC_Ex_Cyf1
Gene expression profiling after 10-day exposure.


title: Bsub_168_LPDM_T2_rep3

type: genomic

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Data files were loaded into Bioconductor and preprocessed through Ringo, using the 'nimblegen' method. Combination of replicates and smoothing was accomplished through Ringo's 'computeRuningMedians' function, using a winHalfSize of 350.
merged and smoothed log2 (ChIP/Input) ratio

molecule: genomic DNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: ChIP_DNA from Bsub 168, T2 phase

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.ChIP DNA is labelled with Cy5 and CONTROL DNA with Cy3. See www.nimblegen.com.

growth_protocol: Cells of strain 168 (mock precipitation) were grown in LPDM and 100 mM IPTG with vigorous shaking at 37oC. Two hours after the onset of phosphate starvation state (T2), 50 ml were treated with formaldehyde.

extract_protocol: Crosslinking was performed by the addition of formaldehyde to a final concentration of 1% followed by 20 min incubation at room temperature with slow shaking. The cultures were then quenched with Glycine (0.36M final concentration) for 5 min at room temperature. Cells were collected by centrifugation at 4oC and the pellets were washed twice with 50 ml ice-cold Buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) before being snap frozen in a dry ice / ethanol bath.   Pellets were thawed at 37oC and resuspended in 0.5ml buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% Triton X-100) supplemented with 3 mg ml-1 lysozyme and 0.1 mg ml-1 RNaseA (final concentrations) and incubated for 30 min at 37oC, then the sample volume was adjusted to 1 ml with buffer B and samples placed on ice for 10 min. Genomic DNA was sheared by sonication (Diagenode Bioruptor Twin sonicator) into fragments between 0.2 and 1 kb. Sonicated samples were centrifuged for 10 min at 20 000 g (4oC) to remove insoluble debris. Fifty microliteres of the cleared lysates was removed to serve as the CONTROL sample, to which 50 microliters of 10X buffer C (10 mM Tris-HCl pH 8, 10% SDS, 10 mM EDTA) and 400 microliters buffer B were added and the sample was stored on ice. The remaining cleared lysates were each added to 40 microliters anti-FLAG M2-agarose resin (Sigma-Aldrich; A2220) equilibrated with ice-cold buffer B (according to manufacturers’ instructions) and incubated for two hours at 4oC with mild agitation. Beads were then collected by centrifugation for 1 min at 5000 g (4oC) and washed three times with 0.5 ml ice-cold buffer B. To reverse the crosslinking beads were transferred to new 1.5 ml eppendorf tubes, resuspended in 0.5 ml 1X buffer C and incubated along with the CONTROL samples for ~20 hours at 65oC with shaking (950 rpm). ChIP samples were collected by centrifugation for 1 min at 13 300 rpm (4oC).  DNA from both ChIP and CONTROL samples was purified using the QIAquick PCR purification kit (Qiagen, 28106), eluted in 50 microliters H2O and treated with 0.02 mg ml-1 RNaseA (Roche, 11119915001) for 30 min at 37oC. RNase was eliminated using the QIAquick PCR purification kit and samples were eluted in 30 microliters H2O.  Equal concentrations of ChIP DNA and CONTROL samples were amplified using the GenomePlex complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich; WGA2-50RXN) as per manufacturers’ instructions and purified using the QIAquick PCR purification kit and eluted in 30 microliters H2O. Ten microliters of each of the purified amplified samples was subjected to a second round of amplification using the WGA kit as per manufacturer’s instructions, purified using the QIAquick PCR purification kit and eluted in 30 microliters H2O.  3.5-4  micrograms of twice-amplified ChIP DNA and CONTROL samples (of both tagged and mock precipitation experiments) at a concentration of ~250 ng per microliter (A260/A280 ≥1.7 and A260/A230 ≥ 1.6) from three separate ChIP experiments were submitted TO NimbleGen.  Crosslinking was performed by the addition of formaldehyde to a final concentration of 1% followed by 20 min incubation at room temperature with slow shaking. The cultures were then quenched with Glycine (0.36M final concentration) for 5 min at room temperature. Cells were collected by centrifugation at 4oC and the pellets were washed twice with 50 ml ice-cold Buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) before being snap frozen in a dry ice / ethanol bath.

tag: strain

tag: growth phase

tag: chip antibody

value: mouse anti-FLAG M2 (Sigma)

source_name: Control_DNA from Bsub 168, T2 phase


title: Ex_10d_cyfluthrin_labC_rep3

description:
LabC_Ex_Cyf3
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labC_rep5

description:
LabC_Ex_Cyf5
Gene expression profiling after 10-day exposure.


title: Bsub_168_LPDM_T2_rep2


title: 145_W18_H05.CEL


title: Ex_10d_cyfluthrin_labC_rep2

description:
LabC_Ex_Cyf2
Gene expression profiling after 10-day exposure.


title: 147_W0_G07.CEL


title: 150_W0_F05.CEL


title: Bsub_168_LPDM_T2_rep1


title: 142_W18_G07.CEL


title: 144_W0_F07.CEL


title: 144_W18_A07.CEL


title: 147_W18_F09.CEL


title: 145_W0_C09.CEL


title: Ex_10d_cyfluthrin_labC_rep8

description:
LabC_Ex_Cyf8
Gene expression profiling after 10-day exposure.


title: Bsub_168_LPDM_exp_rep3

source_name: ChIP_DNA from Bsub 168, exponential phase

growth_protocol: Cells of strain 168 (mock precipitation) were grown in LPDM and 100 mM IPTG with vigorous shaking at 37oC. At early exponential growth phase (OD600nm~0.2), 200 ml were treated with formaldehyde.

value: exponential

source_name: Control_DNA from Bsub 168, exponential phase


title: 142_W0_F09.CEL


title: Bsub_168_LPDM_exp_rep2


title: 140_W18_F05.CEL


title: 140_W0_E07.CEL


title: 135_W18_E09.CEL


title: Bsub_168_LPDM_exp_rep1


title: 243_W0_C07.CEL


title: Bsub_LSB003_LPDM_T2_rep1

organism: Bacillus subtilis

source_name: ChIP_DNA from Bsub strain expressing WalR-SPA protein, T2 phase

growth_protocol: Cells of strain LSB003 were grown in LPDM with the addition of 1 µg ml-1 erythromycin plus 25 µg ml-1 lincomycin (MLS) and 100 mM IPTG with vigorous shaking at 37oC. Two hours after the onset of phosphate starvation state (T2), 50 ml were treated with formaldehyde.

extract_protocol: Crosslinking was performed by the addition of formaldehyde to a final concentration of 1% followed by 20 min incubation at room temperature with slow shaking. The cultures were then quenched with Glycine (0.36M final concentration) for 5 min at room temperature. Cells were collected by centrifugation at 4oC and the pellets were washed twice with 50 ml ice-cold Buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) before being snap frozen in a dry ice / ethanol bath.   Pellets were thawed at 37oC and resuspended in 0.5ml buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% Triton X-100) supplemented with 3 mg ml-1 lysozyme and 0.1 mg ml-1 RNaseA (final concentrations) and incubated for 30 min at 37oC, then the sample volume was adjusted to 1 ml with buffer B and samples placed on ice for 10 min. Genomic DNA was sheared by sonication (Diagenode Bioruptor Twin sonicator) into fragments between 0.2 and 1 kb. Sonicated samples were centrifuged for 10 min at 20 000 g (4oC) to remove insoluble debris. Fifty microliteres of the cleared lysates was removed to serve as the CONTROL sample, to which 50 microliters of 10X buffer C (10 mM Tris-HCl pH 8, 10% SDS, 10 mM EDTA) and 400 microliters buffer B were added and the sample was stored on ice. The remaining cleared lysates were each added to 40 microliters anti-FLAG M2-agarose resin (Sigma-Aldrich; A2220) equilibrated with ice-cold buffer B (according to manufacturers’ instructions) and incubated for two hours at 4oC with mild agitation. Beads were then collected by centrifugation for 1 min at 5000 g (4oC) and washed three times with 0.5 ml ice-cold buffer B. To reverse the crosslinking beads were transferred to new 1.5 ml eppendorf tubes, resuspended in 0.5 ml 1X buffer C and incubated along with the CONTROL samples for ~20 hours at 65oC with shaking (950 rpm). ChIP samples were collected by centrifugation for 1 min at 13 300 rpm (4oC).  DNA from both ChIP and CONTROL samples was purified using the QIAquick PCR purification kit (Qiagen, 28106), eluted in 50 microliters H2O and treated with 0.02 mg ml-1 RNaseA (Roche, 11119915001) for 30 min at 37oC. RNase was eliminated using the QIAquick PCR purification kit and samples were eluted in 30 microliters H2O.  Equal concentrations of ChIP DNA and CONTROL samples were amplified using the GenomePlex complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich; WGA2-50RXN) as per manufacturers’ instructions and purified using the QIAquick PCR purification kit and eluted in 30 microliters H2O. Ten microliters of each of the purified amplified samples was subjected to a second round of amplification using the WGA kit as per manufacturer’s instructions, purified using the QIAquick PCR purification kit and eluted in 30 microliters H2O.  3.5-4  micrograms of twice-amplified ChIP DNA and CONTROL samples (of both tagged and mock precipitation experiments) at a concentration of ~250 ng per microliter (A260/A280 ≥1.7 and A260/A230 ≥ 1.6) from three separate ChIP experiments were submitted TO NimbleGen.  Crosslinking was performed by the addition of formaldehyde to a final concentration of 1% followed by 20 min incubation at room temperature with slow shaking. The cultures were then quenched with Glycine (0.36M final concentration) for 5 min at room temperature. Cells were collected by centrifugation at 4oC and the pellets were washed twice with 50 ml ice-cold Buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) before being snap frozen in a dry ice / ethanol bath.   Pellets were thawed at 37oC and resuspended in 0.5ml buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% Triton X-100) supplemented with 3 mg ml-1 lysozyme and 0.1 mg ml-1 RNaseA (final concentrations) and incubated for 30 min at 37oC, then the sample volume was adjusted to 1 ml with buffer B and samples placed on ice for 10 min. Genomic DNA was sheared by sonication (Diagenode Bioruptor Twin sonicator) into fragments between 0.2 and 1 kb. Sonicated samples were centrifuged for 10 min at 20 000 g (4oC) to remove insoluble debris. Fifty microliteres of the cleared lysates was removed to serve as the CONTROL sample, to which 50 l of 10X buffer C (10 mM Tris-HCl pH 8, 10% SDS, 10 mM EDTA) and 400 l buffer B were added and the sample was stored on ice. The remaining cleared lysates were each added to 40 l anti-FLAG M2-agarose resin (Sigma-Aldrich; A2220) equilibrated with ice-cold buffer B (according to manufacturers’ instructions) and incubated for two hours at 4oC with mild agitation. Beads were then collected by centrifugation for 1 min at 5000 g (4oC) and washed three times with 0.5 ml ice-cold buffer B. To reverse the crosslinking beads were transferred to new 1.5 ml eppendorf tubes, resuspended in 0.5 ml 1X buffer C and incubated along with the CONTROL samples for ~20 hours at 65oC with shaking (950 rpm). ChIP samples were collected by centrifugation for 1 min at 13 300 rpm (4oC).  DNA from both ChIP and CONTROL samples was purified using the QIAquick PCR purification kit (Qiagen, 28106), eluted in 50 l H2O and treated with 0.02 mg ml-1 RNaseA (Roche, 11119915001) for 30 min at 37oC. RNase was eliminated using the QIAquick PCR purification kit and samples were eluted in 30 l H2O.  Equal concentrations of ChIP DNA and CONTROL samples were amplified using the GenomePlex complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich; WGA2-50RXN) as per manufacturers’ instructions and purified using the QIAquick PCR purification kit and eluted in 30 l H2O. Ten microliters of each of the purified amplified samples was subjected to a second round of amplification using the WGA kit as per manufacturer’s instructions, purified using the QIAquick PCR purification kit and eluted in 30 l H2O.  3.5-4  micrograms of twice-amplified ChIP DNA and CONTROL samples (of both tagged and mock precipitation experiments) at a concentration of ~250 ng l-1 (A260/A280 ≥1.7 and A260/A230 ≥ 1.6) from three separate ChIP experiments were submitted TO NimbleGen.

source_name: Control_DNA from Bsub strain expressing WalR-SPA protein, T2 phase


title: Bsub_LSB003_LPDM_T2_rep3


title: Bsub_LSB003_LPDM_T2_rep2


title: Bsub_LSB003_LPDM_exp_rep2

source_name: ChIP_DNA from Bsub strain expressing WalR-SPA protein, exponential phase

growth_protocol: Cells of strain LSB003 were grown in LPDM with the addition of 1 µg ml-1 erythromycin plus 25 µg ml-1 lincomycin (MLS) and 100 mM IPTG with vigorous shaking at 37oC. At early exponential growth phase (OD600nm~0.2), 200 ml were treated with formaldehyde.

source_name: Control_DNA from Bsub strain expressing WalR-SPA protein, exponential phase


title: Bsub_LSB003_LPDM_exp_rep3


title: Bsub_LSB003_LPDM_exp_rep1


title: 133_W18_G09.CEL

source_name: Abdominal subcutaneous adipose tissue


title: 134_W0_H05.CEL


title: 125_W18_E05.CEL


title: 135_W0_H09.CEL


title: 134_W18_E05.CEL


title: 120_W18_A05.CEL


title: 133_W0_H07.CEL


title: 120_W0_B09.CEL


title: 106_W18_D09.CEL


title: 125_W0_C07.CEL


title: 130_W18_C05.CEL


title: Male-Cerebellum-Folic acid-20 mg-rep2

city: Staten Island

first: Mohammed

middle: A.

last: Junaid

state: NY

address: 1050 Forest Hill Road

department: Developmental Biochemistry

institute: New York State Institute for Basic Research in Developmental Disabilities

description: Maternal folic acid supplementation at 20 mg/kg diet throughout the gestational period.

hyb_protocol: A total of 600ng of cRNA from sample was fragmented and hybridized to the SurePrint G3 mouse gene expression 8 x 60 k arrays (G4852A) (Agilent Technologies, Santa Clara, CA), at 65°C for 17hr in Agilent Microarray  Hybridization Chambers (Agilent Technologies, Santa Clara, CA).

scan_protocol: Slides were scanned immediately on Agilent G2539A DNA scanner using one-color setting for 8x60k slides at 3 µm resolution using Green channel at 100%.

data_processing:
The data were processed in Feature Extraction software v10.7.3.1 for image analysis and initial quality control.
Quantile-Normalization to normalize the expression data and log-transformed.

source_name: Male-Cerebellum-Folic acid-20 mg

label_protocol: Total RNA was reverse-transcribed and cyanine-3-labelled cRNA was generated by following the manufacturer’s instructions using the one-color, low-input QuickAmp labelling kit (Agilent Technologies, Santa Clara, CA).  Following purification of cRNA with RNeasy kit (Qiagen, Valencia, CA), the incorporation of cyanine-3 was assessed by Nano Drop spectrometer.

extract_protocol: Cerebellum tissues of P1 pups were pooled (n=3/gender) for the 2 mg/kg group with three male pups (each from an independent dam) and three female pups (each from an independent dam).  Tissues from 20 mg/kg group were similarly processed.  RNA extractions for 20 mg group were further repeated from a different batch (pooled samples, n=3/gender, with each mouse from a different dam).  Total RNA  was extracted with Trizol reagent (Life Technologies, Carlsbad, CA) and further purified by Qiagen RNeasy kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. To remove any DNA contamination, on-column DNase digestion for each sample was performed.  The integrity of RNA was assessed by formaldehyde-gel electrophoresis and the quality of RNA was assessed by measuring the absorbance ratio at 260/280 nm by using NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA).

treatment_protocol: One week prior to mating C57BL/6J female mice were separated into two groups and supplemented with a custom AIN-93G amino acid–based diet (Research Diet, Inc. New-Brunswick, NJ). Control group were supplemented  with folic acid at 2 mg/kg diet, while the test group received folic acid at 20 mg/kg diet.

tag: strain background

value: Whole brain

value: Post natal day 1


title: Female-Cerebellum-Folic acid-20 mg-rep1

source_name: Female-Cerebellum-Folic acid-20 mg


title: Male-Cerebellum-Folic acid-20 mg-rep1

value: Male


title: Female-Cerebellum-Folic acid-20 mg-rep2


title: Male-Cerebellum-Folic acid-2 mg

description: Maternal folic acid supplementation at 2 mg/kg diet throughout the gestational period.

source_name: Male-Cerebellum-Folic acid-2 mg


title: Zebrafish cardiac tissue 72 hpf ccm2 mutant sample 1

city: Potsdam

first: Salim

last: Abdelilah-Seyfried

address: Karl-Liebknecht Strasse 24-25, Bldg. 26

department: Animal Physiology

country: Germany

institute: University of Potsdam

description:
cardiac gene expression after Bmp2b overexpression
251916110291 subarray 1_3

hyb_protocol: 1.5 µg of labeled cRNA were hybridized to Zebrafish (V2) Gene Expression Microarrays (G2519F-019161, 4x44K)

scan_protocol: Spot intensities were recorded on a G2565BA scanner (Agilent Technologies)

data_processing: Scanned images were analyzed after all the Feature Extraction processing steps were completed. In the case of one color, Processsed Signal contains the Multiplicatively Detrended Background Subtracted Signal if the detrending is selected and helps. If the detrending does not help, this column will contain the Background Subtracted Signal.

organism: Danio rerio

source_name: cardiac tissue, pooled from embryo extractions 72 hpf, ccm2 m201 mutant

label_protocol: For each sample, 200ng of intact (RIN > 8) total RNA was subjected to a single amplification step and Cy3 labeling reaction.

extract_protocol: Whole hearts were extracted manually from 72 hpf embryos as described in Burns and MacRae, 2006. Total RNA was extracted with RNeasy Micro Kit (Qiagen)

treatment_protocol: ccm2 m201 mutant and WT embryos were raised to 72 hpf.

value: cardiac tissue

value: ccm2 m201 mutant


title: Female-Cerebellum-Folic acid-2 mg

source_name: Female-Cerebellum-Folic acid-2 mg


title: Zebrafish cardiac tissue 72 hpf ccm2 mutant sample 2

description:
cardiac gene expression after Bmp2b overexpression
251916110291 subarray 1_1


title: 130_W0_H07.CEL


title: Zebrafish cardiac tissue 72 hpf WT sample 1

description:
cardiac gene expression in WT
251916110291 subarray 1_2

source_name: cardiac tissue, pooled from embryo extractions 72 hpf, WT

value: WT


title: Zebrafish cardiac tissue 72 hpf WT sample 2

description:
cardiac gene expression in WT
251916110291 subarray 1_4


title: 106_W0_E09.CEL


title: G1ME_GATA1s_rep3

description: G1ME Gata1- murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1s. GFP-positive cells isolated by FACS 42 hours following transduction. Replicate 3.

hyb_protocol: Manufacturer's (Affymetrix) protocol

scan_protocol: Manufacturer's (Affymetrix) protocol

data_processing: The raw intensity values from CEL files were processed using RMA method implemented by the Bioconductor R affy package.

label: Phycoerythrin

source_name: G1ME cells: immortalized, developmentally arrested megakaryocyte-erythroid progenitors (MEPs) derived from in vitro differentiation of murine Gata1– ES cells

label_protocol: Manufacturer's (Affymetrix) protocol

growth_protocol: G1ME cells were grown in alpha-MEM supplemented with 20% fetal bovine serum, 1% penicillin/streptomycin (10 U/mL stock), 1% L-glutamine (mM stock), and 20 ng/mL thrombopoietin. After transduction, cells were cultured in the same media plus 2U/mL of erythropoietin.

extract_protocol: Total RNA was extracted using Trizol and the Qiagen RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Cells transduced with MIGR1-GFP vector expressing GATA1s. GFP-positive cells isolated by FACS 42 hours following transduction.

value: 42 hours post transduction with MIGRI-GFP vector expressing GATA1s

tag: cell type

value: megakaryocyte-erythroid progenitors


title: KO, + MTX, biological rep2

status: Public on Jan 24 2015

city: Essen

first: Elke

last: Cario

state: NRW

address: Virchowstr. 171

department: Division of Gastroenterology and Hepatology

institute: University of Duisburg-Essen, University Hospital of Essen

hyb_protocol: 15µg of labeled and fragmented cDNA was hybridized to GeneChip Mouse Gene 1.1 ST array plates (Affymetrix) according to the manufacturer's instructions. Hybridization, washing, staining, and scanning was performed automatically in a GeneTitan instrument (Affymetrix).

scan_protocol: Scanned images were subjected to visual inspection to control for hybridization artefacts and proper grid alignment and analyzed with AGCC 3.0 (Affymetrix) to generate CEL files.

data_processing: RMA was used for array normalization and signal calculation

source_name: prox. jejunum from healthy TLR2 KO mouse, MTX treatment

label_protocol: Double-stranded cDNA was synthesized from 100ng of total RNA using the WT Expression Kit (Ambion) according to the manufacturer's instructions.

extract_protocol: Total RNA from murine proximal jejunum was extracted (RiboPure, Ambion) and purified including the RNase-free DNase digestion step (RNeasy Mini Kit, Qiagen), according to the manufacturer's instructions.

value: proximal jejunum

value: MTX [40mg/kg BW/d] for 4 days


title: KO, + MTX, biological rep3


title: KO, + MTX, biological rep1


title: WT, + MTX, biological rep1

source_name: prox. jejunum from healthy WT mouse, MTX treatment

value: wildtype [C57BL6/J]


title: WT, + MTX, biological rep3


title: KO, - MTX, biological rep2

source_name: prox. jejunum from healthy TLR2 KO mouse, no treatment


title: double mutant vs triple mutant 3

city: Paris

first: frederic

last: devaux

address: 15 rue de l'ecole de medecine

country: France

institute: Universite Pierre et Marie Curie

description: ch1 and ch2 strains were grown in YPD

hyb_protocol: We used the Agilent hyb protocol described in the Agilent booklet. 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in wash 1 buffer at room temperature and one minute in wash 2 buffer at 37°C. The array slides are then air dryed and ready for scanning

scan_protocol: The slides were scan using a Agilent microarray scanner.

data_processing: Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/ (http://transcriptome.ens.fr/goulphar/index.php). GenePix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalization method.

organism: Saccharomyces cerevisiae

source_name: yor1pdr5 double mutant

label_protocol: We used the aminoallyl indirect labelling technique. 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

growth_protocol: Yeast cells were grown in YPD. Growth was carried out in an automatic shaker at 30 ºC until an OD600nm of about 0.6.

extract_protocol: Total RNA was isolated using the standard hot acidic phenol protocol described at http://www.transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php.

value: SEY6210 background pdr5-∆1::hisG yor1-1::hisG

source_name: yor1pdr5pdr1 triple mutant

value: SEY6210 background pdr1::kanMX4 pdr5-∆1::hisG yor1-1::hisG


title: G1ME_GATA1s_rep2

description: G1ME Gata1- murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1s. GFP-positive cells isolated by FACS 42 hours following transduction. Replicate 2.

tag: developmental stage


title: KO, - MTX, biological rep3


title: double mutant vs triple mutant 4

description: ch1 and ch2 strains were grown in YPD


title: WT, - MTX, biological rep2

source_name: prox. jejunum from healthy WT mouse, no treatment


title: double mutant vs triple mutant 1

description: ch1 and ch2 strains were grown in YPD


title: G1ME_GATA1s_rep1

description: G1ME Gata1- murine megakaryocyte-erythrocyte progenitor cell line, transduced with MIGR1-GFP vector expressing GATA1s. GFP-positive cells isolated by FACS 42 hours following transduction. Replicate 1.


title: double mutant vs wild type 4

description: ch1 and ch2 strains were grown in YPD

source_name: wild type


title: HCC38_24h+Wnt3a_rep3

city: PARIS

first: Thierry

last: Dubois

address: 26 rue d’Ulm

department: Recherche Center

institute: Institut Curie

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with the brainarray HuGene11stv1_Hs_ENTREZG version 14 custom chipset definition file for the HuGene11stv1 affymetrix array. The data were first log2 transformed and normalized with RMA.

label_protocol: After RNA quality and quantity controls, samples were hybridized onto Gene st 1.1 Affymetrix chips. Samples were processed as described on the website of the company.

growth_protocol: HCC38 and MDA-MB-468 cells were obtained from the American Type Culture Collection and authenticated in 2013 by short tandem repeat profiling. MDA-MB-468 cells were maintained in RPMI-1640 containing Glutamax and supplemented with 10% FBS. HCC38 cells were cultured in RPMI-1640 with Glutamax containing 10% FBS, 1.5g/L sodium bicarbonate, 10mM Hepes and 1mM sodium pyruvate. Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit from Qiagen (Courtaboeuf, France) following the manufacturer’s recommendations.

treatment_protocol: Cells were seeded in six-well plates, serum starved overnight, and then treated with Wnt3a for the indicated times (6, 12 or 24 hours). Triplicates for each condition were included in the experiment.

tag: wnt3a treatment

value: yes

tag: time after treatment (hours)

tag: cell line


title: HCC38_12h+Wnt3a_rep3


title: WT, + MTX, biological rep2


title: WT, - MTX, biological rep1


title: KO, - MTX, biological rep1


title: double mutant vs triple mutant 2

description: ch1 and ch2 strains were grown in YPD


title: HCC38_24h-Wnt3a_rep3

value: no


title: HCC38_6h-Wnt3a_rep3


title: double mutant vs wild type 3

description: ch1 and ch2 strains were grown in YPD


title: HCC38_12h-Wnt3a_rep3


title: double mutant vs wild type 2

description: ch1 and ch2 strains were grown in YPD


title: double mutant vs wild type 1

description: ch1 and ch2 strains were grown in YPD


title: MDA-MB-468_24h-Wnt3a_rep3


title: HCC38_6h+Wnt3a_rep3


title: MDA-MB-468_6h-Wnt3a_rep3


title: 4973 TM cell control

city: Tokyo

first: Akira

last: Matsuda

address: 2-1-1 Hongo

department: Ophthalmology

country: Japan

institute: Juntendo University School of Medicine

description: Gene expression of control sample

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, 480ng probe was hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters. Gene spring GX version 12.5 was used for data nomalization using default setting (percentile sift=75).

source_name: Trabecular meshwork cell lot 4973

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the NucleoSpin RNA II Purification kit (Machery-Nagel, Duren, Germany) following the manufacturer's recommendations.  The protocol includes lysis of trabecular meshwork cells, and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer

treatment_protocol: Trabecular meshwork cells were cultured in Dulbecco's Minimum Essential Medium with 10% fetal calf serum, with and without 100nM dexamethasone for 14 days. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Primary human trabecular meshwork cells

tag: cell line vendor

value: ScienCell Ltd

tag: cell line lot #

tag: cultured with

value: none (control)


title: MDA-MB-468_6h+Wnt3a_rep3


title: WT, - MTX, biological rep3

tag: tissue


title: MDA-MB-468_12h-Wnt3a_rep3


title: HCC38_24h+Wnt3a_rep2


title: 4973 TM cell DEX treated

description: Gene expression after 14 days DEX treatment

value: 100nM dexamethsone for 14 days


title: MDA-MB-468_24h+Wnt3a_rep3


title: HCC38_12h+Wnt3a_rep2


title: Sample 18-Disease

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Disease

data_processing: Raw data were loaded on GenEx Pro version 5.4.3.710 from MultiD.  After interplate calibration, data was tested for outliers with cutoff SD (cycles) = 0.25 and Grubbs test was performed with confidence level = 0.95. All outliers were deleted as recommended. Values above Cq > 37 were treated as background. All non-numerical values were replaced and miRNAs with ≥ 75% missing values, both within biological replicates and altogether, were removed from analysis. Missing values within biological replicates were generated by imputing while missing values were assigned a maximum of Cq = 38.

source_name: plasma

label_protocol: For comprehensive miRNA analysis, qPCR was performed on samples from 6 wild-type, mice  and 14 GEMM OS mice using Exiqon miRNome platform (mouse panels I+II, V2), which utilizes ready-to-use PCR panels and analyzes 752 miRNAs.

growth_protocol: A GEMM of OS used in this project was developed in our laboratory.  It contains a germline 2.3kb Col-α1(I) promoter region upstream of the Cre-recombinase gene along with one or both Trp53 alleles flanked by LoxP recombination sites (8).  In this model osteoblast-specific deletion of Trp53 results primarily in OS (8).  Heterozygous mice with osteoblast-specific Cre and deletion of a single copy of wild-type Trp53 (F/+) develop de novo localized OS at a median age of 54 weeks, whereas homozygous mice with the loss of both copies of wild-type Trp53 (F/F) tend to develop metastatic OS at a median age of 38 weeks (described further in Zhao et al., accepted Oncogene).  Mice were maintained in barrier facilities at Baylor College of Medicine (BCM) and provided with food and water ad libitum. All animal experiments were conducted according to institutional animal care and use committee (IACUC) protocols after approval was obtained from the BCM Institutional Review Board (BCM Animal Protocols AN-336 and AN-5225). Once mice developed a tumor, they were sedated with isoflurane per IACUC protocols and blood was obtained by cardiac puncture and placed into ethylene-diamine-tetra-acetic acid (EDTA) blood collection vials.  Wild-type littermates were randomly selected and sacrificed for control samples.  The blood samples were centrifuged at 1,300g for 25 min at 4°C.  The resultant plasma was isolated and centrifuged at 1000g for 5 min to remove debris.  All plasma was stored at -80°C until further processing.  Necropsy was completed and slides were prepared with hematoxylin and eosin stains to confirm an OS diagnosis.

extract_protocol: Strand cDNA synthesis was performed from 1 ml of RNA (in 10 ml reactions) using the miRCURY universal cDNA synthesis kit per manufacturer instructions (Exiqon, Copenhagen).

tag: disease state

value: Osteosarcoma

tag: genotype/variation

value: GEMM OS


title: Sample 19-Disease

description: Disease


title: MDA-MB-468_12h+Wnt3a_rep3


title: Sample 17-Disease

description: Disease


title: Sample 16-Disease

description: Disease


title: MDA-MB-468_12h+Wnt3a_rep2


title: Sample 15-Disease

description: Disease


title: Sample 14-Control

description: Control

value: healthy

value: wild type


title: MDA-MB-468_24h-Wnt3a_rep2


title: MDA-MB-468_12h-Wnt3a_rep2


title: HCC38_24h-Wnt3a_rep2


title: HCC38_6h+Wnt3a_rep2


title: HCC38_6h-Wnt3a_rep2


title: MDA-MB-468_24h+Wnt3a_rep2


title: HCC38_12h-Wnt3a_rep1


title: Sample 11-Disease

description: Disease


title: MDA-MB-468_6h+Wnt3a_rep2


title: HCC38_12h+Wnt3a_rep1


title: HCC38_24h-Wnt3a_rep1


title: Sample 12-Disease

description: Disease


title: Sample 10-Disease

description: Disease


title: HCC38_12h-Wnt3a_rep2


title: HCC38_24h+Wnt3a_rep1


title: Sample 04-Control

description: control


title: MDA-MB-468_6h-Wnt3a_rep2


title: HCC38_6h-Wnt3a_rep1


title: MDA-MB-468_24h+Wnt3a_rep1


title: Sample 13-Control

description: Control


title: Sample 03-Control

description: control


title: HCC38_6h+Wnt3a_rep1


title: Sample 02-Control

description: control


title: Sample 01-Control

description: control


title: MDA-MB-468_24h-Wnt3a_rep1


title: MDA-MB-468_12h-Wnt3a_rep1


title: MDA-MB-468_6h+Wnt3a_rep1


title: MDA-MB-468_6h-Wnt3a_rep1


title: MDA-MB-468_12h+Wnt3a_rep1


title: 3423 TM cell DEX treated

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters. Gene spring GX version 12.6 was used for data nomalization using default setting (percentile sift=75).


title: 2584 TM cell DEX treated

treatment_protocol: Trabecular meshwork cells were cultured in Dulbecco's Minimum Essential Medium with 10% fetal calf serum, with and without 100nM dexamethasone for 14 days. The cultures were incubated for 6 or 24 hours at 37C in a humidified incubator with 5% CO2.


title: 3423 TM cell control

description: Gene expression of control sample


title: Cell line VU-SCC-OE: CD98high fraction tumor 3

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridization was performed on a human GE 4x44K formatted expression array spotted with 60-mer oligonucleotides representing over 43,000 well-characterized coding and non-coding sequences (G4112F, Agilent Technologies, Amstelveen, The Netherlands).  Input: 825 ng RNA.

scan_protocol: Scanning was performed using a microarray scanner G2505B (Agilent Technologies). Feature Extraction v9.5 using the manufacturer's protocols (Agilent Technologies).

data_processing:
Preprocessing of the gene expression data comprised RMA background correction, loess within-array normalization and A-quantile between-array normalization and was performed in R. Single channel data were used to accommodate the unbalanced design (four CD98high samples versus three CD98low samples).
The moderated t-test implemented in Limma, employing empirical Bayes estimation of the variance, was used to evaluate the difference in gene expression between the two groups. Sample origin and CyDye were taken along as possible confounders. The Benjamini-Hochberg procedure was applied to the raw p-values to control the False Discovery Rate (FDR).

source_name: CD98high: fraction tumor 3

label_protocol: cDNA synthesis and labeling were performed according to the recommendations of the manufacturer (Agilent Technologies, Amstelveen, The Netherlands), including quality controls (QCs).

growth_protocol: VU-SCC-OE cells were harvested from culture and inoculated subcutaneously in nu/nu mice.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen).

treatment_protocol: Tumors were minced and enzymatically treated to create single cell suspensions. Cells were incubated with fluorescently labeled CD98 antibodies. CD98high and CD98low fractions were isolated by FACS sorting.

value: VU-SCC-OE

tag: tumor

tag: cd98 fraction

value: high


title: Cell line VU-SCC-OE: CD98low fraction tumor 1, rep1

source_name: CD98low: fraction tumor 1

value: low


title: Cell line VU-SCC-OE: CD98low fraction tumor 4

source_name: CD98low: fraction tumor 4


title: Listeria monocytogenes S10 [160908] replicate 3

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

description:
Biological replicate 3 of 3. Listeria monocytogenes strains indentified in a Iberian pork plant, S10 [160908]  in presence of 1.25 mg/L
S10_1 [160908]-rep3

hyb_protocol: The hybridization and washing steps were carried out according to the Agilent’s “Two Color Microarray-Based Gene Expression Analysis” protocol.

scan_protocol: Image acquisition and scanning was performed on an Agilent G2565AA scanner according to the manufacturer’s instructions.

data_processing: Background-subtracted data were log-transformed, LOWESS-normalized, and analyzed for the detection of differentially expressed genes using BRBArrayTools Software developed by Dr. Richard Simon and the BRB-ArrayTools Development Team [http://linus.nci.nih.gov/BRB-ArrayTools.html].

organism: Listeria monocytogenes

label_protocol: A total of 100 ng of total RNA of each sample replicate was reverse transcripted and labeled by using the Low-Input Quick Amp Labeling Kit, Two color (Agilent Technologies) according to the protocol provided by the manufacturer. The yield and the specific activity of each labeling reaction were determined in a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE).

growth_protocol: Tryptic soy Extract Broth with 1.25 mg/L of Benzalkonium, 37C during 24 hours

extract_protocol: Total RNA was isolated  by using RNeasy Protect Bacteria Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. The quality and concentration of RNA was determined by using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only high-quality RNA samples (RIN > 8) were used.

tag: strain

tag: strain source

value: Iberian pork plant

tag: incubation time

value: 24 hours

tag: growth temperature

tag: growth media

source_name: EGD-e

value: EGD-e

value: Tryptic soy Extract Broth


title: Listeria monocytogenes S1 [160908] replicate 2

description:
Biological replicate 2 of 3. Listeria monocytogenes strains indentified in a Iberian pork plant, S1 [160908]  in presence of 1.25 mg/L
S1 [160908]-rep2

value: Tryptic soy Extract Broth with 1.25 mg/L of Benzalkonium


title: Listeria monocytogenes S10 [160908] replicate 1

description:
Biological replicate 1 of 3. Listeria monocytogenes strains indentified in a Iberian pork plant, S10 [160908]  in presence of 1.25 mg/L
S10_1 [160908]-rep1


title: Listeria monocytogenes S10 [160908] replicate 2

description:
Biological replicate 2 of 3. Listeria monocytogenes strains indentified in a Iberian pork plant, S10 [160908]  in presence of 1.25 mg/L
S10_1 [160908]-rep2


title: Listeria monocytogenes S1 [160908] replicate 1

description:
Biological replicate 1 of 3. Listeria monocytogenes strains indentified in a Iberian pork plant, S1 [160908]  in presence of 1.25 mg/L
S1 [160908]-rep1


title: Cell line VU-SCC-OE: CD98high fraction tumor 2

source_name: CD98high: fraction tumor 2


title: Cell line VU-SCC-OE: CD98low fraction tumor 3

source_name: CD98low: fraction tumor 3


title: Cell line VU-SCC-OE: CD98low fraction tumor 1, rep2


title: 2584 TM cell control

description: Gene expression of control sample

tag: cell type


title: Listeria monocytogenes S1 [160908] replicate 3

description:
Biological replicate 3 of 3. Listeria monocytogenes strains indentified in a Iberian pork plant, S1 [160908]  in presence of 1.25 mg/L
S1 [160908]-rep3


title: Cell line VU-SCC-OE: CD98high fraction tumor 4

source_name: CD98high: fraction tumor 4


title: Cell line VU-SCC-OE: CD98high fraction tumor 1

source_name: CD98high: fraction tumor 1


title: BA TNBC, TUM054

status: Public on Jan 23 2015

description: Breast tumor sample from IHC defined Triple Negative subgroup

data_processing: Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using GC-RMA. Batch and hybridization effects were corrected using a linear model in which they were treated as fixed effects. Samples with technical replicates were subsequently averaged.

label_protocol: Following RNA quality and quantity control, 2 µg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.

growth_protocol: Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),

extract_protocol: Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturers’ instructions.

value: TNBC

tag: hybridation batch


title: BA TNBC, TUM067_repB

source_name: Breast tumor sample from IHC defined Triple Negative subgroup


title: BA TNBC, TUM068


title: BA Her2, TUM062

description: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: BA Her2, TUM063

source_name: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: BA Luminal A, TUM082

description: Breast tumor sample from IHC defined Luminal A subgroup

value: Luminal A


title: BA Her2, TUM060


title: BA Her2, TUM058_repB


title: BA TNBC, TUM069


title: BA TNBC, TUM065


title: BA TNBC, TUM071


title: BA TNBC, TUM048_repB


title: BA Her2, TUM058_repA


title: BA TNBC, TUM070


title: BA TNBC, TUM064_repB


title: BA TNBC, TUM049


title: BA TNBC, TUM053


title: BA Her2, TUM066


title: BA Luminal A, TUM073

source_name: Breast tumor sample from IHC defined Luminal A subgroup


title: BA Her2, TUM044


title: BA TNBC, TUM050


title: BA Her2, TUM042


title: BA TNBC, TUM052


title: BA Her2, TUM047


title: BA TNBC, TUM043_repB


title: BA Her2, TUM061


title: BA Her2, TUM041


title: BA Her2, TUM040


title: BA Her2, TUM046


title: BA TNBC, TUM039


title: BA Her2, TUM037


title: BA Her2, TUM038_repB


title: BA Her2, TUM038_repA


title: BA Her2, TUM020_repB


title: BA Her2, TUM036


title: BA TNBC, TUM025


title: BA Her2, TUM031


title: BA Her2, TUM026_repB


title: BA Her2, TUM021_repB


title: BA TNBC, TUM012


title: BA TNBC, TUM003


title: BA TNBC, TUM017_repB


title: BA Her2, TUM022


title: BA TNBC, TUM023


title: BA TNBC, TUM011


title: BA TNBC, TUM029


title: BA Her2, TUM016_repB


title: BA TNBC, TUM008


title: BA TNBC, TUM014


title: BA TNBC, TUM010_repB


title: BA Her2, TUM019


title: BA TNBC, TUM033


title: BA Her2, TUM027


title: BA Her2, TUM021_repA


title: BA TNBC, TUM007


title: BA TNBC, TUM034


title: BA Her2, TUM002_repB


title: BA TNBC, TUM004


title: BA TNBC, TUM001_repB


title: BA TNBC, TUM018_repB


title: PAO1-dPA4203-2 [expression]

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

institute: Max Rubner-Institute

hyb_protocol: According to Affymetrix GeneChip protocol

scan_protocol: Washing and staining of the arrays were performed according to the manufacturer’s instructions using a fluidics station 450 (Affymetrix). Microarray slides were scanned using the 2500 GeneArray Scanner (Agilent Technologies) and Affymetrix MAS 5.0.

data_processing: Raw Affymetrix data were pre-processed in R environment using BioConductor packages including “affy”, “affyPLM”, “simpleaffy” and 222 “limma”. The primary processing includes: (i) background correction based on the robust multichip average (RMA) convolution model; (ii) quantile normalization to make expression values from different arrays more comparable and (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA. Only fold change ratios with adjusted P-values below 0.05 were included as statistically significant. Microarray analysis was performed on all three biological replicates.

organism: Pseudomonas aeruginosa PAO1

source_name: PA4203 mutant

label_protocol: Fragmented cDNA was labeled with GeneChip DNA labeling reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega)

growth_protocol: All strains were grown in LB at 37°C with agitation in an Innova 4000 New Brunswick incubator (200 rpm).

extract_protocol: RNeasy Mini Kit (Qiagen), DNAse I treatment, reverse transcription with SuperScript II (Invitrogen), cDNA was fragmented with DNAse I (Promega) to 50-200 bp

treatment_protocol: no treatment

value: PA4203 mutant


title: BA CellLine, MDA-MB-231

description: Sample from breast cancer derived cell line MDA-MB-231

value: CellLine


title: PAO1-dPA4203-1 [expression]


title: BA CellLine, MDA-MB-157

description: Sample from breast cancer derived cell line MDA-MB-157


title: PAO1-WT-1 [expression]

source_name: PAO1 wild type


title: BA Healthy, H5

description: Healthy breast sample from mammoplasty surgery

value: Healthy


title: BA Healthy, H14

source_name: Healthy breast sample from mammoplasty surgery


title: BA CellLine, HCC70

description: Sample from breast cancer derived cell line HCC70


title: EM-low 2

city: Kashiwa

first: Shingo

last: Kawano

state: Chiba

institute: National Cancer Center Hospital East

hyb_protocol: The procedures for target hybridization, washing, and staining with signal amplification were conducted according to the supplier's protocols.

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The intensity of each feature of the array was calculated using GeneSpring GX Software, version 12.6 (Agilent).

source_name: Colorectal cancer tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 - 200 ng total RNA using a 3' IVT Express Kit.

extract_protocol: TRIzol / RNeasy minicolumn protocol (QIAGEN) were performed according to the manufacturer's instructions.

value: CRC

tag: dukes stage

value: B

tag: age

value: 60 years

tag: gender

value: Male

tag: elastic module


title: BA Healthy, H4


title: EM-high 1

value: 76 years

value: Female


title: PAO1-WT-2 [expression]

value: wild type


title: EM-high 2

value: 78 years


title: EM-low 3


title: BA CellLine, MDA-MB-468

description: Sample from breast cancer derived cell line MDA-MB-468

tag: cell line


title: Control siRNA

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix) in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix) followed the manufacturer’ s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies).

source_name: Control cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were cultured at 37°C in 5% CO2 in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’ s instructions

tag: transfection

value: control


title: 253949410878-1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent: 200.0 ng at 65 degree_C during 17 hours.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

source_name: SKOV3ipL, sh51

label_protocol: Agilent: Low RNA Input QuickAmp.

extract_protocol: Trizol

treatment_protocol: Stable knock down of CD63 was performed in SKOV3ipL ovarian carcinoma cell line using 2 shRNAs lentiviral constructs (sh49 and sh51), and as a negative control, a shNT construct. Parental cells, control shNT and the 2 shCD63 cell lines were seeded 24 hours prior to RNA isolation on a 10 cm dish.

value: ovarian carcinoma cell line

tag: shRNA

tag: amount in (µg)

tag: rin number


title: 253949410878-5


title: 253949410878-3

source_name: SKOV3ipL, shNT

value: negative control (shNT)


title: BA CellLine, BT-549

description: Sample from breast cancer derived cell line BT-549


title: EM-high 3

tag: disease state

value: 84 years


title: POH1 siRNA

source_name: POH1 siRNA transfected cells

value: POH1 siRNAs


title: EM-low 1

value: 64 years


title: 253949410878-6

source_name: SKOV3ipL, sh49


title: 253949410878-2


title: BA Healthy, H15


title: BA Healthy, H11


title: CellLine, MDA-MB-231

source_name: Sample from breast cancer derived cell line MDA-MB-231


title: 253949410878-4

source_name: SKOV3ipL, parental


title: 253949410878-7


title: 253949410878-8


title: BA Healthy, H12


title: BA CellLine, MCF-12A

description: Sample from breast cancer derived cell line MCF-12A


title: BA CellLine, HCC38

description: Sample from breast cancer derived cell line HCC38


title: CellLine, HCC70

source_name: Sample from breast cancer derived cell line HCC70


title: BA CellLine, Hs 578T

description: Sample from breast cancer derived cell line Hs 578T

value: Hs 578T


title: CellLine, MDA-MB-157

source_name: Sample from breast cancer derived cell line MDA-MB-157

value: CellLine


title: BA Healthy, H18

value: Healthy


title: Healthy, H5


title: CellLine, BT-549

source_name: Sample from breast cancer derived cell line BT-549


title: Healthy, H14


title: Healthy, H4


title: CellLine, Hs 578T

source_name: Sample from breast cancer derived cell line Hs 578T


title: CellLine, HCC38

source_name: Sample from breast cancer derived cell line HCC38


title: CellLine, MDA-MB-468

source_name: Sample from breast cancer derived cell line MDA-MB-468


title: Healthy, H18


title: Healthy, H11


title: CellLine, MCF-12A

source_name: Sample from breast cancer derived cell line MCF-12A


title: Healthy, H12


title: CellLine, BT20

description: Sample from breast cancer derived cell line BT20


title: BA CellLine, HCC1937

description: Sample from breast cancer derived cell line HCC1937


title: BA Healthy, H10


title: Healthy, H15


title: CellLine, HCC1937

source_name: Sample from breast cancer derived cell line HCC1937


title: BA CellLine, HCC1187

description: Sample from breast cancer derived cell line HCC1187


title: BA CellLine, HCC1143

description: Sample from breast cancer derived cell line HCC1143


title: Healthy, H10

source_name: Healthy breast sample from mammoplasty surgery


title: BA CellLine, BT20

source_name: Sample from breast cancer derived cell line BT20


title: Healthy, H9


title: CellLine, HCC1143

source_name: Sample from breast cancer derived cell line HCC1143


title: CellLine, HCC1187

source_name: Sample from breast cancer derived cell line HCC1187


title: BA CellLine, MDA-MB-436

description: Sample from breast cancer derived cell line MDA-MB-436


title: CellLine, MDA-MB-436

source_name: Sample from breast cancer derived cell line MDA-MB-436


title: CellLine, 184B5

description: Sample from breast cancer derived cell line 184B5


title: Healthy, H13


title: Luminal B, TUM129

description: Breast tumor sample from IHC defined Luminal B subgroup

value: Luminal B


title: BA Healthy, H13


title: BA Healthy, H9


title: Luminal B, TUM130

source_name: Breast tumor sample from IHC defined Luminal B subgroup


title: Healthy, H3


title: BA Healthy, H3


title: Luminal B, TUM123


title: Luminal B, TUM128


title: Luminal B, TUM127


title: Luminal B, TUM126


title: Luminal B, TUM122


title: Luminal B, TUM125


title: Luminal B, TUM124


title: Luminal B, TUM119


title: BA CellLine, 184B5

source_name: Sample from breast cancer derived cell line 184B5


title: Luminal B, TUM118


title: Luminal B, TUM115


title: Luminal B, TUM113


title: Luminal B, TUM120


title: Luminal B, TUM121


title: BA Luminal B, TUM125


title: Luminal B, TUM117


title: Luminal B, TUM114


title: BA Luminal B, TUM126


title: Luminal B, TUM112


title: Luminal B, TUM108


title: Luminal B, TUM116


title: Luminal B, TUM109


title: BA Luminal B, TUM122


title: Luminal B, TUM107


title: Luminal B, TUM111


title: Luminal B, TUM110


title: Luminal B, TUM104


title: Luminal B, TUM103


title: Luminal B, TUM102


title: Luminal B, TUM101


title: Luminal B, TUM105


title: Luminal A, TUM099

description: Breast tumor sample from IHC defined Luminal A subgroup

value: Luminal A


title: Luminal A, TUM100

source_name: Breast tumor sample from IHC defined Luminal A subgroup


title: Luminal A, TUM097


title: Luminal A, TUM098


title: Luminal A, TUM096


title: Luminal A, TUM095


title: Luminal B, TUM106


title: Luminal A, TUM094


title: BA Luminal B, TUM117


title: Luminal A, TUM091


title: Luminal A, TUM093


title: Luminal A, TUM090


title: Luminal A, TUM088


title: Luminal A, TUM089


title: Luminal A, TUM087


title: Luminal A, TUM092


title: BA Luminal B, TUM115


title: Luminal A, TUM085


title: Luminal A, TUM081


title: Luminal A, TUM086


title: BA Luminal B, TUM112


title: Luminal A, TUM084


title: Luminal A, TUM083


title: DNA from PB S51, SGA, no rhGH treatment

city: Kiel

first: Susanne

last: Bens

address: Arnold-Heller-Str.3 (Haus 10)

department: Institute of Human Genetics

institute: Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein

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

scan_protocol: Arrays were scanned using the Illumina iScan

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0)

label: Cy5 and Cy3

source_name: peripheral blood (PB) cells from child born small for gestational age (SGA), no treatment

label_protocol: Standard Illumina Protocol

extract_protocol: various DNA extraction methods

tag: tissue

value: Peripheral Blood (PB)

tag: diagnosis

value: born small for gestational age (SGA)

tag: rhgh treatment

value: no treatment


title: Luminal A, TUM082


title: Luminal A, TUM079


title: Luminal A, TUM077


title: BA Luminal B, TUM111


title: Luminal A, TUM078


title: DNA from PB S49, SGA, no rhGH treatment


title: BA Luminal B, TUM109


title: DNA from PB S52, SGA, no rhGH treatment


title: DNA from PB S53, SGA, no rhGH treatment


title: DNA from PB S50, SGA, no rhGH treatment


title: Luminal A, TUM080


title: Luminal A, TUM076


title: Luminal A, TUM075


title: Luminal A, TUM074


title: BA Luminal B, TUM108


title: Luminal A, TUM073


title: Luminal A, TUM072


title: TNBC, TUM069

description: Breast tumor sample from IHC defined Triple Negative subgroup

value: TNBC


title: TNBC, TUM067_repB

source_name: Breast tumor sample from IHC defined Triple Negative subgroup


title: TNBC, TUM068


title: TNBC, TUM065


title: TNBC, TUM070


title: DNA from PB S47, SGA, no rhGH treatment


title: TNBC, TUM067_repA


title: DNA from PB S41, SGA, no rhGH treatment


title: TNBC, TUM071


title: Her2, TUM066

description: Breast tumor sample from IHC defined Er- Her2+ subgroup


title: TNBC, TUM064_repA


title: TNBC, TUM064_repB