title: K14Snail_Mts24negative_keratinocytes

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

description: Sample preparation was done at VIB-UGent (Ghent, Belgium), from labeling on experiments were done at Nucleomics (Leuven, Belgium), result interpretation was done at VIB-UGent (Ghent, Belgium)

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse Gene 1.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA as implemented in the XPS package of Bioconductor. Reported values are on log2-scale.

source_name: Mts24 negative keratinocytes from K14Snail mice

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: Mice were housed and experiments were done in accordance with the institutional guidelines regarding the care and use of laboratory animals.

extract_protocol: RNA was prepared with Trisure (Bioline cat #BIO-38032) following the manufacturer’s instructions

treatment_protocol: Preparation of keratinocytes of 8-week old mice: the back skins of adult mice were incubated overnight on a 1X trypsin solution (Gibco BRL cat # 25050-014). Harvesting of keratinocytes was done the next day according to the procedure described in (1). CD34 positive cells were selected with a biotinylated CD34 antibody (eBioscience cat #13-0341-85) using the easySEP mouse biotin kit (Stem Cell Technologies cat #18556) and easySEP magnet (Stem Cell Technologies cat #18000) following the manufacturer’s instructions. Mts24 positive cells were selected using a specific antibody (2), followed by incubation with an anti-rat PE labelled secondary antibody (BD Biosciences #550767). Cells were then purified further using the easySEP mouse PE kit (Stem Cell Technologies cat #18554) and easySEP magnet, following the manufacturer’s instructions. References (1) Jensen KB, Driskell RR, Watt FM. Assaying proliferation and differentiation capacity of stem cells using disaggregated adult mouse epidermis. Nat Protoc 2010; 5 (5): 898-911., (2) Raymond K, Richter A, Kreft M, Frijns E, Janssen H, Slijper M, et al. Expression of the orphan protein Plet-1 during trichilemmal differentiation of anagen hair follicles. The Journal of investigative dermatology 2010 Jun; 130 (6): 1500-1513.

tag: strain/background

tag: gender

value: male+female

tag: number

value: pool of 9 mice

value: 8 weeks

value: skin

value: Mts24 negative keratinocytes


title: HCT15_330-2

status: Public on Jul 09 2014

type: RNA

city: Manchester

first: Anna

last: Marusiak

address: Wilmslow Road

country: United Kingdom

institute: CRUK Manchester Institute

description:
gene expression data after MLK4-Y330H induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 2

hyb_protocol: Triplicate samples were hybridized in the oven at 45°C for 16 hrs with rotation at 60rpm on Affymetrix Human U133 Plus 2.0 array in Affymetrix GeneChip Hybridisation Oven 640. Washing and staining is carried out in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 with Autoloader Software used: Affymetrix GeneChip Command Console (version 4.0.0)

data_processing: The data was analysed using the method RMA implemented in the Affymetrix's tool 'apt-probeset-summarize'

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: cell line HCT15

label_protocol: Amplified cDNA is produced from the total RNA samples using the Ovation Pico WTA System V2 (NuGEN Technologies, item 3302-60). The amplified cDNA is fragmented and labelled using the Encore Biotin Module (NuGEN Technologies, item 4200-60). A 5µg input is used.

growth_protocol: HCT15 and HT115 cells were cultured in RPMI supplemented with 10% FCS, 1% penicillin/streptomycin and 2 mM L-glutamine. Cell lines were obtained from ATCC.

extract_protocol: Cells were lysed using RLT buffer (Qiagen) and mRNA was isolated using Qiagen RNeasy Plus Mini Kit according to the manufacturer's instructions.

treatment_protocol: HCT15 and HT115 were split into 6-well plates and the next day cell lines were treated with tetracycline for 24 hours in order to induce MLK4 expression.

tag: cell line

tag: cell type

value: colorectal cancer


title: HCT15_WT_3_Tet

description:
gene expression data after MLK4-WT induction in colon cancer cell lines harboring loss-of-function mutations in MLK4
repeat 3


title: HCT15_330-1

description:
gene expression data after MLK4-Y330H induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 1


title: HCT15_330-3_Tet

description:
gene expression data after MLK4-Y330H induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 3


title: HT115_314-1

description:
gene expression data after MLK4-E314K induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 1

source_name: cell line HT115


title: HCT15_330-2_Tet


title: K14Snail_Mts24positive_keratinocytes

country: Belgium

organism: Mus musculus

source_name: Mts24 positive keratinocytes from K14Snail mice

tag: genotype

tag: age

tag: tissue

value: Mts24 positive keratinocytes


title: HT115_314-2_Tet

description:
gene expression data after MLK4-E314K induction in colon cancer cell lines harboring loss-of-function mutations in MLK4 (control experiment)
repeat 2


title: Wildtype_Mts24positive_keratinocytes

source_name: Mts24 positive keratinocytes from Wild type mice

value: wild type


title: K14Snail_CD34positive_keratinocytes

source_name: CD34 positive keratinocytes from K14Snail mice

value: pool of 11 mice

value: CD34 positive keratinocytes


title: HT115_314-1_Tet


title: Wildtype_Mts24negative_keratinocytes

source_name: Mts24 negative keratinocytes from Wild type mice


title: HCT15_330-3


title: HCT15_330-1_Tet


title: HCT15_WT_3


title: HCT15_WT_1

description:
gene expression data after MLK4-WT induction in colon cancer cell lines harboring loss-of-function mutations in MLK4
repeat 1


title: HCT15_WT_2_Tet

description:
gene expression data after MLK4-WT induction in colon cancer cell lines harboring loss-of-function mutations in MLK4
repeat 2


title: HCT15_WT_1_Tet


title: Wildtype_CD34negative_keratinocytes

source_name: CD34 negative keratinocytes from Wild type mice

value: CD34 negative keratinocytes


title: HCT15_WT _2


title: K14Snail_CD34negative_keratinocytes

source_name: CD34 negative keratinocytes from K14Snail mice


title: HBCx34_TamR_m70

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 48C on Human Gene 1.1 ST array. GeneChips were washed and stained in the Affymetrix GeneTitan.

scan_protocol: GeneChips were scanned in the Affymetrix GeneTitan.

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

source_name: HBCx34 tamoxifen-resistant

label_protocol: RNA was amplified by WT expression kit (Ambion) and Biotinylated by WT terminal labeling kit (Affymetrix)

extract_protocol: Total RNA were extracted by miRNeasy kit (Qiagen)

tag: model

tag: resistance

value: tamoxifen-resistant

value: luminal breast cancer tumor


title: TKO-Mock

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

country: USA

institute: Walter Reed Army Institute of Research

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was Quantile normalized and log2 transformed to median of samples

label: Biotin

source_name: Mouse embryonic fibroblast

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

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained from e13.5 embryos by a standard procedure and cultured in DMEM with 10% FBS.

extract_protocol: Total RNA was extracted with RNeasy Mini kit (Qiagen). RNA quality was analyzed by Bionalyzer RNA 6000 Nano (Agilent Technologies).

treatment_protocol: Cells were transfected with 4µg/ml of double strand DNA (ISD) for 6 hours.

tag: strain

value: MEFs

value: Sting -/-


title: Wildtype_CD34positive_keratinocytes

source_name: CD34 positive keratinocytes from Wild type mice


title: HBCx34_TamR_m58


title: HBCx34_OvaR_m8

source_name: HBCx34 ovariectomy-resistant

value: ovariectomy-resistant


title: HBCx34_TamR_m22


title: WT-Mock

description: SAMPLE 6


title: HBCx34_TamR_m21


title: WT-ISD

description: SAMPLE 5


title: HBCx34_m7

source_name: HBCx34 parental


title: TKO-ISD

description: SAMPLE 3

value: Sting +/+


title: 16 (Trex-/- STING-/-)

description:
Genotypes : Sting -/-
SAMPLE 12

data_processing: Data was Quantile normalized and log2 transformed to median of all samples

source_name: Heart from Trex-/- STING-/-

growth_protocol: Mice were maintained by Institutional Animal Care Facility

treatment_protocol: No treatment. Each mouse has different genotypes.

value: heart

value: Trex-/- STING-/-


title: HBCx34_OvaR_m4


title: 13 (Trex+/+ STING-/-)

description:
Genotypes : Sting +/+
SAMPLE 9

source_name: Heart from Trex+/+ STING-/-

value: Trex+/+ STING-/-


title: HBCx34_TamR_m40


title: HBCx34_OvaR_m3


title: 11 (Trex-/- STING+/-)

description:
Genotypes : Sting +/+
SAMPLE 8

source_name: Heart from Trex-/- STING+/-

value: Trex-/- STING+/-


title: 15 (Trex-/- STING-/-)

description:
Genotypes : Sting -/-
SAMPLE 11


title: STKO-ISD

description: SAMPLE 1


title: 14 (Trex+/+ STING-/-)

description:
Genotypes : Sting -/-
SAMPLE 10


title: STKO-Mock

description: SAMPLE 2


title: HBCx34_OvaR_m1


title: HBCx34_OvaR_m10


title: HBCx34_m29


title: HBCx34_m24


title: 10 (Trex-/- STING+/-)

description:
Genotypes : Sting +/+
SAMPLE 7


title: 7 (Trex-/- STING+/+)

description:
Genotypes : Sting -/-
SAMPLE 5

source_name: Heart from Trex-/- STING+/+

value: Trex-/- STING+/+


title: HBCx34_m22


title: HBCx34_m53


title: HBCx22_TamR_m27

source_name: HBCx22 tamoxifen-resistant


title: HBCx22_TamR_m58


title: HBCx22_TamR_m69


title: HBCx22_m46

source_name: HBCx22 parental


title: HBCx22_OvaR_m60

source_name: HBCx22 ovariectomy-resistant


title: HBCx22_TamR_m68


title: HBCx22_OvaR_m83


title: HBCx22_m66


title: HBCx22_m99


title: 8 (Trex-/- STING+/+)

description:
Genotypes : Sting -/-
SAMPLE 6


title: HBCx22_OvaR_m20


title: HBCx22_OvaR_m66


title: HBCx22_TamR_m31


title: 5 (Trex+/+ STING+/-)

description:
Genotypes : Sting -/-
SAMPLE 4

source_name: Heart from Trex+/+ STING+/-

value: Trex+/+ STING+/-


title: 2 (Trex+/+ STING+/+)

description:
Genotypes : Sting +/+
SAMPLE 2

source_name: Heart from Trex+/+ STING+/+

value: Trex+/+ STING+/+


title: HBCx22_m67


title: 3D7/HP1OFF generation 2 24-32hpi

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

country: Switzerland

institute: Swiss Tropical and Public Health Institute

hyb_protocol: Microarray hybridizations were carried out as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Microarrays were scanned as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: All probes on the array were remapped to P. falciparum genome sequence released on PlasmoDBv9.0 (www.plasmodb.org) using NCBI Blast 2.2 with an Evalue cut-off 0.1. Data normalization was done using Limma package of R [Smyth,W.A. (2005). Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R.Gentleman, V.Carey, S.Dudoit, R.Irizarry, and W.Huber, eds. (New York: Springer), pp. 397-420]. Briefly, log2 ratios of Cy5/Cy3 signal intensities were calculated for each spot after ‘normexp’ background correction [Ritchie,M.E., Silver,J., Oshlack,A., Holmes,M., Diyagama,D., Holloway,A., and Smyth,G.K. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics. 23, 2700-2707] and normalized by locally estimated scatterplot smoothing (LOESS) within arrays and quantile normalized between arrays [Yang, Y. H. and Thorne, N. P. (2003). Normalization for two-color cDNA microarray data. In Statistics and Science: A Festschrift for Terry Speed. D.R.Goldstein, ed. (Ohio, Institute of Mathematical Statistics), IMS Lecture Notes - Monograph Series, 40, pp. 403-418]. Flagged spots and spots with both Cy3 and Cy5 intensities lower than 1.5 fold the corresponding microarray background were discarded.

organism: Plasmodium falciparum 3D7

source_name: RNA extracted from 3D7/HP1OFF generation 2 24-32hpi

label_protocol: Labeling was carried out as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]

extract_protocol: Total RNA was extracted using Ribozol (Amresco) following manufacturer's instructions.

treatment_protocol: Pre-synchronized 3D7/HP1ON cultures were synchronized twice 16 hours apart to achieve a tight eight hour growth window. After the last synchronization at 4-12hpi, parasites were split and cultured in presence (3D7/HP1ON) and absence (3D7/HP1OFF) of Shield-1.

value: Plasmodium falciparum clone 3D7/HP1-GFP-DD

tag: sample type

value: cDNA

tag: treatment

value: 4nM WR

tag: time point

value: 24-32 hours post-invasion

tag: generation

value: whole organism

source_name: reference pool RNA

value: cDNA reference pool consisting of of time points 2, 3, 4, 5, 6


title: 3D7/HP1OFF generation 2 16-24hpi

source_name: RNA extracted from 3D7/HP1OFF generation 2 16-24hpi

value: 16-24 hours post-invasion


title: 3D7/HP1OFF generation 2 32-40hpi

source_name: RNA extracted from 3D7/HP1OFF generation 2 32-40hpi

value: 32-40 hours post-invasion


title: HBCx22_OvaR_m21

value: ovariectomy-resistant

value: luminal breast cancer tumor


title: HBCx22_m65


title: 3D7/HP1OFF generation 2 8-16hpi

source_name: RNA extracted from 3D7/HP1OFF generation 2 8-16hpi

value: 8-16 hours post-invasion


title: 1 (Trex+/+ STING+/+)

description:
Genotypes : Sting +/+
SAMPLE 1

value: heart


title: 3D7/HP1OFF generation 2 4-12hpi

source_name: RNA extracted from 3D7/HP1OFF generation 2 4-12hpi

value: 4-12 hours post-invasion


title: 3D7/HP1OFF generation 1 40-48hpi

source_name: RNA extracted from 3D7/HP1OFF generation 1 40-48hpi

value: 40-48 hours post-invasion


title: HD11-stress-1Hpost

city: New Haven

first: Robert

middle: D

last: Beech

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Peripheral blood

extract_protocol: Total RNA was isolated from 10 cc whole blood using the PAXgene Blood RNA Isolation kit (QIAGEN, Valencia, CA) per the manufacturer's instructions, and depleted of globin mRNA message using GLOBINclear hybridization capture technology (Ambion, Austin, TX). Quality control was performed with Agilent Bioanalyser.

value: blood

tag: drinking group

value: H

tag: subject number

tag: imagery condition

value: stress

tag: timepoint

value: 1 hr post

tag: Sex

value: m

tag: age (in years)

tag: race/ ethnicity

value: W


title: 3D7/HP1OFF generation 1 24-32hpi

source_name: RNA extracted from 3D7/HP1OFF generation 1 24-32hpi

tag: genotype

value: Plasmodium falciparum clone 3D7/HP1-GFP-DD

value: cDNA

value: 4nM WR

value: 24-32 hours post-invasion


title: HD11-alcohol-1Hpost

value: alcohol


title: 4 (Trex+/+ STING+/-)

description:
Genotypes : Sting +/+
SAMPLE 3

value: Trex+/+ STING+/-


title: 3D7/HP1OFF generation 1 32-40hpi

source_name: RNA extracted from 3D7/HP1OFF generation 1 32-40hpi

value: 32-40 hours post-invasion

value: whole organism

value: cDNA reference pool consisting of of time points 2, 3, 4, 5, 6


title: HD11-stress-immed

value: immed.


title: 3D7/HP1ON generation 2 24-32hpi

source_name: RNA extracted from 3D7/HP1ON generation 2 24-32hpi

value: 4nM WR + 625 nM Shield-1


title: HD11-alchol-immed

value: blood


title: 3D7/HP1OFF generation 1 16-24hpi

source_name: RNA extracted from 3D7/HP1OFF generation 1 16-24hpi

value: 16-24 hours post-invasion


title: 3D7/HP1ON generation 2 32-40hpi

source_name: RNA extracted from 3D7/HP1ON generation 2 32-40hpi


title: 3D7/HP1ON generation 2 16-24hpi

source_name: RNA extracted from 3D7/HP1ON generation 2 16-24hpi


title: HD11-neutral-1Hpost

value: H

value: neutral


title: HD10-alcohol-1Hpost

value: 1 hr post

value: m


title: 3D7/HP1ON generation 2 40-48hpi

source_name: RNA extracted from 3D7/HP1ON generation 2 40-48hpi

value: Plasmodium falciparum clone 3D7/HP1-GFP-DD

value: 40-48 hours post-invasion


title: 3D7/HP1ON generation 2 8-16hpi

source_name: RNA extracted from 3D7/HP1ON generation 2 8-16hpi

value: cDNA

value: 8-16 hours post-invasion


title: HD10-alcohol-immed

value: alcohol

value: W


title: HD10-alchol-baseline

value: baseline


title: 3D7/HP1OFF generation 2 40-48hpi

source_name: RNA extracted from 3D7/HP1OFF generation 2 40-48hpi

value: 4nM WR

value: whole organism


title: HD11-alcohol-baseline


title: 3D7/HP1ON generation 1 40-48hpi

source_name: RNA extracted from 3D7/HP1ON generation 1 40-48hpi

value: cDNA reference pool consisting of of time points 2, 3, 4, 5, 6


title: 3D7/HP1ON generation 2 4-12hpi

source_name: RNA extracted from 3D7/HP1ON generation 2 4-12hpi

value: 4nM WR + 625 nM Shield-1

value: 4-12 hours post-invasion

source_name: reference pool RNA


title: HD9-neutral-1Hpost

value: blood

value: f


title: 3D7/HP1OFF generation 1 8-16hpi

source_name: RNA extracted from 3D7/HP1OFF generation 1 8-16hpi


title: HD9-neutral-immed

value: H

value: neutral

value: immed.


title: HD11-stress-baseline

value: stress

value: m


title: HD9-neutral-baseline


title: HD11-neutral-immed


title: HD10-stress-1Hpost

value: 1 hr post


title: 3D7/HP1ON generation 1 8-16hpi

source_name: RNA extracted from 3D7/HP1ON generation 1 8-16hpi

value: Plasmodium falciparum clone 3D7/HP1-GFP-DD

value: cDNA

value: 8-16 hours post-invasion


title: HD9-alcohol-1Hpost

value: alcohol

value: W


title: HD10-neutral-baseline

value: baseline


title: HD9-alcohol-immed


title: HD9-stress-1Hpost


title: HD10-stress-baseline


title: HD9-stress-immed


title: HD11-neutral-baseline


title: HD9-stress-baseline


title: 3D7/HP1ON generation 1 16-24hpi

source_name: RNA extracted from 3D7/HP1ON generation 1 16-24hpi

value: Plasmodium falciparum transgenic clone 3D7/HP1-GFP-DD

value: 16-24 hours post-invasion

value: whole organism

value: cDNA reference pool consisting of of time points 2, 3, 4, 5, 6


title: ERp_val_58

city: Berlin

first: Jan

last: Budczies

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite - Universitaetsmedizin Berlin

data_processing: Illumina CubSpline Normalization

source_name: breast cancer tissue

label_protocol: Standard Illumina label protocol

extract_protocol: QIAamp DNA Mini Kit (Qiagen)

value: breast cancer tissue

tag: er


title: ERp_val_60

tag: tissue


title: 3D7/HP1ON generation 1 32-40hpi

source_name: RNA extracted from 3D7/HP1ON generation 1 32-40hpi

value: 4nM WR + 625 nM Shield-1

value: 32-40 hours post-invasion


title: ERp_val_56


title: 3D7/HP1ON generation 1 24-32hpi

source_name: RNA extracted from 3D7/HP1ON generation 1 24-32hpi

value: 24-32 hours post-invasion


title: HD8-alcohol-immed

source_name: Peripheral blood

value: blood

value: H

value: immed.


title: HD8-alcohol-1Hpost

value: 1 hr post

value: m


title: ERp_val_54


title: HD10-stress-immed

value: stress


title: HD9-alcohol-baseline

value: alcohol

value: f


title: HD8-alcohol-baseline

value: baseline

value: W


title: HD10-neutral-immed

value: neutral


title: HD10-neutral-1Hpost


title: HD8-neutral-1Hpost


title: HD8-stress-1Hpost


title: ERp_val_55


title: ERp_val_43


title: ERp_val_46


title: ERp_val_49


title: HD8-stress-immed


title: HD8-stress-baseline


title: ERp_val_38


title: MD11-neutral-immed

value: M


title: ERp_val_39


title: ERp_val_37


title: MD11-neutral-1Hpost


title: ERp_val_36


title: HD8-neutral-baseline


title: ERp_val_30


title: ERp_val_33


title: HD8-neutral-immed


title: ERp_val_31


title: MD11-stress-1Hpost


title: MD11-alcohol-1Hpost


title: MD11-stress-immed


title: HD7-stress-1Hpost

value: AA


title: MD11-alcohol-baseline


title: MD11-neutral-baseline


title: HD7-stress-immed


title: ERp_val_42

value: breast cancer tissue


title: ERp_val_26


title: ERp_val_25


title: MD11-stress-baseline


title: MD11-alcohol-immed


title: ERp_val_23


title: ERp_val_22


title: ERp_val_16


title: ERp_val_20

value: unknown


title: ERp_val_17


title: ERp_val_14


title: HD7-alcohol-1Hpost


title: MD10-stress-baseline


title: ERp_val_18


title: HD7-alcohol-immed


title: ERp_val_19


title: ERp_val_6


title: MD10-neutral-1Hpost


title: HD7-alcohol-baseline


title: ERp_val_21


title: HD7-stress-baseline


title: MD10-neutral-immed


title: MD10-stress-1Hpost


title: ERp_val_4


title: MD10-stress-immed


title: ERp_val_12


title: ERp_val_8


title: HD7-neutral-1Hpost


title: HD7-neutral-immed


title: MD10-alcohol-1Hpost


title: ERp_val_2


title: MD10-neutral-baseline


title: ERp_val_11


title: ERn_val_24


title: MD9-stress-1Hpost


title: ERn_val_22


title: HD7-neutral-baseline


title: ERn_val_21


title: ERn_val_15


title: ERn_val_18


title: MD9-stress-immed


title: ERn_val_9


title: ERn_val_10


title: ERn_val_11


title: ERp_train_137


title: ERp_train_140


title: ERn_val_4


title: MD9-neutral-baseline


title: MD10-alcohol-immed


title: ERp_train_139


title: ERn_val_19


title: MD9-neutral-immed


title: ERn_val_16


title: MD9-neutral-1Hpost


title: MD9-alcohol-immed


title: MD9-stress-baseline


title: MD10-alcohol-baseline


title: ERn_val_7


title: MD8-alcohol-1Hpost


title: MD9-alcohol-1Hpost


title: MD9-alcohol-baseline


title: MD8-alcohol-immed


title: MD8-neutral-1Hpost


title: MD8-alcohol-baseline


title: MD8-neutral-immed


title: ERp_val_48


title: ERp_train_135


title: ERp_train_132


title: ERp_train_134


title: ERp_train_128


title: ERp_train_126


title: ERp_train_127


title: ERp_train_133


title: ERp_train_129


title: ERp_train_125


title: ERp_train_122


title: MD8-stress-1Hpost


title: MD8-neutral-baseline


title: ERp_train_123


title: ERp_train_124


title: MD8-stress-immed


title: MD7-neutral-1Hpost


title: MD8-stress-baseline


title: MD7-stress-baseline


title: ERp_train_116


title: ERp_train_113


title: MD7-neutral-immed


title: MD7-alcohol-immed


title: ERp_train_115


title: ERp_train_119


title: MD7-stress-immed


title: MD7-neutral-baseline


title: ERp_train_112


title: MD7-stress-1Hpost


title: MD6-neutral-1Hpost


title: ERp_train_109


title: ERp_train_107


title: ERp_train_106


title: MD7-alcohol-baseline


title: MD7-alcohol-1Hpost


title: MD6-neutral-immed


title: ERp_train_105


title: ERp_train_110


title: MD6-stress-1Hpost


title: ERp_train_103


title: MD6-stress-immed


title: MD6-neutral-baseline


title: ERp_train_101


title: MD6-alcohol-1Hpost


title: MD6-stress-baseline


title: MD6-alcohol-baseline


title: HD6-stress-1Hpost


title: MD6-alcohol-immed


title: ERp_train_95


title: ERp_train_92


title: ERp_train_99


title: ERp_train_94


title: ERp_train_98


title: HD6-stress-immed


title: ERp_train_93


title: HD6-stress-baseline


title: ERp_train_86


title: ERp_train_89


title: MD5-neutral-1Hpost


title: MD4-neutral-immed


title: ERp_train_83


title: ERp_train_84


title: MD5-neutral-baseline


title: ERp_train_79


title: ERp_train_82


title: ERp_train_88


title: MD4-neutral-1Hpost


title: ERp_train_77


title: ERp_train_78


title: ERp_train_76


title: MD5-stress-1Hpost


title: MD5-neutral-immed


title: HD6-neutral-immed


title: MD5-alcohol-1Hpost


title: ERp_train_81


title: MD5-alcohol-immed


title: MD5-alcohol-baseline


title: MD5-stress-baseline


title: ERp_train_70


title: HD6-neutral-1Hpost


title: ERp_train_72


title: MD4-neutral-baseline


title: MD5-stress-immed


title: HD6-neutral-baseline


title: ERp_train_69


title: ERp_train_71


title: ERp_train_61


title: ERp_train_63


title: ERp_train_73


title: ERp_train_64


title: HD6-alcohol-immed


title: ERp_train_57


title: ERp_train_55


title: ERp_train_75


title: HD6-alcohol-1Hpost


title: ERp_train_59


title: ERp_train_67


title: ERp_train_53


title: MD4-stress-baseline


title: HD6-alcohol-baseline


title: MD4-stress-immed


title: HD5-stress-immed


title: MD4-alcohol-immed


title: ERp_train_52


title: ERp_train_51


title: ERp_train_49


title: MD4-alcohol-baseline


title: HD5-stress-1Hpost


title: MD4-alcohol-1Hpost


title: HD5-neutral-immed


title: HD5-neutral-1Hpost


title: ERp_train_50


title: HD5-stress-baseline


title: MD4-stress-1Hpost


title: ERp_train_47


title: ERp_train_48


title: HD5-alcohol-1Hpost


title: ERp_train_45


title: HD5-alcohol-baseline


title: HD5-neutral-baseline


title: ERp_train_38


title: ERp_train_40


title: HD4-neutral-baseline


title: HD4-neutral-immed


title: HD4-neutral-1Hpost


title: ERp_train_35


title: HD5-alcohol-immed


title: HD4-stress-1Hpost


title: ERp_train_43


title: ERp_train_34


title: ERp_train_37


title: ERp_train_36


title: HD4-alcohol-immed


title: HD4-alcohol-1Hpost


title: ERp_train_33


title: HD4-stress-immed


title: HD4-stress-baseline


title: HD4-alcohol-baseline


title: ERp_train_26


title: MD3-stress-1Hpost


title: MD3-stress-immed


title: ERp_train_24


title: ERp_train_23


title: ERp_train_20


title: ERp_train_29


title: MD3-neutral-1Hpost


title: ERp_train_13


title: ERp_train_16


title: ERp_train_11


title: ERp_train_7


title: ERp_train_19


title: ERp_train_5


title: mbd11 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 3

city: delhi

first: Adwaita

middle: Prasad

last: Parida

state: Delhi

address: Benito Juarez Road

department: plant molecular biology

country: India

institute: university of delhi, south campus

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: Data were RMA-normalized using R (v.2.11) and filterd by p_value 0.05.

organism: Arabidopsis thaliana

source_name: mbd11 mutant_10 days old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each genotype were surface sterilized with 70% ethanol followed by 2 % sodium hypochloride with repeated rinses with dd-water, and were grown in MS media for ten days.

extract_protocol: Trizol extraction of total RNA of whole seedlings was performed according to the manufacturer's instructions followed by cleanup using the Qiagen RNA mini kit.

tag: ecotype

tag: genotype/variation

value: mbd11 mutant

value: 10 days old seedling


title: ERp_train_14


title: mbd11 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 1


title: ERp_train_4


title: ERp_train_12


title: MD3-alcohol-1Hpost

value: blood


title: mbd11 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 2


title: mbd6 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 3

source_name: mbd6 mutant_10 days old seedling

value: mbd6 mutant


title: MD3-alcohol-immed

value: immed.


title: mbd6 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 1


title: MD3-neutral-immed


title: mbd6 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 2


title: MD2-neutral-1Hpost

value: 1 hr post


title: ERn_train_40


title: ERp_train_2


title: MD3-neutral-baseline


title: ERn_train_38


title: ERn_train_33


title: ERn_train_35


title: MD3-alcohol-baseline


title: ERn_train_32


title: mbd4 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 3

source_name: mbd4 mutant_10 days old seedling

value: mbd4 mutant


title: MD2-neutral-immed

value: m


title: ERn_train_37


title: MD2-neutral-baseline


title: wild type Arabidopsis thaliana 10-day-old seedling, Biological replicate 3

description: Wild 3

source_name: WT_10 days old seedling

value: wildtype


title: ERn_train_26


title: ERn_train_36


title: ERn_train_29


title: ERn_train_19


title: mbd4 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 1


title: mbd4 mutant of Arabidopsis thaliana 10-day-old seedling, Biological replicate 2


title: wild type Arabidopsis thaliana 10-day-old seedling, Biological replicate 2

description: Wild 2


title: ERn_train_18


title: ERn_train_21


title: ERn_train_25


title: wild type Arabidopsis thaliana 10-day-old seedling, Biological replicate 1

description: Wild 1


title: MD2-stress-baseline

value: stress


title: MD2-stress-1Hpost


title: ERn_train_31


title: MD2-alcohol-1Hpost

value: alcohol


title: MD2-alcohol-immed

value: W


title: MD2-stress-immed


title: Le136

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

institute: Centre for cellular and molecular biology

description: Biological replicate 5 of 6 T-ALL

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark) following manufacturer's instructions usign Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the slides were scanned and stored in an ozone free environment (ozon level below 2.0 ppb) in order to prevent potential bleaching of the flourescent dyes.

scan_protocol: Scanned on an Agilent G2565BA Microarray scanner. Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery,Inc.,USA).

data_processing: Background corrected (Normexp with offset value 10 – Ritchie et al.,2007) and normalized using Lowess regression algorithm.

source_name: T-ALL PB

label_protocol: One µg total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark).

extract_protocol: Total RNA was extracted using mirVana™ miRNA isolation kit following manufacturer's instructions.

tag: gender

value: Male

tag: age (years)

source_name: Common reference pool

tag: reference rna

value: pool of human, rat, mouse


title: Le139

description: Biological replicate 6 of 6 T-ALL

source_name: T-ALL BM


title: ERn_train_17


title: Le134N

description: Biological replicate 5 of 5 Control

source_name: normal blood

value: Female


title: Le132N

description: Biological replicate 3 of 5 Control


title: ERn_train_12

value: breast cancer tissue


title: ERn_train_6


title: ERn_train_7


title: Le131N

description: Biological replicate 2 of 5 Control


title: ERn_train_14


title: ERn_train_4


title: Le130N

description: Biological replicate 1 of 5 Control


title: alcohol_rep8

city: Indianapolis

first: James

middle: A

last: Marrs

state: IN

address: 723 West Michigan Street

department: Biology

institute: Indiana University-Purdue University Indianapolis

description: Gene expression data from alcohol-treated embryo.

hyb_protocol: Affymetrix standard protocol, except hybridization for 17 hours.

scan_protocol: Scanned using 3000-7G controlled by Affymetrix GCOS.

data_processing: Affymetrix MAS5 data scaled to intensity of 1000.

organism: Danio rerio

source_name: Total RNA from alcohol-treated embryos

label_protocol: Total RNA was labeled using the 3' IVT express kit from Affymetrix.

growth_protocol: Embryos were grown by incubation in embryo medium, in Petri dishes wrapped with parafilm and maintained at 28.5ºC.

extract_protocol: Total RNA was extracted from approximately 20 treated and untreated embryos at 8 hpf using TRIzol reagent (Sigma, St. Louis, MO USA).

treatment_protocol: Embryos were exposed to ethanol by incubation in embryo medium containing 100 mM (0.6% vol./vol.) ethanol from 2 hours post fertilization (hpf) until the completion of the experiment, in Petri dishes wrapped with parafilm and maintained at 28.5ºC.

tag: strain

value: TL

tag: age

value: 8 hours postfertilization

value: whole body

tag: treatment

tag: treatment duration

value: 6 hrs


title: control_rep5

description: Gene expression data from control embryos.

source_name: Total RNA from control embryos

value: control


title: MD2-alcohol-baseline

value: blood

tag: drinking group

value: M

tag: subject number

tag: imagery condition

value: baseline


title: Le117

description: Biological replicate 5 of 5 B-ALL

source_name: B-ALL PB


title: HD3-alcohol-1Hpost

value: H

tag: timepoint

value: 1 hr post

tag: Sex

value: m

tag: age (in years)


title: Le115

description: Biological replicate 4 of 6 T-ALL


title: control_rep8


title: Le114

description: Biological replicate 3 of 6 T-ALL


title: HD3-alcohol-baseline

value: alcohol

tag: race/ ethnicity


title: HD3-stress-immed

tag: tissue

value: stress

value: immed.

value: W


title: alcohol_rep6


title: HD3-alcohol-immed


title: Le82

description: Biological replicate 2 of 6 T-ALL

value: Male

value: pool of human, rat, mouse


title: alcohol_rep4

value: TL


title: Le74

description: Biological replicate 4 of 5 B-ALL


title: HD3-stress-1Hpost


title: HD3-stress-baselin


title: Le70

description: Biological replicate 3 of 5 B-ALL

value: Female


title: Le53

description: Biological replicate 2 of 5 B-ALL


title: control_rep6

value: 8 hours postfertilization

value: whole body


title: alcohol_rep3

value: 6 hrs


title: Le33

description: Biological replicate 1 of 6 T-ALL


title: control_rep4

value: control


title: alcohol_rep5


title: control_rep2


title: HD3-neutral-1Hpost

value: blood

value: neutral


title: alcohol_rep1


title: alcohol_rep2


title: control_rep3


title: MD3-stress-baseline

value: M

value: baseline

value: f


title: HD3-neutral-baseline

value: H

value: m


title: HD3-neutral-immed

value: immed.


title: Le52

description: Biological replicate 1 of 5 B-ALL


title: dptB-H genes deletion mutant_ grown for 12h_rep2

city: Shanghai

first: Bo

last: Cao

address: 1954 Huashan Road

country: China

institute: Shanghai Jiaotong University

description: Gene expression of phosphorothioate modificaiton and restriction genes mutant strain

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Salmonella enterica

source_name: dptB-H genes deletion mutant grown for 12h_rep2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Strains were grown at 37 ˚C on liquid Luria-Bertani (LB) medium. To obtain cells from different growth phases, the overnight bacterial cultures were diluted into 5 ml of LB medium at a concentration of 5000 cells/ml and the cell growth was monitored by the optical density 600 nm (OD600). The cells grown for 8h, 12h, 16h were considered to be at their early-, late-exponential and stationary phase, respectively.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The cells were collected from theLB medium by centrifugation at 12,000 rpm for 1 min, resuspended in 1 mL TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US), and broken in a precellys homogenizer (6,500 rpm, 1×30 s; Peqlab) with glass beads (150–212 μm, Sigma). Cell debris was removed by centrifugation at 12,000 rpm for 5 min, and the extracted supernatants were stored at -80°C.

tag: growth time

tag: serovar

value: Cerro 87

tag: genotype

value: dptB-H genes deletion


title: control_rep1


title: dptB-H genes deletion mutant_ grown for 12h_rep3

source_name: dptB-H genes deletion mutant grown for 12h_rep3


title: MRMAX8

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

country: Spain

institute: Institute of Aquaculture Torre de la Sal (CSIC)

hyb_protocol: Each sample (1.65 µg) was hybridized to the gilthead sea bream array at 65 ºC for 17 h using Agilent GE hybridization kit.

scan_protocol: Arrays were scanned with Agilent scanner G2505B.

data_processing: Spot intensities and other quality control features were extracted with Agilent Feature Extraction software version 10.4.0.0, and was further analyzed, including percentile shift normalization, one-way ANOVA, principal components analysis and k-means clustering of differentially expressed genes, by means of GeneSpring GX 11.5.1 software (Agilent).

organism: Sparus aurata

source_name: Red muscle, maximum ration size

label_protocol: Total RNA (100 ng) from each individual sample was amplified and Cy3-labeled with Agilent One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling kit) along with Agilent One-color RNA SpikeIn kit. After labeling, cRNA was purified with RNeasy mini spin columns (Qiagen).

extract_protocol: Total RNA from target tissues was isolated with the ABI PRISM™ 6100 Nucleic Acid PrepStation (Applied Biosystems, Foster City, CA, USA).

treatment_protocol: Fish were fed from May to August (11 weeks) with a commercial diet (D-2 Excel 1P, Skretting, Stavanger, Norway) twice per day at two different feeding levels: full ration until visual satiety (MAX group), and maintenance ration (30% of the satiation level) (MANT group).

value: red skeletal muscle

tag: muscle type

value: aerobic

tag: ration size

value: maximum (MAX)


title: dptB-H genes deletion mutant_ grown for 8h_rep1

source_name: dptB-H genes deletion mutant grown for 8h_rep1


title: MRMAX7


title: MRMAX6


title: HD2-neutral-immed

value: W


title: MRMAX5


title: HD2-neutral-1Hpost

value: 1 hr post


title: MRMAX2


title: MRMAX3


title: HD2-stress-baseline

value: stress


title: MRMANT7

source_name: Red muscle, maintenance ration

value: maintenance (MANT)


title: MRMANT8


title: HD2-stress-1Hpost

source_name: Peripheral blood

value: blood


title: dptB-H genes deletion mutant_ grown for 12h_rep1

source_name: dptB-H genes deletion mutant grown for 12h_rep1


title: HD2-stress-immed


title: Le133N

description: Biological replicate 4 of 5 Control

tag: gender

value: Female

tag: age (years)

tag: reference rna

value: pool of human, rat, mouse


title: HD2-neutral-baseline

value: neutral

value: baseline


title: MRMANT3


title: MRMAX4


title: dptBCED genes deletion mutant_ grown for 16h_rep3

description: Gene expression of phosphorothioate modificaiton genes mutant strain

source_name: dptBCED genes deletion mutant grown for 16h_rep3

value: dptBCDE genes deletion


title: dptB-H genes deletion mutant_ grown for 8h_rep3

source_name: dptB-H genes deletion mutant grown for 8h_rep3


title: HD2-alcohol-immed

value: H

value: alcohol

value: f


title: dptB-H genes deletion mutant_ grown for 8h_rep2

source_name: dptB-H genes deletion mutant grown for 8h_rep2

value: Cerro 87

value: dptB-H genes deletion


title: HD2-alcohol-baseline


title: MBMAX7

source_name: White muscle, maximum ration size

value: white skeletal muscle

value: anaerobic


title: MRMAX1

value: red skeletal muscle

value: aerobic

value: maximum (MAX)


title: MRMANT1

value: maintenance (MANT)


title: HD2-alcohol-1Hpost

value: blood

value: 1 hr post

value: W


title: MD1-alcohol-1Hpost

value: M


title: dptBCED genes deletion mutant_ grown for 16h_rep2

source_name: dptBCED genes deletion mutant grown for 16h_rep2


title: dptBCED genes deletion mutant_ grown for 12h_rep2

source_name: dptBCED genes deletion mutant grown for 12h_rep2


title: MBMAX2


title: MBMAX6


title: dptBCED genes deletion mutant_ grown for 12h_rep3

source_name: dptBCED genes deletion mutant grown for 12h_rep3


title: MD1-alcohol-immed

value: immed.


title: MD1-alcohol-baseline

value: baseline


title: MBMANT8

source_name: White muscle, maintenance ration


title: MD1-neutral-1Hpost

value: neutral


title: MRMANT6


title: MD1-neutral-immed


title: MD1-stress-1Hpost

value: stress


title: MBMAX8


title: dptBCED genes deletion mutant_ grown for 12h_rep1

source_name: dptBCED genes deletion mutant grown for 12h_rep1

value: dptBCDE genes deletion


title: p47phox-deleted macrophages

city: Chicago

first: Ravi

last: Ranjan

state: IL

address: 840 S Wood St

department: Medicine

institute: University of Illinois at Chicago

description:
p47phox-/-
microRNA

data_processing: The data was analyzed by using the ddCT method by using the manufacturer-provided software (www.SABiosciences.com/pcrarraydataanalysis.php).

label: FAM

source_name: Bone marrow-derived macrophages from p47phox-/-/HLL mice

label_protocol: Converted using the specific cDNAs from mature miRNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) and the cDNAs were loaded onto TaqMan Rodent MicroRNA array-A kit chips (Applied Biosystems) using the Megaplex RT Primers, Rodent Pool A (Applied Biosystems). Quantitative real-time PCR was performed using the 7900HT Fast Real-Time PCR instrument (Applied Biosystems).

growth_protocol: Femoral and tibia bone marrow were isolated from mice (WT-HLL and p47phox-/-/HLL). Mouse bone marrow cells were flushed from femurs and tibias with Ca2+/Mg2+-free Hanks' balanced salt solution (HBSS, Mediatech Inc). Bone marrow progenitor cells were cultured in DMEM (Mediatech, Inc.) containing 10% heat-inactivated FBS (HyClone), 100 U Penicillin-Streptomycin (Mediatech, Inc.) and supplemented with 10% L929 Cell Culture Media (LCCM). After 7 days, bone marrow-derived macrophages were collected for the experiments.

extract_protocol: Total microRNA was isolated by using the mirVana miRNA isolation kit (Ambion).

treatment_protocol: The primary mouse macrophages (left untreated) were used for microRNA isolation.

tag: strain/background

value: HLL (transgenic mouse expressing luciferase)

tag: genotype/variation

value: p47phox-/- (knock-down of p47phox gene)

tag: cell type

value: bone marrow-derived macrophages


title: dptBCED genes deletion mutant_ grown for 8h_rep3

source_name: dptBCED genes deletion mutant grown for 8h_rep3

value: Cerro 87


title: MBMAX5

value: white skeletal muscle

value: anaerobic


title: MBMANT7


title: MD1-neutral-baseline

tag: drinking group

tag: subject number

tag: imagery condition

value: f


title: dptBCED genes deletion mutant_ grown for 8h_rep2

source_name: dptBCED genes deletion mutant grown for 8h_rep2


title: Wild type macrophages

description:
WT
microRNA

source_name: Bone marrow-derived macrophages from WT-HLL mice

value: wild type


title: MBMANT6

value: maintenance (MANT)


title: Wild-type strain_ grown for 16h_rep2

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 16h_rep2


title: MD1-stress-immed

value: blood

tag: timepoint

tag: Sex

tag: age (in years)


title: MBMANT5

tag: tissue


title: dptBCED genes deletion mutant_ grown for 8h_rep1

source_name: dptBCED genes deletion mutant grown for 8h_rep1

tag: growth time

tag: serovar


title: Wild-type strain_ grown for 16h_rep1

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 16h_rep1

tag: genotype


title: CMAX8

source_name: Heart, maximum ration size

value: heart

tag: muscle type

value: aerobic

tag: ration size

value: maximum (MAX)


title: SP 23 (GFP+RFP+), technical rep1

city: Dresden

first: Sonja

last: Schallenberg

state: Saxony

address: Fetscherstrasse 105

department: Research Group Molecular and Cellular Immunology/Immune Regulation

institute: Technische Universität Dresden; DFG-Center for Regenerative Therapies Dresden

description: Gene expression data from Treg cells

hyb_protocol: 7.5 µg biotinylated cRNA was hybridized to an identical lot of Affymetrix GeneChip MOE430 2.0 (16 hours, 45°C) following the manufacturer’s instructions. Washing and SA-PE staining was performed on a fluidics station 450 following the mini_euk2v3_FS450 protocol.

scan_protocol: Images were scanned using a GeneChip® Scanner 3000 and GCOS 1.3 software (both Affymetrix).

data_processing:
Array normalization and expression value calculation was performed using DNA-Chip Analyzer (www.dchip.org).
Summarization Algorithm: RMA
Technology: Affymetrix.GeneChip.Mouse430_2
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: GFP+RFP+ Treg cells from spleen

label_protocol: 50 ng of total RNA were used for biotin labeling (3´ IVT Express kit; Affymetrix).

growth_protocol: Organs of 14-17 week old mice were used.

extract_protocol: RNA was extracted using Qiagen RNAeasy according to manufacturer's manual.

treatment_protocol: Mice were left untreated.

tag: developmental stage

value: thymically induced Treg

tag: cell population

value: GFP+RFP+


title: MBMANT4


title: HD1-stress-1Hpost

source_name: Peripheral blood

value: H

value: stress

value: 1 hr post

value: m

tag: race/ ethnicity

value: W


title: CMAX4


title: HD1-stress-baseline

value: baseline


title: SP 24 (GFP+RFP+), technical rep2

description: Gene expression data from Treg cells


title: CMAX7


title: SP 22 (GFP-RFP+), technical rep2

description: Gene expression data from Treg cells

source_name: GFP-RFP+ Treg cells from spleen

value: peripherally induced Treg

value: GFP-RFP+


title: MD1-stress-baseline

value: M

value: f


title: CMAX3


title: HD1-stress-immed

value: immed.


title: Wild-type strain_ grown for 12h_rep2

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 12h_rep2

value: Cerro 87

value: wild type


title: Wild-type strain_ grown for 16h_rep3

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 16h_rep3


title: HD1-alcohol-1Hpost

value: blood

value: alcohol


title: CMAX5

value: heart

value: aerobic

value: maximum (MAX)


title: CMAX2


title: HD1-alchol-immed

value: H


title: LN 23 (GFP+RFP+), technical rep1

description: Gene expression data from Treg cells

source_name: GFP+RFP+ Treg cells from lymph nodes

value: thymically induced Treg

value: GFP+RFP+


title: Wild-type strain_ grown for 8h_rep2

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 8h_rep2


title: HD1-alcohol-baseline

value: m

value: W


title: CMANT6

source_name: Heart, maintenance ration

value: maintenance (MANT)


title: HD1-neutral-1Hpost

value: neutral

value: 1 hr post


title: SP 21 (GFP-RFP+), technical rep1

description: Gene expression data from Treg cells

value: peripherally induced Treg

value: GFP-RFP+


title: CMAX1


title: dptBCED genes deletion mutant_ grown for 16h_rep1

source_name: dptBCED genes deletion mutant grown for 16h_rep1

value: Cerro 87

value: dptBCDE genes deletion


title: Wild-type strain_ grown for 12h_rep1

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 12h_rep1

value: wild type


title: Wild-type strain_ grown for 8h_rep3

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 8h_rep3


title: LN 24 (GFP+RFP+), technical rep2

description: Gene expression data from Treg cells


title: CMANT7


title: LN 22 (GFP-RFP+), technical rep2

description: Gene expression data from Treg cells

source_name: GFP-RFP+ Treg cells from lymph nodes


title: cikA null 24h Light

status: Public on Jul 08 2014

first: Michael

middle: Joseph

last: Rust

address: 900 E 57th ST

department: Molecular Genetics and Cell Biology

institute: University of Chicago

hyb_protocol: Each array was hybridized with 600 ng of Cyanine 3-labeled cRNA and incubated with rotation (10 rpm) at 65C for 17 hours in an Agilent hybridization oven

scan_protocol: After hybridization, arrays were washed  in wash buffer I and II and scanned immediately at wavelength 532 nm to extract Tiff image files using GenePix 4000B scanner (GenePix pro 6.0 software) at 5-µm resolution with PMT voltage setting to 690 and power (%) to 100 for Cy3 channel (Axon instrument, Inc).

data_processing: The data was extracted by Agilent Feature Extraction Software v9.5 from the image files.  Log intensity for each probe was subsequently normalized by linear regression against RNA spike-in standards.  Data were further processed by normalizing the median of the probes for each ORF across the time course to give mean = 0 and amplitude = 2 for the WT data.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: cikA null 24h Light

label_protocol: 60 ng of total RNA was converted to cDNA and amplified into Cyanine 3-CTP  labeled cRNA using Low Input Quick Amp WT Labeling kit according to Agilent One Color Microarray Based Exon Analysis (Agilent, Inc).

growth_protocol: S. elongatus cells were grown in modified BG-11M liquid medium supplemented with 20 mM HEPES pH 8.0 at 30C under continuous illumination (LL) 50-55 µmol photons m-2 s-1; cool white fluorescent light (Phillips)] with shaking at 200 rpm.

extract_protocol: Cells were lysed in 65°C phenol/SDS by vortexing and total RNA was purified by phenol/chloroform extraction. Then total RNA was subjected to DNase I (Promega, Madison, WI, SA) treatment followed by a second phenol/chloroform extraction.The quality and quantity of RNA sample were checked using a 2100 Bioanalyzer (Agilent) and Nanodrop 1000 (Thermo ientific), respectively.

treatment_protocol: Synechococcus cultures (both wildtype and ΔcikA null cells) were synchronized with two light-dark (12h:12h) cycle before release into continuous light. Samples were collected at 4 h intervals for the next 24 h, total RNA was isolated from samples collected at each time points and genome-wide expression was measured using custom-designed microarrays

tag: genotype/variation

value: cikA null

tag: time point

value: 24h Light


title: Wild-type strain_ grown for 8h_rep1

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 8h_rep1


title: HD1-neutral-immed

value: blood

tag: drinking group

value: immed.


title: CMANT4

value: heart

value: aerobic


title: cikA null 20h Light

source_name: cikA null 20h Light

value: 20h Light


title: HD1-neutral-baseline

value: H

tag: subject number

value: baseline

value: m


title: LN 21 (GFP-RFP+), technical rep1

description: Gene expression data from Treg cells


title: cikA null 12h Light

source_name: cikA null 12h Light

value: 12h Light


title: cikA null 8h Light

source_name: cikA null 8h Light

value: 8h Light


title: cikA null 16h Light

source_name: cikA null 16h Light

value: 16h Light


title: WT 20h Light

source_name: WT 20h Light

value: WT


title: WT 16h Light

source_name: WT 16h Light


title: WT 8h Light

source_name: WT 8h Light


title: conventional TS1

city: Kofu

first: Yasuhide

last: Ohinata

state: Yamanashi

address: 4-4-37 Kakeda

department: Faculty of Life and Environmental Science

country: Japan

institute: Yamanashi University

hyb_protocol: Labeled RNA was hybridized to Mouse 4x44K Ver.2.0 arrays.

scan_protocol: Arrays were scanned on an Agilent Technologies Microarray scanner.

data_processing: Signal intensities were calculated in Agilent Feature Extraction 10.7.3.1 software.

source_name: Trophoblast stem cells established in serum, FGF4, heparin,and  MEF conditioned medium containing culture condition.

label_protocol: Microarray targets from 200 ng total RNA were synthesized and labelled using the Low RNA Input Linear Amp Kit (Agilent).

extract_protocol: Total RNA was purified by using RNeasy Mini kit (QIAGEN).

treatment_protocol: The following condition, termed CDM/FAXY, was used to derive and maintain undifferentiated TS cells from pre-implantation E3.5 blastocysts and post-implantation E6.5 extraembryonic ectoderms. CDM/FAXY was generated by combining 250 ml of Neurobasal (Invitrogen), 250 ml of DMEM/F12 (Ham’s) (1:1) (Invitrogen), 2.5 ml N2 supplement (Invitrogen), B27 supplement (Invitrogen), 5 ml penicillin–streptomycin–L-glutamine solution (Invitrogen), bovine serum albumin (Sigma, 0.05% final concentration), 1-thioglycerol (Sigma, 1.5 × 10-4 M final concentration), recombinant mouse basic FGF (R&D, 12.5–50 ng/ml final concentration), recombinant human activin A (R&D, 20 ng/ml final concentration), XAV939 (Calbiochem, 10 nM final concentration), and Y27632 (Stemgent, 5 nM/ml final concentration). E3.5 blastocysts and E6.5 extraembryonic ectoderms were placed on 96-well plates coated with 15 μg/ml human plasma fibronectin (Millipore) for at least 1 hour at 37℃ in CDM/FAXY. Initial outgrowths of proliferating TS cells were evident by day 5; these outgrowths were dissociated into single cells using TripLE Select (Invitrogen) 5–8 days following plating. The newly established cell lines were further propagated on fibronectin-coated dishes by TripLE Select and then either frozen using a Cellbanker 2 (Mitsubishi Chemical Medience) or used for further analysis. Medium was replaced every 2 days. KnockOut™ serum replacement (Invitrogen, 1% final concentration) can be used in CDM/FAXY and result in positive cell adherent effect (data not shown). Dishes coated with 0.2% Matrigel (BD Biosciences) were used for TS cell culture when Y27632 was not added. Conventional TS cells (129B6F1) were derived and maintained with FGF4, heparin, and serum containing MEF-conditioned medium as described [10].

tag: gender

value: male

tag: strain


title: WT 24h Light

source_name: WT 24h Light


title: conventional TS2


title: cikA null 4h Light

source_name: cikA null 4h Light

value: 4h Light


title: WT 12h Light

source_name: WT 12h Light


title: new TS1

source_name: Trophoblast stem cells established in serum-free, FGF2, Activin A, XAV939, and Y27632  containing chemically defined culture condition.


title: CMANT2

source_name: Heart, maintenance ration

value: maintenance (MANT)


title: WT 4h Light

source_name: WT 4h Light


title: V583_19

type: genomic

city: Tromso

first: Christopher

last: Fenton

state: Norge

address: MH bygget

department: GSCT

country: Norway

institute: Universiry of Tromso

hyb_protocol: Hybridization of 4X2K CustomArrays were performed as described by the manufacturer (CustomArray Inc, Mukilteo, WA) at 52°C for 15 hours. Immediately after scanning, the arrays were stripped for 90 minutes according to the manufacturer’s protocol. Control scans were performed each time to monitor possible background of the subsequent re-hybridization. The arrays were stripped up to 6 times.

scan_protocol: Arrays were subsequently scanned using an Axon GenePix ® 4000B scanner

data_processing: Mean signal intensity was used for multiple replicate probes on array (1 to 5 probes). Arrays were normalized using quantile normalization.

molecule: genomic DNA

organism: Enterococcus faecalis

source_name: Blood

label_protocol: Total DNA (2 µg) was fluorescent labelled using the Kreatech labeling kit with ULS-Cy5 according to the manufacturer instructions (Kreatech Biotechnologies, Amsterdam, The Netherlands), and degree of labelling (DoL) was calculated by measuring absorbance at 260 and 650 nm using a Nanodrop spectrophotometer.

extract_protocol: Total DNA for microarray hybridization and PCR was extracted using E.Z.N.A Bacterial DNA kit (Omega Bio-Tek Inc., Norcross, GA) with the following modifications; cell walls were digested with 1.5 mg lysozyme and 20 U mutanolysin for 20 minutes at 30°C, and DNA was eluted in ddH2O. For hybridization, DNA was broken down to 100-600 bp fragments by 1 min sonication at 2 µm amplitude.

tag: taxonomy

value: Bacteria, Firmicutes, Bacilli, Lactobacillales, Enterococcacea

tag: lineage

tag: year of isolation


title: V583_18


title: V583_20


title: V583_21


title: V583_22


title: V583_16


title: V583_15


title: V583_11


title: V583_12


title: new TS2


title: V583_08


title: V583_10


title: V583_14


title: V583_17


title: V583_13


title: V583_07


title: V583_06


title: V583_05


title: Wild-type strain_ grown for 12h_rep3

description: Gene expression of wild-type strain

source_name: Wild-type strain grown for 12h_rep3

tag: growth time

value: Cerro 87

value: wild type


title: V583_01


title: V583_09


title: 916/07

source_name: Faeces


title: 1638/07

source_name: Urine


title: V583_03


title: V583_04


title: Sample7_iPS-R1

city: La Jolla

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing: We performed preprocessing and normalization utilizing the statistical programming language R (http://www.r-project.org/) (version 3.0.1) and the R package minfi (v.1.6.0). Briefly, IDATs files were control normalized and probes with detection p-values > 0.01 in at least one sample were discarded. The samples were then normalized using the SWAN normalization option in the minfi package and M-values were exported. The R script, ComBat was used to eliminate batch effects.

label: Cy5 and Cy3

source_name: induced Pluripotent Stem Cell

label_protocol: Standard Illumina Protocol

growth_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Cells were transduced by retro virus-based iPSC vectors as previously reported (Lowry, W. E. et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proceedings of the National Academy of Sciences of the United States of America 105, 2883-2888, doi:10.1073/pnas.0711983105 (2008)). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).

extract_protocol: DNA was isolated (QIAGEN Gentra Puregene Cell Kit), quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) and bisulfite converted (EZDNA Methylation Kit, Zymo Research) according to the manufacturer’s protocol.

treatment_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Genetically matched iPSCs were generated by transductions of the same HDF culture with  retroviral or Sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols.

tag: cell type

value: Human Pluripotent Stem Cell

tag: cell line

value: Retro-Virus Derived


title: V583_02


title: Sample9_iPS-S1

value: Sendai-Virus Derived


title: 3992/09


title: UW7784


title: Sample8_iPS-R2


title: Sample10_iPS-S2


title: UW1833


title: Sample6_hESO8

source_name: Human Embryonic Stem Cell

value: IVF Derived


title: 1665/07


title: 3962/09


title: UW7789


title: Sample11_HDF

source_name: Human Dermal Fibroblast

value: Fibroblast

value: Parental


title: 340/07


title: UW5744


title: Sample5_hESO7


title: Sample3_NT3

source_name: Nuclear Transfer Stem Cell

value: Nuclear Transfer Derived


title: UW7753


title: Sample4_NT4


title: Sample2_NT2


title: E3450


title: UW7782


title: VRE-115


title: BIP_9cRA

city: kawasaki

first: Daiki

last: Taniguchi

address: higashimita 1-1-1

institute: Meiji University

hyb_protocol: After amplification and labeling, cyanine incorporation and the cRNA quantity were determined using an Agilent Bioanalyzer and a Nanodrop ND-1000 spectrophotometer. For each hybridization, 1.65 μg of Cy3-labeled cRNA was fragmented and hybridized at 65degC for 17 h to an Agilent Bos taurus (Bovine) Oligo Microarray v2 (Design ID: 023647).

scan_protocol: The microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: The intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtraction. We only used the features that were flagged as having no errors (flags present), whereas we excluded features that were not positive, not significant, not uniform, not above the background, saturated, or population outliers (marginal and absent flags).

organism: Bos taurus

source_name: treated with 9cRA (1 μM)

label_protocol: The total RNA was amplified and labeled with Cyanine 3 (Cy3) using an Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) according to the manufacturer’s instructions. In brief, 100 ng of total RNA was reverse transcribed to double-stranded cDNA using a poly dT-T7 promoter primer. The primer, template RNA, and quality-control transcripts with known concentrations and quality were denatured at 65degC for 10 min and then incubated for 2 h at 40degC with 5× First-Strand Buffer, 0.1 M dithiothreitol, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was inactivated at 70degC for 15 min and the cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. The cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3 labeled-CTP and then incubated at 40degC for 2 h. The labeled cRNAs were purified using RNeasy mini spin columns (QIAGEN GmbH, Hilden, Germany) and eluted in 30 μL of nuclease-free water.

growth_protocol: BIP cells were cultured according to previously reported methods (Aso et al. 1995, Mizoguchi et al. 2014).

extract_protocol: BIP cells were harvested at 0 (D0) and 6 days (D6) after adipogenic stimulation. Total RNA samples were extracted from BIP cells using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and then treated with DNase I (Takara Bio Inc., Shiga, Japan).

treatment_protocol: Confluent cultures were transferred to fresh Dulbecco’s modified Eagle’s medium, which contained 50 ng/mL insulin, 0.25 μM dexamethasone, 5 mM octanoate, 10 mM acetic acid, 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin. The cells were cultured for up to 6 days and the medium was changed every 2 days. BIP cells were treated with ATRA (1 μM), 9cRA (1 μM), or they received no treatment (control).

value: bovine intramuscular preadipocytes

tag: culture days


title: 217691


title: 2724


title: UW7001


title: BIP_atRA

source_name: treated with ATRA (1 μM)


title: Sample1_NT1


title: E1828


title: VRE-0673

organism: Enterococcus faecium


title: Sample21_Leigh_NT

data_processing:
Genotyping calls were made with GenomeStudio (Illumina, Inc.) via the cluster files provided by the manufacturer. The GenCall (v. 6.3.0) threshold was set to 0.15, and the call rates were greater than 0.998. Reproducibility and heritability were calculated in GenomeStudio (Illumina, Inc.). CNVs were identified using the cnvPartition Plug-in v 3.2.0 in GenomeStudio (Illumina, Inc.). The cnvPartition confidence threshold was set at 100, with a minimum number of SNPs per CNV region of 10. All CNVs were visually verified by assessing both the B-allele-frequency and Log R ratios.
Name is the SNP ID, Chr (Chromosome), Position (location on Chr), Genotype: AA,AB,BB,or NC (No Call), Score, Thera, R, B Allele, Log R Ratio

label: C-Bio and A-DNP

extract_protocol: All DNA was isolated (QIAGEN Gentra Puregene Cell Kit) except the sperm sample (PicoPure DNA Extraction Kit, Life Technologies, Inc.), and quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) according to the manufacturer’s protocol.

treatment_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Genetically matched iPSCs were generated by transductions of the same HDF culture with  retroviral or Sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols  (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).

value: Human Pluripotent Stem Cell from Patient with Leigh Syndrome


title: Sample20_Leigh_iPS3


title: UW6765


title: BIP_D0

source_name: untreated


title: BIP_D6


title: Sample18_Leigh_HDF

value: Fibroblast from Patient with Leigh Syndrome

value: Tissue


title: VRE-106


title: Sample16_iPSS4


title: 229710


title: Sample17_iPSS5


title: HPH3


title: UW6880


title: UW6847


title: E4076


title: Sample11_HDF


title: Sample14_Leigh_iPS2


title: Sample13_Sperm

source_name: Donor Sperm

value: Sperm

value: Donor Sperm


title: E1626

source_name: Peritoneal fluid

value: STX


title: Sample19_Leigh_iPS1


title: U0262

value: Bacteria, Firmicutes, Bacilli, Lactobacillales, Enterococcacea


title: U0367


title: VRE-84

source_name: Ventricle aspirate


title: E1644


title: Sample10_iPS-S2


title: E2603


title: Sample9_iPS-S1


title: Sample15_iPSS3


title: Oocyte

description: Oocyte

source_name: Donor Oocyte

value: Oocyte

value: Donor Oocyte


title: Sample7_iPS-R1

value: Human Pluripotent Stem Cell


title: VRE-10


title: U0106


title: Sample5_hESO7


title: Sample6_hESO8


title: Sample4_NT4


title: Sample3_NT3


title: NIZP292/02

source_name: Wound


title: O2T878


title: Sample1_NT1


title: Sample2_NT2


title: Sample8_iPS-R2

value: Retro-Virus Derived


title: E1463


title: U0218


title: UW6900


title: TUH 2-18


title: Vin2_SC7/ Con2_SC8

status: Public on Jul 07 2014

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Vinclozolin sample 2 verses control sample 2 is compared to vinclozolin sample 3 verses control sample 3

hyb_protocol: Roche Nimblegen’s Rat DNA Methylation 3×720 K CpG Island Plus RefSeq Promoter Array was used, which contains three identical sub-arrays, with 713,670 probes per sub-array, scanning a total of 15,287 promoters (3,880 bp upstream and 970 bp downstream from transcription start site). Probe sizes range from 50–75 mer in length with the median probe spacing of 100 bp. Three different comparative (amplified MeDIP vs. amplified MeDIP) hybridizations experiments included in three sub-arrays were performed by Nimblegen. Each comparative hybridization experiment contained one biological replicate of Sertoli cell Whole Genome Amplified-MeDIP-DNA sample from each lineage-treatment.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For each comparative hybridization experiment, raw data from both the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), checked for quality and converted to MA values (M = Cy5-Cy3; A = (Cy5+Cy3)/2). The following normalization procedure was conducted: within each array, probes were separated into groups by GC content and each group was separately normalized, between Cy3 and Cy5 using the loess normalization procedure. This allowed for GC groups to receive a normalization curve specific to that group. After each array had its CG groups normalized within the array, the arrays were then normalized across arrays using the A quantile normalization procedure. Following normalization each probe within each array was normalized and M values were replaced with the median value of all probe normalized M values across all arrays within a 600 bp window. If the number of probes present in the window was less than 3, no value was assigned to that probe. Each probe’s A values were likewise normalized using the same procedure. Following normalization each probe’s M value represents the median intensity difference between vinclozolin generation and control generation of a 600 bp window. Significance (p<10−5) was assigned to probe differences between treatment-generation samples and control generation samples by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the normalized M. A Z-score and P-value were computed for each probe from that distribution. The statistical analysis was performed in pairs of comparative IP hybridizations between treatment-lineage (T) and control-lineage (C). T1-C1 and T2-C2 gave 715 sites; T1-C1 and T3-C3 gave 633 sites; T2-C2 and T3-C3 gave 807 sites. In order to assure the reproducibility of the candidates obtained, only the candidates showing significant changes in all three of the paired comparisons were chosen as having a significant change in DNA methylation between the experimental group and controls. This is a very stringent approach to select for changes, since it only considers those changes repeated in all paired analyses. Clustered Regions of interest were then determined by combining consecutive probes within 600 bases of each other, and based on whether their mean M values were positive or negative, with significance p-values less than 10−5. The statistically significant differential DNA methylated regions were identified and p-value associated with each region presented. Each region of interest was then annotated for gene and CpG content. This list was further reduced to those regions with an average intensity value exceeding 9.5 (log scale) and a CpG density ≥1 CpG/100 bp. The web-based tool FIMO (Found Individual Motifs Occurrences) was used for determining the incidence of motifs in sets of sequences
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study. Value Definitions for processed data files: #ClusterID = ID and chromosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control), #Chromosome = Chromosome number, #cSTART = Cluster start site, #cSTOP = Cluster stop site, #meanM = mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group, #meanA = mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group, #minP = p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files.  P-value must be p<1.0E-5 or less for inclusion, #nProbes = number of consecutive probes with p<1.0E-5 included in cluster, #GC = GC content of cluster, #CpG = CpG content of cluster, and #CpGdensity = number of CpGs per hundred base pairs.

organism: Rattus norvegicus

source_name: MeDIP ChIP DNA from F3 vinclozolin sertoli cell DNA

label_protocol: MeDIP DNA samples from experimental groups were labeled with Cy5 and MeDIP DNA samples from the control groups were labeled with Cy3

growth_protocol: The F0 generation gestating female Sprague-Dawley rats were exposed to vinclozolin (100 mg/kg/day) during days 8–14 (E8–14) of fetal development. The F1 generation progeny were bred to obtain the F2 generation and the F2 bred to obtain the F3 generation. No sibling or cousin breeding was used in order to avoid any inbreeding artifacts. Corresponding control (vehicle DMSO) lineage F1, F2 and F3 generations were obtained to compare to the vinclozolin lineage males. Some of the direct exposure F1 generation and transgenerational F3 generation control and vinclozolin lineage males were aged to 1 year and testes collected.

extract_protocol: Sertoli cells were isolated from the testes of 20-day-old rats (P20) using a sequential enzymatic digestion procedure. This pubertal period allows the optimum purity cells prior to disease onset. Three pools of P20 Sertoli cells were produced per treatment, with each pool containing cells from 2 to 6 animals. In brief, decapsulated testes were minced with razor blades and then tissue fragments were digested with trypsin (1.5 mg/ml, Life Technologies, Gaithersburg, MD) to remove the interstitial cells. This was followed by incubation with collagenase (1 mg/ml type I, Sigma) for removal of peritubular cells and then hyaluronidase (1 mg/ml, Sigma) for removal of germ cells. The purity of the Sertoli cell preparations were determined by immunohistochemistry to be >98%. Final Sertoli cell pellets were then resuspended in 1 ml Trizol™ (Invitrogen) for further RNA and DNA extractions. DNA was isolated using the Trizol™ (Invitrogen) method as per the manufacturer protocol, from the same Sertoli cell Trizol™ preparations that were used for RNA isolations. Therefore, three independent DNA Trizol™ fractions from Sertoli cells per group were used to obtain three different biological replicates of DNA samples from each of the two treatment groups. Each of these DNA samples were then used for methylated DNA immunoprecipitation (MeDIP). MeDIP was performed as follows: 6 mg of genomic DNA was subjected to a series of three 20 pulse sonications at 20% amplitude. The appropriate fragment size (200–1000 ng) was verified through 2% agarose gels. The sonicated genomic DNA was resuspended in 350 ul TE and denaturated for 10 min at 95°C and then immediately placed on ice for 5 min; 100 ul of 5X IP buffer (50 mM Na-phosphate pH7, 700 mM NaCl, 0.25% Triton X-100) was added to the sonicated and denatured DNA. An overnight incubation of the DNA was performed with 5 ug of antibody anti-5-methylCytidine monoclonal from Diagenode S.A (Denville, NJ) at 4°C on a rotating platform. Protein A/G beads from Santa Cruz (Santa Cruz, CA) were prewashed on PBS-BSA 0.1% and resuspended in 40 ul 1X IP buffer. Beads were then added to the DNA-antibody complex and incubated 2 h at 4°C on a rotating platform. Beads bound to DNA-antibody complex were washed 3 times with 1 ml 1X IP buffer; washes included incubation for 5 min at 4°C on a rotating platform and then centrifugation at 6000 rpm for 2 min. Beads-DNA-antibody complex were then resuspended in 250 ul digestion buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 0.5% SDS) and 3.5 ul of proteinase K (20 mg/ml) was added to each sample and then incubated overnight at 55°C on a rotating platform. DNA purification was performed first with phenol and then with chloroform:isoamyl alcohol. Two washes were then performed with 70% ethanol, 1 M NaCl and glycogen. MeDIP selected DNA was then resuspended in 30 ul TE buffer. Whole-genome amplification was then performed with the WGA2 kit (Sigma-Aldrich) on each MeDIP sample to be used in the microarray comparative hybridization analysis.

treatment_protocol: Vinclozolin

tag: generation

value: Sprague-Dawley

source_name: MeDIP ChIP DNA from F3 control sertoli cell DNA

treatment_protocol: Control


title: Vin3_SC3/ Con3_SC4

description: Vinclozolin sample 1 verses control sample 1 is compared vinclozolin sample 3 verses control sample 3


title: U0229

source_name: Blood


title: Vin1_SC6/ Con1_SC2

description: Vinclozolin sample 1 verses control sample 1 is compared vinclozolin sample 2 verses control sample 2


title: Flavopiridol treated HeLa cells

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

description:
Gene expression data from Flavopiridol treated HeLa cells
Flavopirodol

hyb_protocol: The RNA prepared was hybridized and stained onto the Human Genome U133 Plus 2.0 array (Affymetrix Inc.) using the GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc.).

scan_protocol: Signals were detected using the GeneChip® Scanner 3000G (Affymetrix Inc.).

data_processing: The data was analyzed with a bioconductor package 'affy'.  No global normalization was peformed for this study.

source_name: Flavopiridol treated HeLa cells

label_protocol: RNA was prepared for microarray expression analysis by the GeneChip® 3’ IVT Expression Kit (Affymetrix Inc.) according to the manufacturer’s instructions.

growth_protocol: HeLa cells were plated in a 6-cm culture dish at a density of 1 × 105 cells per dish.

extract_protocol: Total RNA extraction using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: Cells were incubated with FIT-039 or flavopiridol at 4 M or 800 nM, respectively.

value: HeLa cell

tag: agent

value: Flavopiridol


title: vehicle treated HeLa cells

description:
Gene expression data from vehicle treated HeLa cells
DMSO

source_name: vehicle treated HeLa cells

value: vehicle


title: HNSCC sample patient 070

city: Jackson

first: Sharon

last: Lobert

state: MS

address: 2500 N. State St.

department: School of Nursing

institute: University of Mississippi Medical Center

description:
Gene expression data from HNSCC patient 070
070T

hyb_protocol: RNA samples were processed per manufacturers’ protocols using Ambion® Whole-Transcript (WT) Expression kit, and Affymetrix® GeneChip WT Terminal Labeling and Controls Reagent kit on Affymetrix equipment (Scanner 3000 7G System). Hybridized chips were automatically washed, stained and scanned at the UMMC Institutional Molecular and Genomics Core.

data_processing:
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-1_0-st-v1
program-name = Expression Console

source_name: HNSCC

extract_protocol:
The tissues were placed in RNAlater® (Qiagen, Valencia, CA) immediately after surgical removal. Eighty-two paired normal and tumor tissue samples were obtained prior to treatment (164 samples total).  The normal tissue sample was taken at the same time as the tumor sample but from a site distant to the tumor. Of these, 33 pairs met our criteria for RNA quality: concentration sufficient for qRT-PCR analysis, A260/280 > 1.8 and RIN > 6.0.  The RNA Integrity Number (RIN) limit was set empirically from Agilent Lab Chip electropherograms of tissue sample RNA.  Although other individual samples in the pool of 164 samples met our criteria, we only included samples where both the normal and tumor sample were acceptable.
RNA was isolated from 15 paired normal and HNSCC tumor tissues (a subset of the total 33 paired tissues) and evaluated for quality and integrity (Bio-Rad Experion™ System) as done previously (Westbrook et. al., 2014). Whole genome transcript analysis was performed using Affymetrix 3000 7G System platform using Human GeneChip 1.0ST arrays. The Human GeneChip 1.0ST covers >30,000 coding transcripts, along with a small number of lincRNA transcripts.

tag: patient

tag: scca site

value: Right piriform sinus

tag: Stage

tag: hpv status

value: pos

tag: age

tag: tissue

value: HNSCC

tag: patient 2 yr disease free survival outcome

value: no


title: HNSCC sample patient 077

description:
Gene expression data from HNSCC patient 077
077T

scan_protocol: Hybridized chips were automatically washed, stained and scanned at the UMMC Institutional Molecular and Genomics Core.

label_protocol: Affymetrix® GeneChip WT Terminal Labeling and Controls Reagent kit

value: Supraglottic

value: neg


title: Normal tissue distant to HNSCC, patient 072

description:
Gene expression data from normal tissue patient 072
072N

source_name: Normal tissue distant to HNSCC

value: Normal tissue distant to HNSCC


title: HNSCC sample patient 072

description:
Gene expression data from HNSCC patient 072
072T


title: Normal tissue distant to HNSCC, patient 057

description:
Gene expression data from normal tissue patient 057
057N

value: Left tongue base


title: HNSCC sample patient 075

description:
Gene expression data from HNSCC patient 075
075T

value: Glottis

value: unknown


title: Normal tissue distant to HNSCC, patient 076

description:
Gene expression data from normal tissue patient 076
076N

value: yes


title: Normal tissue distant to HNSCC, patient 077

description:
Gene expression data from normal tissue patient 077
077N


title: HNSCC sample patient 076

description:
Gene expression data from HNSCC patient 076
076T


title: HNSCC sample patient 057

description:
Gene expression data from HNSCC patient 057
057T


title: Normal tissue distant to HNSCC, patient 066

description:
Gene expression data from normal tissue patient 066
066N


title: Normal tissue distant to HNSCC, patient 070

description:
Gene expression data from normal tissue patient 070
070N


title: Normal tissue distant to HNSCC, patient 043

description:
Gene expression data from normal tissue patient 043
043N

value: Left AE fold


title: FIT-039 treated HeLa cells

description:
Gene expression data from FIT-039 treated HeLa cells
FIT-039

source_name: FIT-039 treated HeLa cells


title: HNSCC sample patient 054

description:
Gene expression data from HNSCC patient 054
054T

value: Left piriform sinus


title: HNSCC sample patient 021

description:
Gene expression data from HNSCC patient 021
021T


title: HNSCC sample patient 043

description:
Gene expression data from HNSCC patient 043
043T


title: Normal tissue distant to HNSCC, patient 075

description:
Gene expression data from normal tissue patient 075
075N


title: Normal tissue distant to HNSCC, patient 033

description:
Gene expression data from normal tissue patient 033
033N

value: Right AE fold


title: Normal tissue distant to HNSCC, patient 054

description:
Gene expression data from normal tissue patient 054
054N


title: HNSCC sample patient 018

description:
Gene expression data from HNSCC patient 018
018T


title: Normal tissue distant to HNSCC, patient 021

description:
Gene expression data from normal tissue patient 021
021N


title: HNSCC sample patient 033

description:
Gene expression data from HNSCC patient 033
033T


title: HNSCC sample patient 066

description:
Gene expression data from HNSCC patient 066
066T


title: Normal tissue distant to HNSCC, patient 018

description:
Gene expression data from normal tissue patient 018
018N


title: HNSCC sample patient 017

description:
Gene expression data from HNSCC patient 017
017T


title: Normal tissue distant to HNSCC, patient 017

description:
Gene expression data from normal tissue patient 017
017N


title: HNSCC sample patient 007

description:
Gene expression data from HNSCC patient 007
007T

value: Left soft palate


title: HNSCC sample patient 014

description:
Gene expression data from HNSCC patient 014
014T

value: Tongue base


title: Normal tissue distant to HNSCC, patient 014

description:
Gene expression data from normal tissue patient 014
014N


title: DN-Clim Luminal Cells (CD29hiCD24+), biological rep2

city: Irvine

middle: L

last: Salmans

address: 250 Sprague Hall

institute: University of California Irvine

description: Gene expression data from sorted DN-Clim luminal (CD29loCD24+Lin-) cells of 10 week old mouse

hyb_protocol: cRNA was hybridized on MouseGene 1.0ST array according to Affymetrix protocol in Affymetrix GeneChip Hybridization Oven 640 and washed and stained in GeneChip Fluidics Station 450

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

data_processing: The data were analyzed with the PLIER algorithm using Affymetrix default analysis settings.

source_name: Mouse mammary gland luminal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Mice were grown according to regulatory guidelines approved by the International Animal Care and Use Committee of the University of California Irvine

extract_protocol: For laser capture microdissected samples: Qiagen RNeasy Mini; for sorted cells: Direct-zol RNA MiniPrep (Zymo Research)

treatment_protocol: For laser capture microdissection, mammary glands were frozen embedded in OCT, sectioned at 8 microns, and H&E stained prior to microdissection. For sorted cells, single cell isolations of mammary glands were generated and labeled with CD24, C29, and lineage markers (CD31, CD45, and TER119) prior to sorting.

value: Mammary gland luminal cells

tag: genotype

value: DN-Clim

value: 10 weeks

tag: genetic background


title: WT Luminal Cells (CD29hiCD24+), biological rep1

description: Gene expression data from sorted WT luminal (CD29loCD24+Lin-) cells of 10 week old mouse

value: Wild type


title: WT Basal Cells (CD29hiCD24+), biological rep1

description: Gene expression data from sorted WT basal (CD29hiCD24+Lin-) cells of 10 week old mouse

source_name: Mouse mammary gland basal cells

value: Mammary gland basal cells


title: DN-Clim Duct at 8 weeks, biological rep3

description: Gene expression data from laser capture microdissected DN-Clim mammary gland ducts of 8 week old mouse

source_name: Mouse mammary gland at late puberty

value: Mammary gland duct

value: 8 weeks


title: DN-Clim Basal Cells (CD29hiCD24+), biological rep2

description: Gene expression data from sorted DN-Clim basal (CD29hiCD24+Lin-) cells of 10 week old mouse


title: DN-Clim Duct at 10 weeks, biological rep2

description: Gene expression data from laser capture microdissected DN-Clim mammary gland ducts of 10 week old mouse

source_name: Mouse mammary gland at early adulthood


title: DN-Clim Luminal Cells (CD29hiCD24+), biological rep1


title: WT Basal Cells (CD29hiCD24+), biological rep2


title: DN-Clim Duct at 10 weeks, biological rep3


title: Normal tissue distant to HNSCC, patient 007

description:
Gene expression data from normal tissue patient 007
007N

value: neg

value: Normal tissue distant to HNSCC

value: no


title: WT Luminal Cells (CD29hiCD24+), biological rep2


title: DN-Clim TEB at 10 weeks, biological rep2

description: Gene expression data from laser capture microdissected DN-Clim mammary gland TEBs of 10 week old mouse

value: Mammary gland TEB


title: DN-Clim Duct at 6 weeks, biological rep2

description: Gene expression data from laser capture microdissected DN-Clim mammary gland ducts of 6 week old mouse

source_name: Mouse mammary gland at mid puberty

value: 6 weeks


title: DN-Clim TEB at 8 weeks, biological rep1

description: Gene expression data from laser capture microdissected DN-Clim mammary gland TEBs of 8 week old mouse


title: DN-Clim TEB at 10 weeks, biological rep1


title: DN-Clim Duct at 8 weeks, biological rep1


title: DN-Clim TEB at 8 weeks, biological rep3


title: DN-Clim TEB at 6 weeks, biological rep2

description: Gene expression data from laser capture microdissected DN-Clim mammary gland TEBs of 6 week old mouse


title: DN-Clim Basal Cells (CD29hiCD24+), biological rep1


title: DN-Clim TEB at 10 weeks, biological rep3


title: DN-Clim Duct at 10 weeks, biological rep1


title: DN-Clim TEB at 8 weeks, biological rep2


title: DN-Clim TEB at 4 weeks, biological rep3

description: Gene expression data from laser capture microdissected DN-Clim mammary gland TEBs of 4 week old mouse

source_name: Mouse mammary gland at early puberty

value: 4 weeks


title: DN-Clim TEB at 4 weeks, biological rep1


title: DN-Clim Duct at 8 weeks, biological rep2


title: DN-Clim TEB at 6 weeks, biological rep1


title: DN-Clim Duct at 4 weeks, biological rep2

description: Gene expression data from laser capture microdissected DN-Clim mammary gland ducts of 4 week old mouse


title: DN-Clim TEB at 4 weeks, biological rep2


title: DN-Clim Duct at 4 weeks, biological rep3


title: DN-Clim Duct at 6 weeks, biological rep1


title: WT TEB at 10 weeks, biological rep2

description: Gene expression data from laser capture microdissected WT mammary gland TEBs of 10 week old mouse


title: WT TEB at 10 weeks, biological rep1


title: DN-Clim Duct at 4 weeks, biological rep1


title: WT Duct at 8 weeks, biological rep2

description: Gene expression data from laser capture microdissected WT mammary gland TEBs of 8 week old mouse


title: WT Duct at 10 weeks, biological rep2


title: WT Duct at 8 weeks, biological rep1

description: Gene expression data from laser capture microdissected WT mammary gland ducts of 8 week old mouse


title: WT TEB at 8 weeks, biological rep2


title: WT Duct at 10 weeks, biological rep1

description: Gene expression data from laser capture microdissected WT mammary gland ducts of 10 week old mouse


title: WT TEB at 6 weeks, biological rep3

description: Gene expression data from laser capture microdissected WT mammary gland TEBs of 6 week old mouse


title: WT TEB at 6 weeks, biological rep2


title: WT TEB at 4 weeks, biological rep3

description: Gene expression data from laser capture microdissected WT mammary gland TEBs of 4 week old mouse


title: WT TEB at 6 weeks, biological rep1


title: WT Duct at 6 weeks, biological rep1

description: Gene expression data from laser capture microdissected WT mammary gland ducts of 6 week old mouse


title: WT Duct at 6 weeks, biological rep3


title: WT TEB at 4 weeks, biological rep1


title: WT TEB at 4 weeks, biological rep2


title: H37RvΔphoPR::phoPR-TB / H37RvΔphoPR::phoPR-bovis

city: Paris

first: Alexandre

last: Pawlik

address: 28 rue du Dr. Roux

institute: Institut Pasteur

description: data table include data for 4 replicates (merge dye-swap)

hyb_protocol: The hybridization procedure has been done according to the manufacturer (Agilent).

scan_protocol: Fluorescent signals were acquired with a Genepix 4200AL microarray scanner (Axon Instruments) with 5 microns per pixel resolution. The PMT gain for the 635 and 532nm wavelengths were automatically set with control yellow hybridizations (sample hybridized versus itself). The quantification of the signal for each spot was performed with the image analysis GenePix Pro 6.0 software (Axon Instruments).

data_processing: All the data generated by the scan were imported into the statistical data analysis system R. The data were globally normalized using the Lowess regression approach. Data were then converted to relative ratio of fold activation changes. Differential analysis was conducted using the limma package. To ensure the robustness of the results, the resulting raw P values were adjusted according to the Benjamini and Hochberg method and a cutoff of significance was set to 0.05.

organism: Mycobacterium tuberculosis

label_protocol: Labeled cDNA obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen).

growth_protocol: Strains were cultured aerobically using Middlebrook 7H9 liquid medium containing 10% ADC and 0.05 % Tween 80. When necessary, media were supplemented with 50µg.ml-1 hygromycin and 40µg.ml-1 kanamycin.

extract_protocol: Total RNA was extracted from cultures harvested during the exponential phase of growth (OD at 600nm between 0.6 and 0.7). To minimize RNA degradation, cells were resuspended in 1 ml RNA protect reagent (Qiagen) after centrifugation and incubated for 5 min at room temperature before to be again centrifuged. The cells resuspended in a lysis buffer and phenol:chloroform were lysed using glass beads (Qbiogene) and a ribolyser (Fast-prep instrument). After extraction, precipitation, rinsing and resuspension in RNase-free water, the RNA samples were treated with DNase (TURBO DNA-free Kit, Ambion). The RNA concentrations were measured with a Nanodrop ND-1000 spectrophotometer. The RNA integrity/quality was monitored with a Bioanalyzer RNA nano assay.

treatment_protocol: No treatment

tag: strain

tag: variant


title: H37RvΔphoPR::phoPR-TB / H37RvΔphoPR

value: ΔphoPR


title: H37RvΔphoPR::phoPR-bovis / H37RvΔphoPR


title: WT Duct at 4 weeks, biological rep3

description: Gene expression data from laser capture microdissected WT mammary gland ducts of 4 week old mouse


title: WT Duct at 6 weeks, biological rep2


title: WT TEB at 8 weeks, biological rep1


title: H37RvΔphoPR / H37Rvwt

value: wt


title: GC1237ΔphoPR::phoPR-TB / GC1237ΔphoPR::phoPR-bovis


title: GC1237ΔphoPR::phoPR-bovis / GC1237ΔphoPR


title: WT Duct at 4 weeks, biological rep1


title: GC1237ΔphoPR::phoPR-TB / GC1237ΔphoPR


title: GC1237ΔphoPR / GC1237wt


title: NN control, biological rep3

city: Nanjing

first: Yongli

last: Wang

address: Weigang No.1

department: Agricultural college

institute: Nanjing Agricultural University

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

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

organism: Glycine max

source_name: NN soybean leaves from insect non-induced plants

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

growth_protocol: Seeds of Wanxianbaidongdou and Nannong99-10 soybean lines were sown in 15 cm plastic pots that contained a sterile soil mixture (top soil:sand:vermiculite, 3:2:1). The seedlings were grown in a greenhouse maintained at 30 ± 5°C, 70 ± 10% RH, and a 14 h/10 h (day/night) photoperiod with supplementary metal-halide illumination.

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

treatment_protocol: Treatments of cotton worm (obtained from a colony maintained on an artificial diet) feeding and untreated (control) plants were applied to soybean plants at the V4 (vegetative stage with four nodes) stage of growth. Defoliation (about 20–30%) was induced by placing three third or four instar cotton worm larvaes on the first and second trifoliate leaf for 48 hours, after which the larvae were removed.

value: trifoliate leaf

value: vegetative stage with four nodes


title: NN control, biological rep2


title: Control_rep3

city: Guelph

first: Brenda

last: Coomber

state: Ontario

address: 50 Stone Road

department: Department of Biomedical Sciences

country: Canada

institute: University of Guelph

hyb_protocol: As per Affymetrix Instructions

scan_protocol: As per Affymetrix Instructions

data_processing: Cel Files imported into Partek Genomics Suite, RMA prenormalization.

source_name: HCCT116 cell line, Control

label_protocol: As per Affymetrix Instructions

growth_protocol: Human colorectal cancer cells, HCT116  were cultured in DMEM + 10% fetal bovine serum + 50 μg/ml gentamicin+ 1mM sodium pyruvate at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA was isolated using TRIPure according to manufacturer’s instructions.

treatment_protocol: Control:  No treatment.  Low Oxygen:  As above, except with 5% CO2, 95% N2.  Low Glucose: As above, except with Glucose/pyruvate free media.

tag: condition

value: untreated


title: NN control, biological rep1


title: Low_Oxygen_rep2

source_name: HCCT116 cell line, Low Oxygen

value: low oxygen


title: NN insect treated, biological rep3

source_name: NN soybean leaves from insect induced plants