title: GM0637 at T8

description: Gene expression data from MCFs after DNA damage

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

source_name: GM0637 Fibroblast

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The GM0637 cells were plated on multiple 100-mm dishes for each line in 10% fetal calf serum and Dulbecco's modified Eagle's medium (DMEM) in 37℃ with 5% CO2.

treatment_protocol: GM0637 cells were treated with or without DNA damaging reagent neocarzinostatin (NCS),  a radiomimetic drug that generates DSBs. Cells were harvested at varying time points (0-8 h).

value: Human Fibroblast


title: Atm-/- MEFs at T0

status: Public on Jan 17 2013

type: RNA

city: Houston

first: Guohui

last: Wan

state: TX

address: 7777 Knight Road

department: Cancer Biology

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

description: Gene expression data from MEFs after DNA damage

hyb_protocol: Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. 1 ug of each labeled cRNA was  fragmented by adding 11 ul 10 x Blocking Agent and 2.2 ul of 25 x Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 ul 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 100 ul of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 3 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic fibroblast

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from 1 ug total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The MEFs were plated on multiple 100-mm dishes for each line in 15% fetal calf serum and Dulbecco's modified Eagle's medium (DMEM) in 37? with 5% CO2.

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

treatment_protocol: The MEFs were treated with or without DNA damaging reagent neocarzinostatin (NCS),  a radiomimetic drug that generates DSBs. Cells were harvested at varying time points (0-24h).

tag: tissue

value: Mouse embryonic fibroblast

tag: genotype

value: Atm-/-

tag: treatment


title: Deletion hippocampus DEL_HPC_1011MK0069-20110510

city: New York

first: Bin

last: XU

state: NY

address: 1051 Riverside Drive

institute: columbia university

hyb_protocol: According to Affymetrix Standard Protocols

data_processing: The CEL files were analyzed using Bioconductor of R project. The raw intensity data of all PFC samples or HPC samples were first RMA normalized and log2 transformed. differential expression analysis was conducted using limma package.

label: biotin

growth_protocol: Adult male mice were collected

extract_protocol: Total RNA were extracted and purified with the miRNeasy Mini-kit (Qiagen).

value: 22q11.2 microdeletion

value: hippocampus

tag: age

value: adult


title: Δmec1 Δsml1 30 min S phase DNA profile Replicate 2

type: genomic

city: Seattle

first: Jairo

last: Rodriguez

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: According to Nimblegen suggested protocol

data_processing: Raw data was processed using NimbleScan software from Nimblegen. Processed data for each sample are reported as the bi-weight adjusted mean of the log(2) Cy5/Cy3 ratio.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Genomic DNA from Δmec1 Δsml1 cells by 30 min in S phase

label_protocol: 3 µg of DNA were used for a dUTP incorporation reaction with klenow Exo-, random hexamers and a dNTP mix containing 5% dUTP. Unincorporated hexamers and dNTPS were eliminated running the samples through Biospin 30 columns. Samples were cleaned up by phenol/chloroform extraction and ethanol precipitation. The recovered DNA was then subject to fragmentation by UDG and APE1. 4 µg of the fragmented DNA were labeled with either Cy5 (test sample) or Cy3 (Input) with Terminal transferase. Unincorporated Cyes were eliminated by running the samples through Biospin 30 columns. Equal amounts of Cy5 and Cy3 labeled DNA were hybridized.

growth_protocol: Cells were grown in rich media to O.D.660 0.25, then arrested in G1 with α-factor. Cells were synchronously released from α-factor induced G1 arrest into S phase by filtration, and harvested 30 minutes after release.

extract_protocol: Genomic DNA (gDNA) was purified using 20G columns (Qiagen) according to manufacturer's instructions. gDNA was fragmented to an average size of 150-200 bp with DNAseI and purified by Phenol/Chloroform extraction and ethanol precipitation.

treatment_protocol: Cells were released into rich media at 24°C

tag: strain/genotype

value: Δmec1 Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

tag: antibody

value: None, input DNA

source_name: Input DNA from Δmec1 Δsml1 cells arrested in G1

growth_protocol: Cells were grown in rich media to O.D.660 0.25, then arrested in G1 with α-factor. Cells were harvested during G1 arrest.

value: none, input DNA


title: Δmec1 Δsml1 30 min S phase H3 ChIP Replicate 2

scan_protocol: According to Nimblegen suggested protocol

source_name: H3 ChIP from Δmec1 Δsml1 cells by 30 min in S phase

extract_protocol: Genomic DNA from ChIP samples was purified using PCR purification columns (Qiagen) according to manufacturer's protocol. Samples were then amplified using an LM-PCR strategy.

value: H3 C-terminal domain

source_name: Input DNA from Δmec1 Δsml1 cells by 30 min in S phase


title: Δmec1 Δsml1 G1 H3 ChIP no HU Replicate 2

source_name: H3 ChIP from Δmec1 Δsml1 cells arrested in G1

source_name: Input DNA from Δmec1 Δsml1 G1 arrested cells


title: Δmec1 Δsml1 30 min S phase mononucleosome signal Replicate 2

source_name: Mononucleosome signal from Δmec1 Δsml1 cells by 30 min in S phase

extract_protocol: Genomic DNA from MNase treated cells was recovered by G500 tip purification (Qiagen) according to manufacturer's instructions. Mononucleosome-sized DNA was excised from agarose gels and DNA was recovered by electroelution and ethanol precipitation.

tag: experiment type

value: in vivo MNase digested chromatin


title: Δmec1 Δsml1 30 min S phase Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from Δmec1 Δsml1 cells by 30 min in S phase

value: FLAG


title: Δmec1 Δsml1 G1 mononucleosome signal no HU Replicate 2

source_name: Mononucleosome signal from Δmec1 Δsml1 cells arrested in G1


title: Epcam patient A

city: Barcelona

first: Alexandre

last: CALON

address: Dr. Aiguader, 88

country: Spain

institute: Hospital del Mar Medical Research Institute (IMIM)

description: expression data from epithelial cells

hyb_protocol: Affymetrix HG-U133  +PM arrays were hybridized with 8 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: We used RMA background correction, quantile normalization and RMA summarization(Gautier et al., 2004).

organism: Homo sapiens

source_name: patient A

label_protocol: RNA was labeled (biotin) using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

extract_protocol: RNA was processed and amplified as previously described(Gonzalez-Roca et al., 2010).

tag: individual

value: patient A

tag: marker

value: Epcam

tag: disease state

value: human CRC

tag: cell population

value: epithelial cells


title: Deletion pre-frontal cortex DEL_pfc_1011MK0076-20110510

scan_protocol: According to Affymetrix Standard Protocols

value: pre-frontal cortex


title: Reference hippocampus REF_HPC_1011MK0066-20110510

label_protocol: According to Affymetrix Standard Protocols

value: heterozygous balanced copy number


title: FAP patient A

description: expression data from fibroblasts

value: FAP

value: fibroblasts


title: Deletion hippocampus DEL_HPC_1011MK0065-20110510

value: 22q11.2 microdeletion


title: Deletion hippocampus DEL_HPC_1011MK0064-20110510

value: hippocampus


title: Reference hippocampus REF_HPC_1011MK0063-20110510

value: adult


title: GM0637 at T4

value: Human Fibroblast

tag: cell line

value: DNA damaging agent neocarzinostatin (NCS)


title: GM0637 at T0


title: Atm+/+ MEFs at T4

value: Mouse embryonic fibroblast

value: Atm+/+


title: Atm+/+ MEFs at T8


title: Atm+/+ MEFs at T0


title: Reference hippocampus REF_HPC_1011MK0058-20110510


title: Δmec1 Δsml1 G1 H3 ChIP no HU Replicate 1

value: Δmec1 Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

value: H3 C-terminal domain

value: none, input DNA


title: Atm+/+ MEFs at T24


title: Reference hippocampus REF_HPC_1011MK0059-20110510


title: Duplication pre-frontal cortex DUP_pfc_1011MK0074-20110510

value: 22q11.2 microduplication


title: Duplication hippocampus DUP_HPC_1011MK0062-20110510


title: Deletion hippocampus DEL_HPC_1011MK0061-20110510


title: Δmec1 Δsml1 30 min S phase H3 ChIP Replicate 1


title: Δmec1 Δsml1 30 min S phase mononucleosome signal Replicate 1

value: in vivo MNase digested chromatin


title: Δmec1 Δsml1 30 min S phase Pol1-3FLAG ChIP Replicate 1

value: FLAG


title: Δmec1 Δsml1 G1 mononucleosome signal no HU Replicate 1


title: Purkinje cells animal2-2

city: Uruma

first: Nozomu

middle: H

last: Nakamura

state: Okinawa

address: 12-22 Suzaki

department: Molecular Neuroscience Unit

country: Japan

institute: Okinawa Institute of Science and Technology

description: Gene expression data from mouse cerebellar Purkinje cells

hyb_protocol: The samples were hybridized to DNA microarray, according to standard protocols of Affymetrix GeneChip Expression Analysis (Mouse Genome 430 2.0 Array, GeneChip Hybridization, Wash and Stain Kit, Affymetrix).

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

data_processing: A dataset of each sample was analyzed with GeneChip Operating Software (GCOS 1, Affymetrix). The present (P), marginal (M), or absent (A) call for each data point was calculated by the standard algorithm. Each probe set contained 11 probes. Here, we chose 26,351 probe sets, corresponding to 17,197 genes, each of which contained more than nine probes matched to the defined cDNAs having gene symbols in the ENSEMBL or NCBI (reference sequence) database, and used them for further analysis.

source_name: Cerebellum of 8-week-old C57BL/6J male

label_protocol: cDNAs were synthesized from mRNAs in approximately 1 ng of total RNA, amplified and labeled, according to standard protocols of Affymetrix GeneChip Expression Analysis (GeneChip Two-Cycle Target Labeling, Control Reagents, Affymetrix).

growth_protocol: Intact 8-week-old mice were used

extract_protocol: Cells were dissolved in RNA extraction buffer and stored at -80 ºC according to the manufacturer's instructions.

treatment_protocol: Brains were rapidly removed and frozen in liquid nitrogen-chilled isopentane, and then stored at -80 ºC. Brains were sagittally sectioned at 12 μm thickness using cryostat at -20 ºC. Sections were fixed with a mixture of ethanol/acetic acid (19:1) on dry ice and dried out. Cells were cut using laser capture microdissection

tag: strain

tag: gender

value: male

value: Cerebellum

tag: cell type

value: cerebellar Purkinje cells


title: Purkinje cells animal1-2


title: Purkinje cells animal2-1


title: Duplication hippocampus DUP_HPC_1011MK0060-20110510


title: Duplication hippocampus DUP_HPC_1011MK0057-20110510


title: Purkinje cells animal1-1


title: Δmec1 Δsml1 30 min S phase DNA profile Replicate 1

value: None, input DNA


title: Granule cell layer animal1-2

description: Gene expression data from mouse cerebellar granule cell layer

value: cerebellar granule cell layer


title: Duplication hippocampus DUP_HPC_1011MK0056-20110510

value: hippocampus


title: Reference pre-frontal cortex REF_pfc_1011MK0082-20110510

value: heterozygous balanced copy number

value: pre-frontal cortex

value: adult


title: Granule cell layer animal1-1


title: Deletion hippocampus DEL_HPC_1011MK0055-20110510

value: 22q11.2 microdeletion


city: Göteborg

first: Tobias

last: Österlund

address: Kemivägen 10

department: Dept. of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from NC strain_anaerobic conditions_biological rep3

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Images were analyzed using R 2.10.1 software and Bioconductor packages. Briefly, data normalization was carried out using the method of Probe Logarithmic Intensity Error (PLIER) with perfect match probe only (PM-only).

source_name: Saccharomyces cerevisiae strain with no amyalse productions at anaerobic batch fermentations

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: All fermentations were performed in DasGip 1.0-liter stirrer-pro vessels (Drescher Amold Schneider, Germany) with a working volume of 500ml of SD-SCAA media, at 30°C, 600 rpm agitation.

extract_protocol: RNA was isolated using the RNeasy Minikit (Qiagen) and processed to cRNA using the Genechip 3’ IVT Express Kit (Affymetrix) and hybridized/scanned on the Yeast Genome 2.0 Array (Affymetrix) to create CEL files.

treatment_protocol: Samples for microarray analysis were taken at approximatly OD=1, and centrifuged at 4 degree for 3min, depleted supernatant, and stored in liquid nitrogen for short time and stored at -80 °C until processing

value: CEN. PK 530-1C with TPI1 promoter (2 μm POT1)


title: Duplication hippocampus DUP_HPC_1011MK0053-20110510


title: Hypothalamus from HF-fed control rats

city: Villeneuve d'Ascq

first: christophe

last: breton

address: Cité Scientifique

country: France

institute: University of Lille 1

description: Hyp control HF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation with GenomeStudio (Illumina)

organism: Rattus norvegicus

source_name: Rat hypothalamus

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin-aRNA Labeling for Illumina System

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the manufacturer's instructions

value: Wistar

value: 4 months

value: Hypothalamus

tag: diet

value: HF-fed

tag: rats

value: control rats


title: Hypothalamus from HF-fed FR30 rats

description: Hyp FR30 HF

tag: tissue

value: FR30 rats


title: Hypothalamus from control rats

description: Hyp control

value: standard


title: Hypothalamus from FR30 rats

description: Hyp FR30


description: Gene expression data from NC strain_anaerobic conditions_biological rep2

tag: genotype


description: Gene expression data from AAP strain_anaerobic conditions_biological rep3

source_name: Saccharomyces cerevisiae strain with less amyalse productions at anaerobic batch fermentations

value: CEN. PK 530-1C with pTEF1-alpha factor leader amylase (2 μm POT1)


title: Reference hippocampus REF_HPC_1011MK0051-20110510


title: Δsml1 30 min S phase mononucleosome signal Replicate 2

source_name: Mononucleosome signal from Δsml1 cells by 30 min in S phase

value: Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

value: in vivo MNase digested chromatin

source_name: Input DNA from Δsml1 cells by 30 min in S phase

value: none, input DNA


title: Δsml1 G1 H3 ChIP no HU Replicate 2

source_name: H3 ChIP from Δsml1 cells arrested in G1

value: H3 C-terminal domain

source_name: Input DNA from Δsml1 G1 arrested cells


description: Gene expression data from NC strain_anaerobic conditions_biological rep1


description: Gene expression data from AAP strain_anaerobic conditions_biological rep2


title: Δsml1 30 min S phase H3 ChIP Replicate 2

source_name: H3 ChIP from Δsml1 cells by 30 min in S phase


title: Δsml1 G1 mononucleosome signal no HU Replicate 2

source_name: Mononucleosome signal from Δsml1 cells arrested in G1


title: Deletion hippocampus DEL_HPC_1011MK0049-20110510

value: hippocampus


title: WT_rep3

city: University of NSW

first: Alister

last: Funnell

address: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of NSW

hyb_protocol: RNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

scan_protocol: Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.5 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

source_name: E13.5 TER119+ fetal liver wildtype

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: All mice were housed in standard University of NSW facilities, under SPF conditions

extract_protocol: RNA extraction was performed using TRI-Reagent, according to manufacturer’s guidelines (Sigma-Aldrich). RNA samples were further purified using RNeasy columns (Qiagen)

treatment_protocol: TER119+ cells were purified from E13.5 fetal liver using Magnetic Activated Cell Sorting with Anti-TER119 MicroBeads (Miltenyi Biotech) and MS columns as per supplier’s instructions.

tag: developmental stage

value: embryonic day E13.5

value: FVB/NJ

value: fetal liver

value: wildtype


title: Δsml1 30 min S phase DNA profile Replicate 2

source_name: Genomic DNA from Δsml1 cells by 30 min in S phase

value: None, input DNA

source_name: Input DNA from Δsml1 cells arrested in G1


title: Δsml1 30 min S phase H3 ChIP Replicate 1


title: Duplication hippocampus DUP_HPC_1011MK0050-20110510

value: 22q11.2 microduplication

tag: age

value: adult


title: WT_rep4


title: Δsml1 30 min S phase Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from Δsml1 cells by 30 min in S phase

tag: strain/genotype

value: FLAG


description: Gene expression data from AAC strain_anaerobic conditions_biological rep3

source_name: Saccharomyces cerevisiae strain with high amyalse productions at anaerobic batch fermentations

value: CEN. PK 530-1C with pTPI1-alpha factor leader amylase (2 μm POT1)


title: WT_rep2


title: WT_rep1


title: Δsml1 G1 H3 ChIP no HU Replicate 1

tag: antibody


title: Δsml1 30 min S phase mononucleosome signal Replicate 1

tag: experiment type


title: Δsml1 G1 mononucleosome signal no HU Replicate 1


description: Gene expression data from AAC strain_anaerobic conditions_biological rep2


title: Klf8gt_rep3

source_name: E13.5 TER119+ fetal liver Klf8gt/gt


description: Gene expression data from NC strain_aerobic conditions_biological rep3

source_name: Saccharomyces cerevisiae strain with no amyalse productions at aerobic batch fermentations

value: CEN. PK 530-1C with TPI1 promoter (2 μm POT1)


title: wt P6 prefrontal cortex biological replicate 9

data_processing: The CEL files were normalized and analyzed using packages in Bioconductor project. The raw intensity data of all PFC samples or HPC samples were first RMA normalized and log2 transformed. differential expression analysis was conducted using limma package.

source_name: wt_P6_PFC_biological replicate_9

growth_protocol: Embryoic day 17 and postnatal day 6 littermates were collected

value: wt

value: prefrontal cortex

tag: genetic background


title: wt P6 prefrontal cortex biological replicate 11

source_name: wt_P6_PFC_biological replicate_11


description: Gene expression data from AAC strain_anaerobic conditions_biological rep1


title: wt P6 prefrontal cortex biological replicate 10

source_name: wt_P6_PFC_biological replicate_10


description: Gene expression data from NC strain_aerobic conditions_biological rep1


title: Klf8gt_rep1


title: Klf8gt_rep2


title: WT 35 min S phase mononucleosome signal Replicate 2

source_name: Mononucleosome signal from WT cells by 35 min in S phase

growth_protocol: Cells were grown in rich media to O.D.660 0.25, then arrested in G1 with α-factor. Cells were synchronously released from α-factor induced G1 arrest into S phase by filtration, and harvested 35 minutes after release.

value: WT, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

source_name: Input DNA from WT cells by 35 min in S phase


title: wt P6 prefrontal cortex biological replicate 6

source_name: wt_P6_PFC_biological replicate_6


title: Klf3KO_rep3

source_name: E13.5 TER119+ fetal liver Klf3-/-


title: Δsml1 30 min S phase DNA profile Replicate 1

value: Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.


title: WT 35 min S phase DNA profile Replicate 2

source_name: Genomic DNA from WT cells by 35 min in S phase

source_name: Input DNA from WT cells arrested in G1

value: none, input DNA


title: WT G1 mononucleosome signal no HU Replicate 2

source_name: Mononucleosome signal from WT cells arrested in G1

value: in vivo MNase digested chromatin

source_name: Input DNA from WT G1 arrested cells


title: Klf8gt_rep4


title: wt P6 prefrontal cortex biological replicate 7

source_name: wt_P6_PFC_biological replicate_7


title: wt P6 prefrontal cortex biological replicate 8

source_name: wt_P6_PFC_biological replicate_8


title: Δsml1 30 min S phase Pol1-3FLAG ChIP Replicate 1

source_name: Pol1-3FLAG ChIP from Δsml1 cells by 30 min in S phase

source_name: Input DNA from Δsml1 cells by 30 min in S phase


description: Gene expression data from AAP strain_aerobic conditions_biological rep3

source_name: Saccharomyces cerevisiae strain with less amyalse productions at aerobic batch fermentations

value: CEN. PK 530-1C with pTEF1-alpha factor leader amylase (2 μm POT1)


description: Gene expression data from AAP strain_aerobic conditions_biological rep2


title: Klf3KO_rep2

value: embryonic day E13.5


title: WT 30 min S phase mononucleosome signal Replicate 1

source_name: Mononucleosome signal from WT cells by 30 min in S phase

source_name: Input DNA from WT cells by 30 min in S phase


description: Gene expression data from AAP strain_aerobic conditions_biological rep1


description: Gene expression data from AAP strain_anaerobic conditions_biological rep1

source_name: Saccharomyces cerevisiae strain with less amyalse productions at anaerobic batch fermentations


description: Gene expression data from AAC strain_aerobic conditions_biological rep3

source_name: Saccharomyces cerevisiae strain with high amyalse productions at aerobic batch fermentations


title: wt P6 prefrontal cortex biological replicate 5

source_name: wt_P6_PFC_biological replicate_5


title: wt P6 prefrontal cortex biological replicate 2

source_name: wt_P6_PFC_biological replicate_2


title: wt P6 prefrontal cortex biological replicate 1

source_name: wt_P6_PFC_biological replicate_1


title: WT G1 H3 ChIP no HU Replicate 1

source_name: H3 ChIP from WT cells arrested in G1

value: H3 C-terminal domain


title: wt P6 prefrontal cortex biological replicate 4

source_name: wt_P6_PFC_biological replicate_4


title: Deletion hippocampus DEL_HPC_1011MK0052-20110510

value: 22q11.2 microdeletion

value: hippocampus


title: DKO_rep4

source_name: E13.5 TER119+ fetal liver Klf3-/- Klf8gt/gt

value: FVB/NJ

value: fetal liver

value: Klf3-/- Klf8gt/gt


description: Gene expression data from AAC strain_aerobic conditions_biological rep1


title: WT G1 mononucleosome signal no HU Replicate 1

source_name: Mononucleosome signal from WT cells arrested in G1


title: DKO_rep3


title: WT 30 min S phase H3 ChIP Replicate 1

source_name: H3 ChIP from WT cells by 30 min in S phase


title: DKO_rep1


title: Klf3KO_rep1

source_name: E13.5 TER119+ fetal liver Klf3-/-


title: DKO_rep2


title: Df16(A)+/- P6 prefrontal cortex biological replicate 9

source_name: MUT_P6_PFC_biological replicate_9


title: wt P6 prefrontal cortex biological replicate 3

source_name: wt_P6_PFC_biological replicate_3


title: Ovary carcinoma cell line skov3

city: Sungnam

first: Hee

last: An

address: 351 Yatap-dong

department: Pathology

country: South Korea

institute: CHA University

description: Sample name: skov3

data_processing:
Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3  (Gene Expression Module v3.3.8).
We performed version 2 microarray for the test samples (4 samples), whereas the control sample (SKOV3) was used version 1 microarray. The matched probes between version 1 and version 2 were 500 or more, so the probes were filtered by detection p value filtering in the merging process.
Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Nearly half of probes were p> 0.05, therefore, they were excluded  before normalization.  Selected probe signal value was then transformed by logarithm and normalized using quantile normalization with ArrayAssist® 5.5.1 (Stratagene, La Jolla, USA).

source_name: Ovary adenocacinoma

label_protocol: Standard Illumina lavbeling protocol

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

tag: chemo-resistance

value: Paclitaxel-sensitive parental cell line


title: Chemo-resistant subcell line 4 produced from skov3

description: Sample name: skp46

value: Paclitaxel-resistant subcell line


title: Chemo-resistant subcell line 3 produced from skov3

description: Sample name: skp44


description: Gene expression data from AAC strain_aerobic conditions_biological rep2

value: CEN. PK 530-1C with pTPI1-alpha factor leader amylase (2 μm POT1)


title: Df16(A)+/- P6 prefrontal cortex biological replicate 8

source_name: MUT_P6_PFC_biological replicate_8


title: WT 30 min S phase Pol1-3FLAG ChIP Replicate 1

source_name: Pol1-3FLAG ChIP from WT cells by 30 min in S phase

value: FLAG


title: Df16(A)+/- P6 prefrontal cortex biological replicate 7

source_name: MUT_P6_PFC_biological replicate_7

value: prefrontal cortex


title: WT G1 Pol1-3FLAG ChIP no HU Replicate 1

source_name: Pol1-3FLAG ChIP from WT cells arrested in G1

value: WT, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

source_name: Input DNA from WT G1 arrested cells


title: mec1-100 Δsml1 30 min HU DNA profile Replicate 3

source_name: Genomic DNA from mec1-100 Δsml1 cells by 30 min in HU

treatment_protocol: Cells were released into rich media containing 200 mM Hydroxyurea (HU)

value: mec1-100 Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

value: None, input DNA

source_name: Input DNA from mec1-100 Δsml1 cells arrested in G1


title: mec1-100 Δsml1 30 min HU H3 ChIP Replicate 2

source_name: H3 ChIP from mec1-100 Δsml1 cells by 30 min in HU

source_name: Input DNA from mec1-100 Δsml1 cells by 30 min in HU

value: none, input DNA


title: Df16(A)+/- P6 prefrontal cortex biological replicate 2

source_name: MUT_P6_PFC_biological replicate_2


title: mec1-100 Δsml1 40 min HU DNA profile Replicate 3

source_name: Genomic DNA from mec1-100 Δsml1 cells by 40 min in HU

growth_protocol: Cells were grown in rich media to O.D.660 0.25, then arrested in G1 with α-factor. Cells were synchronously released from α-factor induced G1 arrest into S phase by filtration, and harvested 40 minutes after release.


title: mec1-100 Δsml1 G1 H3 ChIP Replicate 2

source_name: H3 ChIP from mec1-100 Δsml1 cells arrested in G1

source_name: Input DNA from mec1-100 Δsml1 G1 arrested cells


title: Df16(A)+/- P6 prefrontal cortex biological replicate 4

source_name: MUT_P6_PFC_biological replicate_4


title: Df16(A)+/- P6 prefrontal cortex biological replicate 6

source_name: MUT_P6_PFC_biological replicate_6


title: Df16(A)+/- P6 prefrontal cortex biological replicate 3

source_name: MUT_P6_PFC_biological replicate_3


title: wt P6 hippocampus biological replicate 11

source_name: wt_P6_HPC_biological replicate_11

value: wt


description: Gene expression data from NC strain_aerobic conditions_biological rep2

source_name: Saccharomyces cerevisiae strain with no amyalse productions at aerobic batch fermentations

value: CEN. PK 530-1C with TPI1 promoter (2 μm POT1)


title: WT 30 min S phase DNA profile Replicate 1

source_name: Genomic DNA from WT cells by 30 min in S phase

source_name: Input DNA from WT cells arrested in G1


title: wt P6 hippocampus biological replicate 10

source_name: wt_P6_HPC_biological replicate_10


title: Df16(A)+/- P6 prefrontal cortex biological replicate 1

source_name: MUT_P6_PFC_biological replicate_1


title: Chemo-resistant subcell line 2 produced from skov3

description: Sample name: skp43

source_name: Ovary adenocacinoma


title: Chemo-resistant subcell line 1 produced from skov3

description: Sample name: skp41


title: wt P6 hippocampus biological replicate 8

source_name: wt_P6_HPC_biological replicate_8


title: mec1-100 Δsml1 30 min HU Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from mec1-100 Δsml1 cells by 30 min in HU


title: mec1-100 Δsml1 30 min HU H3 ChIP Replicate 1

source_name: H3 ChIP from mec1-100 Δsml1 cells by 30 min in HU

value: H3 C-terminal domain

source_name: Input DNA from mec1-100 Δsml1 cells by 30 min in HU


title: Df16(A)+/- P6 prefrontal cortex biological replicate 5

source_name: MUT_P6_PFC_biological replicate_5


title: mec1-100 Δsml1 30 min HU mononucleosome signal Replicate 2

source_name: Mononucleosome signal from mec1-100 Δsml1 cells by 30 min in HU

value: in vivo MNase digested chromatin


title: mec1-100 Δsml1 G1 mononucleosome signal Replicate 2

source_name: Mononucleosome signal from mec1-100 Δsml1 cells arrested in G1

source_name: Input DNA from mec1-100 Δsml1 G1 arrested cells


title: mec1-100 Δsml1 30 min HU DNA profile Replicate 2

source_name: Genomic DNA from mec1-100 Δsml1 cells by 30 min in HU

source_name: Input DNA from mec1-100 Δsml1 cells arrested in G1


title: wt P6 hippocampus biological replicate 7

source_name: wt_P6_HPC_biological replicate_7

value: hippocampus


title: wt P6 hippocampus biological replicate 5

source_name: wt_P6_HPC_biological replicate_5


title: wt P6 hippocampus biological replicate 2

source_name: wt_P6_HPC_biological replicate_2


title: wt P6 hippocampus biological replicate 4

source_name: wt_P6_HPC_biological replicate_4


title: wt P6 hippocampus biological replicate 6

source_name: wt_P6_HPC_biological replicate_6


title: wt P6 hippocampus biological replicate 3

source_name: wt_P6_HPC_biological replicate_3


title: wt P6 hippocampus biological replicate 1

source_name: wt_P6_HPC_biological replicate_1


title: mec1-100 Δsml1 30 min HU mononucleosome signal Replicate 1


title: mec1-100 Δsml1 30 min HU Pol1-3FLAG ChIP Replicate 1


title: Df16(A)+/- P6 hippocampus biological replicate 9

source_name: MUT_P6_HPC_biological replicate_9


title: Df16(A)+/- P6 hippocampus biological replicate 7

source_name: MUT_P6_HPC_biological replicate_7


title: mec1-100 Δsml1 60 min HU DNA profile Replicate 2

source_name: Genomic DNA from mec1-100 Δsml1 cells by 60 min in HU

growth_protocol: Cells were grown in rich media to O.D.660 0.25, then arrested in G1 with α-factor. Cells were synchronously released from α-factor induced G1 arrest into S phase by filtration, and harvested 60 minutes after release.


title: Δmec1 Δsml1 30 min HU mononucleosome signal Replicate 2

source_name: Mononucleosome signal from Δmec1 Δsml1 cells by 30 min in HU

value: Δmec1 Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

source_name: Input DNA from Δmec1 Δsml1 cells by 30 min in HU


title: mec1-100 Δsml1 G1 mononucleosome signal Replicate 1


title: Df16(A)+/- P6 hippocampus biological replicate 6

source_name: MUT_P6_HPC_biological replicate_6


title: Df16(A)+/- P6 hippocampus biological replicate 5

source_name: MUT_P6_HPC_biological replicate_5


title: Df16(A)+/- P6 hippocampus biological replicate 8

source_name: MUT_P6_HPC_biological replicate_8


title: mec1-100 Δsml1 G1 H3 ChIP Replicate 1

source_name: H3 ChIP from mec1-100 Δsml1 cells arrested in G1

source_name: Input DNA from mec1-100 Δsml1 G1 arrested cells


title: Δmec1 Δsml1 30 min HU H3 ChIP Replicate 2

source_name: H3 ChIP from Δmec1 Δsml1 cells by 30 min in HU


title: Δmec1 Δsml1 G1 mononucleosome signal Replicate 2

source_name: Mononucleosome signal from Δmec1 Δsml1 cells arrested in G1

source_name: Input DNA from Δmec1 Δsml1 G1 arrested cells


title: Δmec1 Δsml1 30 min HU Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from Δmec1 Δsml1 cells by 30 min in HU


title: Df16(A)+/- P6 hippocampus biological replicate 3

source_name: MUT_P6_HPC_biological replicate_3


title: wt E17 prefrontal cortex biological replicate 9

source_name: wt_E17_PFC_biological replicate_9


title: Df16(A)+/- P6 hippocampus biological replicate 2

source_name: MUT_P6_HPC_biological replicate_2


title: Δmec1 Δsml1 G1 H3 ChIP Replicate 1

source_name: H3 ChIP from Δmec1 Δsml1 cells arrested in G1


title: mec1-100 Δsml1 60 min HU DNA profile Replicate 1

source_name: Input DNA from mec1-100 Δsml1 cells arrested in G1


title: wt E17 prefrontal cortex biological replicate 10

source_name: wt_E17_PFC_biological replicate_10


title: wt P6 hippocampus biological replicate 9

source_name: wt_P6_HPC_biological replicate_9


title: Δmec1 Δsml1 30 min HU H3 ChIP Replicate 1

source_name: Input DNA from Δmec1 Δsml1 cells by 30 min in HU


title: Δmec1 Δsml1 30 min HU mononucleosome signal Replicate 1

source_name: Mononucleosome signal from Δmec1 Δsml1 cells by 30 min in HU


title: Δmec1 Δsml1 30 min HU DNA profile Replicate 2

source_name: Genomic DNA from Δmec1 Δsml1 cells by 30 min in HU

source_name: Input DNA from Δmec1 Δsml1 cells arrested in G1


title: wt E17 prefrontal cortex biological replicate 8

source_name: wt_E17_PFC_biological replicate_8


title: wt E17 prefrontal cortex biological replicate 7

source_name: wt_E17_PFC_biological replicate_7


title: mec1-100 Δsml1 30 min HU DNA profile Replicate 1

source_name: Genomic DNA from mec1-100 Δsml1 cells by 30 min in HU


title: Δmec1 Δsml1 G1 H3 ChIP Replicate 2


title: Δmec1 Δsml1 G1 mononucleosome signal Replicate 1

source_name: Mononucleosome signal from Δmec1 Δsml1 cells arrested in G1


title: Δmec1 Δsml1 30 min HU DNA profile Replicate 1


title: Δsml1 G1 H3 ChIP Replicate 2

source_name: H3 ChIP from Δsml1 cells arrested in G1

value: Δsml1, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.

source_name: Input DNA from Δsml1 G1 arrested cells


title: Df16(A)+/- P6 hippocampus biological replicate 1

source_name: MUT_P6_HPC_biological replicate_1


title: wt E17 prefrontal cortex biological replicate 3

source_name: wt_E17_PFC_biological replicate_3


title: wt E17 prefrontal cortex biological replicate 6

source_name: wt_E17_PFC_biological replicate_6


title: Df16(A)+/- E17 prefrontal cortex biological replicate 9

source_name: MUT_E17_PFC_biological replicate_9


title: Δsml1 30 min HU H3 ChIP Replicate 2

source_name: H3 ChIP from Δsml1 cells by 30 min in HU

source_name: Input DNA from Δsml1 cells by 30 min in HU


title: Df16(A)+/- E17 prefrontal cortex biological replicate 8

source_name: MUT_E17_PFC_biological replicate_8


title: wt E17 prefrontal cortex biological replicate 4

source_name: wt_E17_PFC_biological replicate_4


title: wt E17 prefrontal cortex biological replicate 5

source_name: wt_E17_PFC_biological replicate_5


title: wt E17 prefrontal cortex biological replicate 2

source_name: wt_E17_PFC_biological replicate_2


title: Df16(A)+/- E17 prefrontal cortex biological replicate 10

source_name: MUT_E17_PFC_biological replicate_10


title: Δmec1 Δsml1 30 min HU Pol1-3FLAG ChIP Replicate 1

source_name: Pol1-3FLAG ChIP from Δmec1 Δsml1 cells by 30 min in HU

source_name: Input DNA from Δmec1 Δsml1 cells by 30 min in HU


title: wt E17 prefrontal cortex biological replicate 1

source_name: wt_E17_PFC_biological replicate_1


title: Δsml1 30 min HU Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from Δsml1 cells by 30 min in HU


title: Δsml1 60 min HU DNA profile Replicate 2

source_name: Genomic DNA from Δsml1 cells by 60 min in HU

source_name: Input DNA from Δsml1 cells arrested in G1


title: Δsml1 G1 mononucleosome signal Replicate 2

source_name: Mononucleosome signal from Δsml1 cells arrested in G1

source_name: Input DNA from Δsml1 G1 arrested cells


title: Df16(A)+/- P6 hippocampus biological replicate 4

source_name: MUT_P6_HPC_biological replicate_4


title: Δsml1 30 min HU mononucleosome signal Replicate 2

source_name: Mononucleosome signal from Δsml1 cells by 30 min in HU


title: Df16(A)+/- E17 prefrontal cortex biological replicate 7

source_name: MUT_E17_PFC_biological replicate_7


title: Δsml1 30 min HU mononucleosome signal Replicate 1

source_name: Input DNA from Δsml1 cells by 30 min in HU


title: Δsml1 30 min HU DNA profile Replicate 2

source_name: Genomic DNA from Δsml1 cells by 30 min in HU


title: Df16(A)+/- E17 prefrontal cortex biological replicate 6

source_name: MUT_E17_PFC_biological replicate_6


title: Δsml1 30 min HU Pol1-3FLAG ChIP Replicate 1


title: WT 40 min HU DNA profile Replicate 4

source_name: Genomic DNA from WT cells by 40 min in HU

source_name: Input DNA from WT cells arrested in G1


title: Δsml1 30 min HU H3 ChIP Replicate 1

source_name: H3 ChIP from Δsml1 cells by 30 min in HU


title: Δsml1 60 min HU DNA profile Replicate 1


title: Δsml1 30 min HU DNA profile Replicate 1


title: Δsml1 G1 mononucleosome signal Replicate 1


title: wt E17 hippocampus biological replicate 10

source_name: wt_E17_HPC_biological replicate_10


title: Df16(A)+/- E17 prefrontal cortex biological replicate 3

source_name: MUT_E17_PFC_biological replicate_3


title: Df16(A)+/- E17 prefrontal cortex biological replicate 4

source_name: MUT_E17_PFC_biological replicate_4


title: wt E17 hippocampus biological replicate 8

source_name: wt_E17_HPC_biological replicate_8


title: Δmec1 Δsml1 60 min HU DNA profile Replicate 1

source_name: Genomic DNA from Δmec1 Δsml1 cells by 60 min in HU

source_name: Input DNA from Δmec1 Δsml1 cells arrested in G1


title: wt E17 hippocampus biological replicate 9

source_name: wt_E17_HPC_biological replicate_9


title: WT 30 min HU DNA profile Replicate 4

source_name: Genomic DNA from WT cells by 30 min in HU


title: Δsml1 G1 H3 ChIP Replicate 1

source_name: H3 ChIP from Δsml1 cells arrested in G1

source_name: Input DNA from Δsml1 G1 arrested cells


title: WT 30 min HU DNA profile Replicate 3


title: Df16(A)+/- E17 prefrontal cortex biological replicate 2

source_name: MUT_E17_PFC_biological replicate_2


title: WT 60 min HU DNA profile Replicate 3

source_name: Genomic DNA from WT cells by 60 min in HU


title: Df16(A)+/- E17 prefrontal cortex biological replicate 1

source_name: MUT_E17_PFC_biological replicate_1


title: wt E17 hippocampus biological replicate 7

source_name: wt_E17_HPC_biological replicate_7


title: wt E17 hippocampus biological replicate 4

source_name: wt_E17_HPC_biological replicate_4


title: WT 60 min HU H3 ChIP Replicate 2

source_name: H3 ChIP from WT cells by 60 min in HU

source_name: Input DNA from WT cells by 60 min in HU


title: wt E17 hippocampus biological replicate 1

source_name: wt_E17_HPC_biological replicate_1


title: WT 60 min HU H3 ChIP Replicate 1


title: wt E17 hippocampus biological replicate 6

source_name: wt_E17_HPC_biological replicate_6


title: wt E17 hippocampus biological replicate 2

source_name: wt_E17_HPC_biological replicate_2


title: WT 60 min HU DNA profile Replicate 2

source_name: Input DNA from WT cells arrested in G1


title: wt E17 hippocampus biological replicate 5

source_name: wt_E17_HPC_biological replicate_5


title: WT G1 H3 ChIP Replicate 2

source_name: H3 ChIP from WT cells arrested in G1

source_name: Input DNA from WT G1 arrested cells


title: WT 60 min HU Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from WT cells by 60 min in HU


title: Df16(A)+/- E17 hippocampus biological replicate 10

source_name: MUT_E17_HPC_biological replicate_10


title: wt E17 hippocampus biological replicate 3

source_name: wt_E17_HPC_biological replicate_3


title: WT 60 min HU mononucleosome signal Replicate 2

source_name: Mononucleosome signal from WT cells by 60 min in HU


title: Df16(A)+/- E17 prefrontal cortex biological replicate 5

source_name: MUT_E17_PFC_biological replicate_5


title: WT G1 mononucleosome signal Replicate 2

source_name: Mononucleosome signal from WT cells arrested in G1


title: WT G1 Pol1-3FLAG ChIP Replicate 2

source_name: Pol1-3FLAG ChIP from WT cells arrested in G1


title: Df16(A)+/- E17 hippocampus biological replicate 8

source_name: MUT_E17_HPC_biological replicate_8


title: Df16(A)+/- E17 hippocampus biological replicate 6

source_name: MUT_E17_HPC_biological replicate_6


title: Df16(A)+/- E17 hippocampus biological replicate 9

source_name: MUT_E17_HPC_biological replicate_9


title: WT G1 H3 ChIP Replicate 1


title: WT G1 Pol1-3FLAG ChIP Replicate 1


title: Df16(A)+/- E17 hippocampus biological replicate 5

source_name: MUT_E17_HPC_biological replicate_5


title: Df16(A)+/- E17 hippocampus biological replicate 4

source_name: MUT_E17_HPC_biological replicate_4


title: Df16(A)+/- E17 hippocampus biological replicate 3

source_name: MUT_E17_HPC_biological replicate_3


title: Df16(A)+/- E17 hippocampus biological replicate 7

source_name: MUT_E17_HPC_biological replicate_7


title: WT 60 min HU Pol1-3FLAG ChIP Replicate 1

source_name: Input DNA from WT cells by 60 min in HU


title: Df16(A)+/- E17 hippocampus biological replicate 2

source_name: MUT_E17_HPC_biological replicate_2


title: WT 30 min HU DNA profile Replicate 1

source_name: Genomic DNA from WT cells by 30 min in HU

source_name: Input DNA from WT cells arrested in G1


title: vulvar normal tissue 1102-0325 expression

status: Public on Jan 16 2013

city: oslo

first: Francesca

last: Micci

address: Ullernchausseen 70

department: Institute for medical informatics

country: Norway

institute: Oslo Universitetssykehus

hyb_protocol: 750 ng of biotin-labeled cRNA was hibridized to the HumanHT-12 v.4 Illumina Sentrix BeadCHip according to the manufacturer's instructions.

data_processing: Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples, as well as imputing missing data using the k-nearest neighbor algorithm  (Tech note: Inputing HumanHT-12 Expression BeadChip Data; Illumina, Inc.). The text file was imported into J-Express Pro 2011, and signal intensity values were quantile normalized (Bolstad et al. 2003) and log transformed (base 2). Significance Analysis of Microarrays (SAM) was used to look for differentially expressed genes. To obtain manageable datasets, differentially expressed genes were defined by a fold change ≥2 and q-value = 0.

source_name: normal tissue

extract_protocol: RNA was extracted with Trizol reagent. Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled. The amount and quality of labeled CDNA were measured using both a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.

tag: differentiation

value: normal tissue

tag: individual

value: normal vulva


title: WT G1 mononucleosome signal Replicate 1

source_name: Input DNA from WT G1 arrested cells


title: vulvar normal tissue 1102-0354 expression

label_protocol: Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled.


title: WT 60 min HU mononucleosome signal Replicate 1

source_name: Mononucleosome signal from WT cells by 60 min in HU


title: Col-0 vs lsm1a lsm1b-3

city: Madrid

first: Carlos

last: Perea-Resa

address: Ramiro de Maeztu,9

institute: CIB-CSIC

description:
Biological replicate 3 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.
Rep 3.gpr

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization). Limma software was used for the normalization.

organism: Arabidopsis thaliana

source_name: lsm1a lsm1b

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Plants were grown in pots containing a mixture of organic substrate and vermiculite (3:1 v/v) for two weeks in 16h light/8 h dark at 22ºC conditions.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. Then, total RNA was purified using the Rneasy MiniKit from QIAGEN following manufacturer's instructions.

tag: genotype/variation

value: lsm1a lsm1b

value: Rosette

value: control


title: Col-0 vs lsm1a lsm1b-2

description:
Biological replicate 2 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.
Rep 2.gpr


title: vulvar normal tissue 1102-0405 expression


title: SCC of the vulva 09-818 expression

source_name: tumor

value: moderately differentiated

value: squamous cell carcinoma tumor


title: WT 60 min HU DNA profile Replicate 1

source_name: Genomic DNA from WT cells by 60 min in HU

value: WT, Pol1-3FLAG strain congenic to W303-1a in which the weak rad5 mutant allele in the original W303 has been corrected.


title: vulvar normal tissue 1102-0370 expression


title: SCC of the vulva 03-830 expression


title: SCC of the vulva 03-1088 expression

value: well differentiated


title: SCC of the vulva 02-1171 expression

value: not specified


title: SCC of the vulva 06-125 expression


title: SCC of the vulva 09-733 expression


title: vulvar normal tissue 1102-0395 expression


title: SCC of the vulva 06-709 expression


title: SCC of the vulva 06-19 expression

value: poorly differentiated


title: SCC of the vulva 02-167 expression


title: SCC of the vulva 03-1011 expression

value: moderately and well differentiated


title: SCC of the vulva 02-1060 expression


title: SCC of the vulva 02-869 expression

value: well, moderately and poorly differentiated


title: SCC of the vulva 02-848 expression


title: GRASS_884606 at time H03 [control_Blood]

city: Bethesda

first: Sai

last: Kanaparthi

state: MD

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

description: Gene Expression data from GRASS_884606 at time H03

hyb_protocol: Hybridization cocktail is prepared using the Hybridization, Wash, and Stain kit (Affymetrix), applied to arrays, and incubated at 45C for 16 hours.  Following hybridization, arrays are washed and stained using standard Affymetrix procedures.

scan_protocol: Completed arrays were scanned using the GeneChip® Scanner 3000 7G and analyzed with the Affymetrix GeneChip Operation System.

data_processing: R package aroma.affymetrix was used for normalization and QA.

label_protocol: RNA samples are converted to sense-stranded cDNA using the Ambion® WT Expression Kit and subsequently labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit. The WT Expression kit is optimized for use with human, mouse and rat Affymetrix GeneChip® Sense Target (ST) Arrays. Briefly, 200ng of total RNA undergoes a reverse transcription step designed to exclude priming of ribosomal RNA.  Primers are designed using a proprietary-oligonucleotide matching algorithm that avoids rRNA binding, thereby providing comprehensive coverage of the transcriptome while significantly reducing coverage of rRNA. This method also avoids the 3’ bias inherent in method that prime exclusively with oligo-dT-based primers.  The resulting sense-strand cDNA is next fragmented and labeled using uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) which recognizes and fragments the cDNA at dUTP residues, which were incorporated during the 2nd-cycle. Next, DNA is labeled by terminal deoxynucleotidyle transerase (TdT) using the Affymetrix DNA Labeling Reagent.

extract_protocol: Whole blood RNA extractions were conducted from ABI Tempus™ Whole Blood Collection tubes using the ABI PRISM® 6100 Nucleic Acid PrepStation and Tempus™ 12-Port RNA Isolation Kit (Ambion).  The resulting RNA was quantitated by spectrophotometry using a NanoDrop ND-8000 (Thermo), and was evaluated for integrity using the RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent). Purified RNAs were stored at -80°C.  CD4+ T cells from PBMCs were enriched by negative selection using EasySep CD4+ T cell enrichment kit according to manufacturers instructions (StemCell Technologies, Vancouver, BC, Canada). RNA extractions were conducted using the RNeasy method (Qiagen).  Briefly, cell pellets were lysed in RLT buffer (with beta mercaptoethanol) and transferred to collection tubes.  They were then loaded into a QIAcube automated sample prep instrument where they were homogenized and RNA was extracted. The resulting RNA was quantitated by spectrophotometry using a NanoDrop ND-8000 (Thermo) and evaluated for integrity using the RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent). Purified RNAs were stored at -80°C.

treatment_protocol: Control: subjects received nasal challenge with diluent at visit-2; Treatment: the same set of subjects received nasal challenge with titrated timothy grass pollen (Aquagen, phleum pratense; ALK) at visit-3 (14±2 days after visit2). For both control and treatment, peripheral blood was collected before nasal challenge (Base) and at 3 (H03), 6 (H06) and 24 hours (H24) following nasal challenge.

value: Blood

tag: time

tag: group


title: Lung cancer cells_H2AX knockdown_rep1

city: Beijing

first: Chengrong

last: Lu

address: Fucheng road 30

department: Aviation Medicine Research lab

country: China

institute: General Hospital of Air Force

description: Gene expression data from luang cancer cells_H2AX knockdown, treated with VP16.

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

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

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

source_name: Lung cancer cells_P1 treated with VP-16

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: A549 stable cells (C and P1) were seeded in 10 cm dishes and cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) until they reached 80% confluence.

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

treatment_protocol: The cells (C and P1) were then treated with VP16 (100M) for 48 h after serum starvation overnight

tag: cell line

value: H2AX knockdown


title: Lung cancer cells_control_rep2

description: Gene expression data from luang cancer cells_control treated with VP16.

source_name: Lung cancer cells_control treated with VP-16


title: GRASS_884606 at time H06 [control_Blood]

description: Gene Expression data from GRASS_884606 at time H06


title: Lung cancer cells_control_rep1


title: Lung cancer cells_H2AX knockdown_rep3


title: GRASS_884606 at time H06 [treatment_Blood]

value: treatment


title: Lung cancer cells_control_rep3


title: Lung cancer cells_H2AX knockdown_rep2


title: GRASS_884606 at time H24 [control_Blood]

description: Gene Expression data from GRASS_884606 at time H24


title: GRASS_884606 at time Base [treatment_Blood]

description: Gene Expression data from GRASS_884606 at time Base

value: Base


title: GRASS_884606 at time H24 [treatment_Blood]


title: GRASS_884606 at time H03 [treatment_Blood]


title: GRASS_860883 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_860883 at time H03


title: GRASS_884606 at time Base [control_Blood]


title: GRASS_860883 at time H06 [treatment_Blood]

description: Gene Expression data from GRASS_860883 at time H06


title: GRASS_860883 at time H06 [control_Blood]


title: GRASS_860883 at time H03 [control_Blood]


title: GRASS_860883 at time H24 [treatment_Blood]

description: Gene Expression data from GRASS_860883 at time H24


title: GRASS_860883 at time H24 [control_Blood]


title: GRASS_811955 at time H06 [treatment_Blood]

description: Gene Expression data from GRASS_811955 at time H06


title: GRASS_811955 at time H06 [control_Blood]


title: GRASS_811955 at time H24 [control_Blood]

description: Gene Expression data from GRASS_811955 at time H24


title: GRASS_811955 at time Base [control_Blood]

description: Gene Expression data from GRASS_811955 at time Base


title: GRASS_811955 at time H03 [control_Blood]

description: Gene Expression data from GRASS_811955 at time H03


title: Col-0 vs lsm1a lsm1b-1

description:
Biological replicate 1 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.
Rep 1.gpr


title: GRASS_811955 at time H24 [treatment_Blood]


title: GRASS_860883 at time Base [treatment_Blood]

description: Gene Expression data from GRASS_860883 at time Base


title: GRASS_811955 at time Base [treatment_Blood]


title: GRASS_811955 at time H03 [treatment_Blood]


title: GRASS_652140 at time H24 [treatment_Blood]

description: Gene Expression data from GRASS_652140 at time H24


title: GRASS_577927 at time H06 [treatment_Blood]

description: Gene Expression data from GRASS_577927 at time H06


title: GRASS_577927 at time Base [control_Blood]

description: Gene Expression data from GRASS_577927 at time Base


title: GRASS_577927 at time H24 [treatment_Blood]

description: Gene Expression data from GRASS_577927 at time H24


title: GRASS_577927 at time H03 [control_Blood]

description: Gene Expression data from GRASS_577927 at time H03


title: GRASS_652140 at time H06 [control_Blood]

description: Gene Expression data from GRASS_652140 at time H06


title: GRASS_577927 at time Base [treatment_Blood]


title: GRASS_577927 at time H06 [control_Blood]


title: GRASS_652140 at time H24 [control_Blood]


title: GRASS_572228 at time H24 [control_Blood]

description: Gene Expression data from GRASS_572228 at time H24


title: GRASS_577927 at time H03 [treatment_Blood]


title: GRASS_652140 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_652140 at time H03


title: GRASS_652140 at time Base [control_Blood]

description: Gene Expression data from GRASS_652140 at time Base


title: GRASS_577927 at time H24 [control_Blood]


title: GRASS_572228 at time H06 [control_Blood]

description: Gene Expression data from GRASS_572228 at time H06


title: GRASS_652140 at time Base [treatment_Blood]


title: GRASS_652140 at time H03 [control_Blood]


title: GRASS_572228 at time H03 [control_Blood]

description: Gene Expression data from GRASS_572228 at time H03


title: GRASS_572228 at time H03 [treatment_Blood]


title: GRASS_572228 at time H24 [treatment_Blood]


title: GRASS_860883 at time Base [control_Blood]


title: GRASS_652140 at time H06 [treatment_Blood]


title: GRASS_532035 at time H24 [control_Blood]

description: Gene Expression data from GRASS_532035 at time H24


title: GRASS_532035 at time H06 [control_Blood]

description: Gene Expression data from GRASS_532035 at time H06


title: GRASS_572228 at time Base [control_Blood]

description: Gene Expression data from GRASS_572228 at time Base


title: GRASS_572228 at time H06 [treatment_Blood]


title: GRASS_572228 at time Base [treatment_Blood]


title: GRASS_532035 at time H24 [treatment_Blood]


title: GRASS_532035 at time Base [control_Blood]

description: Gene Expression data from GRASS_532035 at time Base


title: Df16(A)+/- E17 hippocampus biological replicate 1

source_name: MUT_E17_HPC_biological replicate_1

value: hippocampus


title: GRASS_524464 at time H24 [control_Blood]

description: Gene Expression data from GRASS_524464 at time H24


title: GRASS_532035 at time H06 [treatment_Blood]


title: GRASS_532035 at time Base [treatment_Blood]


title: GRASS_532035 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_532035 at time H03


title: GRASS_461692 at time Base [treatment_Blood]

description: Gene Expression data from GRASS_461692 at time Base


title: GRASS_532035 at time H03 [control_Blood]


title: GRASS_524464 at time H24 [treatment_Blood]


title: GRASS_524464 at time Base [control_Blood]

description: Gene Expression data from GRASS_524464 at time Base


title: GRASS_461692 at time H06 [treatment_Blood]

description: Gene Expression data from GRASS_461692 at time H06


title: GRASS_524464 at time H06 [control_Blood]

description: Gene Expression data from GRASS_524464 at time H06


title: GRASS_524464 at time Base [treatment_Blood]


title: GRASS_461692 at time H24 [treatment_Blood]

description: Gene Expression data from GRASS_461692 at time H24


title: GRASS_461692 at time H24 [control_Blood]


title: GRASS_461692 at time Base [control_Blood]


title: GRASS_290908 at time H06 [control_Blood]

description: Gene Expression data from GRASS_290908 at time H06


title: GRASS_524464 at time H03 [control_Blood]

description: Gene Expression data from GRASS_524464 at time H03


title: GRASS_524464 at time H06 [treatment_Blood]


title: GRASS_290908 at time H24 [treatment_Blood]

description: Gene Expression data from GRASS_290908 at time H24


title: GRASS_461692 at time H06 [control_Blood]


title: GRASS_290908 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_290908 at time H03


title: GRASS_290908 at time H06 [treatment_Blood]


title: GRASS_290908 at time Base [control_Blood]

description: Gene Expression data from GRASS_290908 at time Base


title: GRASS_524464 at time H03 [treatment_Blood]


title: GRASS_290908 at time H24 [control_Blood]


title: GRASS_461692 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_461692 at time H03


title: GRASS_290908 at time H03 [control_Blood]


title: GRASS_290908 at time Base [treatment_Blood]


title: GRASS_141635 at time H06 [treatment_Blood]

description: Gene Expression data from GRASS_141635 at time H06


title: GRASS_209904 at time H24 [treatment_Blood]

description: Gene Expression data from GRASS_209904 at time H24


title: GRASS_209904 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_209904 at time H03


title: GRASS_884606 at time H03 [treatment_CD4+]

description: Gene Expression data from GRASS_884606 at time H03

value: CD4+ T cells from PBMC


title: GRASS_884606 at time H24 [treatment_CD4+]

description: Gene Expression data from GRASS_884606 at time H24


title: GRASS_141635 at time H24 [control_Blood]

description: Gene Expression data from GRASS_141635 at time H24


title: GRASS_209904 at time Base [control_Blood]

description: Gene Expression data from GRASS_209904 at time Base


title: GRASS_209904 at time H06 [treatment_Blood]

description: Gene Expression data from GRASS_209904 at time H06


title: GRASS_884606 at time H06 [control_CD4+]

description: Gene Expression data from GRASS_884606 at time H06


title: GRASS_141635 at time Base [treatment_Blood]

description: Gene Expression data from GRASS_141635 at time Base


title: GRASS_141635 at time H24 [treatment_Blood]


title: GRASS_209904 at time H24 [control_Blood]


title: GRASS_141635 at time H03 [treatment_Blood]

description: Gene Expression data from GRASS_141635 at time H03


title: GRASS_884606 at time H24 [control_CD4+]


title: GRASS_209904 at time H06 [control_Blood]


title: GRASS_141635 at time H06 [control_Blood]


title: GRASS_209904 at time H03 [control_Blood]


title: GRASS_884606 at time Base [treatment_CD4+]

description: Gene Expression data from GRASS_884606 at time Base


title: GRASS_884606 at time H06 [treatment_CD4+]


title: GRASS_141635 at time Base [control_Blood]


title: GRASS_860883 at time H06 [control_CD4+]

description: Gene Expression data from GRASS_860883 at time H06


title: GRASS_141635 at time H03 [control_Blood]


title: GRASS_860883 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_860883 at time H24


title: GRASS_884606 at time Base [control_CD4+]


title: GRASS_884606 at time H03 [control_CD4+]


title: GRASS_860883 at time H24 [treatment_CD4+]


title: GRASS_860883 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_860883 at time H03


title: GRASS_860883 at time H03 [treatment_CD4+]


title: GRASS_811955 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_811955 at time H24


title: GRASS_811955 at time H06 [treatment_CD4+]

description: Gene Expression data from GRASS_811955 at time H06


title: GRASS_811955 at time H24 [treatment_CD4+]


title: GRASS_461692 at time H03 [control_Blood]

description: Gene Expression data from GRASS_461692 at time H03


title: GRASS_860883 at time Base [control_CD4+]

description: Gene Expression data from GRASS_860883 at time Base


title: GRASS_811955 at time H06 [control_CD4+]


title: GRASS_652140 at time H03 [treatment_CD4+]

description: Gene Expression data from GRASS_652140 at time H03


title: GRASS_860883 at time H06 [treatment_CD4+]


title: GRASS_652140 at time H24 [treatment_CD4+]

description: Gene Expression data from GRASS_652140 at time H24


title: GRASS_811955 at time H03 [treatment_CD4+]

description: Gene Expression data from GRASS_811955 at time H03


title: GRASS_652140 at time H03 [control_CD4+]


title: GRASS_860883 at time Base [treatment_CD4+]


title: GRASS_652140 at time H06 [treatment_CD4+]

description: Gene Expression data from GRASS_652140 at time H06


title: GRASS_652140 at time H06 [control_CD4+]


title: GRASS_652140 at time Base [treatment_CD4+]

description: Gene Expression data from GRASS_652140 at time Base


title: GRASS_811955 at time Base [control_CD4+]

description: Gene Expression data from GRASS_811955 at time Base


title: GRASS_209904 at time Base [treatment_Blood]

description: Gene Expression data from GRASS_209904 at time Base


title: GRASS_577927 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_577927 at time H03


title: GRASS_577927 at time H06 [treatment_CD4+]

description: Gene Expression data from GRASS_577927 at time H06


title: GRASS_577927 at time Base [control_CD4+]

description: Gene Expression data from GRASS_577927 at time Base


title: GRASS_577927 at time H06 [control_CD4+]


title: GRASS_811955 at time Base [treatment_CD4+]


title: GRASS_577927 at time Base [treatment_CD4+]


title: GRASS_811955 at time H03 [control_CD4+]


title: GRASS_652140 at time H24 [control_CD4+]


title: GRASS_577927 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_577927 at time H24


title: GRASS_652140 at time Base [control_CD4+]


title: GRASS_577927 at time H03 [treatment_CD4+]


title: GRASS_577927 at time H24 [treatment_CD4+]


title: GRASS_532035 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_532035 at time H03


title: GRASS_572228 at time H03 [treatment_CD4+]

description: Gene Expression data from GRASS_572228 at time H03


title: GRASS_572228 at time H06 [control_CD4+]

description: Gene Expression data from GRASS_572228 at time H06


title: GRASS_572228 at time H03 [control_CD4+]


title: GRASS_572228 at time H06 [treatment_CD4+]


title: GRASS_532035 at time H03 [treatment_CD4+]


title: GRASS_532035 at time Base [control_CD4+]

description: Gene Expression data from GRASS_532035 at time Base


title: GRASS_532035 at time Base [treatment_CD4+]


title: GRASS_572228 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_572228 at time H24


title: GRASS_572228 at time Base [treatment_CD4+]

description: Gene Expression data from GRASS_572228 at time Base


title: GRASS_572228 at time H24 [treatment_CD4+]


title: GRASS_532035 at time H24 [treatment_CD4+]

description: Gene Expression data from GRASS_532035 at time H24


title: GRASS_524464 at time H06 [control_CD4+]

description: Gene Expression data from GRASS_524464 at time H06


title: GRASS_524464 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_524464 at time H03


title: GRASS_572228 at time Base [control_CD4+]


title: GRASS_524464 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_524464 at time H24


title: GRASS_524464 at time Base [control_CD4+]

description: Gene Expression data from GRASS_524464 at time Base


title: GRASS_524464 at time Base [treatment_CD4+]


title: GRASS_524464 at time H03 [treatment_CD4+]


title: GRASS_524464 at time H24 [treatment_CD4+]


title: GRASS_461692 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_461692 at time H24


title: GRASS_532035 at time H06 [treatment_CD4+]

description: Gene Expression data from GRASS_532035 at time H06


title: GRASS_461692 at time H06 [control_CD4+]

description: Gene Expression data from GRASS_461692 at time H06


title: GRASS_532035 at time H24 [control_CD4+]


title: GRASS_524464 at time H06 [treatment_CD4+]


title: GRASS_532035 at time H06 [control_CD4+]


title: GRASS_461692 at time H06 [treatment_CD4+]


title: GRASS_461692 at time H24 [treatment_CD4+]


title: GRASS_461692 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_461692 at time H03


title: GRASS_290908 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_290908 at time H24


title: GRASS_290908 at time H24 [treatment_CD4+]


title: GRASS_290908 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_290908 at time H03


title: GRASS_290908 at time Base [control_CD4+]

description: Gene Expression data from GRASS_290908 at time Base


title: GRASS_461692 at time Base [treatment_CD4+]

description: Gene Expression data from GRASS_461692 at time Base


title: GRASS_461692 at time H03 [treatment_CD4+]


title: GRASS_290908 at time H06 [treatment_CD4+]

description: Gene Expression data from GRASS_290908 at time H06


title: GRASS_290908 at time Base [treatment_CD4+]


title: GRASS_290908 at time H06 [control_CD4+]


title: GRASS_209904 at time H24 [control_CD4+]

description: Gene Expression data from GRASS_209904 at time H24


title: GRASS_209904 at time H24 [treatment_CD4+]


title: GRASS_209904 at time Base [control_CD4+]

description: Gene Expression data from GRASS_209904 at time Base


title: GRASS_290908 at time H03 [treatment_CD4+]


title: GRASS_461692 at time Base [control_CD4+]


title: GRASS_209904 at time Base [treatment_CD4+]


title: GRASS_141635 at time H06 [control_CD4+]

description: Gene Expression data from GRASS_141635 at time H06


title: GRASS_141635 at time H03 [control_CD4+]

description: Gene Expression data from GRASS_141635 at time H03


title: GRASS_141635 at time Base [control_CD4+]

description: Gene Expression data from GRASS_141635 at time Base


title: GRASS_209904 at time H03 [treatment_CD4+]

description: Gene Expression data from GRASS_209904 at time H03


title: GRASS_141635 at time Base [treatment_CD4+]


title: GRASS_141635 at time H03 [treatment_CD4+]


title: human iNSC derived from human fibroblasts CRL-2097, replicate1

city: San Francisco

first: Saiyong

last: Zhu

address: 1650 Owens Street, GICD, 4P,

institute: The Gladstone Institute

hyb_protocol: GeneChip Expression Analysis Technical Manual 701021 Rev.3

data_processing: Affymetrix Expression Console V1.1

label_protocol: NuGEN Ovation Pico WTA V2 and NuGEN Encore Biotin Module

growth_protocol: CRL was cultured in fibroblast medium; B3 and ONE3 were cultured in neural stem cell medium.

treatment_protocol: No treatment.

tag: protocol

value: neural stem cell medium


title: GRASS_141635 at time H24 [treatment_CD4+]

description: Gene Expression data from GRASS_141635 at time H24


title: human iNSC derived from human fibroblasts CRL-2097, replicate2


title: GRASS_141635 at time H06 [treatment_CD4+]


title: GRASS_209904 at time H06 [treatment_CD4+]

description: Gene Expression data from GRASS_209904 at time H06


title: GRASS_141635 at time H24 [control_CD4+]


title: human fibroblast cell line CRL-2097 from ATCC, replicate1

value: fibroblast medium


title: human fibroblast cell line CRL-2097 from ATCC, replicate2


title: human NSC differentiated from human ESCs, replicate2


title: KO kidney pool 2

city: Lausanne

first: Daniel

last: Pouly

address: Rue du Bugnon 27

department: Department of Pharmacology and Toxicology

country: Switzerland

institute: University of Lausanne

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 5 micrograms of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: whole kidney from KO mice

label_protocol: Equal amounts of RNA extracted from 3 mice from the same group were combined as a pool. For all samples, 300 ng of total RNA was used to perform target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).

growth_protocol: Mice were housed for 3 weeks in 12h Light:12h Dark under standard conditions

extract_protocol: Total RNA from mice kidney was isolated with the Trizol and phenol chloroform extraction and was purified with RNAqeuous kit. RNA quality and concentration was verified with an Agilent Bioanalyzer 2100

treatment_protocol: 6 pairs of littermate male Usp2-KO and WT mice were dissected at the age of 12 weeks at Zeitgeber Time 12, the acrophase of Usp2 expression

tag: strain


title: WT kidney pool 1

source_name: whole kidney from WT mice

value: WT


title: MUC1 peptide:MUC1.Tg 72h Rep 3

first: Adam

middle: M

last: Farkas

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description:
Replicate 3
SAMPLE 12

data_processing: The data were processed with quantile 99 normalization followed by cube root transformation using caGEDA (Lyons-Weiler, J. Cancer Infomatics, 2008)

label: Biotin

source_name: MUC1 peptide_MUC1.Tg 72h

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

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

treatment_protocol: Mice were immunized (i.v.) with 1*10^6 bone marrow-derived dendritic cells loaded overnight with 30ug/mL of synthetic, human MUC1 100mer peptide and matured with 30ug/mL Poly:ICLC.

tag: strain background

value: MUC1 transgenic

tag: immunized with

value: dendritic cells loaded with sythetic, human MUC1 peptide

tag: tissue

value: spleen


title: MUC1 peptide:MUC1.Tg 72h Rep 1

description:
Replicate 1
SAMPLE 10


title: Muller control 24h rep3

city: Shanghai

first: Xin

last: Wang

address: Fenyang road

institute: Fudan University

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

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Muller cells cultured under the same conditions but with no applied mechanical strain for 24 h

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

tag: glutamine synthetase

value: positive

tag: passages

value: between 2 and 4

tag: cell type

value: retinal Muller cells

tag: treatment

value: control

value: Sprague-Dawley


title: WT kidney pool 2


title: KO kidney pool 1


title: Muller stretched 24h rep3

source_name: Muller cells under mechanical stretching for 24 h

value: stretched

tag: genetic background


title: MUC1 peptide:WT 24h Rep 2

description:
Replicate 2
SAMPLE 2

source_name: MUC1 peptide_WT 24h

value: wild type


title: MUC1 peptide:WT 72h Rep 1

description:
Replicate 1
SAMPLE 7

source_name: MUC1 peptide_WT 72h


title: MUC1 peptide:MUC1.Tg 24h Rep 2

description:
Replicate 2
SAMPLE 5

source_name: MUC1 peptide_MUC1.Tg 24h


title: MUC1 peptide:MUC1.Tg 72h Rep 2

description:
Replicate 2
SAMPLE 11


title: Muller control 24h rep1


title: MUC1 peptide:MUC1.Tg 24h Rep 3

description:
Replicate 3
SAMPLE 6


title: MUC1 peptide:WT 72h Rep 3

description:
Replicate 3
SAMPLE 9


title: human NSC differentiated from human ESCs, replicate1


title: MUC1 peptide:MUC1.Tg 24h Rep 1

description:
Replicate 1
SAMPLE 4


title: MUC1 peptide:WT 24h Rep 3

description:
Replicate 3
SAMPLE 3


title: Muller stretched 24h rep1


title: Muller control 1h rep3

source_name: Muller cells cultured under the same conditions but with no applied mechanical strain for 1 h

value: 1 h


title: Muller control 1h rep2


title: Muller control 24h rep2


title: Muller stretched 24h rep2


title: Muller stretched 1h rep3

source_name: Muller cells under mechanical stretching for 1 h


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 52

city: bethesda

first: abdel

last: elkahloun

address: 50 south dr

institute: nih

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cDNAs was hybridized  to Affymetrix U133A_2.0 GeneChips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

scan_protocol: Fluorescent intensities were measured with an Affymetrix GeneChip Scanner 3000.

data_processing:
Prior to statistical analysis of the MAS5 data, all probe sets for each microarray were globally scaled to a target intensity of 500 in the Affymetrix software (GCOS v1.4). Only transcripts with a present (P) flag in 75% or more of the chips from a given class were analyzed.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HG-U133A_2
program-name = Expression Console
program-version = 1.2.1.20
program-company = Affymetrix
affymetrix-algorithm-param-apt-engine = ProbesetSummarizeEngine
affymetrix-algorithm-param-apt-program-name = Expression Console
affymetrix-algorithm-param-apt-opt-analysis-name = rma
affymetrix-algorithm-param-apt-opt-set-analysis-name = rma
affymetrix-algorithm-param-apt-opt-analysis-spec = rma-bg,quant-norm.sketch=0.bioc=true.lowprecision=false.usepm=true.target=0.doavg=f
alse.subsetmd5=37a9e6fae3eaa22bda0bb220c6bc054d,pm-only,med-polish.FixFeatureEffect=false.UseInputModel=false.FitFeatureResponse=true.
expon=false.attenuate=true.l=0.005.h=-1,expr.genotype=false.strand=false.allele-a=false
affymetrix-algorithm-param-apt-opt-do-residuals = false
affymetrix-algorithm-param-apt-opt-do-feature-effects = false
affymetrix-algorithm-param-apt-opt-write-sketch = false
affymetrix-algorithm-param-apt-opt-write-profile = false
affymetrix-algorithm-param-quantification-name = med-polish
affymetrix-algorithm-param-quantification-version = 1.0
affymetrix-algorithm-param-quantification-scale = log2
affymetrix-algorithm-param-quantification-type = signal

source_name: peripheral blood

label_protocol: 1.5 μg of total RNA was used for standard target preparation and hybridization (Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents). 10 ug of labeled cRNA was fragmented according to the protocol recommendations.

extract_protocol: PBMCs were isolated from whole blood using ficoll-based Lymphocyte Separation Medium (MP Biomedicals). The cell pellets were resuspended in Trizol (Invitrogen Corp.) for 5 min and stored at -80oC until the samples from this study could be processed together. Total RNA was isolated from the PBMC lysates by alcohol precipitation and the RNA samples were subject to further purification via RNEasy columns (Qiagen, Inc.). The concentration and quality of RNA samples was determined using spectrophotometry and the 2100 Bioanalyzer (Agilent Technlogies, Inc.). The RNA samples all had 260:280 ratios between 1.8 and 2.1 and were of good quality as evidenced by intact 18S and 28S rRNA bands

treatment_protocol: All blood specimens were processed within 60 minutes of drawing to minimize ex vivo changes in gene expression

value: peripheral blood mononuclear cells

tag: genotype

value: TNFRSF1A mutation carrier

tag: disease causing mutation

tag: disease state

value: other autoinflammatory disease


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 51


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 40


title: Muller stretched 1h rep1


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 53


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 41


title: MUC1 peptide:WT 72h Rep 2

description:
Replicate 2
SAMPLE 8

tag: genotype/variation


title: MUC1 peptide:WT 24h Rep 1

description:
Replicate 1
SAMPLE 1


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 34


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 33


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 28


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 42


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 27


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 30

value: not known


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 46


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 50


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 44


title: Muller stretched 1h rep2

tag: time


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 25


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 38


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 35


title: Muller control 1h rep1


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 20


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 29


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 21


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 22


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 19


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 23


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 24


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 18


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 7


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 5


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 2


title: TNFRSF1A mutation carrier JR TRAPS 2007 Sample 1


title: healthy children  control 6_20_07 Sample 9

value: healthy children  control


title: healthy children  control 6_20_07 Sample 12


title: healthy children  control 6_20_07 Sample 13


title: healthy children  control 6_20_07 Sample 11


title: healthy children  control 6_20_07 Sample 7


title: PSTPIP1 mutation carrier 10_11_07 Sample 15

value: PSTPIP1 mutation carrier


title: healthy children  control 6_20_07 Sample 14


title: healthy children  control 6_20_07 Sample 2


title: PSTPIP1 mutation carrier 10_11_07 Sample 14


title: healthy children  control 6_20_07 Sample 4


title: healthy children  control 6_20_07 Sample 1


title: healthy children  control 6_20_07 Sample 6


title: healthy children  control 6_20_07 Sample 8


title: healthy children  control 6_20_07 Sample 5


title: PSTPIP1 mutation carrier 10_11_07 Sample 13


title: PSTPIP1 mutation carrier 10_11_07 Sample 12


title: healthy children  control 6_20_07 Sample 3


title: PSTPIP1 mutation carrier 10_11_07 Sample 11


title: healthy children  control 6_20_07 Sample 10


title: MVK mutations  10_11_07 Sample 9

value: MVK mutations


title: MVK mutations  10_11_07 Sample 8

value: V377I/ex3 del


title: PSTPIP1 mutation carrier 10_11_07 Sample 10


title: MVK mutations  10_11_07 Sample 7


title: MVK mutations  10_11_07 Sample 4


title: MVK mutations  10_11_07 Sample 5


title: MVK mutations  10_11_07 Sample 2


title: healthy adult control JR TRAPS 2007 Sample 47

value: healthy adult control


title: healthy adult control JR TRAPS 2007 Sample 54


title: two MVK mutations  10_11_07 Sample 1

value: two MVK mutations


title: MVK mutations  10_11_07 Sample 3


title: SCC of the vulva 02-1171 aCGH

hyb_protocol: aCGH was performed using Agilent SurePrint G3 Human CGH Microarray 4 x 180K arrays (Agilent Technologies Inc., Palo Alto, CA, USA).

scan_protocol: All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.

data_processing: Genomic Workbench software (Agilent Technologies Inc.) was used with design file 022060.xml.

source_name: tumor tissue

label_protocol: DNA was labeled according to the manufacturer’s instructions.

extract_protocol: Genomic DNA was extracted from fresh-frozen tissue using the MagAttract DNA Mini M48 kit (Qiagen Inc., Valencia, CA, USA).

tag: differentiation

value: not specified

value: squamous cell carcinoma tumor

tag: individual

source_name: control DNA (supplied by Agilent)

tag: sample type

value: Cat nr G1521 Human Genomic DNA Female from Promega


title: SCC of the vulva 02-869 aCGH

value: well, moderately and poorly differentiated


title: SCC of the vulva 03-1011 aCGH

value: well and moderately differentiated


title: healthy adult control JR TRAPS 2007 Sample 49


title: SCC of the vulva 06-709 aCGH

value: moderately differentiated


title: SCC of the vulva 03-1088 aCGH

value: well differentiated


title: SCC of the vulva 02-167 aCGH


title: SCC of the vulva 02-848 aCGH


title: SCC of the vulva 03-830 aCGH


title: healthy adult control JR TRAPS 2007 Sample 43

value: peripheral blood mononuclear cells


title: Vulvar hyperplasia 03-48 aCGH

value: atypical hyperplasia


title: healthy adult control JR TRAPS 2007 Sample 36


title: SCC of the vulva 09-733 aCGH


title: healthy adult control JR TRAPS 2007 Sample 39


title: SCC of the vulva 02-1060 aCGH


title: SCC of the vulva 09-818 aCGH


title: healthy adult control JR TRAPS 2007 Sample 37


title: SCC of the vulva 06-125 aCGH


title: healthy adult control JR TRAPS 2007 Sample 6


title: healthy adult control JR TRAPS 2007 Sample 13


title: healthy adult control JR TRAPS 2007 Sample 14


title: healthy adult control JR TRAPS 2007 Sample 26


title: healthy adult control JR TRAPS 2007 Sample 17


title: healthy adult control JR TRAPS 2007 Sample 4


title: healthy adult control JR TRAPS 2007 Sample 10


title: healthy adult control JR TRAPS 2007 Sample 12


title: healthy adult control JR TRAPS 2007 Sample 3


title: healthy adult control JR TRAPS 2007 Sample 32


title: NLRP3 mutation carrier 11_30_05 Sample 5

description: total RNA from patient with active disease

value: NLRP3 mutation carrier

value: heterozygous for A374D

value: CAPS


title: NLRP3 mutation carrier 11_30_05 Sample 3

value: heterozygous for V351L


title: NLRP3 mutation carrier 08_16_07 Sample 8

value: heterozygous forL353P


title: NLRP3 mutation carrier 11_30_05 Sample 1

value: heterozygous for T348M


title: NLRP3 mutation carrier 08_16_07 Sample 7

value: heterozygous for R260W


title: NLRP3 mutation carrier 08_16_07 Sample 5

value: heterozygous for D303N


title: NLRP3 mutation carrier 08_16_07 Sample 4


title: NLRP3 mutation carrier 08_13_05 Sample 9

value: heterozygous for L264F


title: NLRP3 mutation carrier 08_16_07 Sample 2


title: NLRP3 mutation carrier 08_16_07 Sample 3


title: NLRP3 mutation negative 08_13_05 Sample 6

value: NLRP3 mutation negative

value: not known


title: NLRP3 mutation carrier 08_13_05 Sample 8


title: NLRP3 mutation carrier 08_16_07 Sample 6


title: NLRP3 mutation carrier 08_13_05 Sample 12

value: heterozygous for F443L


title: NLRP3 mutation carrier 08_13_05 Sample 11

value: heterozygous for V262A


title: lsm8-1 vs Col-0

city: Pozuelo de Alarcón

first: Tamara

last: Hernández-Verdeja

state: Madrid

address: Autovia M-40, Km 38

department: Centre for Plant Biotechnology and Genomics

institute: Universidad Politécnica de Madrid

description: The .CEL files correspond to independent biological replicates.

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix with 7.5 ug of labeled DNA. Array washing and staining as in standard  protocol for tiling array from Affymetrix using GeneChip® Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Tiling Analysis software (TAS) from Affymetrix technology was used to analyze Tiling Array data (.CEL files). The option Two Sample Comparison Analysis was chosen for comparing Col and lsm8-1 hybridizations and both groups were normalized together using quantile normalization plus scaling (scale to target intensity=500).

label_protocol: Double stranded cDNAs were synthesized from 7 ug total RNA primed with random hexamers and incorporating dUTP during first and second strand synthesis. Afterwards, dU-incorporated dsDNAs were fragmented using apurinic/apyrimidinic endonuclease (APE 1) and uracil DNA glycosylase (UDG), and fragments were end-labeled with biotin using terminal deoxynucleotidyl transferase (TdT). All the steps were carried out with GeneChip® Whole Transcript (WT) Double-Stranded Target Assay Kit, following manufacturer instructions. Finally, 7.5 ug of labeled DNA was used for hybridization

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and was purified using Rneasy Mini Kit (QIAGEN) following manufacturer's instructions.

tag: age

value: Rosette

tag: genetotype

value: wt


title: healthy adult control JR TRAPS 2007 Sample 45

value: peripheral blood mononuclear cells

value: healthy adult control


title: ES Lhx6_GFP-

first: Joshua

last: Pollack

state: CA

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

description: Gene expression in differentiated Lhx6-GFP- cells from ES cell culture

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: Dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: FACS purified Lhx6-GFP- cells from differentiated J14 cells

label_protocol: RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays.

growth_protocol: For MGE-Lhx6-GFP+ cells, there is no growth protocol. Cells were isolated fresh from sacrificed embryos. For differentiated ES cells, ES cells were subjected to MGE-differentiated protocol as described in Chen et al., 2013 (PLOS ONE) manuscript. Briefly, ES cells were dissociated into single cells with 0.25% trypsin-EDTA (Invitrogen) and quickly re-aggregated in the differentiation media (GMEM medium supplemented with 10% KSR, 1 mM sodium pyruvate, 0.1 mM NEAA, 0.1 mM 2-ME) containing 100 ng/ml Dkk-1 (5000 cells/100 µl/well) using 96-well low cell adhesion plates (Lipidure-coat plate A-U96, NOF America). On day 3 of differentiation (D3), 20 µl of differentiation media containing SAG (Alexis Biochemicals) was added into each well so that the final concentration of SAG was 6 nM. On D6, ES cell aggregates (embryoid body (EB) aggregates) were transferred to a 10-cm bacterial-grade dish with DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and 6 nM SAG.

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

treatment_protocol: For MGE-Lhx6-GFP+ cells, embryonic 12.5 (E12.5) MGE from Lhx6-GFP transgenic mouse (in CD-1 background) brains were dissected and dissociated into single cells with 0.05% ypsin/EDTA (UCSF CCF) with 10 µg/ml DNase I (Roche) at 37C for 15 min. For differentiated ES cells, On day 12 of MGE differentiation protocol, ES embroic body aggregates from 20 96-wells plates were collected (1920 aggregates) and dissociated with the enzyme solution of the Neural Tissue Dissociation Kit (Sumitomo Bakelite, MB-X9901). Rock inhibitor Y-27632 (10 µM) was added in all the solutions to prevent cell death. Cells were stained with Sytox Blue (Invitrogen, to eliminate dead cells) in 1% BSA/HBSS 15 minutes before FACsorting to distinguish dead vs. live cells. Lhx6-GFP+ cells were sorted with BD FACSAria II using 100µm nozzle and collected in 10% FBS/DMEM/F-12.

tag: strain background

value: 129S4/SvJae strain-derived ES cells (J14) with Lhx6-GFP BAC transgene and 692-mCherry enhancer-reporter viral gene

tag: gender

value: male

value: Differentiated ES cells

tag: developmental stage

value: Differentiated ES cells (12 days in the MGE differentiating protocol)

tag: gfp marker

value: GFP negative


title: Mammary tumor RNA from AKXD RI Strain 25

status: Public on Jan 15 2013

first: Natalie

last: Goldberger

address: 9000 Rockville Pike

institute: NCI

hyb_protocol: Slides were hybridized at 56C for 16 hrs following the miRCURY LNA microRNA Array Power Labeling kit (Exiquon Inc) instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Agilent Feature Extraction Software (version A.7.5) was used for LOWESS normalized and background subtraction.

source_name: mammary tumor

label_protocol: Total RNA (1 ug) was labeled using the miRCURY LNA microRNA Array Power Labeling kit (Exiquon Inc) following manufacturer's instructions.

extract_protocol: Total RNA was extracted using the mirVana Isolation Kit (Ambion) following manufacturer's instructions.

tag: strain

value: [FVB/N-TgN(MMTV-PyVT)634Mul x AKXD R1]F1 sublines

tag: tissue

value: mammary tumor

source_name: FirstChoice Total RNA Ambion (AM7800)

value: Swiss Webster mice

value: various


title: Mammary tumor RNA from AKXD RI Strain 27


title: Mammary tumor RNA from AKXD RI Strain 28


title: NLRP3 mutation carrier 08_13_05 Sample 10

tag: cell type

value: NLRP3 mutation carrier

value: heterozygous for T348M

value: CAPS


title: NLRP3 mutation carrier 08_12_05 Sample 5

tag: genotype

value: heterozygous for G326E


title: Mammary tumor RNA from AKXD RI Strain 24


title: ES Lhx6_GFP+

description: Gene expression in differentiated Lhx6-GFP+ cells from ES cell culture

source_name: FACS purified Lhx6-GFP+ cells from differentiated J14 cells

value: GFP positive


title: Mammary tumor RNA from AKXD RI Strain 23


title: NLRP3 mutation carrier 08_12_05 Sample 7

tag: disease causing mutation

value: heterozygous for D303N


title: NLRP3 mutation carrier 08_13_05 Sample 13

value: peripheral blood mononuclear cells

value: heterozygous for L632F

tag: disease state