title: Blood_15mg silica, 1 week post-exposure_rep4

source_name: 15mg/m3 silica, 1 week post-exposure rat 68 blood

tag: strain

tag: gender

value: 3 mo

tag: tissue

value: blood

value: 1 week post-exposure


title: ECRG4 set: BC30

status: Public on Dec 02 2011

type: RNA

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA using a quantile normalization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human breast cancer tumors

label_protocol: Affymetrix standard protocol

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalB

value: breast cancer tumor


title: 10403S_BMM_4hrs_repB

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

country: USA

institute: The University of Chicago

description:
WT 10403S LM in BMM  B
Biological replicate 2 of 2.

hyb_protocol: Applied to spotted arrays in binding buffer containing HEPES, SSC, tRNA, and SDS at 63 °C for 48 hours (see Leber et al., PloS Pathogens, 2008 (PMID 18193943) for more detail).

scan_protocol: Images were scanned on a Molecular Devices GenePix 4100B scanner using GenePix Pro software.

data_processing: Background-subtracted data obtained from log2 of processed Red signal/processed Green signal using GenePix Pro software.

organism: Listeria monocytogenes

source_name: WT 10403S LM grown in BMM

label_protocol: 5 ug amplified RNA was reacted with Cy dye for 60 min, and purified using Zymo clean and concentrate columns (see Leber et al., PloS Pathogens, 2008 (PMID 18193943) for more detail).

growth_protocol: WT C57BL6 mouse bone marrow-derived macrophages (BMM), 37 °C, 4 hours post-infection.

extract_protocol: Trizol with silica beads in MP FastPrep.

tag: genotype

value: wild-type

tag: host

value: mouse bone marrow-derived macrophages

tag: time post-infection

value: 4 hours

source_name: Pooled reference total RNA from all 4 samples used in this experiment

tag: sample type

value: reference


title: Blood_15mg silica, 16 week post-exposure_rep5

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description: The labeling and hybridization of microarray were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc (San Diego, CA), each labeled cRNA sample was hybridized to RatRef-12 v1.0 expression beadchip (Illumina, Inc) for 20 hrs at 580C. Following hybridization, microarrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc). This was followed by a non-stringent washing to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, following the protocol provided by the manufacturer (Illumina, Inc, San Diego, CA).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the expression data were carried out in R/Bioconductor using the 'lumi' and 'limma' packages. The 'lumi' Bioconductor package covered the data input, quality control, force positive background correction, variance stabilization, normalization and gene annotation (http://bioconductor.org/packages/2.2/bioc/vignettes/lumi/inst/doc/lumi.pdf). Robust spline normalization was used to generate the values in the matrix table. After normalization, Lumi code deletes undetected genes, resulting in a subset of genes detected on the array. A linear model analysis using the 'limma' package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes. Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

organism: Rattus norvegicus

source_name: 15mg/m3 silica, 16 week post-exposure rat 5 blood

label_protocol: Biotin-labeled cRNA was generated from 375 ng RNA samples each by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72± 50 F), and humidity (50 ± 20%) with free access to food and water.

extract_protocol: Total RNA was isolated from the blood samples using Mouse RibopureTM Blood isolation kit (Ambion Inc, Austin, TX) following the protocol provided by the kit manufacturer. The total RNA isolated was digested with RNase-free DNase and further purified using RNeasy Mini kit (Qiagen Inc, Valencia, CA) following the recommendations of the supplier. The globin mRNA present in abundance in the blood RNA samples was depleted using the GlobinclearTM – Mouse/Rat globin mRNA removal kit (Ambion Inc, Austin, TX).

treatment_protocol: Rats were exposed to air (control) or crystalline silica by inhalation (1, 2, or 15 mg/m3, 6 hours/day, 5 days). Rats exposed to 1 or 2 mg/m3, 6 hours/day, 5 days and the corresponding control were sacrificed at 16-hours following the last silica exposure. Rats exposed to 15 mg/m3, 6 hours/day, 5 days and corresponding controls were sacrificed at post-exposure time intervals of 0, 1, 2, 4, 8, and 16 weeks.

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: tissue

tag: treatment

value: 15mg silica

tag: time

value: 16 week post-exposure


title: 10403S_BMM_4hrs_repA

description:
WT 10403S LM in BMM  A
Biological replicate 1 of 2.


title: ECRG4 set: BC31

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

value: Basal


title: D105-1A-T_2

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Gene expression data from LMD nascent tumor cells

hyb_protocol: According to manf. protocol

scan_protocol: According to manf. Protocol Genechip 3000 Scanner

data_processing: Affymetrix Microarray Analysis Suite version 5.0., arrays were then imported into PartekGS (Partek Inc) and RMA normalized using default settings

organism: Mus musculus

source_name: Day 105, LMD

label_protocol: RNA from both PC and OG samples were put through two rounds of linear amplification using Affymetrix’s GeneChip 2-cycle cDNA Synthesis Kit according to the manufacturer’s protocol. The quality of the amplified and fragmented RNAs was assessed by the RNA 6000 Nano Labchip /2100  Bioanalyzer (Agilent). 20-50 ng of total intact RNA was labeled, fragmented and biotin labled.

growth_protocol: 8 week old mice

extract_protocol: Frozen sections of ip oil granulomata were fixed in 70% ethanol for 20 seconds, stained to identify plasma cells using methyl green pyronin (MGP) (Sigma)17 that also contained 300 U/mL of an RNase inhibitor (Superasin, Ambion) for two minutes with slight agitation, destained by a quick dip in RNAase-free water followed by two changes of 100% ethanol (3 and 30 seconds, respectively), dehydrated in two changes of xylene for 2 minutes each, and allowed to air dry. MGP-positive cells were microdissected on a Leica LMD6000 into 0.5 mL RNase-free tube caps containing 50 μL of RLT extraction buffer (Qiagen). Total RNA from both laser-microdissected MGP-positive cells (PC samples) and whole, undissected tissue (OG samples) sections was isolated using Allprep DNA/RNA Micro kits (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed via both NanoDrop 2000 Spectrophotometer (Thermo) and Agilent’s RNA 6000 Pico Labchip and 2100 Bioanalyzer. Samples showing degradation were not used in this investigation.

treatment_protocol: Two independent cohorts of BALB/c.iMycEμ mice were aged at least 8 weeks, allocated to 2 study groups and injected intraperitoneally with 0.5 ml of pristane (2,6,10,14-tetramethylpentadecane) oil.

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 2


title: D49-2A-T_1

source_name: Day 49, LMD


title: D49-2A-T_3


title: Blood_0mg silica, 8week post-exposure_rep4

institute: National Institute for Occupational Safety and Health

source_name: 0mg/m3 silica, 8 week post-exposure rat 28 blood

value: 3 mo

value: 0mg silica

value: 8week post-exposure


title: D49-1A-T_3


title: ECRG4 set: BC29

value: IDC

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalA


title: D49-1A-T_1


title: Blood_0mg silica, 1 week post-exposure_rep4

source_name: 0mg/m3 silica, 1 week post-exposure rat 76 blood

tag: strain

tag: gender

tag: age

tag: tissue

value: blood

tag: treatment

value: 1 week post-exposure


title: Blood_0mg silica, 2 week post-exposure_rep3

source_name: 0mg/m3 silica, 2 week post-exposure rat 59 blood

tag: time

value: 2 week post-exposure


title: ECRG4 set: BC26

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

value: breast cancer tumor


title: Blood_15mg silica, 4 week post-exposure_rep4

source_name: 15mg/m3 silica, 4 week post-exposure rat 36 blood

value: 4 week post-exposure


title: D33-3A-T_1

source_name: Day 33, LMD

tag: background strain

tag: tissue type

tag: experiment


title: ECRG4 set: BC27

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt


title: D33-3A-T_3


title: ECRG4 set: BC28

value: TUB

tag: dfs time (months)

tag: molecular subtype


title: Blood_15mg silica, 0 week post-exposure_rep4

source_name: 15mg/m3 silica, 0 week post-exposure rat 84 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: tissue

tag: treatment

value: 0 week post-exposure


title: Blood_0mg silica, 0 week post-exposure_rep3 (control for 15mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 91 blood (control for 15mg/m3 silica)

tag: time


title: ECRG4 set: BC25

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

value: Basal


title: ec-brac-ex-15_4

city: North Chicago

first: J

middle: Wade

last: Davis

address: 1 N Waukegan Rd

institute: AbbVie

hyb_protocol: 130 µl of hybridization solution containing 50 ng/µl of fragmented aRNA was hybridized to the porcine genome array genechip (Affymetrix, Santa Clara, CA) at 45ºC for 20 hrs.  After hybridization, the chips were washed and stained with R-phycoerythrin-streptavidin on Affymetrix fluidics station 450 using fluidics protocol Midi_euk2v3-450.

scan_protocol: The microarrays were then scanned and data acquired using an Afflymetrix GeneChip Scanner 3000 driven by GCOS 1.2 software (Afflymetrix)

data_processing: The RAW CEL files were analyzed primarily with the Bioconductor affy package. Probel-level summaries were constructed using the expresso function with the following settings: bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=medianpolish. Non-specific filtering was then run using the Bioconductor genefilter package wiht the nsFilter function with following settings: require.entrez=FALSE, require.GOBP=FALSE, require.GOCC=FALSE, require.GOMF=FALSE, require.CytoBand=FALSE, remove.dupEntrez=FALSE, var.func=IQR, var.cutoff=0.5, var.filter=TRUE, filterByQuantile=TRUE, feature.exclude=c(^AFFX,^RPTR)

organism: Sus scrofa

source_name: endothelial cells, brachial artery, exercised pig

label_protocol: Half microgram of porcine tissue total RNA was used to make the biotin-labeled antisense RNA (aRNA) target using the MessageAmpTM Premier RNA amplification kit (Ambion, Austin, TX) by following the manufacturer’s procedures.  Briefly, the total RNA was reverse transcribed to first strand cDNA with a oligo(dT) primer bearing a 5’-T7 promoter using ArrayScript reverse transcriptase.  The first strand cDNA then underwent second-strand synthesis to convert into double stranded cDNA template for in vitro transcription.  The biotin-labeled aRNA was synthesized using T7 RNA transcriptase with biotin-NTP mix.  After purification, the aRNA was fragmented in 1X fragmentation buffer at 94ºC for 35 min.

extract_protocol: After completion of the exercise intervention or sedentary confinement, and ~24 h following the last exercise bout, pigs were sedated with ketamine (25 mg/kg im) and Rompun (2.25 mg/kg im). Pigs were then anesthetized with phentobarbital sodium (20 mg/kg iv), intubated and ventilated with room air, and euthanized by removal of the heart in full compliance with the American Veterinary Medical Association Guidelines on Euthanasia.  Immediately following sacrifice, the brachial and internal mammary arteries were harvested, rinsed with ice-cold Krebs saline, and stored in 10 volumes of a cold RNA stabilizing agent (RNAlater, Ambion).  On the same day as sacrifice, and while remaining wetted with the RNAlater solution, arteries were dissected clean of excess adventitia, opened with one full-length longitudinal cut through the vessel wall and laid open, lumen side up.  Excess solution was gently blotted away with a clean kimwipe and the vessel’s luminal surface was covered with a minimal volume of TRI Reagent.  After 30 seconds of incubation, the endothelium was gently scraped with a sterile scalpel blade.  The remainder of a 1 ml volume of TRI Reagent was pipetted across the lumen surface and the wash/endothelial cell slurry was collected into a 1.5 ml microcentrifuge tube.  Each sample was passed through a 20 ga needle attached to a plastic syringe 10 times to insure a homogenous lysate.   This method of scraping the luminal surface yields an endothelial enriched sample, as demonstrated by us (42) and others (8, 25, 44).  Phenol-chloroform isolation of total RNA was performed for each sample per the TRI Reagent manufacturer’s protocol (Ambion).  Product was eluted in a 26 µl volume with a 2 µl aliquot being used for spectrophotometric quantification.  Twenty-five nanograms of each sample were used in an Experion StdSens RNA Analysis to confirm concentration and quality of RNA.

treatment_protocol: The pigs in the exercise group completed a 16-20 week endurance training program on the treadmill. The intensity and duration of exercise bouts increased steadily so that by week 10 of training the pigs ran 85 min/day, 5 days/week.  The 85-min training bouts consisted of a 5 min warm-up, a 15 min sprint run at 6-8 mph, a 60 min endurance run at 4-6 mph, and a 5 min cool-down.  Pigs assigned to the sedentary group were restricted to their enclosures and did not exercise.

value: Endothelial cells

value: exercised

tag: artery type

value: brachial

tag: pigid

tag: date

tag: quality grade

value: B-

tag: totalrna amount

tag: dna core


title: ec-brac-ex-15_2


title: ec-brac-ex-14_3

value: B


title: ec-brac-ex-12_5


title: D33-2D-T_2

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 2


title: D33-1C-T_4


title: ECRG4 set: BC24

value: IDC

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalB

tag: tissue


title: D33-1B-T_1


title: ECRG4 set: BC23

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade


title: ECRG4 set: BC22

value: LuminalA


title: D33-2A-T_1


title: ec-brac-ex-11_3

tag: treatment

tag: artery type

tag: pigid

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: Blood_15mg silica, 2 week post-exposure_rep6

source_name: 15mg/m3 silica, 2 week post-exposure rat 54 blood

tag: strain

tag: gender

tag: age

value: 3 mo

value: blood

value: 15mg silica

tag: time

value: 2 week post-exposure


title: ec-brac-ex-10_5

tag: tissue


title: Blood_0mg silica, 4week post-exposure_rep3

source_name: 0mg/m3 silica, 4 week post-exposure rat 43 blood

value: CDF Fisher 344

value: male

value: 0mg silica

value: 4week post-exposure


title: Blood_0mg silica, 8week post-exposure_rep1

source_name: 0mg/m3 silica, 8 week post-exposure rat 25 blood

value: 8week post-exposure


title: ec-brac-ex-10_1

value: Endothelial cells

value: exercised

value: brachial


title: ECRG4 set: BC21

source_name: human breast cancer tumors

tag: age at diagnosis

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: breast cancer tumor


title: ec-brac-sed-17_1

source_name: endothelial cells, brachial artery, sedentary pig

tag: treatment

value: sedentary

tag: artery type

tag: pigid

tag: date

value: B-


title: Blood_15mg silica, 2 week post-exposure_rep2

source_name: 15mg/m3 silica, 2 week post-exposure rat 50 blood

tag: strain


title: ECRG4 set: BC18

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

value: Basal


title: ec-brac-sed-12_3

tag: tissue

tag: quality grade

value: B+

tag: totalrna amount

tag: dna core


title: Blood_15mg silica, 0 week post-exposure_rep2

source_name: 15mg/m3 silica, 0 week post-exposure rat 82 blood

tag: gender

tag: age

value: 3 mo

value: blood

tag: time

value: 0 week post-exposure


title: D17-2A-T_3

source_name: Day 17, LMD

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 2


title: ec-brac-sed-15_1

tag: treatment

tag: artery type

tag: pigid


title: ECRG4 set: BC19

tag: age at diagnosis

tag: histology

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalA


title: D17-3B-T_3


title: D7-3A-T_3

source_name: Day 7, LMD


title: ECRG4 set: BC16

tag: pt

tag: pn

tag: sbr grade

value: LuminalB

tag: tissue


title: ec-brac-sed-11_1

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: ECRG4 set: BC15

tag: age at diagnosis

value: ILC


title: ECRG4 set: BC20

tag: histology

value: other


title: D17-3B-T_2

tag: background strain

tag: tissue type

tag: experiment


title: Blood_0mg silica, 16week post-exposure_rep3

source_name: 0mg/m3 silica, 16 week post-exposure rat 11 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

value: 0mg silica

tag: time

value: 16week post-exposure


title: ec-brac-sed-11_4

value: Endothelial cells

value: sedentary

tag: artery type

value: brachial

tag: pigid


title: D17-1B-T_1


title: ECRG4 set: BC14

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: Basal

tag: tissue

value: breast cancer tumor


title: ec-brac-sed-10_2

tag: date

tag: quality grade

value: B+

tag: totalrna amount

tag: dna core


title: Blood_0mg silica, 0 week post-exposure_rep1 (control for 15mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 89 blood (control for 15mg/m3 silica)

tag: strain

tag: gender

tag: age

value: 3 mo

value: blood

tag: treatment

tag: time

value: 0 week post-exposure


title: Blood_0mg silica, 2 week post-exposure_rep4

source_name: 0mg/m3 silica, 2 week post-exposure rat 60 blood

value: 2 week post-exposure


title: ec-brac-sed-13_2

tag: artery type

tag: pigid

value: B-


title: Blood_15mg silica, 4 week post-exposure_rep2

source_name: 15mg/m3 silica, 4 week post-exposure rat 34 blood

value: 15mg silica

value: 4 week post-exposure


title: ECRG4 set: BC13

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

value: LuminalB


title: ECRG4 set: BC17

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

tag: tissue


title: ec-ima-ex-15_2

source_name: endothelial cells, internal mammary artery, sedentary pig

tag: treatment

value: exercised

value: internal mammary

tag: date

tag: quality grade

value: B

tag: totalrna amount

tag: dna core


title: Blood_15mg silica, 16 week post-exposure_rep7

source_name: 15mg/m3 silica, 16 week post-exposure rat 7 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: time

value: 16 week post-exposure


title: D17-1B-T_2

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 2


title: D7-2A-T_2


title: Blood_0mg silica, 1 week post-exposure_rep1

source_name: 0mg/m3 silica, 1 week post-exposure rat 73 blood

value: 0mg silica

value: 1 week post-exposure


title: D17-2A-T_4


title: D7-1B-T_1


title: Blood_15mg silica, 1 week post-exposure_rep2

source_name: 15mg/m3 silica, 1 week post-exposure rat 66 blood

value: 3 mo

value: blood


title: ECRG4 set: BC11

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

value: Basal

value: breast cancer tumor


title: ec-ima-ex-11_3

tag: tissue

value: Endothelial cells

tag: treatment

tag: artery type

tag: pigid

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: ec-ima-ex-10_5

value: B+


title: ec-ima-ex-15_4

value: exercised


title: D7-3A-T_2

tag: background strain

tag: tissue type

tag: experiment


title: Blood_15mg silica, 8 week post-exposure_rep6

source_name: 15mg/m3 silica, 8 week post-exposure rat 22 blood

tag: strain

tag: gender

tag: age

value: 15mg silica

tag: time

value: 8 week post-exposure


title: ec-ima-ex-12_2

value: internal mammary

value: B


title: ECRG4 set: BC7

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: dfs evt

tag: dfs time (months)

tag: molecular subtype

value: LuminalA


title: ec-ima-ex-10_1

tag: tissue

tag: treatment

tag: artery type

tag: pigid

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: ec-ima-ex-14_3


title: Blood_15mg silica, 0 week post-exposure_rep3

source_name: 15mg/m3 silica, 0 week post-exposure rat 83 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: time

value: 0 week post-exposure


title: ec-ima-sed-17_1

value: sedentary


title: D7-1B-T_2

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 2


title: ec-ima-sed-15_1


title: Blood_0mg silica, 4week post-exposure_rep1

source_name: 0mg/m3 silica, 4 week post-exposure rat 41 blood

value: 3 mo

value: blood

value: 0mg silica

value: 4week post-exposure


title: ECRG4 set: BC5

source_name: human breast cancer tumors

tag: age at diagnosis

tag: histology

value: IDC

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: breast cancer tumor


title: ec-ima-ex-12_5

tag: tissue

value: Endothelial cells

tag: treatment

value: exercised

tag: artery type

tag: pigid

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: D7-2A-T_3

tag: background strain

tag: tissue type

tag: experiment


title: D33-5

description: Gene expression data from nascent tumor cells

source_name: Day 33, whole tissue

value: Whole tissue sections of ip oil granulomata

value: study 1


title: D104-4687-3

source_name: Day 104, whole tissue


title: ECRG4 set: BC12

tag: age at diagnosis

tag: histology

tag: pt

tag: pn

tag: sbr grade

tag: er ihc

tag: molecular subtype

value: Basal


title: Blood_0mg silica, 0 week post-exposure_rep4 (control for 15mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 92 blood (control for 15mg/m3 silica)

tag: strain

value: CDF Fisher 344

tag: gender

tag: age

tag: tissue

tag: treatment

tag: time


title: ECRG4 set: BC9

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalB


title: ECRG4 set: BC4

tag: age at diagnosis

tag: histology


title: Blood_15mg silica, 2 week post-exposure_rep7

source_name: 15mg/m3 silica, 2 week post-exposure rat 55 blood

value: male

value: 15mg silica

value: 2 week post-exposure


title: ec-ima-sed-12_3

value: sedentary

tag: artery type

value: internal mammary

tag: pigid

tag: date

tag: quality grade

value: B

tag: totalrna amount

tag: dna core


title: ECRG4 set: BC2

tag: pn

tag: sbr grade

tag: er ihc

tag: molecular subtype


title: ECRG4 set: BC8

tag: pt

tag: pr ihc

value: Normal

tag: tissue


title: D104-4687-2

tag: background strain

tag: tissue type

tag: experiment


title: ECRG4 set: BC10

tag: age at diagnosis

tag: histology

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)


title: D17-10B

source_name: Day 17, whole tissue


title: D7-3B

source_name: Day 7, whole tissue


title: Blood_0mg silica, 2 week post-exposure_rep2

source_name: 0mg/m3 silica, 2 week post-exposure rat 58 blood

tag: strain

tag: gender

tag: age

value: 3 mo

value: blood

tag: treatment

value: 0mg silica

tag: time


title: ECRG4 set: NB3

hyb_protocol: see Affymetrix standard protocols

scan_protocol: see Affymetrix standard protocols

data_processing: RMA. Controls were removed, like all genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples. Data were then log2 transformed.

source_name: Normal Breast

label_protocol: see Affymetrix standard protocols

tag: center

value: IPC

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs

tag: mfsdel (month)


title: D104-4687-1

tag: background strain

tag: tissue type

tag: experiment


title: D33-16


title: ec-ima-sed-10_2

tag: tissue

value: Endothelial cells

tag: treatment

tag: artery type

tag: pigid

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: D17-10A

value: Whole tissue sections of ip oil granulomata


title: D7-3A

value: study 1


title: Blood_0mg silica, 16week post-exposure_rep1

source_name: 0mg/m3 silica, 16 week post-exposure rat 9 blood

tag: strain

tag: gender

tag: age

tag: time

value: 16week post-exposure


title: ECRG4 set: NB4

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs


title: Blood_15mg silica, 1 week post-exposure_rep3

source_name: 15mg/m3 silica, 1 week post-exposure rat 67 blood

tag: strain

value: CDF Fisher 344

tag: gender

tag: age

tag: tissue

tag: treatment

tag: time

value: 1 week post-exposure


title: Blood_15mg silica, 4 week post-exposure_rep3

source_name: 15mg/m3 silica, 4 week post-exposure rat 35 blood

value: male

value: 4 week post-exposure


title: ECRG4 set: NB2

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: mfsdel (month)


title: D33-14

tag: background strain

tag: tissue type

tag: experiment


title: D7-1


title: ECRG4 set: BC6

tag: age at diagnosis

value: IDC

tag: sbr grade

tag: er ihc

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

tag: tissue

value: breast cancer tumor


title: Blood_0mg silica, 1 week post-exposure_rep3

source_name: 0mg/m3 silica, 1 week post-exposure rat 75 blood

tag: strain

tag: gender

tag: age

tag: treatment

tag: time


title: ec-ima-sed-13_2

source_name: endothelial cells, internal mammary artery, sedentary pig

value: sedentary

tag: artery type

value: internal mammary

tag: pigid

tag: date

tag: quality grade

tag: totalrna amount

tag: dna core


title: Blood_0mg silica, 0 week post-exposure_rep2 (control for 15mg silica)

source_name: 0mg/m3 silica, 0 week post-exposure rat 90 blood (control for 15mg/m3 silica)

value: 0 week post-exposure


title: D17-12

tag: background strain

tag: tissue type

tag: experiment


title: Day104_4687_12-21-06

source_name: Day 104, LMD

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata


title: Blood_0mg silica, 4week post-exposure_rep4

source_name: 0mg/m3 silica, 4 week post-exposure rat 44 blood

value: 3 mo

value: blood

value: 4week post-exposure


title: Day104_4687_10-2-06


title: ECRG4 set: BC11979

source_name: Breast cancer

tag: center

value: IPC

tag: type

value: IBC

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

value: DUC

tag: pt

tag: pn

value: pos

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

value: neg

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs

tag: mfsdel (month)


title: Breast cancer tumor sample301

description: Primary breast tumor

source_name: human breast cancer tumors

tag: age at diagnosis

value: positive

tag: er ihc

value: negative

tag: prihc

tag: molecular subtype

value: Basal

tag: tissue


title: Blood_0mg silica, 2 week post-exposure_rep1

source_name: 0mg/m3 silica, 2 week post-exposure rat 57 blood

tag: strain

value: CDF Fisher 344

tag: gender

value: male

tag: age

tag: treatment

value: 0mg silica

tag: time

value: 2 week post-exposure


title: Blood_0mg silica, 16week post-exposure_rep2

source_name: 0mg/m3 silica, 16 week post-exposure rat 10 blood

value: 16week post-exposure


title: ECRG4 set: BC3

tag: pn

tag: sbr grade

tag: pr ihc

tag: p53 ihc

tag: ki67 ihc

tag: dfs evt

tag: dfs time (months)

value: LuminalB

value: breast cancer tumor


title: Blood_0mg silica, 8week post-exposure_rep3

source_name: 0mg/m3 silica, 8 week post-exposure rat 27 blood

value: 3 mo

value: blood

value: 8week post-exposure


title: Blood_15mg silica, 2 week post-exposure_rep1

source_name: 15mg/m3 silica, 2 week post-exposure rat 49 blood

value: 15mg silica


title: ECRG4 set: BC1

tag: age at diagnosis

tag: histology

value: IDC

tag: pt


title: Breast cancer tumor sample260

description: Primary breast tumor

tag: er ihc

tag: prihc

tag: molecular subtype


title: ec-ima-sed-11_4

tag: tissue

value: Endothelial cells

value: sedentary

tag: artery type

value: internal mammary

tag: pigid

tag: date

tag: quality grade

value: C

tag: totalrna amount

tag: dna core


title: Blood_15mg silica, 8 week post-exposure_rep2

source_name: 15mg/m3 silica, 8 week post-exposure rat 18 blood

tag: strain

tag: gender

tag: age

tag: treatment

tag: time

value: 8 week post-exposure


title: ec-ima-sed-11_1

value: B


title: Day104_4687_3-13-07

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 1


title: Breast cancer tumor sample251

description: Primary breast tumor

tag: age at diagnosis

tag: pt

tag: pn

value: negative

tag: er ihc

tag: prihc

value: positive

value: Basal


title: Blood_0mg silica, 1 week post-exposure_rep2

source_name: 0mg/m3 silica, 1 week post-exposure rat 74 blood

value: CDF Fisher 344

value: male

tag: tissue

value: 0mg silica

value: 1 week post-exposure


title: Day46B_4547_4-2-07

source_name: Day 46, LMD


title: Blood_15mg silica, 16 week post-exposure_rep6

source_name: 15mg/m3 silica, 16 week post-exposure rat 6  blood

value: 3 mo

value: blood

value: 15mg silica

value: 16 week post-exposure


title: porcine primary umbilical cord cell p4

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: RNA from pUC cultured in DMEM/10%FBS, 4ng/ml FGF2 medium

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The expression data were extracted using the Micro-Array Suite 5.0 software (Affymetrix).

source_name: primary cultures established from explants of porine umbilical cord at day 34 of pregnancy

label_protocol: 10 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix)

growth_protocol: pESK cells cultured in KP/CH medium on MEF feeder

extract_protocol: RNA from pESK cells and porcine primary umbilical cord cells was extracted using STAT-60 reagent.

treatment_protocol: ICMs were subjected lentiviral transduction with hKLF4 and M2rtTA virus under 4% O2 and 5% CO2 air at 38.5ºC. Two days following transduction the blastomeres were plated onto irradiated MEF feeders and cultured two weeks for development of stem cell colonies.

tag: breed

value: Landrace

value: unknown


title: Breast cancer tumor sample243

description: Primary breast tumor

tag: molecular subtype

value: breast cancer tumor


title: Day_33_1-25-07

source_name: Day 33, LMD


title: Breast cancer tumor sample309

description: Primary breast tumor

value: LuminalA


title: Blood_15mg silica, 1 week post-exposure_rep1

source_name: 15mg/m3 silica, 1 week post-exposure rat 65 blood


title: ECRG4 set: NB1

source_name: Normal Breast

tag: center

value: IPC

tag: type

tag: age of diagnosis (year)

tag: histology

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs

tag: mfsdel (month)


title: pESK II, passage 5

description: RNA from pESK II cultured in KP/CH medium on MEF feeder for 3 days

source_name: ICMs isolated by immunosurgery from in vitro-produced d 5.5 porcine blastocysts were transduced with human KLF4 by lentiviral and stem cell colonies were derived.

tag: breed

tag: gender

value: Male


title: Day_7_003

source_name: Day 7, LMD

tag: background strain

tag: tissue type

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

tag: experiment

value: study 1


title: Day46_4546_4-9-07


title: Blood_15mg silica, 0 week post-exposure_rep1

source_name: 15mg/m3 silica, 0 week post-exposure rat 81 blood

tag: strain

tag: age

tag: tissue

tag: treatment

tag: time

value: 0 week post-exposure


title: Day46A_4547_4-2-07


title: Breast cancer tumor sample242

description: Primary breast tumor

tag: age at diagnosis

tag: pn

value: negative

tag: er ihc

tag: prihc

tag: molecular subtype

value: Normal


title: pESK I, passage 14

description: RNA from pESK I cultured in KP/CH medium on MEF feeder for 3 days

source_name: Physically dissociated ICMs from in vitro-produced d 5.5 porcine blastocysts were transduced with human KLF4 by lentiviral and stem cell colonies were derived.


title: Blood_0mg silica, 4week post-exposure_rep2

source_name: 0mg/m3 silica, 4 week post-exposure rat 42 blood

value: CDF Fisher 344

value: male

value: 0mg silica

value: 4week post-exposure


title: Day104_4687_4-9-07

source_name: Day 104, LMD


title: Blood_15mg silica, 16 week post-exposure_rep1

source_name: 15mg/m3 silica, 16 week post-exposure rat 1 blood

value: 3 mo

value: blood

value: 15mg silica


title: Breast cancer tumor sample237

description: Primary breast tumor

source_name: human breast cancer tumors

tag: pt

value: Basal


title: Breast cancer tumor sample238

description: Primary breast tumor

value: positive

value: breast cancer tumor


title: Breast cancer tumor sample249

description: Primary breast tumor


title: Day104_4687_3-26-07


title: Breast cancer tumor sample241

description: Primary breast tumor


title: Blood_15mg silica, 4 week post-exposure_rep1

source_name: 15mg/m3 silica, 4 week post-exposure rat 33 blood

value: 4 week post-exposure


title: Blood_0mg silica, 8week post-exposure_rep2

source_name: 0mg/m3 silica, 8 week post-exposure rat 26 blood

value: 8week post-exposure


title: Day33_14_12-19-06

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata


title: Breast cancer tumor sample235

description: Primary breast tumor


title: Breast cancer tumor sample231

description: Primary breast tumor


title: Day46_4544_12-19-06

value: study 1


title: Day46_4544_3-19-07


title: Blood_15mg silica, 8 week post-exposure_rep1

source_name: 15mg/m3 silica, 8 week post-exposure rat 17 blood

value: 8 week post-exposure


title: Day33_14_12-21-06


title: Day33_5-1_9-3-06


title: A498-Vector-rep1

city: Boston

first: Chuan

last: Shen

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: A498 cells inducibly express Luciferase Replicate 1

hyb_protocol: The fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The Human ST 1.0 array chips are then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing: Raw expression data was processed using DNA-Chip Analyzer (dChip) custom software (http://www.dChip.org/).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in 37 degree incubator with 5% CO2

extract_protocol: Total RNA was extracted with Rneasy kit according to the manufacturer's recommendation

treatment_protocol: Doxycyline (1 ug/ml) was used for doxycycline-inducible cells

tag: cell type

value: renal carcinoma cells

tag: cell line

tag: infection

value: Vector


title: Day33_5-2_9-3-06

tag: background strain


title: A498-HIF1A-rep2

description: A498 cells inducibly express HIF1alpha Replicate 2


title: A498-HIF1A-rep1

description: A498 cells inducibly express HIF1alpha Replicate 1


title: Breast cancer tumor sample233

description: Primary breast tumor

value: negative


title: Breast cancer tumor sample230

description: Primary breast tumor


title: Breast cancer tumor sample221

description: Primary breast tumor


title: Caki-2-Scr-shRNA-rep2

description: Caki-2 cells stably express scramble shRNA Replicate 2

value: Scr-shRNA


title: Caki-2-HIF1A-shRNA-rep2

description: Caki-2 cells stably express HIF1alpha shRNA Replicate 1


title: Caki-2-Scr-shRNA-rep1

description: Caki-2 cells stably express scramble shRNA Replicate 1


title: Breast cancer tumor sample210

description: Primary breast tumor


title: Caki-2-HIF1A-shRNA-rep1


title: Day17_11-1_9-2-06

source_name: Day 17, LMD

tag: tissue type


title: Breast cancer tumor sample222

description: Primary breast tumor


title: Day17_12_1-18-07

tag: experiment


title: Day17_4-3_9-2-06


title: preMBT_H3K4me3 Repl1

type: genomic

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (ChIP/Input) with biweight mean of values subtracted

molecule: genomic DNA

organism: Danio rerio

source_name: preMBT H3K4me3 ChIP DNA

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: Fish and embryos grown as per AAALAC certification

extract_protocol: Histone ChIPs were done as described (Dahl, Collas, 2007) using 0.5 A260 units chromatin per ChIP. In short, dechorionated embryos were cross-linked with 1% formaldehyde for 8 min and quenched with glycine. Lysis buffer was added and samples incubated for 5 min on ice. Cells were sonicated on ice using a Bioruptor (Diagenode) to produce fragments of 400 bp or less. The lysate was centrifuged, the supernatant collected, and chromatin was incubated with 2.4 μg antibody coupled to Dynabeads Protein A (Invitrogen) for 2 h ro overnight at 4oC. ChIP material was washed, elution buffer containing 1 % SDS and 50 µg/ ml Proteinase K was added and samples incubated for 2 h at 68oC on a Thermomixer (Eppendorf); after a second extraction both supernatants were pooled. ChIP DNA was purified by phenol-chloroform isoamylalcohol extraction, ethanol-precipitated and dissolved in 50 μl TE buffer. 5 µg (10 µl) RNase A (Roche) was added before ChIP DNA elution. ChIP DNA samples were dissolved in 16 μl MilliQ water. Input DNA (channel 2) was purified by phenol-chloroform isoamylalcohol extraction and RNAse-treated as above.

value: Embryonic cells

tag: source

value: AB strain zebrafish embryos

tag: developmental stage

value: preMBT, 2.5 hpf, 256-cell stage

tag: chip antibody

tag: vendor

value: Diagenode pAb-003-050

source_name: preMBT H3K4me3 Input DNA

tag: antibody


title: Breast cancer tumor sample188

description: Primary breast tumor

tag: age at diagnosis

tag: tissue


title: A498-Vector-rep2

description: A498 cells inducibly express Luciferase Replicate 2


title: SLR24-HIF1A-rep2

description: SLR24 cells inducibly express HIF1alpha Replicate 2


title: postMBT_polii Repl1

source_name: postMBT polii ChIP DNA

value: postMBT, 5.3 hpf, 50% epiboly

value: RNA Pol II

value: Santa Cruz sc-899

source_name: postMBT polii Input DNA


title: Day7_8_1-18-07


title: Day17_3-1_9-2-06


title: SLR24-HIF1A-rep1

description: SLR24 cells inducibly express HIF1alpha Replicate 1


title: postMBT_H3K9me3 Repl2

source_name: postMBT H3K9me3 ChIP DNA

value: Diagenode pAb-056-50

source_name: postMBT H3K9me3 Input DNA


title: Day17_11-2_9-2-06


title: postMBT_H3K9me3 Repl1


title: SLR24-Vector-rep2

description: SLR24 cells inducibly express Luciferase Replicate 2


title: postMBT_H3K36me3 Repl2

source_name: postMBT H3K36me3 ChIP DNA

value: Diagenode pAb-058-050

source_name: postMBT H3K36me3 Input DNA


title: Day7_5-7_9-3-06

source_name: Day 7, LMD


title: preMBT_polii Repl1

source_name: preMBT polii ChIP DNA

source_name: preMBT polii Input DNA


title: preMBT_H3K9me3 Repl1

source_name: preMBT H3K9me3 ChIP DNA

source_name: preMBT H3K9me3 Input DNA


title: preMBT_H3K27me3 Repl1

source_name: preMBT H3K27me3 ChIP DNA

value: Millipore 07-449

source_name: preMBT H3K27me3 Input DNA


title: postMBT_H3K36me3 Repl1


title: postMBT_H3K4me3 Repl1

source_name: postMBT H3K4me3 ChIP DNA

source_name: postMBT H3K4me3 Input DNA


title: Breast cancer tumor sample187

description: Primary breast tumor

source_name: human breast cancer tumors

tag: er ihc

value: Basal

value: breast cancer tumor


title: Day7_3-1_1-18-07

value: Laser-captured nascent plasma cell tumor cells from ip oil granulomata

value: study 1


title: SLR24-Vector-rep1

description: SLR24 cells inducibly express Luciferase Replicate 1

value: renal carcinoma cells

value: Vector


title: Breast cancer tumor sample124

description: Primary breast tumor

tag: pn

value: positive

value: negative

tag: prihc


title: postMBT_H3K4me3 Repl2

value: Embryonic cells

value: AB strain zebrafish embryos


title: postMBT_polii Repl2


title: Breast cancer tumor sample180

description: Primary breast tumor

tag: pt

tag: molecular subtype


title: Breast cancer tumor sample200

description: Primary breast tumor


title: Breast cancer tumor sample141

description: Primary breast tumor


title: postMBT_H3K27me3 Repl2

source_name: postMBT H3K27me3 ChIP DNA

tag: cell type

source_name: postMBT H3K27me3 Input DNA


title: Ab 07-751

type: other

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

description:
http://www.millipore.com/catalogue/item/07-751
IgG

hyb_protocol: Abs were diluted 1:1000 from stocks (maintained at -20 deg. C. in) in peptide binding buffer (PBB): [50 mM Tris (Mallinckrodt Baker, Phillipsburg, NJ) pH 7.5, 150 mM NaCl (Mallinckrodt AR, Phillipsburg NJ), 0.05% NP-40 (Sigma) + 2.5% fetal calf serum (FCS, Omega Scientific, Tarzana, CA)]. Post primary incubation, washed arrays were incubated with 0.375ug/ml Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA)

scan_protocol: Arrays were scanned using an Axon digital scanning system (Molecular Devices, Sunnyvale, CA)

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

molecule: other

organism: Oryctolagus cuniculus

source_name: polyclonal antibody

tag: commercial source

value: Millipore


title: Day7_5-1_9-3-06

description: Gene expression data from LMD nascent tumor cells

tag: background strain


title: Breast cancer tumor sample137

description: Primary breast tumor


title: SLR25-Scr-shRNA-rep2

description: SLR25 cells stably express scramble shRNA Replicate 2

tag: cell line

tag: infection

value: Scr-shRNA


title: ab62335

description:
http://www.abcam.com/Histone-H2B-acetyl-K15-antibody-EP955Y-ab62335.html
IgG

source_name: monoclonal antobody

value: Abcam


title: preMBT_H3K36me3 Repl1

source_name: preMBT H3K36me3 ChIP DNA

tag: source

value: preMBT, 2.5 hpf, 256-cell stage

source_name: preMBT H3K36me3 Input DNA


title: postMBT_H3K27me3 Repl1

tag: developmental stage

value: postMBT, 5.3 hpf, 50% epiboly


title: 769P-HIF1A-rep2

description: 769P cells inducibly express HIF1alpha Replicate 2


title: SLR25-Scr-shRNA-rep1

description: SLR25 cells stably express scramble shRNA Replicate 1


title: SLR25-HIF1A-shRNA-rep1

description: SLR25 cells stably express HIF1alpha shRNA Replicate 1


title: SLR25-HIF1A-shRNA-rep2


title: MBT_H3K9me3 Repl2

source_name: MBT H3K9me3 ChIP DNA

value: MBT, 3.5 hpf, 1000+-cell stage

tag: chip antibody

value: Diagenode pAb-056-50

source_name: MBT H3K9me3 Input DNA


title: Breast cancer tumor sample120

description: Primary breast tumor

value: Basal


title: ab40886

description:
http://www.abcam.com/Histone-H2B-acetyl-K5-antibody-EP857Y-ChIP-Grade-ab40886.html
IgG


title: MBT_polii Repl2

source_name: MBT polii ChIP DNA

value: RNA Pol II

tag: vendor

value: Santa Cruz sc-899

source_name: MBT polii Input DNA


title: ab52988

description:
http://www.abcam.com/Histone-H2B-acetyl-K20-antibody-EP859Y-ab52988.html
IgG

tag: antibody


title: 769P-Vector-rep1

description: 769P cells inducibly express Luciferase Replicate 1


title: ab18977

description:
http://www.abcam.com/Histone-H2B-antibody-ab18977.html
IgG


title: 769P-Vector-rep2

description: 769P cells inducibly express Luciferase Replicate 2


title: Breast cancer tumor sample39

description: Primary breast tumor

tag: age at diagnosis

value: breast cancer tumor


title: 769P-HIF1A-rep1

description: 769P cells inducibly express HIF1alpha Replicate 1

value: renal carcinoma cells


title: Breast cancer tumor sample93

description: Primary breast tumor

tag: tissue


title: Breast cancer tumor sample58

description: Primary breast tumor

tag: er ihc


title: CAF rep3

status: Public on Dec 01 2011

city: Galveston

first: Celia

last: Chao

state: TX

address: 301 University Boulevard

department: Surgery

institute: Univ TX Medical Branch

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: CAF

label_protocol: Biotinylated cRNA were prepared with Enzo's BioArray Synthesis Kit (PN 42406-10) from >7 ug total RNA .

growth_protocol: DMEM, 10% FCS, 1% ITS, 1% nonessential amino acids (Invitrogen), and 1% penicillin-streptomycin

extract_protocol: Total RNA was Extracted with Ambion's RNAqueous (Cat# 1911) according to the manufacturer's instructions.

tag: disease state

value: colon cancer stage II

value: carcinoma associated fibroblast


title: Breast cancer tumor sample21

description: Primary breast tumor

tag: pn

value: negative

tag: prihc


title: CD133- rep1

value: CD133-  carcinoma cell


title: CD133+ rep2

value: CD133+  carcinoma cell


title: CD133- rep3


title: CD133+ rep3


title: CD133+ rep1


title: CD133- rep2


title: SET7 PKMT + pan methyl Ab (ab23366)

description:
http://www.abcam.com/Methylated-Lysine-mono-methyl-di-methyl-antibody-ab23366.html
IgG

value: SET7 PKMT + pan methyl Ab (ab23366)


title: MBT_H3K4me3 Repl2

source_name: MBT H3K4me3 ChIP DNA

value: Embryonic cells

value: AB strain zebrafish embryos

value: Diagenode pAb-003-050

source_name: MBT H3K4me3 Input DNA


title: human bronchial epithelial cells exposed to A. alternata spores 2

city: Blacksburg

first: Christopher

last: Lawrence

state: Virginia

address: Washington Street

institute: Virginia Bioinformatics Institute, Virginia Tech

description: Treated cells with A. alternata spores.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized at 45C overnight at 60rpm on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 3000.

scan_protocol: GeneChips were scanned using Affimetrix scanner 3000

data_processing: MAS 5.0

source_name: human brochial epithelial cells exposed to A. alternata spores

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: 37°C and 5% CO2

extract_protocol: Total RNA via a hybrid protocol using TRIzol and the RNeasy Cleanup Kit

treatment_protocol: 24h exposure to  5 x 105 A. alternata spores

tag: treatment

value: 5 x 10^5 A. alternata spores


title: human bronchial epithelial cells exposed to A. alternata spores 1

description: Treated cells with A. alternata spores.


title: Aza_G669043_1500nM_rep2

city: Waltham

first: Paul

last: Mason

address: 153 Second Ave

institute: Genzyme Corporation

description: Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669043(1500 nM)

hyb_protocol: The hybridization cocktail and the fragmented cRNA mixture were heated to 99oC for 5 minutes, and incubated at 45oC for 5 minutes After a final spin to collect the samples, hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station.

scan_protocol: Arrays were washed and stained on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G

data_processing: Intensity data was preprocessed using the robust multiarray average (RMA) algorithm in Expression Console v1.1 (Affymetrix). Statistical analysis was carried out in JMP Genomics v4.1 (SAS). 36,116 probe sets were retained after filtering out probe sets with low intensity signals.

label_protocol: With standard processing, 2ug were used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX). Labeled cRNA was fragmented in a 0.5ug/uL reaction and used for array hybridization and washing, according to the standard Affymetrix protocol. In brief, labeled cRNA was resuspended in 5X fragmentation buffer and incubated at 94oC for 35 minutes then stored on ice.

growth_protocol: HCT116 cells were obtained from ATCC and maintained in RPMI1640 medium containing 5% FBS.

extract_protocol: Cells were collected after treatment, and RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) according to manufacturer's information

treatment_protocol: HCT116 cells were treated for 72 hours with 1/1000th volume 1000X compound stocks in DMSO at final concentrations as indicated, or an equivalent amount of DMSO.


title: human bronchial epithelial cells 3

description: Untreated cells

source_name: human brochial epithelial cells

value: Negative control


title: Aza_G669043_150nM_rep2

description: Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669043(150 nM)


title: Aza_G669043_150nM_rep1

source_name: HCT116 cells were treated for 72 hours with prodrug_G669043(150 nM)


title: human bronchial epithelial cells 2

description: Untreated cells


title: MBT_polii Repl1

tag: cell type

value: MBT, 3.5 hpf, 1000+-cell stage


title: ester_G668684_150nM_rep1

description: Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G668684(150 nM)


title: human bronchial epithelial cells 1

description: Untreated cells


title: ester_G668684_150nM_rep2

source_name: HCT116 cells were treated for 72 hours with prodrug_G668684(150 nM)


title: Aza_1500nM_rep1

description: Gene expression data from HCT116 cells were treated for 72 hours with Azacytidine(1500 nM)


title: Aza_150nM_rep1

description: Gene expression data from HCT116 cells were treated for 72 hours with Azacytidine(150 nM)


title: Aza_1500nM_rep2

source_name: HCT116 cells were treated for 72 hours with Azacytidine(1500 nM)


title: Aza_G669043_1500nM_rep1

source_name: HCT116 cells were treated for 72 hours with prodrug_G669043(1500 nM)


title: Aza_150nM_rep2

source_name: HCT116 cells were treated for 72 hours with Azacytidine(150 nM)


title: ester_G668684_7uM_rep2

description: Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G668684(7uM)


title: MBT_H3K9me3 Repl1

value: Diagenode pAb-056-50


title: ester_G668684_7uM_rep1

source_name: HCT116 cells were treated for 72 hours with prodrug_G668684(7uM)


title: human bronchial epithelial cells exposed to A. alternata spores 3

description: Treated cells with A. alternata spores.


title: MBT_H3K27me3 Repl2

source_name: MBT H3K27me3 ChIP DNA

value: Millipore 07-449

source_name: MBT H3K27me3 Input DNA


title: MBT_H3K36me3 Repl2

source_name: MBT H3K36me3 ChIP DNA

value: Diagenode pAb-058-050

source_name: MBT H3K36me3 Input DNA


title: phos_G669071_6uM_rep2

description: Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669071(6nM)


title: MBT_H3K36me3 Repl1


title: DAC_5uM_rep2

description: Gene expression data from HCT116 cells were treated for 72 hours with Decitabine (5uM)


title: phos_G669071_6uM_rep1

source_name: HCT116 cells were treated for 72 hours with prodrug_G669071(6nM)


title: DMSO_rep_4

description: Gene expression data from HCT116 cells were treated for 72 hours with DMSO


title: phos_G669071_63uM_rep2

description: Gene expression data from HCT116 cells were treated for 72 hours with prodrug_G669071(120nM)


title: DAC_120nM_rep1

description: Gene expression data from HCT116 cells were treated for 72 hours with Decitabine (120nM)


title: DAC_120nM_rep2

source_name: HCT116 cells were treated for 72 hours with Decitabine (120nM)


title: DAC_5uM_rep1

source_name: HCT116 cells were treated for 72 hours with Decitabine (5uM)


title: DMSO_rep_1

source_name: HCT116 cells were treated for 72 hours with DMSO


title: DMSO_rep_2


title: phos_G669071_63uM_rep1

source_name: HCT116 cells were treated for 72 hours with prodrug_G669071(120nM)


title: MBT_H3K4me3 Repl1

source_name: MBT H3K4me3 ChIP DNA

source_name: MBT H3K4me3 Input DNA


title: MDMs with IFN infected with HIV at T8

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

description:
Gene expression data from IFNα2 pre-treated macrophages at 8hours post-infection with HIV
MS_8_IFN.HIV

hyb_protocol: 15ug of fragmented cRNA were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays  (Affymetrix, Santa Clara, CA) for 16 h at 45°C with constant rotation at 60 rpm. The arrays were washed and stained using the Affymetrix Fluidics Station 450 (protocol EukGE-WS2v5_450).

scan_protocol: Arrays were read using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GC Robust Multi-array Average (GCRMA) for normalization

source_name: IFNα2 pre-treated monocytes-derived macrophages infected 8 hrs with HIV

label_protocol: 100 ng of total RNA were converted to cDNA, which was amplified and transcribed to produce biotinylated cRNA using the Two-Cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA)

growth_protocol: Monocytes were plated into 25cc flasks in RPMI 1640 supplemented with 10% human serum and incubated at 37°C.

extract_protocol: Total RNA was isolated for each condition and time point using the TRIzol method according to the manufacturer’s protocol

treatment_protocol: Purified primary macrophages were treated with 1000 IU/ml of IFNα2, for 18 hours before infection. Pre-treated macrophages were infected with the Bal strain of HIV-1 at an MOI of 1

value: monocytes-derived-macrophages

tag: ifn pre-treatment

value: yes

tag: hiv infection

value: HIV-1 strain NL4-3balenv

tag: time

value: 8 hours


title: MDMs with IFN at T24

description:
Gene expression data from IFNα2 pre-treated macrophages at 24hours
MS_24_IFN

source_name: IFNα2 pre-treated monocytes-derived macrophages

value: 24 hours


title: DMSO_rep_3

tag: cell line


title: MDMs with IFN infected with HIV at T16

description:
Gene expression data from IFNα2 pre-treated macrophages at 16hours post-infection with HIV
MS_16_IFN.HIV

source_name: IFNα2 pre-treated monocytes-derived macrophages infected 16 hrs with HIV

value: 16 hours


title: MDMs with IFN at T2

description:
Gene expression data from IFNα2 pre-treated macrophages at 2hours
MS_2_IFN

value: 2 hours


title: MDMs with IFN at T4

description:
Gene expression data from IFNα2 pre-treated macrophages at 4hours
MS_4_IFN

value: 4 hours


title: TAX577688 (HumanOmni1)

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Standard Illumina protocol for HumanOmni 1M Quad Beadchip

data_processing: Copy number (Log R) and B allele frequency estimates were obtained from GenomeStudio (Illumina). Genomic profiles from 1M data were partitioned using the R implementation of GLAD.

label: C-Bio and A-DNP

source_name: Breast tumor

extract_protocol: Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps.

value: Breast cancer (HER2+)

tag: er

tag: osbin

tag: os

tag: age

tag: ln

tag: primary

tag: grade


title: MDMs with IFN at T16

description:
Gene expression data from IFNα2 pre-treated macrophages at 16hours
MS_16_IFN


title: MDMs with IFN at T8

description:
Gene expression data from IFNα2 pre-treated macrophages at 8hours
MS_8_IFN


title: MDMs with IFN at T0

description:
Gene expression data from IFNα2 pre-treated macrophages at 0hours
MS_0_IFN

value: 0 hours


title: MDMs with IFN infected with HIV at T2

description:
Gene expression data from IFNα2 pre-treated macrophages at 2hours post-infection with HIV
MS_2_IFN.HIV

source_name: IFNα2 pre-treated monocytes-derived macrophages infected 2 hrs with HIV


title: MDMs CTL at T16

description:
Gene expression data from macrophages at 16hours
MS_16_CTL

source_name: monocytes-derived-macrophages

value: no


title: MDMs with IFN infected with HIV at T4

description:
Gene expression data from IFNα2 pre-treated macrophages at 4hours post-infection with HIV
MS_4_IFN.HIV

source_name: IFNα2 pre-treated monocytes-derived macrophages infected 4 hrs with HIV


title: MDMs CTL at T24

description:
Gene expression data from macrophages at 24 hours
MS_24_CTL


title: MDMs CTL at T2

description:
Gene expression data from macrophages at 2 hours
MS_2_CTL


title: TAX577712 (HumanOmni1)

scan_protocol: Standard Illumina protocol for HumanOmni 1M Quad Beadchip


title: MDMs CTL at T0

description:
Gene expression data from macrophages at 0 hours
MS_0_CTL


title: MDMs CTL at T4

description:
Gene expression data from macrophages at 4 hours
MS_4_CTL


title: MDMs CTL at T8

description:
Gene expression data from macrophages at 8 hours
MS_8_CTL


title: THP1-cells infected by MAD2.2 strains at 48h

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

country: United Kingdom

institute: University of Bristol

hyb_protocol: The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).

scan_protocol: An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays

data_processing: These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.

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

value: THP-1 cells

tag: m. tuberculosis strain

tag: infection time


title: MBT_H3K27me3 Repl1

source_name: MBT H3K27me3 ChIP DNA

value: Embryonic cells

tag: source

value: AB strain zebrafish embryos

tag: developmental stage

tag: chip antibody

tag: vendor

source_name: MBT H3K27me3 Input DNA

tag: antibody


title: THP1-cells infected by MAD2.2 strains at 18h


title: THP1-cells infected by MAD2.2 strains at 4h


title: THP1-cells infected by H37Rv strains at 48h, Replication 2


title: THP1-cells infected by 19.5 strains at 4h


title: THP1-cells infected by H37Rv strains at 18h, Replication 2


title: THP1-cells infected by 19.5 strains at 48h


title: THP1-cells infected by CHN50.2 strains at 4h


title: THP1-cells infected by H37Rv strains at 4h, Replication 2


title: THP1-cells infected by R17.3 strains at 4h


title: TAX577654 (HumanOmni1)

label_protocol: Standard Illumina protocol for HumanOmni 1M Quad Beadchip

tag: disease state


title: THP1-cells infected by H37Rv strains at 48h, Replication 1


title: THP1-cells infected by CHN50.2 strains at 18h


title: THP1-cells infected by H37Rv strains at 18h, Replication 1


title: THP1-cells infected by 19.5 strains at 18h


title: TAX577646 (HumanOmni1)


title: THP1-cells infected by R17.3 strains at 18h


title: THP1-cells infected by R17.3 strains at 48h


title: THP1-cells infected by H37Rv strains at 4h, Replication 1


title: THP1-cells infected by MAD2.1 strains at 48h


title: THP1-cells infected by MAD2.1 strains at 18h


title: THP1-cells infected by MAD2.1 strains at 4h


title: THP1-cells infected by CHN50.2 strains at 48h


title: THP1-cells infected by R19.4 strains at 48h


title: THP1-cells infected by R19.4 strains at 18h


title: TAX577718 (HumanOmni1)


title: THP1-cells infected by CHN50.1 strains at 18h


title: THP1-cells infected by CHN50.1 strains at 4h


title: THP1-cells infected by ZA9.4 strains at 18h


title: THP1-cells infected by R19.4 strains at 4h


title: MDMs with IFN infected with HIV at T24

description:
Gene expression data from IFNα2 pre-treated macrophages at 24hours post-infection with HIV
MS_24_IFN.HIV

source_name: IFNα2 pre-treated monocytes-derived macrophages infected 24 hrs with HIV

tag: cell type

tag: ifn pre-treatment

tag: hiv infection

tag: time


title: THP1-cells infected by ZA9.4 strains at 4h

tag: cell line


title: THP1-cells infected by ZA9.2 strains at 48h


title: THP1-cells infected by ZA9.2 strains at 18h


title: THP1-cells infected by CHN50.1 strains at 48h


title: THP1-cells infected by R17.1 strains at 18h


title: THP1-cells infected by R17.1 strains at 48h


title: THP1-cells infected by R1.4 strains at 4h


title: PMA-treated THP-1 cells as non-infection control

value: Control


title: THP1-cells infected by ZA9.2 strains at 4h


title: THP1-cells infected by R17.1 strains at 4h


title: day20 non-laminar replicate 2

city: Madison

first: David

last: Gamm

address: 1500 Highland Avenue

department: Department of Ophthalmology & Visual Sciences

institute: University of Wisconsin at Madison

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using an AFX GC3000 G7 scanner.

data_processing: The data were analyzed with RMA algorithm using affy package in Bioconductor.

label: Biotin

source_name: forebrain progenitor cells, derived from human embryonic stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: human ES cells were differentiated following protocol in manuscript in chemically defined medium.

extract_protocol: Tri reagent (Ambioin) extraction of total RNA was performed according to the manufacturer's instructions. The integrity of RNA was checked by Agilent 2100 Bioanalyzer

treatment_protocol: DNA was removed by RNase-free DNase treatment using standard procedure.

value: forebrain progenitor cells


title: day20 non-laminar replicate 1


title: day20 laminar replicate 3

source_name: retinal progenitor cells, derived from human embryonic stem cells

value: retinal progenitor cells


title: THP1-cells infected by R1.4 strains at 48h


title: THP1-cells infected by R1.4 strains at 18h


title: day20 laminar replicate 1


title: day20 non-laminar replicate 3


title: scram_hi_9

city: Philadelphia

first: Hiroshi

last: Nakagawa

state: PA

address: 415 Curie Blvd.

department: Gastroenterology Division

institute: University of Pennsylvania

description: no KD, hi Ca, rep3

hyb_protocol: Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

scan_protocol: Scanning of Affymetrix chips were performed according manufacturer's instructions

data_processing: .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the N3 knockdown cell experiments

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.

extract_protocol: RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.

value: epithelial cells (keratinocytes)

tag: genotype

value: hTERT-immortalized, non-transformed

tag: genotype/variation

value: STR-pGIPZ scramble

tag: treatment


title: n3_hi_10

description: N3 KD, hi Ca, rep1

value: STR-pGIPZ shNotch3


title: day20 laminar replicate 2


title: scram_hi_7

description: no KD, hi Ca, rep1


title: n3_hi_12

description: N3 KD, hi Ca, rep3


title: THP1-cells infected by ZA9.4 strains at 48h


title: n3_lo_5

description: N3 KD, low Ca, rep2


title: n3_lo_6

description: N3 KD, low Ca, rep3


title: n3_lo_4

description: N3 KD, low Ca, rep1


title: scram_lo_3

description: no KD, low Ca, rep3


title: n3_hi_11

description: N3 KD, hi Ca, rep2


title: scram_lo_1

description: no KD, low Ca, rep1


title: Hs578T CDH13 ODN

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
Gene expression data of the human breast cancer cell line Hs578T treated with ODN 2006.

0464_016_HsODN_h01_SJ_240506

hyb_protocol: 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.

data_processing: The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).

label_protocol: 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.

extract_protocol: Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol:
BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.

In more detail:
Cells were treated with a 200 nM final concentration of different oligonucleotides:
CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.

value: breast cancer


title: scram_lo_2

description: no KD, low Ca, rep2


title: Hs578T CDH13 ODN CTL

description:
Gene expression data of the human breast cancer cell line Hs578T treated with ODN 2006 CTL.

0465_016_HsODN-CT_h01_SJ_240506

source_name: Hs578T, ODN 2006 CTL

value: ODN 2006 CTL


title: Hs578T set 1 CDH13 U

description:
Gene expression data of the human breast cancer cell line Hs578T treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.

0416_016_Hs578T-U_h01_SJ_130406

source_name: Hs578T, unmethylated CDH13 sequence (CDH13 U)

value: CDH13 U


title: Hs578T set 2 CDH13 U

description:
Gene expression data of the human breast cancer cell line Hs578T treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.

0463_016_Hs578T-U_h01_SJ_240506


title: Skeletal muscle (vastus lateralis) 13 (set B)

city: Helsinki

first: Suvi

last: Savola

address: Haartmaninkatu 3

department: Pathology

country: Finland

institute: University of Helsinki

description: Vastus lateralis muscle

scan_protocol: Standard Affymetrix protocol

data_processing: The R statistical software was applied for data analysis. The RMA method was used for global background correction and qspline was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test was used to calculate p-values.

source_name: Vastus lateralis muscle

label_protocol: One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit.

extract_protocol: Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

tag: diagnosis

value: normal

tag: tissue

value: vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 15 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 12 (set B)

description: Vastus lateralis muscle


title: Hs578T set 1 CDH13 M

description:
Gene expression data of the human breast cancer cell line Hs578T treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.

0415_016_Hs578T-M_h01_SJ_130406

source_name: Hs578T, methylated CDH13 sequence (CDH13 M)

value: CDH13 M


title: Skeletal muscle (vastus lateralis) 7 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 18 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 6 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 8 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 11 (set B)

description: Vastus lateralis muscle


title: Hs578T set 2 CDH13 M

description:
Gene expression data of the human breast cancer cell line Hs578T treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.

0462_016_Hs578T-M_h01_SJ_240506


title: Skeletal muscle (vastus lateralis) 2 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 10 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 9 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 17 (set B)

description: Vastus lateralis muscle


title: Skeletal muscle (vastus lateralis) 3 (set B)

description: Vastus lateralis muscle


title: Ewing sarcoma patient sample R62 (set B)

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000

data_processing: Images were analysed using GeneChip Operating Software

source_name: fresh frozen tissue sample

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneChip One-Cycle Target Labelling protocol from 5 ug of total RNA.

growth_protocol: Cell lines were cultured according to Manara et al., 2002

extract_protocol: RNA was extracted using Invitrogen TRIzol extraction kit according to manufacture's instructions

treatment_protocol: not applicable

tag: sample id

value: Ewing

value: tumor

tag: state

value: Primary

tag: age

tag: sex

value: M

tag: efs (months)

tag: ovs (months)

tag: status

value: NED


title: Ewing sarcoma patient sample R81 (set B)

value: Metastasis

value: Dead


title: Ewing sarcoma patient sample R74 (set B)

value: PNET


title: Ewing sarcoma patient sample R78 (set B)

value: F


title: Ewing sarcoma patient sample R84 (set B)


title: scram_hi_8

description: no KD, hi Ca, rep2

tag: cell type

value: epithelial cells (keratinocytes)

value: hTERT-immortalized, non-transformed

value: STR-pGIPZ scramble


title: Ewing sarcoma patient sample R79 (set B)


title: Ewing sarcoma patient sample R69 (set B)


title: Ewing sarcoma patient sample R75 (set B)


title: Ewing sarcoma patient sample R55 (set B)


title: Ewing sarcoma patient sample R61 (set B)


title: Ewing sarcoma patient sample R67 (set B)


title: Ewing sarcoma patient sample R72 (set B)


title: Ewing sarcoma patient sample R63 (set B)


title: Ewing sarcoma patient sample R51 (set B)

value: Askin


title: Ewing sarcoma patient sample R83 (set B)


title: Ewing sarcoma patient sample R65 (set B)


title: Ewing sarcoma patient sample R80 (set B)


title: Ewing sarcoma patient sample R54 (set B)

value: Recurrence


title: Ewing sarcoma patient sample R58 (set B)


title: Ewing sarcoma patient sample R48 (set B)


title: Ewing sarcoma patient sample R53 (set B)


title: Ewing sarcoma patient sample R52 (set B)


title: Ewing sarcoma patient sample R46 (set B)


title: Ewing sarcoma patient sample R50 (set B)


title: Ewing sarcoma patient sample R49 (set B)


title: Ewing sarcoma patient sample R64 (set B)


title: Ewing sarcoma patient sample R44 (set B)


title: Ewing sarcoma patient sample R41 (set B)


title: Ewing sarcoma patient sample R60 (set B)


title: Ewing sarcoma patient sample R39 (set B)


title: Ewing sarcoma patient sample R40 (set B)


title: Ewing sarcoma patient sample R45 (set B)


title: Ewing sarcoma patient sample R42 (set B)


title: Ewing sarcoma patient sample R43 (set B)


title: Ewing sarcoma patient sample R38 (set B)


title: Ewing sarcoma patient sample R35 (set B)


title: Ewing sarcoma patient sample R37 (set B)


title: Ewing sarcoma patient sample R30 (set B)


title: Ewing sarcoma patient sample R57 (set B)


title: Ewing sarcoma patient sample R196 (set B)


title: Ewing sarcoma patient sample R29 (set B)


title: Ewing sarcoma patient sample R194 (set B)


title: Ewing sarcoma patient sample R34 (set B)

value: AWD


title: Ewing sarcoma patient sample R33 (set B)


title: Ewing sarcoma cell line IOR-NGR (set A)

source_name: in vitro cultured cell line

value: not applicable

tag: gender

value: IOR-NGR


title: Ewing sarcoma cell line IOR-RCH (set A)

value: IOR-RCH


title: Ewing sarcoma cell line 6647 (set A)


title: Ewing sarcoma patient sample R84 (set A)

source_name: freshfrozen tissue sample

value: Ewing

value: tumor


title: Ewing sarcoma cell line LAP35 (set A)


title: Ewing sarcoma cell line SKES1 (set A)


title: Ewing sarcoma cell line SKNMC (set A)

value: SKNMC


title: Ewing sarcoma patient sample R83 (set A)

value: NED


title: Ewing sarcoma cell line TC71 (set A)


title: Ewing sarcoma cell line IOR-BRZ (set A)

value: IOR-BRZ


title: Ewing sarcoma cell line IOR-CAR (set A)

value: IOR-CAR


title: Ewing sarcoma patient sample R81 (set A)

value: Metastasis

value: M

value: Dead


title: Ewing sarcoma cell line RDES (set A)

value: RDES


title: Ewing sarcoma cell line IOR-CLB (set A)

value: IOR-CLB


title: Ewing sarcoma patient sample R80 (set A)

value: PNET

value: Primary

value: F


title: Ewing sarcoma patient sample R74 (set A)


title: Ewing sarcoma patient sample R72 (set A)


title: Ewing sarcoma patient sample R63 (set A)


title: Ewing sarcoma patient sample R64 (set A)


title: Ewing sarcoma patient sample R79 (set A)


title: Ewing sarcoma patient sample R61 (set A)


title: Ewing sarcoma patient sample R75 (set A)


title: Ewing sarcoma patient sample R60 (set A)


title: Ewing sarcoma patient sample R65 (set A)


title: Ewing sarcoma patient sample R67 (set A)


title: Ewing sarcoma patient sample R57 (set A)


title: Ewing sarcoma patient sample R78 (set A)


title: Ewing sarcoma patient sample R53 (set A)


title: Ewing sarcoma patient sample R55 (set A)


title: Ewing sarcoma patient sample R50 (set A)


title: Ewing sarcoma patient sample R51 (set A)

value: Askin


title: Ewing sarcoma patient sample R45 (set A)

value: Recurrence


title: Ewing sarcoma patient sample R62 (set A)


title: Ewing sarcoma patient sample R69 (set A)


title: Ewing sarcoma patient sample R54 (set A)


title: Ewing sarcoma patient sample R48 (set A)


title: Ewing sarcoma patient sample R52 (set A)


title: Ewing sarcoma patient sample R46 (set A)


title: Ewing sarcoma patient sample R58 (set A)


title: Ewing sarcoma patient sample R49 (set A)


title: Ewing sarcoma patient sample R41 (set A)


title: Ewing sarcoma patient sample R43 (set A)


title: Ewing sarcoma patient sample R35 (set A)


title: Ewing sarcoma patient sample R38 (set A)


title: Ewing sarcoma patient sample R40 (set A)


title: Ewing sarcoma patient sample R34 (set A)

value: AWD


title: Ewing sarcoma patient sample R30 (set A)

value: Ewing


title: Ewing sarcoma patient sample R44 (set A)

value: tumor


title: Ewing sarcoma patient sample R33 (set A)


title: Ewing sarcoma patient sample R37 (set A)


title: Ewing sarcoma patient sample R39 (set A)


title: Ewing sarcoma patient sample R42 (set A)


title: Ewing sarcoma patient sample R196 (set A)


title: Ewing sarcoma patient sample R29 (set A)


title: Ewing sarcoma patient sample R194 (set A)


title: p29060513_m23027331_expression

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: The Inflammation and the Host Response to Injury Collaborative Research Program.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: Dchip normalized expression values PM only model

source_name: Early Recovery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix).

extract_protocol: Total RNA was harvested using the RNeasy RNA Isolation kit standard protocol (Qiagen, Valencia, CA)

tag: Peripheral blood leukocyte

tag: Early Recovery


title: p27820153_m24583089_expression

source_name: Late Recovery

tag: Late Recovery


title: p28105148_m27887462_expression


title: p28128372_m1661344_expression


title: p26657616_m14289387_expression


title: p26259680_m7252498_expression


title: p32582723_m32964739_expression


title: p29663633_m10591358_expression


title: p33580296_m21409180_expression


title: p25499319_m7343477_expression


title: p34466944_m21296423_expression


title: p23836873_m10922614_expression


title: p25598097_m4572919_expression


title: p17686459_m24188284_expression


title: p21266782_m28285208_expression


title: p34629304_m16370670_expression


title: p18320652_m34243783_expression


title: p29670554_m27151980_expression


title: p30822033_m9559523_expression


title: p16622938_m7443586_expression


title: p17747412_m31688510_expression


title: p15629307_m5246244_expression


title: p18878883_m10323125_expression


title: p19645406_m954757_expression


title: p20008375_m26588800_expression


title: p18814936_m298508_expression


title: p15429976_m10117881_expression


title: p17992882_m8132681_expression


title: p14922137_m20591163_expression


title: p8873662_m13541004_expression


title: p9209587_m30563371_expression


title: p10208165_m33753201_expression


title: p16435097_m12990526_expression


title: p13289348_m31006699_expression


title: p9973279_m395154_expression


title: p7191554_m14423980_expression


title: p12600235_m16218394_expression


title: p3513825_m26904971_expression


title: p5211601_m145804_expression


title: p1352072_m29098958_expression


title: p1614058_m30159648_expression


title: p6706622_m14925403_expression


title: p7938695_m7837933_expression


title: p1274923_m17427026_expression


title: p5225241_m29290397_expression


title: p4239521_m24369165_expression


title: APM_48h_4

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

country: Germany

institute: UFZ Helmholtz Centre for Environmental Research

description: Gene expression of embryos treated with APM for 48 h (2-50 hpf)

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit following manufacturer's instructions.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.1.1).

data_processing: Feature extraction files (processed signals) were used for statistics, quantile normalisation of all processed signals before significance testing.

label_protocol: Synthesis of cDNA, cRNA and cRNA-labeling was performed with the Agilent Low RNA Input Linear Amplification Kit according to the manufacturer’s instructions. cRNA was labelled with Cy3.

growth_protocol: Zebrafish embryos were collected directly after fertilisation and treated starting 2 hpf in exposure medium.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: 50 embryos per treatment, treatments: control, 5,83 µM azinphos-methyl (APM), 509 µM 1,4-dimethoxybenzene (DMB), 14,2 µM 2,4-dinitrophenol (DNP), 24 h and 48 h (26-50 and 2-50 hpf), respectively; all in 4 independent replicates

tag: developmental stage

value: embryo

tag: exposure time

value: APM 5,83 µM


title: APM_48h_1

source_name: embryos treated with APM for 48 h (2-50 hpf)

tag: treatment


title: p309805_m2484259_expression


title: APM_48h_2


title: APM_48h_3


title: DMB_48h_3

description: Gene expression of embryos treated with DMB for 48 h (2-50 hpf)

value: DMB 509 µM


title: DMB_48h_4

source_name: embryos treated with DMB for 48 h (2-50 hpf)


title: p845580_m2020468_expression


title: DMB_48h_1


title: DMB_48h_2


title: DNP_48h_3

description: Gene expression of embryos treated with DNP for 48 h (2-50 hpf)

value: DNP 14,2 µM


title: IgG1

city: La Jolla

first: Sara

last: Weis

state: CA

address: 3855 Health Sciences Drive #0803

institute: Univ of California San Diego

description:
Control - 1
TaqMan 384-well low density qPCR microfluidic card

scan_protocol: 7900 HT Fast Real Time PCR system

data_processing: Microsoft Excel and the ddCT method was used for data analysis

source_name: aortic vascular smooth muscle cells

extract_protocol: VSMCs were cultured on Jag1 or IgG-coated plates as described above. RNA was extracted using RNA isolation kit (Qiagen). Reverse-transcription PCR was done with RNA-to-cDNA kit (Applied Biosystems). cDNA was run on a TaqMan Low-Density Array, human angiogenesis panel (Applied Biosystems , Cat#4378725), amplified on a 7900 HT Fast Real Time PCR system (Applied Biosystems) according to manufacturer’s instructions.

value: aortic vascular smooth muscle cells

value: IgG


title: DNP_48h_1

source_name: embryos treated with DNP for 48 h (2-50 hpf)


title: EpCAM-Unbound_biologicalreps1-3

city: Huntsvilee

first: Kruti

last: Patel

state: AL

address: 601 Genome Way, Suite 2100

institute: Thermo Fisher Scientific

description: biological triplicates

hyb_protocol: Standard hybridization protocol for Agilent

scan_protocol: Arrays were scanned using a GenePix 4200A scanner (Molecular Devices, Sunnyvale, CA) at 635 nm and 532 nm using 5 µm resolution.

data_processing: Microarray images were imported into Feature Extraction 9.5.1 for quantitation of processed signal values following background subtraction.  Extraction of data for each probe was performed using manufacturer generated extraction protocols and grid files specific for Decode barcode microrarrays. Microarray data were imported into GeneSpring GX 10.0.2 for analysis of shRNA abundance.  For each channel, background subtracted data were lowess normalized, log2 transformed and baselined to the median of all samples.  Log ratios for probes were calculated for both bound to reference and unbound to reference.   Probes were next filtered to remove those which did not pass a signal cutoff of greater than 2-fold median background in the reference samples in 6 out of the 6 microarrays (Cy5 median signal ≥ 75) followed with filtering by expression using the 25th and 99th percentiles as lower and upper cutoffs, respectively.  Resulting data were analyzed for statistical significance by unpaired student’s t-test (p≤0.05) comparing the unbound to bound fractions.  The list of significant probes was then filtered based on a fold change ≥ 2.0

source_name: enriched for non-EpCAM expressing cells

label_protocol: 250bp amplicons were amplified (and subsequently column purified) from the gDNA containing shRNA unique molecular barcode sequences (barcode sequences are probed on custom microarray).  Labeled Bound and Unbound samples with Cy3 and Reference with Cy5 using Agilent's Genomic DNA Enzymatic Labeling Kit

growth_protocol: OVCAR8 cells were maintained in DMEM supplemented with 10% FBS

extract_protocol: gDNA was isolated from bound, unbound and reference (transduced OVCAR8 cells without MACS cell sorting) cells using Qiagen Dneasy Blood and Tissue Kit.

treatment_protocol: OVCAR8 cells were transduced with shRNA pools and maintained for 7 days followed by phenotypic selection for EpCAM enriched or EpCAM depleted cells using MACS magnetic cell sorting

tag: cell line

tag: cell population

value: enriched for non-EpCAM expressing cells

source_name: Transduced Reference 1


title: EpCAM-Bound_biologicalreps1-3

description: biological triplicates

source_name: enriched for EpCAM expressing cells

value: enriched for EpCAM expressing cells

value: reference (transduced OVCAR8 cells without MACS cell sorting)


title: Jag1

description:
Test - 1
TaqMan 384-well low density qPCR microfluidic card

tag: tissue

value: Jag


title: IgG2

description:
Control - 2
TaqMan 384-well low density qPCR microfluidic card


title: Jag2

description:
Test - 2
TaqMan 384-well low density qPCR microfluidic card


title: C_48h_4

description: Gene expression of control embryos after 50 hpf - treated parallel to the 48 h exposed embryos

value: control


title: DNP_48h_2


title: C_48h_3

source_name: control embryos after 50 hpf - treated parallel to the 48 h exposed embryos


title: DNP_48h_4


title: C_48h_1


title: YPD wt 6

city: Princeton

first: Noorossadat

last: Torabi

state: NJ

address: 110 Carl Icahn Lab

department: Molecular Biology

institute: Princeton University

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

organism: Saccharomyces cerevisiae

source_name: BYxRM diploid hybrid

label_protocol: DNA was labeled using the BioPrime Array CGH Genomic Labeling Module (Invitrogen; 18095-012) with the sample being labeled with Cy3 dUTP and the reference being labeled with Cy5 dUTP. We used a BY/RM diploid as the reference for all hybridizations.

growth_protocol: Pooled Mata segregants from either wt or sup35 BYxRM cross were plated on YPD alone(control) or YPD+drug (selection) plates and were incubated at 30C for two days.

extract_protocol: DNA was extracted from the grown cells using Genomic-tip 100/G columns (Qiagen; 10243)

tag: genetic background

value: BYxRM diploid hybrid

tag: selection

tag: genotype

value: wild type

source_name: BYxRM wt selected segregant on YPD

tag: sample type

value: Pooled BYxRM wt segregant grown on YPD biological replicate6

value: BYxRM

value: Pooled BYxRM wt segregant grown on YPD

value: BYxRM wt segregant


title: C_48h_2

value: embryo


title: YPD wt 2

value: Pooled BYxRM wt segregant grown on YPD biological replicate2


title: APM_24h_1

description: Gene expression of embryos treated with APM for 24 h (26-50 hpf)

value: APM 5,83 µM


title: APM_24h_2

source_name: embryos treated with APM for 24 h (26-50 hpf)


title: YPD wt 3

value: Pooled BYxRM wt segregant grown on YPD biological replicate3


title: YPD wt 4

value: Pooled BYxRM wt segregant grown on YPD biological replicate4


title: DMB_24h_4

description: Gene expression of embryos treated with DMB for 24 h (26-50 hpf)

value: DMB 509 µM


title: DMB_24h_3

source_name: embryos treated with DMB for 24 h (26-50 hpf)


title: APM_24h_4


title: YPD wt 5

value: Pooled BYxRM wt segregant grown on YPD biological replicate5


title: YPD sup35 5

source_name: BYxRM sup35 selected segregant on YPD

value: Pooled BYxRM sup35 segregant grown on YPD biological replicate5

value: BYxRM sup35 segregant


title: DMB_24h_2


title: APM_24h_3


title: YPD sup35 6

value: Pooled BYxRM sup35 segregant grown on YPD biological replicate6


title: YPD sup35 3

value: Pooled BYxRM sup35 segregant grown on YPD biological replicate3


title: YPD wt 1

value: BYxRM diploid hybrid

value: Pooled BYxRM wt segregant grown on YPD biological replicate1


title: YPD sup35 4

value: wild type

value: Pooled BYxRM sup35 segregant grown on YPD biological replicate4


title: YPD sup35 2

value: Pooled BYxRM sup35 segregant grown on YPD biological replicate2

value: BYxRM


title: YPD sup35 1

value: Pooled BYxRM sup35 segregant grown on YPD biological replicate1


title: DNP_24h_4

description: Gene expression of embryos treated with DNP for 24 h (26-50 hpf)

value: embryo

value: DNP 14,2 µM


title: DNP_24h_1

source_name: embryos treated with DNP for 24 h (26-50 hpf)


title: DNP_24h_3


title: AcK16.T [Agilent-027811]

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

description: AcK16H4 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

hyb_protocol: 5 ug labeled material was mixed with blocking agent and hybridization buffer (Agilent Technologies) followed by denaturing at 95°C for 3 min and incubating at 37°C for 30 min. The mixtures were applied to microarrays in Agilent microarray hybridization chambers, and hybridizations were carried out for 40 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA) at 10 rpm.  Hybridized microarrays were washed and dried according to the Agilent CGH microarray wash protocol.

scan_protocol: Microarrays were scanned with Agilent G2565BA microarray scanner and data were extracted using Feature Extraction Software (Agilent Technologies) with recommended data extraction protocol for array CGH.

data_processing:
Bioconductor packages limma and Ringo were used for data processing. The median signals of non-control probes were selected and normalized using Tukey-biweight scaling procedure.
Normalized log2 ratio (Cy5/Cy3) representing ChIP/WCE (do not include control probes)

source_name: SW480 cells, 2mM H2O2, 30min

label_protocol: 2 ug of ligation-mediated PCR fragments was mixed with 2.5x random primer solution (Agilent Technologies) and incubated at 95°C for 5 minutes. Labeling reactions were performed using a BioPrime Array CGH Genomic Labeling Module (Invitrogen) and Cydine-5 or Cydine-3 dUTP (Perkin Elmer) at 37°C for 3 hours.  The labeled sample was purified, concentrated with affinity columns and buffers provided in the kit. Both nucleic acid and dye concentrations of purified material were determined by NanoDrop ND-1000

growth_protocol: SW480 cells were obtained from American Type Culture Collection and maintained at 37°C and 5% CO2 in McCoy's 5a, supplemented with 10% fetal bovine serum.

extract_protocol: ChIP-on-chip was performed as previously described (McGarvey et al., Cancer Res. 2008 Jul 15;68(14):5753-9.), following Agilent's instructions.

treatment_protocol: Cells were either untreated or treated with 2mM H2O2 for 30min at 37°C

value: Human colorectal adenocarcinoma cell line SW480 (CCL-228)

tag: antibody

tag: fraction

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: Neomycin wt 2

source_name: BYxRM wt selected segregant on Neomycin

value: Pooled BYxRM wt segregant grown on YPD+Neomycin biological replicate2

value: BYxRM wt segregant


title: DNP_24h_2


title: Tunicamycin sup35 1

source_name: BYxRM sup35 selected segregant on Tunicamycin

value: Pooled BYxRM sup35 segregant grown on YPD+Tunicamycin biological replicate1

value: BYxRM sup35 segregant


title: Tunicamycin sup35 2

value: Pooled BYxRM sup35 segregant grown on YPD+Tunicamycin biological replicate2


title: C_24h_2

description: Gene expression of control embryos after 50 hpf - treated parallel to the 24 h exposed embryos

value: control


title: Tunicamycin wt 1

value: BYxRM diploid hybrid

source_name: BYxRM wt selected segregant on Tunicamycin

value: Pooled BYxRM wt segregant grown on YPD+Tunicamycin biological replicate1