title: genomic DNA from tumor tissue sample id 47

description: colorectal tumor tissue

value: Male

value: Proximal

tag: lymphovascular invasion

tag: tils

tag: cimp

tag: sample type

tag: disease state


title: genomic DNA from tumor tissue sample id 109

status: Public on Jul 18 2012

type: genomic

city: Singapore

first: Marie

last: Loh

address: 14 Medical Drive

country: Singapore

institute: National University of Singapore

description: colorectal tumor tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised according to standard IlluminaGoldengate Methylation Array protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: colorectal tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from approximately 25 mg of tissue using standard phenol-chloroform extraction

tag: gender

value: Female

tag: age

tag: site

value: Distal

tag: acps stage

value: Yes

tag: extramural vascular invasion

value: No

tag: perineural invasion

value: Negative

tag: msi

tag: kras

tag: braf

value: colorectal tissue

value: tumor


title: genomic DNA from tumor tissue sample id 45

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 50

description: colorectal tumor tissue

value: Positive


title: CBMC Twin 1082 sib2

city: Parkville

first: Richard

last: Saffery

state: Victoria

address: Flemington Rd

department: Cancer, Disease and Developmental Epigenetics

country: Australia

institute: Murdoch Children's Research Institute

description:
CBMCs from twin sibling
T1082.2C

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: Raw data was exported from BeadStudio and analysed in the programming language R, specifically using the package lumi.

source_name: cord blood mononuclear cells

extract_protocol: DNA was extracted using phenol/chloroform.

treatment_protocol: CBMCs were purified using density gradient centrifugation.

tag: zygosity

value: MZ

tag: chorionicity

value: DC

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

value: cord blood mononuclear cells

tag: twin

value: Twin 1082


title: CBMC Twin 1130 sib1

description:
CBMCs from twin sibling
T1130.1C

value: Twin 1130


title: CBMC Twin 1138 sib1

description:
CBMCs from twin sibling
T1138.1C

value: M

value: Twin 1138


title: CBMC Twin 1114 sib1

description:
CBMCs from twin sibling
T1114.1C

value: MC

value: Twin 1114


title: CBMC Twin 2071 sib1

description:
CBMCs from twin sibling
T2071.1C

value: Twin 2071


title: genomic DNA from tumor tissue sample id 44

description: colorectal tumor tissue

value: Male

value: Distal

tag: lymphovascular invasion

tag: tils

tag: cimp

tag: sample type

tag: disease state


title: genomic DNA from tumor tissue sample id 39

description: colorectal tumor tissue

tag: gender

value: Female

tag: age

tag: site

value: Proximal

tag: acps stage

value: No

tag: extramural vascular invasion

value: Negative


title: genomic DNA from tumor tissue sample id 41

description: colorectal tumor tissue

tag: perineural invasion

tag: msi

tag: kras

tag: braf

value: colorectal tissue

value: tumor


title: genomic DNA from tumor tissue sample id 38

description: colorectal tumor tissue

value: Positive


title: CBMC Twin 1114 sib2

description:
CBMCs from twin sibling
T1114.2C

tag: zygosity

value: MZ

tag: chorionicity

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

value: cord blood mononuclear cells


title: MouseBrain-KO-samp2-rep2

type: RNA

city: San Diego

first: Eric

last: Scott

state: California

address: 9500 Gilman Dr.

department: School of Medicine

country: USA

institute: UC San Diego

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Mus musculus

source_name: Brain

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

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: tissue

value: MouseBrain

tag: sample

tag: replicate

tag: phenotype

value: KO


title: MouseBrain-KO-samp3-rep2

tag: gender


title: MouseBrain-WildType-samp2-rep2

value: WildType


title: MouseBrain-KO-samp1-rep2


title: genomic DNA from tumor tissue sample id 36

description: colorectal tumor tissue

tag: age

tag: site

tag: lymphovascular invasion

value: Yes

tag: tils

tag: cimp

tag: sample type

tag: disease state


title: MouseBrain-WildType-samp1-rep2


title: CBMC Twin 1074 sib2

description:
CBMCs from twin sibling
T1074.2C

tag: zygosity

value: DZ

value: DC

value: M

tag: cell type

tag: twin

value: Twin 1074


title: MouseBrain-WildType-samp2-rep1

value: Male


title: CBMC Twin 1074 sib2 rep

description:
CBMCs from twin sibling
T1074.2C_rep

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance


title: CBMC Twin 1074 sib1

description:
CBMCs from twin sibling
T1074.1C

tag: gestational age (wk)


title: CBMC Twin 1065 sib1

description:
CBMCs from twin sibling
T1065.1C

value: Twin 1065


title: CBMC Twin 1082 sib1

description:
CBMCs from twin sibling
T1082.1C

value: Twin 1082


title: MouseBrain-KO-samp2-rep1

tag: tissue

tag: sample

tag: replicate


title: genomic DNA from tumor tissue sample id 34

description: colorectal tumor tissue

tag: gender

tag: age

value: Distal

tag: acps stage

value: No

tag: extramural vascular invasion

tag: perineural invasion

tag: msi

tag: kras

value: Negative

tag: braf

value: colorectal tissue


title: MouseBrain-KO-samp1-rep1.2

tag: phenotype


title: MouseBrain-WildType-samp1-rep1.2


title: genomic DNA from tumor tissue sample id 33

description: colorectal tumor tissue

tag: site

tag: lymphovascular invasion

tag: tils

value: Positive

tag: cimp

tag: sample type

tag: disease state

value: tumor


title: CBMC Twin 1065 sib2

description:
CBMCs from twin sibling
T1065.2C

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

value: cord blood mononuclear cells

tag: twin


title: MouseBrain-KO-samp1-rep1

tag: tissue

value: MouseBrain

tag: sample

tag: replicate

tag: gender

value: KO


title: CBMC Twin 1049 sib2

description:
CBMCs from twin sibling
T1049.2C

value: Twin 1049


title: CBMC Twin 1049 sib1

description:
CBMCs from twin sibling
T1049.1C

value: DZ


title: genomic DNA from tumor tissue sample id 32

description: colorectal tumor tissue

value: Female

tag: age

tag: site

tag: acps stage

tag: extramural vascular invasion

tag: perineural invasion

tag: msi

tag: kras

tag: braf


title: Neuron-Affected-samp3-rep1.2

source_name: Neuron

value: Neuron

tag: phenotype

value: Affected


title: MouseBrain-WildType-samp1-rep1

value: Male

value: WildType


title: Neuron-Affected-samp3-rep1


title: CBMC Twin 1048 sib2

description:
CBMCs from twin sibling
T1048.2C

tag: zygosity

tag: chorionicity

value: DC

value: M

tag: birth weight (g)

tag: birth weight discordance

value: Twin 1048


title: Neuron-Affected-samp3-rep2

tag: tissue


title: Neuron-Affected-samp3-rep2.3

tag: sample


title: Neuron-Affected-samp2-rep1

tag: replicate


title: Neuron-Affected-samp3-rep3

tag: gender


title: Neuron-Affected-samp3-rep2.2


title: CBMC Twin 1022 sib2

description:
CBMCs from twin sibling
T1022.2C

value: MZ

value: MC

tag: gestational age (wk)

tag: cell type

tag: twin

value: Twin 1022


title: genomic DNA from tumor tissue sample id 30

description: colorectal tumor tissue

tag: age

tag: site

value: Distal

tag: acps stage

tag: lymphovascular invasion

value: Yes

tag: extramural vascular invasion

value: No

tag: tils

value: Positive

tag: cimp

value: Negative

tag: sample type

value: colorectal tissue

tag: disease state

value: tumor


title: genomic DNA from tumor tissue sample id 31

description: colorectal tumor tissue

tag: perineural invasion

tag: msi

tag: kras

tag: braf


title: Neuron-Affected-samp1-rep1

tag: tissue

value: Neuron

tag: sample

tag: replicate

tag: gender

tag: phenotype


title: Neuron-WildType-samp1-rep2


title: CBMC Twin 1048 sib1

description:
CBMCs from twin sibling
T1048.1C

tag: zygosity

value: DZ

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

value: cord blood mononuclear cells

tag: twin


title: Neuron-WildType-samp4-rep2

value: Male

value: WildType


title: CBMC Twin 1022 sib1

description:
CBMCs from twin sibling
T1022.1C

value: M


title: genomic DNA from tumor tissue sample id 29

description: colorectal tumor tissue

tag: age

tag: site

value: Proximal

tag: acps stage

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: tils

tag: cimp

tag: sample type

tag: disease state


title: genomic DNA from tumor tissue sample id 28

description: colorectal tumor tissue

tag: gender

tag: perineural invasion

tag: msi

tag: kras

tag: braf


title: Neuron-WildType-samp4-rep1

tag: tissue

tag: sample

tag: replicate

tag: phenotype


title: Neuron-WildType-samp1-rep1


title: CBMC Twin 1021 sib2

description:
CBMCs from twin sibling
T1021.2C

tag: zygosity

tag: chorionicity

value: DC

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

tag: twin

value: Twin 1021


title: CBMC Twin 1021 sib1

description:
CBMCs from twin sibling
T1021.1C

value: F


title: genomic DNA from tumor tissue sample id 26

description: colorectal tumor tissue

value: Female

tag: age

tag: site

value: Distal

tag: acps stage

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: tils

tag: cimp

tag: sample type

tag: disease state


title: NPC-Affected-samp3-rep2

source_name: Neural Progenitor Cells

tag: tissue

value: NPC

tag: sample

tag: replicate

tag: gender

tag: phenotype

value: Affected


title: NPC-Affected-samp3-rep1


title: NPC-WildType-samp1-rep3


title: NPC-WildType-samp1-rep1


title: genomic DNA from tumor tissue sample id 22

description: colorectal tumor tissue

value: Yes

tag: perineural invasion

value: No

value: Negative

tag: msi

tag: kras

tag: braf


title: NPC-Affected-samp2-rep2


title: NPC-Affected-samp2-rep1


title: CBMC Twin 1019 sib2

description:
CBMCs from twin sibling
T1019.2C

tag: zygosity

value: MZ

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

tag: twin

value: Twin 1019


title: NPC-Affected-samp1-rep2


title: MouseBrain-KO-samp3-rep1

value: MouseBrain

value: KO


title: genomic DNA from tumor tissue sample id 20

description: colorectal tumor tissue

tag: age

tag: site

tag: acps stage

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: tils

tag: cimp

value: Positive

tag: sample type

value: colorectal tissue

tag: disease state

value: tumor


title: CBMC Twin 1016 sib2

description:
CBMCs from twin sibling
T1016.2C

value: DC

tag: gender

value: M

value: cord blood mononuclear cells

value: Twin 1016


title: CBMC Twin 1019 sib1

description:
CBMCs from twin sibling
T1019.1C

tag: zygosity


title: IPS-Affected-samp3-rep4

source_name: Induced Pluripotent Stem Cells

tag: tissue

value: IPS

tag: sample

tag: replicate

value: Male

tag: phenotype


title: IPS-Affected-samp3-rep3

value: Affected


title: genomic DNA from tumor tissue sample id 19

description: colorectal tumor tissue

value: Distal

tag: perineural invasion

tag: msi

tag: kras

tag: braf


title: IPS-Affected-samp3-rep2


title: genomic DNA from tumor tissue sample id 21

description: colorectal tumor tissue

value: Female

tag: age

tag: site

value: Proximal

tag: acps stage

value: Yes

value: No


title: CBMC Twin 1012 sib2

description:
CBMCs from twin sibling
T1012.2C

value: MZ

tag: chorionicity

value: MC

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

tag: twin

value: Twin 1012


title: IPS-Affected-samp2-rep1.2

tag: tissue

tag: gender


title: genomic DNA from tumor tissue sample id 18

description: colorectal tumor tissue

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: tils

value: Positive

tag: cimp

value: Negative

tag: sample type

value: colorectal tissue

tag: disease state

value: tumor


title: CBMC Twin 1016 sib1

description:
CBMCs from twin sibling
T1016.1C

tag: zygosity

value: DC

value: M

value: cord blood mononuclear cells

value: Twin 1016


title: genomic DNA from tumor tissue sample id 16

description: colorectal tumor tissue

tag: age

tag: site

tag: perineural invasion

tag: msi

tag: kras

tag: braf


title: genomic DNA from tumor tissue sample id 24

description: colorectal tumor tissue

value: Distal

tag: acps stage


title: IPS-Affected-samp2-rep1

value: IPS

tag: sample

tag: replicate

value: Male

tag: phenotype

value: Affected


title: IPS-WildType-samp1-rep3

tag: tissue

tag: gender

value: WildType


title: IPS-Affected-samp2-rep4


title: IPS-Affected-samp2-rep2


title: CBMC Twin 1012 sib1

description:
CBMCs from twin sibling
T1012.1C

value: MZ

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

tag: twin


title: genomic DNA from tumor tissue sample id 14

description: colorectal tumor tissue

value: Female

tag: age

tag: site

tag: lymphovascular invasion

value: No

tag: extramural vascular invasion

tag: tils

tag: cimp

tag: sample type

tag: disease state


title: IPS-WildType-samp1-rep2

tag: sample

tag: replicate

tag: phenotype


title: genomic DNA from tumor tissue sample id 13

description: colorectal tumor tissue

tag: gender

tag: acps stage

tag: perineural invasion

value: No data

tag: msi

tag: kras

tag: braf


title: CBMC Twin 1002 sib2

description:
CBMCs from twin sibling
T1002.2C

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: cell type

tag: twin

value: Twin 1002


title: CBMC Twin 1002 sib1

description:
CBMCs from twin sibling
T1002.1C


title: IPS-Affected-samp2-rep3

tag: tissue


title: IPS-WildType-samp1-rep1

tag: sample


title: CBMC Twin 1001 sib2

description:
CBMCs from twin sibling
T1001.2C

value: DZ

value: F

value: Twin 1001


title: CBMC Twin 1001 sib1

description:
CBMCs from twin sibling
T1001.1C

value: DC


title: Fibroblast-WildType-samp1-rep1

source_name: Fibroblast

value: Fibroblast

tag: replicate


title: Fibroblast-Affected-samp3-rep2

tag: phenotype


title: Fibroblast-WildType-samp1-rep2

tag: gender


title: Fibroblast-Affected-samp2-rep3


title: Fibroblast-Affected-samp2-rep2


title: NPC-Affected-samp4-rep1

value: NPC


title: Sbds(ATG)/p53(ATG)-injected embryo rep 4

status: Public on Jul 17 2012

city: Baltimore

first: Steven

last: Leach

state: MD

address: 733 N. Broadway, BRB 471

department: The Department of Surgery and Institute for Genetic Medicine

institute: Johns Hopkin University

description: replicate 4

hyb_protocol: Standard Agilent One-Color Microarray-Based Gene Expression Analysis Protocol, version 5.5 protocol

data_processing: The data were normalised using LOESS normalization with limma in Bioconductor

organism: Danio rerio

source_name: 24 hpf zebrafish embryos

growth_protocol: 28 degree centigrade

extract_protocol: Sigma Trizol reagent extraction

treatment_protocol: Morpholinos were resuspended in water and injected at experimentally determined concentrations. Morpholinos were injected into 1-4 cell zebrafish embryos, which were then raised at 28C, in embryo water plus PTU to inhibit pigmentation.

value: embryo

tag: treatment


title: Sbds(ATG)/p53(ATG)-injected embryo rep 3

description: replicate 3

scan_protocol: Standard Agilent One-Color Microarray-Based Gene Expression Analysis Protocol, version 5.5 protocol


title: Fibroblast-Affected-samp3-rep1


title: Fibroblast-Affected-samp2-rep1


title: IPS-WildType-samp3-rep5


title: p53(ATG) MO injected embryo rep2

description: replicate 2

label_protocol: Standard Agilent One-Color Microarray-Based Gene Expression Analysis Protocol, version 5.5 protocol

value: p53(ATG) MO injected


title: p53(ATG) MO injected embryo rep3

description: replicate 3


title: p53(ATG) MO injected embryo rep4

description: replicate 4


title: Sbds(ATG) MO-injected embryo rep2

description: replicate 2

value: Sbds(ATG) MO-injected


title: p53(ATG) MO injected embryo rep1

description: replicate 1


title: 6dpf_wt.cy3_mut.cy5

city: Utrecht

first: Leonie

last: Huitema

state: Utrecht

address: Uppsalalaan 8

department: Schulte-Merker group

country: Netherlands

institute: Hubrecht Institute

description: Samples were run in dye swap

hyb_protocol: Labeled samples were hybridized for 17 hours at 60 degrees Celcius to a 4x44K zebrafish expression array using the Gene Expression Hybrdization Kit (Agilent technologies). Arrays were washed according to the manufactures protocol.

scan_protocol: The microarray was scanned using the G2505C Agilent DNA microarray scanner using default parameters.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: cDNA synthesis and labeling were performed using the two color Low Input  Quick-Amp labeling kit (5190-2306, Agilent Technologies) and samples were purified using the Rneasy Mini kit (Qiagen). Concentration and cy3 and cy5 incorporation were determined using a nanodrop spectrophotometer.

growth_protocol: Embryos from mutant versus wild type crosses were raised in standard E3 medium at 28 degrees Celcius. At 3 and 6 dpf embryos were sacrificed by an overdosis of ms222 and frozen in liquid nitrogen

extract_protocol: Total RNA from (n=30) msp mutants versus wild types was isolated using the Rnaesy mini kit (Qiagen) according to the manufactures protocol.

treatment_protocol: no treatment

value: whole embryos

tag: strain

value: wik

tag: genotype/variation

value: wildtype

tag: developmental stage

value: 6 dpf

value: Msp mutant


title: Sbds(ATG) MO-injected embryo rep4

description: replicate 4


title: Sal 3h (F1) rep1

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

country: Japan

institute: Yokohama City University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix Gene Array Scanner 2500A with the original setting (This means that scanning steps are conducted at a high level of sensitivity to focus on those genes that function in hormone signaling, because their transcripts are relatively less abundant. Under these conditions, signals of highly abundant transcripts may reach saturation)

label: biotin

organism: Arabidopsis thaliana

source_name: 7 day old seedlings

label_protocol: One-cycle target labeling reagents (Affymetrix)

growth_protocol: Seedlings were grown for 7 days at 23 degrees.

extract_protocol: guanidine-hydrochloride method

treatment_protocol: Seedlings were treated with an inhibitor for 3 h or 12h.

tag: genotype/ecotype

value: 10µM salicylic acid

tag: time point


title: MO-injected embryo rep3

description: replicate 3

value: MO-injected


title: 3dpf_wt.cy5_mut.cy3

description: Samples were run in dye swap

value: 3 dpf


title: Sbds(ATG) MO-injected embryo rep3

description: replicate 3


title: Sbds(ATG)/p53(ATG)-injected embryo rep 1

description: replicate 1


title: B9 3h (F1) rep2

value: 10 µM daminozide


title: Ibup 3h (F1) rep2

value: 10 µM ibuprofen


title: PNO8 10µM3h (G) rep2

value: 10 µM PNO8


title: 6dpf_wt.cy5_mut.cy3

description: Samples were run in dye swap


title: MO-injected embryo rep4

description: replicate 4


title: Sbds(ATG) MO-injected embryo rep1

description: replicate 1


title: B9 3h (F1) rep1


title: MO-injected embryo rep2

description: replicate 2


title: Sbds(ATG)/p53(ATG)-injected embryo rep 2

description: replicate 2


title: MO-injected embryo rep1

description: replicate 1


title: 3dpf_wt.cy3_mut.cy5

description: Samples were run in dye swap


title: Ibup 3h (F1) rep1


title: PNO8 1µM3h (F1) rep2

value: 1 µM PNO8


title: Sal 3h (F1) rep2


title: PNO8 1µM12h (F2) rep1


title: CHX 3h (F1) rep1

value: 10 µM CHX


title: MG132 3h (F1) rep1


title: PNO8 1µM12h (F2) rep2


title: AVG 3h (F1) rep2

value: 10 µM AVG


title: MG132 3h (F1) rep2


title: AgNO3 3h (F1) rep2

value: 10 µM AgNO3


title: PNO8 1µM3h (F1) rep1


title: mock 3h (G) rep2

value: mock


title: AVG 3h (F1) rep1


title: CHX 3h (F1) rep2


title: Brz220 3µM3h (G) rep1

value: 3 µM Brz220


title: Brz220 3µM3h (G) rep2


title: Brz91 3h (F1) rep2

value: 10 µM Brz91


title: Brz220 10µM3h (F1) rep1

value: 10 µM Brz220


title: Brz220 10µM12h (F2) rep2


title: mock 3h (G) rep1


title: Brz91 12h (F2) rep1


title: Brz220 10µM3h (F1) rep2


title: NPA 3h (F1) rep2

value: 10 µM NPA


title: PCIB 3h (F1) rep2

value: 10 µM PCIB


title: NPA 3h (F1) rep1


title: Brz91 3h (F1) rep1


title: TIBA 3h (F1) rep1

value: 10 µM TIBA


title: TIBA 3h (F1) rep2


title: PX 12h (F2) rep1

value: 10 µM prohexadione


title: Brz220 10µM12h (F2) rep1


title: Brz91 12h (F2) rep2


title: PCIB 3h (F1) rep1


title: AgNO3 3h (F1) rep1


title: PX 3h (F1) rep2


title: 246T 3h (F1) rep2


title: PX 12h (F2) rep2


title: Pac 12h (F2) rep1

value: 10 µM paclobutrazol


title: Pac 3h (F1) rep1


title: Pac 12h (F2) rep2


title: Pac 3h (F1) rep2


title: 246T 3h (F1) rep1


title: PX 3h (F1) rep1


title: Hgd+/- Fah-/- hepatocytes, repopulated (off NTBC), replicate 3

city: Pittsburgh

first: Andrew

middle: W.

last: Duncan

state: PA

address: 450 Technology Drive, Suite 300

department: Pathology

institute: University of Pittsburgh

description: Biological replicate 3 of 4.

hyb_protocol: Labeled DNA of the test samples and gender-mismatched references was purified using a MultiScreen-PCRμ96 Filter Plate (Millipore), pooled, and hybridized to an array for ~40h at 65°C.

scan_protocol: The post-hybridization slides were washed and scanned into image files using an Agilent Microarray Scanner (PN G2565BA).

data_processing: Microarray image files were quantified using Agilent Feature Extraction software (version 9.5), and text file outputs were imported into Agilent Genomic Workbench software (version 6.5). To identify chromosomal aneuploidy and genomic copy number variations, data were analyzed using the Aberration Detection Method 2 (ADM2) statistical algorithm, which uses an iterative procedure to identify all genomic regions for which the weighted average by log2 ratio of the measured probe signals is different from the expected value of 0 by more than a given threshold. “Fuzzy Zero” and “Centralization” default algorithms of DNA Analytics were utilized. To minimize the detection of non-relevant variants, data analyses were performed using threshold 6.0 and changes detected by less than 150 probes (<300 kb) were filtered. Data were also analyzed using ADM2 with threshold 3.0 and using algorithm ADM1 with or without filters, which detected no additional low-level mosaicism of aneuploidy.

source_name: hepatocytes, Hgd+/- Fah-/-

label_protocol: 1 μg of genomic DNA from test (i.e., hepatocytes) and reference (i.e., splenocytes) samples was digested with AluI and RsaI (Promega) at 37°C for 2h, and labeled by cyanine 5-dCTP (for the test sample) or cyanine 3-dCTP (for the reference sample) (Perkin Elmer) at 37°C for 2h using the Bioprime CGH Labeling Module (Invitrogen).

extract_protocol: Genomic DNA was isolated from suspensions of hepatocytes and splenocytes using the DNeasy Blood and Tissue Kit (Qiagen).

tag: genotype

value: Hgd+/- Fah-/-

value: hepatocytes

tag: ntbc selection

value: yes

value: female

source_name: splenocytes, wild type

value: wild type

value: splenocytes

value: male

tag: sample type

value: reference


title: Hgd+/- Fah-/- hepatocytes, repopulated (off NTBC), replicate 4

description: Biological replicate 4 of 4.


title: Unic 3h (F1) rep1

value: 10 µM uniconazole


title: Hgd+/- Fah-/- hepatocytes, repopulated (off NTBC), replicate 1

description: Biological replicate 1 of 4.


title: PPI 12h (F2) rep2

value: 10 µM propiconazole


title: Hgd+/- Fah-/- hepatocytes, repopulated (off NTBC), replicate 2

description: Biological replicate 2 of 4.


title: PPI 3h (F1) rep1


title: PPI 3h (F1) rep2


title: PPI 12h (F2) rep1


title: Unic 3h (F1) rep2


title: Unic 12h (F2) rep1


title: mock 12h (F2) rep2

value: mock


title: Unic 12h (F2) rep2


title: Hgd-/- Fah-/- hepatocytes (off NTBC), replicate 1

description: Biological replicate 1 of 2.

source_name: hepatocytes, Hgd-/- Fah-/-

value: Hgd-/- Fah-/-


title: det2mock 3h (A9) rep2

source_name: 7 day old seedling

growth_protocol: Seedlings were grown for 7 days at 22 degrees.

treatment_protocol: Seedlings were treated with plant hormones for 30 min, 1 h, or 3 h.

value: 3 h


title: Wild type hepatocytes, replicate 2

description: Biological replicate 2 of 2.

source_name: hepatocytes, wild type

value: no


title: mock 3h (F1) rep1


title: mock 12h (F2) rep1


title: det2mock 3h (A9) rep1


title: det2+BL 3h (A9) rep2

value: 10 nM BL


title: det2mock 1h (A8) rep2

value: 1 h


title: det2mock 1h (A8) rep1


title: det2+BL 1h (A8) rep2


title: det2mock 30m (A7) rep2

value: 30 min


title: mock 3h (F1) rep2


title: det2mock 30m (A7) rep1


title: det2+BL 3h (A9) rep1


title: Hgd-/- Fah-/- hepatocytes (off NTBC), replicate 2

description: Biological replicate 2 of 2.


title: det2+BL 30m (A7) rep2


title: Wild type hepatocytes, replicate 1

description: Biological replicate 1 of 2.


title: ga1+GA 3h (A6) rep1

value: 1 µM GA3


title: det2+BL 1h (A8) rep1


title: det2+BL 30m (A7) rep1


title: ga1mock 3h (A6) rep1


title: ga1+GA 3h (A6) rep2


title: PNO8 10µM3h (G) rep1

value: 10 µM PNO8


title: ga1+GA 1h (A5) rep1


title: ga1+GA 30m (A4) rep1


title: ga1mock 1h (A5) rep1


title: BL 3h (A3) rep2


title: ga1mock 3h (A6) rep2


title: ACC 3h (A3) rep2

value: 10 µM ACC


title: ga1mock 30m (A4) rep2


title: ga1mock 1h (A5) rep2


title: ga1mock 30m (A4) rep1


title: ga1+GA 1h (A5) rep2


title: BL 3h (A3) rep1


title: ga1+GA 30m (A4) rep2


title: GA 3h (A3) rep2


title: MJ 3h (A3) rep2

value: 10 µM MJ


title: ABA 3h (A3) rep2

value: 10 µM ABA


title: IAA 3h (A3) rep2

value: 1 µM IAA


title: Zeatin 3h (A3) rep2

value: 1 µM zeatin


title: GA 3h (A3) rep1


title: ABA 3h (A3) rep1


title: MJ 3h (A3) rep1


title: Zeatin 3h (A3) rep1


title: ACC 3h (A3) rep1


title: mock 3h (A3) rep2


title: IAA 3h (A3) rep1


title: BL 1h (A2) rep2


title: mock 3h (A3) rep1


title: rat hippocampus (CA1 region), 72 hours novel environment stress, subject 68, cohort 1

city: Lexington

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: hippocampus CA1 region

hyb_protocol: 20ug biotin-labeled cRNA was applied to a rat RGU34A GeneChip (Affymetrix) for hybridization (one chip per animal).

scan_protocol: Standard Affymetrix

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.

organism: Rattus norvegicus

source_name: hippocampus (CA1 region)

label_protocol: For each sample, 20 ug of biotin-labeled cRNA was generated from 5ug of total RNA according to manufacturer’s instructions (Affymetrix).

extract_protocol: RNA was extracted from each CA1 tissue block, as described previously (Blalock et al., 2003; Kadish et al., 2009; Rowe et al., 2007) using TRIzol (Invitrogen) followed by ethanol precipitation, and was reconstituted in RNase-free water.

treatment_protocol: 72 hours novel environment stress (72NES)

value: Male

value: Fisher 344


title: rat hippocampus (CA1 region), 72 hours novel environment stress, subject 73, cohort 1

description: hippocampus CA1 region

value: 72 hours novel environment stress (72NES)


title: rat hippocampus (CA1 region), 72 hours novel environment stress, subject 70, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 67, cohort 1

description: hippocampus CA1 region

treatment_protocol: 24 hours novel environment stress (24NES)


title: rat hippocampus (CA1 region), 72 hours novel environment stress, subject 69, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours novel environment stress, subject 71, cohort 1

description: hippocampus CA1 region


title: ACC 1h (A2) rep1


title: BL 1h (A2) rep1


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 66, cohort 1

description: hippocampus CA1 region

value: 24 hours novel environment stress (24NES)


title: ACC 1h (A2) rep2


title: rat hippocampus (CA1 region), 72 hours novel environment stress, subject 72, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 64, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 65, cohort 1

description: hippocampus CA1 region


title: ABA 1h (A2) rep2


title: GA 1h (A2) rep2


title: MJ 1h (A2) rep1


title: MJ 1h (A2) rep2


title: Zeatin 1h (A2) rep2


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 63, cohort 1

description: hippocampus CA1 region


title: GA 1h (A2) rep1


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 62, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 61, cohort 1

description: hippocampus CA1 region


title: IAA 1h (A2) rep2


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 59, cohort 1

description: hippocampus CA1 region


title: IAA 1h (A2) rep1


title: Zeatin 1h (A2) rep1


title: mock 1h (A2) rep2

value: mock


title: ABA 1h (A2) rep1


title: mock 1h (A2) rep1


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 60, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 57, cohort 2

description: hippocampus CA1 region

treatment_protocol: 72 hours sleep deprived (72SD)

value: 72 hours sleep deprived (72SD)


title: BL 30m (A1) rep1


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 56, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 55, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 54, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours novel environment stress, subject 58, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 52, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 53, cohort 2

description: hippocampus CA1 region


title: ACC 30m (A1) rep1


title: MJ 30m (A1) rep1


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 49, cohort 2

description: hippocampus CA1 region


title: ABA 30m (A1) rep2


title: GA 30m (A1) rep2


title: BL 30m (A1) rep2


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 51, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 50, cohort 2

description: hippocampus CA1 region


title: ABA 30m (A1) rep1


title: GA 30m (A1) rep1


title: Zeatin 30m (A1) rep2


title: MJ 30m (A1) rep2


title: ACC 30m (A1) rep2


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 47, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 43, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 48, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 39, cohort 1

description: hippocampus CA1 region


title: IAA 30m (A1) rep2


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 41, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 38, cohort 1

description: hippocampus CA1 region


title: IAA 30m (A1) rep1


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 42, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 35, cohort 2

description: hippocampus CA1 region

treatment_protocol: 24 hours sleep deprived (24SD)

value: 24 hours sleep deprived (24SD)


title: Zeatin 30m (A1) rep1


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 36, cohort 1

description: hippocampus CA1 region


title: mock 30m (A1) rep2


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 34, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 46, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 31, cohort 2

description: hippocampus CA1 region


title: mock 30m (A1) rep1


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 37, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 30, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 72 hours sleep deprive, subject 40, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 32, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 33, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-42

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description:
LWT-42
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281057_A

hyb_protocol: Labeled cRNA samples were hybridized to Human Ref-8 BeadChips (Illumina) according to the manufacturer's instructions, using equipment specified by the manufacturer (Illumina).

scan_protocol: Processed arrays were read using a BeadStation array reader (Illumina) according to the manufacturer's instructions.

data_processing: quantile normalization

source_name: synaptosomes from frontal cortex

label_protocol: Samples which passed quality were amplified one round and biotin-labeled, using the Illumina TotalPrep Kit (Ambion) according to the manufacturer's instructions. Concentration and quality were assessed using the Nanodrop Spectrophotometer and the Agilent Bioanalyzer Nano Chip System.

extract_protocol: Trizol

tag: age

value: wild type

value: Low (1mg/kg) dose EUK189

value: synaptosomes

tag: genetic background


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 29, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-46

description:
WT-46
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281037_F

value: untreated


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-50

description:
WT-50
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281054_F


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-45

description:
WT-45
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281030_E


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-43

description:
WT-43
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281014_B


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-48

description:
WT-48
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281039_H


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-51

description:
WT-51
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281057_C


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-47

description:
WT-47
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281039_C


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-44

description:
WT-44
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281028_C


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 28, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-41

description:
LWT-41
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281054_H


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-40

description:
LWT-40
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281054_D


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 25, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 24, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 22, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 23, cohort 1

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-38

description:
LWT-38
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281039_B


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 21, cohort 1

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-39

description:
LWT-39
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281054_E


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-37

description:
LWT-37
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281039_E


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 19, cohort 1

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-36

description:
LWT-36
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281039_A


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 18, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 14, cohort 2

description: hippocampus CA1 region

treatment_protocol: home cage (HC)

value: home cage (HC)


title: rat hippocampus (CA1 region), home cage, subject 16, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-33

description:
LWT-33
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281030_C


title: rat hippocampus (CA1 region), 24 hours sleep deprive, subject 20, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 12, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 13, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-30

description:
LKO-30
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281057_F

value: Sod2 KO


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-35

description:
LWT-35
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281037_H


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-32

description:
LWT-32
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281014_G


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-31

description:
LKO-31
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281057_H


title: rat hippocampus (CA1 region), home cage, subject 10, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 15, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-29

description:
LKO-29
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281057_B


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-26

description:
LKO-26
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281037_B


title: rat hippocampus (CA1 region), home cage, subject 7, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-28

description:
LKO-28
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281054_B


title: rat hippocampus (CA1 region), home cage, subject 6, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 17, cohort 2

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 8, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-27

description:
LKO-27
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281039_F


title: rat hippocampus (CA1 region), home cage, subject 11, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-25

description:
LKO-25
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281030_H


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-24

description:
LKO-24
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281030_A


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-22

description:
LKO-22
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281014_E


title: rat hippocampus (CA1 region), home cage, subject 3, cohort 1

description: hippocampus CA1 region


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-18

description:
HWT-18
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281039_D

value: High (30mg/kg) dose EUK189


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-16

description:
HWT-16
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281037_C


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-19

description:
HWT-19
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281054_C


title: rat hippocampus (CA1 region), home cage, subject 5, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 2, cohort 1

description: hippocampus CA1 region


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out  LKO-23

description:
LKO-23
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 knock out
4432281014_H


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-20

description:
HWT-20
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281057_D


title: rat hippocampus (CA1 region), home cage, subject 4, cohort 1

description: hippocampus CA1 region


title: rat hippocampus (CA1 region), home cage, subject 9, cohort 2

description: hippocampus CA1 region


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-17

description:
HWT-17
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281037_D


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-14

description:
HWT-14
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281030_B


title: Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt LWT-34

description:
LWT-34
Synaptosomal RNA from Low Dose treated (EUK8) Constitutive Sod2 wt
4432281037_E


title: rat hippocampus (CA1 region), home cage, subject 1, cohort 1

description: hippocampus CA1 region


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-15

description:
HWT-15
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281030_D


title: Synaptosomal RNA from untreated Constitutive Sod2 wt WT-49

description:
WT-49
Synaptosomal RNA from untreated Constitutive Sod2 wt
4432281054_A


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-12

description:
HWT-12
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281014_F


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-10

description:
HKO-10
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281057_G


title: Gata2+9.5_090111_mutantG

city: Madison

first: Kirby

middle: Dean

last: Johnson

state: WI

address: 1300 University Avenue

department: Pharmacology

institute: University of Wisconsin-Madison

description:
Gene expression in CD31+-enriched cells from Gata2 +9.5 mutant  E12.5 embyo
Gata2+9.5-/- sample 4

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 Mouse GE 8x60 Microarray (GPL13912), microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), both containing 0.005% Triton X-102Slides were air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the 8x60K G3 one color Microarray format. Dye channel is green, scan area 61x21.65 mm, scan resolution 3 um, Tiff is 20 bit.

data_processing: We median centered the arrays of four independent wild type  and +9.5-/- embryos and filtered out the bottom 10% of the probes with the lowest standard deviation across combined wild-type and mutant samples. The differential expression analysis between the mutant and the wild-type samples was conducted with the R package Limma

source_name: E12.5 murine CD31+ cells,Gata2 +9.5 mutant embryo G from litter 2

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

growth_protocol: Gata2 +9.5 mutant and wild type E12.5 littermates were obtained from matings of Gata2 +9.5+/- males and females.

extract_protocol: Total RNA was extracted from CD31+ cells using Trizol reagent (Invitrogen) and futher purified using Qiagen microRNA columns following manufacturer's recommendations.  RNA was quantified using NanoDrop-1000 and and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CD31+ cells were enriched from individual embryo carcasses lacking fetal livers and brains. Single cell suspensions were prepared by collagenase treatment and mechanical dissociation.  CD31+ cells were isolated with anti-CD31 antibody-bound magnetic beads.

tag: litter

value: Gata2 +9.5 mutant

value: embryo

tag: cell type

value: Magnetic bead-enriched CD31+ cells


title: Gata2+9.5_083111_mutantD

description:
Gene expression in CD31+-enriched cells from Gata2 +9.5 mutant  E12.5 embyo
Gata2+9.5-/- sample 2

source_name: E12.5 murine CD31+ cells,Gata2 +9.5 mutant embryo D  from litter 1


title: Gata2+9.5_083111_mutantC

description:
Gene expression in CD31+-enriched cells from Gata2 +9.5 mutant  E12.5 embyo
Gata2+9.5-/- sample 1

source_name: E12.5 murine CD31+ cells,Gata2 +9.5 mutant embryo C  from litter 1


title: 3_UKE1_6h_ITF2357-

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of untreated UKE1 cell line, replicate 3.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hr 30 minutes at 45°C on a GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The Gene 1.0 ST arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: HEL and UKE1 samples were processed separately as two independent datasets following the described procedures. Expression Console Software (Affymetrix Inc.) was used for probe set summarization, robust multi-array average (RMA) normalization and log2 transformation. Probe sets mapping on the same gene were considered as single series of expression value by means of a median summarization approach. The supervised gene expression analyses were performed using Rank Product method by the RankProd R package available on Bioconductor repository (http://www.bioconductor.org/). The up-regulated or down-regulated genes were selected from the lists generated by RankProd using a filter on percentage of false positive predictions (pfp < 0.05) and a second filter on the difference in gene expression value (fold change > 2). Only the matching list of the differentially expressed genes either in HEL and UKE-1 cell lines was considered for further study.

source_name: erythroleukemia cell line UKE1, untreated

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: The UKE1 cell line was maintained in RPMI 1640 medium (Lonza, Basel, Switzerland) supplemented with 2 mM glutamine (Euroclone), 110 µM gentamycin (PHT Pharma, Milano, Italy) and 10% FCS plus 10% horse serum (GIBCO Invitrogen Corp., Paisley, United Kingdom), 10 µM hydrocortisone and 25 mM HEPES buffer solution (Sigma-Aldrich, Milan, Italy).

extract_protocol: Cell pellets were resuspended in TRIzol Reagent (Life Technologies, Inc., Rockville, MD, USA), and total RNA was then purified using the RNeasy® total RNA Isolation Kit (Qiagen, Valencia, CA).

treatment_protocol: Exponentially growing UKE1 cells were cultured in absence of ITF2357 for 6 hours.

tag: cell line

value: JAK2V617F mutation

value: erythroleukemia cells


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-11

description:
HWT-11
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281014_C


title: 4_UKE1_6h_ITF2357+

description: Gene expression profiling data of ITF2357-treated UKE1 cell line, replicate 1.

source_name: erythroleukemia cell line UKE1, ITF2357

treatment_protocol: Exponentially growing UKE1 cells were cultured in the presence of 250 nM ITF2357 for 6 hours.

tag: treatment dosage

tag: treatment time


title: Gata2+9.5_090111_mutantD

description:
Gene expression in CD31+-enriched cells from Gata2 +9.5 mutant  E12.5 embyo
Gata2+9.5-/- sample 3

source_name: E12.5 murine CD31+ cells,Gata2 +9.5 mutant embryo D  from litter 2


title: 5_UKE1_6h_ITF2357+

description: Gene expression profiling data of ITF2357-treated UKE1 cell line, replicate 2.


title: Gata2+9.5_083111_wtA

description:
Gene expression in CD31+-enriched cells from wild type E12.5 embyo
Wild Type sample 1

source_name: E12.5 murine CD31+ cells, wild type embryo A from litter 1


title: Gata2+9.5_090111_wtA

description:
Gene expression in CD31+-enriched cells from wild type E12.5 embyo
Wild Type sample 3

source_name: E12.5 murine CD31+ cells, wild type embryo A from litter 2


title: Gata2+9.5_090111_wtF

description:
Gene expression in CD31+-enriched cells from wild type E12.5 embyo
Wild Type sample 4

source_name: E12.5 murine CD31+ cells, wild type embryo F from litter 2


title: 9384

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 label) was hybridised on Agilent's whole genome rat gene expression microarrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.7.3.1) . Intensities were base 2 log-transformed. Control probes were removed.

source_name: 3C3 B

label_protocol: Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Standard RNA extraction protocol according to Quiagen RNA micro kit

value: Fischer

tag: gender

value: male

tag: tissue

value: bone marrow


title: 6_UKE1_6h_ITF2357+

description: Gene expression profiling data of ITF2357-treated UKE1 cell line, replicate 3.

tag: treatment


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-8

description:
HKO-8
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281054_G


title: Gata2+9.5_083111_wtE

description:
Gene expression in CD31+-enriched cells from wild type E12.5 embyo
Wild Type sample 2

source_name: E12.5 murine CD31+ cells, wild type embryo E from litter 1

tag: strain

tag: genotype/variation


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-7

description:
HKO-7
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281039_G


title: 9386

source_name: RMAPC-1 B


title: 9381

source_name: Fi2 B

value: female

value: blastocyst


title: 2_UKE1_6h_ITF2357-

description: Gene expression profiling data of untreated UKE1 cell line, replicate 2.


title: 1_UKE1_6h_ITF2357-

description: Gene expression profiling data of untreated UKE1 cell line, replicate 1.


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-6

description:
HKO-6
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281037_G


title: 5_HEL_6h_ITF2357+

description: Gene expression profiling data of ITF2357-treated HEL cell line, replicate 2.

source_name: erythroleukemia cell line HEL, ITF2357

growth_protocol: The HEL cell line was maintained in RPMI 1640 medium (Lonza, Basel, Switzerland) supplemented with 2 mM glutamine (Euroclone), 110 µM gentamycin (PHT Pharma, Milano, Italy) and 10% FCS (Euroclone, Wetherby, West Yorkshire, U.K.).

treatment_protocol: Exponentially growing HEL cells were cultured in the presence of 250 nM ITF2357 for 6 hours.

value: HEL


title: 6_HEL_6h_ITF2357+

description: Gene expression profiling data of ITF2357-treated HEL cell line, replicate 3.


title: 9387

source_name: RClone-2 B

value: mesenchymal control


title: 9383

source_name: CL19 B


title: 9382

source_name: Wk8 B

value: Wistar-Kyoto


title: 9380

source_name: Fi1 B


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-5

description:
HKO-5
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281037_A

source_name: synaptosomes from frontal cortex

value: synaptosomes


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-9

description:
HKO-9
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281057_E


title: 4_HEL_6h_ITF2357+

description: Gene expression profiling data of ITF2357-treated HEL cell line, replicate 1.


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-4

description:
HKO-4
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281030_F


title: 9378

source_name: RMAPC-1 A


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-2

description:
HKO-2
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281014_D


title: 9375

source_name: CL19 A


title: 9376

source_name: 3C3 A


title: 3_HEL_6h_ITF2357-

description: Gene expression profiling data of untreated HEL cell line, replicate 3.

source_name: erythroleukemia cell line HEL, untreated

treatment_protocol: Exponentially growing HEL cells were cultured in the absence of ITF2357 for 6 hours.

value: untreated


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-3

description:
HKO-3
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281030_G

value: Sod2 KO


title: wt_P2-hyp-reps1&2

city: Hamilton

first: Turlough

last: Finan

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

description: HYP

hyb_protocol: Standard NimbleGen protocol: hybridized to the microarrays for 16 hours at 42°C

scan_protocol: NimbleGen scanned at 5μm resolution using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The raw data (.pair file) was subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185). Feature expression (value) was the uncorrected median of normalized probe intensity for each experiment (GLY,GAL,HYP,HYPN) data, pooled from two replicates. Only features with at least 6 unique probes were used as defined by our genome analysis of each probe sequence. Background was estimated from the median of the normalized null probes for each experiment.

organism: Sinorhizobium meliloti

label_protocol: Standard NimbleGen protocol: RNA converted to cDNA, random prime lagelled with Cy3

growth_protocol: Growth medium: M9 minimal salts with the addition of  0.25 mM CaCl2, 1 mM MgSO4, 0.5 mg/ml biotin, 43 nM CoCl2; Growth temperature: 30C; exponential phase cells, aerated mid-log phase cultures (OD600 0.4 to 0.6)

extract_protocol: Following extraction, the RNA was further purified and DNA removed using RNeasy minikits (Qiagen).

treatment_protocol: RNA was isolated as previously described (MacLellan et al., 2006. Microbiol  152: 1751-1763.) from aerated mid-log phase cultures (OD600 0.4 to 0.6).

tag: carbon source

value: 10 mM 4-L-hydroxyproline

tag: nitrogen source

value: 1 mg/ml NH4Cl


title: 9379

source_name: RClone-2 A


title: wt_P2-hyp-N-reps1&2

description: HYPN


title: 2_HEL_6h_ITF2357-

description: Gene expression profiling data of untreated HEL cell line, replicate 2.

tag: genotype


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt HWT-13

description:
HWT-13
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 wt
4432281028_A

value: wild type

value: High (30mg/kg) dose EUK189


title: 7603, left breast tumor

city: Nashville

first: Justin

last: Balko

state: TN

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

description: RMA normalized gene expression data from frozen surgical tumor

hyb_protocol: 7.5ug of samples were fragmented and 6ug was put into hyb cocktail for use with the Gene Titan

scan_protocol: Samples were hybridized and scanned using the Gene Titan Affyemtrix instrument according to manufacturer's protocols

data_processing: Data were normalized by RMA in R using the Affy package

source_name: 7603, left breast tumor

label_protocol: Reactions were run with 100ng of Total RNA used per reaction in the Affymetrix IVT-Express Kit (Part #901225, Lot#0901008, Exp 040110) on 030310. The reactions were run through First and Second Strand synthesis, followed by In Vitro Transcription (IVT) using a 16 hour incubation to generate aRNA.

growth_protocol: Surgical tumor specimens from ER+ breast cancer patients were utilized for RNA extraction and hybridization to Affymetrix Gene expression microarrays

extract_protocol: TriZOL followed by RNEasy extraction

treatment_protocol: The patient was treated with 16 days of letrozole leading up to definitive breast surgery of both the left and right bilateral tumors

tag: kras

value: WT

value: Amplified

tag: tumor type

value: Breast

tag: Stage

value: I

value: Letrozole; 16 days


title: wt_P2-gly-reps1&2

description: GLY

value: 0.5% glycerol


title: 9373

source_name: Fi2 A

value: Fischer

value: female

value: blastocyst


title: 7603, right breast tumor

source_name: 7603, right breast tumor

tag: age

value: II


title: wt_P2-gal-reps1&2

description: GAL

value: 15 mM galactitol


title: 1_HEL_6h_ITF2357-

description: Gene expression profiling data of untreated HEL cell line, replicate 1.

value: HEL

value: JAK2V617F mutation

value: erythroleukemia cells

value: untreated


title: 9374

source_name: Wk8 A

value: Wistar-Kyoto


title: 9372

source_name: Fi1 A

value: male


title: 744B9 undiff.

status: Public on Jul 16 2012

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: undifferentiated hiPSCs

hyb_protocol: According to manufature's protocol.

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

label_protocol: According to manufature's protocol.

growth_protocol: HiPSCs were maintained on feeder layers of mitomycin C-treated SNL cells in Primate ES medium (ReproCELL) supplemented with 4 ng/ml recombinant human basic fibroblast growth factor (bFGF).

extract_protocol: Total RNA was purified with a miRNeasy mini kit (QIAGEN) according to the manufacturer’s protocol.

tag: disease

value: healthy

value: human iPSCs

tag: original tissue

value: peripheral blood


title: 751B4 undiff.

description: undifferentiated hiPSCs

tag: cell type

value: adult dermal fidroblast


title: 751A3 undiff.

description: undifferentiated hiPSCs


title: CiRA-PD27 undiff.

description: undifferentiated hiPSCs

source_name: PD #2

value: Parkinson’s disease


title: 201B7 CXCR4- #4

description: CXCR4-negative cell populations sorted by flowcytometry after 7 days of endodermal differentiation

hyb_protocol: According to manufature's protocol

label_protocol: According to manufature's protocol

tag: clone


title: 201B7 CXCR4- #1

value: CXCR4-negative cell populations sorted by flowcytometry after 7 days of endodermal differentiation


title: 744A2 undiff.

description: undifferentiated hiPSCs


title: CiRA-PD29 undiff.

description: undifferentiated hiPSCs


title: CiRA-PD24 undiff.

description: undifferentiated hiPSCs

source_name: PD #1


title: Tailbud SU5402 3 hour 3

city: New Haven

first: Michael

middle: Jeremy

last: Stulberg

state: CT

address: 219 Prospect St

department: MCDB

institute: Yale University

hyb_protocol: Labeled cRNA was fragmented and placed on zebrafish 44k whole genome microarray for 17 hours at 65°C.

scan_protocol: Arrays were washed and scanned at 5uM resolution on an Agilent G2565CA High Resolution Scanner.

data_processing: Data was processed through Feature Extraction software version 10.7.3.1 using the protocol GE1_107_Sep09 and the 44k grid file 026437_D_F_20091215.

source_name: tailbud, 3hr, SU5402 treatment, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amp Labeling Protocol (V.6) (Agilent) according to manufacturor's instructions, followed by RNeasy column purification (Qiagen). Labeling efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol: Zebrafish embryos were grown in E2 and at the 4 somite stage chorions were removed and embryos were subjected to chemical treatment.

extract_protocol: total RNA from dissected tailbuds was extracted using RNA XS (Macherey-Nagel) and cleaned an additional time with RNA Clean and Concentrator kit (Zymo Research). RNA was shipped to Ambry Genetics for labeling, hybridization, and running of the arrays.

treatment_protocol: Dechorionated embryos were treated with 0.3M LiCl, 50uM SU5402, or E2 and tailbuds dissected following 3 hours or 7 hours (E2 and SU5402 only).

value: tailbud

tag: time

value: 3 h

value: TLAB


title: Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out  HKO-1

description:
HKO-1
Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out
4432281014_A

value: Sod2 KO

value: High (30mg/kg) dose EUK189

tag: sample type

value: synaptosomes

tag: genetic background


title: CiRA-PD22 undiff.

description: undifferentiated hiPSCs


title: CiRA-PD23 undiff.

description: undifferentiated hiPSCs


title: CiRA-PD28 undiff.

description: undifferentiated hiPSCs


title: 201B6 CXCR4- #4


title: Tailbud SU5402 7 hour 3

source_name: tailbud, 7hr, SU5402 treatment, replicate 3

tag: tissue

tag: treatment

value: 7 h


title: Tailbud WT 7 hour 2

source_name: tailbud, 7hr, no treatment, replicate 2

tag: strain


title: Tailbud SU5402 7 hour 1

source_name: tailbud, 7hr, SU5402 treatment, replicate 1


title: CiRA-PD25 undiff.

description: undifferentiated hiPSCs


title: 201B6 CXCR4- #3


title: 201B7 CXCR4- #2


title: 201B7 CXCR4+ #4

description: CXCR4-positive cell populations sorted by flowcytometry after 7 days of endodermal differentiation


title: CiRA-PD26 undiff.

description: undifferentiated hiPSCs


title: 201B6 CXCR4- #2


title: 201B7 CXCR4- #3


title: Tailbud WT 7 hour 3

source_name: tailbud, 7hr, no treatment, replicate 3


title: 201B6 CXCR4- #1


title: Tailbud SU5402 7 hour 2

source_name: tailbud, 7hr, SU5402 treatment, replicate 2


title: Tailbud LiCl 3 hour 1

source_name: tailbud, 3hr, LiCl treatment, replicate 1

value: LiCl


title: 201B7 CXCR4+ #1

value: CXCR4-positive cell populations sorted by flowcytometry after 7 days of endodermal differentiation


title: 201B7 CXCR4+ #2


title: Tailbud LiCl 3 hour 3

source_name: tailbud, 3hr, LiCl treatment, replicate 3


title: 201B7 CXCR4+ #3


title: 201B6 CXCR4+ #4


title: Tailbud SU5402 3 hour 2

source_name: tailbud, 3hr, SU5402 treatment, replicate 2


title: Tailbud SU5402 3 hour 1

source_name: tailbud, 3hr, SU5402 treatment, replicate 1


title: Tailbud WT 3 hour 2

source_name: tailbud, 3hr, no treatment, replicate 2


title: Tailbud WT 3 hour 3

source_name: tailbud, 3hr, no treatment, replicate 3


title: Tailbud LiCl 3 hour 2

source_name: tailbud, 3hr, LiCl treatment, replicate 2


title: 201B7 undiff. #3

description: undifferentiated hiPSCs

value: undifferentiated hiPSCs


title: 201B6 CXCR4+ #2


title: Tailbud WT 7 hour 1

source_name: tailbud, 7hr, no treatment, replicate 1


title: Tailbud WT 3 hour 1

source_name: tailbud, 3hr, no treatment, replicate 1


title: 201B6 undiff. #4

description: undifferentiated hiPSCs


title: 201B6 CXCR4+ #1


title: 201B7 undiff. #2

description: undifferentiated hiPSCs


title: PN21 mouse retina, biological rep4 Edn2+/+

city: Toronto

first: Alexa

middle: Natalie

last: Bramall

address: 101 College St.

institute: Hospital for Sick Children

description: Gene expression data from retinas at PN21

hyb_protocol: EukGE-WS2v5. 15 ug of cRNA were hybridized.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the Robust Multi-array Averaging algorithm (RMA) with Affymetric GeneChip Operating Software (GCOS). The scaling target signal was set to 150.

label_protocol: Biotinylated cRNA were prepared according to the standard Afymetrix protocol from 2.5 ug total RNA (Affymetrix one-cycle kit and IVT kit)

growth_protocol: mice of the appropriate genotype were sacrificed at PN21 for extraction of retinal RNA

extract_protocol: Total RNA from two retinas (one mouse) was homogenized in GIT buffer and isolated by cesium chloride density gradient centrifugation.

treatment_protocol: Eyes were dissected in ice-cold 1X PBS by removing the corneas and peeling off the retina from the underlying sclera and choroid

value: whole retina

value: postnatal day 21


title: PN21 mouse retina, biological rep 4 Edn2-/-


title: 201B6 CXCR4+ #3


title: 201B7 undiff. #4

description: undifferentiated hiPSCs


title: PN21 mouse retina, biological rep4 Tg(RHO P347S) Edn2-/-

value: Tg(RHO P347S) Edn2-/-


title: 201B7 undiff. #1

description: undifferentiated hiPSCs


title: 201B6 undiff. #3

description: undifferentiated hiPSCs


title: PN21 mouse retina, biological rep4 Tg(RHO P347S) Edn2+/+

value: Tg(RHO P347S) Edn2+/+


title: PN21 mouse retina, biological rep 2 Edn2-/-


title: 201B6 undiff. #2

description: undifferentiated hiPSCs

value: adult dermal fidroblast


title: PN21 mouse retina, biological rep3 Tg(RHO P347S) Edn2+/+


title: PN21 mouse retina, biological rep2 Tg(RHO P347S) Edn2-/-


title: PN21 mouse retina, biological rep1 Edn2-/-


title: PN21 mouse retina, biological rep2 Tg(RHO P347S) Edn2+/+


title: PN21 mouse retina, biological rep1 Tg(RHO P347S) Edn2-/-


title: PN21 mouse retina, biological rep3 Tg(RHO P347S) Edn2-/-


title: PN21 mouse retina, biological rep1 Edn2+/+


title: PN21 mouse retina, biological rep2 Edn2+/+


title: PN21 mouse retina, biological rep3 Edn2+/+


title: 201B6 undiff. #1

description: undifferentiated hiPSCs


title: PN21 mouse retina, biological rep1 Tg(RHO P347S) Edn2+/+


title: RC_MC030065

city: Tokushima

first: Toyomasa

last: Katagiri

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: The University of Tokushima

hyb_protocol: Labeled cDNAs were mixed with microarray hybridization solution version 2 (Amersham) and formamide (Sigma) to a final concentration of 50%. After hybridization for 14-16 hours at 42 oC in Automated Slide Processor, the slides were washed in 2xSSC and 1% SDS for 10min at 55C, washed in 0.2xSSC and 0.1% SDS for 10min at 55C, and washed in 0.1xSSC for 1 min at room temperature in Automated Slide Processor.

scan_protocol: Microarray slides were scanned using the Array Scanner Generation III (Amersham) after hybridization.

data_processing: Images were gridded and the fluorescent intensity of each spot (Cy5/Cy3) was evaluated photometrically by the ArrayVision computer program (Imaging Research, Inc., St. Catharines, Ontario, Canada) . The fluorescent intensities of Cy5 (tumor) and Cy3 (control) for each target spot were adjusted so that the mean Cy3/Cy5 ratio of the 52 housekeeping genes was equal to one. Because data derived from low signal intensities are less reliable, we determined a cut-off value on each slide and excluded genes from further analysis when both Cy3 and Cy5 dyes yielded signal intensities lower than the cut-off value. For other genes, we calculated the Cy5/Cy3 ratio using the raw data of each sample. Experiments were performed using 6 sets of slides (slide set 1-6  corresponding to ID_REF 1-27648).

source_name: clear cell renal cell carcinoma (ccRCC)

label_protocol: 2.5 ug aliquots of aRNA from tumor cells or normal cells were annealed with random primer for 10 min at 70oC. They were labeled in a 50ul volume by reverse transcription reaction for 2 hours at 37oC using Superscript II reverse transcriptase (Invitrogen) with 1mM Cy5-dCTP for tumor cells or Cy3-dCTP for normal cells (Amersham) and 25mM each dATP, dGTP, and dTTP. The labeling reaction was stopped by adding 6ul 2.5 N NaOH and incubation for 30 min at 65oC and neutralized by 20ul 1M Tris-HCl (pH7.4) and 7ul 2.5N HCl. The labeled cDNAs were purified by QIAquick PCR Purification Kit (QIAGEN).

extract_protocol: Celar cell renal cell carcinoma cells that were microdissected from tissue samples of surgically-resected renal cell carcinoma. 100,00-200,000 tumor cells or normal cells were isolated selectively using the EZ cut system with a pulsed ultraviolet narrow beam-focus laser (SL Microtest GmbH, Germany) in accordance with the manufacturer’s protocols. Total RNAs were isolated from captured cells with QIAGNE RNAeasy Kit (QIAGEN). After DNAse I treatment, total RNAs were subjected to two rounds of T7-based amplification using MEGAscript High Yield Transcription Kit (Ambion), which yielded 50-100 ug of amplified RNA (aRNA) from each sample.

tag: gender

value: female

tag: pt

tag: grade

tag: tissue origin

value: Clear cell renal cell carcinoma cells

source_name: Universal control of normal renal cortex

value: A mixture of normal renal cortex cells in kidney tissues from 11 patients


title: RC_518

value: male

value: surgically-resected renal cell carcinoma


title: RC_KI04028


title: RC_MC030058


title: RC_KI04001


title: RC_KI04037


title: RC_MC030063


title: cell line H-STS

city: Graz

first: Carina

last: Fischer

address: Stiftingtalstr. 24

country: Austria

institute: ZMF

hyb_protocol: according to Affymetrix SNP 6.0 protocol

scan_protocol: ACGG

data_processing: SNP 6.0 data were imported and normalized using the Genotyping Console 4.0  program default settings. All samples passing QC criteria were subsequently  genotyped using the Birdseed (v2) algorithm. We used 60 raw HapMap data  generated with the Affymetrix Genome-Wide Human SNP Array 6.0 as reference.

source_name: cell line

extract_protocol: according to Qiagen QIAamp DNA Mini Kit Protocol

value: cell line


title: RC_MC030067


title: primary tumor p-TU

source_name: tissue

label_protocol: according to Affymetrix SNP 6.0 protocol

value: primary tumor


title: cell line L-STS


title: RC_KI04029


title: RC_MC030069


title: RC_KI04036


title: RC_KI04006


title: RC_KI04005


title: RC_KI04007


title: DCIR2_zDCKO_3

city: New York

first: Matthew

last: Meredith

state: New York

address: 1230 York Ave

institute: The Rockefeller University

description:
ZKO_DCIR2_3
Mice were treated with Flt3L in vivo to expand DCs.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GeneSpring using default RMA normalization. The normalized values are log2 scaled, where the median is set as zero.

source_name: spleen cDCs, zDC KO, DCIR2+

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

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

tag: strain/background

tag: genotype

value: zDC knockout

value: 6-8 weeks

value: spleen

value: classical dendritic cells (cDCs)

tag: cell population


title: cell line P-STS


title: RC_KI04018

tag: age


title: PN21 mouse retina, biological rep 3 Edn2-/-


title: DCIR2_zDCKO_1

description:
ZKO_DCIR2_1
Mice were treated with Flt3L in vivo to expand DCs.


title: DCIR2_zDCKO_2

description:
ZKO_DCIR2_2
Mice were treated with Flt3L in vivo to expand DCs.


title: DEC_zDCKO_1

description:
ZKO_DEC_1
Mice were treated with Flt3L in vivo to expand DCs.

source_name: spleen cDCs, zDC KO, DEC-205+


title: DEC_zDCKO_2

description:
ZKO_DEC_2
Mice were treated with Flt3L in vivo to expand DCs.


title: DEC_zDCKO_3

description:
ZKO_DEC_3
Mice were treated with Flt3L in vivo to expand DCs.


title: siRNA transfected cells, biological rep2

status: Public on Jul 15 2012

city: Sydney

middle: J

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

institute: University of Sydney

description: Exon expression data from HeLa cells, transfected with siRNA only

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Human Exon 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix).

data_processing: The samples were individually normalized using robust-multi-array analysis (RMA) in the R application (version 2.11.1). A two-stage statistical analysis was used. The first stage was to identify differentially expressed transcripts between the RBM4-specific siRNA and control siRNA sets of samples. For a typical transcript g (log-likelihood ratio) we averaged expression values among all exons within transcript g and computed the fold-change and moderated t-statistics between groups.  Then we generated a candidate list of differentially-expressed genes with an absolute moderated t-statistics of 2 and above, and greater than 1.5-fold change between groups. These procedures use functions in the limma library of the Bioconductor software package.

source_name: HeLa cells

label_protocol: 1 μg of total RNA was prepared for hybridisation according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix).

growth_protocol: The cervical cancer cells HeLa  were obtained from the American Type Culture Collection and cultured at 37°C under 5% CO2 in DMEM (Invitrogen), supplemented with 0.1 mM non-essential amino acids and 1.0 mM sodium pyruvate. Ten percent FCS (Invitrogen) and penicillin/streptomycin (5000 u/mL; Invitrogen) were added to the medium.

extract_protocol: HeLa cells were harvested after 40 h of incubation. RNeasy kit (Qiagen) was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with RBM4-specific siRNA (Dharmacon) by lipofection using Lipofectamine 2000 according to the manufacturer’s instructions (Invitrogen) at a transfection efficiency of over 90%.

tag: cell line

value: HeLa

value: siRNA transfected


title: HepG2 vs. HepG2-DDX20 knockdown

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: normalized log2 ratio (HepG2-DDX20KD/HepG2-PCDH)

hyb_protocol: Hybridized for 16h at 37C with rotary shake (250rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: Cells were maintained in Dulbecco's modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from cells using Trizol Reagent (Invitrogen, Carlsbad, CA) following manufacturer's instructions.

treatment_protocol: HepG2 cells were transduced with control-shRNA lentiviral particles and DDX20 (Gemin3)-shRNA (Santa Cruz Biotechnology) and then selected on puromycin.

tag: genotype/variation

value: control


title: RBM4-specific siRNA transfected cells, biological rep1

description: Exon expression data from HeLa cells, transfected with RBM4-specific siRNA

value: RBM4-specific siRNA transfected cells


title: RBM4-specific siRNA transfected cells, biological rep2


title: RBM4-specific siRNA transfected cells, biological rep3


title: Untransfected cells, biological rep2

description: Exon expression data from HeLa cells, untransfected

value: untransfected


title: Hematopoietic stem cell, biological replicate 1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
HSC_1
Cell purification by FACS as follows: Lineage (CD4, CD8, CD3, B220, Ter119, Mac1, Gr1, Il7ra) negative, Sca1+, ckit+, CD34-, flk2-, PI-.

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The microarrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: The data were normalized using GCRMA and Bioconductor 2.8 with default parameters.

source_name: Hematopoietic stem cells purified from primary bone marrow

label_protocol: Total RNA from the samples was normalized to 50 ng/ul, and the GeneChip 3' IVT Express Protocol was used for amplification in a semi-automated process. The total RNA underwent reverse transcription to synthesize first-strand cDNA. This cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the samples for hybridization on the microarray.

growth_protocol: Cells were purified directly from primary bone marrow (HSC, MEP) or primary skin tissue (CLDC, EPro, EDif) without any phase of in vitro culture.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's recommendation.

treatment_protocol: Cells were sorted on a BD Biosciences FACSAria II cell sorter according to the listed cell type specific criteria.

tag: cell type

value: hematopoietic stem cells

tag: tissue lineage

value: blood


title: siRNA transfected cells, biological rep3


title: mock, biological rep3

description: Exon expression data from HeLa cells, mock

value: mock


title: Megakaryocyte-erythroid progenitor, biological replicate 1

description:
MEP_1
Cell purification by FACS as follows: Lineage (CD4, CD8, CD3, B220, Ter119, Mac1, Gr1 Il7ra) negative, Sca1-, ckit+, fcgamma receptor low/neg, CD34-, PI-.

source_name: Megakaryocyte-erythroid progenitor cells purified from primary bone marrow


title: Epidermis differentiated cell, biological replicate 2

description:
EDif_2
Cell purification by FACS as follows: K14-GFP negative, K10-RFP positive, alpha 6 integrin low, Sca1 low.

source_name: Epidermis differentiated cells purified from primary skin tissue

value: epidermis differentiated cells

value: skin


title: Epidermis progenitor cell, biological replicate 2

description:
EPro_2
Cell purification by FACS as follows: K14-GFP positive, K10-RFP negative, alpha 6 integrin high, Sca1 positive.

source_name: Epidermis progenitor cells purified from primary skin tissue

value: epidermis progenitor cells


title: Epidermis progenitor cell, biological replicate 1

description:
EPro_1
Cell purification by FACS as follows: K14-GFP positive, K10-RFP negative, alpha 6 integrin high, Sca1 positive.


title: Epidermis differentiated cell, biological replicate 1

description:
EDif_1
Cell purification by FACS as follows: K14-GFP negative, K10-RFP positive, alpha 6 integrin low, Sca1 low.


title: Hematopoietic stem cell, biological replicate 2

description:
HSC_2
Cell purification by FACS as follows: Lineage (CD4, CD8, CD3, B220, Ter119, Mac1, Gr1, Il7ra) negative, Sca1+, ckit+, CD34-, flk2-, PI-.


title: Companion layer differentiated cell, biological replicate 2

description:
CLDC_2
Cell purification by FACS as follows: Lhx2-GFP negative, K6-RFP positive, beta 1 integrin negative, CD34 negative.

source_name: Companion layer differentiated cells purified from primary skin tissue

value: companion layer differentiated cells


title: Megakaryocyte-erythroid progenitor, biological replicate 2

description:
MEP_2
Cell purification by FACS as follows: Lineage (CD4, CD8, CD3, B220, Ter119, Mac1, Gr1 Il7ra) negative, Sca1-, ckit+, fcgamma receptor low/neg, CD34-, PI-.


title: mock, biological rep1


title: Untransfected cells, biological rep1


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _EGTA+Ionomycin Treatment_TP5_6hr

city: Singapore

first: Ramya

last: Ramadoss

address: 60 Nanyang Drive, 04n-18, School of Biological Sciences

institute: Nanyang Technological University, School of Biological Sciences

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

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

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum 3D7

source_name: P.falciparum 3d7 strain (in-vitro) treated with EGTA+ionomycin

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

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

value: lab strain 3d7

tag: culture type

value: in-vitro culture

tag: time point

tag: time post-treatment

source_name: P. falciparum 3d7 RNA reference pool

value: Lab Strain 3D7

tag: sample type

value: mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Untransfected cells, biological rep3

tag: treatment


title: siRNA transfected cells, biological rep1


title: Companion layer differentiated cell, biological replicate 1

description:
CLDC_1
Cell purification by FACS as follows: Lhx2-GFP negative, K6-RFP positive, beta 1 integrin negative, CD34 negative.

tag: strain


title: mock, biological rep2


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _EGTA+Ionomycin Treatment_TP1_30mins


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _EGTA+Ionomycin Treatment_TP4_4hr


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _EGTA+Ionomycin Treatment_TP3_2hr


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _Ionomycin Treatment_TP5_6hr

source_name: P.falciparum 3d7 strain (in-vitro) treated with ionomycin


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _Ionomycin Treatment_TP4_4hr


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _Ionomycin Treatment_TP2_1hr


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _control_TP5_6hr

source_name: P.falciparum 3d7 strain (in-vitro) untreated_control


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _Ionomycin Treatment_TP1_30mins


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _Ionomycin Treatment_TP3_2hr


title: WT+pXYLA,XKS1 grown in xylose, rep 3

city: Ottawa

first: Linda

last: Harris

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

description: Gene expression in wild-type yeast with additional exogenous genes in Xylose

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Yeast Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Robbins Model 400 hybridization oven (Robbins Scientific) and an Agilent Rotator Rack. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then a 10 seconds Acetonitrile Wash (Agilent) followed by a 30 seconds Stabilization and Drying Solution wash (Agilent).

scan_protocol: Slides were scanned immediately after washing using a GenePix 4200A (Molecular Devices) using only the cy3 channel, scanning each each array individually (scan area 2088 x 3112 pixels). Scan resolution 10 µm, lines to average= 1, focus position 0µm. Laser set at 100% and PMT between 330 and 370 according to strength of the individual array.

data_processing: The scanned images were analyzed with GenePix 6.0 (Molecular Devices) using default parameters to obtain background subtracted. To generate the normalized data, we have performed a global median intensity standardization manually to correct for position and scale for the arrays. Features flagged in GenePix as absent or non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: wild type yeast with additional exogenous genes XYLA and XKS1, grown in xylose

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Protocol version 5.7 (Agilent) according to the manufacturer's instructions, except using half of the reagents amount in step 2, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Overnight cultures were diluted to 0.05 at OD 600nm in fresh YPD or YEP-Xylose and incubated at 30ºC to an optical density of 0.6 (OD600nm).

extract_protocol: Total RNA was extracted from yeast cells using TRI reagent (Sigma) as per the manufacturers protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were grown in either 2% YEP-Glucose or YEP-Xylose till at mid-log phase

value: YKB2178 (YKB731 + pXYLA,XKS1)


title: WT+pXYLA,XKS1 grown in xylose, rep 4


title: WT+pXYLA,XKS1 grown in xylose, rep 2


title: WT+pXYLA,XKS1 grown in glucose, rep 3

description: Gene expression in wild-type yeast with additional exogenous genes in glucose

source_name: wild type yeast with additional exogenous genes XYLA and XKS1, grown in glucose


title: WT+pXYLA,XKS1 grown in glucose, rep 4


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _control_TP1_30mins


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _control_TP4_4hr


title: WT+pXYLA,XKS1 grown in glucose, rep 2


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _control_TP2_1hr


title: P.falciparum 3D7_schizonts_A23187_TP4_4hr post treatment

source_name: P.falciparum 3d7 strain (in-vitro) treated with A23187


title: WT+pXYLA,XKS1 grown in xylose, rep 1


title: WT+pXYLA grown in xylose, rep 5

source_name: wild type yeast with additional exogenous gene XYLA,grown in xylose

value: YKB2179 (YKB731+pXYLA)


title: WT+pXYLA grown in xylose, rep 4


title: P.falciparum 3D7_schizonts_A23187_TP3_2hr post treatment


title: P.falciparum 3D7_schizonts_extracellular calcium chelation _control_TP3_2hr


title: P.falciparum 3D7_schizonts_Ionomycin_TP5_6hr post treatment


title: P.falciparum 3D7_schizonts_A23187_TP1_30mins post treatment


title: P.falciparum 3D7_schizonts_A23187_TP5_6hr post treatment


title: WT+pXYLA grown in xylose, rep 6


title: WT+pXYLA,XKS1 grown in glucose, rep 1


title: WT+pXYLA grown in xylose, rep 3


title: P.falciparum 3D7_schizonts_A23187_TP2_1hr post treatment


title: P.falciparum 3D7_schizonts_Ionomycin_TP4_4hr post treatment


title: WT+pXYLA grown in glucose, rep 3

source_name: wild type yeast with additional exogenous gene XYLA,grown in glucose


title: P.falciparum 3D7_schizonts_Ionomycin_TP2_1hr post treatment


title: WT+pXYLA grown in glucose, rep 4


title: Wildtype strain grown in xylose, rep 3

description: Gene expression in wild-type yeast grown in xylose

source_name: wild type yeast, treated with xylose


title: WT+pXYLA grown in xylose, rep 1


title: WT+pXYLA grown in xylose, rep 2


title: Wildtype strain grown in xylose, rep 2


title: WT+pXYLA grown in glucose, rep 1


title: P.falciparum 3D7_schizonts_Ionomycin_TP3_2hr post treatment


title: P.falciparum 3D7_schizonts_control_TP5_6hr post treatment


title: P.falciparum 3D7_schizonts_Ionomycin_TP1_30mins post treatment


title: WT+pXYLA grown in glucose, rep 2


title: P.falciparum 3D7_schizonts_control_TP4_4hr post treatment


title: Wildtype strain grown in xylose, rep 1


title: P.falciparum 3D7_schizonts_control_TP3_2hr post treatment


title: Calcium ionophore_A23187 treatment/Timepoint 4_4 hour post treatment

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy3) divided by the corresponding measurement in the reference channel (Cy5, Untreated P. falciparum parasites).

organism: Plasmodium falciparum

source_name: P. falciparum parasites (in-vitro) treated with A23187

extract_protocol: Total genomic DNA extracted using phenol-chlorofom method as previously described : Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009)

value: lab strain DD2

value: 4 hr

source_name: Untreated P. falciparum parasites (in-vitro)


title: Calcium ionophore_A23187 treatment/Timepoint 5_6 hour post treatment

value: 6 hr


title: P.falciparum 3D7_schizonts_control_TP2_1hr post treatment


title: Wildtype strain grown in glucose, rep 2

description: Gene expression in wild-type yeast grown in glucose

source_name: wild type yeast, no treatment


title: Calcium ionophore_ionomycin treatment/Timepoint 5_6 hour post treatment

source_name: P. falciparum parasites (in-vitro) treated with ionomycin