title: HepG2 treated with PH Array 2

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across PH treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated PH labeled with Cy5

value: PH


title: HepG2 treated with CHR Array 1

status: Public on Apr 18 2012

type: RNA

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

hyb_protocol: Hybridization was performed by incubation in a hybridization oven at 62°C for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58°C, 1× SSC for 2 min at RT, and 0.2× SSC for 3 min at room temperature [RT]), slides were dried by centrifugation at 800 rpm for 3 min at RT.

scan_protocol: Images of the hybridized slides were captured using a GenePix 4000B scanner (Axon Instruments, USA). Scanned images were analyzed with GenePix 5.1 software (Axon Instruments) to obtain gene expression ratios.

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across CHR treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 treated CHR labeled with Cy5

label_protocol: Platinum Biochip Reagent Kit

extract_protocol: Trizol extraction

tag: agent

value: CHR

tag: cell line

value: HepG2 (hepatocellular carcinoma)

source_name: HepG2 treated DMSO labeled with Cy3

value: DMSO


title: HepG2 treated with CHR Array 3


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 5

city: Madrid

first: David

last: Santamaría

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

hyb_protocol: Samples were hybridized to Mouse WMG 4X44K (Agilent).

scan_protocol: Microarrays were scanned on a G2565C DNA microarray scanner (Agilent).

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.1.1).
Bioconductor's limma package was employed for preprocessing and normalization, thus, background was corrected using normexp method and data were normalized using loess and quantiles method for within-array and inter-array normalization, respectively
Normalized log2 ratio representing KO/WT in all cases including dye-swap experiment column (Sample 4).

organism: Mus musculus

source_name: WT

label_protocol: 1µg per sample was labeled with Two-Color Microarray-Based Gene Expression Analysis (Agilent) and purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: MEFs were grown in DMEM supplemented with 10% fetal bovine serum in 5%CO2 incubator. Following adenoviral infection MEFs were splitted when necessary to maintain sub-confluent cultures.

extract_protocol: RNA was extracetd using RNeasy kit (Quiagen) 7 days after adenoviral infection. RNA integrity was assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

treatment_protocol: MEFs were infected with 100MOI of Ad5-CMVCre or Ad5-CMVGFP.

tag: cell type

value: Adeno-GFP infected Cdk7lox/lox MEFs

tag: strain

value: Mixed (129 x C57Bl/6)

tag: genotype

value: WT

source_name: KO

value: Adeno-Cre infected Cdk7lox/lox MEFs

value: KO


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 4


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 2


title: HepG2 treated with CHR Array 2


title: Nogays Caucasus Male nogay42

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium Human610-Quad v1.0  Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label: biotin

molecule: genomic DNA

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: Nogays

tag: region

value: Caucasus

tag: tissue

value: blood


title: HepG2 treated with PH Array 1


title: HepG2 treated with NP Array 1

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across NP treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated NP labeled with Cy5

value: NP


title: HepG2 treated with NP Array 3


title: HepG2 treated with DBA Array 3

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across DBA treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated DBA labeled with Cy5

value: DBA


title: HepG2 treated with 3MC Array 3

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across 3MC treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated 3MC labeled with Cy5


title: 7-week-old chicken leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep3

city: Guangzhou

first: Hongmei

last: Li

address: Guangzhou tianhe wushan street

country: China

institute: south china agricultural university

description:
Meat-type chickens.
The body weight of dwarf chickens was about 30% less than that of normal chickens.
3 chickens used per breed for each sample.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two-color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

organism: Gallus gallus

source_name: normal chicken leg muscle

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore). The small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) following the manufacturer's recommended protocol.

tag: breed

value: normal recessive White Rock

value: leg muscle

tag: age

value: 7 weeks

tag: identifier

source_name: dwarf chicken leg muscle

value: dwarf recessive White Rock


title: Uveal melanoma 30

city: Genova

first: Valentina

last: Mirisola

address: Largo Benzi 10

department: Functiona Genomics

country: Italy

institute: National Cancer Institute

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Expression Console

source_name: Uveal melanoma

label_protocol: Standard Affymetrix procedures

extract_protocol:
Tumour samples were homogenized in the tissue lyser Mixer Mill in total RNA extraction lysis buffer Qiazol (Qiagen).
Total RNA was extracted from the tissue lysate using an miRNeasy mini kit (Qiagen).

value: uveal melanoma

value: female

tag: eye

value: right


title: HepG2 treated with DBA Array1

value: HepG2 (hepatocellular carcinoma)

value: DMSO


title: 7-week-old chicken leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep2


title: HepG2 treated with NP Array 2


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 3

value: Adeno-GFP infected Cdk7lox/lox MEFs

value: Mixed (129 x C57Bl/6)

value: WT

value: Adeno-Cre infected Cdk7lox/lox MEFs


title: HepG2 treated with DBA Array 2


title: HepG2 treated with 3MC Array 2


title: Adeno-Cre vs. Adeno-GFP infected Cdk7lox/lox MEFs rep 1

value: KO


title: ALL derived TOM-1 cell line after 6 hours of treatment with LH589 T3

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HuGene 1.0 ST chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

data_processing: RMA  (R/Bioconductor processing)

source_name: ALL derived TOM-1 cell line after 6 hours of treatment with LH589 growth in vitro

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Cell lines were maintained in culture in RPMI 1640 medium supplemented with 10% fetal bovine serum and with 1% penicillin-streptomicin and 2% hepes (Gibco-BRL, Burlington, Ontario, Canada) at 37ºC in a humid atmosphere containing 5% CO2.

extract_protocol: The cells were harvested with Ultraspec Reagent (Biotecx. Houston, TX, USA)   and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: In vitro ALL-derived cell lines were treated with LBH589 at 50nM of concentration and maintained in culture for up to 6 hours.


title: HepG2 treated with 3MC Array 1


title: ALL derived TOM-1 cell line after 6 hours of treatment with LH589 T1


title: ALL derived TOM-1 cell line after 6 hours of treatment with LH589 T2


title: ALL derived TOM-1 cell line control T3

source_name: ALL derived TOM-1 cell line growth in vitro


title: HepG2 treated with BaP Array 3

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios of below 10 were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across BaP treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated BaP labeled with Cy5

value: BaP


title: HepG2 treated with BaP Array 2


title: ALL derived TOM-1 cell line control T1


title: 14-day-old embryo leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep1

description:
Meat-type chickens.
The body weight of dwarf chickens was about 30% less than that of normal chickens.
3 embryos used per breed for each sample.

source_name: normal embryo leg muscle

tag: developmental stage

value: 14-day-old embryo

source_name: dwarf embryo leg muscle


title: 14-day-old embryo leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep2


title: HepG2 treated with BaP Array 1


title: ALL derived MOLT-4 cell line after 6 hours of treatment with LH589 T1

source_name: ALL derived MOLT-4 cell line after 6 hours of treatment with LH589 growth in vitro


title: ALL derived MOLT-4 cell line after 6 hours of treatment with LH589 T2


title: ALL derived TOM-1 cell line control T2


title: ALL derived MOLT-4 cell line control T3

source_name: ALL derived MOLT-4 cell line growth in vitro


title: HepG2 treated with PH Array 3

source_name: HepG2 treated PH labeled with Cy5

value: PH

source_name: HepG2 treated DMSO labeled with Cy3


title: Nogays Caucasus Male nogay49

value: Male

value: Nogays

value: Caucasus

value: blood


title: ALL derived MOLT-4 cell line control T2


title: T cell Acute Lymphoblastic Leukemia 1

source_name: The same T cell ALL as LALT obtained from the spleen of mouse

growth_protocol: Samples 421, 739, 1 and 226 have been obtained from spleen of immunodeficient mice.

extract_protocol: The cells were harvested with Ultraspec Reagent (Biotecx. Houston, TX, USA)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

value: T cell ALL


title: T cell Acute Lymphoblastic Leukemia 226


title: ALL derived MOLT-4 cell line control T1


title: Chicken embryonic cerebral cortex: High dose replicate 4

city: Ottawa

first: Cristina

last: Cassone

address: 620 Kochar Drive

country: Canada

institute: University of Ottawa

description: Biological replicate 4 of 5. HD

hyb_protocol: Samples were hybridized to Agilent 4X44K chicken gene expression microarrays at 65 degrees celcius for 17 hours according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Agilent G2505B scanner at 5 um resolution.

data_processing: Agilent Feature Extraction Software (v. 10.7.3.1) was used for data processing.

source_name: Chicken embryonic cerebral cortex dosed with 38,000 ng/g PFHxS

label_protocol: Samples were labeled using Quick Amp Labeling kits (Agilent) according to the manufacturer's instructions.

growth_protocol: Fertilized chicken embryos were grown in a rotating incubator set to 37.5 degrees celcius and 57% humidity.

extract_protocol: Total RNA was extracted using RNeasy mini kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Single dose was injected into the air cell of chicken embryos and set in incubator.

value: Cerebral cortex

value: day 21-22 embryo

source_name: Total RNA pooled from equal parts of all control and treated samples


title: Chicken embryonic cerebral cortex: High dose replicate 1

description: Biological replicate 1 of 5. HD


title: HepG2 treated with IND Array 1

data_processing: After analysis of scanned images, spots judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Spots with dust artifacts or spatial defects were manually flagged and excluded. In an attempt to filter out unreliable data, spots with signal-to-noise ratios were also excluded. Data were normalized by global, lowless, print-tip, and scaled normalization methods. A volcano plot of genes that behaved similarly across IND treatments was created using GeneSpring GX 7.3.1 software. We utilized an algorithm based on Pearson's correlation to separate genes with similar patterns

source_name: HepG2 treated IND labeled with Cy5

value: IND

value: HepG2 (hepatocellular carcinoma)


title: Chicken embryonic cerebral cortex: Low dose replicate 4

description: Biological replicate 4 of 4. LD

source_name: Chicken embryonic cerebral cortex dosed with 890 ng/g PFHxS


title: Chicken embryonic cerebral cortex: High dose replicate 3

description: Biological replicate 3 of 5. HD


title: Primary sample of T cell Acute Lymphoblastic Leukemia

source_name: Peripheral Blood of primary T cell ALL


title: HepG2 treated with IND Array 2

value: DMSO


title: Cortical_Kidney_male_BR4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

hyb_protocol: Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C).

scan_protocol: Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 3 µm resolution.

data_processing: Data were quantile normalized and log2 transformed using R (2.13.0) and the Bioconductor package limma (3.8.2).

organism: Rattus norvegicus

source_name: cortical kidney tissue, male

label_protocol: For each array, 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Animals were housed at the animal facility of the Medical Faculty of the University of Göttingen under conventional housing conditions (22°C, 55% humidity, and 12 h day/night cycle) and given free access to water and rat chow. Acclimatization period was at least 14 days before use.

extract_protocol: The kidneys of four male and four female rats were extracted directly post mortem, washed in cold PBS and cooled on ice. After removal of the kidneys capsules, cortical slices were prepared and stored overnight in RNAlater® (Applied Biosystems, Germany) at 4°C. Total RNA was isolated from kidney cortical slices using the RNeasy® Mini Kit (Qiagen, Germany) according to the manufacturer´s recommendations.

value: RCCHanTMWIST

value: cortical kidney

value: male

value: adult


title: Chicken embryonic cerebral cortex: High dose replicate 2

description: Biological replicate 2 of 5. HD


title: Nogays Caucasus Male nogay44

source_name: blood


title: Chicken embryonic cerebral cortex: Low dose replicate 3

description: Biological replicate 3 of 4. LD


title: HepG2 treated with IND Array 3


title: Chicken embryonic cerebral cortex: Low dose replicate 2

description: Biological replicate 2 of 4. LD


title: Cortical_Kidney_male_BR3


title: 7-week-old chicken leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep1

source_name: normal chicken leg muscle

value: normal recessive White Rock

value: leg muscle

value: 7 weeks

source_name: dwarf chicken leg muscle

value: dwarf recessive White Rock


title: Cortical_Kidney_male_BR2


title: Primary sample of B cell Acute Lymphoblastic Leukemia

source_name: Peripheral Blood of primary B cell ALL

value: B cell ALL


title: Chicken embryonic cerebral cortex: DMSO control replicate 5

description: Biological replicate 5 of 5. Control

source_name: Chicken embryonic cerebral cortex dosed with DMSO


title: Cortical_Kidney_male_BR1


title: Chicken embryonic cerebral cortex: DMSO control replicate 4

description: Biological replicate 4 of 5. Control


title: Chicken embryonic cerebral cortex: DMSO control replicate 2

description: Biological replicate 2 of 5. Control


title: T cell Acute Lymphoblastic Leukemia S605

description: ALL sample

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: The same T cell ALL as LALT obtained from the spleen of mouse treated with 5mg/Kg of LBH589

label_protocol: Standard Illumina Protocol

growth_protocol: Samples S421, S739, S1 and S226 have been obtained from spleen of immunodeficient mice.

extract_protocol: genomic DNA was extracted using QIAmp DNA Mini Kit following the manufacturer´s instructions (Qiagen, Hilden, Germany).

treatment_protocol: treatment was initiated 24 hours after injection of leukemic cells and included 3 cycles of 5 consecutive days of LBH589 with 2 days of rest between cycles.

value: Female

value: Peripheral Blood


title: Chicken embryonic cerebral cortex: DMSO control replicate 1

description: Biological replicate 1 of 5. Control


title: B cell Acute Lymphoblastic Leukemia S162

description: ALL sample

source_name: The same B cell ALL as LALB obtained from the spleen of mouse treated with 5mg/Kg of LBH589

value: Male


title: B cell Acute Lymphoblastic Leukemia S158

description: ALL sample


title: Cortical_Kidney_female_BR2

source_name: cortical kidney tissue, female

value: female


title: B cell Acute Lymphoblastic Leukemia 421

source_name: The same B cell ALL as LALB obtained from the spleen of mouse


title: Cortical_Kidney_female_BR3


title: Cortical_Kidney_female_BR1


title: T cell Acute Lymphoblastic Leukemia S602

description: ALL sample

value: T cell ALL


title: Cortical_Kidney_female_BR4


title: B cell Acute Lymphoblastic Leukemia 739


title: B cell Acute Lymphoblastic Leukemia S160

description: ALL sample


title: Chicken embryonic cerebral cortex: DMSO control replicate 3

description: Biological replicate 3 of 5. Control

value: Cerebral cortex

value: day 21-22 embryo


title: Chicken embryonic cerebral cortex: Low dose replicate 1

description: Biological replicate 1 of 4. LD


title: T cell Acute Lymphoblastic Leukemia S226

description: ALL sample


title: T cell Acute Lymphoblastic Leukemia S604

description: ALL sample


title: Primary sample of T cell Acute Lymphoblastic Leukemia LALT

description: ALL sample


title: ALL derived MOLT-4 cell line after 6 hours of treatment with LH589 T3

source_name: ALL derived MOLT-4 cell line after 6 hours of treatment with LH589 growth in vitro


title: 14-day-old embryo leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep3

source_name: normal embryo leg muscle

value: 14-day-old embryo

source_name: dwarf embryo leg muscle


title: Knockdown of BmSCM gene

city: Fukuoka

first: zhiqing

last: li

address: Higashi-ku, Hakozaki 6-10-1

department: Department of Bioresource Sciences

country: Japan

institute: Kyushu University

hyb_protocol: Cy5-dCTP-labeled (test samples) and Cy3-dCTP-labeled (reference samples) double-stranded cDNA were dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from images using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing:
Lowess-normalized, background-subtracted data obtained from log2 of processed Red signal/processed Green signal. The software from CapitalBio Crop was used. Cluster 3.0 and Mev software (version 4.2.01) were also used in further data processing.
Probes with signal intensity lower than 400 after subtracting the background were considered as unexpressed genes.

organism: Bombyx mori

source_name: Knockdown of BmSCM gene in silkworm BmN4-SID1 cells

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: BmN4-SID1 cells was cultured at 27 ºC in IPL-41 medium (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco).

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: An RNA interference (RNAi) experiment was performed by adding dsRNA specific for the BmSCM gene into the cultured medium. BmN4-SID1 cells were harvested at 7 days post-incubation.

tag: treatment

value: knockdown of the BmSCM gene

source_name: Knockdown of EGFP gene in silkworm BmN4-SID1 cells

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference sample), respectively.

treatment_protocol: An RNA interference (RNAi) experiment was performed by adding dsRNA specific for the EGFP gene into the cultured medium. BmN4-SID1 cells were harvested at 7 days post-incubation.

value: knockdown of the EGFP gene


title: Knockdown of BmESC gene

source_name: Knockdown of BmESC gene in silkworm BmN4-SID1 cells

treatment_protocol: An RNA interference (RNAi) experiment was performed by adding dsRNA specific for the BmESC gene into the cultured medium. BmN4-SID1 cells were harvested at 7 days post-incubation.

value: knockdown of the BmESC gene


title: T cell Acute Lymphoblastic Leukemia 226

hyb_protocol: According to manufacturer's protocol.

scan_protocol: According to manufacturer's protocol.

data_processing: The CEL files were analyzed using the aroma.affymetrix package of R/Bioconductor (CRLMM-algorithm to produce genotype calls and SNPRMA to produce the summarized signal).

source_name: The same T cell ALL as LALT obtained from the spleen of mouse

label_protocol: According to manufacturer's protocol.


title: Primary sample of B cell Acute Lymphoblastic Leukemia LALB

description: ALL sample


title: B cell Acute Lymphoblastic Leukemia S421

description: ALL sample


title: Chicken embryonic cerebral cortex: High dose replicate 5

description: Biological replicate 5 of 5. HD

source_name: Chicken embryonic cerebral cortex dosed with 38,000 ng/g PFHxS

source_name: Total RNA pooled from equal parts of all control and treated samples


title: Knockdown of BmPHO gene

source_name: Knockdown of BmPHO gene in silkworm BmN4-SID1 cells

treatment_protocol: An RNA interference (RNAi) experiment was performed by adding dsRNA specific for the BmPHO gene into the cultured medium. BmN4-SID1 cells were harvested at 7 days post-incubation.

value: knockdown of the BmPHO gene


title: T cell Acute Lymphoblastic Leukemia 1


title: P. pacificus germline ablated animals versus un-ablated wild type animals. Biological Replicate 3 of 3, Dye-flip.

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

country: USA

institute: New England Biolabs

description:
Test sample: Germline ablated P. pacificus young adults, fed on E. coli OP50
Refernce sample: Un-ablated P. apcificus young adults, fed on E. coli OP50

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent P. pacificus oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Pristionchus pacificus

source_name: P. pacificus young adults, germline intact (un-ablated)

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: P. pacificus J2 stage were picked into 2.8 ul PBS on a agar pad containing 1mM NaN3. Ablations were done within 1 hour of hatching at 20°C. After ablation nematodes were stored at 20°C and successful ablation was verified 48 hours later. Nematodes unablated were grown in parallel and acted as controls. For microarrays, 20 P. pacificus (either Z2 or Z3 ablated or unablated) were picked onto 5 separate NGM plates either spread with E. coli OP50 or the pathogens S. marcescens and incubated at 25°C for 8 hours. About 100 nematodes for each condition were then picked into 500 ul of Trizol and stored at -80°C until RNA extaction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

value: young adults

tag: bacteria

value: E. coli OP50

source_name: P. pacificus young adults, germline ablated


title: B cell Acute Lymphoblastic Leukemia S739

description: ALL sample


title: B cell Acute Lymphoblastic Leukemia 739


source_name: Peripheral Blood of primary T cell ALL


title: Knockdown of BmSCE gene

source_name: Knockdown of BmSCE gene in silkworm BmN4-SID1 cells

treatment_protocol: An RNA interference (RNAi) experiment was performed by adding dsRNA specific for the BmSCE gene into the cultured medium. BmN4-SID1 cells were harvested at 7 days post-incubation.

value: knockdown of the BmSCE gene


title: Immune response of germline ablated P. pacificus exposed to S. marcescens. Biological Replicate 1 of 4.

description: Test sample: Germline-ablated P. pacificus young adults, exposed to pathogen S. marcescens for 8 hours. Reference sample: Germline-ablated P. pacificus young adults, exposed to pathogen E. coli OP50 for 8 hours.

source_name: P. pacificus young adults, germline ablated, exposed to S. marcescens for 8 hours

growth_protocol: P. pacificus J2 stage were picked into 2.8 ul PBS on a agar pad containing 1mM NaN3. Ablations were done within 1 hour of hatching at 20C. After ablation nematodes were stored at 20C and successful ablation was verified 48 hours later. Nematodes unablated were grown in parallel and acted as controls. For microarrays, 20 P. pacificus (either Z2 or Z3 ablated or unablated) were picked onto 5 separate NGM plates either spread with E. coli OP50 or the pathogens S. marcescens and incubated at 25C for 8 hours. About 100 nematodes for each condition were then picked into 500 ul of Trizol and stored at -80C until RNA extaction.

tag: germline

value: ablated

value: S. marcescens

source_name: P. pacificus young adults, germline ablated, exposed to E. coli OP50 for 8 hours


title: Immune response of germline ablated P. pacificus exposed to S. marcescens. Biological Replicate 4 of 4. Dye-swap.


title: Immune response of germline ablated P. pacificus exposed to S. marcescens. Biological Replicate 2 of 4.


title: P. pacificus germline ablated animals versus un-ablated wild type animals. Biological Replicate 2 of 3, Dye-flip.


title: Immune response of germline ablated P. pacificus exposed to S. marcescens. Biological Replicate 3 of 4. Dye-swap.


title: B cell Acute Lymphoblastic Leukemia 421

source_name: The same B cell ALL as LALB obtained from the spleen of mouse

value: B cell ALL


title: L149R Mac-MCSF

status: Public on Apr 17 2012

city: Chicago

first: Chiang-Ching

last: Huang

state: IL

address: 680 N. Lake Shore Dr., Suite 1400

institute: Northwestern University

description:
SAMPLE 70
replicate 1

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was log transformed and then quantile normalized based on the output of Illumina BeadStudio software. Batch effect was adjusted using ComBat algorithm. The supplementary data includes both raw and normalized data, which can be loaded using Bioconductor lumi package.

source_name: macrophage

label_protocol: standard as recommended by illumina

extract_protocol: Mononuclear cells were isolated from peripheral blood and subsequently in vitro differentiated into macrophages.  RNA was extracted and cDNA and biotinylated cRNA were created with the Illumina TotalPrep RNA Amplification Kit for each sample.

value: blood

value: macrophage

tag: lupus status

value: case

tag: atherosclerosis status

value: yes


title: L165c Mono

description:
SAMPLE 71
replicate 1

source_name: monocyte

tag: cell type

value: monocyte

value: control


title: P. pacificus germline ablated animals versus un-ablated wild type animals. Biological Replicate 1 of 3.

growth_protocol: P. pacificus J2 stage were picked into 2.8 ul PBS on a agar pad containing 1mM NaN3. Ablations were done within 1 hour of hatching at 20¡C. After ablation nematodes were stored at 20¡C and successful ablation was verified 48 hours later. Nematodes unablated were grown in parallel and acted as controls. For microarrays, 20 P. pacificus (either Z2 or Z3 ablated or unablated) were picked onto 5 separate NGM plates either spread with E. coli OP50 or the pathogens S. marcescens and incubated at 25¡C for 8 hours. About 100 nematodes for each condition were then picked into 500 ul of Trizol and stored at -80¡C until RNA extaction.

tag: strain


title: L165c Mac-MCSF

description:
SAMPLE 72
replicate 1


source_name: Peripheral Blood of primary B cell ALL


title: L199 Mono

description:
SAMPLE 59
replicate 1


title: L114c Mono

description:
SAMPLE 55
replicate 1


title: L64c Mac-MCSF

description:
SAMPLE 54
replicate 1

value: no


title: L35c mono (2)

description:
SAMPLE 49
replicate 2


title: L49 Mac-MCSF

description:
SAMPLE 51
replicate 1


title: L164c Mac-MCSF

description:
SAMPLE 58
replicate 1


title: L72 Mono

description:
SAMPLE 65
replicate 1


title: L72 Mac-MCSF

description:
SAMPLE 66
replicate 1


title: L149R Mono

description:
SAMPLE 69
replicate 1


title: L153 Mono

description:
SAMPLE 47
replicate 1


title: L64c mono

description:
SAMPLE 53
replicate 1


title: L75c Mono

description:
SAMPLE 67
replicate 1


title: L114c Mac-MCSF

description:
SAMPLE 56
replicate 1


title: L54c mono

description:
SAMPLE 62
replicate 1


title: L49 mono

description:
SAMPLE 52
replicate 1


title: L54c Mac-MCSF

description:
SAMPLE 63
replicate 1


title: L8 mono

description:
SAMPLE 61
replicate 1


title: L35c Mac-MCSF (2)

description:
SAMPLE 50
replicate 2


title: L164c Mono

description:
SAMPLE 57
replicate 1


title: L106c Mono

description:
SAMPLE 43
replicate 1


title: L106c Mac-MCSF

description:
SAMPLE 44
replicate 1


title: L81c Mac-MCSF

description:
SAMPLE 42
replicate 1


title: L130 Mono

description:
SAMPLE 45
replicate 1


title: L130 Mac-MCSF

description:
SAMPLE 46
replicate 1


title: L199 Mac-MCSF

description:
SAMPLE 60
replicate 1


title: T cell Acute Lymphoblastic Leukemia S1

description: ALL sample

value: Female

value: Peripheral Blood

value: T cell ALL


title: L81c Mono

description:
SAMPLE 41
replicate 1


title: L153 Mac-MCSF

description:
SAMPLE 48
replicate 1


title: L60 mono

description:
SAMPLE 29
replicate 1


title: L60 Mac-MCSF

description:
SAMPLE 30
replicate 1


title: L172 Mac-MCSF

description:
SAMPLE 36
replicate 1


title: L8 Mac-MCSF

description:
SAMPLE 37
replicate 1


title: L76c Mac-MCSF

description:
SAMPLE 32
replicate 1


title: L40 Mac-MCSF

description:
SAMPLE 40
replicate 1


title: L128 Mono

description:
SAMPLE 33
replicate 1


title: L40 mono

description:
SAMPLE 39
replicate 1


title: L76c Mono

description:
SAMPLE 31
replicate 1


title: L52 Mac-MCSF

description:
SAMPLE 28
replicate 1


title: L70 Mac

description:
SAMPLE 20
replicate 1


title: L172 Mono

description:
SAMPLE 35
replicate 1


title: L128 Mac-MCSF

description:
SAMPLE 34
replicate 1


title: L112 Mac-MCSF

description:
SAMPLE 24
replicate 1


title: L70 mono

description:
SAMPLE 19
replicate 1


title: L28 Mac-MCSF

description:
SAMPLE 16
replicate 1


title: L56c Mac-MCSF

description:
SAMPLE 22
replicate 1


title: L38c Mac-MCSF

description:
SAMPLE 18
replicate 1


title: L35c Mac-MCSF (1)

description:
SAMPLE 38
replicate 1


title: L112 Mono

description:
SAMPLE 23
replicate 1


title: L51c mono

description:
SAMPLE 25
replicate 1


title: L56c mono

description:
SAMPLE 21
replicate 1


title: L52 mono

description:
SAMPLE 27
replicate 1


title: L38c mono

description:
SAMPLE 17
replicate 1


title: L51c Mac-MCSF

description:
SAMPLE 26
replicate 1


title: L75c Mac-MCSF

description:
SAMPLE 68
replicate 1


title: L9 mono

description:
SAMPLE 13
replicate 1


title: L28 mono

description:
SAMPLE 15
replicate 1


title: L9 Mac-MCSF

description:
SAMPLE 14
replicate 1


title: L124 Mono

description:
SAMPLE 11
replicate 1


title: L46c Mac-MCSF

description:
SAMPLE 7
replicate 1


title: L95R Mono

description:
SAMPLE 9
replicate 1


title: L45 Mac-MCSF

description:
SAMPLE 5
replicate 1


title: L95R Mac-MCSF

description:
SAMPLE 10
replicate 1


title: L35c mono (1)

description:
SAMPLE 3
replicate 1


title: L30c mono

description:
SAMPLE 1
replicate 1


title: mo.h3.sp3.asp

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: human cell line A549 plus monocyte-derived dendritic cells after co-cultivation with A. fumigatus germinated conidia

hyb_protocol: Hybridization for 16 hr at 42C using a Agilent hybridization oven, labeled targets from 500 ng total RNA were used for hybridization

scan_protocol: Arrays were scanned using the ScanArray 4000 (PerkinElmer)

data_processing: The data were analyzed with Bioconductor packages (under R) 1st median value of 4 replicates was calculated, 2nd normalization using quantile-quantile

label_protocol: Labeling according to the LabelStar Array Kit (Qiagen) manual

extract_protocol: Purification from human cell lines using RNeasy Mini Kit and QiaShredder spin columns (Qiagen) as per the manufacturer’s instructions, followed by the amplification of RNA using the MessageAmp II aRNA Amplification Kit (Ambion)

tag: protocol

tag: time


title: mo.h3.sp4

description: human cell line A549 plus monocyte-derived dendritic cells


title: mo.h6.sp3

source_name: human cell line A549 plus monocyte-derived dendritic cells


title: mo.h6.sp3.asp

value: after co-cultivation with A. fumigatus germinated conidia


title: mo.h6.sp4.asp


title: mo.h6.sp4


title: mo.h6.sp1.asp


title: mo.h3.sp4.asp


title: mo.h3.sp3


title: mo.h6.sp1


title: mo.h3.sp1.asp


title: L30c Mac-MCSF

description:
SAMPLE 2
replicate 1


title: L69 Mac-MCSF

description:
SAMPLE 8
replicate 1


title: mo.h0.sp4


title: mo.h3.sp1


title: mo.h0.sp3


title: L46c mono

description:
SAMPLE 6
replicate 1


title: L45 mono

description:
SAMPLE 4
replicate 1


title: mo.h0.sp1


title: h6.sp3.asp

description: human cell line A549 plus myeloid dendritic cells after co-cultivation with A. fumigatus germinated conidia


title: h6.sp2.asp

source_name: human cell line A549 plus myeloid dendritic cells


title: h6.sp1.asp


title: h6.sp2

description: human cell line A549 plus myeloid dendritic cells


title: h3.sp2.asp


title: h3sp3..asp


title: h6.sp1


title: HPAEC2.M0h

description: human endothelial cell

source_name: human cell line HPAEC


title: HPAEC2.M3h

description: human endothelial cell


title: h3.sp1.asp


title: HPAEC2.M6h

description: human endothelial cell


title: h3.sp1


title: HPAEC3.M6h

description: human endothelial cell


title: HPAEC3.M3h

description: human endothelial cell


title: HPAEC3.aC6h

description: human endothelial cell line after co-cultivation with Aspergillus fumigatus conidia


title: h3.sp2


title: h3.sp3


title: HPAEC2.aC3h

value: after co-cultivation with Aspergillus fumigatus conidia


title: HPAEC2.aC6h


title: HPAEC2.aC0h


title: h6.sp3


title: HPAEC1.M6h

description: human endothelial cell


title: HPAEC1.M3h

description: human endothelial cell


title: HPAEC3.aC3h


title: HPAEC3.aC0h


title: HPAEC1.M0h

description: human endothelial cell


title: HPAEC1.aC6h


title: HPAEC1.aC3h


title: A549.3.gtM3h

description: human epithelial cell line after co-cultivation with Aspergillus fumigatus germinated conidia

source_name: human cell line A549


title: A549.3.gtM0h

value: after co-cultivation with Aspergillus fumigatus germinated conidia


title: A549.2.gtM6h


title: A549.3.gtM6h


title: A549.2.gtM3h


title: A549.2.gtM0h


title: A549.1.gtM6h


title: A549.1.gtM3h


title: Neural stem cells from the mouse subventricular zone at postnatal day 7 - Biological replicate 3

city: Milano

first: Rossella

last: Galli

state: MI

address: via Olgettina 58

department: Regenerative Medicine, Stem Cells and Gene Therapy

institute: San Raffaele Scientific Institute

description:
SVZ_7_H_WT_171008
Gene expression data from NSC lines.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: The data were analyzed with R and Bioconductor. The data were normalized using the RMA algorithm.

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

growth_protocol: NSCs and CSCs were cultured in the presence of EGF and FGF2 in agreement with the NeuroSphere Assay.

extract_protocol: Total RNA was extracted by means of the RNeasy kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Neurospheres were collected by centrifugation three-five days after plating.

value: postnatal day 7

value: subventricular zone

value: neural stem cells (NSCs)


title: HPAEC1.aC0h


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_MB_77_SX_TISSUE_040309

description:
MDB_MB_77_SX_TISSUE_040309
Gene expression data from medulloblastoma tissue.

tag: genotype/variation

value: Ptch het p53 wt

value: medulloblastoma


title: A549.1.gtM0h


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_MB_68_SX_TISSUE_220509

description:
MDB_MB_68_SX_TISSUE_220509
Gene expression data from medulloblastoma tissue.


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_MB_68_SX_180209

description:
MDB_MB_68_SX_180209
Gene expression data from CSC lines.

value: cancer stem cells (CSCs)


title: L69 Mono

description:
SAMPLE 64
replicate 1

value: blood

value: case


title: Neural stem cells from the mouse subventricular zone at postnatal day 7 - Biological replicate 1

description:
SVZ_7_F_WT_060608
Gene expression data from NSC lines.


title: A3.M6h

description: human epithelial cell line


title: Neural stem cells from the mouse subventricular zone at postnatal day 7 - Biological replicate 2

description:
SVZ_7_G_WT_060608
Gene expression data from NSC lines.


title: Cancer stem cells from a Ptch het p53 het mouse-derived medulloblastoma - Technical replicate 3, MDB_B_II_300807

description:
MDB_B_II_300807
Gene expression data from CSC lines.

value: Ptch het p53 het


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_MB_83_SX_180209

description:
MDB_MB_83_SX_180209
Gene expression data from CSC lines.


title: L124 Mac-MCSF

description:
SAMPLE 12
replicate 1

value: macrophage

value: yes


title: A3.aC3h

description: human epithelial cell line after co-cultivation with Aspergillus fumigatus conidia


title: A3.aC6h


title: A3.M3h

description: human epithelial cell line

value: control


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_9_SX_IV_TISSUE_300708

description:
MDB_9_SX_IV_TISSUE_300708
Gene expression data from medulloblastoma tissue.


title: A3.aC0h


title: Cancer stem cells from a Ptch het p53 het mouse-derived medulloblastoma - Technical replicate 1, MDB_B_I_010807

description:
MDB_B_I_010807
Gene expression data from CSC lines.


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_MB_49_SX_IV_180209

description:
MDB_MB_49_SX_IV_180209
Gene expression data from CSC lines.


title: Cancer stem cells from a Ptch het p53 het mouse-derived medulloblastoma - Technical replicate 2, MDB_B_I_300807

description:
MDB_B_I_300807
Gene expression data from CSC lines.


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_MB_49_SX_TISSUE_040309

description:
MDB_MB_49_SX_TISSUE_040309
Gene expression data from medulloblastoma tissue.


title: A2.M6h

description: human epithelial cell line


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_92_ST_TISSUE_300708

description:
MDB_92_ST_TISSUE_300708
Gene expression data from medulloblastoma tissue.


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_MB_77_SX_180209

description:
MDB_MB_77_SX_180209
Gene expression data from CSC lines.


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_91_ST_300708

description:
MDB_91_ST_300708
Gene expression data from CSC lines.


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_92_ST_300708

description:
MDB_92_ST_300708
Gene expression data from CSC lines.


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_MB_83_SX_TISSUE_220509

description:
MDB_MB_83_SX_TISSUE_220509
Gene expression data from medulloblastoma tissue.


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_9_SX_IV_300708

description:
MDB_9_SX_IV_300708
Gene expression data from CSC lines.


title: A2.M3h

description: human epithelial cell line


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_74_DX_TISSUE_300708

description:
MDB_74_DX_TISSUE_300708
Gene expression data from medulloblastoma tissue.


title: A2.aC6h


title: Matched Ptch het p53 wt mouse-derived medulloblastoma tissue, MDB_91_ST_TISSUE_300708

description:
MDB_91_ST_TISSUE_300708
Gene expression data from medulloblastoma tissue.


title: A2.M0h

description: human epithelial cell line


title: A2.aC3h


title: A2.aC0h


title: A1.M6h

description: human epithelial cell line


title: A1.M3h

description: human epithelial cell line


title: A1.M0h

description: human epithelial cell line


title: Cancer stem cells from a Ptch het p53 wt mouse-derived medulloblastoma, MDB_74_DX_300708

description:
MDB_74_DX_300708
Gene expression data from CSC lines.


title: A1.aC3h


title: A1.aC0h


title: A1.aC6h


title: Cancer stem cells from a Ptch het p53 het mouse-derived medulloblastoma - Technical replicate 2, MDB_27_II_241007

description:
MDB_27_II_241007
Gene expression data from CSC lines.


title: Cancer stem cells from a Ptch het p53 het mouse-derived medulloblastoma - Technical replicate 1, MDB_27_II_111007

description:
MDB_27_II_111007
Gene expression data from CSC lines.


title: Neural stem cells from the mouse IV ventricle region at postnatal day 7 - Biological replicate 2

description:
IV_VENT_7_G_WT_290508
Gene expression data from NSC lines.

value: IV ventricle region


title: Cancer stem cells from a Ptch het p53 het mouse-derived medulloblastoma - Technical replicate 3, MDB_27_III_131207

description:
MDB_27_III_131207
Gene expression data from CSC lines.


title: Neural stem cells from the mouse cerebellar white matter at postnatal day 7 - Biological replicate 3

description:
CB_7_H_WT_171008
Gene expression data from NSC lines.

value: cerebellar white matter


title: Neural stem cells from the mouse IV ventricle region at postnatal day 7 - Biological replicate 1

description:
IV_VENT_7_F_WT_060608
Gene expression data from NSC lines.


title: Neural stem cells from the mouse IV ventricle region at postnatal day 7 - Biological replicate 3

description:
IV_VENT_7_H_WT_171008
Gene expression data from NSC lines.


title: Neural stem cells from the mouse cerebellar white matter at postnatal day 7 - Biological replicate 2

description:
CB_7_G_WT_060608
Gene expression data from NSC lines.


title: CEN.PK122, 2h oscillation period, 14.53 h

city: Duarte

first: shwe

middle: lynn

last: chin

address: 1500 E Duarte Rd.

department: Biology

institute: Beckman Research Institute

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner M10.

data_processing: MicroArray Suite 6.1 and GCOS were used to quantify and analyze results. The submitted files show raw and unnormalized data adjusted for hybridization efficiency using biotinylated Escherichia coli standards.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: CEN.PK122, 2h oscillation period

label_protocol: Purified total RNA samples were processed as recommended in the Affymetrix GeneChip Expression Analysis Technical Manual. RNA samples were adjusted to a final concentration of 1 mg/ml. Typically, 25-250 ng were loaded onto an RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) and analyzed in an Agilent Bioanalyzer 2100. Double-stranded cDNA was synthesized from 5 mg of total RNA using GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix) and oligo(dT) primers containing a T7 RNA polymerase promoter. Double-stranded cDNA was used as a template to generate biotinylated cRNA using the GeneChip Expression 3'-Amplification Reagents for IVT Labeling. The biotin-labeled cRNA was fragmented to 35-200 bases following the Affymetrix protocol. Five micrograms of fragmented cRNA was hybridized to Yeast 2.0 Affymetrix arrays at 45°C for 16 h in an Affymetrix GeneChip Hybridization Oven 640. The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450, followed by scanning on an Affymetrix GeneArray scanner.

growth_protocol: Samples were from the yeast strain CEN.PK122 grown in continuous cultures under aerobic conditions.

extract_protocol: The samples from the 2 hr oscillation data set were taken every 4 mins through a little over one cycle (31 samples total).

treatment_protocol: The cells spontaneously oscillate in redox state (respiratory and reductive) monitored by the percent of dissolved oxygen in the media.

tag: phase angle

value: 362.01 degrees


title: CEN.PK122, 2h oscillation period, 14.00 h

value: 267.03 degrees


title: CEN.PK122, 2h oscillation period, 14.07 h

value: 278.90 degrees


title: CEN.PK122, 2h oscillation period, 14.13 h

value: 290.77 degrees


title: CEN.PK122, 2h oscillation period, 13.93 h

value: 255.17 degrees


title: CEN.PK122, 2h oscillation period, 14.33 h

value: 326.37 degrees


title: CEN.PK122, 2h oscillation period, 14.47 h

value: 350.11 degrees


title: CEN.PK122, 2h oscillation period, 13.87 h

value: 243.30 degrees


title: CEN.PK122, 2h oscillation period, 14.40 h

value: 338.24 degrees


title: CEN.PK122, 2h oscillation period, 13.67 h

value: 207.69 degrees


title: CEN.PK122, 2h oscillation period, 13.60 h

value: 195.82 degrees


title: Neural stem cells from the mouse cerebellar white matter at postnatal day 7 - Biological replicate 1

description:
CB_7_F_WT_060608
Gene expression data from NSC lines.

value: postnatal day 7

tag: tissue

value: neural stem cells (NSCs)


title: CEN.PK122, 2h oscillation period, 13.80 h

value: 231.43 degrees


title: CEN.PK122, 2h oscillation period, 13.73 h

value: 219.56 degrees


title: CEN.PK122, 2h oscillation period, 14.20 h

value: 302.64 degrees


title: CEN.PK122, 2h oscillation period, 14.27 h

value: 314.51 degrees


title: FHCRCAML2429

city: Berlin

first: Sebastian

middle: K

last: Ochsenreither

state: Berlin

address: Hindenburgdamm 30

department: Hematology/Oncology

institute: Charite Berlin

description:
GSM239487
7AML_34N_D_68M_5_BM_N_2429
Cryopreserved MNCs

hyb_protocol: Hybridization was performed according to Affymetrix protocol.

scan_protocol: Arrays were scanned according to Affymetrix protocol.

data_processing: .DAT files were generated using GCOS 1.2.1 software (Affymetrix). CEL files were generated using MAS 5.0 softare (Affymetrix) with target signals for probe sets scaled to 500. Model-based expression levels were computed from .CEL files using dChip software after normalization by invariant set method.

source_name: leukemia

label_protocol: Target was labeled with Enzo BioArray High Yield RNA Trascript Labeling Kit (Enzo Life Technologies, Farmingdale, NY) according to manufacturer's protocol.

extract_protocol: Total RNA extracted using TRIzol reagent (Invitrogen, Carlsbad, CA)according to manufacturer's protocol.

tag: diagnosis

value: AML

value: Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period, 13.33 h

value: 148.35 degrees


title: CEN.PK122, 2h oscillation period, 13.13 h

value: 112.75 degrees


title: CEN.PK122, 2h oscillation period, 13.20 h

value: 124.62 degrees


title: CEN.PK122, 2h oscillation period, 13.53 h

value: 183.96 degrees


title: CEN.PK122, 2h oscillation period, 13.07 h

value: 100.88 degrees


title: GSM18981 reanalysis

description:
GSM18981
GSM18981

source_name: testis

value: healthy control

value: testis


title: FHCRCAML1818

description:
GSM239460
7AML_34N_M_83F_9_PB_AI_1818
Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period, 13.27 h

value: 136.48 degrees


title: FHCRCAML0482

description:
GSM239346
7AML_34N_D_69M_5_PB_N_0482
Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period, 13.47 h

value: 172.09 degrees


title: CEN.PK122, 2h oscillation period, 13.40 h

value: 160.22 degrees


title: CEN.PK122, 2h oscillation period, 12.93 h

value: 77.14 degrees


title: GSM18982 reanalysis

description:
GSM18982
GSM18982


title: FHCRCAML169052

description:
8AML_1690-52
Cryopreserved MNCs


title: FHCRCAML2557

description:
GSM239488
7AML_34N_D_62M_5_PB_I_2557
Cryopreserved MNCs


title: FHCRCAML16906

description:
GSM239497
7AML_34N_D_41M_5_BM_I_1690-6
Cryopreserved MNCs


title: FHCRCAML169011

description:
GSM239520
7AML_34N_T_36F_5_BM_I_1690-11
Cryopreserved MNCs


title: FHCRCAML16907

description:
GSM239498
7AML_34N_D_58M_5_PB_N_1690-7
Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period, 12.80 h

value: 53.41 degrees


title: CEN.PK122, 2h oscillation period, 12.87 h

value: 65.28 degrees


title: FHCRCAML7209

description:
GSM239495
7AML_34N_D_54F_1_PB_I_7209
Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period, 13.00 h

value: 89.01 degrees


title: FHCRCAML169018

description:
GSM240427
7AML_34N_D_44F_2_BM_I_1690-18
Cryopreserved MNCs


title: FHCRCAML169030

description:
7AML_34N_D_63F_5_BM_U_1690-30
Cryopreserved MNCs


title: FHCRCAML16908

description:
GSM239516
7AML_34N_D_60M_5_PB_N_1690-8
Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period, 12.53 h

value: 5.93 degrees


title: FHCRCAML4500

description:
GSM239493
7AML_34N_D_66M_2_PB_N_4500
Cryopreserved MNCs

value: AML


title: CEN.PK113-7D, 4h oscillation period 17.916667 h

scan_protocol: GeneChips were scanned using an Affymetrix GeneArray scanner according to the manufacturer’s instructions.

source_name: CEN.PK113-7D, 4h oscillation period

label_protocol: GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and oligo(dT) primers containing T7 RNA polymerase promoter was used to synthesize double-stranded cDNA from RNA adjusted to 1 mg/ml for each sample. Then, biotinylated cRNA was synthesized using the GeneChip IVT labeling kit from Affymetrix. After framentation to 35-200 bases according to the Affymetrix protocol, 5 micrograms was hybridized to Affymetrix GeneChip Yeast Genome 2.0 Array (Santa Clara, CA) for 16 h at 45°C. The arrays were washed and stained with streptavidin-phycoerythrin using an Affymetrix Fluidics Station 450.

growth_protocol: CEN.PK113-7D (MATa), grown overnight in 20 ml YPD at 275 rpm and 30C, was inoculated into the fermentor. The fermentor maintained the pH, agitation speed, aeration, and temperature at 4.0, 750 rpm, 150 ml/min, and 30 oC, respectively. Cells were grown in either the B. Braun Biotech Biolab CP (Aylesbury, Buckinghamshire, UK) at 650 ml or the New Brunswick Scientific Bioflo 110 Fermentor/Bioreactor (Edison, NJ) at 850 ml volume. Continuous flow was started after 24-30 h by pumping in fermenter media (19.25 g/l D(+)glucose monohydrate, 5 g/l (NH4)2SO4, 2 g/l KH2PO4, 0.5 g/l MgSO4, 1 g/l yeast extract, 0.2 ml/l antifoam A, 0.1 g/l CaCl2, 0.02 g/l FeSO4, 0.01 g/l ZnSO4, 0.005 g/l CuSO4, 0.001 g/l MnCl2, and 1 ml/l 75% H2SO4) at a dilution rate of 0.086/h. Media with excess cells was pumped out of the fermentor to maintain a constant fermentor volume. The media was maintained at pH 4.0 with 2.5 N NaOH. The dilution rate was adjusted to 0.06-0.086/h to maintain the period.

extract_protocol: RNA was purified from the cells and DNA was digested with DNase 1 using the RiboPureTM Yeast kit (Ambion, Austin, TX) according to the manufacturer’s instructions, except the cells were lysed in a minibead beater (BioSpec Products, Bartlesville, OK) rather than by vortexing. The isolated RNA was analyzed for concentration and purity with the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells with a ~4 h period (49 samples total) were collected every 5 min for one cycle with a small overlap into the next cycle.

value: 606.97 degrees


title: CEN.PK113-7D, 4h oscillation period 18 h

value: 614.63 degrees


title: CEN.PK122, 2h oscillation period, 12.60 h

value: 17.80 degree


title: CEN.PK122, 2h oscillation period, 12.73 h

value: 41.54 degrees


title: FHCRCAML7216

description:
GSM239496
6AML_34P_M_76F_9_PB_N_7216
Cryopreserved MNCs

value: Cryopreserved MNCs


title: FHCRCAML_2762

description:
GSM239490
6AML_34P_M_79M_9_PB_N_2762
Cryopreserved MNCs


title: CEN.PK122, 2h oscillation period,12.67 h

value: 29.67 degrees


title: CEN.PK113-7D, 4h oscillation period 17.5 h

value: 568.70 degrees


title: CEN.PK113-7D, 4h oscillation period 17.833333 h

value: 599.32 degrees


title: CEN.PK113-7D, 4h oscillation period 17.666667 h

value: 584.01 degrees


title: CEN.PK113-7D, 4h oscillation period 17.166667 h

value: 538.09 degrees


title: CEN.PK113-7D, 4h oscillation period 17.25 h

value: 545.74 degrees


title: FHCRCAML1038

description:
GSM239363
7AML_34N_D_38F_5_PB_A_1038
Cryopreserved MNCs


title: CEN.PK113-7D, 4h oscillation period 17.583333 h

value: 576.36 degrees


title: CEN.PK113-7D, 4h oscillation period 17.416667 h

value: 561.05 degrees


title: FHCRCAML169014

description:
GSM239580
6AML_34P_D_67M_4_PB_I_1690-14
Cryopreserved MNCs


title: CEN.PK113-7D, 4h oscillation period 17.333333 h

value: 553.39 degrees


title: CEN.PK113-7D, 4h oscillation period 17.75 h

value: 591.67 degrees


title: FHCRCAML16901970

description:
GSM239485
6AML_34P_M_45M_9_PB_I_1970
Cryopreserved MNCs


title: FHCRCAML3653

description:
GSM239492
7AML_34N_D_52F_1_BM_N_3653
Cryopreserved MNCs


title: FHCRCAML169016F

description:
6AML_34P_E_51M_9_PB_N_1690-16F
Cryopreserved MNCs


title: FHCRCAML1355

description:
GSM239371
6AML_34P_D_68F_1_BM_I_1355
Cryopreserved MNCs


title: FHCRCAML169020

description:
GSM240429
6AML_34P_D_64M_1_PB_I_1690-20
Cryopreserved MNCs


title: FHCRCAML169016

description:
GSM240405
6AML_34P_E_51M_9_PB_N_1690-16
Cryopreserved MNCs


title: FHCRCAML72

description:
GSM239345
6AML_34P_M_53M_9_PB_N_0072
Cryopreserved MNCs


title: FHCRCAML169017

description:
GSM240406
6AML_34P_M_51F_9_PB_I_1690-17
Cryopreserved MNCs


title: FHCRCAML4653

description:
GSM239494
6AML_34P_D_41M_2_PB_I_4653
Cryopreserved MNCs


title: FHCRCAML2619

description:
GSM239489
7AML_34N_D_53M_4_BM_N_2619
Cryopreserved MNCs


title: FHCRCAML2852

description:
GSM239491
6AML_34P_M_51F_9_PB_N_2852
Cryopreserved MNCs


title: FHCRCAML723

description:
GSM239348
6AML_34P_D_61F_0_PB_N_0723
Cryopreserved MNCs


title: PB_DON097

description:
GSM240498
4PB_DON097
Cryopreserved MNCs

source_name: Normal PB

value: healthy control


title: FHCRCAML169048

description:
6AML_34P_D_19 M_U_PB_U_1690-48
Cryopreserved MNCs

value: AML


title: CEN.PK113-7D, 4h oscillation period 17 h

value: 522.78 degrees


title: CEN.PK113-7D, 4h oscillation period 16.833333 h

value: 507.47 degrees


title: CEN.PK113-7D, 4h oscillation period 16.916667 h

value: 515.12 degrees


title: CEN.PK113-7D, 4h oscillation period 17.083333 h

value: 530.43 degrees


title: PB_DON034

description:
GSM240431
4PB_34_M_DON034
Cryopreserved MNCs

value: Cryopreserved MNCs


title: CEN.PK113-7D, 4h oscillation period 16.583333 h

value: 484.51 degrees


title: CEN.PK113-7D, 4h oscillation period 16.666667 h

value: 492.16 degrees


title: CEN.PK113-7D, 4h oscillation period 16.75 h

value: 499.82 degrees


title: PB_DON058

description:
GSM240495
4PB_33_F_DON058
Cryopreserved MNCs


title: PB_DON040

description:
GSM240432
4PB_27_M_DON040
Cryopreserved MNCs


title: PB_DON102

description:
GSM240499
4PB_34_M_DON102
Cryopreserved MNCs


title: Homozygous pool-15 generations-100uM zinc-replicate2-Up

city: Berkeley

first: Chris

last: Vulpe

state: Ca

address: 119 Morgan Hall

department: Nutritional Sciences and Toxicology

institute: UC Berkeley

description: Up tag data processing

hyb_protocol: Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix)

scan_protocol: After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing:
Robust mean Log2 intensity for replicate features calculated with S-plus/R function.
Up and down tags are processed separately and output reported as separate data sets.
Note: Platform GPL8633 contains the array design which will be helpful for users who do not want to use our preprocessing strategy.

label_protocol: The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers

growth_protocol: Growth in zinc defined media (LZM), 30 °C, 200 rpm. Measurements of optical density at 595 nm (OD595) to monitor growth

extract_protocol: Cells were collected and genomic DNA was extracted using the YDER kit (Pierce Biotechnology)

treatment_protocol: Zinc concentration incorporated into growth media, 2 concentrations with 6 biological replicates each, for 5 and 15 generations (g) of growth

tag: pool

value: Homozygous deletion mutants

tag: growth stage

value: 15 generations

tag: agent

value: zinc

tag: concentration


title: Homozygous pool-15 generations-100uM zinc-replicate6-Up

description: Up tag data processing


title: Homozygous pool-15 generations-100uM zinc-replicate3-Up

description: Up tag data processing


title: CEN.PK113-7D, 4h oscillation period 16.333333 h

value: 461.55 degrees


title: PB_DON086

description:
GSM240496
4PB_27_F_DON086
Cryopreserved MNCs


title: PB_DON046

description:
GSM240433
4PB_27_M_DON046
Cryopreserved MNCs


title: PB_DON088

description:
GSM240497
4PB_29_M_DON088
Cryopreserved MNCs


title: CEN.PK113-7D, 4h oscillation period 16.416667 h

value: 469.20 degrees


title: Homozygous pool-15 generations-100uM zinc-replicate4-Up

description: Up tag data processing


title: CEN.PK113-7D, 4h oscillation period 16.5 h

value: 476.85 degrees


title: BM_CD34_TBO3488

description:
GSM239339
0BM_CD34_23_M_TBO3488
Cryopreserved MNCs

source_name: Normal BMCD34


title: BM_CD34_R000121

description:
GSM239338
0BM_CD34_51_M_R000121
Cryopreserved MNCs


title: PB_DON056

description:
GSM240494
4PB_28_F_DON056
Cryopreserved MNCs


title: Homozygous pool-15 generations-100uM zinc-replicate5-Up

description: Up tag data processing


title: BM_CD34_R000030

description:
GSM239170
0BM_CD34_18_M_R000030
Cryopreserved MNCs


title: BM_CD34_TBO2249

description:
GSM239340
0BM_CD34_23_F_TBO2249
Cryopreserved MNCs


title: Homozygous pool-15 generations-100uM zinc-replicate1-Up

description: Up tag data processing


title: BM_CD34_TBO3077

description:
GSM239344
0BM_CD34_32_M_TBO3077
Cryopreserved MNCs


title: BM_CD34_TBO2854

description:
GSM239343
0BM_CD34_18_M_TBO2854
Cryopreserved MNCs


title: BM_CD34_TBO2841

description:
GSM239342
0BM_CD34_36_M_TBO2841
Cryopreserved MNCs


title: BM_CD34_TBO2523

description:
GSM239341
0BM_CD34_16_M_TBO2523
Cryopreserved MNCs


title: CEN.PK113-7D, 4h oscillation period 16.25 h

value: 453.89 degrees


title: wt.ks.sp1

data_processing: The data were analyzed with Bioconductor packages (under R) 1st median value of 4 replicates (flaged spots excluded) was calculated, 2nd normalization using a set of house keeping genes

source_name: human whole blood from healthy blood donors

extract_protocol: Purification from human myeloid dendritic cells using RNeasy Mini Kit and QiaShredder spin columns (Qiagen) as per the manufacturer’s instructions, followed by the amplification of RNA using the MessageAmp II aRNA Amplification Kit (Ambion)

value: human myeloid dendritic cells

value: after co-cultivation with Aspergillus fumigatus germinated conidia


title: wt.ks.sp2


title: wt.ks.sp3


title: wt.con.sp1

value: after co-cultivation with Aspergillus fumigatus conidia


title: rodA.ks.sp3

value: after co-cultivation with Aspergillus fumigatus (rod A knockout) germinated conidia


title: rodA.ks.sp1


title: rodA.ks.sp2


title: CEN.PK113-7D, 4h oscillation period 15.75 h

value: 407.97 degrees


title: HFF actinomycin D 240 min rep 3

city: Newark

first: Ju Youn

last: Lee

state: NJ

address: 185 South Orange Ave. MSB-E501

department: Biochemistry

institute: UMDNJ-New Jersey Medical School

description: This is sample was collected at 240 min after actinomycin D treatment

hyb_protocol: Labeled probes were hybridized to GeneChip  Human Gene 1.0 ST Arrays according to GeneChip® WT Terminal Labeling and Hybridization User Manual provided with the WT Expression Kit   (Affymetrix)

scan_protocol: Labeled hybridized arrays were washed and stained using the Fluidics Station 450 prior to scanning on the GeneChip  Scanner 3000 7G according to GeneChip® Expression Wash, Stain and Scan  Manual (Affymetrix)

data_processing: All the probe sets were applied median normalization by Affymetrix Power Tools (APT) with ‘no adjustment’ option and were normalized to the 5th percentile value of all probe sets on the same array.

source_name: HFFs with actinomycin D, time 240 min

label_protocol: Biotinylated DNA probes were prepared according to Whole Transcript Sense Target Labeling Manual (Affymetrix)

growth_protocol: Human foreskin fibroblasts (HFFs) and genetically identical in Duced pluripotent stem (iPS) cells were purchased from System Biosciences.  The HFFs were cultured in DMEM medium supplemented with 10% FBS, 2mM L-glutamine, 100µM nonessential amino acids, 50U/ml penicillin and 50µg/ml streptomycin.  The iPS cells were cultured in mTeSR®1 medium (Stemcell Technologies Inc) supplemented with 50U/ml penicillin and 50µg/ml streptomycin on plates coated with 0.3mg/ml Matrigel™ Basement Membrane Matrix Growth Factor Reduced (BD Biosciences).  Cells were incubated at 37°C with 5% CO2.

extract_protocol: Cells were collected in Trizol® (Invitrogen) at 0, 15, 30, 160, 120 and 240 minutes after transcription inhibition.  Total RNA was isolated according to the manufacturer’s protocol. RNA quality and concentration were analyzed using a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) and Bioanalyzer (Agilent).

treatment_protocol: To inhibit transcription, cells were treated with 5µg/ml actinomycin D (Invitrogen) for 20 minutes.

value: HFFs (Human foreskin fibroblasts)

tag: treatment

value: actinomycin D

value: 240 min


title: wt.con.sp3


title: CEN.PK113-7D, 4h oscillation period 16.083333 h

value: 438.58 degrees


title: Homozygous pool-15 generations-1uM zinc-replicate5-Up

description: Up tag data processing


title: CEN.PK113-7D, 4h oscillation period 16.166667 h

value: 446.24 degrees


title: CEN.PK113-7D, 4h oscillation period 16 h

value: 430.93 degrees


title: CEN.PK113-7D, 4h oscillation period 15.916667 h

value: 423.27 degrees


title: HFF actinomycin D 120 min rep 2

description: This is sample was collected at 120 min after actinomycin D treatment

source_name: HFFs with actinomycin D, time 120 min

value: 120 min


title: HFF actinomycin D 240 min rep 2


title: Homozygous pool-15 generations-1uM zinc-replicate6-Up

description: Up tag data processing

value: Homozygous deletion mutants

value: 15 generations

value: zinc


title: rodA.con.sp3

value: after co-cultivation with Aspergillus fumigatus (rod A knockout) conidia


title: wt.con.sp2

value: human myeloid dendritic cells


title: Homozygous pool-15 generations-1uM zinc-replicate4-Up

description: Up tag data processing


title: HFF actinomycin D 60 min rep 3

description: This is sample was collected at 60 min after actinomycin D treatment

source_name: HFFs with actinomycin D, time 60 min

value: 60 min


title: HFF actinomycin D 120 min rep 3


title: CEN.PK113-7D, 4h oscillation period 15.666667 h

value: 400.31 degrees


title: CEN.PK113-7D, 4h oscillation period 15.833333 h

value: 415.62 degrees


title: HFF actinomycin D 60 min rep 2


title: Homozygous pool-15 generations-1uM zinc-replicate3-Up

description: Up tag data processing


title: rodA.con.sp1


title: rodA.con.sp2


title: CEN.PK113-7D, 4h oscillation period 15.583333 h

value: 392.66 degrees


title: HFF actinomycin D 240 min rep 1

value: HFFs (Human foreskin fibroblasts)


title: mnt-1.ks.sp3

value: after co-cultivation with Aspergillus fumigatus (mnt-1 knockout) germinated conidia


title: CEN.PK113-7D, 4h oscillation period 15.416667 h

value: 377.35 degrees


title: CEN.PK113-7D, 4h oscillation period 15.5 h

value: 385.00 degrees


title: HFF actinomycin D 60 min rep 1

value: actinomycin D


title: Homozygous pool-15 generations-1uM zinc-replicate2-Up

description: Up tag data processing


title: CEN.PK113-7D, 4h oscillation period 15.333333 h

value: 369.70 degrees


title: Homozygous pool-15 generations-1uM zinc-replicate1-Up

description: Up tag data processing


title: HFF actinomycin D 120 min rep 1


title: CEN.PK113-7D, 4h oscillation period 15.25 h

value: 362.04 degrees


title: HFF actinomycin D 30 min rep 2

description: This is sample was collected at 30 min after actinomycin D treatment

source_name: HFFs with actinomycin D, time 30 min

value: 30 min


title: HFF actinomycin D 30 min rep 3


title: mnt-1.ks.sp2


title: mnt-1.ks.sp1


title: mitA.ks.sp3

value: after co-cultivation with Aspergillus fumigatus (mit A knockout) germinated conidia


title: mitA.ks.sp1


title: mitA.ks.sp2


title: lps.sp3

value: after co-cultivation with LPS


title: CEN.PK113-7D, 4h oscillation period 15.166667 h

value: 354.23 degrees


title: CEN.PK113-7D, 4h oscillation period 14.916667 h

value: 330.63 degrees


title: HFF actinomycin D 0 min rep 3

description: This is sample was collected at 0 min after actinomycin D treatment

source_name: HFFs with actinomycin D, time 0 min

value: 0 min


title: CEN.PK113-7D, 4h oscillation period 14.833333 h

value: 322.77 degrees


title: lps.sp2

value: human myeloid dendritic cells


title: HFF actinomycin D 30 min rep 1


title: HFF actinomycin D 15 min rep 2

description: This is sample was collected at 15 min after actinomycin D treatment

source_name: HFFs with actinomycin D, time 15 min

value: 15 min


title: HFF actinomycin D 15 min rep 1


title: lps.sp1


title: HFF actinomycin D 15 min rep 3


title: CEN.PK113-7D, 4h oscillation period 15 h

value: 338.50 degrees


title: HFF actinomycin D 0 min rep 1

value: HFFs (Human foreskin fibroblasts)


title: HFF actinomycin D 0 min rep 2


title: c.sp2


title: CEN.PK113-7D, 4h oscillation period 15.083333 h

value: 346.37 degrees


title: c.sp3


title: CEN.PK113-7D, 4h oscillation period 14.583333 h

value: 299.17 degrees


title: CEN.PK113-7D, 4h oscillation period 14.5 h

value: 291.30 degrees


title: Homozygous pool-5 generations-100uM zinc-replicate5-Up

description: Up tag data processing

value: Homozygous deletion mutants

value: 5 generations

value: zinc


title: CEN.PK113-7D, 4h oscillation period 14.416667 h

value: 283.44 degrees


title: Homozygous pool-5 generations-100uM zinc-replicate6-Up

description: Up tag data processing


title: iPS actinomycin D 240 min rep 2

source_name: iPSCs with actinomycin D, time 240 min

value: iPS cells (induced pluripotent stem cells)

value: actinomycin D

value: 240 min


title: iPS actinomycin D 240 min rep 3


title: Homozygous pool-5 generations-100uM zinc-replicate3-Up

description: Up tag data processing


title: CEN.PK113-7D, 4h oscillation period 14.666667 h

value: 307.04 degrees


title: Homozygous pool-5 generations-100uM zinc-replicate4-Up

description: Up tag data processing


title: CEN.PK113-7D, 4h oscillation period 14.75 h

value: 314.90 degrees


title: c.sp1


title: iPS actinomycin D 120 min rep 3

source_name: iPSCs with actinomycin D, time 120 min

value: 120 min


title: CEN.PK113-7D, 4h oscillation period 14.166667 h

value: 259.84 degrees


title: CEN.PK113-7D, 4h oscillation period 14.25 h

value: 267.71 degrees


title: CEN.PK113-7D, 4h oscillation period 14.083333 h

value: 251.97 degrees


title: iPS actinomycin D 240 min rep 1


title: iPS actinomycin D 120 min rep 2


title: Homozygous pool-5 generations-100uM zinc-replicate2-Up

description: Up tag data processing


title: iPS actinomycin D 120 min rep 1


title: iPS actinomycin D 60 min rep 3

source_name: iPSCs with actinomycin D, time 60 min

value: 60 min


title: CEN.PK113-7D, 4h oscillation period 14 h

value: 244.11 degrees


title: CEN.PK113-7D, 4h oscillation period 14.333333 h

value: 275.57 degrees


title: CEN.PK113-7D, 2h oscillation period 12.06666634 h

source_name: CEN.PK113-7D, 2h oscillation period

treatment_protocol: For cells with a ~2 h dissolved oxygen period, 32 samples (the pellet from 0.5 ml with the supernatant removed) were removed every 4 min, immediately frozen in liquid nitrogen, and store at -80 C.

value: 743.75 degrees


title: iPS actinomycin D 60 min rep 1


title: Homozygous pool-5 generations-100uM zinc-replicate1-Up

description: Up tag data processing

value: Homozygous deletion mutants


title: ETCs from barley seeds at 12 DAF, biological rep2

city: Gatersleben

first: Johannes

last: Thiel

address: Corrensstrasse 3

institute: IPK-Gatersleben

description:
ETC_12DAF_2
Gene expression data from laser-microdissected tissues at different stages of seed development.

hyb_protocol: After fragmentation, 1.65 µg labelled aRNA was hybridized to Agilent 4x 44K barley gene expression microarrays (Agilent-021623) according to Agilent standard protocols at ATLAS biolabs (www.atlas-biolabs.de).

scan_protocol: Barley microarrays were scanned using the Agilent G2505B DNA microarray scanner with one color scan settings for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol: GE1_105_Dec08 and Grid: 021623_D_F_20100204) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were further processed and analyzed using BioConductor/R software (http://www.bioconductor.org/). Quantile normalization was carried out on the complete data set.

organism: Hordeum vulgare

source_name: endosperm transfer cells, 12 DAF

label_protocol: T7 RNA polymerase-based mRNA amplification was performed using the MessageAmpTM II aRNA kit (Ambion, UK). Two amplification rounds were performed and samples were labelled with amino allyl-UTP during the second round. Cy3 dyes were coupled to amino allyl-modified aRNA. Yield of labelled aRNA and dye incorporation was quantified using NanoDrop ND-1000 UV-Vis spectrophotometer. RNA quality was assessed using Agilent 2100 Bioanalyzer.

growth_protocol: Plants were grown in greenhouses at 18°C under 16/8-h photoperiod and a relative air humidity of 60%.

extract_protocol: Total RNA was extracted from microdissected cells using the Absolutely RNA Nanoprep Kit (Stratagene) according to the manufacturer's instructions, including on-column DNase digestion.

treatment_protocol: None.

tag: cultivar

value: Barke

value: barley seed endosperm transfer cells (ETCs)

tag: developmental stage

value: 12 days after flowering/pollination (DAF)


title: ETCs from barley seeds at 10 DAF, biological rep2

description:
ETC_10DAF_2
Gene expression data from laser-microdissected tissues at different stages of seed development.

source_name: endosperm transfer cells, 10 DAF

value: 10 days after flowering/pollination (DAF)


title: ETCs from barley seeds at 12 DAF, biological rep1

description:
ETC_12DAF_1
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: iPS actinomycin D 60 min rep 2

value: iPS cells (induced pluripotent stem cells)

value: actinomycin D


title: CEN.PK113-7D, 2h oscillation period 11.99999969 h

value: 731.09 degrees


title: ETCs from barley seeds at 10 DAF, biological rep3

description:
ETC_10DAF_3
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: Homozygous pool-5 generations-1uM zinc-replicate6-Up

description: Up tag data processing

value: 5 generations

value: zinc


title: ETCs from barley seeds at 12 DAF, biological rep3

description:
ETC_12DAF_3
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: ETCs from barley seeds at 10 DAF, biological rep1

description:
ETC_10DAF_1
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: Homozygous pool-5 generations-1uM zinc-replicate5-Up

description: Up tag data processing


title: CEN.PK113-7D, 2h oscillation period 11.73333 h

value: 681.04 degrees


title: ETCs from barley seeds at 7 DAF, biological rep3

description:
ETC_7DAF_3
Gene expression data from laser-microdissected tissues at different stages of seed development.

source_name: endosperm transfer cells, 7 DAF

value: 7 days after flowering/pollination (DAF)


title: CEN.PK113-7D, 2h oscillation period 11.66667 h

value: 668.57 degrees


title: CEN.PK113-7D, 2h oscillation period 11.93333304 h

value: 718.44 degrees


title: CEN.PK113-7D, 2h oscillation period 11.79999974 h

value: 693.51 degrees


title: CEN.PK113-7D, 2h oscillation period 11.86666639 h

value: 705.97 degrees


title: ETCs from barley seeds at 7 DAF, biological rep1

description:
ETC_7DAF_1
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: Homozygous pool-5 generations-1uM zinc-replicate4-Up

description: Up tag data processing


title: ETCs from barley seeds at 7 DAF, biological rep2

description:
ETC_7DAF_2
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: iPS actinomycin D 15 min rep 2

source_name: iPSCs with actinomycin D, time 15 min

value: 15 min


title: iPS actinomycin D 30 min rep 2

source_name: iPSCs with actinomycin D, time 30 min

value: 30 min


title: iPS actinomycin D 15 min rep 1


title: iPS actinomycin D 15 min rep 3


title: iPS actinomycin D 0 min rep 3

source_name: iPSCs with actinomycin D, time 0 min

value: 0 min


title: iPS actinomycin D 30 min rep 3


title: CEN.PK113-7D, 2h oscillation period 11.6 h

value: 656.10 degrees


title: Homozygous pool-5 generations-1uM zinc-replicate3-Up

description: Up tag data processing

value: Homozygous deletion mutants


title: ETCs from barley seeds at 5 DAF, biological rep1

description:
ETC_5DAF_1
Gene expression data from laser-microdissected tissues at different stages of seed development.

source_name: endosperm transfer cells, 5 DAF

value: Barke

value: barley seed endosperm transfer cells (ETCs)

value: 5 days after flowering/pollination (DAF)


title: ETCs from barley seeds at 5 DAF, biological rep3

description:
ETC_5DAF_3
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: iPS actinomycin D 30 min rep 1

value: iPS cells (induced pluripotent stem cells)

value: actinomycin D


title: Homozygous pool-5 generations-1uM zinc-replicate2-Up

description: Up tag data processing

value: 5 generations

value: zinc


title: CEN.PK113-7D, 2h oscillation period 11.33333 h

value: 606.23 degrees


title: iPS actinomycin D 0 min rep 2


title: Roquin+/+ mouse, biological replicate 3

city: Canberra

first: Pheh Ping

last: Chang

state: ACT

address: The Australian National University

department: Pathogens and Immunity

country: Australia

institute: The John Curtin School of Medical Research

description: Gene expression data from CD44loCD8+ T cells

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: data analysis was performed with Partek Genomics Suite software

source_name: Roquin+/+ CD44loCD8+ T cells

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

growth_protocol: mice were bred in specific pathogen free conditions at the Australian National University Bioscience Facility and mice of 10 -week old were used.

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

treatment_protocol: Spleen and lymph node cell suspensions were prepared by sieving and gentle pipetting. For 20 minutes fluorescent antibody surface staining, cells were maintained in the dark at 4oC throughout. Stained cells were then subjected to sorting with FACSAria Cell Sorter (BD Biosciences).

value: sorted CD44loCD8+ T cells

tag: genotype

value: Roquin+/+

tag: age

value: 10-week old


title: ETCs from barley seeds at 5 DAF, biological rep2

description:
ETC_5DAF_2
Gene expression data from laser-microdissected tissues at different stages of seed development.


title: CEN.PK113-7D, 2h oscillation period 11.46667 h

value: 631.17 degrees


title: Roquinsan/san mouse, biological replicate 3

source_name: Roquinsan/san  CD44loCD8+ T cells

value: Roquinsan/san(sanroque)


title: CEN.PK113-7D, 2h oscillation period 11.53333 h

value: 643.64 degrees


title: CEN.PK113-7D, 2h oscillation period 11.4 h

value: 618.70 degrees


title: Roquinsan/san mouse, biological replicate 2

source_name: Roquinsan/san CD44loCD8+ T cells


title: CEN.PK113-7D, 2h oscillation period 11.2 h

value: 581.30 degrees


title: Roquin+/+ mouse, biological replicate 2


title: CEN.PK113-7D, 2h oscillation period 11.06667 h

value: 556.36 degrees


title: CEN.PK113-7D, 2h oscillation period 11.26667 h

value: 593.77 degrees


title: Roquinsan/san mouse, biological replicate 1


title: CEN.PK113-7D, 2h oscillation period 11.13333 h

value: 568.83 degrees


title: iPS actinomycin D 0 min rep 1

tag: cell type

value: 0 min


title: Roquin+/+ mouse, biological replicate 1


title: Toh2-Maternal parent

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

country: Singapore

institute: Temasek Life Sciences Laboratory

description: Family Toh2 maternal / Paternal gDNA

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Arrays were scanned with Axon GenePix 4000B scanner as per standard NimbleGen protocol (version 5.1) .

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.6 aCGH data extraction.

organism: Danio rerio

source_name: Female parent gDNA

label_protocol: Labeled according to NimbleGen Dual-Color Labelling Kit protocol.

extract_protocol: Tail fin genomic DNA extracted using QIAGEN Dneasy Blood and Tissue kit according to manufacturer's instructions.

tag: Sex

value: Female

tag: strain

value: Toh

source_name: Paternal gDNA

tag: reference

value: Paternal gDNA


title: Toh2-Male-Offspring1

description: Family Toh2 male offspring 1 / Paternal gDNA

source_name: Male offspring 1 gDNA

value: Male


title: Toh2-Male-Offspring2

description: Family Toh2 male offspring 2 / Paternal gDNA

source_name: Male offspring 2 gDNA


title: Toh2-Paternal parent

description: Family Toh2 paternal / Paternal gDNA

source_name: Male parent gDNA


title: Toh2-Female-Offspring2

description: Family Toh2 female offspring 2 / Paternal gDNA

source_name: Female offspring 2 gDNA


title: Homozygous pool-5 generations-1uM zinc-replicate1-Up

description: Up tag data processing

value: Homozygous deletion mutants

value: 5 generations

value: zinc


title: Toh2-Female-Offspring1

description: Family Toh2 female offspring 1 / Paternal gDNA

source_name: Female offspring 1 gDNA


title: Toh1-Paternal parent

description: Family Toh1 paternal / Paternal gDNA


title: Ccl3_ratio4 numerator

city: Stanford

first: Manuel

last: Lopez

address: Clark Center W200 318 Campus Dr.

institute: Stanford University

description: P58 Ccl3-/-;Npc1-/-

hyb_protocol: Full Services: (cDNA synthesis to data acquisition; includes Bioanalyzer QC) provided by Stanford PAN facility, for protocol used see Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

data_processing:
The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings as normalization method.
Affymetrix Expression Console Software V.1.1, Affymetrix Default Gene Robust Multichip Analysis (RMA), and  Affymetrix MoGene-1_0-st-v1 Probeset Annotations.

source_name: whole cellebrum_Ccl3-/-;Npc1-/-

growth_protocol: Care and handling of mice was in accordance with institutional guidelines. Sibling mice were used when possible.

extract_protocol: Total cerebellar RNA was extracted with Trizol reagent (Invitrogen). Genomic DNA was removed with Turbo DNA-free kit (Ambion) and the RNA further purified with Acid Phenol:ChCl3 (Ambion) and subsequent alcohol precipitation steps.

treatment_protocol: C02 euthanization and dissection/isolation of cerebellum from brain.

tag: background

tag: ~age in days

tag: genotype/variation

value: Niemann-Pick C (NPC) disease animals with Ccl3 gene deletion

value: whole cerebellum


title: CEN.PK113-7D, 2h oscillation period 11 h

source_name: CEN.PK113-7D, 2h oscillation period

tag: phase angle

value: 543.90 degrees


title: CEN.PK113-7D, 2h oscillation period 10.8 h

value: 506.49 degrees


title: Toh1-Male-Offspring1

description: Family Toh1 male offspring 1 / Paternal gDNA


title: CEN.PK113-7D, 2h oscillation period 10.73333 h

value: 494.03 degrees


title: Toh1-Male-Offspring2

description: Family Toh1 male offspring 2 / Paternal gDNA


title: Ccl3_ratio3 numerator

description: P56 Ccl3-/-;Npc1-/-

scan_protocol: Full Services: (cDNA synthesis to data acquisition; includes Bioanalyzer QC) provided by Stanford PAN facility, for protocol used see Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

tag: tissue


title: Ccl3_ratio4 denominator

description: P58 Npc1-/-

source_name: whole cellebrum_Npc1-/-

label_protocol: Full Services: (cDNA synthesis to data acquisition; includes Bioanalyzer QC) provided by Stanford PAN facility, for protocol used see Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

value: Niemann-Pick C (NPC) disease animals


title: Toh1-Maternal parent

description: Family Toh1 maternal / Paternal gDNA


title: CEN.PK113-7D, 2h oscillation period 10.86667 h

value: 518.96 degrees


title: Toh1-Female-Offspring2

description: Family Toh1 female offspring 2 / Paternal gDNA


title: Ccl3_ratio3 denominator

description: P56 Npc1-/-


title: CEN.PK113-7D, 2h oscillation period 10.93333 h

value: 531.43 degrees


title: Ccl3_ratio1/2 denominator

description: P54 Npc1-/-


title: Ccl3_ratio2 numerator

description: P53 Ccl3-/-;Npc1-/-


title: CEN.PK113-7D, 2h oscillation period 10.66667 h

value: 481.56 degrees


title: CEN.PK113-7D, 2h oscillation period 10.6 h

value: 469.09 degrees


title: CEN.PK113-7D, 2h oscillation period 10.53333 h

value: 456.62 degrees


title: AB2-Paternal parent

description: Family AB2 paternal / Paternal gDNA

value: AB


title: Toh1-Female-Offspring1

description: Family Toh1 female offspring 1 / Paternal gDNA

value: Female

value: Toh

value: Paternal gDNA


title: AB2-Male-Offspring2

description: Family AB2 male offspring 2 / Paternal gDNA

value: Male


title: CEN.PK113-7D, 2h oscillation period 10.46667 h

value: 444.16 degrees


title: PN_ratio3 numerator

description: P100+ P;N; Npc1-/-

source_name: whole cellebrum_P;N;Npc1-/-

value: FVB

value: Niemann-Pick C (NPC) disease animals with tTa inducible NPC1-YFP and Purkinje neuron-specific tTA driver

value: Pcp2-tTA+/-;tetO-Npc1+/-; Npc1-/-


title: Ccl3_ratio1 numerator

description: P52 Ccl3-/-;Npc1-/-

value: Niemann-Pick C (NPC) disease animals with Ccl3 gene deletion

value: whole cerebellum


title: CEN.PK113-7D, 2h oscillation period 10.4 h

value: 431.69 degrees


title: PN_ratio2 numerator

description: P71 P;N;Npc1-/-


title: AB2-Male-Offspring1

description: Family AB2 male offspring 1 / Paternal gDNA


title: PN_ratio2 denominator

description: P71 N;Npc1-/-

source_name: whole cellebrum_N;Npc1-/-

value: Niemann-Pick C (NPC) disease animals with tTa inducible NPC1-YFP

value: tetO-Npc1+/-; Npc1-/-


title: CEN.PK113-7D, 2h oscillation period 10.33333 h

value: 419.22 degrees


title: AB2-Maternal parent

description: Family AB2 maternal / Paternal gDNA


title: AB2-Female-Offspring2

description: Family AB2 female offspring 2 / Paternal gDNA


title: AB2-Female-Offspring1

description: Family AB2 female offspring 1 / Paternal gDNA


title: CEN.PK113-7D, 2h oscillation period 10.26667 h

value: 406.75 degrees


title: CEN.PK113-7D, 2h oscillation period 10.2 h

value: 394.29 degrees


title: PN_ratio1 numerator

description: P50 P;N;Npc1-/-


title: CEN.PK113-7D, 2h oscillation period 10.13333 h

value: 381.82 degrees


title: CEN.PK113-7D, 2h oscillation period 10.06667 h

value: 369.35 degrees


title: NPC vs WT_ratio denominator rep1

description: P50 Npc1+/-

source_name: whole cellebrum_Npc1+/-

value: wild type


title: NPC vs WT_ratio numerator rep2 & PN_ratio1/3 denominator rep2

description: P50 N;Npc1-/-


title: NPC vs WT_ratio numerator rep1 & PN_ratio1/3 denominator rep1

description: P50 Npc1-/-

value: Niemann-Pick C (NPC) disease animals


title: NPC vs WT_ratio denominator rep3

description: P50 P;N;Npc1+/-

source_name: whole cellebrum_P;N;Npc1+/-

value: wild type animals with tTa inducible NPC1-YFP and Purkinje neuron-specific tTA driver

value: Pcp2-tTA+/-;tetO-Npc1+/-; Npc1+/-


title: CEN.PK113-7D, 2h oscillation period 10 h

value: 356.87 degrees


title: NPC vs WT_ratio denominator rep2

description: P50 N;Npc1+/-

source_name: whole cellebrum_N;Npc1+/-

value: FVB

value: wild type animals with tTa inducible NPC1-YFP

value: tetO-Npc1+/-; Npc1+/-


title: AB1-Paternal parent

description: Family AB1 paternal / Paternal gDNA

value: Male

value: AB

value: Paternal gDNA


title: AB1-Male-Offspring2

description: Family AB1 male offspring 2 / Paternal gDNA


title: AB1-Male-Offspring1

description: Family AB1 male offspring 1 / Paternal gDNA


title: AB1-Maternal parent

description: Family AB1 maternal / Paternal gDNA

value: Female


title: AB1-Female-Offspring2

description: Family AB1 female offspring 2 / Paternal gDNA


title: AB1-Female-Offspring1

description: Family AB1 female offspring 1 / Paternal gDNA


title: H2AZ ChIP in WT ES cells (Eed+/+ clone 2.21) using anti H2AZ antibody (Abcam ab4174)

status: Public on Apr 16 2012

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Chip-chip in WT mouse ES cells ( Eed+/+ clone 2.21) for H2AZ

hyb_protocol: Samples were hybridized according to standard protocol (http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: Arrays were scanned on MS 200 Microarray scanner as per manufacturer's instructions. Separate TIFF images were created for Cy3 and Cy5 at 2μM resolution.

data_processing: The mean signal intensity of the 4 replicate probes, on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used, within replicates group, to control inter array variability. The log enrichment for each group was calculated by dividing the mean of log2 input intensities by the mean of log2 ChIP enriched intensities.

source_name: Input DNA from WT ES cells  (Eed+/+ clone 2.21)

label_protocol: 1.0 µg of amplified ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were grown on mitomycin C treated primary embryonic fibroblasts (PEFs) derived from E12.5 mouse embryos, in DMEM (Invitrogen) supplemented with 15% foetal calf serum (FCS, Hyclone), 1,000 units/ml LIF, non-essential amino acids, sodium pyruvate, 2-mercaptoethanol, L-glutamine, and Penicillin/Streptomycin. ESCs were trypsinized and the PEFs allowed to re-attach to the tissue culture plastic for 2x 30 minutes in LIF-containing medium, before preparation of chromatin, and nuclear extracts from ESCs.

extract_protocol: ChIP was performed overnight (o/n) with 3 μg H2A.Z antibody and 90 μg chromatin. For polycomb ChIPs; 10 μg Ring1B or EZH2 antibody was incubated with 450 μg chromatin o/n. ChIP and input chromatin was decrosslinked at 65 ° C for 6 hours, RNase A at 37° C for 1 hour, then with Proteinase K at 55° C for 2 hours. The DNA samples were purified using the Qiagen DNA purification kit. Native ChIP for H3K27me3 was described in (Eskeland R, et al. 2010. Mol Cell 38(3) 452-464). 10ng of purified DNA (ChIP and Input) was amplified using the WGA2 kit from sigma (WGA2-50RXN) accoring to manufacturers instructions.

tag: fraction

value: Input DNA

value: WT

value: embryonic stem cells  (Eed+/+ clone 2.21)

source_name: H2AZ ChIP DNA from WT ES Cells  (Eed+/+ clone 2.21)

tag: antibody vendor

value: Abcam

tag: antibody catalog#

tag: antibody

value: ChIP DNA