title: B7bisVsal-V3Kcoc_High_globus_pallidus

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675

hyb_protocol: After checking the labeling efficiency and the product integrity, 825 ng Cy3- and 825 ng Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven, using an Agilent in situ hybridization kit. The slides were washed and then any traces of water were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Slides were scanned using an Agilent G6525 Microarray Scanner at 5-μm resolution. The photo multiplier tube (PMT) levels of the two channels at 635 nm (for Cy5) and 532 nm (for Cy3) were balanced to limit the number of saturated pixels for generating gray scale 16-bit TIFF image files

data_processing: The data were extracted using Feature Extraction software (Agilent).The pre-processing of the data and its quality assessment were done using the MANGO (MicroArray Normalization tool of GODMAP) tools suit (version 1.0, CNRS BioInfome Team [http://bioinfome.cgm.cnrs-gif.fr/]), an R script that allows integrated analysis of two-color microarrays. The background level was calculated using morphological operators (a short closing followed by a large opening) and subtracted. Raw data were normalized using the print-tip lowess method, i.e. local regression normalization within an artificial print-tip block.

label: Cy5-CTP Agilent

source_name: Globus pallidus from mouse submitted to conditioned place preference

label_protocol: Briefly, 75-ng aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies).

extract_protocol: Kit Picopure (Arcturus)

tag: background

value: Globus pallidus

tag: sex

value: received saline solution at D2 D3 D4 of conditioned place preference protocol

label: Cy3-CTP Agilent

value: received cocaine (15 mg/kg) at D2 D3 D4 of conditioned place preference protocol


title: R5bisEcoc-N2Bsal_Low_globus_pallidus

status: Public on May 10 2015

type: RNA

country: France

molecule: total RNA

organism: Mus musculus

tag: tissue

value: male

tag: treatment


title: 600kbdup_23

city: Lausanne

first: Alexandre

last: Reymond

address: Dorigny

department: CIG

country: Switzerland

institute: UNIL

description: Gene expression data from lymphoblastoid cell lines

hyb_protocol: Affymetrix Affymetrix HT HG-U133+ PM Array Plate arrays were hybridized, washed and stained according to the protocol described in Affymetrix GeneChip 3' IVT Express Kit Manual.

scan_protocol: The arrays were scanned using the Affymetrix GeneTitan Instrument and raw data were extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

data_processing: The Affymetrix GeneTitan Instrument was used for automated array processing. Raw data was generated and extracted from the scanned images for analysis with the Affymetrix GeneChip Command Console (AGCC) Software and Expression Console Software packages.

label: biotin

organism: Homo sapiens

source_name: LCL

label_protocol: For each sample, 100 ng of total RNA was processed according to the Affymetrix GeneChip 3' IVT Express Kit manual (P/N 702646 Revision 6) and hybridized to the Affymetrix Human Genome U133 Plus GeneChips.

extract_protocol: Exponentially growing LCLs were harvested and resuspended in TRIzol reagent (Ambion, Carlsbad, CA, USA), after which the manufacturer’s protocol for RNA isolation was performed. Upon RNA isolation, RNA clean-up was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany), including the DNase treatment step, according to the manufacturer’s protocol.

tag: cell type

value: lymphoblastoid

tag: gender

value: F

tag: age

tag: copy number 16p11.2

tag: genotype

tag: family identifier

tag: kinship

value: proband


title: 600kbdup_25

value: M


title: 600kbdup_26

value: pat grandfather


title: MDA-MB-468LN (HumanMethylation450 array)

status: Public on May 11 2015

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

molecule: genomic DNA

source_name: Lymph node metastasis

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cell were growth in DMEM complemented with FBS 10% and a combination of antibiotics and antimicotics

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: tumor

value: lymph node metastasis

tag: cell line

value: breast


title: N5Hsal-R5Ucoc_High_globus_pallidus


title: 600kbdup_24

value: mother


title: 600kbdup_29


title: B7bisVsal-N1Ococ_Low_globus_pallidus

data_processing: The data were extracted using Feature Extraction software (Agilent).The pre-processing of the data and its quality assessment were done using the MANGO (MicroArray Normalization tool of GODMAP) tools suit (version 1.0, CNRS BioInfome Team [http://bioinfome.cgm.cnrs-gif.fr/]), an R script that allows integrated analysis of two-color microarrays. The background level was calculated using morphological operators (a short closing followed by a large opening) and subtracted. Raw data were normalized using the print-tip lowess method, i.e. local regression normalization within an artificial print-tip block


title: 600kbdup_30


title: 600kbdup_22


title: 600kbdup_27

value: father


title: Stable non-targeting shRNA vs. Stable knockdown of P4HA1 shRNA 1 in DU145

city: Ann Arbor

first: Balabhadrapatruni

middle: Venkata Srinivasa Kalyana

last: Chakravarthi

state: Michigan

address: 2900 Huron Parkway, Suite 100

department: MCTP, Pathology

country: USA

institute: Michigan Center for Translational Pathology

description: DU145_Non-T shRNA Vs P4HA shRNA1

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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

source_name: Stable non-targeting shRNA

label_protocol: 1 µg of total RNA were primed with 2 µl of 100 µM T7-oligo-dT DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 400 U MMLV RTase (Agilent), and labeled with T7 polymerase with 100 µM each of dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-label or Cy3-label.

growth_protocol: Cells were cultured in ATCC recommended media supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer's instructions.

value: prostate cancer cell line

tag: shRNA

value: non-targeting

tag: genotype/variation

value: AR negative, ERG fusion negative

source_name: P4HA1 shRNA 1 stable DU145 cells


title: Stable non-targeting shRNA vs. Stable knockdown of P4HA1 shRNA 2 in DU145

description: DU145_Non-T shRNA Vs P4HA shRNA2

source_name: P4HA1 shRNA 2 stable DU145 cells


title: 600kbdup_20


title: IGR39 (HumanMethylation450 array)

source_name: Primary (achromic) cutaneous tumor

value: primary (achromic) cutaneous tumor

value: melanoma


title: R7Qcoc-N2Bsal_High_globus_pallidus

value: Globus pallidus

value: received saline solution at D2 D3 D4 of conditioned place preference protocol


title: 600kbdup_19


title: R5Hsal-R5Ucoc_Low_globus_pallidus

value: male

value: received cocaine (15 mg/kg) at D2 D3 D4 of conditioned place preference protocol


title: 600kbdup_28

value: lymphoblastoid

value: F


title: MDA-MB-468PT (HumanMethylation450 array)

source_name: Mammary gland; breast: pleural effusion

value: primary tumor of mammary gland


title: IGR37 (HumanMethylation450 array)


title: SW480 (HumanMethylation450 array)

source_name: Primary adenocarcinoma of the colon

value: primary adenocarcinoma of the colon

value: colon


title: 600kbdup_31

value: M

value: proband


title: Sw620 (HumanMethylation450 array)

value: lymph node metastasis


title: human hepatic stellate cell sample 4

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: human hepatic stellate cell sample 4

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.12)  under Linux R.3.0.0

source_name: HSC 4

label_protocol: Standard Affymetrix protocol

extract_protocol: Four donors were used in the current study. ADHLSC were obtained subsequently to primary culture of the liver parenchymal fraction previously obtained after a two-step collagenase perfusion, filtration and low speed centrifugation. HSCs were isolated from the corresponding non-parenchymal fraction using a Nycodenz gradient centrifugation step (Myegaard, Oslo, Norway).

value: human hepatic stellate cell


title: B5Gcoc-B4bisJsal_Low_globus_pallidus


title: 600kbdup_14


title: 600kbdup_21


title: 600kbdup_13


title: 600kbdup_12


title: 600kbdup_17


title: 600kbdup_06


title: 600kbdup_03_replicate1


title: 600kbdup_10

value: mother


title: 600kbdup_04


title: 600kbdup_15

value: father


title: 600kbdup_16


title: 600kbdup_11

value: sibling


title: 600kbdup_18


title: 600kbdup_09


title: 600kbdup_08


title: 600kbdel_50


title: B7Scoc-B4bissal_High_globus_pallidus


title: 600kbdel_48


title: 600kbdup_03_replicate2


title: 600kbdup_02


title: 600kbdup_07


title: 600kbdup_01


title: 600kbdel_49


title: 600kbdel_47


title: 600kbdel_42


title: 600kbdel_40


title: 600kbdel_43


title: 600kbdel_45


title: 600kbdel_39


title: 600kbdel_46


title: 600kbdel_44


title: 600kbdel_38


title: 600kbdel_35


title: 600kbdel_34


title: normal breast epithelium,4

city: Singapore

first: Surya Pavan

last: Yenamandra

address: 30, Biopolis street, #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute

hyb_protocol: Affymetrix standard protocol

scan_protocol: Probe arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: MAS5 using a quantile normalization

source_name: human normal breast tissue RNA

label_protocol: Biotin-modified mRNA labeling were carried out using Affymetrix manufacturer’s protocol

extract_protocol: total RNA

tag: age at diagnosis

tag: diagnosis

value: Within normal limits

tag: tumor grade

tag: mininal stage grouping

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)

tag: er

tag: pgr

tag: dfs-month

tag: dfs-event

tag: distant metastasis


title: 600kbdel_30

tag: cell type

tag: gender

tag: age

tag: copy number 16p11.2

tag: genotype

tag: family identifier


title: 600kbdel_33

tag: kinship


title: 600kbdel_37


title: 600kbdel_41


title: 600kbdel_32


title: 600kbdel_36


title: 600kbdel_27


title: 600kbdel_29


title: breast tumor epithelium,52

source_name: human breast tumor tissue RNA

tag: age at diagnosis

tag: diagnosis

value: Adenocarcinoma of breast, ductal

value: IIIC


title: 600kbdel_24


title: breast tumor epithelium,51

tag: tumor grade

tag: mininal stage grouping

value: IIB


title: 600kbdel_26


title: breast tumor epithelium,50

value: I

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)


title: 600kbdel_31

value: lymphoblastoid


title: breast tumor epithelium,49

tag: er

tag: pgr


title: breast tumor epithelium,48

tag: dfs-month

tag: dfs-event


title: 600kbdel_25

tag: cell type


title: 600kbdel_28

tag: gender


title: 600kbdel_22

tag: age


title: 600kbdel_23

value: F

tag: copy number 16p11.2


title: 600kbdel_18

tag: genotype


title: breast tumor epithelium,45

tag: distant metastasis


title: breast tumor epithelium,47

value: IIIA


title: breast tumor epithelium,42


title: 600kbdel_21

tag: family identifier

tag: kinship


title: 600kbdel_17


title: breast tumor epithelium,46

tag: age at diagnosis

tag: diagnosis

value: IIA


title: breast tumor epithelium,41

tag: tumor grade

tag: mininal stage grouping


title: breast tumor epithelium,43

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)


title: breast tumor epithelium,44

value: NX

tag: er

tag: pgr


title: 600kbdel_20

value: M


title: 600kbdel_16

value: proband


title: breast tumor epithelium,40

tag: dfs-month

tag: dfs-event


title: breast tumor epithelium,53

value: Adenocarcinoma of breast, ductal, lobular features


title: 600kbdel_15

tag: cell type

tag: gender


title: normal breast epithelium,3


title: 600kbdel_14

tag: age

tag: copy number 16p11.2


title: 600kbdel_19

tag: genotype


title: breast tumor epithelium,39

tag: distant metastasis


title: 600kbdel_12

tag: family identifier

tag: kinship


title: 600kbdel_09


title: 600kbdel_11


title: 600kbdel_10


title: 600kbdel_13


title: breast tumor epithelium,54

tag: age at diagnosis

tag: diagnosis

value: Adenocarcinoma of breast, ductal, medullary features


title: breast tumor epithelium,38

tag: tumor grade

tag: mininal stage grouping


title: breast tumor epithelium,37

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)


title: breast tumor epithelium,36

tag: er

tag: pgr


title: 600kbdel_05


title: 600kbdel_08


title: breast tumor epithelium,32

tag: dfs-month

tag: dfs-event


title: breast tumor epithelium,35


title: breast tumor epithelium,34


title: 600kbdel_07

tag: cell type

tag: gender


title: breast tumor epithelium,57

value: Adenocarcinoma of breast, lobular


title: 600kbdel_06

tag: age

tag: copy number 16p11.2


title: breast tumor epithelium,30

tag: distant metastasis


title: breast tumor epithelium,33

value: IV


title: 600kbdel_02

tag: genotype

tag: family identifier


title: 600kbdel_01

tag: kinship


title: 600kbdel_03

value: sibling


title: 600kbdel_04


title: Control_15

value: Control


title: breast tumor epithelium,28

tag: age at diagnosis

tag: diagnosis

value: Adenocarcinoma of breast, ductal


title: breast tumor epithelium,31

tag: tumor grade

tag: mininal stage grouping


title: breast tumor epithelium,29

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)


title: breast tumor epithelium,58

value: Carcinoma of breast, squamous cell

tag: er

tag: pgr


title: normal breast epithelium,2

value: Within normal limits

tag: dfs-month

tag: dfs-event


title: Control_17

tag: cell type

tag: gender

value: mother


title: breast tumor epithelium,27


title: Control_11

value: lymphoblastoid

tag: age

tag: copy number 16p11.2

value: unrelated


title: breast tumor epithelium,25

value: I

tag: distant metastasis


title: Control_16

tag: genotype

tag: family identifier

value: father


title: Control_14

tag: kinship


title: Control_09


title: breast tumor epithelium,26

tag: age at diagnosis

tag: diagnosis

value: IIA


title: Control_06

value: M


title: breast tumor epithelium,19

tag: tumor grade

tag: mininal stage grouping

value: IIIA

value: TX


title: Control_13


title: breast tumor epithelium,22

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)


title: breast tumor epithelium,23

value: IIB

tag: er

tag: pgr


title: Control_07


title: Control_12


title: breast tumor epithelium,24

value: IIIC

tag: dfs-month

tag: dfs-event


title: breast tumor epithelium,18


title: breast tumor epithelium,21


title: Control_05

tag: cell type

tag: gender


title: breast tumor epithelium,20


title: Control_08

value: F

tag: age

tag: copy number 16p11.2


title: Control_10

tag: genotype


title: breast tumor epithelium,16

tag: distant metastasis


title: Control_02

tag: family identifier

tag: kinship


title: breast tumor epithelium,15

tag: age at diagnosis

tag: diagnosis

value: EV


title: breast tumor epithelium,17

tag: tumor grade

tag: mininal stage grouping


title: Control_01

value: Control


title: Control_04


title: Control_03


title: breast tumor epithelium,12

value: Adenocarcinoma of breast, ductal

tag: t (extent of primary tumor)

tag: n (lymph node metastasis)


title: breast tumor epithelium,11

tag: er

tag: pgr


title: breast tumor epithelium,56

value: Adenocarcinoma of breast, ductal, recurrent

tag: dfs-month

tag: dfs-event


title: 600kbdup_05

tag: cell type

tag: gender

value: proband


title: breast tumor epithelium,14


title: breast tumor epithelium,13


title: breast tumor epithelium,8


title: R8coc-V8sal-Low-accumbens

hyb_protocol: After checking the labeling efficiency and the product integrity, 750 ng Cy3- and 750 ng Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven, using an Agilent in situ hybridization kit. The slides were washed and then any traces of water were removed by centrifugation at 800 rpm for 1 min.

source_name: Accumbens nucleus from mouse submitted to conditioned place preference

label_protocol: Briefly, 50-ng aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies).

tag: tissue

value: Accumbens nucleus

tag: Sex

value: male

tag: treatment

value: received cocaine (15 mg/kg) at D2 D3 D4 of conditioned place preference protocol

tag: background

value: received saline solution at D2 D3 D4 of conditioned place preference protocol


title: B4biscoc-N7sal_Low-accumbens


title: breast tumor epithelium,6

tag: distant metastasis


title: breast tumor epithelium,7

tag: age at diagnosis


title: V3bissal-R7coc_Low-accumbens


title: R6sal-B7coc_STN_Agilent_scan

data_processing: The resulting images were processed using the GenePix Pro (v6.0.1.26) image analysis software. This included defining the spots, measuring the intensities, flagging the spots having inadequate quality control parameters and evaluating local background The pre-processing of the data and its quality assessment were done using the MANGO (MicroArray Normalization tool of GODMAP) tools suit (version 1.0, CNRS BioInfome Team [http://bioinfome.cgm.cnrs-gif.fr/]), an R script that allows integrated analysis of two-color microarrays. The background level was calculated using morphological operators (a short closing followed by a large opening) and subtracted. Raw data were normalized using the print-tip lowess method, i.e. local regression normalization within an artificial print-tip block.

source_name: Subthalamic nucleus from mouse submitted to conditioned place preference

label_protocol: Briefly, 70ng-aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies)

value: Subthalamic nucleus


title: V3coc-V1bissal_STN_Axon_scan

scan_protocol: Slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) at 5-μm resolution. The photo multiplier tube (PMT) levels of the two channels at 635 nm (for Cy5) and 532 nm (for Cy3) were balanced to limit the number of saturated pixels (less than 0.005%) for generating gray scale 16-bit TIFF image files.

label_protocol: Briefly, 75ng-aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies)


title: breast tumor epithelium,5

tag: diagnosis


title: N3coc-B5sal_STN_Agilent_scan


title: R6sal-B7coc_STN_Axon_scan


title: breast tumor epithelium,9

tag: tumor grade

value: IIA


title: B7sal-B3coc_Low-accumbens


title: R5coc-R2sal_STN_Agilent_scan


title: R5coc-R2sal_STN_Axon_scan

scan_protocol: Slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) at 5-μm resolution. The photo multiplier tube (PMT) levels of the two channels at 635 nm (for Cy5) and 532 nm (for Cy3) were balanced to limit the number of saturated pixels (less than 0.005%) for generating gray scale 16-bit TIFF image files


title: breast tumor epithelium,4

tag: mininal stage grouping


title: V3coc-V1bissal_STN_Agilent_scan


title: N3coc-B5sal_STN_Axon_scan


title: breast tumor epithelium,10

value: IIIB

tag: t (extent of primary tumor)


title: SalN5-Coc B7_accumbens_Agilent_scan


title: breast tumor epithelium,3

tag: n (lymph node metastasis)


title: B4coc-V4sal_Low-accumbens


title: N9sal-V4biscoc_STN_Agilent_scan

hyb_protocol: After checking the labeling efficiency and the product integrity, 750 ng Cy3- and 750 ng Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven, using an Agilent in situ hybridization kit. The slides were washed and then any traces of water were removed by centrifugation at 800 rpm for 1 min


title: N9sal-V4biscoc_STN_Axon_scan


title: breast tumor epithelium,2

tag: er


title: normal breast epithelium,1

value: Within normal limits

tag: pgr


title: SalN5-Coc B7_accumbens_Axon_scan


title: SalN9-CocV4_accumbens__Agilent_scan


title: CocN3-SalB8_accumbens_Axon_scan


title: CocV3-SalB5_accumbens_Agilent_scan

scan_protocol: Slides were scanned using an Agilent G6525 Microarray Scanner at 5-μm resolution. The photo multiplier tube (PMT) levels of the two channels at 635 nm (for Cy5) and 532 nm (for Cy3) were balanced to limit the number of saturated pixels for generating gray scale 16-bit TIFF image files.


title: aldesterone-producing adenoma (APA) tissue from Case7

status: Public on May 09 2015

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

hyb_protocol: The resultant cRNAs were fragmented for 30 min at 60oC in dark. The fragmented cRNAs (600 ng) were hybridized on the microarray at 65oC for 17 h.

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505B.

data_processing:
Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.
Log2-transformed normalized signal intensities (75 percentile global normalization)

source_name: aldesterone-producing adenoma (APA)

label_protocol: Total RNA samples (100 ng) were amplified and labelled with Cy3 using the Low Input QuickAmp Labeling Kit (Agilent).

extract_protocol: Total RNA was isolated using All Prep DNA/RNA Mini kit (Qiagen) according to the manufacturer’s instruction.

tag: subject

value: patients with aldosterone-producing adenoma (APA)

tag: health state

value: primary aldosteronism

tag: tissue type

value: aldesterone-producing adenoma (APA)


title: aldesterone-producing adenoma (APA) tissue from Case5

tag: gender

value: female


title: CocN3-SalB8_accumbens_Agilent_scan

tag: tissue


title: adjacent adrenal gland (AAG) tissue from Case6

source_name: adrenal gland tissue adjacent to APA

value: adrenal gland tissue adjacent to APA (AAG)


title: adjacent adrenal gland (AAG) tissue from Case7


title: SalN9-CocV4_accumbens_Axon_scan

tag: Sex


title: aldesterone-producing adenoma (APA) tissue from Case6


title: adjacent adrenal gland (AAG) tissue from Case4


title: adjacent adrenal gland (AAG) tissue from Case2


title: VO vs CTRL dye-swap

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

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

hyb_protocol: 500 ng of Cy3- and Cy5-labeled cRNAs were combined

scan_protocol: Agilent G2565BA Microarray Scanner

data_processing: Data were extracted using the Agilent Feature Extraction Software 9.5.3; Data normalization (Lowess intesity dependent) was performed by means of GeneSpring GX 10.0.

organism: Sparus aurata

source_name: adipose tissue from CTRL animals

label_protocol: RNA sample were pooled within each group and 250 ng of total RNA was labeled using the Quick Amp Labeling Kit (Agilent) to produce Cyanine 3-CTP or Cyanine 5-CTP labeled cRNA.

extract_protocol: Total RNA from adipose tissue was extracted using a Qiazol and RNeasy Maxi combination protocol (Qiagen)

treatment_protocol: Juvenile gilthead sea bream (Sparus aurata L.) of 16 g initial mean body weight were distributed into 9 fibreglass tanks (500 l) in groups of 60 fish at the research experimental facilities of IATS. Each triplicate group received (from May 23rd to September 19th) one of the three experimental diets nominally CTRL, 66VO and VO. All diets were based on plant proteins and dietary oil was either Scandinavian FO (CTRL diet) or a blend of vegetable oils, replacing the 66% (66VO diet) and 100% (VO diet) of FO.

tag: diet

value: CTRL

source_name: adipose tissue from VO animals

value: VO


title: breast tumor epithelium,1

value: Adenocarcinoma of breast, ductal

value: IIB

tag: dfs-month

tag: dfs-event


title: breast tumor epithelium,55

tag: age at diagnosis

value: Adenocarcinoma of breast, ductal, mucinous

tag: distant metastasis


title: adjacent adrenal gland (AAG) tissue from Case3


title: aldesterone-producing adenoma (APA) tissue from Case3


title: aldesterone-producing adenoma (APA) tissue from Case4


title: VO vs CTRL


title: aldesterone-producing adenoma (APA) tissue from Case1


title: adjacent adrenal gland (AAG) tissue from Case5


title: liver Wrn mutant vitamin C #4 / liver Wrn mutant #4

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

country: Canada

institute: Centre de Recherche du CHU de Québec

description: Biological Wrn vitamin C replicate 4 of 4. Biological Wrn replicate 4 of 4.

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix® 4000B. Data were extracted from images using GenePix® version 6.0 with local background estimation.

data_processing: Data were processed using limma in BioConductor (www.bioconductor.org). The data were background subtracted using normexp and also normalized using the loess method.

source_name: Liver tissue

label_protocol: Protocol from Agilent

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

extract_protocol: Extraction of total RNA protocol described in Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

treatment_protocol: Wrn mutant mice were treated with 0.4% vitamin C in drinking water since weaning. Untreated Wrn mutant mice were the controls.

tag: liver

value: males treated with vitamin C since weaning

tag: age

value: 3 months of age

tag: strain

value: males Wrn mutant (no treatment)


title: aldesterone-producing adenoma (APA) tissue from Case2


title: 66VO vs CTRL dye-swap

source_name: adipose tissue from 66VO animals


title: adjacent adrenal gland (AAG) tissue from Case1


title: CocV3-SalB5_accumbens_Axon_scan

data_processing:
The resulting images were processed using the GenePix Pro (v6.0.1.26) image analysis software. This included defining the spots, measuring the intensities, flagging the spots having inadequate quality control parameters and evaluating local background
The pre-processing of the data and its quality assessment were done using the MANGO (MicroArray Normalization tool of GODMAP) tools suit (version 1.0, CNRS BioInfome Team [http://bioinfome.cgm.cnrs-gif.fr/]), an R script that allows integrated analysis of two-color microarrays. The background level was calculated using morphological operators (a short closing followed by a large opening) and subtracted. Raw data were normalized using the print-tip lowess method, i.e. local regression normalization within an artificial print-tip block.

value: Accumbens nucleus

value: male

tag: treatment

value: received cocaine (15 mg/kg) at D2 D3 D4 of conditioned place preference protocol

label_protocol: Kit Picopure (Arcturus)

extract_protocol: Briefly, 75ng-aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies)

value: received saline solution at D2 D3 D4 of conditioned place preference protocol


title: liver Wrn mutant vitamin C #2 / liver Wrn mutant #2

description: Biological Wrn vitamin C replicate 2 of 4. Biological Wrn replicate 2 of 4.


title: 66VO vs CTRL


title: liver Wrn mutant vitamin C #3 / liver Wrn mutant #3

description: Biological Wrn vitamin C replicate 3 of 4. Biological Wrn replicate 3 of 4.


title: liver Wrn mutant vitamin C #1 / liver Wrn mutant #1

description: Biological Wrn vitamin C replicate 1 of 4. Biological Wrn replicate 1 of 4.


title: 308-001_251807310182_S01_GE1_105_Dec08_1_2_48 HrsTreated

city: Lincoln

first: Dhairyasheel

last: Desai

state: Canterbury

address: Ellesmere Junction Road/Spring Road

department: Bio-Protection Research Centre

country: New Zealand

institute: Lincoln University

description: Gene expression 48hr after Xcc inoculation

hyb_protocol: Cy3-labeled cRNA (1.65 µg) from each sample was hybridized to an Agilent Brassica 95k EST microarray chip.  The hybridized array was then washed and scanned

scan_protocol: data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: The raw data was imported into Genespring GX 11 and normalised by intensity dependent Lowess (per spot per chip) method.

organism: Brassica oleracea var. capitata

source_name: Cabbage leaf, 48h after Xcc inoculation, replicate 4

label_protocol: Five hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

growth_protocol: Seedlings of cabbage (Brassica oleracea var capitata L.) cultivar ‘County green’were grown in a heated glasshouse in 6 packs containing a soil / sand based potting mix Innoculations and sampling were initiated at the 7 week mark. Xanthomonas campestris pv campestris  # 4013 from the ICMP (International collection of microorganisms from plants,  Landcare Research http://www.landcareresearch.co.nz/resources/collections/icmp )  is an isolate of Xcc derived from cabbage grown in Pukekohe, New Zealand, in 1974.  This isolate reliably produced characteristic V shaped lesions of blackened veins on ‘County green’ cabbage leaves.  Bacterial suspensions were grown overnight in  Luria Bertani broth at 28C, pelleted and resuspended in a 10mM MgSO4 solution to and OD600 of  0.2.

extract_protocol: RNA was extracted from frozen leaf disks with a RNeasy Plus mini kit (Qiagen cat # 74904), using glass beads and a beadbeater (Biospec) combined with qiashredder columns (Qiagen) to disrupt plant material, followed by a gDNA eliminator column for removal of genomic DNA.  Samples were analysed on an agarose gel under denaturing conditions (2% formamide loading buffer, 65 degrees 5 min), and quantified using a Qbit flourometer (Invitrogen).   A minimum of 80 and maximum of 480 ng/ul of RNA was sent on dry ice to Cogenics corporation (Morrinsville, North Carolina) for hybridisation on the Brassica 95k EST microarray chip.

treatment_protocol: bacterial suspension was loaded in a 1ml syringe with needle and the midvein of the first fully opened leaf inoculated 3 times just above the petiole. This delivered approximately 2-4 µl of bacterial suspension to the leaf.   Plants were returned to the glasshouse and sampled at 6, 24 and 48 hours post inoculation.  Humidity was kept at 95% for 24 hpi, and at 75% for the remainder of the experiment.

value: Leaf

value: 7 week old seedling


title: 308-001_251807310182_S01_GE1_105_Dec08_1_1_48 HrsTreated

source_name: Cabbage leaf, 48h after Xcc inoculation, replicate 3


title: Bre98p2_ChIP_input

city: Darlinghurst

first: Warwick

middle: James

last: Locke

state: NSW

address: 384 Victoria St

department: Cancer Deparment

country: Australia

institute: The Garvan Institute of Medical Research

description:
Formalin Fixed 10min 37C + Sonicated to ~500bp mean fragment size
Fixed Chromatin

hyb_protocol: Hybridisation was performedt according to the conditions set ou by Affymetrix

scan_protocol: Scan was performedt according to the conditions set ou by Affymetrix

data_processing: Low level analysis and Model-based Analysis of Tiling arrays (MAT) normalisation of ChIP-chip data was performed using the R package aroma.affymetrix. Array signal across all promoters on the array was determined using the R package Repitools. ChIP data was then summarised to a t-statistic for a region of ±2 kb of all TSS with the Repitools function “blocksStats”

label: Biotin

source_name: HMEC, none

label_protocol: DNA was amplified using the whole genome amplification (Genomeplex WGA2 Kit, Sigma Aldrich). WGA material was cleaned-up with the GeneChip® Sample Cleanup Module (Affymetrix, Santa Clara CA, USA) and 7.5 μg was then fragmented and labelled for array hybridisation with the GeneChip® WT Double-Stranded Target Assay (Affymetrix, Santa Clara CA, USA) according to the manufacturer’s protocol.

growth_protocol: HMEC lines were generated from tissue taken from healthy women with informed donor consent as part of breast reduction mammoplasty (institutional ethics approval provided by the Sydney Adventist Hospital Ethics Committee, Project ID 06/03). At the time of surgery, all donors were aged between 23 and 43 years of age. Breast tissue was diced and then digested with collagenase to generate organoids. To establish HMEC lines, organoids were allowed to expand in MBD170 serum free basal medium (Life Technologies, Carlsbad CA, USA) until large colonies (1-2 cm) were observed (5-10 days). Organoid colonies were partially trypsinised to remove stromal cells and the remaining epithelial cells were transferred into a new tissue culture flask to generate passage 1 HMEC. vHMEC lines were then generated by serial passage of HMEC until proliferation slowed and the cells entered the selection phase. Selection phase HMEC were maintained with twice-weekly media changes until large, actively growing colonies (1-2 cm) were observed. Growing cells were trypsinised and transferred to a new culture vessel, generating the vHMEC lines.

extract_protocol: Cell peeltes were resuspended in SDS cell lysis solution (Millipore) and IP performed using the millipore Chromatin Immunoprecipitation (ChIP) Assay Kit using 10ug of antibody (Anti-H3K27me3 or anti-H3K9ac)

treatment_protocol: ~2x10^6 cells (per immunoprecipitation) fixed for 10 minutes at 37°C in culture media containing 2.7% (w/v) formaldehyde. Media was discarded and cells were washed in ice cold PBS, then scraped in cold PBS and pelleted and stored at -80C until required.

value: Breast

tag: passage


title: Bre98p8_ChIP_input

source_name: vHMEC, none


title: Bre98p14_ChIP_input


title: Bre98p8_ChIP_H3K27me3

description:
Formalin Fixed 10min 37C + Sonicated to ~500bp mean fragment size + Anti-H3K27me3
Fixed Chromatin

source_name: vHMEC, Anti-H3K27me3


title: Bre67p7_ChIP_input


title: Bre98p14_ChIP_H3K27me3


title: Bre67p2_ChIP_input


title: Bre67p7_ChIP_H3K27me3


title: Bre67p2_ChIP_H3K27me3

source_name: HMEC, Anti-H3K27me3


title: Bre67p14_ChIP_input


title: Bre98p2_ChIP_H3K27me3


title: Bre67p14_ChIP_H3K27me3


title: Bre38p7_ChIP_input


title: Bre38p7_ChIP_H3K27me3


title: Bre38p7_ChIP_H3K9ac

description:
Formalin Fixed 10min 37C + Sonicated to ~500bp mean fragment size + Anti-H3K9ac
Fixed Chromatin

source_name: vHMEC, Anti-H3K9ac


title: Bre38p3_ChIP_input


title: Bre38p3_ChIP_H3K9ac

source_name: HMEC, Anti-H3K9ac


title: Bre38p3_ChIP_H3K27me3


title: Bre38p26_ChIP_input


title: Bre38p26_ChIP_H3K9ac


title: Bre38p26_ChIP_H3K27me3


title: Bre12p8_ChIP_input


title: Bre12p8_ChIP_H3K9ac


title: Bre12p3_ChIP_input


title: Bre12p8_ChIP_H3K27me3


title: Bre98p8_vHMEC_mRNA

hyb_protocol: Hybridised according to affymetrix protocol

scan_protocol: Scan performed according to conditions as set out by Affymetrix

data_processing: GeneChip® array data was analysed using the aroma.affymetrix R package [154] which utilises Robust Multi-Array (RMA) normalisation to summarise gene-probe intensities.

source_name: vHMEC

label_protocol: RNA was converted to labelled cDNA using the Affymetrix Whole Transcript (WT) Sense Target Labelling Assay kit accordin go the manufactureres protocol

extract_protocol: Total RNA was extracted using TRIzol (invitrogen) according to the manufactureres protocol

treatment_protocol: Cells were cultured under normal conditions


title: Microvesicles derived from normal cultured MSC

city: Nanjing

first: Yan

last: Wang

address: 300 Guangzhou Road

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: normall cultured MSC

label_protocol: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: The MSC was cultured in DMEM/F12 with 10% FBS and 2% penicillin/ streptomycin with or without 100IU/ML EPO for 48h,then the cell supernanent were collected to be centrifuged  at 3000 g for 20 min then stored at -80℃

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs.

treatment_protocol: The free-cell debris supernatants were centrifuged at 100 000 g for 1h at 4°C, washed in serum-free medium 199(M199) ,following submitted to a second ultracentrifugation at the same conditions, and then resuspension with M199.

tag: msc culture

value: complete medium for 48h


title: Microvesicles derived from erythropoietin co-cultured MSC

description: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.

source_name: erythropoietin co-cultured MSC

value: complete medium with EPO for 48h


title: Bre12p3_ChIP_H3K9ac


title: 308-001_251807310180_S01_GE1_105_Dec08_1_2_48 HrsControl

description: Gene expression 48hr after mock inoculation

source_name: Cabbage leaf, 48h after mock treatment, replicate 4


title: 308-001_251807310050_S01_GE1_105_Dec08_1_1_6 HrsTreated

description: Gene expression 6hr after Xcc inoculation

source_name: Cabbage leaf, 6h after Xcc inoculation, replicate 1


title: Bre98p14_vHMEC_mRNA


title: Bre98p2_HMEC_mRNA

source_name: HMEC


title: 308-001_251807310181_S01_GE1_105_Dec08_1_2_48 HrsTreated

source_name: Cabbage leaf, 48h after Xcc inoculation, replicate 2


title: 308-001_251807310051_S01_GE1_105_Dec08_1_2_6 HrsTreated

source_name: Cabbage leaf, 6h after Xcc inoculation, replicate 4


title: 308-001_251807310178_S01_GE1_105_Dec08_1_2_24 HrsTreated

description: Gene expression 24hr after Xcc inoculation

source_name: Cabbage leaf, 24h after Xcc inoculation, replicate 4


title: Bre12p3_ChIP_H3K27me3


title: Bre67p7_vHMEC_mRNA


title: 308-001_251807310179_S01_GE1_105_Dec08_1_1_48 HrsControl

source_name: Cabbage leaf, 48h after mock treatment, replicate 1


title: 308-001_251807310179_S01_GE1_105_Dec08_1_2_48 HrsControl

source_name: Cabbage leaf, 48h after mock treatment, replicate 2


title: 308-001_251807310175_S01_GE1_105_Dec08_1_2_24 HrsControl

description: Gene expression 24hr after mock inoculation

source_name: Cabbage leaf, 24h after mock treatment, replicate 2


title: 308-001_251807310175_S01_GE1_105_Dec08_1_1_24 HrsControl

source_name: Cabbage leaf, 24h after mock treatment, replicate 1


title: 308-001_251807310049_S01_GE1_105_Dec08_1_2_6 HrsControl

description: Gene expression 6hr after mock inoculation

source_name: Cabbage leaf, 6h after mock treatment, replicate 4


title: Bre12p14_ChIP_input

source_name: vHMEC, none


title: 308-001_251807310176_S01_GE1_105_Dec08_1_1_24 HrsControl

source_name: Cabbage leaf, 24h after mock treatment, replicate 3


title: 308-001_251807310178_S01_GE1_105_Dec08_1_1_24 HrsTreated

source_name: Cabbage leaf, 24h after Xcc inoculation, replicate 3


title: 308-001_251807310050_S01_GE1_105_Dec08_1_2_6 HrsTreated

source_name: Cabbage leaf, 6h after Xcc inoculation, replicate 2


title: 308-001_251807310048_S01_GE1_105_Dec08_1_1_6 HrsControl

source_name: Cabbage leaf, 6h after mock treatment, replicate 1


title: 308-001_251807310177_S01_GE1_105_Dec08_1_1_24 HrsTreated

source_name: Cabbage leaf, 24h after Xcc inoculation, replicate 1


title: 308-001_251807310048_S01_GE1_105_Dec08_1_2_6 HrsControl

source_name: Cabbage leaf, 6h after mock treatment, replicate 2


title: 308-001_251807310049_S01_GE1_105_Dec08_1_1_6 HrsControl

source_name: Cabbage leaf, 6h after mock treatment, replicate 3


title: 308-001_251807310180_S01_GE1_105_Dec08_1_1_48 HrsControl

source_name: Cabbage leaf, 48h after mock treatment, replicate 3


title: 308-001_251807310177_S01_GE1_105_Dec08_1_2_24 HrsTreated

source_name: Cabbage leaf, 24h after Xcc inoculation, replicate 2


title: 308-001_251807310176_S01_GE1_105_Dec08_1_2_24 HrsControl

source_name: Cabbage leaf, 24h after mock treatment, replicate 4


title: 308-001_251807310051_S01_GE1_105_Dec08_1_1_6 HrsTreated

source_name: Cabbage leaf, 6h after Xcc inoculation, replicate 3


title: Bre67p2_HMEC_mRNA

source_name: HMEC


title: Bre12p14_ChIP_H3K9ac

source_name: vHMEC, Anti-H3K9ac


title: Bre67p14__vHMEC_mRNA

source_name: vHMEC


title: Bre38p11_vHMEC_mRNA_ReplicateB


title: Neonatal fibroblasts

city: Brno

first: Tomas

last: Barta

address: Pekarska 53

department: International Clinical Research Center (FNUSA-ICRC)

country: Czech Republic

institute: St. Anne's University Hospital Brno

hyb_protocol: Hybridisation process was done following the Agilent protocol "miRNA Microarray System with miRNA Complete Labelling and Hyb Kit" version 2.1 adapted for the spike-in use with the specifications of the "miRNA Microarray System" version 1.7 protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting.

data_processing: Arrays where normalized using RMA background correction and quantile normalization.

source_name: Neonatal dermal fibroblasts

label_protocol: 100 ng of RNA were used for fluorescent labelling with "Cyanine 3-pCp".

growth_protocol: Human iPSCs were cultured in undifferentiated, pluripotent state as discrete colonies on feeder layers of mitotically inactivated mouse embryonic fibroblasts (MEF) with medium containing Knockout Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Paisley, U.K., http:// www.invitrogen.com), 1 mM L-glutamine (Invitrogen), 100 mM nonessential amino acids (Invitrogen), 20% serum replacement (Invitrogen) and 8 ng/ml fibroblast growth factor 2 (FGF2; Invitrogen). To avoid feeder cell inclusions, two pasages before RNA extraction cells were transferred to Matrigel Basement Membrane Matrix (BD Biosciences) coated dishes and cultured in MEF-conditioned media. Human neonatal fibroblasts were cultured in media containing: Knockout DMEM medium, 20% fetal bovine serum, 1 mM L-glutamine, 100 mM MEM non-essential amino acid solution.

extract_protocol: RNA was prepared using mirVana (Ambion) kit according to manufacturer's instructions. RNA quality was controlled using Bioanalyzer 2100. RNA samples were diluted to 100ng/μl and checked with NanoDrop.

tag: cell type

value: Neonatal fibroblasts


title: Bre38p5_HMEC_mRNA_ReplicateB


title: aldesterone-producing adenoma (APA) tissue from Case7 [methylation]

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing:
Genome Studio V2011.2; the non_normalized.txt contains unmethylated and methylated signal intensities.
Detection P-value and normalized average beta value. The methylation level of each of the >  480,000 CpG sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using Normalization to Internal Controls and Background Subtraction options implemented in the Methylation Module 1.9.0.

source_name: aldesterone-producing adenoma (APA)

extract_protocol: Genomic DNA was isolated using All Prep DNA/RNA Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.

tag: subject

value: patients with aldosterone-producing adenoma (APA)

tag: health state

value: primary aldosteronism

value: aldesterone-producing adenoma (APA)


title: Bre38p14_vHMEC_mRNA_ReplicateB


title: Bre38p5_HMEC_mRNA_ReplicateA


title: Bre38p11_vHMEC_mRNA_ReplicateA


title: Induced pluripotent stem cells

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: Bre38p14_vHMEC_mRNA_ReplicateA


title: adjacent adrenal gland (AAG) tissue from Case7 [methylation]

source_name: adrenal gland tissue adjacent to APA

tag: gender

tag: tissue type

value: adrenal gland tissue adjacent to APA (AAG)


title: Bre12p3_HMEC_mRNA_ReplicateA

tag: tissue


title: Bre12p16_vHMEC_mRNA_ReplicateA


title: Bre12p10_vHMEC_mRNA_ReplicateB


title: Bre12p16_vHMEC_mRNA_ReplicateB


title: Bre12p3_HMEC_mRNA_ReplicateB


title: Bre12p10_vHMEC_mRNA_ReplicateA


title: 308-001_251807310181_S01_GE1_105_Dec08_1_1_48 HrsTreated

source_name: Cabbage leaf, 48h after Xcc inoculation, replicate 1


title: WT_leaf_palisade _paerenchyma+upper_epidermis_5uM_Zn_Rep3

status: Public on May 08 2015

city: Warsaw

first: Maria

last: Kendziorek

address: Miecznikowa 1

department: Biology

country: Poland

institute: Uniwersity of  Warsaw

description: gene expression in LCM -excised palisade paerenchyma + upper epidermis from leaves of Wild type tomato

hyb_protocol: RNA hybridization to tomato cDNA microarray Affymetrix Tomato Genome Array was conducted at Corelab, Laboratory of Microarray Analyses (University of Warsaw and Institute of Biochemistry and Biophysics, PAS) using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) according to manufacturer’s protocol

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix UK Ltd., High Wycombe, UK)

data_processing: Microarray hybridization signals were recorded and processed using Affymetrix® GeneChip® Command Console® Software (AGCC).

organism: Solanum lycopersicum

source_name: 25 days old tomato plants exposed to 5 uM Zn for 15 days

label_protocol: Labelling of RNA samples was performed by use of the Affymetrix 3’ IVT-Express kit (Affymetrix UK Ltd., High Wycombe, UK) following standard Affymetrix protocols (Affymetrix UK Ltd., High Wycombe, UK).

growth_protocol: Seeds were surface-sterilized in 70% ethanol and rinsed with sterile deionised water. Germination and the first stage of seedlings development took place in the glass jars containing the basic medium supplemented with 2% (w/v) sucrose solidified with 1% agar (w/v) for 10 days. Obtained 10-day-old seedlings were transferred to 2-L pots and grown for 15 days under hydroponic conditions on quarter-strength Knop’s medium. The nutrient solution was replaced every 2 days. Plants were grown in a controlled growth chamber, at 23/16°C day/night temperatures, 40–50% humidity, with a 16-h photoperiod at a quantum flux density (PAR) of 250 μmol m−2 s−1 using fluorescent Flora tubes.

extract_protocol: PicoPure RNA Isolation Kit (Arcturus Engineering)  following the manufacturer’s instructions, including treatment with the RNase-Free DNase Set (Qiagen, USA). Isolated RNA was amplified with the RiboAmp HS PLUS (Arcturus Engineering) amplification system following the manufacturer’s protocol.

treatment_protocol: The plants of the same size were transferred to basic nutrient solution (1/4 Knop's medium) supplemented with 5 µM Zn (added as ZnS04) for 15 days.

tag: organ

value: leaves

value: palisade paerenchyma + upper epidermis (EPP)

tag: genotype

value: var. Beta wild type


title: 35S:AtHMA4_leaf_palisade _paerenchyma+upper_epidermis_5uM_Zn_Rep2

description: gene expression in LCM -excised palisade paerenchyma + upper epidermis from leaves of 35S:AtHMA4 expressing tomato

value: var.Beta, 35S:AtHMA4 expressing line 4


title: 35S:AtHMA4_leaf_palisade _paerenchyma+upper_epidermis_5uM_Zn_Rep3


title: 35S:AtHMA4_leaf_spongy _paerenchyma+lower_epidermis_5uM_Zn_Rep1

description: gene expression in LCM -excised spongy paerenchyma + lower epidermis from leaves of 35S:AtHMA4 expressing  tomato

value: spongy paerenchyma + lower epidermis (ESP)


title: WT_leaf_spongy _paerenchyma+lower_epidermis_5uM_Zn_Rep3

description: gene expression in LCM -excised spongy paerenchyma + lower epidermis from leaves of Wild type tomato


title: WT_leaf_palisade _paerenchyma+upper_epidermis_5uM_Zn_Rep2


title: aldesterone-producing adenoma (APA) tissue from Case6 [methylation]

label_protocol: Standard Illumina labelling protocol

value: female


title: 35S:AtHMA4_leaf_spongy _paerenchyma+lower_epidermis_5uM_Zn_Rep3

description: gene expression in LCM -excised spongy paerenchyma + lower epidermis from leaves of 35S:AtHMA4 expressing tomato


title: WT_leaf_spongy _paerenchyma+lower_epidermis_5uM_Zn_Rep2


title: 35S:AtHMA4_leaf_palisade _paerenchyma+upper_epidermis_5uM_Zn_Rep1


title: 35S:AtHMA4_root_stele_5uM_Zn_Rep3

description: gene expression in LCM -excised stele from roots of 35S::AtHMA4 expressing tomato

value: roots

value: stele (S)


title: adjacent adrenal gland (AAG) tissue from Case5 [methylation]


title: 35S:AtHMA4_leaf_spongy _paerenchyma+lower_epidermis_5uM_Zn_Rep2


title: 35S:AtHMA4_root_epidermis+cotrex_5uM_Zn_Rep3

description: gene expression in LCM -excised epidermis + cortex from roots of 35S::AtHMA4 expressing tomato

value: epidermis + cortex (EC)


title: WT_leaf_palisade _paerenchyma+upper_epidermis_5uM_Zn_Rep1


title: adjacent adrenal gland (AAG) tissue from Case4 [methylation]


title: aldesterone-producing adenoma (APA) tissue from Case4 [methylation]


title: WT_leaf_spongy _paerenchyma+lower_epidermis_5uM_Zn_Rep1


title: 35S:AtHMA4_root_stele_5uM_Zn_Rep2


title: 35S:AtHMA4_root_epidermis+cotrex_5uM_Zn_Rep2


title: adjacent adrenal gland (AAG) tissue from Case6 [methylation]


title: aldesterone-producing adenoma (APA) tissue from Case1 [methylation]


title: aldesterone-producing adenoma (APA) tissue from Case2 [methylation]


title: aldesterone-producing adenoma (APA) tissue from Case5 [methylation]


title: 35S:AtHMA4_root_epidermis+cotrex_5uM_Zn_Rep1


title: WT_root_epidermis+cotrex_5uM_Zn_Rep3

description: gene expression in LCM -excised epidermis + cortex from roots of Wild type tomato


title: WT_root_stele_5uM_Zn_Rep1

description: gene expression in LCM -excised stele from roots of Wild type tomato


title: WT_root_epidermis+cotrex_5uM_Zn_Rep1


title: WT_root_epidermis+cotrex_5uM_Zn_Rep2


title: adjacent adrenal gland (AAG) tissue from Case2 [methylation]


title: WT_root_stele_5uM_Zn_Rep3


title: aldesterone-producing adenoma (APA) tissue from Case3 [methylation]


title: EXP-485: ovary_TCGA-61-2109

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Ovary

tag: Sex

value: FEMALE

tag: disease staging

value: IIIC

tag: cancer site

value: OVARY

tag: clinical diagnosis

value: Serous Cystadenocarcinoma

tag: individual

tag: tumor grading

tag: external id

tag: organism part

value: ovary


title: EXP-485: ovary_TCGA-61-2098

scan_protocol: See mage-tab files linked to series entry for additional details

tag: age


title: EXP-485: ovary_TCGA-61-2110

data_processing: See mage-tab files linked to series entry for additional details

value: NOT SPECIFIED


title: EXP-485: ovary_TCGA-61-2095

label_protocol: See mage-tab files linked to series entry for additional details


title: EXP-485: ovary_TCGA-61-2092

extract_protocol: See mage-tab files linked to series entry for additional details


title: adjacent adrenal gland (AAG) tissue from Case3 [methylation]

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

value: patients with aldosterone-producing adenoma (APA)

value: primary aldosteronism


title: EXP-485: ovary_TCGA-61-2094


title: adjacent adrenal gland (AAG) tissue from Case1 [methylation]

value: adrenal gland tissue adjacent to APA (AAG)


title: EXP-485: ovary_TCGA-61-2113

value: IIC


title: EXP-485: ovary_TCGA-61-2101


title: EXP-485: ovary_TCGA-61-2096

value: IC


title: EXP-485: ovary_TCGA-61-2087


title: EXP-485: ovary_TCGA-61-2088


title: EXP-485: ovary_TCGA-61-2104


title: EXP-485: ovary_TCGA-61-2097


title: EXP-485: ovary_TCGA-61-2018


title: Bre12p14_ChIP_H3K27me3

description:
Formalin Fixed 10min 37C + Sonicated to ~500bp mean fragment size + Anti-H3K27me3
Fixed Chromatin

source_name: vHMEC, Anti-H3K27me3

value: Breast

tag: passage


title: EXP-485: ovary_TCGA-61-2017


title: EXP-485: ovary_TCGA-61-2000


title: EXP-485: ovary_TCGA-61-2009


title: EXP-485: ovary_TCGA-61-2008


title: EXP-485: ovary_TCGA-61-2012


title: EXP-485: ovary_TCGA-61-2002


title: EXP-485: ovary_TCGA-61-2003


title: EXP-485: ovary_TCGA-61-1918

value: IV


title: EXP-485: ovary_TCGA-61-1995


title: EXP-485: ovary_TCGA-61-1919


title: EXP-485: ovary_TCGA-61-1915


title: EXP-485: ovary_TCGA-61-1911

value: IIA


title: EXP-485: ovary_TCGA-61-1904


title: EXP-485: ovary_TCGA-61-1910


title: EXP-485: ovary_TCGA-61-1906


title: EXP-485: ovary_TCGA-61-1913

value: IIIB


title: EXP-485: ovary_TCGA-61-1914


title: EXP-485: ovary_TCGA-61-1998


title: EXP-485: ovary_TCGA-61-1901


title: EXP-485: ovary_TCGA-61-1917


title: EXP-485: ovary_TCGA-61-1903

value: IB


title: EXP-485: ovary_TCGA-61-1900


title: EXP-485: ovary_TCGA-61-1743


title: EXP-485: ovary_TCGA-61-1895


title: 35S:AtHMA4_root_stele_5uM_Zn_Rep1

value: roots

value: stele (S)

value: var.Beta, 35S:AtHMA4 expressing line 4


title: EXP-485: ovary_TCGA-61-1737

value: FEMALE

value: OVARY


title: EXP-485: ovary_TCGA-61-1740

value: IIIC

value: Serous Cystadenocarcinoma

value: ovary


title: EXP-485: ovary_TCGA-61-1907


title: EXP-485: ovary_TCGA-61-1730


title: EXP-485: ovary_TCGA-61-1722


title: EXP-485: ovary_TCGA-59-2351


title: EXP-485: ovary_TCGA-61-1899


title: EXP-485: ovary_TCGA-61-1736


title: EXP-485: ovary_TCGA-61-1733


title: EXP-485: ovary_TCGA-61-1721

value: NOT SPECIFIED


title: EXP-485: ovary_TCGA-61-1724


title: EXP-485: ovary_TCGA-61-1727


title: EXP-485: ovary_TCGA-59-2354


title: EXP-485: ovary_TCGA-59-2363

value: IIIA


title: EXP-485: ovary_TCGA-61-1725


title: EXP-485: ovary_TCGA-59-2350


title: EXP-485: ovary_TCGA-61-2111


title: EXP-485: ovary_TCGA-59-2352


title: EXP-485: ovary_TCGA-59-2355


title: EXP-485: ovary_TCGA-59-2348


title: EXP-485: ovary_TCGA-59-2349

value: IA


title: EXP-485: ovary_TCGA-57-1994


title: EXP-485: ovary_TCGA-57-1586


title: EXP-485: ovary_TCGA-57-1993


title: EXP-485: ovary_TCGA-57-1992

value: IC


title: WT_root_stele_5uM_Zn_Rep2

value: var. Beta wild type


title: EXP-485: ovary_TCGA-36-1580


title: EXP-485: ovary_TCGA-36-1576


title: EXP-485: ovary_TCGA-57-1582


title: EXP-485: ovary_TCGA-36-1577

value: IIC


title: EXP-485: ovary_TCGA-57-1584


title: EXP-485: ovary_TCGA-36-1575


title: EXP-485: ovary_TCGA-36-1570


title: EXP-485: ovary_TCGA-36-1569


title: EXP-485: ovary_TCGA-36-1581


title: EXP-485: ovary_TCGA-57-1583


title: EXP-485: ovary_TCGA-36-1574


title: EXP-485: ovary_TCGA-36-1568


title: EXP-485: ovary_TCGA-57-1585


title: EXP-485: ovary_TCGA-36-1571


title: EXP-485: ovary_TCGA-61-2102


title: EXP-485: ovary_TCGA-36-1578

value: IV


title: EXP-485: ovary_TCGA-31-1956

value: IIIB


title: EXP-485: ovary_TCGA-31-1951


title: EXP-485: ovary_TCGA-31-1959


title: EXP-485: ovary_TCGA-61-2016


title: EXP-485: ovary_TCGA-31-1946


title: EXP-485: ovary_TCGA-30-1892


title: EXP-485: ovary_TCGA-31-1950


title: EXP-485: ovary_TCGA-30-1891


title: EXP-485: ovary_TCGA-31-1953


title: EXP-485: ovary_TCGA-30-1866


title: EXP-485: ovary_TCGA-30-1867

value: GX


title: EXP-485: ovary_TCGA-30-1887


title: EXP-485: ovary_TCGA-30-1880


title: EXP-485: ovary_TCGA-30-1862


title: EXP-485: ovary_TCGA-30-1857


title: EXP-485: ovary_TCGA-30-1718


title: EXP-485: ovary_TCGA-30-1860


title: EXP-485: ovary_TCGA-29-2428


title: EXP-485: ovary_TCGA-30-1855


title: EXP-485: ovary_TCGA-30-1853


title: EXP-485: ovary_TCGA-30-1859


title: EXP-485: ovary_TCGA-30-1856


title: EXP-485: ovary_TCGA-29-2425


title: EXP-485: ovary_TCGA-29-1777


title: EXP-485: ovary_TCGA-29-1784


title: EXP-485: ovary_TCGA-29-2427


title: EXP-485: ovary_TCGA-29-1785


title: EXP-485: ovary_TCGA-29-1783


title: EXP-485: ovary_TCGA-29-1778


title: EXP-485: ovary_TCGA-61-1734


title: EXP-485: ovary_TCGA-30-1714


title: EXP-485: ovary_TCGA-61-1728


title: EXP-485: ovary_TCGA-29-1775


title: EXP-485: ovary_TCGA-29-1771


title: EXP-485: ovary_TCGA-29-1774


title: EXP-485: ovary_TCGA-29-2414


title: EXP-485: ovary_TCGA-29-1781


title: EXP-485: ovary_TCGA-29-1768


title: EXP-485: ovary_TCGA-29-1762


title: EXP-485: ovary_TCGA-29-1711


title: EXP-485: ovary_TCGA-61-1741


title: EXP-485: ovary_TCGA-61-1738


title: EXP-485: ovary_TCGA-29-1761


title: EXP-485: ovary_TCGA-29-1710


title: EXP-485: ovary_TCGA-29-1776


title: EXP-485: ovary_TCGA-29-1703


title: EXP-485: ovary_TCGA-29-1705


title: EXP-485: ovary_TCGA-29-1770


title: EXP-485: ovary_TCGA-29-1707


title: EXP-485: ovary_TCGA-29-1769


title: EXP-485: ovary_TCGA-29-1702


title: EXP-485: ovary_TCGA-29-1699


title: EXP-485: ovary_TCGA-29-1701


title: EXP-485: ovary_TCGA-29-1764


title: EXP-485: ovary_TCGA-29-1763


title: EXP-485: ovary_TCGA-29-1698


title: EXP-485: ovary_TCGA-29-1695


title: EXP-485: ovary_TCGA-25-2408


title: EXP-485: ovary_TCGA-29-1696


title: EXP-485: ovary_TCGA-29-1697


title: EXP-485: ovary_TCGA-29-1690


title: EXP-485: ovary_TCGA-29-1691


title: EXP-485: ovary_TCGA-29-1688


title: EXP-485: ovary_TCGA-25-2404


title: EXP-485: ovary_TCGA-25-2401


title: EXP-485: ovary_TCGA-25-2398


title: EXP-485: ovary_TCGA-25-2392


title: EXP-485: ovary_TCGA-25-2409


title: EXP-485: ovary_TCGA-29-1693


title: EXP-485: ovary_TCGA-25-2399


title: EXP-485: ovary_TCGA-25-2400


title: EXP-485: ovary_TCGA-29-1694


title: EXP-485: ovary_TCGA-25-2397


title: EXP-485: ovary_TCGA-25-2391


title: EXP-485: ovary_TCGA-25-2042


title: EXP-485: ovary_TCGA-25-1877


title: EXP-485: ovary_TCGA-25-1871


title: EXP-485: ovary_TCGA-25-1633


title: EXP-485: ovary_TCGA-25-2393


title: EXP-485: ovary_TCGA-25-1870


title: EXP-485: ovary_TCGA-25-1627


title: EXP-485: ovary_TCGA-25-1631


title: EXP-485: ovary_TCGA-25-1635


title: EXP-485: ovary_TCGA-25-1628


title: EXP-485: ovary_TCGA-25-2396


title: EXP-485: ovary_TCGA-25-1634


title: EXP-485: ovary_TCGA-30-1861


title: EXP-485: ovary_TCGA-31-1944


title: EXP-485: ovary_TCGA-25-1632


title: EXP-485: ovary_TCGA-25-1626


title: EXP-485: ovary_TCGA-25-1329


title: EXP-485: ovary_TCGA-25-1326


title: EXP-485: ovary_TCGA-25-1625


title: EXP-485: ovary_TCGA-25-1328


title: EXP-485: ovary_TCGA-25-1324


title: EXP-485: ovary_TCGA-25-1322


title: EXP-485: ovary_TCGA-25-1323


title: EXP-485: ovary_TCGA-25-1320


title: EXP-485: ovary_TCGA-25-1319


title: EXP-485: ovary_TCGA-25-1325


title: EXP-485: ovary_TCGA-25-1623


title: EXP-485: ovary_TCGA-25-1318


title: EXP-485: ovary_TCGA-24-2295


title: EXP-485: ovary_TCGA-25-1314


title: EXP-485: ovary_TCGA-29-1766

value: PERITONEUM (OVARY)


title: EXP-485: ovary_TCGA-25-1313


title: EXP-485: ovary_TCGA-25-1312


title: EXP-485: ovary_TCGA-24-2297


title: EXP-485: ovary_TCGA-24-2298


title: EXP-485: ovary_TCGA-25-1317


title: EXP-485: ovary_TCGA-25-1316


title: EXP-485: ovary_TCGA-25-1315


title: EXP-485: ovary_TCGA-24-2293


title: EXP-485: ovary_TCGA-25-1321


title: EXP-485: ovary_TCGA-25-1878


title: EXP-485: ovary_TCGA-24-2288


title: EXP-485: ovary_TCGA-24-2289


title: EXP-485: ovary_TCGA-24-2271


title: EXP-485: ovary_TCGA-24-2261


title: EXP-485: ovary_TCGA-24-2267

value: IIB


title: EXP-485: ovary_TCGA-24-2290


title: EXP-485: ovary_TCGA-24-2254


title: EXP-485: ovary_TCGA-24-2260


title: EXP-485: ovary_TCGA-24-2280


title: EXP-485: ovary_TCGA-24-2281

value: IIA


title: EXP-485: ovary_TCGA-24-2262

value: FEMALE


title: EXP-485: ovary_TCGA-24-2036


title: EXP-485: ovary_TCGA-24-2038

value: OVARY

value: GB


title: EXP-485: ovary_TCGA-24-2035

value: IIIC

value: Serous Cystadenocarcinoma


title: EXP-485: ovary_TCGA-24-2026

value: ovary


title: EXP-485: ovary_TCGA-24-2024


title: EXP-485: ovary_TCGA-24-2027


title: EXP-485: ovary_TCGA-24-2023

value: IIIA


title: EXP-485: ovary_TCGA-24-2020


title: EXP-485: ovary_TCGA-24-2019


title: EXP-485: ovary_TCGA-24-1930


title: EXP-485: ovary_TCGA-24-1920


title: EXP-485: ovary_TCGA-24-1923


title: EXP-485: ovary_TCGA-24-1928

value: NOT SPECIFIED


title: EXP-485: ovary_TCGA-24-1850


title: EXP-485: ovary_TCGA-24-2030


title: EXP-485: ovary_TCGA-24-1846


title: EXP-485: ovary_TCGA-24-1924


title: EXP-485: ovary_TCGA-24-2029


title: EXP-485: ovary_TCGA-24-1845


title: EXP-485: ovary_TCGA-24-1849


title: EXP-485: ovary_TCGA-24-2033


title: EXP-485: ovary_TCGA-24-1844


title: EXP-485: ovary_TCGA-24-1847


title: EXP-485: ovary_TCGA-24-1614


title: EXP-485: ovary_TCGA-24-1567


title: EXP-485: ovary_TCGA-24-1604


title: EXP-485: ovary_TCGA-24-1565


title: EXP-485: ovary_TCGA-24-1564


title: EXP-485: ovary_TCGA-24-1616


title: EXP-485: ovary_TCGA-24-1843


title: EXP-485: ovary_TCGA-24-1560


title: EXP-485: ovary_TCGA-24-1842


title: EXP-485: ovary_TCGA-24-1603


title: EXP-485: ovary_TCGA-24-1558


title: EXP-485: ovary_TCGA-24-1563


title: EXP-485: ovary_TCGA-24-1553


title: EXP-485: ovary_TCGA-25-1630


title: EXP-485: ovary_TCGA-24-1549


title: EXP-485: ovary_TCGA-24-1474


title: EXP-485: ovary_TCGA-24-1435


title: EXP-485: ovary_TCGA-24-1436


title: EXP-485: ovary_TCGA-24-1467


title: EXP-485: ovary_TCGA-24-1428


title: EXP-485: ovary_TCGA-24-1562


title: EXP-485: ovary_TCGA-24-1555


title: EXP-485: ovary_TCGA-24-1430


title: EXP-485: ovary_TCGA-24-1550


title: EXP-485: ovary_TCGA-24-1544


title: EXP-485: ovary_TCGA-24-1431


title: EXP-485: ovary_TCGA-24-1548


title: EXP-485: ovary_TCGA-24-1469


title: EXP-485: ovary_TCGA-24-1556


title: EXP-485: ovary_TCGA-24-1463


title: EXP-485: ovary_TCGA-24-1545


title: EXP-485: ovary_TCGA-24-1551


title: EXP-485: ovary_TCGA-24-1470


title: EXP-485: ovary_TCGA-24-1426


title: EXP-485: ovary_TCGA-24-1425


title: EXP-485: ovary_TCGA-24-1464


title: EXP-485: ovary_TCGA-24-1557


title: EXP-485: ovary_TCGA-24-1424


title: EXP-485: ovary_TCGA-24-1546


title: EXP-485: ovary_TCGA-24-1466


title: EXP-485: ovary_TCGA-24-1434


title: EXP-485: ovary_TCGA-24-1423


title: EXP-485: ovary_TCGA-24-1419


title: EXP-485: ovary_TCGA-24-1418


title: EXP-485: ovary_TCGA-24-1417


title: EXP-485: ovary_TCGA-24-1413


title: EXP-485: ovary_TCGA-24-1471


title: EXP-485: ovary_TCGA-24-1422


title: EXP-485: ovary_TCGA-24-1427


title: EXP-485: ovary_TCGA-24-1552


title: EXP-485: ovary_TCGA-24-1105


title: EXP-485: ovary_TCGA-23-2081


title: EXP-485: ovary_TCGA-24-0975


title: EXP-485: ovary_TCGA-24-0980


title: EXP-485: ovary_TCGA-24-0968


title: EXP-485: ovary_TCGA-24-1104


title: EXP-485: ovary_TCGA-24-0981


title: EXP-485: ovary_TCGA-23-2078


title: EXP-485: ovary_TCGA-24-0982


title: EXP-485: ovary_TCGA-23-2079


title: EXP-485: ovary_TCGA-23-2084


title: EXP-485: ovary_TCGA-24-0979


title: EXP-485: ovary_TCGA-23-2077


title: EXP-485: ovary_TCGA-24-0966


title: EXP-485: ovary_TCGA-24-0970


title: EXP-485: ovary_TCGA-23-1809


title: EXP-485: ovary_TCGA-23-2072


title: EXP-485: ovary_TCGA-24-1416


title: EXP-485: ovary_TCGA-23-1120


title: EXP-485: ovary_TCGA-23-1123


title: EXP-485: ovary_TCGA-23-1121


title: EXP-485: ovary_TCGA-23-1122


title: EXP-485: ovary_TCGA-23-1117


title: EXP-485: ovary_TCGA-23-1118


title: EXP-485: ovary_TCGA-23-1116


title: EXP-485: ovary_TCGA-23-1111


title: EXP-485: ovary_TCGA-23-1114


title: EXP-485: ovary_TCGA-24-1103


title: EXP-485: ovary_TCGA-23-1110


title: EXP-485: ovary_TCGA-23-1124


title: EXP-485: ovary_TCGA-23-1113


title: EXP-485: ovary_TCGA-23-1109


title: EXP-485: ovary_TCGA-23-1031


title: EXP-485: ovary_TCGA-23-1032


title: EXP-485: ovary_TCGA-23-1027


title: EXP-485: ovary_TCGA-23-1030


title: EXP-485: ovary_TCGA-23-1107


title: EXP-485: ovary_TCGA-23-1022


title: EXP-485: ovary_TCGA-23-1026


title: EXP-485: ovary_TCGA-23-1021


title: EXP-485: ovary_TCGA-20-1684


title: EXP-485: ovary_TCGA-20-1687


title: EXP-485: ovary_TCGA-20-1685


title: EXP-485: ovary_TCGA-20-0996


title: EXP-485: ovary_TCGA-23-1023


title: EXP-485: ovary_TCGA-23-1028


title: EXP-485: ovary_TCGA-20-0991


title: EXP-485: ovary_TCGA-20-0990


title: EXP-485: ovary_TCGA-20-1686


title: EXP-485: ovary_TCGA-13-1511


title: EXP-485: ovary_TCGA-13-2060


title: EXP-485: ovary_TCGA-20-1683


title: EXP-485: ovary_TCGA-23-1029


title: EXP-485: ovary_TCGA-23-1024


title: EXP-485: ovary_TCGA-20-0987


title: EXP-485: ovary_TCGA-13-1512


title: EXP-485: ovary_TCGA-13-1507


title: EXP-485: ovary_TCGA-13-1509


title: EXP-485: ovary_TCGA-20-1682


title: EXP-485: ovary_TCGA-13-1510


title: EXP-485: ovary_TCGA-23-1119


title: EXP-485: ovary_TCGA-13-1506


title: EXP-485: ovary_TCGA-13-1505


title: EXP-485: ovary_TCGA-13-1504


title: EXP-485: ovary_TCGA-13-1501


title: EXP-485: ovary_TCGA-13-1498


title: EXP-485: ovary_TCGA-13-1494


title: EXP-485: ovary_TCGA-13-1500


title: EXP-485: ovary_TCGA-13-1497


title: EXP-485: ovary_TCGA-13-1495


title: EXP-485: ovary_TCGA-13-1489


title: EXP-485: ovary_TCGA-13-1492


title: EXP-485: ovary_TCGA-13-1487


title: EXP-485: ovary_TCGA-13-1488


title: EXP-485: ovary_TCGA-13-1499


title: EXP-485: ovary_TCGA-13-1491


title: EXP-485: ovary_TCGA-13-1485


title: EXP-485: ovary_TCGA-13-1496


title: EXP-485: ovary_TCGA-13-1483


title: EXP-485: ovary_TCGA-13-1481


title: EXP-485: ovary_TCGA-13-1477


title: EXP-485: ovary_TCGA-13-1479


title: EXP-485: ovary_TCGA-13-1412


title: EXP-485: ovary_TCGA-13-1409


title: EXP-485: ovary_TCGA-13-1411


title: EXP-485: ovary_TCGA-13-1408


title: EXP-485: ovary_TCGA-13-1407


title: EXP-485: ovary_TCGA-13-1484


title: EXP-485: ovary_TCGA-13-1405


title: EXP-485: ovary_TCGA-13-1482


title: EXP-485: ovary_TCGA-13-1403


title: EXP-485: ovary_TCGA-13-0924


title: EXP-485: ovary_TCGA-13-0923


title: EXP-485: ovary_TCGA-13-0912


title: EXP-485: ovary_TCGA-13-0913


title: EXP-485: ovary_TCGA-13-0919


title: EXP-485: ovary_TCGA-13-0904


title: EXP-485: ovary_TCGA-13-0899


title: EXP-485: ovary_TCGA-13-0910


title: EXP-485: ovary_TCGA-13-1404


title: EXP-485: ovary_TCGA-13-0916


title: EXP-485: ovary_TCGA-13-0921


title: EXP-485: ovary_TCGA-13-0908


title: EXP-485: ovary_TCGA-13-0903


title: EXP-485: ovary_TCGA-13-0897


title: EXP-485: ovary_TCGA-13-0901


title: EXP-485: ovary_TCGA-13-0905


title: EXP-485: ovary_TCGA-13-0894


title: EXP-485: ovary_TCGA-13-0920


title: EXP-485: ovary_TCGA-13-0906


title: EXP-485: ovary_TCGA-13-0900


title: EXP-485: ovary_TCGA-13-1410


title: EXP-485: ovary_TCGA-13-0911


title: EXP-485: ovary_TCGA-13-0891


title: EXP-485: ovary_TCGA-13-0884


title: EXP-485: ovary_TCGA-13-0890


title: EXP-485: ovary_TCGA-13-0885


title: EXP-485: ovary_TCGA-13-0893


title: EXP-485: ovary_TCGA-13-0886


title: EXP-485: ovary_TCGA-13-0805


title: EXP-485: ovary_TCGA-13-0883


title: EXP-485: ovary_TCGA-13-0803


title: EXP-485: ovary_TCGA-13-0794


title: EXP-485: ovary_TCGA-13-0801


title: EXP-485: ovary_TCGA-13-0795


title: EXP-485: ovary_TCGA-13-0888


title: EXP-485: ovary_TCGA-13-0807


title: EXP-485: ovary_TCGA-13-0791


title: EXP-485: ovary_TCGA-13-0792


title: EXP-485: ovary_TCGA-13-0797


title: EXP-485: ovary_TCGA-13-0762


title: EXP-485: ovary_TCGA-13-0768


title: EXP-485: ovary_TCGA-13-0765


title: EXP-485: ovary_TCGA-13-0804


title: EXP-485: ovary_TCGA-13-0793


title: EXP-485: ovary_TCGA-13-0799


title: EXP-485: ovary_TCGA-13-0889


title: EXP-485: ovary_TCGA-13-0800


title: EXP-485: ovary_TCGA-13-0766


title: EXP-485: ovary_TCGA-13-0802


title: EXP-485: ovary_TCGA-13-0760


title: EXP-485: ovary_TCGA-13-0764


title: EXP-485: ovary_TCGA-13-0761


title: EXP-485: ovary_TCGA-13-0751


title: EXP-485: ovary_TCGA-13-0755


title: EXP-485: ovary_TCGA-13-0758


title: EXP-485: ovary_TCGA-13-0757


title: EXP-485: ovary_TCGA-13-0726


title: EXP-485: ovary_TCGA-13-0730


title: EXP-485: ovary_TCGA-13-0723


title: EXP-485: ovary_TCGA-10-0938


title: EXP-485: ovary_TCGA-13-0725


title: EXP-485: ovary_TCGA-13-0724


title: EXP-485: ovary_TCGA-13-0717


title: EXP-485: ovary_TCGA-13-0720


title: EXP-485: ovary_TCGA-10-0934


title: EXP-485: ovary_TCGA-10-0935


title: EXP-485: ovary_TCGA-10-0937


title: EXP-485: ovary_TCGA-10-0936


title: EXP-485: ovary_TCGA-13-0727


title: EXP-485: ovary_TCGA-10-0933


title: EXP-485: ovary_TCGA-10-0927


title: EXP-485: ovary_TCGA-10-0930


title: EXP-485: ovary_TCGA-10-0928


title: EXP-485: ovary_TCGA-09-2055

value: IC


title: EXP-485: ovary_TCGA-13-0714


title: EXP-485: ovary_TCGA-10-0925


title: EXP-485: ovary_TCGA-09-2050


title: EXP-485: ovary_TCGA-09-2056


title: EXP-485: ovary_TCGA-13-0887


title: EXP-485: ovary_TCGA-10-0931


title: EXP-485: ovary_TCGA-09-2049


title: EXP-485: ovary_TCGA-09-2045


title: EXP-485: ovary_TCGA-09-2054


title: EXP-485: ovary_TCGA-10-0926


title: EXP-485: ovary_TCGA-09-2043


title: EXP-485: ovary_TCGA-09-1670


title: EXP-485: ovary_TCGA-09-1675


title: EXP-485: ovary_TCGA-09-2051


title: EXP-485: ovary_TCGA-09-2044


title: EXP-485: ovary_TCGA-09-2053


title: EXP-485: ovary_TCGA-09-2048


title: EXP-485: ovary_TCGA-09-1666


title: EXP-485: ovary_TCGA-09-1674


title: EXP-485: ovary_TCGA-09-1673


title: EXP-485: ovary_TCGA-09-1661


title: EXP-485: ovary_TCGA-09-1668


title: EXP-485: ovary_TCGA-09-1662


title: EXP-485: ovary_TCGA-09-1665


title: EXP-485: ovary_TCGA-09-1664


title: EXP-485: ovary_TCGA-09-0369


title: EXP-485: ovary_TCGA-09-1659


title: EXP-485: ovary_TCGA-09-1669


title: EXP-485: ovary_TCGA-09-0367


title: EXP-485: ovary_TCGA-09-1667


title: EXP-485: ovary_TCGA-09-0366


title: EXP-485: ovary_TCGA-04-1655


title: EXP-485: ovary_TCGA-09-0365


title: EXP-485: ovary_TCGA-04-1646


title: EXP-485: ovary_TCGA-04-1542


title: EXP-485: ovary_TCGA-04-1648


title: EXP-485: ovary_TCGA-04-1654


title: EXP-485: ovary_TCGA-04-1514


title: EXP-485: ovary_TCGA-04-1530


title: EXP-485: ovary_TCGA-04-1517


title: EXP-485: ovary_TCGA-04-1638


title: EXP-485: ovary_TCGA-04-1536


title: EXP-485: ovary_TCGA-04-1649


title: EXP-485: ovary_TCGA-04-1367


title: EXP-485: ovary_TCGA-09-0364


title: EXP-485: ovary_TCGA-04-1351


title: EXP-485: ovary_TCGA-04-1360

value: IA


title: EXP-485: ovary_TCGA-04-1525


title: EXP-485: ovary_TCGA-04-1652


title: EXP-485: ovary_TCGA-04-1371


title: EXP-485: ovary_TCGA-04-1357


title: EXP-485: ovary_TCGA-04-1651


title: EXP-485: ovary_TCGA-04-1350


title: EXP-485: ovary_TCGA-04-1364


title: EXP-485: ovary_TCGA-04-1349


title: EXP-485: ovary_TCGA-09-1672


title: EXP-485: Cell_TCGA-07-0249

source_name: cell


title: EXP-485: ovary_TCGA-04-1365


title: EXP-485: ovary_TCGA-04-1519


title: EXP-485: ovary_TCGA-04-1348


title: EXP-485: ovary_TCGA-04-1361


title: EXP-485: ovary_TCGA-04-1335

value: IB


title: EXP-485: ovary_TCGA-04-1362

value: IIC


title: EXP-485: ovary_TCGA-04-1356


title: EXP-485: ovary_TCGA-04-1338


title: EXP-485: ovary_TCGA-04-1336

value: IIIB


title: EXP-485: ovary_TCGA-04-1347

value: IV


title: EXP-485: ovary_TCGA-04-1346


title: EXP-485: ovary_TCGA-04-1332


title: EXP-485: ovary_TCGA-04-1343


title: EXP-485: ovary_TCGA-04-1342


title: EXP-485: ovary_TCGA-04-1337


title: EXP-485: ovary_TCGA-01-0628

value: many


title: EXP-485: ovary_TCGA-01-0638


title: EXP-485: ovary_TCGA-01-0637


title: EXP-485: ovary_TCGA-04-1341


title: EXP-485: ovary_TCGA-01-0633


title: EXP-485: ovary_TCGA-01-0639


title: EXP-485: ovary_TCGA-01-0636


title: EXP-485: ovary_TCGA-01-0642


title: EXP-485: ovary_TCGA-01-0629


title: cbt, RNAi flies, ZT15

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were imported to Affymetrix Expression Console program, and data were normalized using Robust Multichips Analysis. Differential expression was tested for probes that had expression levels above 4.0 (log2 scale)  in at least one group (mutants or WT). All other probes were excluded from the analysis.

organism: Drosophila melanogaster

source_name: cbt, RNAi flies, ZT15

label_protocol: RNA was then used to prepare a probe that was hybridized to Drosophila 2.0 gene expression arrays (Affymetrix) according to the manufacturer's protocol.

growth_protocol: Flies were entrained in LD (light: dark) condition for 3-4 days and harvested at two time points: ZT3 and  ZT15.

extract_protocol: Total RNA was prepared (30 heads per sample) using Trizol reagent (Invitrogen) according to the manufacturer's protocol.

value: fly heads

tag: treatment

value: cbt RNAi


title: control flies, ZT3

source_name: control flies, ZT3

value: control


title: cbt over-expression flies, ZT3

source_name: cbt over-expression flies, ZT3

value: cbt over-expression


title: EXP-485: ovary_TCGA-04-1331

value: FEMALE

value: OVARY


title: cbt RNAi flies, ZT3

source_name: cbt RNAi flies, ZT3


title: EXP-485: ovary_TCGA-01-0630


title: EXP-485: ovary_TCGA-01-0631


title: cbt over-expression flies, ZT15

source_name: cbt over-expression flies, ZT15


title: Neurologically healthy control 02

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

hyb_protocol: 12.5µg of cRNA molecules were heat fragmented and applied to the Human U133 Plus 2.0 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data were normalised using puma package (PMID:  23379655). Puma quantifies uncertainty to improve estimation of transcript expression values.

source_name: control_motor neurons

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol:
staining protocol: 10 um cervical spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
isolation protocol: From each individual 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: subject id

tag: patient group

value: Neurologically healthy, non-disease control

value: Laser captured motor neurons


title: control flies, ZT15

source_name: control flies, ZT15


title: Neurologically healthy control 03


title: ALS with C9ORF72 mutation 01

source_name: ALS with C9ORF72 mutation_motor neurons

value: ALS due to mutated C9ORF72


title: Neurologically healthy control 01


title: dOB (OL)

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 100μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. Gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuGene-1_0-st-v1.r3.pgf
meta-probeset file: HuGene-1_0-st-v1.r3.mps

source_name: cultivation cell

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Each cells were cultured at 37℃ in a humid atmosphere with 5% CO2.

extract_protocol: Total RNA were extracted using ISOGENII

treatment_protocol: Not applicable.

tag: cell type

value: dOB (osteoblasts)


title: ALS with C9ORF72 mutation 06

tag: tissue


title: ALS with C9ORF72 mutation 08


title: HEK293T_pLEX-MCS_Truncated FMRP

city: Fuzhou

first: Xianguo

last: Fu

address: Xihuanbei Road

department: Department of Clinical Genetics and Experimental Medicine

institute: Fuzhou General Hospital

description: stable over-expression of truncated FMRP

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: stably transfected HEK 293T cells of  the over-expression of truncated FMRP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: HEK 293T cells were maintained in DMEM/F12 (1:1) medium containing 10% fetal bovine serum. All cells were cultured at 37 °C in an incubator containing 5% CO2.

extract_protocol: Total RNA were isolated from stably transfected HEK293T cells with TRIzol (Invitrogen, Carlsbad, CA), and then followed by a DNase I treatment.

treatment_protocol: Two transfections of pLEX-MCS lentiviral empty vector and pLEX-MCS lentiviral vector with the truncated FMRP were constructed. Transfections were performed with Polyethylenimine for the lentiviral pLEX-MCS vector transfection. For stable transfection, at 24h post transfection, the transiently transfected cells were cultured in DMEM/F12 (1:1) medium containing puromycin for about 2 weeks. Two stable transfectants of empty vector ( pLEX-MCS), pLEX-MCS containing truncated FMR1 (pLEX-MCS-△FMR1) were generated and maintained in culture for further studies.

tag: cell line


title: ALS with C9ORF72 mutation 04


title: HCC1937, replicate 2

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.0.

source_name: HCC1937, replicate 2

label_protocol: One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol.

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA) was used for RNA isolation from cell lines, according to manufacturer’s protocol

treatment_protocol: 10 µM COH29 for 24 h

tag: brca1 expression

value: BRCA1 deficient


title: HCC1937BRCA1, replicate 2

source_name: HCC1937BRCA1, replicate 2

value: WT BRCA1


title: ALS with C9ORF72 mutation 03


title: HCC1937, replicate 1

source_name: HCC1937, replicate 1


title: ALS with C9ORF72 mutation 05


title: HEK293T_pLEX-MCS_Empty Vector

description: stable expression of empty vector

source_name: stably transfected HEK 293T cells of empty lentiviral vector (pLEX-MCS)


title: ALS with C9ORF72 mutation 02


title: HCC1937BRCA1-COH29, replicate 2

source_name: HCC1937BRCA1-COH29, replicate 2


title: ALS with C9ORF72 mutation 07


title: ALS with C9ORF72 mutation 29

description: Lymphoblastoid cells derived from individual with mutated C9ORF72

hyb_protocol: 6-10µg of cRNA molecules were heat fragmented and applied to the Human Exon 1.0ST GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

data_processing:
Data were normalised using puma package (PMID:  23379655).  Puma quantifies uncertainty to improve estimation of transcript expression values. A custom cdf (HuexonSpecificGeneProbes.tsv) and annotation file (ranscripts-human-annotation.R.gz) were obtained through GATExplorer.
The 'transcripts-human-annotation.R.gz' annotation file (http://bioinfow.dep.usal.es/xgate/downloads_v57/transcripts-human-annotation.R.gz) was downloaded from http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=annotationfiles

source_name: ALS with C9ORF72 mutation

extract_protocol: RNA was extracted from approximately 5x10^6 lymphoblasotoid cells using the Qiagen RNeasy Mini Kit (Qiagen).

value: ALS due to mtC9ORF72

value: Cultured lymphoblastoid cells


title: ALS with C9ORF72 mutation 30


title: ALS with C9ORF72 mutation 28


title: ALS without C9ORF72 mutation 21

description: Lymphoblastoid cells derived from individual without mutated C9ORF72

source_name: ALS without C9ORF72 mutation

value: ALS not due to mtC9ORF72


title: ALS without C9ORF72 mutation 23


title: ALS without C9ORF72 mutation 22


title: ALS with C9ORF72 mutation 27


title: ALS with C9ORF72 mutation 25


title: ALS with C9ORF72 mutation 26


title: ALS with C9ORF72 mutation 31


title: HCC1937BRCA1-COH29, replicate 1

source_name: HCC1937BRCA1-COH29, replicate 1


title: ALS with C9ORF72 mutation 23


title: ALS with C9ORF72 mutation 24


title: HCC1937BRCA1, replicate 1

source_name: HCC1937BRCA1, replicate 1


title: dOB (RXOL)


title: ALS with C9ORF72 mutation 20


title: ALS without C9ORF72 mutation 16


title: MSC

value: mesenchymal stem cells (MSC)


title: Hs578T 0nmoles/l FA rep4

city: Southampton

first: Graham

middle: C

last: Burdge

address: IDS Building (Mailpoint 887), Southampton General Hospital, Tremona Road

department: Human Development and Health

institute: University of Southampton

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quintile normalisation with Illumina BeadStudio

source_name: Breast cancer cell line

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

growth_protocol: All cell lines were cultured at 37oC in an atmosphere containing 5% (v/v) CO2, in Dulbecco’s Modified Eagle Medium without FA (Sigma), supplemented with 10% (v/v) fetal bovine serum (FBS), 2mM glutamine, 10U/ml penicillin and 100µg/ml streptomycin. The media for the MCF10a cell line was further supplemented with 20ng/ml epidermal growth factor and 100µg/ml hydrocortisone.

extract_protocol: Total RNA was extracted using TRI reagent (Sigma), followed by clean-up with RNeasy MinElute Cleanup kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

treatment_protocol: Cultures were treated with 0 or 100 nmoles/l folic acid for 72 hours (n=6 replicates/treatment). Background folate concentration derived from FBS in the medium was 1.5 nmoles/l.

tag: folic acid

value: 0 nmoles/l


title: ALS without C9ORF72 mutation 15


title: ALS without C9ORF72 mutation 17


title: Osteoblasts

value: osteoblasts (OB)


title: ALS with C9ORF72 mutation 22


title: Gingival fibroblasts

value: gingival fibroblasts


title: Hs578T 0nmoles/l FA rep5


title: ALS with C9ORF72 mutation 19


title: MSC-OB

value: mesenchymal stem cells (MSC)-osteoblast (OB)


title: HCC1937-COH29, replicate 1

source_name: HCC1937-COH29, replicate 1


title: ALS with C9ORF72 mutation 16


title: ALS without C9ORF72 mutation 20


title: ALS with C9ORF72 mutation 17


title: ALS without C9ORF72 mutation 18


title: ALS without C9ORF72 mutation 13


title: MCF7 0nmoles/l FA rep6


title: ALS with C9ORF72 mutation 21


title: ALS without C9ORF72 mutation 19


title: ALS without C9ORF72 mutation 14


title: ALS without C9ORF72 mutation 11


title: ALS without C9ORF72 mutation 12


title: ALS with C9ORF72 mutation 18


title: ALS with C9ORF72 mutation 15


title: ALS without C9ORF72 mutation 10


title: HCC1937-COH29, replicate 2

source_name: HCC1937-COH29, replicate 2


title: ALS with C9ORF72 mutation 14


title: ALS without C9ORF72 mutation 09


title: MCF10a 100nmoles/l FA rep6

value: 100 nmoles/l


title: Hs578T 100nmoles/l FA rep4


title: MCF10a 100nmoles/l FA rep3


title: MCF7 0nmoles/l FA rep3


title: ALS without C9ORF72 mutation 08


title: ALS with C9ORF72 mutation 12


title: MCF7 0nmoles/l FA rep2


title: ALS with C9ORF72 mutation 07


title: ALS without C9ORF72 mutation 06


title: ALS with C9ORF72 mutation 13


title: ALS with C9ORF72 mutation 06


title: ALS with C9ORF72 mutation 09


title: Hs578T 0nmoles/l FA rep6


title: ALS with C9ORF72 mutation 10


title: ALS with C9ORF72 mutation 08


title: ALS with C9ORF72 mutation 11


title: ALS with C9ORF72 mutation 05


title: ALS with C9ORF72 mutation 04


title: ALS without C9ORF72 mutation 05


title: Hs578T 0nmoles/l FA rep3


title: MCF10a 0nmoles/l FA rep3


title: Hs578T 0nmoles/l FA rep2


title: ALS without C9ORF72 mutation 07


title: MCF7 100nmoles/l FA rep4


title: MCF10a 100nmoles/l FA rep1


title: Neurologically healthy control 07

description: Lymphoblastoid cells derived from non disease individuals

source_name: Neurologically healthy control

value: Control


title: MCF7 0nmoles/l FA rep5


title: ALS with C9ORF72 mutation 02


title: Neurologically healthy control 08


title: ALS without C9ORF72 mutation 01


title: ALS without C9ORF72 mutation 02


title: MCF10a 0nmoles/l FA rep5


title: MCF7 100nmoles/l FA rep1


title: Neurologically healthy control 09


title: ALS with C9ORF72 mutation 01


title: Neurologically healthy control 13


title: MCF7 100nmoles/l FA rep6


title: ALS without C9ORF72 mutation 03


title: Neurologically healthy control 06


title: Neurologically healthy control 15


title: MCF10a 100nmoles/l FA rep2


title: Hs578T 100nmoles/l FA rep3


title: Neurologically healthy control 14


title: ALS without C9ORF72 mutation 04


title: Neurologically healthy control 05


title: ALS with C9ORF72 mutation 03


title: MCF7 0nmoles/l FA rep4


title: Neurologically healthy control 11


title: Hs578T 100nmoles/l FA rep1


title: Neurologically healthy control 04


title: Neurologically healthy control 12


title: Neurologically healthy control 10


title: Neurologically healthy control 03


title: Neurologically healthy control 02


title: GT10 vs GT21_cy5_Biorep 3

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

institute: Agriculture & Agri-Food Canada (AAFC)

description:
Biological replicate 3 of 3
GT10_5_BR3

hyb_protocol: Two-colour hybridizations were performed using the samples from all cold treatments as “test” samples and the N33 room temperature sample as the “reference”. Dye-flip hybridizations were performed for each sample combination with three biological replicates for a total of 42 hybridizations. The labelled probes were combined with a solution containing 2 μl of calf thymus ss-DNA (10mg/ml, Sigma), 2 μl Yeast tRNA (10mg/ml, Invitrogen) and 61 μl of DIG easy hybridization buffer (Roche),  denatured at 70°C for 2 minutes and hybridized with the arrays at 37°C for 8-18 hrs. Following incubation, the arrays were washed three times at 50°C for 15 min in 1X SSC-0.1% SDS, rinsed in 1x SSC and spun 5 min (1000 rpm) at room temperature.

scan_protocol: The slides were scanned sequentially at 532 and 635 nm using a Genepix 4200A microarray scanner (Molecular Devices, Sunnyvale, CA). Features were aligned in Genepix Pro 6.0 using the Irregular Features Spot Finder application and local background subtraction. Low quality features were flagged and filtered from further analysis. The raw data files were named using strain abbreviation, hybridization time date and slide number (i.e. MrN33-080326-13723296.gpr). The complete set of data for the N33 gene expression microarray experiment is available on the GEO.

data_processing: Features were aligned in Genepix Pro 6.0 using the Irregular Features Spot Finder application and local background subtraction. Low quality features were flagged and filtered from further analysis. The raw data files were named using strain abbreviation, hybridization time date and slide number (i.e. MrN33-080326-13723296.gpr). Arrays were imported into Acuity 4 (Molecular Devices, Sunnyvale, CA Axon Instruments Inc.) for data normalization and analysis. The arrays were re-named by test treatment, test dye and biological replicate (i.e. B_3_BR1). LOWESS normalization was applied to each array. Data filtering steps were performed by removing features flagged in Genepix as low quality, removing spike-in controls and ribosomal RNA clones and removing negative control features. Furthermore, we removed substances with “LOWESS A” intensities ≤8 in at least 32 of the arrays (75%). As well, substances were removed from the dataset if they were not present in at least 80% of the arrays. Data processing and filtering resulted in the removal of low intensity features and the preservation of the strong signal subsets. The data type was changed to Lowess M log2 ratio. After subtraction and the filtering steps, 4603 substances remained in the dataset. Pearson centered hierarchical clustering analysis was carried out on the dataset and supported strong reproducibility of the technical and biological replicates across all treatments

organism: Mesorhizobium sp. N33

source_name: GT10=test sample cells grown at 10°C

label_protocol: cDNA synthesis, labelling, purification and hybridization were performed based on a protocol from The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute) (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M007.pdf). Labelled probes were quantified on the NanoDrop ND-1000 Spectrophotometer and yields were calculated in picomoles of cDNA synthesized and Cy-dye incorporation. The labelled cDNA was dried in a vacuum centrifuge with medium heat for 45-60 min and stored at 4°C in the dark. Human clones (~300bp in length), purchased from Michigan State University were used as internal spike-in controls for hybridization.

growth_protocol: Mesorhizobium sp. strain N33 was grown in 100 ml of yeast mannitol broth (YMB) media at 150 rpm at room temperature (~21°C) to mid-log phase (OD600= 0.4-0.6). The purity of colonies was checked by cultivation on yeast extract mannitol agar (YMA) supplemented with 200 μg ml-1 streptomycin and 25 μg ml-1 Congo red. Subsequent purity tests of the strain were followed by performing a nodulation test on Onobrychis viciifolia (sainfoin), and by 16S-rDNA sequencing.

extract_protocol: After each treatment, before harvest of cells, transcription activity was halted by adding a stop solution. The samples were immediately centrifuged (10,000 g) at 4°C for 5 minutes. The pellets were washed once with cold TES buffer (100 mM NaCl, 1 mM EDTA, 10 mM Tris hydrochloride [pH 7.4]), re-centrifuged, and cells frozen in liquid nitrogen and stored at -85°C. Total RNA was purified using the Epicenter Kit (Cat. #MC89010) according to the manufacturer's protocol with additional modifications: i) Small RNAs, proteins, carbohydrates, and DNA were precipitated with 5M LiCl (Ambion). ii) DNA was also removed from RNA samples using DNase I (Ambion). Lack of DNA contamination of RNA samples was verified by standard PCR using one pair of primers from the OrfZ gene of strain N33. RNA concentration was determined using the NanoDrop ND-1000 Spectrophotometer at 260 nm. RNA purity and integrity were assessed by electrophoresis on a density gradient 1% agarose/formaldehyde gel and using the Experion automated electrophoresis system (Biorad).

treatment_protocol: The N33 cells were grown in YMB medium at three steady state temperature conditions (GT21°C= room temperature [21°C] as control, GT4= growth at 4°C in water bath, and GT10= growth at 10°C), and also the room temperature grown cells were downshifted for various times (T1= 2 min, T2= 4 min, T3= 8 min, T4= 60 min, T5= 240 min) at 4°C in water bath under constant agitation. A total of 8 conditions with 3 biological replicates were screened in this experiment. The pellets were collected at mid-log phase (OD600=0.4-0.6) for RNA purification, cDNA synthesis and labelling.

tag: sample type

value: GT10=test sample cells grown at 10°C

source_name: GT21= reference cells grown at 21°C

value: GT21= reference cells grown at 21°C


title: GT10 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
GT10_3_BR3


title: Neurologically healthy control 01


title: GT10 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
GT10_5_BR2


title: GT10 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
GT10_5_BR1


title: T5 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
T5_5_BR1

source_name: T5=test sample cells, grown at 21°C, then cold shock at 4°C for 4 hours


title: T5 vs GT21_cy5_Biorep 3

description:
Biological replicate 3 of 3
T5_5_BR3

value: T5=test sample cells, grown at 21°C, then cold shock at 4°C for 4 hours


title: T5 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
T5_5_BR2


title: MCF7 100nmoles/l FA rep3


title: GT10 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
GT10_3_BR1


title: T4 vs GT21_cy5_Biorep 3

description:
Biological replicate 3 of 3
T4_5_BR3

source_name: T4=test sample cells, grown at 21°C, then cold shock at 4°C for 1 hour


title: T5 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
T5_3_BR1


title: T5 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
T5_3_BR2


title: T5 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
T5_3_BR3


title: MCF7 0nmoles/l FA rep1


title: MCF10a 0nmoles/l FA rep2


title: MCF10a 100nmoles/l FA rep4


title: Hs578T 0nmoles/l FA rep1


title: MCF10a 0nmoles/l FA rep6


title: Hs578T 100nmoles/l FA rep2


title: T4 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
T4_5_BR2

value: T4=test sample cells, grown at 21°C, then cold shock at 4°C for 1 hour


title: Hs578T 100nmoles/l FA rep6


title: MCF10a 0nmoles/l FA rep4


title: MCF7 100nmoles/l FA rep2


title: MCF10a 0nmoles/l FA rep1


title: Hs578T 100nmoles/l FA rep5


title: T4 vs GT21_cy3_Biorep 2

description:
Biological replicate 2 of 3.
T4_3_BR2


title: T4 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
T4_3_BR3


title: T4 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
T4_5_BR1


title: T4 vs GT21_cy3_Biorep 1

description:
Biological replicate 1 of 3.
T4_3_BR1


title: T3 vs GT21_cy5_Biorep 3

description:
Biological replicate 3 of 3
T3_5_BR3

source_name: T3=test sample cells, grown at 21°C, then cold shock at 4°C for 8 minutes


title: T3 vs GT21_cy5_Biorep 2

description:
Biological replicate 2 of 3.
T3_5_BR2

value: T3=test sample cells, grown at 21°C, then cold shock at 4°C for 8 minutes


title: T3 vs GT21_cy5_Biorep 1

description:
Biological replicate 1 of 3.
T3_5_BR1


title: MCF10a 100nmoles/l FA rep5


title: T3 vs GT21_cy3_Biorep 3

description:
Biological replicate 3 of 3
T3_3_BR3