title: wildtype

status: Public on Mar 31 2015

type: RNA

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

country: USA

institute: Huntsman Cancer Institute

description:
6370X1; 6371X1; 6372X1
YBC1894 sample

hyb_protocol: Total RNA samples were fragmented and combined with Agilent Hi-RPM GE Hybridization kit (cat#5190-0403) reagents. These samples were hybridized to the array slides at 65C for 17 hr. The slides were washed in 6x SSPE, 0.005% N-lauroylsarcosine for one min at room temperature and in 0.06x SSPE, 0.005% N-lauroylsarcosine for 1 min at 31C. The slides were then incubated with 0.025mg/mL primary monoclonal mouse anti-RNA DNA hybrid antibody available in a hybridoma cell line from ATCC (HB-8730). This was diluted in 500uL of SB+BSA (100mM MES, pH 6.6, 1M NaCl, 0.05% Tween 20, and 1 mg/mL BSA). The 60 min incubation was at 25C. After this incubation the slides were washed four times for three min in NSWB (6xSSPE, 0.01% Tween 20). The secondary Cy3-labeled goat anti-mouse antibody (KPL, cat#078-18-061) was used at a concentration of 3ug/mL in 500uL of SB+BSA. The slides were incubated with the secondary antibody for 60 min at 25C. Finally the slides are washed four times for three min in NSWB at room temperature.

scan_protocol: Arrays were scanned in an Agilent G2505B Microarray Scanner using extended dynamic range software. Feature extraction of the scanned images was performed using Agilent Feature Extraction Software Version 9.5.1.

data_processing:
Raw feature intensities from three replicates were quantile normalized, median scaled to the mean value of the zebra fish non-hybridizing sequence probes which themselves were scaled to 1, and the combined expression values converted to log2 values.  Probe sequences were mapped to Saccharoymyces cerevisisiae genome release 64 (UCSC sacCer3) and were then associated with the corresponding processed feature score. Processing was done with the BioToolBox (http://code.google.com/p/biotoolbox) programs process_microarray and map_oligo_data2gff.
Quantile normalized log2 values representing absolute expression relative to the mean signal of non-hybridizing zebra fish sequence probes.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: wildtype

growth_protocol: Cells were grown in standard synthetic complete media with 2% glucose at 30C until an optical density at 600 nm of 0.8. Harvested cells were frozen in liquid nitrogen and stored at -80C until ready for processing.

extract_protocol: Cell pellets were pulverized in liquid nitrogen. Approximately 30 mg of lysed cell material was used with the Ambion Mirvana RNA isolation kit following the manufacturer's protocol to isolate total RNA.

tag: strain

tag: genotype/variation

value: wildtype


title: isw1 null rsc1 null rsc2ts

description:
6370X5; 6371X5; 6372X5
YBC3227 sample

source_name: isw1 null rsc1 null rsc2ts

value: isw1 null rsc1 null rsc2ts


title: rsc1 null rsc2ts

description:
6370X2; 6371X2; 6372X2
YBC1111 sample

source_name: rsc1 null rsc2ts

value: rsc1 null rsc2ts


title: Italian_Breast_Cancer_Sample_86 [gene]

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Raw gene expression data were log2 transformed and normalized using Robust Spline Normalization (RSN) from lumi package.

label: biotin

organism: Homo sapiens

source_name: Italian breast cancer sample

label_protocol: Biotinylated cRNA was prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) and treated with RNase-free DNase to remove genomic DNA traces using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: tissue

value: breast tumor

tag: age (years)

tag: gender

value: female

tag: nationality

value: Italy

tag: grade

value: II

tag: size (cm)

tag: lymph node status

tag: er status

tag: pgr status

tag: erbb2 status

tag: er status gene

tag: erbb2 status gene

tag: pam50 subtype

value: luminal-A

tag: ecm1/3 subtype


title: Italian_Breast_Cancer_Sample_94 [gene]

value: III

value: basal


title: Italian_Breast_Cancer_Sample_95 [gene]

value: luminal-B

value: undetermined


title: Italian_Breast_Cancer_Sample_93 [gene]


title: ioc3 null rsc1 null rsc2ts

description:
6370X6; 6371X6; 6372X6
YBC3228 sample

source_name: ioc3 null rsc1 null rsc2ts

value: ioc3 null rsc1 null rsc2ts


title: Italian_Breast_Cancer_Sample_96 [gene]


title: Italian_Breast_Cancer_Sample_87 [gene]


title: ioc3 null

description:
6370X4; 6371X4; 6372X4
YBC2693 sample

source_name: ioc3 null

value: ioc3 null


title: Italian_Breast_Cancer_Sample_90 [gene]


title: Italian_Breast_Cancer_Sample_97 [gene]


title: Italian_Breast_Cancer_Sample_91 [gene]


title: isw1 null

description:
6370X3; 6371X3; 6372X3
YBC1416 sample

source_name: isw1 null

value: isw1 null


title: Italian_Breast_Cancer_Sample_92 [gene]


title: Italian_Breast_Cancer_Sample_88 [gene]


title: Italian_Breast_Cancer_Sample_89 [gene]


title: Italian_Breast_Cancer_Sample_84 [gene]


title: Italian_Breast_Cancer_Sample_85 [gene]


title: Italian_Breast_Cancer_Sample_82 [gene]


title: Italian_Breast_Cancer_Sample_83 [gene]


title: Italian_Breast_Cancer_Sample_81 [gene]


title: Italian_Breast_Cancer_Sample_77 [gene]


title: Italian_Breast_Cancer_Sample_69 [gene]


title: Italian_Breast_Cancer_Sample_80 [gene]


title: Italian_Breast_Cancer_Sample_78 [gene]


title: Italian_Breast_Cancer_Sample_71 [gene]


title: Italian_Breast_Cancer_Sample_75 [gene]


title: Italian_Breast_Cancer_Sample_79 [gene]


title: Italian_Breast_Cancer_Sample_74 [gene]


title: Italian_Breast_Cancer_Sample_62 [gene]


title: Italian_Breast_Cancer_Sample_64 [gene]


title: Italian_Breast_Cancer_Sample_70 [gene]


title: Italian_Breast_Cancer_Sample_66 [gene]


title: Italian_Breast_Cancer_Sample_68 [gene]


title: Italian_Breast_Cancer_Sample_72 [gene]


title: Italian_Breast_Cancer_Sample_58 [gene]


title: Italian_Breast_Cancer_Sample_73 [gene]


title: NS4

city: Wuhan

first: Rong

last: Jia

address: 237 Luoyu Rd

country: China

institute: Wuhan University

description: SAMPLE 6

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed, slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon)

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files were generated after normalization.

source_name: Cal27 cells treated with NS siRNA

label_protocol: For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline (NimbleGen Systems, Inc., Madison, WI, USA).

growth_protocol: Cal27 cells were cultured in Dulbecco's modified Eagle medium (DMEM; HyClone, USA) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic (Gibco, USA)

extract_protocol: Total RNA were collected by Trizol (Invitrogen, USA) according to the manufacture’s instructions

treatment_protocol: Cells were treated with 10nM hnRNP A1 or non-specific (NS) siRNA twice in a 48-hour interval in the presence of Lipofentamine 2000 (Invitrogen, USA) according to the manufacture’s instructions.

tag: cell line

tag: cell type

value: oral squamous cell carcinoma

tag: treated with

value: non-specific (NS) siRNA


title: Italian_Breast_Cancer_Sample_76 [gene]

tag: tissue


title: Italian_Breast_Cancer_Sample_65 [gene]

tag: age (years)


title: Italian_Breast_Cancer_Sample_61 [gene]

tag: gender


title: Italian_Breast_Cancer_Sample_67 [gene]

tag: nationality


title: Italian_Breast_Cancer_Sample_63 [gene]

tag: grade


title: Italian_Breast_Cancer_Sample_57 [gene]

tag: size (cm)


title: Italian_Breast_Cancer_Sample_59 [gene]

tag: lymph node status


title: Italian_Breast_Cancer_Sample_60 [gene]

tag: er status


title: Italian_Breast_Cancer_Sample_55 [gene]

tag: pgr status


title: A3

description: SAMPLE 2

source_name: Cal27 cells treated with hnRNP A1 siRNA

value: hnRNP A1 siRNA


title: A2

description: SAMPLE 1


title: Italian_Breast_Cancer_Sample_47 [gene]

tag: erbb2 status


title: Italian_Breast_Cancer_Sample_51 [gene]

tag: er status gene


title: Italian_Breast_Cancer_Sample_49 [gene]

tag: erbb2 status gene


title: Italian_Breast_Cancer_Sample_53 [gene]

tag: pam50 subtype


title: A5

description: SAMPLE 3


title: NS2

description: SAMPLE 4


title: Italian_Breast_Cancer_Sample_56 [gene]

tag: ecm1/3 subtype


title: Italian_Breast_Cancer_Sample_54 [gene]


title: Italian_Breast_Cancer_Sample_52 [gene]


title: NS3

description: SAMPLE 5

tag: cell line


title: Italian_Breast_Cancer_Sample_39 [gene]


title: Italian_Breast_Cancer_Sample_41 [gene]


title: Italian_Breast_Cancer_Sample_43 [gene]


title: Italian_Breast_Cancer_Sample_45 [gene]


title: Italian_Breast_Cancer_Sample_33 [gene]


title: Italian_Breast_Cancer_Sample_38 [gene]


title: Italian_Breast_Cancer_Sample_37 [gene]


title: Italian_Breast_Cancer_Sample_48 [gene]


title: Italian_Breast_Cancer_Sample_46 [gene]


title: Italian_Breast_Cancer_Sample_50 [gene]


title: Italian_Breast_Cancer_Sample_31 [gene]


title: Italian_Breast_Cancer_Sample_44 [gene]


title: Italian_Breast_Cancer_Sample_35 [gene]


title: Italian_Breast_Cancer_Sample_32 [gene]


title: Italian_Breast_Cancer_Sample_30 [gene]


title: Italian_Breast_Cancer_Sample_34 [gene]


title: Italian_Breast_Cancer_Sample_40 [gene]


title: Italian_Breast_Cancer_Sample_42 [gene]


title: Italian_Breast_Cancer_Sample_36 [gene]


title: Italian_Breast_Cancer_Sample_24 [gene]


title: Italian_Breast_Cancer_Sample_26 [gene]


title: Italian_Breast_Cancer_Sample_22 [gene]


title: Italian_Breast_Cancer_Sample_19 [gene]


title: Italian_Breast_Cancer_Sample_29 [gene]


title: Italian_Breast_Cancer_Sample_27 [gene]


title: Italian_Breast_Cancer_Sample_20 [gene]


title: Italian_Breast_Cancer_Sample_28 [gene]


title: Italian_Breast_Cancer_Sample_21 [gene]


title: Italian_Breast_Cancer_Sample_25 [gene]


title: Italian_Breast_Cancer_Sample_15 [gene]


title: Italian_Breast_Cancer_Sample_17 [gene]


title: Italian_Breast_Cancer_Sample_23 [gene]


title: Italian_Breast_Cancer_Sample_13 [gene]


title: Italian_Breast_Cancer_Sample_11 [gene]


title: Italian_Breast_Cancer_Sample_9 [gene]


title: Italian_Breast_Cancer_Sample_7 [gene]


title: Italian_Breast_Cancer_Sample_14 [gene]


title: Italian_Breast_Cancer_Sample_12 [gene]


title: Italian_Breast_Cancer_Sample_16 [gene]


title: Italian_Breast_Cancer_Sample_10 [gene]


title: Italian_Breast_Cancer_Sample_8 [gene]


title: Italian_Breast_Cancer_Sample_3 [gene]


title: Italian_Breast_Cancer_Sample_18 [gene]


title: Italian_Breast_Cancer_Sample_1 [gene]


title: Italian_Breast_Cancer_Sample_5 [gene]


title: Chinese_Breast_Cancer_Sample_78 [gene]

source_name: Chinese breast cancer sample

value: China


title: Italian_Breast_Cancer_Sample_6 [gene]


title: Chinese_Breast_Cancer_Sample_77 [gene]


title: Chinese_Breast_Cancer_Sample_73 [gene]


title: Chinese_Breast_Cancer_Sample_75 [gene]


title: Italian_Breast_Cancer_Sample_4 [gene]


title: Italian_Breast_Cancer_Sample_2 [gene]


title: Chinese_Breast_Cancer_Sample_76 [gene]


title: Chinese_Breast_Cancer_Sample_69 [gene]


title: Chinese_Breast_Cancer_Sample_72 [gene]


title: Chinese_Breast_Cancer_Sample_65 [gene]


title: Chinese_Breast_Cancer_Sample_71 [gene]


title: Chinese_Breast_Cancer_Sample_63 [gene]


title: Chinese_Breast_Cancer_Sample_67 [gene]


title: Chinese_Breast_Cancer_Sample_61 [gene]


title: Chinese_Breast_Cancer_Sample_59 [gene]


title: Chinese_Breast_Cancer_Sample_64 [gene]


title: Chinese_Breast_Cancer_Sample_55 [gene]


title: Chinese_Breast_Cancer_Sample_60 [gene]


title: Chinese_Breast_Cancer_Sample_66 [gene]


title: Chinese_Breast_Cancer_Sample_68 [gene]


title: Chinese_Breast_Cancer_Sample_74 [gene]


title: Chinese_Breast_Cancer_Sample_62 [gene]


title: Chinese_Breast_Cancer_Sample_49 [gene]


title: Chinese_Breast_Cancer_Sample_70 [gene]


title: Chinese_Breast_Cancer_Sample_57 [gene]


title: Chinese_Breast_Cancer_Sample_53 [gene]


title: Chinese_Breast_Cancer_Sample_51 [gene]


title: Chinese_Breast_Cancer_Sample_46 [gene]


title: Chinese_Breast_Cancer_Sample_56 [gene]


title: Chinese_Breast_Cancer_Sample_54 [gene]


title: Chinese_Breast_Cancer_Sample_58 [gene]


title: Chinese_Breast_Cancer_Sample_52 [gene]


title: Chinese_Breast_Cancer_Sample_47 [gene]


title: Chinese_Breast_Cancer_Sample_45 [gene]


title: Chinese_Breast_Cancer_Sample_44 [gene]


title: Chinese_Breast_Cancer_Sample_38 [gene]


title: Chinese_Breast_Cancer_Sample_43 [gene]


title: Chinese_Breast_Cancer_Sample_41 [gene]


title: Chinese_Breast_Cancer_Sample_37 [gene]


title: Chinese_Breast_Cancer_Sample_48 [gene]


title: Chinese_Breast_Cancer_Sample_40 [gene]


title: Chinese_Breast_Cancer_Sample_42 [gene]


title: Chinese_Breast_Cancer_Sample_50 [gene]


title: Chinese_Breast_Cancer_Sample_36 [gene]


title: Chinese_Breast_Cancer_Sample_34 [gene]


title: Chinese_Breast_Cancer_Sample_30 [gene]


title: Chinese_Breast_Cancer_Sample_28 [gene]


title: Chinese_Breast_Cancer_Sample_32 [gene]


title: Chinese_Breast_Cancer_Sample_33 [gene]


title: Chinese_Breast_Cancer_Sample_26 [gene]


title: Chinese_Breast_Cancer_Sample_31 [gene]


title: Chinese_Breast_Cancer_Sample_35 [gene]


title: Chinese_Breast_Cancer_Sample_29 [gene]


title: Chinese_Breast_Cancer_Sample_39 [gene]


title: Chinese_Breast_Cancer_Sample_20 [gene]


title: Chinese_Breast_Cancer_Sample_24 [gene]


title: Chinese_Breast_Cancer_Sample_27 [gene]


title: Chinese_Breast_Cancer_Sample_22 [gene]


title: 293T pLKO replicate 3

city: Charlestown

first: Johnathan

last: Whestine

state: MA

address: RM7103 Bldg 149 13th Street

department: Cancer Center

institute: MGH

description: LKO #3

hyb_protocol: Cy3 labeled material was hybridized to arrays for 20 hours.  Washing was performed using Roche/Nimblegen wash buffer kit.

scan_protocol: Slides were scanned on an ms200 scanner using automatic gain using high sensitivity settings

data_processing:
Images were spearated, gridded and extracted using Nimblegen DEVA software.  Pair files were generated and used for RMA normaliziation using DEVA software
Deva generated RMA normalized intensitites were used for analysis

source_name: 293T cells

label_protocol: RNA was converted to dsCDNA using Roche cDNA synthesis system.  dsCDNA was labeled using Roche One-color labeling kit.  Both procedures followed the manufacturer's instructions.

growth_protocol: 293T cells were maintained in DMEM with 10% FBS and 1/100 dilution of Penicillin/Streptomycin and L-glutamine

extract_protocol: Total RNA was isolated using Qiagen miRNeasy kit with optional on column Dnase digestion following the manufacturer's protocol

treatment_protocol: Cells were transfected overnight using xTremeGene 9 in Opti-MEM1 growth media.  Media was then replaced with complete DMEM and cells were collected after 72 hours

tag: transfection

value: pLKO


title: 293T pLKO replicate 2

description: LKO #2


title: 293T shKDM4A.6 replicate 3

description: shKDM4A.6 #3

value: shKDM4A.6 (pLKO backbone)


title: 293T shKDM4A.2 replicate 1

description: shKDM4A.2 #1

value: shKDM4A.2 (pSuper backbone)


title: 293T shKDM4A.2 replicate 2

description: shKDM4A.2 #2


title: Chinese_Breast_Cancer_Sample_18 [gene]

value: breast tumor

value: female


title: Chinese_Breast_Cancer_Sample_25 [gene]

value: II


title: 293T shKDM4A.2 replicate 3

description: shKDM4A.2 #3


title: Chinese_Breast_Cancer_Sample_16 [gene]


title: 293T shKDM4A.6 replicate 1

description: shKDM4A.6 #1


title: Chinese_Breast_Cancer_Sample_23 [gene]


title: Chinese_Breast_Cancer_Sample_21 [gene]

value: luminal-A


title: 293T pSuper replicate 1

description: shCTRL #1

value: pSuper


title: 293T shKDM4A.6 replicate 2

description: shKDM4A.6 #2


title: Chinese_Breast_Cancer_Sample_14 [gene]

value: luminal-B


title: Italian_Breast_Cancer_Sample_97 [miRNA]

extract_protocol: Total RNA including miRNA fraction was extracted with miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Italy

value: undetermined


title: Italian_Breast_Cancer_Sample_96 [miRNA]

value: III


title: Italian_Breast_Cancer_Sample_95 [miRNA]


title: Italian_Breast_Cancer_Sample_92 [miRNA]


title: Italian_Breast_Cancer_Sample_93 [miRNA]

value: basal


title: Italian_Breast_Cancer_Sample_94 [miRNA]


title: Chinese_Breast_Cancer_Sample_19 [gene]


title: Chinese_Breast_Cancer_Sample_15 [gene]


title: Chinese_Breast_Cancer_Sample_17 [gene]


title: 293T pSuper replicate 2

description: shCTRL #2


title: Italian_Breast_Cancer_Sample_91 [miRNA]


title: 293T pLKO replicate 1

description: LKO #1


title: 293T pSuper replicate 3

description: shCTRL #3


title: Italian_Breast_Cancer_Sample_89 [miRNA]


title: Italian_Breast_Cancer_Sample_90 [miRNA]


title: Chinese_Breast_Cancer_Sample_12 [gene]


title: Italian_Breast_Cancer_Sample_85 [miRNA]


title: Italian_Breast_Cancer_Sample_87 [miRNA]


title: Italian_Breast_Cancer_Sample_86 [miRNA]


title: Italian_Breast_Cancer_Sample_88 [miRNA]


title: Italian_Breast_Cancer_Sample_84 [miRNA]


title: Chinese_Breast_Cancer_Sample_11 [gene]


title: Chinese_Breast_Cancer_Sample_9 [gene]


title: Chinese_Breast_Cancer_Sample_10 [gene]


title: Chinese_Breast_Cancer_Sample_13 [gene]


title: Chinese_Breast_Cancer_Sample_8 [gene]


title: Chinese_Breast_Cancer_Sample_7 [gene]


title: Italian_Breast_Cancer_Sample_83 [miRNA]


title: Italian_Breast_Cancer_Sample_82 [miRNA]


title: Italian_Breast_Cancer_Sample_78 [miRNA]


title: Italian_Breast_Cancer_Sample_79 [miRNA]


title: Italian_Breast_Cancer_Sample_80 [miRNA]


title: Italian_Breast_Cancer_Sample_81 [miRNA]


title: Chinese_Breast_Cancer_Sample_4 [gene]


title: Chinese_Breast_Cancer_Sample_2 [gene]


title: Chinese_Breast_Cancer_Sample_6 [gene]


title: Hypoxia-adapted/21% O2, post-eclosion adult, biological rep1

city: La Jolla

first: Merril

last: Gersten

state: CA

address: 9500 Gilman Drive #0412

institute: UCSD

description: Gene expression data from a pool of 25 male and 25 female 0.5-3 hour post-eclosion adults adapted to 4% O2 and reverted to 21% O2

hyb_protocol: 10 ug of fragmented cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner.

data_processing: Data were analyzed using the Plier algorithm implemented in the Affymetrix Expression Console software using the default settings.

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA.

growth_protocol: Flies were cultured on standard media and maintained in chambers adjusted to 4% or 21% O2, depending on experimental group.

extract_protocol: Total RNA was extracted from whole flies homogenized in TRIzol (Invitrogen, Carlsbad, CA) followed by a clean-up with RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Hypoxia-adapted Drosophila melanogaster were grown in chambers maintained at 4% O2 or reverted to 21% O2 for 5 generations, and generation-matched control flies were maintained in chambers at 21% O2.  Cultures were visually inspected and flies were collected from three developmental stages: third instar larvae, 0.5-3 hr post-eclosion adults, and 7-9 day old adults.

tag: developmental stage

value: 0.5-3 hours post-eclosion adult


title: Italian_Breast_Cancer_Sample_76 [miRNA]

tag: tissue


title: Italian_Breast_Cancer_Sample_77 [miRNA]

tag: age (years)


title: Chinese_Breast_Cancer_Sample_3 [gene]

tag: gender


title: Chinese_Breast_Cancer_Sample_5 [gene]

tag: nationality


title: Hypoxia-adapted/21% O2, post-eclosion adult, biological rep2


title: Chinese_Breast_Cancer_Sample_1 [gene]

tag: grade


title: Italian_Breast_Cancer_Sample_75 [miRNA]

tag: size (cm)


title: Hypoxia-adapted/21% O2, larva, biological rep3

description: Gene expression data from 25 control third instar larvae adapted to 4% O2 and reverted to 21% O2

source_name: Hypoxia-adapted/21% O2, larva

value: Third instar larva


title: Hypoxia-adapted/21% O2, post-eclosion adult, biological rep3


title: Hypoxia-adapted/4% O2, larva, biological rep1

description: Gene expression data from 25 control third instar larvae adapted to and maintained in 4% O2

source_name: Hypoxia-adapted/4% O2, larva


title: Control, post-eclosion adult, biological rep1

description: Gene expression data from a pool of 25 male and 25 female 0.5-3 hour post-eclosion adults maintained in 21% O2

source_name: Control, post-eclosion adult


title: Hypoxia-adapted/4% O2, larva, biological rep3


title: Hypoxia-adapted/4% O2, post-eclosion adult, biological rep3

description: Gene expression data from a pool of 25 male and 25 female 0.5-3 hour post-eclosion adults adapted to and maintained in 4% O2


title: Hypoxia-adapted/4% O2, post-eclosion adult, biological rep1


title: Control, post-eclosion adult, biological rep2


title: Control, post-eclosion adult, biological rep3


title: Control, larva, biological rep1

description: Gene expression data from 25 control third instar larvae maintained in 21% O2

source_name: Control, larva


title: Hypoxia-adapted/4% O2, post-eclosion adult, biological rep2


title: Italian_Breast_Cancer_Sample_74 [miRNA]

tag: lymph node status


title: Hypoxia-adapted/4% O2, larva, biological rep2


title: Control, larva, biological rep3


title: Italian_Breast_Cancer_Sample_72 [miRNA]

tag: er status


title: Hypoxia-adapted/21% O2, larva, biological rep1


title: Control, larva, biological rep2


title: Italian_Breast_Cancer_Sample_73 [miRNA]

tag: pgr status


title: Hypoxia-adapted/21% O2, adult, biological rep3

description: Gene expression data from a pool of 25 male and 25 female 7-9 day old adults adapted to 4% O2 and reverted to 21% O2

source_name: Hypoxia-adapted/21% O2, adult

value: 7-9 day adult


title: Hypoxia-adapted/21% O2, larva, biological rep2


title: Italian_Breast_Cancer_Sample_67 [miRNA]

tag: erbb2 status


title: Italian_Breast_Cancer_Sample_68 [miRNA]

tag: er status gene


title: Italian_Breast_Cancer_Sample_69 [miRNA]

tag: erbb2 status gene


title: Italian_Breast_Cancer_Sample_70 [miRNA]

tag: pam50 subtype


title: Hypoxia-adapted/21% O2, adult, biological rep2


title: Hypoxia-adapted/21% O2, adult, biological rep1


title: Italian_Breast_Cancer_Sample_65 [miRNA]

tag: ecm1/3 subtype


title: Hypoxia-adapted/4% O2, adult, biological rep3

description: Gene expression data from a pool of 25 male and 25 female 7-9 day old adults adapted to and maintained in 4% O2

source_name: Hypoxia-adapted/4% O2, adult


title: Italian_Breast_Cancer_Sample_66 [miRNA]


title: Italian_Breast_Cancer_Sample_71 [miRNA]


title: Control, adult, biological rep1

description: Gene expression data from a pool of 25 male and 25 female 7-9 day old adults maintained in 21% O2

source_name: Control, adult


title: Italian_Breast_Cancer_Sample_62 [miRNA]


title: Italian_Breast_Cancer_Sample_64 [miRNA]


title: Italian_Breast_Cancer_Sample_61 [miRNA]


title: Italian_Breast_Cancer_Sample_63 [miRNA]


title: Hypoxia-adapted/4% O2, adult, biological rep2


title: Italian_Breast_Cancer_Sample_60 [miRNA]


title: Control, adult, biological rep3


title: Italian_Breast_Cancer_Sample_56 [miRNA]


title: Italian_Breast_Cancer_Sample_59 [miRNA]


title: Italian_Breast_Cancer_Sample_58 [miRNA]


title: Italian_Breast_Cancer_Sample_57 [miRNA]


title: Hypoxia-adapted/4% O2, adult, biological rep1


title: PHM1-31 cells, TNF-stimulated; Immunoprecipitation with RelA antiserum V2

type: genomic

city: Sheffield

first: Neil

middle: Robert

last: Chapman

state: South Yorkshire

address: Tree Root Walk

department: Oncology and Metabolism

country: United Kingdom

institute: University of Sheffield

description: Myometrial (womb) smooth muscle

hyb_protocol: Hybridisation of Affymetrix GeneChIP 1.0R Human promoter was performed in the Array Core Facility, SITrAN, University of Sheffield. Experimental details were registered in the GeneChip® Operating Software (GCOS) which was installed on a Dell precision T1500 Workstation in the Affymetrix Core Facility Laboratory, Sheffield Institute for Translational Neuroscience (SITrAN), The University of Sheffield. The details entered on the GCOS software included experiment name, probe array type (Human promoter array 1.0R), sample name, sample type (myometrial cell DNA) and project. These fields establish a sample hierarchy that organised GeneChip data on GCOS.    The GeneChip® Fluidics Station 450 was used to wash and stain the human promoter arrays and is operated by GCOS.

scan_protocol: The GeneChip Scanner 3000 7G was used to scan the Human promoter 1.0R Array, this was also operated by the GCOS software. Following the fluidics protocol, Tough Spots® label dots were applied to each septa to prevent any liquid leaking during scanning. The Run Scanner option was selected from the menu bar and this prompted the loading of the array into the scanner. Once the array was loaded start scan was selected and the array was scanned. During the scanning process the array appeared as a pseudo colour image on the screen, this was later saved as a .DAT file.

data_processing:
Upon completion of scanning of the hybridised array slides, the .CEL files (raw data) were imported into Partek Genomics Suite 6.6 following manufacturer's tiling protocol.
Robust Multi-array Average (RMA) background correction, quantile normalisation and Log (base2) transformation utilising the software’s tiling workflow. IgG values served as the baseline and were matched to correponding slides by slide scan date. Baseline  was subtracted from normalised data. There are three Partek data files included: 1) Original imported data from the .CEL files. 2) Normalised but retaining all control IgG data after normalisation. 3) Normalised but IgG baseline data subsequently removed after the normalisation.

label: Biotin

molecule: genomic DNA

source_name: PHM1-31 immortalised myometrial cell

label_protocol: ChIP DNA was amplified using the Sigma Whole Genome Amplification Kit (WGA) as detailed in the manufacturers’ instructions (Sigma) with slight modifications. One microlitre of ChIP DNA was diluted with 9 µl of ultrapure water. Two microlitres of library preparation buffer together with 1 µl of library stabilisation solution was added to this and heated at 95ºC for 2 minutes before cooling on ice. One microlitre of library preparation enzyme was then added and the reaction incubated in the thermal cycler for the following times: 20 minutes at 16ºC (pre-cooled to this temperature); 20 minutes at 20ºC; 20 minutes at 37ºC; 5 minutes at 75ºC and 4ºC hold. During the incubation a master mix containing 7.5µl of 10x amplification master mix, 47.5 µl ultrapure water and 5µl (2 units/µl) of Whole Genome Amplification (WGA) DNA polymerase was prepared. This was added to each sample and incubated in the thermal cycler for the following times: 3 minutes at 95ºC; then 25 cycles of: 15 seconds at 95ºC; 5 minutes at 65ºC and 4ºC hold.  Ten percent of the amplified DNA was run on an agarose gel to ensure a DNA smear of the correct size was obtained. The remainder of the DNA was purified using Sigma Genelute™ PCR Clean-Up Kit following the manufacturer’s guidelines. One round of amplification does not routinely produce enough DNA for successive array hybridisation experiments, therefore, the amplified DNA was re-amplified using the WGA re-amplification kit to generate the 7.5 µg required. Also, as the dNTPs are provided separately to the master mix in this protocol it enables them to be added as directed in the Affymetrix protocol, which includes the addition of dUTP for subsequent fragmentation reactions. The method was as follows: 1 µl of amplified DNA was added to 9 µl of ultrapure water. As master mix containing 47.5 µl ultrapure water, 7.5 µl amplification master mix, 5 µl (2 units/µl) WGA polymerase and 3 µl dNTPS (10 mM dGTP, 10 mM dCTP, 10 mM dTTP, 8 mM dATP and 2 mM dUTP) was prepared. This was added to each sample and incubated in the thermal cycler for the following times: 3 minutes at 95ºC; then 25 cycles of: 15 seconds at 95ºC; 5 minutes at 65ºC and 4ºC hold.  Ten percent of the amplified DNA was run on an agarose gel to ensure a DNA smear of the correct size was obtained. The remainder of the DNA was purified using Sigma Genelute™ PCR Clean-Up Kit following the manufacturer’s guidelines. The DNA was quantified using the nanophotometer.  The re-amplified DNA was fragmented according to the Affymetrix® Chromatin Immunoprecipitation Protocol using the GeneChip® WT Double-Stranded DNA Terminal Labelling Kit. A reaction mix was prepared containing 7.5 µg DNA, 4.8 µl 10x cDNA fragmentation buffer, 1.5 µl (15U) Uracil DNA glycosylase (UDG), 2.25 µl (225U) apurinic/apyrmidinic endonuclease I (APE I) and made up to 48 µl with ultrapure water. The reaction was incubated on the thermal cycler as follows: 2 hours at 37ºC; 2 minutes at 93ºC; 2 minutes at 4ºC; 4ºC hold. Three microlitres of fragmented DNA was run on a 3% (w/v) agarose gel to check the efficiency of the fragmentation reaction.  A double stranded DNA labelling mix was prepared by combining 12 µl 5x Terminal deoxynucleotidyl transferase (TdT); buffer, 2 units TdT enzyme and 1 µl DNA labelling reagent (5 mM). This was added to the remaining fragmented DNA and incubated for the following times: 1 hour at 37ºC; 10 minutes at 70ºC; 2 minutes at 4ºC and 4ºC hold.  Two 1 µl aliquots of fragmented and biotinylated samples were removed, placed into fresh tubes and heated to 70ºC for 2 minutes. To one of the aliquots 5 µl of 2 mg /ml Neutravidin diluted in PBS was added. To the second aliquot 5 µl of PBS was added as a control. Both samples were incubated at room temperature for 5 minutes. Both samples were then electrophoresed on a 4 – 20% TBE gel at 120V for 2 hours. The gel was then soaked in ethidium bromide and visualised under UV.

growth_protocol: Cells grown to 90% confluence in DMEM supplemented with 10%(v/v) FCS, 2mM L-glutamine, 0.1mg/ml geneticin. Grown in a humidified atmosphere at 37C and 5%CO2

extract_protocol: PHM1-31 cells grown to ~2.6-2.8X10E6 cells/T75cm2 flask and then stimulated for one hour with TNF (10ng/ml). Cells then fixed in formaldehyde and the ChIP assay completed using the Magna-ChIP kit (#17-611; Millipore) following manufacturer's guidelines.

treatment_protocol: 2.8X10E6 cells/T75cm2 flask; TNF stimulated, 60 mins

tag: cell type

value: PHM1-31 cells

tag: antibody

value: RelA-containing NF-kappaB transcription factor proteins

tag: antibody vendor/catalog

value: sc-372 (Santa Cruz)

tag: stimulation

value: TNF-stimulated


title: PHM1-31 cells, TNF-stimulated; Immunoprecipitation with control IgGv2

description: Myometrial (womb) smooth muscle

value: non-specific proteins with control IgG


title: PHM1-31 cells, unstimulated; Immunoprecipitation with RelA antiserum V3sw

description: Myometrial (womb) smooth muscle

treatment_protocol: 2.8X10E6 cells/T75cm2 flask; Un-stimulated

value: unstimulated


title: PHM1-31 cells, TNF-stimulated; Immunoprecipitation with control IgGv3sw

description: Myometrial (womb) smooth muscle


title: PHM1-31 cells, TNF-stimulated; Immunoprecipitation with RelA antiserum

description: Myometrial (womb) smooth muscle


title: PHM1-31 cells, TNF-stimulated; Immunoprecipitation with control IgG

description: Myometrial (womb) smooth muscle


title: PHM1-31 cells, TNF-stimulated; Immunoprecipitation with RelA antiserum V3sw

description: Myometrial (womb) smooth muscle


title: Italian_Breast_Cancer_Sample_54 [miRNA]

tag: tissue

value: breast tumor

tag: age (years)

value: female


title: Italian_Breast_Cancer_Sample_55 [miRNA]

tag: gender

tag: nationality


title: PHM1-31 cells, unstimulated; Immunoprecipitation with RelA antiserum V2

description: Myometrial (womb) smooth muscle


title: Italian_Breast_Cancer_Sample_53 [miRNA]

tag: grade

value: II

tag: size (cm)

value: luminal-A


title: PHM1-31 cells, unstimulated; Immunoprecipitation with control IgG V3sw

description: Myometrial (womb) smooth muscle


title: PHM1-31 cells, unstimulated; Immunoprecipitation with RelA antiserum

description: Myometrial (womb) smooth muscle


title: PHM1-31 cells, unstimulated; Immunoprecipitation with control IgG V2

description: Myometrial (womb) smooth muscle


title: Control, adult, biological rep2

tag: developmental stage


title: PHM1-31 cells, unstimulated; Immunoprecipitation with control IgG

description: Myometrial (womb) smooth muscle


title: Italian_Breast_Cancer_Sample_52 [miRNA]

value: Italy

tag: lymph node status

tag: er status

tag: pgr status


title: Italian_Breast_Cancer_Sample_51 [miRNA]

tag: erbb2 status

tag: er status gene

tag: erbb2 status gene

value: undetermined


title: Italian_Breast_Cancer_Sample_50 [miRNA]

tag: pam50 subtype

tag: ecm1/3 subtype


title: Italian_Breast_Cancer_Sample_49 [miRNA]


title: Italian_Breast_Cancer_Sample_48 [miRNA]


title: SPL-Mem

type: SAGE

anchor: NlaIII

city: London

first: Lucie

last: Abeler-Dörner

address: Great Maze Pond

department: Immunobiology

institute: King's College London

description: tag count is approximate

data_processing:
supplementary files include data normalized to 100,000 tags
Analysis was performed using SAGE300 and eSAGE software

organism: Mus musculus

source_name: Splenic Thy1.1+ CD8+ T cells, transferred into and recovered from LCMV-infected Thy1.2 mice

extract_protocol:
Total RNA was isolated with an RNeasy RNA isolation kit from Qiagen and processed as in the supplied protocol (see also Shires et al (2001), Immunity, 15, 419-34
Complete SAGE protocol provided in Series supplementary file Hayday_SAGE_Protocol_Nov 2001.pdf

treatment_protocol: Thy1.1+ splenovytes were injected into Thy1.2+ recepients which were subsequently infected with LCMV Armstrong. After 80 days, Thy1.1+ CD8+ T cells were reisolated by sorting.

tag: cell type

tag: strain


title: IEL gd

source_name: Intestinal TCRγδ IEL

extract_protocol:
Total RNA was isolated with trizol and processed as in the supplied protocol (see also Shires et al (2001), Immunity, 15, 419-34
Complete SAGE protocol provided in Series supplementary file Hayday_SAGE_Protocol_Nov 2001.pdf

treatment_protocol: IEL were isolated from murine gut as described in Shires et al (2001) Immunity, 15, 419-34

value: Intestinal TCRγδ IEL


title: SPL-Nai

description: tag count is approximate

source_name: Splenic Thy1.1+ CD8+ T cells, from uninfected mice

treatment_protocol: CD8+ Thy1.1+ T cells were sorted from uninfected mice


title: IEL-ab

source_name: Intestinal TCRαβ IEL

value: Intestinal TCRαβ IEL


title: Italian_Breast_Cancer_Sample_46 [miRNA]

source_name: Italian breast cancer sample

tag: tissue

value: III

value: basal


title: Italian_Breast_Cancer_Sample_43 [miRNA]

tag: age (years)


title: Italian_Breast_Cancer_Sample_44 [miRNA]

tag: gender


title: Italian_Breast_Cancer_Sample_42 [miRNA]

tag: nationality


title: Act-DETC

source_name: DETC, activated with anti-CD3

treatment_protocol: DETC were isolated from murine epidermis, stimulated in vitro on anti-CD3 coated plates (1 μg/ml) for 24 hours, cultured in IL-2 for four weeks, then restimulated with 1 μg/ml plate-bound anti-CD3 for 24 hours.

value: DETC, activated with anti-CD3


title: Italian_Breast_Cancer_Sample_39 [miRNA]

tag: grade


title: Italian_Breast_Cancer_Sample_41 [miRNA]

tag: size (cm)


title: Italian_Breast_Cancer_Sample_38 [miRNA]


title: Italian_Breast_Cancer_Sample_45 [miRNA]


title: Italian_Breast_Cancer_Sample_40 [miRNA]


title: Italian_Breast_Cancer_Sample_37 [miRNA]


title: Italian_Breast_Cancer_Sample_36 [miRNA]


title: Italian_Breast_Cancer_Sample_47 [miRNA]


title: RSC and rsc-null mononucleosome occupancy

description:
Mononucleosomal DNA from RSC and rsc-null strains in ISW1 background, repeat 1-3
6185E1; 6186E1; 6190E1

hyb_protocol: Fluorescently labeled DNA samples were heat denatured after being combined with cot-1 DNA, Agilent aCGH blocking agent and Agilent Hi-RPM hybridization solution.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization Oven and were incubated at 65ºC for 24 hours with a rotational speed of 20 rpm.  Following incubation, the microarray slide was washed for 5 minute in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minute in aCGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31ºC).  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

data_processing: Raw feature intensities from three replicates were quantile normalized together, median scaled to 1, and the combined values converted to a log2 value. Probe sequences were mapped to Saccharoymyces cerevisisiae genome release 64 (UCSC sacCer3) and were then associated with the corresponding processed feature value. Processing was done with the BioToolBox (http://code.google.com/p/biotoolbox) programs process_microarray and map_oligo_data2gff.

source_name: rsc-null ISW1 mononucleosome DNA

label_protocol: ISW1 wildtype samples were amplified using PCR with a random primer. Mononucleosome DNA was denatured, incubated with a random primer (GTTTCCCAGTCACGATCNNNNNNNNN), and extended using Sequenase enzyme (US Biochemical) in the presence of dNTP. The reaction was denatured again and extended a second time with fresh Sequenase enzyme. A portion of the primed products was then amplified in a standard PCR reaction using the primer GTTTCCCAGTCACGATC and Platinum Taq (Invitrogen). For isw1 mutant samples, the mononucleosome DNA was amplified by ligation-mediated PCR. Mononucleosome DNA ends were polished using T4 kinase (NEB) and ligated to annealed primers AGAAGCTTGAATTCGAGCAGTCAG and CTGCTCGAATTCAAGCTTCT. The ligated product was then amplified using standard PCR reaction with primer CTGCTCGAATTCAAGCTTCT and Platinum Taq. After amplification, products were purified by Qiagen PCR cleanup columns and verified by gel electrophoresis. A normalized amount (3 µg) of amplified product was then labeled using Klenow enzyme, the respective PCR primer, 1 mM each of dATP, dTTP, dGTP, Cy3-dCTP or Cy5-dCTP, and 0.5 mM dCTP. Labeled products were purified using Qiagen PCR cleanup column with an additional 250 µl wash of 35% guanidine HCl.

growth_protocol: Yeast cultures were grown in 100 ml YP -ura -trp media with 1% raffinose and 50 mM CuSO4 at 27C with agitation until optical density of 0.8. Galactose was added to the media to 1% final concentration to induce UBR1 expression. After 1 hour of induction, the incubator was shifted to 37C to induce Sth1 protein degradation. After 2 hours of high temperature, cells were harvested. Cells were crosslinked for 5 minutes by addition of formaldehyde to 1% final concentration in the media and quenched by the addition of 1M glycine to 0.1M final concentration. Cells were harvested by centrifugation and washed twice with Tris-Buffered Saline. Cells were stored at -80C until preparation.

extract_protocol: Cells (equivalent to 50 ml culture) were suspended in spheroplasting solution (1M sorbitol, 10 mM Tris pH 7.5, 10 mM 2-MercaptoEthanol, protease inhibitors) and incubated with prepared zymolyase (Sigma) at 37C until the optical density of a 1:100 dilution in 1% SDS dropped to 0.01. Spheroplasts were gently harvested by low-speed centrifugation and stored on ice until ready. Spheroplasts were resuspended with MNase Digestion buffer (50 mM Tris pH 7.5, 100 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.1% Triton X-100) and digested with MNase at 37C for 25 minutes. The amount of MNase was empirically determined to yield an estimated 60% mono-, 30% di-, and 10% tri-nucleosomes. MNase digestion was stopped by the addition of 0.1X volumes of stop solution (250 mM EDTA. 5% SDS). Proteinase K was added to the samples, incubated at 37C for 2 hours, and then 65C overnight to reverse cross links. Protein was precipitated from the samples by addition of 8M potassium acetate to 1.2M final concentration, cooling on ice, and centrifugation. DNA was recovered by ethanol precipitation. Mononucleosome DNA was isolated by RNAase treatment, electrophoresis on a 1.2% agarose gel, excision, and purification with a Qiagen Gel Extraction Kit.

tag: genotype/variation

value: sth1td ubr1-null ISW1

source_name: RSC ISW1 mononucleosome DNA

value: sth1td pGAL-UBR1 ISW1


title: Italian_Breast_Cancer_Sample_35 [miRNA]

tag: lymph node status


title: Italian_Breast_Cancer_Sample_30 [miRNA]

tag: er status

value: luminal-B


title: Italian_Breast_Cancer_Sample_33 [miRNA]

tag: pgr status


title: Italian_Breast_Cancer_Sample_31 [miRNA]

tag: erbb2 status


title: Ioc3 ChIP in SD

description:
Ioc3 ChIP vs Input in SD media, repeat 1 and 2
5289E4; 5290E4

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image was saved as a TIF file. TIF files were loaded into Agilent Feature Extraction Software version 9.1.3.1 and feature intensities were calculated and exported as a text file.

data_processing: Raw feature intensities from two replicates were quantile normalized together, median scaled to 100, and the combined experiment values expressed as a log2 ratio of ChIP over Input. Probe sequences were mapped to Saccharoymyces cerevisisiae genome release 64 (UCSC sacCer3) and were then associated with the corresponding processed feature score. Processing was done with the BioToolBox (http://biotoolbox.googlecode.com) programs process_microarray and map_oligo_data2gff.

source_name: Ioc3 Input DNA

label_protocol: Purified ChIP eluate or Input DNA was denatured, incubated with a random primer (GTTTCCCAGTCACGATCNNNNNNNNN), and extended using Sequenase enzyme (US Biochemical) in the presence of dNTP. The reaction was denatured again and extended a second time with fresh Sequenase enzyme. A portion of the primed products was then amplified in a standard PCR reaction using the primer GTTTCCCAGTCACGATC and Platinum Taq (Invitrogen). Amplified products were purified by Qiagen PCR cleanup columns and verified by gel electrophoresis. A normalized amount (3 µg) was then labeled using Klenow enzyme, the primer GTTTCCCAGTCACGATC, 1 mM each of dATP, dTTP, dGTP, Cy3-dCTP or Cy5-dCTP, and 0.5 mM dCTP. Labeled products were purified using Qiagen PCR cleanup column with an additional 250 µl wash of 35% guanidine HCl.

growth_protocol: Yeast strains were grown in either standard rich glucose media (YPD) or minimal synthetic glucose (SD) media (supplemented only with uracil to compensate for auxotrophic deficiencies in the strains) to mid log phase (optical density of 1.0) at 30C in 500 ml culture flasks with agitation. Prior to harvesting, cells were fixed by the addition of formaldehyde to 1% final concentration in the media culture and agitated for 30 minutes, then quenched with the addition of 1M glycine to a final concentration of 0.1M. Cells were harvested by centrifugation and washed twice with Tris-Buffered Saline. Cells were stored at -80C until preparation.

extract_protocol: Chromatin was prepared by resuspending the cells in lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, protease inhibitors) and bead beating with 0.7 mm zirconium beads for six rounds of 2 minutes, interspersed with cooling on ice. Cells were collected by centrifugation, the supernatant was discarded, and the pellet resuspended in lysis buffer. The lysate was sonicated for seven rounds of 30 seconds, 90% duty cycle, with a Misonix sonifier. Cellular debris was removed by centrifugation. For immunoprecipitation, anti-mouse magnetic Dynabeads (Invitrogen) were prepared by incubating with anti-cMyc (9E11) in phosphate-buffered saline containing 5 mg/ml BSA for several hours with rotation. Normalized amounts of protein was then incubated with the prepared beads in ChIP buffer (lysis buffer with 0.1% sodium deoxycholate). Immunoprecipitations were performed at 4C overnight with gentle rotation. Beads were harvested by magnetic field and washed twice with ChIP buffer, twice with ChIP buffer supplemented to 500 mM NaCl, twice with LiCl wash buffer (10 mM Tris pH 8, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and once with TE. Captured complexes were eluted and cross-links reversed by incubating the beads in buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5% SDS) at 65C overnight. DNA was purified using Qiagen PCR Clean-up columns using the manufacturer's protocol.

tag: media

value: SD

source_name: Ioc3 ChIP DNA

tag: growth media

tag: chip antibody

value: Anti-c-Myc antibody [9E11]

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Italian_Breast_Cancer_Sample_32 [miRNA]

value: breast tumor

tag: er status gene

tag: erbb2 status gene

tag: pam50 subtype

tag: ecm1/3 subtype


title: Rsc8 ChIP in YPD

description:
Rsc8 ChIP vs Input in YPD media, repeat 1 and 2
5289E1; 5290E1

source_name: Rsc8 Input DNA

tag: strain

value: YPD

source_name: Rsc8 ChIP DNA


title: Italian_Breast_Cancer_Sample_29 [miRNA]

tag: tissue

tag: age (years)

tag: gender

value: female

tag: nationality

tag: grade


title: RSC and rsc-null mononucleosome occupancy in isw1-null

description:
Mononucleosomal DNA from RSC and rsc-null strains in isw1-null background, repeat 1-3
6776E1; 6777E1; 6778E1

scan_protocol: Fluorescently labeled DNA samples were heat denatured after being combined with cot-1 DNA, Agilent aCGH blocking agent and Agilent Hi-RPM hybridization solution.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization Oven and were incubated at 65ºC for 24 hours with a rotational speed of 20 rpm.  Following incubation, the microarray slide was washed for 5 minute in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minute in aCGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31ºC).  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

source_name: rsc-null isw1-null mononucleosome DNA

tag: genotype/variation

value: sth1td ubr1-null isw1-null

source_name: RSC isw1-null mononucleosome DNA

value: sth1td pGAL-UBR1 isw1-null


title: Ioc3 ChIP in YPD

description:
Ioc3 ChIP vs Input in YPD media, repeat 1 and 2
5289E3; 5290E3


title: Italian_Breast_Cancer_Sample_34 [miRNA]

value: Italy

tag: size (cm)

tag: lymph node status

tag: er status

tag: pgr status

tag: erbb2 status


title: Italian_Breast_Cancer_Sample_28 [miRNA]

value: luminal-A


title: Rsc8 ChIP in SD

description:
Rsc8 ChIP vs Input in SD media, repeat 1 and 2
5289E2; 5290E2

tag: media

tag: growth media

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #


title: Italian_Breast_Cancer_Sample_26 [miRNA]

tag: er status gene

tag: erbb2 status gene

tag: pam50 subtype

tag: ecm1/3 subtype

value: undetermined


title: Italian_Breast_Cancer_Sample_27 [miRNA]

tag: tissue

tag: age (years)

tag: gender

tag: nationality

value: II


title: Metformin at 8h, biological rep2

city: Shanghai

first: houkai

last: li

state: Shanghai

address: 1200 Cailun Road, Building 1, Room 1531, Pudong New District

institute: Shanghai University of Traditional Chinese Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_PLUS_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: LoVo cells treated with 10mM Metformin for 8h

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

growth_protocol: Human colon cancer LoVo cells (CCL-229) from ATCC were routinely cultured in 10cm dishes at 37 ℃ in a humidified atmosphere of 5% CO2 in 10% FBS DMEM supplemented with 100 U/ml penicillin and 100 mg/ml streptomycin.

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

treatment_protocol: Cells were treated with 10mM metformin for 8,and 24h, respectively, before the harvest for RNA extraction.

tag: cell line

value: LoVo (ATCC CCL-229)


title: Control at 24h, biological rep2

source_name: LoVo cells cultured for 24h


title: Control at 8h, biological rep2

source_name: LoVo cells cultured for 8h


title: Metformin at 24h, biological rep3

source_name: LoVo cells treated with 10mM Metformin for 24h


title: Control at 24h, biological rep1


title: Control at 24h, biological rep3


title: Metformin at 24h, biological rep1


title: Metformin at 8h, biological rep3


title: Metformin at 24h, biological rep2


title: hNPC_Non

city: Tokyo

first: Mari

last: Katsura

address: 2-11-16 Yayoi, Bunkyo-ku

department: Isotope Science Center

country: Japan

institute: The University of Tokyo

description: Gene expression after chronic radiation from sealed Cs-137 for 72hr

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Undifferentiated hNPC derived from embryonic stem (ES) cells

growth_protocol: The EBs were seeded onto ornithine–laminin511 (O/L)-coated 24-well plates or ornithine–laminin511 (O/L)-coated111 35 mm dishes to promote proliferation and neuronal differentiation with the sequential exchange of neuronal proliferation media and differentiation media..

extract_protocol: Total RNA was extracted with RNeasy Micro Kits.

treatment_protocol: After confluence, they were exposed to chronic radiation for 72h.

value: hNPC

tag: cell type

value: human neural progenitor cells (hNPC)

tag: irradiated with

value: none (control)


title: Italian_Breast_Cancer_Sample_24 [miRNA]

tag: grade

tag: size (cm)

tag: lymph node status

tag: er status

tag: pgr status

tag: erbb2 status


title: Italian_Breast_Cancer_Sample_22 [miRNA]

value: III

tag: er status gene

value: luminal-B


title: hNPC_496mGy

value: 496mGy; 0.085 mGy/min for 72hrs


title: Italian_Breast_Cancer_Sample_25 [miRNA]

tag: erbb2 status gene


title: Italian_Breast_Cancer_Sample_21 [miRNA]

tag: pam50 subtype


title: HUVEC_124mGy

source_name: HUVECs synchronized in G1 cell cycle phase

growth_protocol: Human umbilical vein endothelial cell (HUVEC) from sixth to twelfth passages was grown in endothelial cell basal medium-2 (EBM-2) (Lonza) with 5% fetal bovine serum (FBS).

treatment_protocol: After confluence medium was replaced with that containing 0.5% FBS to synchronize for sixteen hours. Then they were exposed to chronic radiation for 72h. .

value: HUVEC

value: human umbilical vein endothelial cell (HUVEC)

value: 124mGy; 0.029 mGy/min for 72hrs


title: HUVEC_496mGy


title: Control at 8h, biological rep1


title: Italian_Breast_Cancer_Sample_23 [miRNA]

value: breast tumor

value: female

tag: ecm1/3 subtype


title: Italian_Breast_Cancer_Sample_19 [miRNA]

tag: tissue


title: Italian_Breast_Cancer_Sample_18 [miRNA]

tag: age (years)


title: Italian_Breast_Cancer_Sample_17 [miRNA]

tag: gender


title: HUVEC_Non


title: Control at 8h, biological rep3


title: Italian_Breast_Cancer_Sample_20 [miRNA]

tag: nationality


title: hNPC_124mGy

tag: cell line


title: HUVEC_31mGy

tag: cell type

value: 31mGy; 0.0072 mGy/min for 72hrs


title: Italian_Breast_Cancer_Sample_14 [miRNA]

value: Italy


title: Italian_Breast_Cancer_Sample_15 [miRNA]

value: luminal-A


title: Italian_Breast_Cancer_Sample_16 [miRNA]

value: undetermined


title: Italian_Breast_Cancer_Sample_13 [miRNA]

value: II


title: Italian_Breast_Cancer_Sample_8 [miRNA]


title: Italian_Breast_Cancer_Sample_10 [miRNA]


title: Italian_Breast_Cancer_Sample_11 [miRNA]


title: Italian_Breast_Cancer_Sample_9 [miRNA]


title: Italian_Breast_Cancer_Sample_12 [miRNA]


title: hNPC_31mGy

tag: irradiated with


title: PHM1-31 cells, TNF-stimulated 3

hyb_protocol: A hybridisation cocktail containing 33.3 µl (12.5 µg) fragmented and labelled aRNA, 4.2 µl control oligonucleotide B2 (3nM), 12.5 µl 20x hybridisation controls (bioB, bioC, bioD and cre), 125 µl 2x hybridisation mix, 25 µl DMSO and 50 µl nuclease free water. The probe array was equilibrated to room temperature and the hybridisation cocktail was heated to 99ºC for 5 minutes and then transferred to a 45ºC heat block for 5 minutes. The probe array was then pre wet by addition of 200 µl pre hybridisation mix through one of the septa and incubated for 10 minutes at 45ºC rotating at 60rpm in a GeneChip hybridisation oven 640. The pre hybridisation mix was then removed from the array and the hybridisation cocktail was pipetted into the array through the septum. The array was then incubated for 16 hours at 45ºC rotating at 60 rpm in the GeneChip Hybridisation Oven 640. Experimental details were registered in the GeneChip® Operating Software (GCOS) which was installed on a Dell precision T1500 Workstation in the Affymetrix Core Facility Laboratory, SITrAN, The University of Sheffield. The details entered on the GCOS software included experiment name, probe array type , sample name, sample type (myometrial cell DNA) and project. These fields establish a sample hierarchy that organised GeneChip data on GCOS. The GeneChip® Fluidics Station 450 was used to wash and stain and is operated by GCOS.

scan_protocol: The GeneChip Scanner 3000 7G was used to scan the U133plus2 Human Expression Arrays, this was also operated by the GCOS software.

data_processing: The .CEL files (raw data) were imported into Partek Genomics Suite 6.6 and categorised into un-stimulated or TNF-stimulated. Differentially expressed genes were identified using ANOVA which generated p values. Linear contrast as use to calculate fold change and mean ratio from the contrast between un-stimulated and TNF stimulated samples. Genes with fold change ≥ 2 or fold change ≤ -1.5 and with p values ≤ 0.05 were identified using RefSeq.

source_name: PHM1-31 immortalised myometrial (womb) smooth muscle cells

label_protocol: Biotinylated aRNA was prepared according to Affymetrix' guidelines

growth_protocol: ~2.6-2.8X10E6 cells/T75cm2 flask werebathed in DMEM supplemented with 10%(v/v) FCS, 2mM L-glutamine, 0.1mg/ml genetic and then grown in a humidified atmosphere at 37C and 5%CO2.

extract_protocol: Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was subsequently treated with DNAseI to remove residual genomic DNA contamination. The quality of RNA was tested using Agilent’s Eukaryote Total RNA Nano (5067 – 1511) Chip in conjunction with the Agilent 2100 bioanalyzer.

treatment_protocol: PHM1-31 cells grown to ~2.6-2.8X10E6 cells/T75cm2 flask and then stimulated for one hour with TNF (10ng/ml) or left un-stimulated for the same time period. Total RNA was subsequently isolated from both treatment groups.

tag: stimulation

value: stimulated with TNF 60 mins


title: Italian_Breast_Cancer_Sample_7 [miRNA]

source_name: Italian breast cancer sample

tag: grade

tag: size (cm)


title: Italian_Breast_Cancer_Sample_6 [miRNA]

tag: lymph node status

tag: er status

value: basal


title: PHM1-31 cells, TNF-stimulated 2

description: immortalised myometrial (womb) smooth muscle cells


title: PHM1-31 cells, TNF-stimulated 1


title: PHM1-31 cells, unstimulated 2

value: un-stimulated


title: 51_4h_BV6

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: mononuclear cells from peripheral blood

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Primary CLL samples were cultivated using RPMI 1640 (Biochrom AG, Berlin, Germany), supplemented with 10% FCS (Sigma-Aldrich, St. Louis, MO, USA), 2 mM L-Glutamin (Biochrom AG), and Penicillin/Streptomycin (GIBCO, Invitrogen Corporation, Grand Island, NY, USA). Prior to treatment, cells were stained with trypan blue (Sigma-Aldrich), counted, and diluted to a density of 1.0x106 cells/ml. Thawing of viably frozen samples followed the DSMZ (German Collection of microorganisms and cell lines, Braunschweig) guideline. Agents used to treat primary AML sample for 4 and 20 hours in vitro were DMSO (control/carrier; dimethyl sulfoxide; Sigma-Aldrich), and BV6 was synthesized at Genentech, Inc. (South San Francisco, CA, USA).

value: m

tag: sample source

value: PB

tag: karyotype

tag: igvh status

value: mutated

tag: tp53 mutation

value: WT

tag: treatment time

tag: treatment


title: PHM1-31 cells, unstimulated 3


title: 50_4h_BV6

tag: age (years)

value: unmutated


title: 23_4h_D

tag: gender

value: normal

value: MUT

value: DMSO


title: 44_20h_D

value: 13q- bidel


title: 51_4h_D


title: 50_20h_BV6


title: 50_4h_D


title: 50_20h_D


title: Italian_Breast_Cancer_Sample_4 [miRNA]

tag: tissue

value: breast tumor

value: female

tag: nationality

tag: pgr status

tag: erbb2 status

tag: er status gene

tag: erbb2 status gene

tag: pam50 subtype

tag: ecm1/3 subtype


title: Italian_Breast_Cancer_Sample_2 [miRNA]

value: Italy

tag: grade

value: III

tag: size (cm)

tag: lymph node status

tag: er status


title: Italian_Breast_Cancer_Sample_3 [miRNA]

value: undetermined


title: 44_20h_BV6

tag: sample source

tag: karyotype

tag: igvh status

tag: tp53 mutation


title: Italian_Breast_Cancer_Sample_5 [miRNA]

tag: age (years)

tag: gender

value: II

value: luminal-A


title: Chinese_Breast_Cancer_Sample_78 [miRNA]

source_name: Chinese breast cancer sample

tag: tissue

tag: nationality

value: China

value: luminal-B


title: Italian_Breast_Cancer_Sample_1 [miRNA]

tag: pgr status

tag: erbb2 status


title: Chinese_Breast_Cancer_Sample_77 [miRNA]

tag: er status gene

tag: erbb2 status gene


title: 23_4h_BV6

value: m

value: PB

tag: treatment time

tag: treatment


title: Chinese_Breast_Cancer_Sample_76 [miRNA]

tag: grade

tag: size (cm)

tag: pam50 subtype

value: basal

tag: ecm1/3 subtype


title: PHM1-31 cells, unstimulated 1

tag: cell type

tag: stimulation

value: un-stimulated


title: Chinese_Breast_Cancer_Sample_75 [miRNA]

tag: lymph node status

tag: er status


title: Chinese_Breast_Cancer_Sample_74 [miRNA]

tag: age (years)

tag: gender


title: Chinese_Breast_Cancer_Sample_72 [miRNA]

tag: tissue

tag: nationality


title: Chinese_Breast_Cancer_Sample_73 [miRNA]

tag: pgr status

tag: erbb2 status


title: Chinese_Breast_Cancer_Sample_70 [miRNA]

tag: er status gene

tag: erbb2 status gene


title: Patient G Healthy Control

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: RMA (using packages from R/Bioconductor)

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: RNA amplification and reverse transcription into cDNA was performed with the NuGen Ovation Pico RNA amplification system V2. Subsequently, cDNA was fragmented with the NuGen Biotin Module according to the manufacturer’s protocol

tag: condition

value: Healthy

tag: patient

value: G

tag: Stage

value: Normal

value: skin


title: Chinese_Breast_Cancer_Sample_71 [miRNA]

value: breast tumor

tag: grade

tag: size (cm)

tag: pam50 subtype


title: 23_20h_D

tag: sample source

tag: karyotype

value: normal

tag: igvh status

value: unmutated

tag: tp53 mutation

value: MUT

tag: treatment time

tag: treatment

value: DMSO


title: Chinese_Breast_Cancer_Sample_69 [miRNA]

tag: tissue

tag: age (years)

tag: gender

value: female

tag: nationality

value: II

tag: lymph node status

tag: er status

tag: ecm1/3 subtype


title: Patient H Healthy Control

tag: condition

tag: patient

value: H

tag: Stage


title: 23_20h_BV6


title: Patient 9 with Cutaneus Tcell Lymphoma. Stage: tumor

value: Cutaneus Tcell Lymphoma

value: tumor


title: Patient D Healthy Control

value: D


title: Patient A Healthy Control

value: A


title: Patient 66 with Cutaneus Tcell Lymphoma. Stage: tumor


title: Patient F Healthy Control

value: F


title: Metformin at 8h, biological rep1

tag: cell line

value: LoVo (ATCC CCL-229)


title: Patient E Healthy Control

value: Healthy

value: E


title: Chinese_Breast_Cancer_Sample_66 [miRNA]

value: China

tag: grade

tag: size (cm)

tag: pgr status

tag: erbb2 status

tag: er status gene

tag: erbb2 status gene

tag: pam50 subtype

value: luminal-A


title: Patient 56 with Cutaneus Tcell Lymphoma. Stage: patch

value: patch

tag: tissue

value: skin


title: Chinese_Breast_Cancer_Sample_68 [miRNA]

value: breast tumor

tag: age (years)

tag: gender

value: III

value: undetermined


title: Chinese_Breast_Cancer_Sample_67 [miRNA]

value: female

tag: nationality

value: II

tag: lymph node status


title: Patient 43 with Cutaneus Tcell Lymphoma. Stage: tumor

value: Cutaneus Tcell Lymphoma


title: Patient B Healthy Control

value: B

value: Normal


title: Patient C Healthy Control

value: C


title: Chinese_Breast_Cancer_Sample_62 [miRNA]

tag: er status

value: luminal-B

tag: ecm1/3 subtype


title: Chinese_Breast_Cancer_Sample_61 [miRNA]

value: basal


title: Chinese_Breast_Cancer_Sample_63 [miRNA]


title: Chinese_Breast_Cancer_Sample_64 [miRNA]


title: Chinese_Breast_Cancer_Sample_60 [miRNA]


title: Patient 41 with Cutaneus Tcell Lymphoma. Stage: plaque

tag: condition

tag: patient

value: plaque


title: Patient 4 with Cutaneus Tcell Lymphoma. Stage: folliculotropic

tag: Stage

value: folliculotropic


title: Patient 24 with Cutaneus Tcell Lymphoma. Stage: plaque


title: Chinese_Breast_Cancer_Sample_65 [miRNA]

value: China

tag: grade


title: Chinese_Breast_Cancer_Sample_57 [miRNA]

tag: size (cm)


title: Chinese_Breast_Cancer_Sample_58 [miRNA]

tag: pgr status


title: Patient 3 with Cutaneus Tcell Lymphoma. Stage: plaque


title: Patient 17 with Cutaneus Tcell Lymphoma. Stage: plaque


title: Patient 29 with Cutaneus Tcell Lymphoma. Stage: tumor

value: tumor


title: Patient 25 with Cutaneus Tcell Lymphoma. Stage: plaque


title: Patient 18 with Cutaneus Tcell Lymphoma. Stage: plaque


title: Chinese_Breast_Cancer_Sample_56 [miRNA]

tag: erbb2 status


title: Chinese_Breast_Cancer_Sample_55 [miRNA]

tag: er status gene


title: Chinese_Breast_Cancer_Sample_54 [miRNA]

tag: erbb2 status gene


title: Chinese_Breast_Cancer_Sample_53 [miRNA]

tag: pam50 subtype

value: luminal-A


title: Chinese_Breast_Cancer_Sample_52 [miRNA]

tag: tissue


title: Chinese_Breast_Cancer_Sample_59 [miRNA]

tag: age (years)


title: Patient 11 with Cutaneus Tcell Lymphoma. Stage: plaque

value: skin


title: Patient 14  with Cutaneus Tcell Lymphoma. Stage: patch

value: patch


title: IL-17A-treated dendritic cells, biological rep 5 (DC7-G17)

city: Oullins

first: Karene

last: Mahtouk

address: 165 Chemin du Grand Revoyet : BP12

department: LBMC

country: France

institute: CNRS UMR5239

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16hr at 45°C one Genechip human genome U133 Plus 2.0 Affymetrix arrays.

scan_protocol: The arrays were read with a confocal laser (Genechip laser 3000, Affymetrix)

data_processing: Expression values and absent/present/marginal calls were calculated using the GCOS v1.4 software (Affymetrix). Absolute expression transcript levels were normalized for each chip by globally scaling all probe sets to a target signal intensity of 500.

source_name: IL-17A-treated dendritic cells, in the presence of IFN-g

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human dendritic cells (DC) were generated in vitro from CD14+ monocytes purified from peripheral blood from healthy donors and cultured for six days with 100 ng/mL GM-CSF and 10 ng/mL IL-4. After six days of culture, DC were harvested, washed and cultured in the absence or presence of IL-17A, with or without 2ng/mL IFN-gamma. RNA was extracted from untreated DC at day 0 (DC) or DC cultured for 12 days with IL-17A (DC-17), without or with IFN-g (DC-G17).

treatment_protocol: No treatment prior to extraction

tag: generation

value: cells generated in vitro from blood monocytes

tag: cell type

value: dendritic cells

tag: treatment

value: IL-17A and IFN-g


title: IL-17A-treated dendritic cells, biological rep 2 (DC4-17)

source_name: IL-17A-treated dendritic cells, in the absence of IFN-g


title: IL-17A-treated dendritic cells, biological rep 3 (DC3-G17)


title: Chinese_Breast_Cancer_Sample_51 [miRNA]

value: breast tumor

tag: gender

value: female

tag: nationality

value: II

tag: lymph node status

tag: er status


title: Chinese_Breast_Cancer_Sample_50 [miRNA]

value: III

tag: ecm1/3 subtype


title: Chinese_Breast_Cancer_Sample_49 [miRNA]

tag: grade

value: undetermined


title: Chinese_Breast_Cancer_Sample_43 [miRNA]

tag: size (cm)


title: Chinese_Breast_Cancer_Sample_42 [miRNA]

tag: pgr status


title: Chinese_Breast_Cancer_Sample_44 [miRNA]

tag: erbb2 status


title: Chinese_Breast_Cancer_Sample_40 [miRNA]

tag: er status gene


title: Chinese_Breast_Cancer_Sample_39 [miRNA]

tag: erbb2 status gene


title: Untreated dendritic cells, biological rep 3 (DC3)

source_name: Untreated dendritic cells

value: untreated


title: Chinese_Breast_Cancer_Sample_35 [miRNA]

tag: pam50 subtype


title: Chinese_Breast_Cancer_Sample_45 [miRNA]

tag: tissue

value: basal


title: Chinese_Breast_Cancer_Sample_47 [miRNA]

tag: age (years)


title: Chinese_Breast_Cancer_Sample_46 [miRNA]


title: Chinese_Breast_Cancer_Sample_48 [miRNA]


title: IL-17A-treated dendritic cells, biological rep 4 (DC4-G17)

tag: generation


title: IL-17A-treated dendritic cells, biological rep 1 (DC6-17)

tag: cell type


title: Chinese_Breast_Cancer_Sample_34 [miRNA]


title: Chinese_Breast_Cancer_Sample_41 [miRNA]

value: luminal-B


title: Chinese_Breast_Cancer_Sample_33 [miRNA]


title: Untreated dendritic cells, biological rep 4 (DC5)

tag: treatment


title: Chinese_Breast_Cancer_Sample_37 [miRNA]

tag: gender


title: lncMycN siRNA No. 2 transfected

city: Randwick

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute Australia

description:
MYCN-amplified neuroblastoma cells
Gene expression data from neuroblastoma cells knocking-down of lncMycN

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing:
Images were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
Results were further analysed in R (http://www.r-project.org/) with bioconductor package (http://www.bioconductor.org/).

source_name: neuroblasotma Kelly cells transfected with lncMycN siRNA

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

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

treatment_protocol:
Kelly neuroblastoma cells were cultured in Roswell Park Memorial Institute Medium (RPMI) 1640 supplemented with 10% fetal calf serum and 1% L-glutamine.
Kelly cells were transfected with control siRNA, lncMycN siRNA-1, lncMycN siRNA-2, N-Myc siRNA-1 or N-Myc siRNA-2 for 48 hours.

value: peripheral nervous system tumour cell

tag: transfection

value: lncMycN siRNA


title: Chinese_Breast_Cancer_Sample_36 [miRNA]

tag: nationality

value: China

tag: lymph node status


title: Chinese_Breast_Cancer_Sample_38 [miRNA]

tag: er status

tag: ecm1/3 subtype


title: Chinese_Breast_Cancer_Sample_32 [miRNA]

tag: grade

tag: size (cm)


title: Untreated dendritic cells, biological rep 2 (DC2)


title: Untreated dendritic cells, biological rep 1 (DC1)


title: Chinese_Breast_Cancer_Sample_31 [miRNA]

tag: pgr status

tag: erbb2 status


title: Chinese_Breast_Cancer_Sample_21 [miRNA]

tag: er status gene

tag: erbb2 status gene

value: luminal-A


title: Chinese_Breast_Cancer_Sample_20 [miRNA]

tag: tissue

tag: pam50 subtype


title: Chinese_Breast_Cancer_Sample_29 [miRNA]

tag: age (years)


title: lncMycN siRNA No. 1 transfected


title: Chinese_Breast_Cancer_Sample_22 [miRNA]


title: Chinese_Breast_Cancer_Sample_24 [miRNA]


title: Chinese_Breast_Cancer_Sample_30 [miRNA]


title: Chinese_Breast_Cancer_Sample_28 [miRNA]


title: Chinese_Breast_Cancer_Sample_26 [miRNA]


title: Chinese_Breast_Cancer_Sample_27 [miRNA]


title: Chinese_Breast_Cancer_Sample_23 [miRNA]


title: Chinese_Breast_Cancer_Sample_25 [miRNA]


title: N-Myc siRNA No. 1 transfected

description:
MYCN-amplified neuroblastoma cells
Gene expression data from neuroblastoma cells knocking-down of N-Myc

source_name: neuroblasotma Kelly cells transfected with N-Myc siRNA

value: N-Myc siRNA


title: Chinese_Breast_Cancer_Sample_18 [miRNA]


title: N-Myc siRNA No. 2 transfected


title: Chinese_Breast_Cancer_Sample_14 [miRNA]


title: Chinese_Breast_Cancer_Sample_19 [miRNA]


title: Chinese_Breast_Cancer_Sample_13 [miRNA]


title: Chinese_Breast_Cancer_Sample_12 [miRNA]


title: Chinese_Breast_Cancer_Sample_10 [miRNA]


title: control siRNA transfected

description:
MYCN-amplified neuroblastoma cells
Gene expression data from control neuroblastoma cells

source_name: control neuroblastoma Kelly cells

value: control siRNA


title: Chinese_Breast_Cancer_Sample_11 [miRNA]


title: Chinese_Breast_Cancer_Sample_15 [miRNA]


title: Chinese_Breast_Cancer_Sample_17 [miRNA]


title: Chinese_Breast_Cancer_Sample_16 [miRNA]


title: Chinese_Breast_Cancer_Sample_9 [miRNA]


title: Chinese_Breast_Cancer_Sample_1 [miRNA]


title: Chinese_Breast_Cancer_Sample_3 [miRNA]


title: Chinese_Breast_Cancer_Sample_5 [miRNA]


title: Chinese_Breast_Cancer_Sample_4 [miRNA]


title: Chinese_Breast_Cancer_Sample_8 [miRNA]


title: Chinese_Breast_Cancer_Sample_6 [miRNA]


title: Chinese_Breast_Cancer_Sample_7 [miRNA]


title: Chinese_Breast_Cancer_Sample_2 [miRNA]


title: SKOV3__miR365_2

city: Houston

first: Prahlad

middle: T.

last: Ram

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were output from genestudio and quantile normalised using the Lumi package in R

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep Amplification kit

extract_protocol: RNA was extracted with Trizol reagent in the miRVana miRNA isolation KIT in accordance with the prescribed protocol provided with the kit

tag: cell line

value: 48 hour miR-365a-3p


title: SKOV3__miR365_3

description: replicate 3

tag: treatment


title: Liver_TAA_2w_NC miR

city: Osaka

first: Yoshinari

last: Matsumoto

institute: Osaka City University

description: Gene expression after 5 weeks TAA liver fibrosis induction and 2 weeks NC miR injection

hyb_protocol: 600 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. On completion of the fragmentation reaction, fragmentation mixture was hybridized to SurePrint G3 Mouse Gene Expression 8x60K Microarray Kit <G4852A> (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven <G2545A，G2530-60029> (Agilent Technologies).  After hybridization, microarrays were washed by Gene Expression Wash Buffer Kit <5188-5327> (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Scanner <G2539A> (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and R/G PMT gain is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction <version 10.10.1.1> (Agilent Technologies) using default parameters (protocol GE１_1010_Sep10 and Grid template: 028005_D_F_20131202 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was analyzed with GeneSpring GX <version 13.0.0> (Agilent Technologies).

source_name: Liver, 5 weeks TAA treatment, 2 weeks NC miR injection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the Low Input Quick Amp Labeling Kit, one-color <5190-2305> (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy mini kit <74106> column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the Nanodrop ND1000 <version 3.5.2> (Thermo).

growth_protocol: After five weeks liver fibrosis induction period, mouse have been observed for one week (1w) or two weeks (2w) and negative control nucleotide (N.C) or miR-29a were injected every 3 days on this period.

extract_protocol: Liver total RNA was extracted by miRNAeasy® kit (QIAGEN, Venlo, Netherlands), following manufacture’s instruction. Total RNA was quantified using a Nanodrop ND1000 <version 3.5.2> (Thermo) and quality was monitored with Agilent 2100 Bioanalyzer <G2939A> (Agilent Technologies).

treatment_protocol: Mice were sacrificed on anesthesia treatment (isoflurane) and blood was drawn from inferior vena cava. Liver samples were collected and frozen immidiately by liquid mitrogen. Liver samples were stored at -80℃ until RNA extraction.

value: liver

tag: gender

value: male


title: SKOV3__ctrl_miR_2

description: replicate 2

value: 48 control miRNA


title: Liver_TAA_1w_NC miR

description: Gene expression after 5 weeks TAA liver fibrosis induction and 1 week NC miR injection

source_name: Liver, 5 weeks TAA treatment, 1 week NC miR injection


title: Liver_TAA_2w_miR-29a

description: Gene expression after 5 weeks TAA liver fibrosis induction and 2 weeks miR-29a injection

source_name: Liver, 5 weeks TAA treatment, 2 weeks miR-29a injection


title: MDAMB231__ctrl_miR_2

description: replicate 2


title: MDAMB231__ctrl_miR_3

description: replicate 3


title: SKOV3__ctrl_miR_1

description: replicate 1


title: SKOV3__miR365_1

description: replicate 1


title: Liver_CCl4_1w_miR-29a

description: Gene expression after 5 weeks CCl4 liver fibrosis induction and 1 week miR-29a injection

source_name: Liver, 5 weeks CCl4 treatment, 1 week miR-29a injection


title: E13_3day_OSM_Mist1_2

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. On completion of the fragmentation reaction, hybridized to Agilent Whole Mouse Genome Microarray 4×44k for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute with Gene Expression Wash Buffer (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting.

data_processing:
The scanned images were analyzed with Feature Extraction (Agilent).
Normalized signal intensity (log2 transformed and 75%tile shift normalized) calculated from the green processed signal after Feature Extraction using the GeneSpring software version 11.0.

source_name: E13 hepatoblasts cultured for 3day under Mist1 retrovirus infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using Low Input Quick Amp Labeling Kit, one-color.

growth_protocol: Dlk+ cells were cultured with infection of mock or Mist1-overexpressing retrovirus. The next day of virus infection, culture medium was exchanged and oncostatin M was added. The cells were cultured for total 3 days.

extract_protocol: Total RNA was purified from the cultured Dlk+ cells using the RNeasy Micro Kit (Qiagen, Limburg, Netherlands), according to the manufacturer’s instructions. RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: strain

tag: tissue origin

value: E13 fetal liver

tag: cell type

value: Dlk+ hepatoblasts

tag: infected with

value: Mist1-overexpressing retrovirus

tag: treated with

value: Oncostatin M


title: E13_3day_OSM_Mist1_1


title: E13_0day_2

source_name: E13 hepatoblasts cultured at 0day


title: Liver_TAA_1w_miR-29a

description: Gene expression after 5 weeks TAA liver fibrosis induction and 1 week miR-29a injection

source_name: Liver, 5 weeks TAA treatment, 1 week, miR-29a injection


title: Liver_CCl4_2w_NC miR

description: Gene expression after 5 weeks CCl4 liver fibrosis induction and 2 weeks NC miR injection

source_name: Liver, 5 weeks CCl4 treatment, 2 weeks NC miR injection


title: E13_3day_OSM_Control_2

source_name: E13 hepatoblasts cultured for 3day under Control retrovirus infection

value: mock control retrovirus


title: Liver_CCl4_2w_miR-29a

description: Gene expression after 5 weeks CCl4 liver fibrosis induction and 2 weeks miR-29a injection

source_name: Liver, 5 weeks CCl4 treatment, 2 weeks miR-29a injection


title: E13_0day_1


title: MDAMB231__ctrl_miR_1

description: replicate 1


title: Tumor LN 383 (1)

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

description: Replicate 1

hyb_protocol: GeneChip Hybridization, Wash and stain Kit Affymetrix

scan_protocol: GeneChip Scanner 3000  Affymetrix

data_processing: Analyzed with Agilent GeneSpring 12.6 using default normalization for Affymetrix Expression data which is RMA (Summarization method).

source_name: C57BL/6 Ebf1+/-Pax5+/- enlarged lymph node

label_protocol: GeneChip 3 ÍVT Express kit Affymetrix

growth_protocol:
230238: 230238 pre-B-cell line cultivated in RPMI1640
FL Ebf1-KO: Cells were cultivated on OP9 stromal cells in OptiMEM with 10% FCS+50μM β-mercaptoethanol +25 mM HEPES supplemented 10ng/mL KIT ligand, 10ng/mL Fms-like tyrosine kinase 3 ligand (FLT3L), and 10ng/mL Interleukin-7.
Tumor LNs:N/A

extract_protocol: RNA Easy  micro kit Qiagen

treatment_protocol:
230238: N/A
FL Ebf1-KO: Infected and GFP-sorted cells were treated with 0.1 uM 4-hydroxytamoxifen for 0, 6, 12 and 24h prior to RNA preparation.
Tumor LNs:

tag: genotype/variation

value: Enlarged lymphnode cells


title: Liver_CCl4_1w_NC miR

description: Gene expression after 5 weeks CCl4 liver fibrosis induction and 1 week NC miR injection

source_name: Liver, 5 weeks CCl4 treatment, 1 week NC miR injection


title: MDAMB231__miR365_1

description: replicate 1


title: MDAMB231__miR365_3

description: replicate 3


title: E13_3day_OSM_Control_1


title: Tumor LN 327 (2)

description: Replicate 2


title: Tumor LN 381 (1)

description: Replicate 1


title: Tumor LN 381 (2)

description: Replicate 2


title: Carnosine-3

city: Fukuoka

first: Yoshinori

last: KATAKURA

state: Fukuoka

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

department: Graduate School of Systems Life Sciences

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Human Genome Microarray Kit v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Caco-2 cells, carnosine-treatment

label_protocol: cRNA was amplified and labelled using a Low Input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Caco-2 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega).

treatment_protocol: Caco-2 cells were treated with 1 mM carnosine for 3 days. Three independent experiments were performed.

value: carnosine


title: P5 28ºC vs P24 28ºC

city: Paterna

first: Estéfani

last: García-Ríos

state: Valencia

address: Avenue Agustín Escardino, 7

department: Biotechnology

country: Spain

institute: Institute of Agrochemistry and Food Technology (IATA-CSIC)

description: Triplicate arrays and Cy5-dCTP and Cy3-dCTP dye-swap assays

hyb_protocol: A mixture of 350 to 400 pmol of the two labeled samples was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed on a Yeast Array (PCR-amplified ORFs of yeast S288c strain, Servei Genomica, Universitat Autonoma Barcelona, Spain) in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight (17 hours). Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 50% deionized formamide, 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with solutions containing decreasing concentrations of filter sterilized SSC 20x and SDS 10% (Sol.1: 1x SSC-0.2% SDS; Sol.2: 0.1x SSC-0.2% SDS; Sol.3: 0.1x SSC; Sol. 4: double deionized water)

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with a GenePix 4100A scanner (AXON, Molecular Devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing:
Microarray data were derived from three independent experiments for a RNA hybridization. Raw data with a global background subtraction were generated from GenePix pro 7.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).
The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found. Only spots with at least three replicates were considered. Finally, replicates were combined and their medians were calculated. Genes with a two-fold log2 ratio values were considered to have significant differential expression if the p-values of the Student’s t-test, after applying the Benjamini and Hochberg (BH) method to adjust for false discovery rate (FDR) were ≤0.05

source_name: P5 strain growing at 28ºC, Synthetic must

label_protocol: 5 µg of each amplified amino-allyl a RNA were indirectly labeled with Cy3 or Cy5 mono-reactive dyes (Amersham GE Healthcare™, Amersham UK) and later on purified with RNeasy Mini Kitto remove not-incorporated dyes. Dye incorporation was monitored by a NanoDrop ND1000.

growth_protocol: Continuous cultures were performance at 15 ºC and 28 ºC in 0.5 L reactor (MiniBio, Applikon Biotechnology) with a working volume of 0.35 L. The dilution rate (D) of the cultures was 0.028 h-1 at both temperatures. A temperature probe connected to a cryostat controlled temperature cultures. pH was measured online and kept constant at 3.3 by the automatic addition of 2M NaOH. The stirrer was set at 100 rpm. The population inoculated in the chemostat was approximately OD = 0.2. Previously to start the continuous culture, cells were allowed to grow, at the same temperature than the continuous culture, to achieve enough biomass in a batch phase. When the batch culture entered in stationary phase, the continuous culture was connected. Steady states were sampled only after all continuous cultures had been running for at least five residence times and the biomass values were constant. A volume of approximately 30 units of OD600 was centrifuged at 10000 g for 3 min at 4 ºC. After supernatant removal, cell suspension was washed with PBS, transferred to a 1.5 to 2 mL microcentrifuge tube and centrifuged again in the same conditions. The pellet was flash-frozen with liquid nitrogen and stored at -80 ºC until its analysis.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Quiagen) according to manufacturer’s instructions. RNA was quantified spectrophotometrically with a NanoDrop ND-1000 (ThermoFisher Scientific) and integrity was determined by electrophoresis in 1% agarose gel. 2.5 μg of total RNA from each sample was linearly amplified and chemically modified with Amino-Allyl-UTP using the SuperScript RNA Amplification System (Invitrogen, Life Technologies).

tag: isolate

value: Commercial wine strain

source_name: P24 strain growing at 28ºC, Synthetic must


title: MDAMB231__miR365_2

description: replicate 2


title: Tumor LN 383 (2)

description: Replicate 2


title: Tumor LN 317 (2)

description: Replicate 2


title: P5 15ºC vs P24 15ºC

source_name: P5 strain growing at 15ºC, Synthetic must

source_name: P24 strain growing at 15ºC, Synthetic must


title: P5 15ºC vs P5 28ºC


title: P24 15ºC vs P24 28ºC


title: Tumor LN 317 (1)

description: Replicate 1


title: Tumor LN 327 (1)

description: Replicate 1


title: Tumor LN 292 (2)

description: Replicate 2


title: Carnosine-2


title: Tumor LN 292 (1)

description: Replicate 1


title: Tumor LN 279 (1)

description: Replicate 1


title: Tumor LN 279 (2)

description: Replicate 2


title: Control-3

source_name: Caco-2 cells, non-treatment


title: Tumor LN 278 (2)

description: Replicate 2


title: Tumor LN 277 (1)

description: Replicate 1


title: Control-2


title: FL Ebf1-KO Ebf1-ER 24h (2)

description: Replicate 2

source_name: E14.5 FL Ebf1-KO cells with Ebf1-ER 24h post tamoxifen addition

tag: time point


title: FL Ebf1-KO Ebf1-ER 12h (2)

description: Replicate 2

source_name: E14.5 FL Ebf1-KO cells with Ebf1-ER 12h post tamoxifen addition


title: Tumor LN 277 (2)

description: Replicate 2


title: ATRA(Cy5) vs. ATRA+ATO(Cy3)

city: Tokushima

first: Daigo

last: Sumi

institute: Tokushima Bunri University

hyb_protocol: The Human GE 4*44 v2 slide was hybridized with 0.825 maicroG of Cy3- and Cy5-labeled cRNA competitively and washed with the Agilent Gene Expression Wash Buffer.

scan_protocol: Scanned on an Agilent technologies Microarray scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: human leukemia HL-60 cells + ATRA

label_protocol: Low Input Quick Amp Labeling Kit was used to synthesize cDNA from total RNA (200 ng) and then to synthesize cRNA from cDNA as a template. Total RNA was reverse-transcribed with a T7 Promoter Primer. After second-strand synthesis, we used the cDNA as a template for Cyanine (Cy)3-/Cy5-labeled cDNA synthesis. cDNA from ATRA-treated cells was labeled with Cy3 and that from ATRA plus ATO-treated cells was labeled with Cy5 or ATRA-treated cells was labeled with Cy5 and that from ATRA plus ATO-treated cells was labeled with Cy3.

growth_protocol: HL-60 cells were obtained from ATCC (Manassas, VA), and were cultured at 37°C in a humidified atmosphere of 5% CO2 using RPMI-1640 containing 10% fetal calf serum, penicillin (100 U/ml) and streptomycin (100 mg/ml).

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

treatment_protocol: HL-60 cells were treated with 0.1 maicroM ATRA or  0.1 maicroM ATRA plus 0.5 maicroM ATO for 24 hours

value: ATRA

source_name: human leukemia HL-60 cells +  ATRA+ATO

value: ATRA+ATO


title: 230238 pMig (EV) (3)

description: Replicate 3

source_name: 230238 preB cell line infected with pMIG (empy vector control)

value: pMIG (empy vector control)


title: ProB WT control 621

description: Wt control 1

source_name: C57BL/6 wt ProB cells

value: wt

value: ProB cells


title: Carnosine-1


title: FL Ebf1-KO Ebf1-ER 6h (2)

description: Replicate 2

source_name: E14.5 FL Ebf1-KO cells with Ebf1-ER 6h post tamoxifen addition


title: FL Ebf1-KO Ebf1-ER 6h (1)

description: Replicate 1


title: 230238 Ebf1-Eng (3)

description: Replicate 3

source_name: 230238 preB cell line infected with pMIG-Ebf1-engrailed


title: Tumor LN 278 (1)

description: Replicate 1


title: FL Ebf1-KO Ebf1-ER 24h (1)

description: Replicate 1


title: ProB WT control 622

description: Wt control 2


title: FL Ebf1-KO Ebf1-ER 0h (1)

description: Replicate 1

source_name: E14.5 FL Ebf1-KO cells with Ebf1-ER 0h post tamoxifen addition


title: ATRA+ATO(Cy5) vs. ATRA(Cy3)


title: 230238 Ebf1-Eng (2)

description: Replicate 2


title: 230238 Ebf1-Eng (1)

description: Replicate 1


title: 230238 pMig (EV) (2)

description: Replicate 2


title: FL Ebf1-KO Ebf1-ER 0h (2)

description: Replicate 2


title: FL Ebf1-KO Ebf1-ER 12h (1)

description: Replicate 1


title: Control-1


title: Control islets replicate3

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

description: mice were treated with tamoxifen(25mg, 21d release) at 4-5 weeks old and islets were collected at 8-12 weeks

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: The "expresso" and "exprs" functions from R Bioconductor to obtain normalized expression set.

source_name: pancreatic islets

label_protocol: Biotinylated cRNA were prepared according to the GeneChip® 3’ IVT Express Kit manual from 150ng total RNA.

tag: background mouse strain

value: mix of C57BL/6, 129/ola and CBA/J

tag: genotyping

value: RIPcreER; Insm1flox/+


title: Control islets replicate8


title: 230238 pMig (EV) (1)

description: Replicate 1


title: Control islets replicate6


title: Control islets replicate7


title: Co-Insm1 mutant islets replicate8

value: RIPcreER; Insm1flox/lacZ


title: cardiac CD11c+MHC II+ cells rep2

first: Yoshitomo

last: Motomura

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

description: for clustering analysis with GSE10246 samples.

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 Array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: PI–CD45+Ly6G–NK1.1–CD11b+CD11c+MHC II+ cells from heart of FK565-treated mice

label_protocol: The cRNA was amplified, labeled using GeneChip 3' IVT Express kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: heart


title: Control islets replicate1


title: Control islets replicate4


title: Co-Insm1 mutant islets replicate4


title: cardiac CD11c+MHC II+ cells rep1


title: Co-Insm1 mutant islets replicate7


title: Control islets replicate2


title: Co-Insm1 mutant islets replicate2


title: Control islets replicate5


title: Jarid2-miPSC#4

city: Hidaka

first: Yasushi

last: Okazaki

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 45

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing: The intensity data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor affy 2.13.1 package using default analysis settings.

source_name: Mouse iPSC clone #4 generated by OSKM plus Jarid2

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

growth_protocol: MEFs were cultured in DMEM (Nacalai Tesque) supplemented with 10% heat-inactivated FBS (Invitrogen) and 1% non-essential amino acids (NEAA; Invitrogen). Mouse iPSCs were maintained on gelatine-coated dishes/plates in mESC medium (DMEM containing 20% knockout serum replacement (KSR; Invitrogen), 1% NEAA, 1% GlutaMAX (Invitrogen), 0.1 mM 2-mercaptoethanol (2-ME; Invitrogen) and 0.5% leukemia inhibitory factor (LIF)-containing conditioned medium from Cos-7 cells transiently transfected with a LIF-expressing plasmid, supplemented with two chemical inhibitors (2i), 3 uM CHIR99021 (Axon Medchem BV) and 1 uM PD0325901 (Axon Medchem BV).

extract_protocol: Total RNA was extracted using the SV Total RNA Isolation System (Promega) or RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MEFs were inoculated with a pMXs retrovirus mixture supplemented with polybrene (Sigma). Viral supernatant was removed after 24 h and then MEFs were cultured in mESC medium for 2 days.

value: iPSC

value: generated by OSKM plus Jarid2

tag: transgene

value: Nanog::EGFP-IRES-PuroR reporter


title: Co-Insm1 mutant islets replicate5


title: MEF_c-Myc_Day3

source_name: MEF transduced with c-Myc, Day 3

value: MEF

value: transduced with c-Myc


title: MEF_OSKM-J2deltaC+Empty_Day3

source_name: MEF transduced with OSKM plus a Jarid2 mutant, Day 3


title: MEF_Empty_Day3

source_name: MEF transduced with empty vector control, Day 3

value: transduced with empty vector


title: Co-Insm1 mutant islets replicate1


title: MEF_c-Myc+Jarid2WT_Day3

source_name: MEF transduced with Jarid2 plus c-Myc, Day 3

value: transduced with Jarid2 plus c-Myc


title: MEF_OSKM+PrEsS_Day3

source_name: MEF transduced with OSKM plus Prdm14, Esrrb, and Sall4a, Day 3


title: MEF_OSKM+Empty_Day3

source_name: MEF transduced with OSKM plus empty vector control, Day 3


title: MEF_Jarid2WT_Day3

source_name: MEF transduced with Jarid2, Day 3

value: transduced with Jarid2


title: Jarid2-miPSC#3

source_name: Mouse iPSC clone #3 generated by OSKM plus Jarid2


title: Co-Insm1 mutant islets replicate6


title: MEF_OSKM-J2deltaC+PrEsS_Day3

source_name: MEF transduced with OSKM plus a Jarid2 mutant, Prdm14, Esrrb, and Sall4a, Day 3


title: ET 4_R1_B02

first: Mike

last: Harr

address: 1275 York Ave.

institute: Memorial Sloan-Ketering Cancer Center

description: Gene expression array

hyb_protocol: Please see Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/support/technical/byproduct.affx?product=amplification)

data_processing: RMA : log2 transromation : quantile normalization : median polish using Partek GS version 6.5

extract_protocol: Extracted using Trizol according to manufacturure's recommendations

treatment_protocol: de novo MPN patients

tag: disease status

value: ET


title: ET 4_G02

description: Gene expression array

scan_protocol: Please see Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/support/technical/byproduct.affx?product=amplification)


title: Co-Insm1 mutant islets replicate3


title: ET 4_H07

description: Gene expression array

label_protocol: Please see Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/support/technical/byproduct.affx?product=amplification)


title: ET 4_F03

description: Gene expression array


title: ET 4_H04

description: Gene expression array


title: ET 4_F10

description: Gene expression array


title: AMM H06

description: Gene expression array

value: AMM


title: ET 4_D09

description: Gene expression array


title: ET 4_E04

description: Gene expression array


title: ET 4_H03

description: Gene expression array