title: Rpb3_BG3_PhRNAi

description:
Control CEL files: Input_BG3_Repl1.CEL, Input_BG3_Repl2.CEL, and Input_BG3_Repl3.CEL
Rpb3 ChIP DNA from Ph RNAi-treated Drosophila ML-DmBG3-c2 cells, 5 days RNAi treatment

value: Rpb3 [custom, Karen Adelman Lab (NIEHS)]

value: Input DNA from Mock RNAi-treated BG3-c2 cells


title: Control serum sample _BioS-CT1

status: Public on Apr 25 2013

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

country: USA

institute: UMDNJ-SOM

hyb_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters and a pixel size of 5um.

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum results were normalized via the compare-function into disease and control subgroups.   IgG autoantibodies providing a relative immunofluorescence with a Z-factor of greater than or equal to 0.4 were considered significant.

label: Alexa Fluor 647

molecule: other

organism: Homo sapiens

label_protocol: standard Invitrogen protocol

extract_protocol: All serum samples were obtained from public and private biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

tag: age

tag: gender

value: Female

tag: sample type

value: serum

tag: disease state

value: Control


title: 252153510008_1_3-T60[A(5)/A(3)]

type: RNA

city: Cambridge

first: Ilan

last: Wapinski

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: Biological replicate A, technical replicate 1

hyb_protocol: Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.  Reported expression values for each gene are median log2 ratios across all probes.

molecule: total RNA

organism: Schizosaccharomyces japonicus

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days).  These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below.  Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Heat Shock: Cultures were grown at 22C to mid-log densities (3x10^7 to 1x10^8 cells/mL) and then vacuum filtered and resuspended in pre-warmed (37C or 42C) media. Samples were harvested at different time intervals (5, 15, 30, 45, 60 mins)

tag: treatment

value: heat shock

tag: time point (minutes)


title: Control serum sample _AST-CT25

value: Male


title: Control serum sample _AST-CT27


title: 252153510008_2_4-T15[B(5)/B(3)]

description: Biological replicate B, technical replicate 3


title: Rad21_PosteriorWingDisc

type: genomic

city: St Louis

first: Cheri

middle: A

last: Schaaf

state: MO

address: 1100 South Grand Ave

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Rad21 ChIP DNA from yw; en-Gal4,UAS-RFP mixed-gender 3rd instar posterior wing imaginal disc

hyb_protocol: Hybridization cocktails were generated using the labeled DNA fragments (2 μg labeled DNA, 1x MES, 3M TMAC, 40 pM Affymetrix control oligo B2, 100 μg/mL salmon sperm DNA, and 0.02% Triton X-100). Each chip was pre-hybridized with 200 μl of 1X MES-triton for 1 hour in the Affymetrix Hybridization 645 oven at 45 rpm and 45oC.  Samples in hybridization cocktail were heated for 10 minutes at 99oC then incubated to a 45oC for 10 minutes. Samples are spun in a microcentrifuge at maximum speed for 3 min.  200 μl of a sample was injected in to a chip. Hybridization was carry out in the hybridization oven at 45 rpm and 45oC for 18 hours. The arrays were washed and stained on the GeneChip Fluidics Station 450 series.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
MAT software (Johnson et al. 2006) was used to calculate ChIP enrichment and sites of significant binding across the non-repetitive Drosophila genome.
matscore.bar files contain MATscores for each probe as generated using MAT software (Johnson et al. 2006). .bed files, also generated using MAT software, indicate binding at p-value less than or equal to 10-3.

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: Immunoprecipitated DNA was amplified using the GenomePlex Complete Whole Genome Amplification Kit (Sigma) and fragmented using controlled DNAse I reactions. Fragmented DNA was labeled with bio-11-ddATP (Perkin Elmer) using a Terminal Transferase  labeling kit (Roche).

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin. Drosophila larvae are grown under standard conditions at 25 degrees.

extract_protocol: BG3 cells were grown to a concentration of 5x106/mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x109/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 uL chromatin aliquots, each representing ~50x106 cells, were snap frozen on dry ice. Wing imaginal disc chromatin was prepared similarly, except that larval tissues were fixed in 1.8% formaldehyde for 20 minutes, and sonicated at a concentration of 75 discs per 100 μL buffer with a BioRuptor Sonicator using 20 cycles of 30 s on, 30 s off. Sonicated discs were diluted with 1-2 volumes of sonication buffer before immunoprecipitation. For immunoprecipitation, 200 μL aliquots of chromatin (50 x 106 BG3 cells, 60-75 whole wing imaginal discs, or 100-120 anterior or posterior wing imaginal discs) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein A/G agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 2 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS withSchneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools. Cohesin RNAi-treated cells were screened for sister chromatid cohesion defects, and none were found, though a mild cell division delay occurred immediately following RNAi treatment.

value: mixed

tag: chip antibody

value: Rad21 [custom, Dale Dorsett Lab (Saint Louis University)]

tag: genotype/variation

value: yw; en-Gal4,UAS-RFP

tag: developmental stage

value: 3rd instar

tag: tissue

value: posterior wing imaginal disc

source_name: Input DNA from Or-R mixed-gender late third instar wing imaginal disc

tag: input


title: 252035510008_1_4-T60[A(5)/A(3)]

organism: Candida albicans

treatment_protocol: Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with NaCl to a final concentration of 0.3M. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)

value: NaCl


title: 252035510014_1_1-T5[C(5)/C(3)]

description: Biological replicate C, technical replicate 1


title: Control serum sample _AST-CT22


title: Rad21_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Rad21 ChIP DNA from Or-R mixed-gender 3rd instar whole wing imaginal disc

value: Or-R

value: whole wing imaginal disc

value: Input DNA from Or-R mixed-gender late third instar wing imaginal disc


title: Control serum sample _AST-CT23


title: 252153510008_1_1-T5[A(5)/A(3)]


title: Rad21_BG3_Mock

description:
Control CEL files: Input_BG3_Repl1.CEL, Input_BG3_Repl2.CEL, and Input_BG3_Repl3.CEL
Rad21 ChIP DNA from Mock RNAi-treated Drosophila ML-DmBG3-c2 cells

value: male

tag: cell type

value: ML-DmBG3-c2 cells derived from developing Drosophila central nervous system

source_name: Input DNA from Mock RNAi-treated BG3-c2 cells


title: Rad21_BG3_PhRNAi

description:
Control CEL files: Input_BG3_Repl1.CEL, Input_BG3_Repl2.CEL, and Input_BG3_Repl3.CEL
Rad21 ChIP DNA from Ph RNAi-treated Drosophila ML-DmBG3-c2 cells, 5 days RNAi treatment

value: Input DNA from Mock RNAi-treated BG3-c2 cells


title: Rad21_AnteriorWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Rad21 ChIP DNA from yw; en-Gal4,UAS-RFP mixed-gender 3rd instar anterior wing imaginal disc

value: anterior wing imaginal disc


title: Control serum sample _AST-CT20

value: Female

value: serum


title: Control serum sample _AST-CT19

value: Control


title: 252153510008_1_4-T30[A(5)/A(3)]

description: Biological replicate A, technical replicate 2

value: heat shock


title: 252153510008_2_2-T45[B(5)/B(3)]

description: Biological replicate B, technical replicate 1


title: 252153510008_1_2-T30[A(5)/A(3)]


title: PolII_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Pol II ChIP DNA from Or-R mixed-gender 3rd instar whole wing imaginal disc

value: mixed

value: Pol II [Covance, catalog #MMS-126R, also known as 8WG16, lot E10015AF]


title: Psc_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Psc ChIP DNA Or-R mixed-gender 3rd instar whole wing imaginal disc

value: Psc [custom, Vincenzo Pirrotta Lab (Rutgers)]


title: Control serum sample _AST-CT14

value: Male


title: 252153510004_2_4-T15[B(5)/B(3)]


title: PcVP_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Pc-VP ChIP DNA from Or-R mixed-gender 3rd instar whole wing imaginal disc

value: Pc-VP [custom, Vincenzo Pirrotta Lab (Rutgers)]

value: 3rd instar


title: Control serum sample _AST-CT13


title: Ph_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Ph ChIP DNA from Or-R mixed-gender 3rd instar whole wing imaginal disc

value: Ph [custom, Vincenzo Pirrotta Lab (Rutgers)]

value: Or-R


title: Control serum sample _AST-CT12


title: PcRJ_PosteriorWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Pc-RJ ChIP DNA from yw; en-Gal4,UAS-RFP mixed-gender 3rd instar posterior wing imaginal disc

value: Pc-RJ [custom, Richard Jones Lab (Southern Methodist University)]

value: yw; en-Gal4,UAS-RFP

value: posterior wing imaginal disc

value: Input DNA from Or-R mixed-gender late third instar wing imaginal disc


title: 252153510008_2_3-T60[B(5)/B(3)]


title: PcRJ_BG3_Rad21RNAi

description:
Control CEL files: Input_BG3_Repl1.CEL, Input_BG3_Repl2.CEL, and Input_BG3_Repl3.CEL
Pc-RJ ChIP DNA from Rad21 RNAi-treated Drosophila ML-DmBG3-c2 cells, 5 days RNAi treatment

value: male

value: Rad21 [custom, Dale Dorsett Lab (Saint Louis University)] RNAi-treated Drosophila ML-DmBG3-c2 cells, 5 days RNAi treatment

value: ML-DmBG3-c2 cells derived from developing Drosophila central nervous system

value: Input DNA from Mock RNAi-treated BG3-c2 cells


title: 252153510008_2_1-T15[B(5)/B(3)]

description: Biological replicate B, technical replicate 2

value: heat shock


title: 252035310005_1_2-T60[B(5)/B(3)]

organism: Naumovozyma castellii


title: PcRJ_BG3_Mock

description:
Control CEL files: Input_BG3_Repl1.CEL, Input_BG3_Repl2.CEL, and Input_BG3_Repl3.CEL
Pc-RJ ChIP DNA from Mock RNAi-treated Drosophila ML-DmBG3-c2 cells


title: Control serum sample _CO17

value: serum

value: Control


title: 252035310004_2_3-T15[B(5)/B(3)]


title: Control serum sample _AST-CT11

value: Female


title: PcRJ_AnteriorWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Pc-RJ ChIP DNA from yw; en-Gal4,UAS-RFP mixed-gender 3rd instar anterior wing imaginal disc

value: mixed

value: anterior wing imaginal disc


title: 252035310004_1_1-T5[A(5)/A(3)]

description: Biological replicate A, technical replicate 1


title: Control serum sample _CO14

value: Male


title: Nipped-B_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
Nipped-B ChIP DNA from Or-R mixed-gender 3rd instar whole wing imaginal disc

value: Nipped-B [custom, Dale Dorsett Lab (Saint Louis University)]

value: 3rd instar

value: whole wing imaginal disc


title: Control serum sample _CO20


title: 252035310004_1_3-T30[A(5)/A(3)]


title: Control serum sample _CO19


title: 252035310004_1_2-T15[A(5)/A(3)]


title: 252035310004_2_2-T5[B(5)/B(3)]


title: 252153510004_2_3-T15[A(5)/A(3)]


title: Control serum sample _CO18


title: Control serum sample _CO15


title: Control serum sample _CO16


title: 252035310004_2_4-T30[B(5)/B(3)]


title: H3K27me3_PosteriorWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
H3K27me3 ChIP DNA from yw; en-Gal4,UAS-RFP mixed-gender 3rd instar posterior wing imaginal disc

value: H3K27me3 [Abcam, catalog # ab6002, lot GR77445-1]

value: yw; en-Gal4,UAS-RFP


title: Control serum sample _CO13


title: H3K27me3_WholeWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
H3K27me3 ChIP DNA from Or-R mixed-gender 3rd instar whole wing imaginal disc

value: Or-R

value: Input DNA from Or-R mixed-gender late third instar wing imaginal disc


title: 252035310004_1_4-T45[A(5)/A(3)]


title: 251507210475_1_1-T60[A(5)/A(3)]

organism: Saccharomyces cerevisiae


title: H3K27me3_AnteriorWingDisc

description:
Control CEL files: Input_WingDisc_Repl1.CEL and Input_WingDisc_Repl2.CEL
H3K27me3 ChIP DNA from yw; en-Gal4,UAS-RFP mixed-gender 3rd instar anterior wing imaginal disc


title: 252035310005_1_1-T45[B(5)/B(3)]


title: Control serum sample _CO12


title: 252035310004_2_1-T60[A(5)/A(3)]


title: Control serum sample _CO3


title: 252035310002_1_3-T30[B(5)/B(3)]

treatment_protocol: Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with hydrogen peroxide to a final concentration of 5 mM. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)

value: hydrogen peroxide


title: 251507210475_1_4-T30[B(5)/B(3)]


title: 251507210474_1_3-T30[A(5)/A(3)]


title: 252035310002_1_2-T15[B(5)/B(3)]


title: Control serum sample _CO10


title: Control serum sample _CO11


title: 251507210474_1_1-T5[A(5)/A(3)]


title: 251507210475_1_3-T15[B(5)/B(3)]


title: 252035310002_1_1-T5[B(5)/B(3)]


title: Control serum sample _CO2


title: 251507210474_1_4-T45[A(5)/A(3)]


title: 251507210474_1_2-T15[A(5)/A(3)]


title: 252035310002_1_4-T60[B(5)/B(3)]


title: Alzheimer's Disease serum sample_AD40

value: Alzheimer's Disease


title: 251507210475_1_2-T5[B(5)/B(3)]


title: Alzheimer's Disease serum sample_AD45


title: 252035310005_2_1-T30[D(5)/D(3)]

description: Biological replicate D, technical replicate 1


title: 252035310002_2_4-T60[C(5)/C(3)]

description: Biological replicate C, technical replicate 1


title: 252035310002_2_3-T30[C(5)/C(3)]


title: Control serum sample _CO1


title: 251507210463_1_3-T30[B(5)/B(3)]

description: Biological replicate B, technical replicate 1


title: Alzheimer's Disease serum sample_AD38


title: 252035310005_2_2-T60[D(5)/D(3)]


title: Alzheimer's Disease serum sample_AD37


title: Alzheimer's Disease serum sample_AD39


title: 251507210504_1_1-T5[D(5)/D(3)]


title: 252035310002_2_2-T15[C(5)/C(3)]


title: 252035310002_2_1-T5[C(5)/C(3)]


title: 251507210472_1_4-T60[E(5)/E(3)]

description: Biological replicate E, technical replicate 1


title: Alzheimer's Disease serum sample_AD36


title: Alzheimer's Disease serum sample_AD35


title: 252035310005_1_3-T5[D(5)/D(3)]


title: 251507210472_1_1-T5[E(5)/E(3)]


title: 251507210463_1_4-T60[B(5)/B(3)]


title: 252035310005_1_4-T15[D(5)/D(3)]


title: Alzheimer's Disease serum sample_AD34


title: 251507210472_1_3-T30[E(5)/E(3)]


title: 251507210473_1_2-T15[F(5)/F(3)]

description: Biological replicate F, technical replicate 1


title: 251507210462_1_1-T5[A(5)/A(3)]


title: 251507210504_1_4-T60[D(5)/D(3)]


title: Alzheimer's Disease serum sample_AD30


title: Alzheimer's Disease serum sample_AD32


title: 251507210473_1_4-T60[F(5)/F(3)]


title: 252035310001_2_1-T5[B(5)/B(3)]

value: NaCl


title: Alzheimer's Disease serum sample_AD31


title: 252035310008_1_4-T60[A(5)/A(3)]


title: 252035310008_2_2-T15[C(5)/C(3)]


title: 251507210463_1_1-T5[B(5)/B(3)]


title: Alzheimer's Disease serum sample_AD33


title: 251507210463_1_2-T15[B(5)/B(3)]


title: 252035310001_2_4-T60[B(5)/B(3)]


title: 252035310008_1_2-T15[A(5)/A(3)]


title: 252035310008_2_3-T30[C(5)/C(3)]


title: Alzheimer's Disease serum sample_AD28


title: 252035310008_1_3-T30[A(5)/A(3)]


title: 252035310008_1_1-T5[A(5)/A(3)]


title: Alzheimer's Disease serum sample_AD27


title: Alzheimer's Disease serum sample_AD26


title: 251507210462_1_2-T15[A(5)/A(3)]


title: 252035310008_2_4-T60[C(5)/C(3)]


title: Alzheimer's Disease serum sample_AD25


title: 252035310001_2_2-T15[B(5)/B(3)]


title: 251507210504_1_2-T15[D(5)/D(3)]


title: Alzheimer's Disease serum sample_AD24


title: 251507210473_1_3-T30[F(5)/F(3)]


title: 252035310008_2_1-T5[C(5)/C(3)]


title: 251507210462_1_4-T60[A(5)/A(3)]


title: Alzheimer's Disease serum sample_AD23


title: Alzheimer's Disease serum sample_AD22


title: 251507210473_1_1-T5[F(5)/F(3)]


title: 251507210504_1_3-T30[D(5)/D(3)]


title: 252047310006_2_2-T30[B(5)/B(3)]

organism: Lachancea waltii

value: heat shock


title: 251507210462_1_3-T30[A(5)/A(3)]


title: Alzheimer's Disease serum sample_AD20

value: serum


title: 252047310006_1_2-T30[A(5)/A(3)]


title: 251507210472_1_2-T15[E(5)/E(3)]


title: 252047310006_2_1-T15[B(5)/B(3)]


title: 252047310006_1_3-T45[A(5)/A(3)]


title: 251507210461_1_4-T60[C(5)/C(3)]


title: 252047310009_2_4-T5[B(5)/B(3)]


title: 251507210461_1_1-T5[C(5)/C(3)]


title: 251507210461_1_3-T30[C(5)/C(3)]


title: Alzheimer's Disease serum sample_AD19


title: Alzheimer's Disease serum sample_AD16


title: Alzheimer's Disease serum sample_AD18


title: Alzheimer's Disease serum sample_AD17


title: 251507210461_1_2-T15[C(5)/C(3)]


title: 252047310009_2_3-T5[A(5)/A(3)]


title: Alzheimer's Disease serum sample_AD15


title: 252047310006_1_1-T15[A(5)/A(3)]


title: 252035310001_2_3-T30[B(5)/B(3)]


title: 252047310006_2_4-T60[B(5)/B(3)]


title: 252047310006_2_3-T45[B(5)/B(3)]


title: Alzheimer's Disease serum sample_AD13


title: Alzheimer's Disease serum sample_AD29


title: 251983810011_2_3-T30[B(5)/B(3)]


title: Alzheimer's Disease serum sample_AD10


title: Alzheimer's Disease serum sample_AD12


title: Alzheimer's Disease serum sample_AD2

value: UNK


title: 251983810011_1_4-T60[A(5)/A(3)]


title: 252047310006_1_4-T60[A(5)/A(3)]


title: Alzheimer's Disease serum sample_AD21


title: Alzheimer's Disease serum sample_AD11

value: Female


title: Alzheimer's Disease serum sample_AD3


title: 251983810011_2_2-T15[B(5)/B(3)]


title: 251983810011_1_1-T5[A(5)/A(3)]


title: Alzheimer's Disease serum sample_AD14


title: 251983810011_2_1-T5[B(5)/B(3)]


title: Alzheimer's Disease serum sample_AD4


title: 251983810011_2_4-T60[B(5)/B(3)]


title: Late third instar yw wing imaginal disc, biological rep3

description: Gene expression data from late third instar yw wing imaginal discs

hyb_protocol: Fragmented RNA was hybridized to each Affymetrix (Santa Clara, CA) GeneChip Drosophila Genome 2.0 array. The arrays were washed and stained on the GeneChip Fluidics Station 450 series.

data_processing: Probe cell intensities for each array were normalized using GCRMA algorithms, which consist of background adjustment and quantile normalization, accounting for probe GC content. Normalization was executed using the R statistical environment [R Foundation for Statistical Computing, Vienna, 2007; ISBN 3-900051-07-0; www.R-project.org] and the Bioconductor package (www.bioconductor.org).

source_name: Late third instar yw wing imaginal disc

label_protocol: Biotin-labeled cRNA  was synthesized from 200 ng of starting RNA and using Affymetrix GeneChip 3′ IVT Express kit according to the manufacturer's instructions.

extract_protocol: Total RNA from wing imaginal discs was isolated using Zymo ZR RNA MicroPrep columns (Zymo Research), or from BG3 cells using Zymo ZR RNA MiniPrep columns (Zymo Research). Twelve to fifteen wing imaginal discs were used per biological replicate, and at least 3 biological replicates were generated per genotype.

treatment_protocol: For RNAi treatment in BG3 cells, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 2 hours. 10 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS withSchneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against the target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools. Ph RNAi constructs target regions of homology between ph-p and ph-d.

value: mixed


title: Alzheimer's Disease serum sample_AD1


title: 251983810011_1_2-T15[A(5)/A(3)]


title: Lgr5ki-villus, ext176

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: cRNA was hybridized to Affymetrix HT MG-430 PM Array Plates according to manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.

data_processing: The expression data extracted from the raw CEL files were normalized with RMAalgorithm from Affymetrix Power Tools. Data were analyzed using the R2 web application, which is freely available at (http://r2.amc.nl).

organism: Mus musculus

source_name: epithelial intestinal villus cells from Lgr5-EGFP-ires-CreERT2 mice

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.

treatment_protocol: Cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice were used, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS-sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow).

tag: strain/background

tag: genotype

value: epithelial intestinal villus cells

tag: lgr5 expression level

value: high


title: Lgr5ki-villus, ext177


title: Lgr5ki-2601-GFPdim, ext167

source_name: FACS-sorted hair follicle cells from Lgr5-EGFP-ires-CreERT2 mice

value: hair follicle cells


title: Lgr5ki-0507-GFPdim, ext182


title: 251983810011_1_3-T30[A(5)/A(3)]


title: Lgr5ki-0511-GFPdim, ext178

source_name: FACS-sorted epithelial intestinal cells from Lgr5-EGFP-ires-CreERT2 mice

value: epithelial intestinal cells


title: Late third instar yw wing imaginal disc, biological rep2


title: Ph RNAi-treated BG3 cells, biological rep2

description: Gene expression data from Ph-depleted BG3 cells

source_name: Ph RNAi-treated BG3 cells, 5 days RNAi treatment

value: male


title: Lgr5ki-2601-GFPdim, ext155


title: Lgr5ki-0501-GFPdim, ext165


title: Late third instar yw wing imaginal disc, biological rep1


title: Lgr5ki-2601-GFPbright, ext156


title: Ph RNAi-treated BG3 cells, biological rep1


title: Mock RNAi-treated BG3 cells, biological rep2

description: Gene expression data from control BG3 cells

source_name: Mock RNAi-treated BG3 cells


title: Lgr5ki-0511-GFPbright, ext179


title: Lgr5ki-0912-GFPbright, ext154

value: low


title: Ph RNAi-treated BG3 cells, biological rep3


title: Lgr5ki-villus, ext175


title: Mock RNAi-treated BG3 cells, biological rep3


title: R10-1698CardA

status: Public on Apr 24 2013

city: Nottingham

first: Graham

middle: Roy

last: Ball

state: Notts

address: Clifton Lane

department: Science and Technology

country: United Kingdom

institute: Nottingham Trent University

data_processing: Results were analyzed using SDS RQ Manager 1.2 (Applied Biosystems, Foster City, CA). The relative miRNA expression level was normalized to the endogenous control RNU6B (MammU6/U6) using qbase PLUS software.

label: FAM

source_name: Luminal A breast cancer

label_protocol: FAM.  Total RNA was reverse transcribed using Megaplex primer pool A (Applied Biosystems) which contained sequence-specific primers for 377 specific miRNAs plus 4 controls (pool A).  An additional panel of 384 miRNAs (377 miRNAs and 4 controls, pool B) was performed on a subset of 4 cancers and 4 controls. Real-time quantitative PCR was performed on the cDNA product, using A and B microfluidic card on an Applied Biosystems 7900HT instrument.

extract_protocol: Total RNA was extracted from blood (1ml) using TRI Reagent BD (Molecular Research Centre, Inc).

treatment_protocol: Venous non-fasting whole blood samples (from both cancers and controls) were collected in BD vacutainers ® containing 18mg dipotassium EDTA anticoagulant (BD-Plymouth, PL6 7BP, UK).

value: F

tag: invasive tumor size

tag: whole tumor size

tag: tumor stage

tag: histolgical tumour type

value: invasive ductal

tag: grade

tag: perineural invasion

value: No

tag: lymphovascular invasion

tag: lymph node status

value: positive, 3/13


title: R10-1144CardA

tag: gender

tag: age

value: 2 tumours:1:20mm and 2:25mm

value: Tumour 1:1, Tumour 2:2

tag: associated dcis

value: Extensive

value: negative 0/1


title: R10-1663CardA

source_name: Control Healthy


title: R10-1667CardA


title: R11-0033CardA

value: 61 mm

value: positive 3/22


title: R10-1659CardA


title: R11-0461CardA


title: R11-0463CardA


title: R11-0470CardA


title: Lgr5ki-0303-GFPbright, ext152


title: R11-0459CardA


title: R11-0388CardA


title: Mock RNAi-treated BG3 cells, biological rep1


title: R10-1277CardA

value: invasive lobular

value: positive 1/28


title: Lgr5ki-0303-GFPdim, ext151


title: Stems of wild type

city: Yangzhou

first: Yijun

last: Wang

state: Jiangsu

address: Wenhui

country: China

institute: Yangzhou University

description: Gene expression data from wild type

hyb_protocol: Following fragmentation, cRNA were hybridized. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: Raw data were normalized by MAS 5.0 algorithm implemented in Expression Console.

organism: Zea mays

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

growth_protocol: All experimental materials were single-grain sowed and nursed with normal agricultural practice.

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

treatment_protocol: No

tag: tissue

value: Stem

value: wild type (Mo17)

tag: developmental stage

value: Tassel emergence


title: R10-1651CardA


title: R11-0457CardA


title: R10-1526CardA

value: Post NA 38mm

value: Yes

value: positive 5/15


title: R10-1387CardA

value: F

value: Post NA 120mm

value: invasive ductal

value: positive 14/16


title: R10-1251CardA

value: No

value: negative (0/7)


title: R10-1062CardA

value: infiltrating ductal

value: Extensive

value: negative (0/2)


title: RA3

city: San Diego

first: John

middle: William

last: Whitaker

state: Ca

address: Gliam Drive

institute: UCSD

hyb_protocol: Infinium Human Methylation 450k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended protocol.

data_processing: GenomeStudio.

label: Cy5 and Cy3

source_name: Fibroblast-like synoviocytes, rheumatoid arthritis

label_protocol: Standard Illumina Protocol.

growth_protocol: Fibroblast-like-synoviocytes were cultured in 10% bovine serum and maintained between 30 and 80% confluence 5% CO2 atmosphere, 37C. Cells were here harvested at 80% confluence. Reference: Rosengren S, Boyle DL, Firestein GS. Acquisition, culture, and phenotyping of synovial fibroblasts. Methods Mol Med 135:365-75 2007.

extract_protocol: Applied Biosystems, MagMax kit was used for extraction. DNA was quantified by Pico-Green and concentrated on Amicon Ultra Spin columns.

treatment_protocol: Cells were not further treated or stimulated. Cells in stable culture were extracted.

tag: disease status

value: rheumatoid arthritis

tag: cell type

value: fibroblast-like synoviocytes

value: male


title: R10-1094CardA

value: Not commented on

value: negative (0/3)


title: R10-1412CardA

value: invasive mucinous

value: negative (0/4)


title: RA2


title: KG1_24H_R406_Replicate2

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

description: The samples were profiled using the HT U133A Gene Expression Arrays (Affymetrix) at the Broad Institute of MIT and Harvard (Cambridge, MA, USA).

hyb_protocol: GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454)

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: Data were extracted from the  CEL files and preprocessed through  the ExpressionFileCreator module implemented  in  GenePattern 3.5.0  software platform (Broad Institute, http://www.broadinstitute.org/cancer/software/genepattern/),  by applying  RMA and the quantile normalization procedures.

source_name: KG-1 cell line, R406 treated for 24 h

label_protocol: Biotin

growth_protocol: Cells were treated with R406 or matched vehicle control for 24 hours in liquid culture. After 24 hours, an equal number of cells were plated at 1:10 (vol/vol) in MethoCult GF+H4435 methylcellulose (StemCell Technologies, #04445) with 1% penicillin-streptomycin and appropriate drug treatment. All plates were incubated at 37 °C and 5% CO2 and colony numbers counted 8–17 days later.

extract_protocol: RNA was extracted using Qiagen Rneasy Mini Kit (74104)

treatment_protocol: MOLM-14, U937, HL-60 and KG-1 cells were treated in triplicate with either DMSO or R406 4μM for 24 hours.

tag: cell line

tag: treatment

tag: time

tag: replicate

value: Replicate 2


title: Stems of D11 mutant

description: Gene expression data from D11

value: Stem

tag: genotype

value: D11 mutant

value: Tassel emergence


title: KG1_24H_R406_Replicate3

value: Replicate 3


title: KG1_24H_DMSO_Replicate1

source_name: KG-1 cell line, DMSO treated for 24 h

value: DMSO

value: Replicate 1


title: KG1_24H_DMSO_Replicate2


title: KG1_24H_R406_Replicate1


title: HL60_R406_Replicate2

source_name: HL-60 cell line, R406 treated for 24 h


title: OA4

value: osteoarthritis


title: KG1_24H_DMSO_Replicate3


title: HL60_DMSO_Replicate3

source_name: HL-60 cell line, DMSO treated for 24 h


title: HL60_DMSO_Replicate2


title: RA1


title: HL60_R406_Replicate3


title: HL60_R406_Replicate1


title: OA2


title: OA5


title: OA3


title: U937_R406_Replicate2

source_name: U937 cell line, R406 treated for 24 h


title: RA4


title: RA5


title: U937_R406_Replicate1


title: U937_R406_Replicate3


title: RA6


title: MOLM_R406_Replicate1

source_name: MOLM-14 cell line, R406 treated for 24 h


title: MOLM_R406_Replicate2


title: HL60_DMSO_Replicate1


title: U937_DMSO_Replicate1

source_name: U937 cell line, DMSO treated for 24 h


title: OA1


title: CNS_Htl[ACT]_rep1

city: London

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

institute: King's College London

description:
B1
Gene expression data from CNS tissue expressing Htl[ACT] in glial cells

hyb_protocol: Hybridisations were performed using the Genechip 3’IVT kit (Affymetrix) on Genechip Drosophila Genome 2.0 Arrays (Affymetrix).

scan_protocol: Imaging of the arrays was performed using the Affymetrix GCS3000 microarray system.

data_processing: Data normalisation was performed using the Microarray Suite version 5 (MAS 5.0) statistical algorithm using the Affymetrix Expression Console software. Probes where the detection p-value (calculated using the intensity value of a perfect match to a mismatch sequence) was >0.062 in any of the samples were classed as absent and excluded from further analysis.

label: Biotin

source_name: CNS tissue from repoGal4/UAS-Htl[ACT] larvae

label_protocol: cRNA was prepared from 500ng of total RNA using the Ambion Premier kit (Ambion).

growth_protocol: Larvae were grown on standard fly food at 25 degrees.

extract_protocol: For the microarray analysis the complete CNS from 10-15 wandering third instar larvae were dissected in PBS and placed into PBS on ice and then transferred into 100ul of lysis buffer from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in triplicate and stored at -80oC.

treatment_protocol: One control and two different experimental genotypes were used: Control (repoGal4/+), Htl[ACT] (repoGal4>UAS-Htl[ACT]) and InR (repoGal4>UAS-InR).

value: CNS


title: MOLM_R406_Replicate3


title: U937_DMSO_Replicate2


title: U937_DMSO_Replicate3


title: CNS_Htl[ACT]_rep2

description:
B2_2
Gene expression data from CNS tissue expressing Htl[ACT] in glial cells


title: CNS_InR_rep1

description:
C1
Gene expression data from CNS tissue overexpressing InR in glial cells

source_name: CNS tissue from repoGal4/UAS-InR larvae


title: MOLM_DMSO_Replicate3

source_name: MOLM-14 cell line, DMSO treated for 24 h


title: CNS_control_rep1

description:
A1
Gene expression data from control CNS tissue

source_name: CNS tissue from repoGal4/+ control larvae


title: CNS_InR_rep3

description:
C3
Gene expression data from CNS tissue overexpressing InR in glial cells


title: MOLM_DMSO_Replicate1


title: CNS_control_rep3

description:
A3
Gene expression data from control CNS tissue


title: CNS_Htl[ACT]_rep3

description:
B3
Gene expression data from CNS tissue expressing Htl[ACT] in glial cells


title: MOLM_DMSO_Replicate2


title: CB1190 pyruvate (H2bicarbonate reference) rep1

city: Berkeley

first: Ariel

last: Grostern

state: CA

address: 209 O'Brien Hall

department: Civil & Environmental Engineering

institute: UC Berkeley

hyb_protocol: Hybridization followed the procedure of the Affymetrix protocol for Modified FlexMidi_euk2v3 for P. aeruginosa Array.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000 scanner.

data_processing: Primary data was generated with RMAExpress 1.05. Quantile normalization with background adjustment was performed across all arrays, and the PLM summarization method was used.

organism: Pseudonocardia dioxanivorans CB1190

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, pyruvate-grown

label_protocol: cDNA was obtained from 3.5 ug of RNA following the Affymetrix protocol for RT. RNA template was degraded with NaOH treatment. cDNA was fragmented with DNaseI, and fragmented cDNA while terminally labeled with biotin.

growth_protocol: Cells were grown in AMS medium amended with pyruvate (31 mM) or bicarbonate (36 mM) and H2 (10% in headspace).

extract_protocol: Nucleic acids were obtained following cell lysis with heating and bead-beating in the presence of SDS and phenol. Phenol/chloroform extraction, followed by column-based purification, was performed. Nucleic acids were treated with DNaseI and RNA was finally purified by RNeasy purification.

treatment_protocol: Cells were harvested by filtration and scraped from the filter into vials that were frozen at -80C.

value: pyruvate


title: CNS_InR_rep2

description:
C2
Gene expression data from CNS tissue overexpressing InR in glial cells


title: Kinesin IP vs. control, AAA array

city: St Augustine

first: Andrea

middle: B

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

institute: University of Florida

description:
Antibody pulldown complex.
1 plate

hyb_protocol: The recommended amount of 750 ng of labeled cRNA was fragmented and hybridized to the arrays using the recommended procedures described in the In situ Hybridization Kit Plus (Agilent Technologies). Controls provided in the In situ Hybridization Kit were spiked in at the time of hybridization. The arrays were washed according to the manufacturer's recommended protocol.

scan_protocol: The arrays were scanned on an Agilent Technologies G2565AA Microarray Scanner. Data were extracted after scanning using Agilent’s Feature Extraction 5.1.1 software.

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using the LOWESS smoothing procedure as implemented in the Agilent Feature Extraction software version 7.0. The background for the Cy3 and Cy5 channels on all arrays analyzed was observed to be nearly identical (41.8 +/- 1.1) over all 44,000 features. No local background subtraction was performed; instead, the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm. Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both the Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis.

organism: Aplysia californica

source_name: Kinesin IP

label_protocol: cRNA production was performed using Agilent’s Low RNA Input Linear Amplification kit (Agilent Technologies). All amplification reactions involved only one round of amplification. The concentration of the cRNA was determined by GeneSpec III and the 2100 Bioanalyzer. The cRNA was labeled either using the direct method in Agilent’s Low RNA Input Linear Amplification kit or with an indirect technique using the MicroMax ASAP RNA labeling kit (PerkinElmer).

growth_protocol: Aplysia californica were obtained from the NIH/University of Miami National Resource for Aplysia and held in 40-400 liter aquaria with circulating fresh seawater at 15-17º C.

extract_protocol: Isolation of an RNA transport complex from the Aplysia central nervous system: Custom antibodies to Aplysia Kinesin were used in a pull-down experiment. mRNAs associated with the kinesin complex were extracted using RNAqueous or RNAqueous-Micro (Ambion, Austin, TX) kits depending on sample size. Before further processing of the RNA, quality was checked using a 2100 Bioanalyzer (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample. Moreover, it provides information about potential DNA contamination and the approximate RNA concentration. Additionally, RNA concentration was measured spectrophotometrically by using the GeneSpec III system (Mirai Bio).

treatment_protocol: Aplysia californica weighing 100-160g were used. Animals were anesthetized by injection of 60% (volume/body weight) isotonic MgCl2 (337mM) prior to removal of the CNS. Ganglia were mechanically removed with fine forceps and scissors, and cells were isolated. Neurons were then fixed in 75% ethanol for several minutes.

value: central nervous system (CNS)

value: neurons

tag: antibody

value: anti-Aplysia kinesin

value: non-specific (secondary) antibody

source_name: Control


title: CB1190 pyruvate (H2bicarbonate reference) rep3


title: CB1190 H2bicarbonate rep1

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, H2/bicarbonate-grown


title: CNS_control_rep2

description:
A2
Gene expression data from control CNS tissue


title: CB1190 pyruvate (H2bicarbonate reference) rep2


title: Multilineage Differentiating Stress-Enduring-Adipose Tissue Cell Replicate 3

city: Washington

first: Saleh

middle: Gamal

last: Heneidi

state: DC

address: 3900 Reservoir Rd, NW, SE404 Med-Dent Building

department: Department of Pharmacology and Physiology

institute: Georgetown University Medical Center

hyb_protocol: Agilent standard protocol

scan_protocol: Chips were scanned using the Agilent Technologies G2505C Microarray Scanner System

data_processing: gProcessedSignal(normalized) columns were further processed using GeneSpringGX version 12.1.0 (Agilent).

source_name: Multilineage Differentiating Stress-Enduring-Adipose Tissue cells

label_protocol: Agilent standard protocol

growth_protocol: Lipoaspirates (100-200g per aspirate) were obtained from subcutaneous abdominal adipose of women undergoing elective liposuction.   Lipoaspirate was repeatedly washed with PBS until blood was completely removed from the tissue, and then incubated with equal volume of DMEM containing collagenase (0.1 %, Sigma Aldrich) for 30 min at 37°C in a shaking incubator at 110 rpm, followed by incubation in 4°C, while still in collagenase and nutritionally deficient medium (no FCS), for 16 hours under severe hypoxia conditions. Digested material was then centrifuged at 1500 rpm for 10 minutes at 4°C. Supernatant containing adipose cell debris (dead adipocytes, macrophages, red blood cells, adipose stem cells among other cell components) was removed by aspiration and the remaining cell pellets were washed several times with PBS.  Pellets were resuspended in PBS and incubated with a red blood cell lysis buffer (eBiosciences, San Diego, CA) for 10 min at R/T (2X). Remaining cell pellets contain cells highly resistant to severe cellular stress, and these were resuspended in Dulbecco’s Modified Eagle Medium 1x (DMEM; CellGro, MediatechInc, Manassas, VA) containing 10% fetal bovine serum (FBS; Thermo Scientific Hyclone, Logan, UT) and 5% antibiotic-antimyocotic solution (CellGro, Mediatech Inc, Manassas, VA) and plated as cells in suspension as well as adherent cells. For ASC isolation, lipoaspirate material was subjected to collagenase digestion (0.1 %, Sigma Aldrich) for 30 min at 37°C in a shaking incubator at 110 rpm, and ASCs were isolated and cultured as previously as previously described (Zuk, et al. Mol Biol Cell. 2002 December; 13(12): 4279–4295).

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen).

value: lipoaspirated adipose tissue


title: Melanoma primary tumor K15582

city: Leiden

first: Linda

last: Gao

address: Einthovenweg 20

department: Dermatology

institute: Leids Universitair Medisch Centrum

description: primary melanoma tumor

hyb_protocol: bisulphite-converted genomic DNA was amplified, fragmented and hybridised to the Infinium HumanMethylation27 Beadchip according to Illumina's standard protocols

scan_protocol: beadchips were imaged using a BeadArray Reader with Illumina's recommended standard scanner settings

data_processing: BeadStudio and R software

label: Cy3 and Cy5

source_name: primary melanoma, malignant

label_protocol: labelling was performed according to Illumina's standard protocols for the HumanMethylation27 BeadChip

extract_protocol: genomic DNA was extracted using Qiagen's Genomic-tip kit according to the kit's standard protocols

value: fresh-frozen primary melanoma

value: Female


title: CB1190 H2bicarbonate rep2


title: Melanoma primary tumor K16334

description: primary melanoma tumor


title: CB1190 H2bicarbonate rep3


title: Cyclomarin_series_10

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 32 SMP3 print tips from Telechem (http://www.arrayit.com ). The M. tuberculosis microarray (Mtbb) probe set is based on 70mer oligonucleotides from Qiagen's Tuberculosis Genome Oligo Set Version 1.0 ( http://oligos.qiagen.com/arrays/omad.php ). Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The Mtbb microarray spot densities are 270 microns (center-to-center). The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) or PowerMatrix Slides (Full Moon Biosystems, # PXP-M) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.

hyb_protocol: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~11 ul recovered for each). Add 1 µl herring sperm DNA (8-10 ug/ul) and 0.2 ul tNRA (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 12 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 12 ul of 2X F-hyb buffer to samples. Load 25 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (on rocking platform), for 2 minute in 1X SSC (with rocking), for 2 minutes in 0.2X SSC (on rocking platform), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry.

scan_protocol: Creator: GenePix Pro 4.0.1.22, Scanner: GenePix 4000B [83871], ScanPower: 100;; 100, LaserPower: 2.88;; 3.7, Temperature: 30.97

data_processing: mAdb Data Processing Protocol (v. 2). Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

organism: Mycobacterium tuberculosis H37Rv

source_name: test culture_0.625uM Cyclomarin [anti TB compound]

label_protocol: Cy5: 4ug total RNA is converted to cDNA using Invitrogen random primers and superscript III at 48C in presence of 10-fold excess of Cy5-dCTP above unlabeled dCTP according to manufacturer's instructions. Cy3: 4ug total RNA is converted to cDNA using Invitrogen random primers and superscript III at 48C in presence of 10-fold excess of Cy3-dCTP above unlabeled dCTP according to manufacturer's instructions.

extract_protocol: Extracted molecule total RNA. Extraction protocol Trizol MTb Extraction. Extraction method: Trizol-QIAgen RNeasy Kit. Mycobacterium tuberculosis was rapidly harvested and cell pellet suspended in Trizol, subjected to 2-3 rounds of bead beating (0.1mm zirconia beads), phase separation performed with CHCl3 and RNA purified with the Quiagen RNeasy clean up kit using Qiagen on-column DNase to remove contaminating DNA.

tag: growth protocol

value: H37Rv at an OD650 of 0.2 in 7H9-based medium

tag: treatment protocol

value: treated for 6h with 0.625uM Cyclomarin

source_name: control culture_DMSO

value: treated for 6h with DMSO vehicle control


title: Melanoma primary tumor K24091

description: primary melanoma tumor

value: Male


title: Melanoma primary tumor  K20015

description: primary melanoma tumor


title: Melanoma primary tumor K5557

description: primary melanoma tumor


title: Cyclomarin_series_11

source_name: test culture_1.25uM Cyclomarin [anti TB compound]

value: treated for 6h with 1.25uM Cyclomarin


title: Melanoma primary tumor K9900

description: primary melanoma tumor


title: Melanoma primary tumor K7393

description: primary melanoma tumor


title: Cyclomarin_series_9

source_name: test culture_0.125uM Cyclomarin [anti TB compound]

value: treated for 6h with 0.125uM Cyclomarin


title: Melanoma primary tumor K14277

description: primary melanoma tumor


title: Melanoma primary tumor K6386

description: primary melanoma tumor


title: Melanoma primary tumor K21160

description: primary melanoma tumor


title: Melanoma primary tumor K20506

description: primary melanoma tumor


title: Melanoma primary tumor K10454

description: primary melanoma tumor


title: Melanoma primary tumor K17155

description: primary melanoma tumor


title: Melanoma primary tumor K5666

description: primary melanoma tumor


title: Multilineage Differentiating Stress-Enduring-Adipose Tissue Cell Replicate 2

value: Multilineage Differentiating Stress-Enduring-Adipose Tissue cells


title: Melanoma primary tumor K4554

description: primary melanoma tumor


title: Melanoma primary tumor K8269

description: primary melanoma tumor


title: Melanoma primary tumor K5912

description: primary melanoma tumor


title: Cyclomarin_series_8

source_name: test culture_0.0625uM Cyclomarin [anti TB compound]

value: treated for 6h with 0.0625uM Cyclomarin


title: Melanoma primary tumor K17716

description: primary melanoma tumor


title: Lipiarmycin_2

source_name: test culture_1uM Lipiarmycin [anti TB compound]

value: treated for 6h with 1uM Lipiarmycin


title: Adipose Stem Cell Replicate 2

source_name: Adipose stem cells

value: Adipose stem cells


title: Cyclomarin_series_6

source_name: test culture_0.1uM Cyclomarin [anti TB compound]

value: treated for 6h with 0.1uM Cyclomarin


title: Multilineage Differentiating Stress-Enduring-Adipose Tissue Cell Replicate 1


title: Cyclomarin_series_7

source_name: test culture_0.5uM Cyclomarin [anti TB compound]

value: treated for 6h with 0.5uM Cyclomarin


title: Melanoma primary tumor K12832

description: primary melanoma tumor


title: Cyclomarin_series_5


title: Melanoma primary tumor K7206

description: primary melanoma tumor


title: Melanoma primary tumor K17504

description: primary melanoma tumor


title: Melanoma primary tumor K5940

description: primary melanoma tumor


title: Melanoma primary tumor K7376

description: primary melanoma tumor


title: Cyclomarin_series_4


title: Cyclomarin_series_3


title: Adipose Stem Cell Replicate 3


title: Cyclomarin_series_2


title: Melanoma primary tumor K14294

description: primary melanoma tumor


title: Adipose Stem Cell Replicate 1


title: Naevus benign K24848

description: benign naevus

source_name: dermal melanocytic naevus, benign

value: fresh-frozen benign naevus


title: Naevus benign K23342

description: benign naevus


title: Naevus benign K22691

description: benign naevus


title: Naevus benign K23142

description: benign naevus


title: Cyclomarin_series_1


title: hASC_Passage3_Rep1

city: Logroño

first: Andrés

last: Sanz-García

state: La Rioja

address: C/ Luis de Ulloa 20

country: Spain

institute: University of La Rioja

description:
ADH3
Gene expression after 10-12 days in culture_hASC cells in xenogeneic-free conditions

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hASC after 10-12 days in culture_Rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 800ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
Isolation  protocol: Fresh liposuctionsfrom healthy donors under aesthetic procedures  were digested in collagenase type I for 90´at 37ºC.Then cells obtained  were washed in 0.5%HSA in HBSS. Once Isolated, hASC were seeded in DMEM suplemented with 6%Human Serum(HS) and maintained in an incubator at 37C and 5%CO2.
Cells were maintained in DMEM+6%HS until reach 80% of confluence.At that moment cells were detached and expanded using Tryple®.

extract_protocol: RNA was extracted using the RNAse kit (Quiagen) following the manufacturer's recommendations and treated with DNAse (Quiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: origin

value: pool from 8 healthy donors

value: Human adipose stem cells (hASCs)


title: hASC_Passage1_Rep1

description:
ADH1
Gene expression after 3-5 days in culture_hASC cells in xenogeneic-free conditions

source_name: hASC after 3-5 days in culture_Rep1


title: hASC_after_isolation_Rep1

description:
G0
Gene expression after isolation_hASC cells in xenogeneic-free conditions

source_name: hASC immediately after isolation_Rep1


title: Lipiarmycin_1


title: hASC_Passage5_Rep1

description:
ADH5
Gene expression after 20 days in culture_hASC cells in xenogeneic-free conditions

source_name: hASC 20 days after isolation _Rep1


title: Naevus benign K24383

description: benign naevus


title: Effect of 24-h herbivory exposure to VHb leaves 2

city: Oulu

first: Suvi

middle: Tuulia

last: Sutela

department: Biology

country: Finland

institute: University of Oulu

description:
VHb_L1_rep2
Replicate 2.

hyb_protocol: Hybridizations and post-washings were conducted following the instructions of 3DNA Array 50 Expression Array Detection Kit (Genisphere Inc).

scan_protocol: Slides were scanned at 633 nm and 543 nm at 98 % laser power, at a resolution of 10 µm with varying PMT values with ScanArray® Gx PLUS (Microarray Scanner, PerkinElmer, Waltham, MA, USA). The fixed-circle method was used in the quantification of spots, and the total-algorithm in the normalization was conducted with the ScanArray Express software (PerkinElmer).

data_processing: The statistical processing of the data was conducted separately on the two lines and different leaf samples by using identical procedures. The low quality spots were downweighted; these included spots with the sum of median pixel intensities less than 300 and spots having the feature pixel intensity less than 55 % above one standard deviation of the background pixel intensity in both wavelengths. The data was normalized by using print-tip loess within and Aquantile (Aq) between array normalizations.

organism: Populus tremula x Populus tremuloides

source_name: Control treatment, VHb L1 leaf

label_protocol: The SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) was used to synthesize cDNAs in accordance with the manufacturer's instructions and the instructions of the 3DNA Array 50 Expression Array Detection Kit For Microarrays (Genisphere Inc, Hatfield, PA, USA).

growth_protocol: The lines were multiplicated on liquid MS medium (full strength of C10H12FeN2NaO8; half strength of other micro and macro nutrients; 2.22 μM BA and 2.85 μM IAA) in RITA® temporary immersion containers (Vitropic, Saint-Mathieu-de-Tréviers, France) under 16:8 h light/dark photoperiod (110-130 μmol m-2s-1) at 22 ºC. Saplings were rooted on MS without plant growth regulators, acclimated in the Botanical Gardens of the University of Oulu (65°03'N, 25°27'E), and potted to limed and fertilised soil, and grown under standard greenhouse conditions.

extract_protocol: The total RNA was extracted as described by Jaakola et al. (Mol. Biotechnol. 19 (2001) 201-203) except for the first centrifugation step which was omitted.

treatment_protocol: The saplings of wt and VHb lines grown 1.5 months under standard greenhouse conditions were used in the experiments. In the herbivory treatment, one larvae of Conistra vaccinii L. (Lepidoptera: Noctuidae) was placed on the leaf inside the veil cloth bag for 24 hours, which after samples were collected to liquid nitrogen.

tag: line

value: V617/45, generated via Agrobacterium mediated gene transfer using pBVHb

value: leaf

tag: leaf type

value: non-treated leaf, LPI 9

tag: plant number

source_name: Herbivory treatment, VHb L1 leaf

value: treated leaf, LPI 7

value: herbivore (chestnut moth larvae)


title: R10-1659CardB

source_name: Control Healthy

tag: gender

value: F

tag: age

tag: invasive tumor size

tag: whole tumor size

tag: tumor stage

tag: histolgical tumour type

tag: grade

tag: associated dcis

tag: perineural invasion

tag: lymphovascular invasion

tag: lymph node status


title: R10-1651CardB


title: Effect of 24-h herbivory exposure to VHb leaves 1

description:
VHb_L1_rep1
Replicate 1.

tag: tissue

value: non-treated leaf, LPI 8

tag: treatment

value: treated leaf, LPI 9


title: R10-1094CardB

source_name: Luminal A breast cancer

value: infiltrating ductal

value: Not commented on

value: negative (0/3)


title: Effect of 24-h herbivory exposure to VHb leaves 3

description:
VHb_L1_rep3
Replicate 3.

value: non-treated leaf, LP8

value: treated leaf, LP9


title: R10-1251CardB

value: invasive ductal

value: No

value: Yes

value: negative (0/7)


title: R10-1412CardB

value: invasive mucinous

value: negative (0/4)


title: R10-1062CardB

value: Extensive

value: negative (0/2)


title: Uninjured wt leaves positioned below herbivory exposure 3

description:
wt_B_rep3
Replicate 3.

source_name: Control treatment, wt B leaf

value: V617, non-transgenic

value: leaf

value: below leaf, LPI 9

source_name: Herbivory treatment, wt B leaf

value: below leaf, LPI 8

value: herbivore (chestnut moth larvae)


title: Uninjured wt leaves positioned below herbivory exposure 2

description:
wt_B_rep2
Replicate 2.


title: Uninjured VHb leaves positioned above herbivory exposure 3

description:
VHb_A_rep3
Replicate 3.

source_name: Control treatment, VHb A leaf

value: V617/45, generated via Agrobacterium mediated gene transfer using pBVHb

value: above leaf, LPI 8

source_name: Herbivory treatment, VHb A leaf


title: R10-1663CardB

value: F


title: Uninjured VHb leaves positioned below herbivory exposure 1

description:
VHb_B_rep1
Replicate 1.

source_name: Control treatment, VHb B leaf

value: below leaf, LPI 11

source_name: Herbivory treatment, VHb B leaf


title: R10-1667CardB


title: Uninjured VHb leaves positioned below herbivory exposure 2

description:
VHb_B_rep2
Replicate 2.

value: below leaf, LPI 10


title: Effect of 24-h herbivory exposure to wt leaves 1

description:
wt_L1_rep1
Replicate 1.

source_name: Control treatment, wt L1 leaf

value: non-treated leaf, LPI 6

source_name: Herbivory treatment, wt L1 leaf

value: treated leaf, LPI 7


title: Effect of 24-h herbivory exposure to wt leaves 3

description:
wt_L1_rep3
Replicate 3.

value: non-treated leaf, LPI 7

value: treated leaf, LPI 6


title: Effect of 24-h herbivory exposure to wt leaves 2

description:
wt_L1_rep2
Replicate 2.


title: Uninjured VHb leaves positioned below herbivory exposure 3

description:
VHb_B_rep3
Replicate 3.


title: Uninjured wt leaves positioned above herbivory exposure 3

description:
wt_A_rep3
Replicate 3.

source_name: Control treatment, wt A leaf

value: above leaf, LPI 6

source_name: Herbivory treatment, wt A leaf

value: above leaf, LPI 5


title: Kinesin IP vs. control, DAA array

description:
Antibody pulldown complex.
1 plate

source_name: Kinesin IP

value: central nervous system (CNS)

tag: cell type

value: neurons

tag: antibody

value: anti-Aplysia kinesin

value: non-specific (secondary) antibody

source_name: Control


title: Uninjured wt leaves positioned above herbivory exposure 2

description:
wt_A_rep2
Replicate 2.

tag: line

value: V617, non-transgenic

value: leaf

tag: leaf type


title: Uninjured VHb leaves positioned above herbivory exposure 1

description:
VHb_A_rep1
Replicate 1.

value: V617/45, generated via Agrobacterium mediated gene transfer using pBVHb

value: above leaf, LPI 7

tag: plant number

value: herbivore (chestnut moth larvae)


title: Liver, Lactobacillus brevis119-2 containing diet administrated for 2 weeks, biological rep4

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Factor Analysis for Robust Microarray Summarization (FARMS) method, using the statistical language R and Bioconductor.

organism: Rattus norvegicus

source_name: Liver, fed Lactobacillus brevis119-2 containing diet for 2 weeks

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolatedusing Trizol reagent (Invitrogen Life Technologies Corp.), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

tag: gender

value: Male

tag: strain

value: Sprague-Dawley

value: Liver

tag: age

value: 7 weeks


title: Liver, control diet administrated for 2 weeks, biological rep4

description: No additional information

source_name: Liver, fed control CRF-1 diet for 2 weeks


title: Uninjured wt leaves positioned below herbivory exposure 1

description:
wt_B_rep1
Replicate 1.

value: below leaf, LPI 8

value: below leaf, LPI 9


title: Uninjured wt leaves positioned above herbivory exposure 1

description:
wt_A_rep1
Replicate 1.

value: above leaf, LPI 6


title: Uninjured VHb leaves positioned above herbivory exposure 2

description:
VHb_A_rep2
Replicate 2.


title: Liver, Lactobacillus brevis119-2 containing diet administrated for 2 weeks, biological rep2

description: No additional information


title: Liver, Lactobacillus brevis119-2 containing diet administrated for 2 weeks, biological rep1

description: No additional information


title: Liver, control diet administrated for 2 weeks, biological rep2

description: No additional information


title: Liver, Lactobacillus brevis119-2 containing diet administrated for 2 weeks, biological rep3

description: No additional information


title: Liver, control diet administrated for 2 weeks, biological rep1

description: No additional information


title: Human induced pluripotent stem cell-derived mesenchymal cells (BC1)-5 weeks bioreactor

city: New York

first: Giuseppe Maria

last: de Peppo

state: NY

address: 3960 Broadway

department: Research and Development

institute: The New York Stem Cell Foundation

description:
Bone marrow cells
pooled

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio software

source_name: Bone marrow cells

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent2100 Bioanalyser.

tag: growth condition

value: 5 weeks bioreactor

tag: cell line


title: Human induced pluripotent stem cell-derived mesenchymal cells (1013A)-5 weeks bioreactor

description:
Dermal fibroblasts
pooled

source_name: Dermal fibroblasts


title: Liver, control diet administrated for 2 weeks, biological rep3

description: No additional information


title: Human embryonic stem cell-derived mesenchymal cells (H13)-5 weeks bioreactor

description:
Inner cell mass
pooled

source_name: Inner cell mass


title: Itgb3 knockdown (Itgb3-17 shRNA) in LSCs, rep2

first: Fatima

last: Al-Shahrour

department: Cancer program

institute: Broad Institute of MIT and Harvard

description:
Itgb3.shRNA.2
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate2

scan_protocol: BeadArrays were scanned with a BeadArray Reader (Illumina) and expression intensities were calculated with Beadstudio software (Illumina).

data_processing: The samples were analyzed by MouseWG-6 v2.0 Expression BeadChip (Illumina). The quality of probe intensities was determined using the BeadArray R package from Bioconductor (Dunning et al., 2007). The quantiles algorithm from the Affymetrix R package was used.

source_name: leukemia stem cells, Itgc3 knockdown

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was isolated using Trizol (Invitrogen).

tag: strain/background

value: C57BL/6 Actin-dsRed

value: bone marrow

value: primary leukemia stem cells

tag: shRNA


title: Human bone marrow-derived mesenchymal cells (donor 1)-5 weeks bioreactor

description:
Bone marrow
pooled

source_name: Bone marrow

tag: individual

value: donor 1


title: Itgb3 knockdown (Itgb3-20 shRNA) in LSCs, rep4

description:
Itgb3.shRNA.4
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate4


title: Human embryonic stem cell-derived mesenchymal cells (H13)

description:
Inner cell mass
pooled


title: Human induced pluripotent stem cell-derived mesenchymal cells (11c)

description:
Dermal fibroblasts
pooled


title: Control shRNA (Luc) in LSCs, rep3

description:
Luc.3
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate3

source_name: leukemia stem cells, control

value: control


title: Human induced pluripotent stem cell-derived mesenchymal cells (BC1)

description:
Bone marrow cells
pooled


title: Fermentation_Xylose_ΔPHO80l_rep3

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

institute: Kobe University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Yeast Microarrays for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Region 61x21.6 mm, Scan resolution 5um, R PMT is set to 100% and G PMT is set to 100%, XRD=0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 Apr08) and Grid: 015072_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities. Quantile normalization of data was performed with Excel.

source_name: Yeast cell, 6hr xylose fermentation, ΔPHO80

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the One-Color Low-input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer, and its quality checked by Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was obtained by following the protocol provided for the Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA, USA). RNA concentration and quality were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.

tag: genotype

value: PHO80 deletion

value: 80g/l xylose


title: Human bone marrow-derived mesenchymal cells (donor 1)

description:
Bone marrow
pooled


title: Itgb3 knockdown (Itgb3-20 shRNA) in LSCs, rep5

city: Cambridge

address: 7 Cambridge Center

description:
Itgb3.shRNA.5
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate5


title: Itgb3 knockdown (Itgb3-17 shRNA) in LSCs, rep3

description:
Itgb3.shRNA.3
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate3


title: Control shRNA (Luc) in LSCs, rep1

description:
Luc.1
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate1


title: Human bone marrow-derived mesenchymal cells (donor 2)

description:
Bone marrow
pooled

value: donor 2


title: Human embryonic stem cell-derived mesenchymal cells (H9)-5 weeks bioreactor

description:
Inner cell mass
pooled


title: Human embryonic stem cell-derived mesenchymal cells (H9)

description:
Inner cell mass
pooled


title: Itgb3 knockdown (Itgb3-17 shRNA) in LSCs, rep1

description:
Itgb3.shRNA.1
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate1


title: Control shRNA (Luc) in LSCs, rep2

description:
Luc.2
Leukemia stem cells (Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi) driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice.
Replicate2


title: Human induced pluripotent stem cell-derived mesenchymal cells (1013A)

description:
Dermal fibroblasts
pooled


title: Fermentation_Xylose_Control_rep2

source_name: Yeast cell, 6hr xylose fermentation, control

value: wild-type


title: Fermentation_Xylose_Control_rep3


title: Fermentation_Xylose_ΔPHO80l_rep1


title: Fermentation_Xylose_ΔPHO80l_rep2


title: Rpb3_BG3_Rad21RNAi

city: St Louis

first: Cheri

last: Schaaf

address: 1100 South Grand Ave

institute: Saint Louis University School of Medicine

description: Rpb3 ChIP from Rad21 RNAi-treated Drosophila ML-DmBG3-c2 cells

hyb_protocol: Hybridization cocktails were generated using the labeled DNA fragments (2 μg labeled DNA, 1x MES, 3M TMAC, 40 pM Affymetrix control oligo B2, 100 μg/mL salmon sperm DNA, and 0.02% Triton X-100). Each chip was pre-hybridized with 200 μl of 1X MES-triton for 1 hour in the Affymetrix Hybridization 645 oven at 45 rpm and 45oC.  Samples in hybridization cocktail were heated for 10 minutes at 99oC then incubated to a 45oC for 10 minutes. Samples are spun in a microcentrifuge at maximum speed for 3 min.  200 μl of a sample was injected in to a chip. Hybridization was carry out in the hybridization oven at 45 rpm and 45oC for 18 hours. The arrays were washed and stained on the GeneChip Fluidics Station 450 series.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
MAT software (Johnson et al. 2006) was used to calculate ChIP enrichment and significance across the non-repetitive Drosophila genome.
matscore.bar files contain MATscores for each probe as generated using MAT software (Johnson et al. 2006). .bed files indicate significant binding at p-value less than or equal to 10-3.

label_protocol: Immunoprecipitated DNA was amplified using the GenomePlex Complete Whole Genome Amplification Kit (Sigma) and fragmented using controlled DNAse I reactions. Fragmented DNA was labeled with bio-11-ddATP (Perkin Elmer) using a Terminal Transferase  labeling kit (Roche).

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin.

extract_protocol: BG3 cells were grown to a concentration of 5x106/mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x109/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 uL chromatin aliquots, each representing ~50x106 cells, were snap frozen on dry ice. For immunoprecipitation, 200 μL aliquots of chromatin (50 x 106 BG3 cells) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein A/G agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 2 hours. 10 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS withSchneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools. Cohesin RNAi-treated cells were screened for sister chromatid cohesion defects, and none were found, though a mild cell division delay occurred immediately following RNAi treatment.

value: male

value: Anti-Rpb3, rabbit (Karen Adelman, NIEHS, NIH)

value: Rad21 RNAi-treated

source_name: Input DNA from ML-DmBG3-c2 cells


title: Rpb3_BG3_Mock

description: Rpb3 ChIP from Mock RNAi-treated Drosophila ML-DmBG3-c2 cells

value: Mock RNAi-treated


title: Ser2P_BG3_Mock

description: Ser2P-Pol II ChIP from Mock RNAi-treated Drosophila ML-DmBG3-c2 cells

value: Anti-Ser2P Pol II, rabbit (ab5095, Abcam, Lot GR5408-1)


title: Ser2P_BG3_Rad21RNAi

description: Ser2P-Pol II ChIP from Rad21 RNAi-treated Drosophila ML-DmBG3-c2 cells


title: Fermentation_Xylose_Control_rep1


title: Neural Stem Cells cultured in feeder free condition (Matrigel) with NSC Media Replicate 2

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

description:
International Stem Cell Corporation
Biological Replicate 2

data_processing: The data (47207 probes) were filtered for detection pValue < 0.01 (33933 probes) and then normalised using robust spline normalisation with lumi in R

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

growth_protocol: Human pluripotent stem cells were differentiated into neural stem cells under feeder-free conditions through a chemically defined method. Neural stem cells were expanded, characterized, and further differentiated into dopaminergic neurons under defined conditions.

extract_protocol: Total RNA was purified using the RNeasy Plus Mini Kit extraction kit (Qiagen), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

value: Female


title: Brain tissue

description:
Cureline
Biological Replicate 1

source_name: Substantia Nigra


title: CycT_BG3_Rad21RNAi

description: Cyclin T ChIP from Rad21 RNAi-treated Drosophila ML-DmBG3-c2 cells

value: Anti-CycT, rabbit (Akira Nakamura, RIKEN Center for Developmental Biology, Japan)


title: Mature dopaminergic neurons cultured in neurobasal Media Replicate 2


title: liver_24 hr after 2/3 PH_rep2

city: Shanghai

first: Dan

last: Xu

address: Xiangyin Road

department: Second Military Medical University

institute: Mus musculus

description: LncRNA expression of mouse liver 24 hr after 2/3 PH

hyb_protocol: A total of 1μg of labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100μl of hybridization solution was then dispensed in the gasket slide and assembled to the lcnRNA expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned.

scan_protocol: The hybridized arrays were scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technologies’ guidelines.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing was performed using the GeneSpringGX v11.0 software package (Agilent Technologies).Following Quantile normalization of the raw data, low intensity are filtered, lncRNAs and mRNAs that at least 1 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: liver, 24 hr after 2/3 PH

label_protocol: Sample labeling and hybridization reactions were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA was linearly amplified and labeled with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol cy3/μg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: All mice were used in accordance with the institutional guidelines for animal care.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. RNA quality was assessed by Nanodrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Mouse liver samples were obtained at 0, 1.5, 12 and 24 hours after 2/3 partial hepatectomy, and three mice were analyzed for each time point.

value: Male

value: Fresh liver tissues

value: six-week-old


title: CycT_BG3_Mock

description: Cyclin T ChIP from Mock RNAi-treated Drosophila ML-DmBG3-c2 cells


title: liver_24 hr after 2/3 PH_rep3


title: Human dermal fibroblast_>30_rep1

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: Human dermal fibroblast

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

tag: doubling time (dt, days)

value: human diploid fibroblasts


title: Human dermal fibroblast_30_rep1


title: liver_24 hr after 2/3 PH_rep1

tag: tissue


title: Cdk12_BG3_Rad21RNAi

description: Cdk12 ChIP from Rad21 RNAi-treated Drosophila ML-DmBG3-c2 cells

value: Anti-Cdk12, rabbit (Arno Greenleaf, Duke University)

tag: treatment


title: Mature dopaminergic neurons cultured in neurobasal Media Replicate 1

description:
International Stem Cell Corporation
Biological Replicate 1


title: Human Pluripotent Stem cell cultured in feeder free condition (Matrigel) with Stempro Media Replicate 1


title: Human dermal fibroblast_14_rep1

tag: cell type


title: Human dermal fibroblast_20_rep1


title: liver_12 hr after 2/3 PH_rep2

description: LncRNA expression of mouse liver 12 hr after 2/3 PH

source_name: liver, 12 hr after 2/3 PH


title: liver_1.5 hr after 2/3 PH_rep3

description: LncRNA expression of mouse liver 1.5 hr after 2/3 PH

source_name: liver, 1.5 hr after 2/3 PH


title: Human Pluripotent Stem cell cultured in feeder free condition (Matrigel) with Stempro Media Replicate 2


title: liver_12 hr after 2/3 PH_rep1


title: Human dermal fibroblast_15_rep1


title: Human dermal fibroblast_12_rep1


title: Cdk12_BG3_Mock

description: Cdk12 ChIP from Mock RNAi-treated Drosophila ML-DmBG3-c2 cells

tag: antibody


title: liver_12 hr after 2/3 PH_rep3


title: Human dermal fibroblast_10_rep1


title: liver_1.5 hr after 2/3 PH_rep2


title: liver_0 hr after 2/3 PH_rep1

description: LncRNA expression of mouse liver 0 hr after 2/3 PH

source_name: liver, 0 hr after 2/3 PH


title: liver_0 hr after 2/3 PH_rep3


title: Human dermal fibroblast_5_rep1


title: Human dermal fibroblast_7_rep1


title: MDA-MB-231_shCD44-2

city: Shiojiri

first: Toru

last: Hiraga

state: Nagano

address: 1780 Gobara-Hirooka

institute: Matsumoto Dental University

hyb_protocol: 1,650 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4x44K v2 Microarrays (G4845A) for 17 hours at 65°C in a hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MDA-MB-231 cells stably expressing shRNA against CD44, shCD44-2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN, Valencia, CA).

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum at 37oC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared using a High Pure RNA Isolation Kit (Roche Diagnostics K.K., Tokyo, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: breast cancer cell line


title: Human dermal fibroblast_2_rep1


title: MDA-MB-231_shCD44-3

source_name: MDA-MB-231 cells stably expressing shRNA against CD44, shCD44-3


title: Human dermal fibroblast_3_rep1


title: Human dermal fibroblast_2_rep2


title: liver_1.5 hr after 2/3 PH_rep1


title: liver_0 hr after 2/3 PH_rep2


title: Col0 vs myb108 KO timepoint2 biorep A

status: Public on Apr 23 2013

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

description: Col0 WT vs myb108 KO at timepoint2

hyb_protocol: The microarray experiments were carried out using the CATMA (version 4) microarray (Allemeersh et al., 2005; http://www.catma.org). Labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004). Raw data were normalized within arrays using a PrintTip lowess transformation and normalized between arrays using the quantile-normalization. The data were fitted to a linear model using a least squares method. P-values were adjusted for multiple testing using Benjamini and Hochberg method to control the false discovery rate (Benjamini and Hochberg, 1995).

organism: Arabidopsis thaliana

source_name: Col0 t2

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]). Four biological replicates were pooled and labelled twice with each dye giving four technical replicates. Comparisons were made pairwise between WT and mutant under each condition.

growth_protocol: Arabidopsis plants Col-0, myb2 and myb108 were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1). The myb2, myb108 lines were T-DNA insertion lines Salk_045455, Salk_024059 respectively (obtained from the Nottingham Arabidopsis Seed Centre).

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Nine 3-week old Col-0, myb2 (genotype IM24) and myb108 (genotype BOS1) rosettes, cut from the root, were transferred to 3 Petri dishes containing water-saturated filter paper and stored at 20oC in complete darkness. Plates were photographed daily and RGB values calculated for leaf 5 of each rosette using the Color Histogram function in ImageJ. RGB intensities were normalized using a white-background reference point and average red/green ratios provided a quantitative measure of leaf yellowing. A red-green ratio of around 0.8 indicates the initiation of senescence. When the average ratio of Col-0 samples was >0.8, leaf 5 for Col-0, myb2 and myb108 lines was harvested (4 biological replicates). The same sampling procedure was then performed on consecutive days to sample as senescence progressed.

value: Col0 WT

tag: time

source_name: myb108 t2


title: Col0 vs myb108 KO timepoint1 biorep B

description: Col0 WT vs myb108 KO at timepoint1

source_name: Col0 t1

source_name: myb108 t1


title: Col0 vs myb108 KO timepoint2 biorep B

description: Col0 WT vs myb108 KO at timepoint2


title: myb108 KO vs Col0 timepoint1 biorep D

description: myb108 KO vs Col0 WT at timepoint1

value: myb108 KO


title: myb108 KO vs Col0 timepoint1 biorep C

description: myb108 KO vs Col0 WT at timepoint1


title: myb108 KO vs Col0 timepoint2 biorep D

description: myb108 KO vs Col0 WT at timepoint2


title: Col0 vs myb108 KO time 30hpi biorep B

description: Col0 WT vs myb108 KO at 30hpi

treatment_protocol: B. cinerea pepper strain spores (Denby et al., 2004) were prepared and Arabidopsis leaves treated as described in Windram et al., Plant Cell 2012 Sep;24(9):3530-57. PMID: 23023172. Col-0, myb2 and myb108 leaves were inoculated with 4-6 (depending on leaf size) evenly spaced 10μl droplets of B. cinerea spores. Infected leaves were harvested to provide 4 biological replicates. Samples for the comparison between myb108 and Col-0 were harvested at 26 and 30 hpi. Samples for the comparison between myb2 knockout line and Col-0 or myb2 knockout line and Col-0 were harvested at 26 and 30 hpi or 24 and 30 hpi respectively.


title: myb108 KO vs Col0 timepoint2 biorep C

description: myb108 KO vs Col0 WT at timepoint2


title: Col0 vs myb2 KO timepoint1 biorep A

description: Col0 WT vs myb2 KO at timepoint1

source_name: myb2 t1


title: Col0 vs myb2 KO timepoint2 biorep A

description: Col0 WT vs myb2 KO at timepoint2

source_name: myb2 t2


title: myb2 KO vs Col0 timepoint2 biorep C

description: myb2 KO vs Col0 WT at timepoint2

value: myb2 KO


title: myb2 KO vs Col0 timepoint1 biorep D

description: myb2 KO vs Col0 WT at timepoint1


title: myb2 KO vs Col0 timepoint2 biorep D

description: myb2 KO vs Col0 WT at timepoint2


title: Neural Stem Cells cultured in feeder free condition (Matrigel) with NSC Media Replicate 1

institute: UCSD


title: Col0 vs myb108 KO timepoint1 biorep A

description: Col0 WT vs myb108 KO at timepoint1


title: Col0 vs myb108 KO time 26hpi biorep C

description: Col0 WT vs myb108 KO at 26hpi


title: Col0 vs myb108 KO time 26hpi biorep D

description: Col0 WT vs myb108 KO at 26hpi


title: myb108 KO vs Col0 time 30hpi biorep D

description: myb108 KO vs Col0 WT at 30hpi


title: myb108 KO vs Col0 time 30hpi biorep C

description: myb108 KO vs Col0 WT at 30hpi


title: myb2 KO vs Col0 timepoint1 biorep C

description: myb2 KO vs Col0 WT at timepoint1


title: Col0 vs myb108 KO time 30hpi biorep A

description: Col0 WT vs myb108 KO at 30hpi


title: Col0 vs myb2 KO time 30hpi biorep A

description: Col0 WT vs myb2 KO at 30hpi


title: Col0 vs myb2 KO time 30hpi biorep B

description: Col0 WT vs myb2 KO at 30hpi


title: myb2 KO vs Col0 time 30hpi biorep C

description: myb2 KO vs Col0 WT at 30hpi


title: Col0 vs myb2 KO time 24hpi biorep D

description: Col0 WT vs myb2 KO at 24hpi


title: myb108 KO vs Col0 time 26hpi biorep B

description: myb108 KO vs Col0 WT at 26hpi


title: Genotype IM4 Time 5 Biorep D

description: Randomised loop design providing dye-swaps between genotypes, time points and bioreps

data_processing:
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Quantified microarray data were Lowess normalied within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy5, Cy3

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis plants were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1). The anac055 line (genotype IM4, col0 background) was T-DNA insertion line Salk_011069 (obtained from the Nottingham Arabidopsis Seed Centre). The anac019 dSpm insertion mutant (genotype 9C11, col5 background) was identified in a pool of SLAT line DNA screened with gene specific primers (Tissier et al., 1999).

treatment_protocol: Leaf 7 was tagged with cotton 18 days after sowing (DAS) and harvested from five randomly selected plants, 8 h into the light period, at 23, 29, 31, 33 and 35 DAS (full senescence).


title: MDA-MB-231_shLuc

source_name: MDA-MB-231 cells stably expressing shRNA against firefly luciferase, shLuc


title: Genotype IM4 Time 5 Biorep A


title: myb108 KO vs Col0 time 26hpi biorep A

description: myb108 KO vs Col0 WT at 26hpi


title: Genotype IM4 Time 4 Biorep D


title: Genotype IM4 Time 5 Biorep C


title: myb2 KO vs Col0 time 24hpi biorep B

description: myb2 KO vs Col0 WT at 24hpi


title: Genotype IM4 Time 4 Biorep C


title: Genotype IM4 Time 3 Biorep E


title: Genotype IM4 Time 4 Biorep A


title: myb2 KO vs Col0 time 24hpi biorep A

description: myb2 KO vs Col0 WT at 24hpi


title: Genotype IM4 Time 3 Biorep B


title: Genotype IM4 Time 5 Biorep B


title: Genotype IM4 Time 3 Biorep A


title: Genotype IM4 Time 4 Biorep B


title: Col0 vs myb2 KO time 24hpi biorep C

description: Col0 WT vs myb2 KO at 24hpi