title: erStress_131grandparents_GM11933_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11933 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_131grandparents_GM11931_tunicamycin

status: Public on Mar 28 2013

type: RNA

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

country: USA

institute: HHMI, University of Pennsylvania

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11931 treated with 4 ug/ml tunicamycin 8 hours.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell lines derived from GM11931

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp Premier RNA Amplification Kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: The cells were grown at a density of 1 million cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

treatment_protocol: 4 ug/ml tunicamycin 8 hours

tag: cell line

tag: treatment

value: 4 ug/ml tunicamycin


title: CD14 7

type: genomic

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

description: Normal

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

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

data_processing: BeadStudio software, Custom R scripts for normalisation provided in supplementary of paper.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from Buccal cells was extracted using the Gentra Puregene Buccal cell kit, USA. CD14 and CD34 cells were extracted using Qiagen QIAamp DNA Blood Mini Kit, Sperm was extracted by Qiagen QIAamp DNA Mini Kit, Placenta (Catalog number D1234200 from Biochain, USA) and Pancreas (Catalog number D1234188 from Biochain, USA) were commercial samples

tag: gender


title: erStress_131grandparents_GM11920_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11920 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11920


title: erStress_131grandparents_GM11932_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11932 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11932

treatment_protocol: DMSO 8 hours

value: DMSO


title: erStress_131grandparents_GM11932_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11932 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_131grandparents_GM11930_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11930 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11930


title: erStress_131grandparents_GM11920_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11920 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11931_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11931 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11917_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11917 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11917


title: erStress_131grandparents_GM11930_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11930 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11918_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11918 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11918


title: Pancreas 2

description: Normal

source_name: Pancreas 2


title: Sperm 1

description: Normal

source_name: Sperm 1


title: Sperm 2

description: Normal

source_name: Sperm 2


title: Jurkat_ImmunoTRAP_rep5 [Agilent-014707]

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: A 5 µg Cy5-labeled and 5 µg of Cy3-labeled DNAs were combined in a total volume of 158 µl. The 158 µl were mixed with 50 µl of 1 mg/ml of Human Cot-1 DNA, 52 µl of 10x Agilent Blocking Agent, 260 µl of 2x Agilent Hybridization Buffer. Samples were heated at 95°C for 3 min, and then incubated at 37°C for 30 min. 490 µl of the sample were applied to the 1x244 promoter array assembled in a chamber and incubated in a rotisserie hybridization oven at 65°C and 20 r.p.m. for 40 h. After hybridization the microarray slide was washed with Oligo aCGH/ChIP-on-chip Wash Buffer for 5 min at room temperature, followed by a wash for 5 min at 31°C.

scan_protocol: Agilent Feature Extraction software v9.5 was used.

data_processing: Data were pre-processed using the variance-stabilizing normalization algorithm with default parameter settings, as implemented in the vsn package (v3.8.0) of the BioConductor open-source library

source_name: Jurkat cells

label_protocol: The DNA was phenol extracted and ethanol precipitated using glycogen as carrier.  The DNA was amplified using the Whole Genome Amplification (WGA) kit (Sigma).

growth_protocol: Jurkat cells were cultured in RPMI (Invitrogen) supplemented with 10% FBS (Wisent), 10 µg/ml penicillin and streptomycin (Invitrogen), and 2 mM L-glutamine (Invitrogen).

extract_protocol: For affinity purification, the cells were scrapped off the slides into an eppendorf tube containing PBS.  The samples were pelleted at 2900g at 4 °C for 25 minutes.  The pellet was resuspended in 5M urea, 2M NaCl, and 10 nM EDTA.  This suspension was then sonicated in a Misonix 3000 sonicator equipped with a Cup Horn in an iced water bath with the following program (5 sec pulse/15 sec pause repeated 15 times at power level 4).  The program was repeated 4 more times with changes of the iced water bath between repetitions.  The sample was then centrifuged at 13000 rpm for 15 minutes at 4 °C.  The supernatant was then dialyzed overnight in PBS.  Streptavidin agarose beads (Invitrogen) were washed three times in PBS and the supernatant was incubated with the beads for 3-4 hours at 4 °C.  The beads were washed with the following buffers in this order: PBS, TSE150 (20 mM tris pH 8.0, 1% triton X-100, 0.1% SDS, 2 mM EDTA, 150 mM NaCl), TSE 500 (20 mM tris pH 8.0, 1% triton X-100, 0.1% SDS, 2 mM EDTA, 500 mM NaCl), and TE (10 mM tris pH 8.0, 1 mM EDTA).  The beads were collected in TE buffer and the formaldehyde cross-links were reversed by shaking the samples at 65 °C overnight.  The slurry was then treated with RNase A (2 µg/ml) (Fermentas) for 30 minutes at 37 °C and then with proteinase K (100 µg/ml) (Fermentas) for 6 hours at 37 °C.

treatment_protocol: After fixation and permeabilization, cells were washed in TS buffer (100 µM tris-HCl, 150 mM NaCl, pH 7.0).  Endogenous peroxidase activity was quenched with 0.5% H2O2 in TS for 10 minutes at RT.  After another TS wash, samples were blocked in 5% donkey serum in TS for 20 minutes.  mAb 5E10 (a gift from R. van Driel, University of Amsterdam, The Netherlands) was used to detect PML protein.  A secondary antibody conjugated with horseradish peroxidase was then added to the samples.  Biotinylated tyramide (Invitrogen) was diluted in 0.1M boric acid and 0.003% H2O2 and then incubated on the samples for 2 minutes.  Washing the cells three times in TS buffer stopped the reaction.  After this, the samples were either processed for immunofluorescence microscopy or for affinity purification of the PML NB-associated chromatin.

tag: antibody

value: IgG

value: Jurkat cells

value: PML ImmunoTRAP


title: erStress_131grandparents_GM11891_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11891 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11891


title: erStress_131grandparents_GM11892_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11892 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11892


title: erStress_131grandparents_GM11918_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11918 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11892_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11892 treated with 4 ug/ml tunicamycin 8 hours.


title: erStress_131grandparents_GM11893_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11893 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11893


title: erStress_131grandparents_GM11893_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11893 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11879_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11879 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11879


title: erStress_131grandparents_GM11891_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11891 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11917_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11917 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11880_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11880 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11880


title: erStress_131grandparents_GM11880_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11880 treated with DMSO 8 hours.


title: erStress_131grandparents_GM11843_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11843 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM11843


title: CD14 1

description: Normal


title: Pancreas 1

description: Normal

source_name: Pancreas 1


title: erStress_131grandparents_GM11879_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11879 treated with DMSO 8 hours.


title: Placenta 2

description: Normal

source_name: Placenta 2


title: Jurkat_ImmunoTRAP_rep1 [Agilent-014707]


title: CD34- 1

description: Normal


title: Jurkat_ImmunoTRAP_rep2 [Agilent-014707]


title: CD34- 2

description: Normal


title: Jurkat_ImmunoTRAP_rep3 [Agilent-014707]


title: Placenta 1

description: Normal

source_name: Placenta 1


title: erStress_131grandparents_GM07347_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07347 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07347


title: Jurkat_ImmunoTRAP_rep5 [Agilent-014706]


title: CD34+ 2

description: Normal


title: erStress_131grandparents_GM11843_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM11843 treated with DMSO 8 hours.


title: erStress_131grandparents_GM07347_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07347 treated with DMSO 8 hours.


title: N2 young adult on Comamonas DA1877 rep 3

city: Worcester

first: Lesley

middle: T

last: MacNeil

state: MA

address: 368 Plantation St

department: Program in Systems Biology

institute: UMass Medical School

description:
DA1877-3
DA1877.3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Expression Console software from Affymetrix was used to determine data quality as well as for generation of pivot files using RMA

organism: Caenorhabditis elegans

source_name: Young adult

label_protocol: Biotinylated cRNA was prepared using the Affymetrix 3' IVT Express Kit from 500ng total RNA

growth_protocol: Animals grown on NGM plates

extract_protocol: RNA prepared with Trizol(life technologies) followed by cleanup with RNeasy columns(Qiagen) as per manufacturer's instructions

tag: genotype

value: wild type (N2)

tag: age

value: Young adult

tag: diet

value: Comamonas DA1877


title: N2 young adult on Comamonas DA1877 rep 2

description:
DA1877-2
DA1877.2


title: erStress_131grandparents_GM07341_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07341 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07341


title: N2 young adult on E. coli HT115 rep 1

description:
HT115-1
HTDE3.1

value: E. coli HT115


title: CD34+ 1

description: Normal


title: erStress_131grandparents_GM07346_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07346 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07346


title: erStress_131grandparents_GM07340_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07340 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07340


title: erStress_131grandparents_GM07346_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07346 treated with 4 ug/ml tunicamycin 8 hours.


title: N2 young adult on E. coli HT115 rep 3

description:
HT115-3
HTDE3.3


title: erStress_131grandparents_GM07049_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07049 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07049


title: erStress_131grandparents_GM07340_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07340 treated with 4 ug/ml tunicamycin 8 hours.


title: Jurkat_ImmunoTRAP_rep3 [Agilent-014706]


title: N2 young adult on Comamonas DA1877 rep 1

description:
DA1877-1
DA1877.1


title: erStress_131grandparents_GM07341_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07341 treated with 4 ug/ml tunicamycin 8 hours.


title: N2 young adult on E. coli OP50 rep 3

description:
OP50-3
OP50.3

value: E. coli OP50


title: N2 young adult on E. coli OP50 rep 1

description:
OP50-1
OP50.1


title: erStress_131grandparents_GM07049_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07049 treated with DMSO 8 hours.


title: Jurkat_ImmunoTRAP_rep2 [Agilent-014706]


title: erStress_131grandparents_GM07045_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07045 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07045


title: N2 young adult on E. coli OP50 rep 2

description:
OP50-2
OP50.2


title: N2 gravid adult on E. coli OP50 rep 2

description:
OP50GA-2
OP2

source_name: Gravid adult

value: Gravid adult


title: N2 gravid adult on E. coli OP50 rep 1

description:
OP50GA-1
OP1


title: Jurkat_ImmunoTRAP_rep4 [Agilent-014706]

source_name: Jurkat cells


title: Jurkat_ImmunoTRAP_rep1 [Agilent-014706]


title: erStress_131grandparents_GM07045_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07045 treated with DMSO 8 hours.


title: Jurkat_ImmunoTRAP_rep4 [Agilent-014707]


title: erStress_131grandparents_GM07017_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07017 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07017


title: erStress_131grandparents_GM07017_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07017 treated with DMSO 8 hours.


title: N2 young adult on E. coli HT115 rep 2

description:
HT115-2
HTDE3.2


title: N2 gravid adult on 1:1000 Comamonas DA1877 rep 3

description:
DIL1877GA-3
DIL3

value: 1:1000 Comamonas DA1877


title: N2 gravid adult on 1:1000 Comamonas DA1877 rep 2

description:
DIL1877GA-2
DIL2


title: N2 gravid adult on Comamonas DA1877 rep 3

description:
DA1877GA-3
DA3


title: erStress_131grandparents_GM06986_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06986 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM06986


title: erStress_131grandparents_GM06986_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM06986 treated with DMSO 8 hours.


title: erStress_131grandparents_GM07016_tunicamycin

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07016 treated with 4 ug/ml tunicamycin 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07016


title: N2 gravid adult on Comamonas DA1877 rep 1

description:
DA1877GA-1
DA1


title: SSA-treted cells, biological replicate 2

city: Toyama

first: Daisuke

last: Kaida

state: Toyama

address: 2630 Sugitani

department: Frontier Research Core for Life Sciences

country: Japan

institute: University of Toyama

description:
nascent transcript
HuEx_S-2_(HuEx-1_0-st-v2).CEL

hyb_protocol: The end-labeled cDNA was applied to GeneChip Human Exon 1.0 ST arrays. Hybridization was performed using F450-001 fluidics wash and stain script on the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G GeneChip Operating Software (GCOS).

data_processing:
Probeset intensities were calculated from the CEL files using the RMA algorithm with default settings at the probeset level in Partek Genomic Suite 6.5, using the core probe sets as defined by Affymetrix. Probesets with maximum RMA intensity of 3 across all samples were excluded to eliminate probesets with low expression levels. Alternative splicing multi-way ANOVA was applied using Partek defaults.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HeLa cells_SSA

label_protocol: Labeled cDNA targets were prepared using the Ambion WT Expression Kit (Life Technologies) and GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer’s directions.

growth_protocol: HeLa cells were grown in DMEM + 10% FBS in humdified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol according to manufacturer's recommendation. Nascent RNA was purified using Click-It Nascent RNA Capture Kit.

treatment_protocol: Cells were treated with methanol or spliceostatin A for 3 hours and the nascent RNA was labelled with EU for 1 hour.

value: HeLa

tag: treated with

value: spliceostatin A (SSA) for 3 hrs


title: SSA-treted cells, biological replicate 3

description:
nascent transcript
HuEx_S-3_(HuEx-1_0-st-v2).CEL


title: N2 gravid adult on 1:1000 Comamonas DA1877 rep 1

description:
DIL1877GA-1
DIL1


title: N2 gravid adult on Comamonas DA1877 rep 2

description:
DA1877GA-2
DA2


title: Control cells, biological replicate 3

description:
nascent transcript
HuEx_M-3_(HuEx-1_0-st-v2).CEL

source_name: HeLa cells_Methanol

value: methanol for 3 hrs


title: HT22 cells plus J147 compound at 1 hour exposure

city: La Jolla

first: Jennifer

middle: Lynn

last: Ehren

state: CA

address: 10010 N Torrey Pines Road

department: Cellular Neurobiology

institute: Salk Institute

description:
HT22 is a nerve cell line derived from mouse brain.  Tissues were not examined via microarray.
Gene expression data from hippocampal cell line HT22-treated with J147 compound for 1 hour.

hyb_protocol: The hybridization and processing of the GeneChips were conducted by Salk Institute’s Functional Genomics Core Facility using the following systems: GeneChip® Hybridization Oven 640 and GeneChip® Fluidics Station 450 to the wash and stain operation of Affymetrix GeneChip® arrays.

scan_protocol: GeneChip® Scanner 3000 7G

data_processing: Affymetrix Expression Console Software (version 1.0) was used to perform quality assessment of the microarray scan/experiments. Array data were normalized via scaling to adjust the average intensity of each array to be similar. GeneChips were analyzed by the GeneChip Operating Software (Affymetrix, Santa Clara, CA, USA) with the default settings except that the target signal was set to 200 for GeneChip quality control. Raw data were analyzed through the gcRMA-algorithm using the Affymetrix package in R software for statistical computing and graphics. The median microarray intensity for all microarrays was normalized to 100.

organism: Mus musculus

source_name: HT22 is a nerve cell line derived from mouse brain and is widely used to study nerve cell physiology.

label_protocol: After RNA isolation for each sample, double stranded cDNA was synthesized from 500 ng total RNA and biotin-labeled using the GeneChip 3’ IVT Express Kit (Affymetrix, #901228-A) per the manufacturer’s instructions and protocol.

growth_protocol: HT22 cells were plated in DMEM plus 10% FCS and placed in a 37C incubator overnight.

extract_protocol: RNA was isolated with the use of RNeasy Mini kit (Qiagen, #74104; Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The next day after plating, the cells were treated with 10mM J147 for 1 hr before RNA isolation.


title: HT22 cells plus DMSO vehicle at 1 hour exposure

description:
HT22 is a nerve cell line derived from mouse brain.  Tissues were not examined via microarray.
Gene expression data from hippocampal cell line HT22-untreated.

value: untreated


title: metr-1(ok521) fed Comamonas DA1877 rep 2

growth_protocol: Animals grown on NGM plates with a diet of Comamonas DA1877


title: SSA-treted cells, biological replicate 1

description:
nascent transcript
HuEx_S-1_(HuEx-1_0-st-v2).CEL


title: Control cells, biological replicate 2

description:
nascent transcript
HuEx_M-2_(HuEx-1_0-st-v2).CEL


title: pcca-1(ok2282) fed Comamonas DA1877 rep1


title: metr-1(ok521) fed Comamonas DA1877 rep 1


title: pcca-1(ok2282) fed Comamonas DA1877 rep3


title: pcca-1(ok2282) fed Comamonas DA1877 rep2


title: N2 gravid adult fed Comamonas DA1877 rep 3


title: N2 gravid adult fed Comamonas DA1877 rep 1


title: WT vs. MO-grnA injected, replicate 1

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Biological replicate 1 of 3.

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

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

organism: Danio rerio

source_name: MO-grnA morphant

label_protocol: Agilent's Quick Amp Labeling Kit generates fluorescent cRNA with a sample input RNA 1 μg of total RNA for two-color processing.The method uses T7 RNA polymerase,which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: The zebrafish were maintained at our own facility in a controlled environment with a 14/10-h light-dark cycle at 28 °C.  The fertilized eggs were collected at the 1-cell stage.

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

treatment_protocol: An injection volume from 2-3 nl of MOs was injected into 1-cell-stage embryos.

value: 22 hpf

value: MO-grnA

source_name: WT embryo


title: metr-1(ok521) fed Comamonas DA1877 rep 3


title: N2 gravid adult fed Comamonas DA1877 rep 2


title: WT vs. MO-grnA injected, replicate 2

description: Biological replicate 2 of 3.


title: WT vs. MO-grnA injected, dye swap

description: Biological replicate 3 of 3.


title: Control cells, biological replicate 1

description:
nascent transcript
HuEx_M-1_(HuEx-1_0-st-v2).CEL


title: GAF 2-4 hr OR Embryo D.melanogaster ChIP Rep2

status: Public on Mar 27 2013

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

source_name: GAF 2-4 hr OR Em. ChIP expt.2580 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: strain

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

tag: developmental stage

value: Embryo 2-4hr OR

value: wild type


title: GAF 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: GAF 2-4 hr OR Em. ChIP expt.2131 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.


title: GAF 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2131.Mvalues.bedgraph

source_name: GAF 2-4 hr OR Em. Input expt.2100 channel_1


title: H4K20me 2nd lot 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H4K20me 2nd lot 2-4 hr OR Em. ChIP expt.1222 channel_1


title: H4K20me 2nd lot 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 1222.Mvalues.bedgraph

source_name: H4K20me 2nd lot 2-4 hr OR Em. Input expt.910 channel_1


title: H4K20me 2nd lot 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H4K20me 2nd lot 2-4 hr OR Em. ChIP expt.1223 channel_1


title: H3K9me2 antibody2 OR Head Nuclear D.melanogaster ChIP Rep2

source_name: H3K9me2 antibody2 OR Head Nuc. ChIP expt.195 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Collection of fly heads from whole adults using sieves of varying sizes.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Mixed Adult


title: H3K9me2 antibody2 OR Head Nuclear D.melanogaster ChIP Rep3

source_name: H3K9me2 antibody2 OR Head Nuc. ChIP expt.561 channel_1


title: H3K9me2 antibody2 OR Head Nuclear D.melanogaster ChIP Rep1

source_name: H3K9me2 antibody2 OR Head Nuc. ChIP expt.142 channel_1


title: H4K20me 2nd lot 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1223.Mvalues.bedgraph

source_name: H4K20me 2nd lot 2-4 hr OR Em. Input expt.909 channel_1


title: cultured human pulp cells (slow)-2

city: Seoul

first: Sang Hyuk

last: Park

address: Dongdaemungu, Hoegidong 1

country: South Korea

institute: Kyung Hee University

description: primary cell

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

source_name: cultured human pulp cells (slow)-2

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Immediately after the teeth were extracted, dental pulp tissues were collected from vertically cut tooth 1mm under the cemento-enamel junction.  Then tissues from each tooth were cut into small pieces for cell culture in medium made by mixing Dulbecco's modified Eagle's medium (Gibco BRL, Life Technologies, Grand Island, NY, USA), 10% fetal bovine serum (Gibco BRL, Life Technologies, Grand Island, NY, USA) and antibiotics, consisting of penicillin-G (100U/ml), streptomycin (100 ㎍/ml), Fungizone (0.25 g/ml) (Gemini Bio-Products, Inc., Woodland, CA, USA), in a humidified atmosphere of 5% CO2 at 37℃.   Dental pulp cells out-grown from the tissues were subcultured and grown to confluence. Then subcultures were successively passed at 1:2 ratio until three passages. Dental pulp cells that had been cultured through three passages were used in the experiments.

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

treatment_protocol: For rapid freezing, the premolars were placed in cryopreservation vials containing 10% dimethyl sulfoxide (Me2SO: Sigma Chemical, St. Louis. MO, USA) within 5 minutes and stored in a liquid nitrogen at -196℃ for 1 week. Then thawing and culture method was same with the slow freezing group. For slow freezing treatment, the premolars were placed in cryopreservation vials containing 10% dimethyl sulfoxide (Me2SO: Sigma Chemical, St. Louis, MO, USA) within 5 minutes.  For a constant cooling rate, they were placed in cell freezer container with 100% isopropanol and stored in a -80℃ deep freezer for twenty-four hours and they stored in liquid nitrogen at -196℃ for 1 week then thawed in a water bath rapidly at 37℃ for 3 minutes. For the experiment, dental pulp cells out-grown from the tissues had been cultured in the same way with control group.

tag: cell type

value: cryopreserved human pulp cells


title: cultured human pulp cells (slow)-3

description: primary cell

source_name: cultured human pulp cells (slow)-3


title: cultured human pulp cells (rapid)-3

description: primary cell

source_name: cultured human pulp cells (rapid)-3


title: GAF 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2580.Mvalues.bedgraph

source_name: GAF 2-4 hr OR Em. Input expt.2099 channel_1


title: H3K9me2 antibody2 OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 142.Mvalues.bedgraph

source_name: H3K9me2 antibody2 OR Head Nuc. Input expt.138 channel_1


title: RIN_ChIP replicate 3

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

description: Biological replicate 3 of 3 for RIN ChIP-chip analysis. Dye-swap

hyb_protocol: Hybridization was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

scan_protocol: Scan was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

data_processing: Data were processed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/dataguide/index.html).

organism: Solanum lycopersicum

source_name: Input DNA from the ripening tomato fruits

label_protocol: The ChIPed and input (no ChIP) DNAs were amplified using the GenomePlex WGA2 kit (Sigma). The amplified DNAs (1 µg each) were used for the following analysis. Labeling was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

growth_protocol: Tomato fruits were harvested at the ripening stage.

extract_protocol: Chromatin immunoprecipitated (ChIPed) DNA bound by RIN was prepared from the ripening tomato fruits basically as previously described (Ito et al., 2008; Fujisawa et al., 2011). Briefly, fruits were sliced and fixed in a vacuum with 1% formaldehyde for 10 min, followed by the addition of 125 mM glycine for 5 min. After rinsed with ice-cold water, the fruit tissue was frozen in liquid nitrogen and powdered by a mortar and pestle. Chromatin was extracted from the lysed nuclei corrected from the powder. The chromatin solution was sonicated for 10 sec twenty times on 10% power (setting 3) using a Sonifier 450 (Branson). The sonicated chromatin suspension was immunoprecipitated with anti-RIN serum. The anti-RIN antibody that interacted with RIN-DNA complex was corrected with Protein A-Agarose (Santa Cruz Biotechnology). After reverse cross-linking, proteins were digested with proteinase K (Takara biotech, Japan) and DNA fragments were recovered by phenol-chloroform purification and ethanol precipitation.

tag: tissue

value: ripening fruit

tag: chip antibody

value: none, input DNA

source_name: RIN ChIP DNA from the ripening tomato fruits

value: anti-RIN antibody


title: H3K9me2 antibody2 OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 195.Mvalues.bedgraph

source_name: H3K9me2 antibody2 OR Head Nuc. Input expt.197 channel_1


title: RPD3 Q3451 L3 Nuclear D.melanogaster ChIP Rep2

source_name: RPD3 Q3451 L3 Nuc. ChIP expt.1158 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: 3rd Instar Larvae


title: H3K9me2 antibody2 OR Head Nuclear D.melanogaster Input Rep3

description: Served as Input for: 561.Mvalues.bedgraph

source_name: H3K9me2 antibody2 OR Head Nuc. Input expt.487 channel_1


title: cultured human pulp cells (control)-3

description: primary cell

source_name: cultured human pulp cells (control)-3

value: human pulp cells


title: cultured human pulp cells (control)-2

description: primary cell

source_name: cultured human pulp cells (control)-2


title: cultured human pulp cells (slow)-1

description: primary cell

source_name: cultured human pulp cells (slow)-1


title: N2 gravid adult on E. coli OP50 rep 3

description:
OP50GA-3
OP3

source_name: Gravid adult

value: wild type (N2)

value: Gravid adult

value: E. coli OP50


title: RPD3 Q3451 L3 Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1158.Mvalues.bedgraph

source_name: RPD3 Q3451 L3 Nuc. Input expt.1004 channel_1


title: cultured human pulp cells (rapid)-2

description: primary cell

source_name: cultured human pulp cells (rapid)-2


title: cultured human pulp cells (rapid)-1

description: primary cell

source_name: cultured human pulp cells (rapid)-1


title: RPD3 Q3451 L3 Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1157.Mvalues.bedgraph

source_name: RPD3 Q3451 L3 Nuc. Input expt.1003 channel_1


title: RPD3 Q3451 L3 Nuclear D.melanogaster ChIP Rep1

source_name: RPD3 Q3451 L3 Nuc. ChIP expt.1157 channel_1


title: cultured human pulp cells (control)-1

description: primary cell

source_name: cultured human pulp cells (control)-1


title: RIN_ChIP replicate 1

description: Biological replicate 1 of 3 for RIN ChIP-chip analysis.


title: RIN_ChIP replicate 2

description: Biological replicate 2 of 3 for RIN ChIP-chip analysis.


title: H3K4me2 JBC 1360331 Ovary D.melanogaster Input Rep1

description: Served as Input for: 1285.Mvalues.bedgraph

source_name: H3K4me2 JBC 1360331 Ovary Input expt.1040 channel_1

extract_protocol:
Growth conditions and collection protocol to harvest ovaries from female flies raised in bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Adult Female

tag: Sex

value: Female


title: HP1 wa191 Ovary D.melanogaster ChIP Rep2

source_name: HP1 wa191 Ovary ChIP expt.1041 channel_1


title: HP1 wa191 Ovary D.melanogaster ChIP Rep1

source_name: HP1 wa191 Ovary ChIP expt.1039 channel_1


title: H3K4me2 JBC 1360331 Ovary D.melanogaster ChIP Rep1

source_name: H3K4me2 JBC 1360331 Ovary ChIP expt.1269 channel_1


title: HP1 wa191 Ovary D.melanogaster Input Rep2

description: Served as Input for: 1041.Mvalues.bedgraph

source_name: HP1 wa191 Ovary Input expt.1047 channel_1


title: H3K9me2 Ab2 new lot Ovary D.melanogaster Input Rep2

description: Served as Input for: 1268.Mvalues.bedgraph

source_name: H3K9me2 Ab2 new lot Ovary Input expt.1047 channel_1


title: H3K9me2 Ab2 new lot Ovary D.melanogaster ChIP Rep2

source_name: H3K9me2 Ab2 new lot Ovary ChIP expt.1284 channel_1


title: H3K9me2 Ab2 new lot Ovary D.melanogaster Input Rep1

description: Served as Input for: 1284.Mvalues.bedgraph

source_name: H3K9me2 Ab2 new lot Ovary Input expt.1040 channel_1


title: H3K4me2 JBC 1360331 Ovary D.melanogaster ChIP Rep2

source_name: H3K4me2 JBC 1360331 Ovary ChIP expt.1285 channel_1


title: murine atherosclerotic plaque on 10 month high fat diet Replicate 1, b

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

description: Biological replicate 1 of 3. advanced atherosclerotic plaque

data_processing: Taqman low density arrays were run on the 7900 HT Sequence Detection system.  The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.  Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRs from card A and B was used for analysis. Data were calculated using Real Time StatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].  Input data for analysis consisted of all samples. CT values were normalized to the most stable endogenous controls (snoRNA202, snoRNA135, snoRNA429 and MammU6 for Card A and B) according to the Genorm algorithm.

label: FAM

extract_protocol: RecoverAll total nucleic acid isolation kit (Applied Biosystems) see  http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_056616.pdf

treatment_protocol: mice were fed on 10 month high fat diet

value: apoe-/-

value: 6-8 weeks

value: aortic root


title: murine atherosclerotic plaque on 10 month high fat diet Replicate 3, b

description: Biological replicate 3 of 3. advanced atherosclerotic plaque


title: murine atherosclerotic plaque on 10 month high fat diet Replicate 2, b

description: Biological replicate 2 of 3. advanced atherosclerotic plaque


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 3, b

description: Biological replicate 3 of 4. early atherosclerotic plaque

treatment_protocol: mice were fed on 3 month high fat diet


title: murine un-diseased arterial tissue on 10 month high fat diet Replicate 2, b

description: Biological replicate 2 of 3. un-diseased arterial tissue on 10 month high fat diet

value: artery


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 4, b


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 1, b

description: Biological replicate 1 of 4. early atherosclerotic plaque


title: murine un-diseased arterial tissue on 10 month high fat diet Replicate 1, b

description: Biological replicate 1 of 3. un-diseased arterial tissue on 10 month high fat diet


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 4, b

description: Biological replicate 4 of 4. un-diseased arterial tissue on 3 month high fat diet


title: HP1 wa191 Ovary D.melanogaster Input Rep1

description: Served as Input for: 1039.Mvalues.bedgraph

source_name: HP1 wa191 Ovary Input expt.1040 channel_1

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: wild type


title: murine un-diseased arterial tissue on 10 month high fat diet Replicate 3, b

description: Biological replicate 3 of 3. un-diseased arterial tissue on 10 month high fat diet


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 3, b

description: Biological replicate 3 of 4. un-diseased arterial tissue on 3 month high fat diet


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 1, b

description: Biological replicate 1 of 4. un-diseased arterial tissue on 3 month high fat diet


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 4


title: H3K9me2 Ab2 new lot Ovary D.melanogaster ChIP Rep1

source_name: H3K9me2 Ab2 new lot Ovary ChIP expt.1268 channel_1


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 2

description: Biological replicate 2 of 4. un-diseased arterial tissue on 3 month high fat diet


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 1


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 3


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 3


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 1


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 2

description: Biological replicate 2 of 4. early atherosclerotic plaque


title: murine atherosclerotic plaque on 10 month high fat diet Replicate 2

description: Biological replicate 2 of 3. advance atherosclerotic plaque


title: murine atherosclerotic plaque on 10 month high fat diet Replicate 3

description: Biological replicate 3 of 3. advance atherosclerotic plaque


title: murine atherosclerotic plaque on 10 month high fat diet Replicate 1


title: murine un-diseased arterial tissue on 10 month high fat diet Replicate 3

value: carotid artery


title: murine atherosclerotic plaque on 3 month high fat diet Replicate 2, b


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 2, b


title: murine un-diseased arterial tissue on 10 month high fat diet Replicate 1


title: murine un-diseased arterial tissue on 10 month high fat diet Replicate 2


title: murine un-diseased arterial tissue on 3 month high fat diet Replicate 4


title: 10 week Infected replicate 4

city: Charlottetown

first: Fraser

last: Clark

state: PEI

address: 550 University Ave

department: Pathology and Microbiology

institute: University of Prince Edward Island

description:
Biological replicate 4 of 5 for 10 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

hyb_protocol: Labeled aRNA and cDNA were quantified spectrophotometrically (NanoDrop ND-1000) and 140 ng of cDNA and 100 pmol of labeled aRNA were used for microarray hybridization.  Prior to hybridization, labeled aRNA was fragmented using 1 µL 10x Fragmentation solution and incubation for 10 min at 70°C followed by 1 µL of Stop solution (Life Technologies Inc.).  Hybridizations were performed using A2 chambers on a Tecan 400 HS Pro hybridization system (Tecan, NC, USA).  Briefly, microarrays were incubated at 65°C for 10 min, washed twice with hybridization buffer 1 (5x SSC, 0.01% SDS, 0.2% BSA) for 20s at room temperature, incubated at 50°C for 13 min, washed once with buffer 1 for 20s, incubated at 48°C for 13 min, washed once with buffer 1 for 1 min and once with buffer 4 (5x SSC) for 1 min.  The sample was then injected and hybridized to the microarray with sample agitation at 48°C for 16 h.  The microarray was washed with buffer 2 (2x SSC, 0.2% SDS) at 40°C for 1 min and incubated at 40°C for 2 min, washed with buffer 2 at 30°C for 1 min and with buffer 5 at 30°C for 1 min, incubated at 30°C for 2 min, washed with buffer 5 at 23°C for 1 min, and buffer 3 (0.2x SSC) at 23°C for 1 min.  Finally the microarray was incubated at 23°C for 2 min followed by a wash with buffer 3 for 1 min and then dried with nitrogen gas for 3 min.

scan_protocol: Microarrays were imaged using a GenePix 4000B scanner (Molecular Devices, PA, USA) and features were extracted using SpotReader v 1.3.1 (Niles Scientific, CA, USA).

data_processing: Data was analyzed using TM4/MeV v4.8.1 (Saeed et al., 2003).  Two colour gene expression arrays were normalized by LOWESS and flagged using the MIDAS (Microarray Data Analysis Software) v2.2.2 software (Quackenbush, 2002).  The data was used to generate log2 ratios of sample to reference gene intensity so that all arrays could be compared.

label: Alexa Flour 555

organism: Homarus americanus

source_name: 10 week Infected

label_protocol: Alexa Fluor® 555 labeled single strand cDNA was generated from 20 µg high quality sample RNA using 20 µg of RNA using a SuperScript™ Plus Indirect cDNA Labeling System (Life Technologies Inc., Burlington, ON, Canada). Reference aRNA was generated from 5 µg of pooled lobster hepatopancreatic RNA using an Amino Allyl MessageAmp™ II aRNA Amplification kit (Life Technologies Inc.). Reference aRNA was Alexa Fluor® 647  labeled using 12 µg of aRNA and a Superscript™ Plus Indirect cDNA Labeling System (Life Technologies Inc.).

growth_protocol: H. americanus were individually housed in a recirculating artificial sea water system with UV and 1 µm filter.

extract_protocol: Total RNA was extracted using a phenol-chloroform extraction method with the aqueos phase cleaned up using an Rneasy kit following manufacturers instructions.

treatment_protocol: Infected lobster were injected with A. haemophila.

tag: moult status

value: Intermoult

value: male

value: Hepatopancreas

label: Alexa Flour 647

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue

tag: sample complexity

value: standard reference pooled sample

value: hepatopancreas


title: Spleen Mock infected 6h Rep 4 (SC84)

city: Mississauga

first: Claude

last: Lachance

address: 1329 Meyerside Drive

institute: Bio-Rad

description: Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were first raw-filtered in order to identify and remove probesets that were not detected and then normalised using robust spline normalization with FlexArray v1.6

label: Biotin

source_name: Spleen Mock infected 6h

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

growth_protocol: Bacterial culture was prepared by transferring 10 μl of 1/1,000 dilutions of 8-h cultures into 30 ml of THB, which was incubated for 16 h at 37°C without agitation. Stationary-phase bacteria were washed twice in PBS (pH 7.3). The bacterial pellet was then resuspended and adjusted to a concentration of 5 × 10^8 c.f.u. ml-1.

extract_protocol: RNA was homogenized from RNAlater-stabilized spleen tissus, extracted and DNAse I treated using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain SC84 or mock-infected with bacterial growth medium (THB).

value: Spleen


title: 10 week Infected replicate 5

description:
Biological replicate 5 of 5 for 10 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 10 week Infected replicate 3

description:
Biological replicate 3 of 5 for 10 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 8 week Infected replicate 2

description:
Biological replicate 2 of 4 for 8 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 8 week Infected


title: 10 week Infected replicate 2

description:
Biological replicate 2 of 5 for 10 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen S. suis SC84 6h Rep 3 (SC84)

description: Replicate 3

source_name: Spleen S. suis SC84 6h


title: Spleen S. suis SC84 6h Rep 2 (SC84)

description: Replicate 2


title: Spleen S. suis SC84 6h Rep 1 (SC84)

description: Replicate 1


title: 8 week Infected replicate 4

description:
Biological replicate 4 of 4 for 8 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 8 week Infected replicate 3

description:
Biological replicate 3 of 4 for 8 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen Mock infected 6h Rep 1 (SC84)

description: Replicate 1


title: 10 week Infected replicate 1

description:
Biological replicate 1 of 5 for 10 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen S. suis P1/7 6h Rep 4 (P1/7)

description: Replicate 4

source_name: Spleen S. suis P1/7 6h

treatment_protocol: Mice were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain P1/7 or mock-infected with bacterial growth medium (THB).


title: Spleen S. suis SC84 6h Rep 4 (SC84)

description: Replicate 4


title: 8 week Infected replicate 1

description:
Biological replicate 1 of 4 for 8 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen S. suis P1/7 6h Rep 2 (P1/7)

description: Replicate 2


title: 5-7 week Infected replicate 10

description:
Biological replicate 10 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 5-7 week Infected


title: Spleen Mock infected 6h Rep 2 (SC84)

description: Replicate 2


title: Spleen S. suis P1/7 6h Rep 3 (P1/7)

description: Replicate 3


title: 5-7 week Infected replicate 7

description:
Biological replicate 7 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 5-7 week Infected replicate 8

description:
Biological replicate 8 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 5-7 week Infected replicate 9

description:
Biological replicate 9 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen Mock infected 6h Rep 3 (SC84)

description: Replicate 3


title: Spleen S. suis P1/7 6h Rep 1 (P1/7)

description: Replicate 1


title: MKN7, miR-29c, replicate 2

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

description: Gene expression after 24hr in miRNA oligo transfected cells

hyb_protocol: 1.65 ug of Cy3-labelled 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 manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F, Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 10% and 100%, extended dynamic range scan mode).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent Technologies) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MKN7, miR-29c, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300ng RNA using the One-Color Quick Amp labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% heat-inactivated fetal bovine serum and  incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from cell lines using a RNeasy mini kit (QIAGEN) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were transfected with miR-29c oligo or negative control oligo (10nM) (Ambion) using lipofectamin RNAiMAX (Invitrogen). At 24h after, total RNA was extracted.

value: miR-29c overexpression


title: 5-7 week Infected replicate 6

description:
Biological replicate 6 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 5-7 week Infected replicate 11

description:
Biological replicate 11 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 5-7 week Infected replicate 5

description:
Biological replicate 5 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: erStress_131grandparents_GM07016_dmso

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM07016 treated with DMSO 8 hours.

source_name: Lymphoblastoid cell lines derived from GM07016

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

value: DMSO


title: Spleen Mock infected 6h Rep 3 (P1/7)

description: Replicate 3


title: Spleen Mock infected 6h Rep 2 (P1/7)

description: Replicate 2


title: 5-7 week Infected replicate 3

description:
Biological replicate 3 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen Mock infected 6h Rep 1 (P1/7)

description: Replicate 1


title: Spleen S. suis 89-1591 6h Rep 3 (89-1591)

description: Replicate 3

source_name: Spleen S. suis 89-1591 6h

treatment_protocol: Mice were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain 89-1591 or mock-infected with bacterial growth medium (THB).


title: Spleen S. suis 89-1591 6h Rep 4 (89-1591)

description: Replicate 4


title: MKN74, miR-29c, replicate 1

source_name: MKN74, miR-29c, replicate 1


title: 5-7 week Infected replicate 2

description:
Biological replicate 2 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen Mock infected 6h Rep 4 (P1/7)

description: Replicate 4


title: 5-7 week Infected replicate 1

description:
Biological replicate 1 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen S. suis 89-1591 6h Rep 2 (89-1591)

description: Replicate 2


title: 5-7 week Infected replicate 4

description:
Biological replicate 4 of 11 for 5-7 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 3-4 week Infected replicate 4

description:
Biological replicate 4 of 5 for 3-4 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 3-4 week Infected


title: MKN7, miR-29c, replicate 1

source_name: MKN7, miR-29c, replicate 1


title: MKN74, miR-29c, replicate 2

source_name: MKN74, miR-29c, replicate 2


title: Spleen S. suis 89-1591 6h Rep 1 (89-1591)

description: Replicate 1


title: MKN7, Negative control, replicate 1

source_name: MKN7, Negative control, replicate 1

value: negative control


title: 3-4 week Infected replicate 5

description:
Biological replicate 5 of 5 for 3-4 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 3-4 week Infected replicate 3

description:
Biological replicate 3 of 5 for 3-4 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Spleen Mock infected 6h Rep 4 (89-1591)

description: Replicate 4

value: Female


title: MKN45, miR-29c, replicate 2

source_name: MKN45, miR-29c, replicate 2


title: 3-4 week Infected replicate 2

description:
Biological replicate 2 of 5 for 3-4 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: MKN7, Negative control, replicate 2

source_name: MKN7, Negative control, replicate 2


title: MKN74, Negative control, replicate 2

source_name: MKN74, Negative control, replicate 2


title: Spleen Mock infected 6h Rep 3 (89-1591)

description: Replicate 3


title: MKN45, miR-29c, replicate 1

source_name: MKN45, miR-29c, replicate 1


title: H3K4me2 JBC 1360331 Ovary D.melanogaster Input Rep2

description: Served as Input for: 1269.Mvalues.bedgraph

source_name: H3K4me2 JBC 1360331 Ovary Input expt.1047 channel_1

value: Adult Female


title: MKN45, Negative control, replicate 2

source_name: MKN45, Negative control, replicate 2


title: Spleen Mock infected 6h Rep 2 (89-1591)

description: Replicate 2

source_name: Spleen Mock infected 6h


title: MKN74, Negative control, replicate 1

source_name: MKN74, Negative control, replicate 1


title: 1 week Infected replicate 2

description:
Biological replicate 2 of 4 for 1 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 1 week infected

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue


title: 1 week Infected replicate 4

description:
Biological replicate 4 of 4 for 1 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: PanB3_B

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

institute: Barts & The London School of Medicine (QMUL)

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
238pb.cel

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

scan_protocol: The arrays were scanned using GeneChip scanner 3000 7G

data_processing: RMA normalisation

source_name: PanIN lesion family B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol. The quantity and quality of the samples were assessed using Thermo Scientific NanoDrop 1000 spectrophotometer and Agilant 2100 Bioanalyzer, respectively.

tag: disease state

value: PanIN lesion

value: pancreas


title: PanB2_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
232aa.cel


title: PanB1_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
223pa1.cel


title: 3-4 week Infected replicate 1

description:
Biological replicate 1 of 5 for 3-4 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 1 week Infected replicate 1

description:
Biological replicate 1 of 4 for 1 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: PanB2_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
232ab.cel


title: PanA1_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
118pa.cel

source_name: PanIN lesion family A


title: PanC2_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
046p2a.cel

source_name: PanIN lesion family C


title: Proximal nail matrix_Rep 1

city: New York

first: Makoto

last: Takeo

state: NY

address: 522 First Ave.

institute: New York University School of Medicine

hyb_protocol: We used AffymertixGeneChip 3 IVT Express Kit for hybridization according to manufacture's protocol.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring GX using Affymetrix default analysis settings and global scaling as normalization method.

source_name: 8 weeks old mouse, intact proximal matrix

label_protocol: We used AffymertixGeneChip 3 IVT Express Kit for labeling according to manufacture's protocol.

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

value: isolated proximal nail matrix


title: 1 week Infected replicate 3

description:
Biological replicate 3 of 4 for 1 week Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: 48 h Infected replicate 3

description:
Biological replicate 3 of 4 for 48 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 48 h Infected


title: PanB3_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
238pa.cel


title: Proximal nail matrix_Rep 2


title: Distal nail matrix_Rep 2

source_name: 8 weeks old mouse, intact distal matrix

value: isolated distal nail matrix


title: Distal nail matrix_Rep 1


title: PanB1_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
223pb1.cel


title: 48 h Infected replicate 4

description:
Biological replicate 4 of 4 for 48 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: PanA1_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
118pb.cel


title: 48 h Infected replicate 2

description:
Biological replicate 2 of 4 for 48 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: PanC2_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
046pb.cel


title: Palatal mesenchymal cells treated with SB431542 and TGF-beta2

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

description: Gene expression data from palatal mesenchymal cells treated with TGF-beta2 in the presence with the TGF-beta type I receptor inhibitor SB431542

hyb_protocol: The biotin-labeled RNAs were fragmented and hybrixized to a GeneChip at 45oC for 16 hours.

scan_protocol: The chips were scanned by GENEChip Scanner 3000 7G System

data_processing: The data were analyzed by Affymetrix GeneChip-related software packages GCOS, Data mining Tool and Affymetrix web database 'NetAffx'.

source_name: Palatal mesenchymal cells; treated with TGF-beta2 and with SB431542

label_protocol: 500 ng of total RNA was amplified and biotin-labeled according to the GeneChip 3'IVT Expression Kit User Manual (Affymetrix).

growth_protocol: Palatal mesenchymal cell cultures were established from E14.0 mouse embryos.

extract_protocol: Total RNAs were isolated using an Rneasy kit (Qiagen)

treatment_protocol: Cells were treated either with SB431542 (group 3) or 5Z-7-Oxozeaenol  (group 4) for 60 minutes and stimulated with TGF-beta2 for 120 minutes. Control cells were treated with TGF-beta2 (group2) for 120 minutes or not treated at all (group 1).

value: treated with SB431542 and TGF-beta2

value: Palatal mesenchymal cells

value: outbred wild-type


title: PanC1_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
025pa.cel


title: PanC1_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
025pb.cel


title: Palatal mesenchymal cells treated with 5Z-7-Oxozeaenol and TGF-beta2

description: Gene expression data from palatal mesenchymal cells treated with TGF-beta2 in the presence with the Tak1 kinase inhibitor 5Z-7-Oxozeaenol

source_name: Palatal mesenchymal cells; treated with TGF-beta2 and with5Z-7-Oxozeaenol


title: Px7_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
Va6PB.CEL

source_name: PanIN lesion family X


title: Px5_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
235_304_A.CEL


title: Px6_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
235_313_B.CEL


title: Px6_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
235_313_A.CEL


title: 24 h Infected replicate 4

description:
Biological replicate 4 of 4 for 24 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 24 h Infected

value: Intermoult

value: male


title: 48 h Infected replicate 1

description:
Biological replicate 1 of 4 for 48 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

value: Hepatopancreas

value: standard reference pooled sample


title: Spleen Mock infected 6h Rep 1 (89-1591)

description: Replicate 1

value: Spleen


title: Px7_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
Va6PA.CEL


title: Px4_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
235_289_A.CEL


title: Palatal mesenchymal cells treated with TGF-beta2

description: Gene expression data from palatal mesenchymal cells treated with TGF-beta2

source_name: Palatal mesenchymal cells; treated with TGF-beta2

value: treated with TGF-beta2


title: Px3_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
049pa.cel


title: Px3_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
049pb.cel


title: 24 h Infected replicate 3

description:
Biological replicate 3 of 4 for 24 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

value: hepatopancreas


title: 10 week control replicate 4

description:
Biological replicate 4 of 4 for 10 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 10 week control


title: Px4_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
235_289_B.CEL


title: Px5_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
235_304_B.CEL


title: Px2_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
016pa.cel


title: 24 h Infected replicate 1

description:
Biological replicate 1 of 4 for 24 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Untreated palatal mesenchymal cells

description: Gene expression data from untreated palatal mesenchymal cells

source_name: Palatal mesenchymal cells; untreated

value: untreated


title: Akatsuki_0D

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

hyb_protocol: Glass slides were hybridized overnight at 65 °C in a hybridization buffer containing a portion of Cy3 -labeled cRNA. After hybridization, slides were washed in Agilent Gene Expression Wash Buffer 1 (Agilent) with 0.005% Triton X-102 for 1 min at room temperature and Agilent Gene Expression Wash Buffer 2 (Agilent) with 0.005% Triton X-102 for 1 min at 37 °C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565A) 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 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Prunus persica

source_name: melting peach 'Akatsuki' fruit

label_protocol: Total RNA (250 ng) was labelled with Cy3 according to the instructions for the Quick Amp Labeling Kit (Agilent, Palo Alto, CA). Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

extract_protocol: Total RNA was extracted from frozen samples by the hot borate method (Wan and Wilkins, 1994).

treatment_protocol: Melting peach ‘Akatsuki’ fruit were sampled at 92, 98, 104 and 106 DAB; stony peach ‘Manami’ and ‘Odoroki’ were harvested at commercial maturity and treated with air or 5000 µl l–1 propylene for 3 days (Tatsuki et al., 2006).

tag: cultivar

value: Akatsuki

tag: harvest

value: commercial maturity

value: fruit


title: PaCa6_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
pa.cel

source_name: pancreatic cancer

value: pancreatic cancer

value: pancreas


title: Px2_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
016pb.cel

value: PanIN lesion


title: Px1_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
010pb.cel


title: PaCa6_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
pb.cel


title: 10 week control replicate 2

description:
Biological replicate 2 of 4 for 10 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

tag: gender


title: PaCa1_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
194bA.CEL


title: 8 week control replicate 2

description:
Biological replicate 2 of 3 for 8 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 8 week control


title: PaCa5_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
ftb.cel


title: PaCa5_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
fta.cel


title: Manami_P3

source_name: stony hard peach 'Manami' fruit treated wity propylen for 3 days

value: Manami

tag: treatment

value: 5000μl/l propylene for 3 days


title: N3_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
NpaVB.CEL

source_name: normal donor pancreas

value: normal


title: 8 week control replicate 3

description:
Biological replicate 3 of 3 for 8 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

value: Intermoult

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue


title: N2_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
NpaGA.CEL


title: 10 week control replicate 3

description:
Biological replicate 3 of 4 for 10 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

value: male


title: N1_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
NpaA.CEL


title: Odoroki_C3

source_name: stony hard peach 'Odoroki' fruit with air for 3 days

value: Odoroki

value: air for 3 days


title: PaCa2_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
205a.cel


title: Manami_C3

source_name: stony hard peach 'Manami' fruit with air for 3 days


title: PaCa2_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
205b.cel


title: Akatsuki-Jly21

source_name: melting peach 'Akatsuki' fruit 106 DAB

value: 106 Day After full Bloom


title: 24 h control replicate 3

description:
Biological replicate 3 of 3 for 24 h control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

source_name: 24 h control

value: Hepatopancreas

value: standard reference pooled sample


title: Odoroki_P3

source_name: stony hard peach 'Odoroki' fruit treated wity propylen for 3 days


title: N3_A

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
NpaVA.CEL


title: MKN45, Negative control, replicate 1

description: Gene expression after 24hr in miRNA oligo transfected cells

source_name: MKN45, Negative control, replicate 1

value: negative control

tag: cell line


title: 24 h control replicate 2

description:
Biological replicate 2 of 3 for 24 h control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

value: hepatopancreas


title: PaCa1_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
194bB.CEL


title: 8 week control replicate 1

description:
Biological replicate 1 of 3 for 8 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: N2_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
NpaGB.CEL


title: Akatsuki_Jly13

source_name: melting peach 'Akatsuki' fruit 98 DAB

value: Akatsuki

value: 98 Day After full Bloom


title: 24 h control replicate 1

description:
Biological replicate 1 of 3 for 24 h control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: Akatsuki-Jly19

source_name: melting peach 'Akatsuki' fruit 104 DAB

value: 104 Day After full Bloom

value: fruit


title: 10 week control replicate 1

description:
Biological replicate 1 of 4 for 10 week control
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.


title: N1_B

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
NpaB.CEL

value: pancreas


title: Akatsuki_Jly07

source_name: melting peach 'Akatsuki' fruit 92 DAB

value: 92 Day After full Bloom


title: 6 h goniothalamin-treated seedlings vs control: replicate 2

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

institute: Tokyo University of Agriculture & Technology

description:
US90500268_252116911354_S01_GE2_105_Dec08_1_2.txt
Biological replicate 2 of 2

hyb_protocol: Mixtures of 0.825 µg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 °C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 4 60-mer oligo-microarray.

scan_protocol: The slides were then washed and scanned with an Agilent G2505B Scanner to detect fluorescence intensity.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio (treated/control). Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field),

organism: Arabidopsis thaliana

source_name: 6 h goniothalamin-treated seedlings

label_protocol: Two-color spike mix was added to the total RNA, and the RNA was labeled with a Quick Amp Labeling Kit, two-color (Agilent Technologies), according to the manufacturer’s protocol. Fluorescent cRNA was generated from total RNA: 500 ng of RNA was reverse-transcribed with MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently transcribed in vitro using T7 RNA polymerase, resulting in Cy3-labeled (control) and Cy5-labeled (cis-CA-treated) cRNAs. The cRNAs were purified through RNeasy Mini Spin columns (Qiagen) and then quantified with a NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: The sterilized seeds were placed on 0.8% agar (Nakalai Tesque, Inc., Kyoto, Japan) with Murashige and Skoog Plant Salt Mixture (Nihon Pharmaceutical Co., Ltd., Tokyo, Japan) and 1% sucrose (Wako Pure Chemical Industries, Osaka, Japan) in a sterilized Petri dish (90-mm diameter). The seeds were held at 4 °C overnight in darkness and then transferred to a growth chamber. Emerging plants were maintained in the growth chamber under a schedule of 16-h light (22 °C) and 8-h dark (20 °C).

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

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and  transferred to 20 ml of deionized water in petri-dish, and then transferred to 20 ml of deionized water containing 100 ppm  goniothalamin and1 % dimethyl sulfoxide, and then incubated under light. Plants were collected at 0 (control), 2, and 6 h and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.

value: Col. 0

tag: age

value: day 14

value: seedling

source_name: control seedlings


title: 6 h  goniothalamin-treated seedlings vs control: replicate1

description:
US90500268_252116911354_S01_GE2_105_Dec08_1_1.txt
Biological replicate 1 of 2


title: B-cell precursors at S3_FBM30_S3_RNA expression

status: Public on Mar 26 2013

first: Seung-Tae

last: Lee

state: - None -

address: 50 Iron-Dong KanangmGu

department: Laboratory Medicine & Genetics

institute: Samsung Medical Center

description: Gene expression data of early B-cell precursors from human fetuses ranging in age between 20 and 24 weeks of gestation

hyb_protocol: Following fragmentation, cRNA were hybridized onto GeneChip Human Gene 1.0 ST Array (Affymetrix) according to Affymetrix's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix genechip scanner

data_processing: Data was processed and normalized using the Expression Console software (Affymetrix) with the standard Robust Multi-array Average (RMA) algorithm

source_name: B-cell precursors at S3

label_protocol: 1 μg of high-quality total RNA was amplified and labeled (NuGen Ovation)

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions

treatment_protocol: Four stages of B-cell precursors were isolated via flow cytometry sorting

value: B-cell precursors at S3, predominantly pre-B-II cells

value: fetal bone marrow

tag: subjects

value: fetuses at San Francisco area


title: B-cell precursors at S4_FBM21_S4_RNA expression

source_name: B-cell precursors at S4

value: B-cell precursors at S4, predominantly immature B cells

value: fetuses ranging in age between 20 and 24 weeks of gestation


title: B-cell precursors at S4_FBM17_S4_RNA expression


title: B-cell precursors at S4_FBM13_S4_RNA expression


title: B-cell precursors at S4_FBM8_S4_RNA expression


title: B-cell precursors at S4_FBM1_S4_RNA expression


title: B-cell precursors at S3_FBM10_S3_RNA expression


title: B-cell precursors at S4_FBM29_S4_RNA expression


title: B-cell precursors at S4_FBM25_S4_RNA expression


title: B-cell precursors at S3_FBM22_S3_RNA expression


title: B-cell precursors at S2_FBM31_S2_RNA expression

source_name: B-cell precursors at S2

value: B-cell precursors at S2, predominantly pre-B-I cells


title: B-cell precursors at S3_FBM7_S3_RNA expression


title: B-cell precursors at S2_FBM15_S2_RNA expression


title: B-cell precursors at S2_FBM6_S2_RNA expression


title: B-cell precursors at S3_FBM26_S3_RNA expression


title: B-cell precursors at S3_FBM18_S3_RNA expression


title: B-cell precursors at S3_FBM14_S3_RNA expression


title: B-cell precursors at S2_FBM3_S2_RNA expression


title: B-cell precursors at S2_FBM19_S2_RNA expression


title: B-cell precursors at S1_FBM5_S1_RNA expression

source_name: B-cell precursors at S1

value: B-cell precursors at S1, predominantly multipotent progenitors and common lymphoid progenitors


title: B-cell precursors at S3_FBM2_S3_RNA expression


title: B-cell precursors at S1_FBM4_S1_RNA expression


title: B-cell precursors at S2_FBM27_S2_RNA expression


title: B-cell precursors at S2_FBM11_S2_RNA expression