title: chorionic villi sample 47

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: chorionic villi sample

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: chorionic villi sample 47

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the High Pure PCR Template Preparation Kit (Roche Diagnostics, Mannheim, Germany)

tag: karyotype

value: chorionic villi sample


title: Caco2_CON_0_1hr-1

status: Public on Dec 15 2012

type: RNA

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

country: USA

institute: Oregon State University

description: Gene expression data from Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 1hr

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Caco-2/HT29-MTX cells exposed to 0 ug/ml control for 1hr, biological rep1

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Caco-2, human colorectal adenocarcinoma cells (ATCC HTB-37, Lot 57863838) were maintained in EMEM media supplemented with 10% FBS (ATCC cat# 30-2003 & 30-2020) and incubated at 37°C – 5% CO2. HT29-MTX, human colon adenocarcinoma cells treated with methotrexate (Lesuffleur et al. 1993) were obtained from Dr. Thécla Lesuffleur (INSERM, Paris, France) and were maintained in DMEM with Glutamax and 10% Hi-FBS (Invitrogen) at 37°C - 5% CO2. Both cell lines were subcultured at 80-90% confluence.  Caco-2 (passage 49 and 63) and HT29-MTX cells (passage 29 and 33) were cultured to obtain several Corning T75 flasks. At 80-90% confluence, the cells were trypsinized and flasks were pooled. Cells were counted using a hemocytometer and then mixed together at a 75:25 Caco-2:HT29-MTX ratio and placed in the HT29-MTX medium with 1% penicillin-streptomycin. Combined cells were mechanically mixed and 1 mL was added to 6-transwell plates to obtain 0.4 x 106 cells per well (8.9 x 104 cells/cm2) (Hilgendorf et al. 2000). Prior to NP exposure, cells were incubated at 37°C - 5% CO2 for 14 days, replacing the medium every other day, to achieve post-confluent differentiation, polarization, and tight-junction formation.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: For NP exposures, 1.5 ml multi-walled carbon nanotubes (MWCNT) or titanium nanobelts (TiO2-NB)  suspensions at 10 or 100 µg/ml media were placed in the top compartment (apical) of the 6 Transwell™ plate containing the 14 days co-cultured cells. The bottom compartment (basolateral) contained 2.5 ml of fresh medium. Control groups received only fresh medium in both compartments. The treated cells were incubated at 37°C – 5% CO2 for 3 and 24 h for proteomics analysis, and for 1 and 24 h for transcriptomics analysis, as described below.

tag: cell line

tag: cell type

value: human colorectal/colon adenocarcinoma

tag: treatment

value: control

tag: dose

value: 0 ug/ml

tag: time

value: 1 hr


title: 12hr_DMSO_NoCyto_1

status: Public on Dec 14 2012

city: CAMBRIDGE

first: Danny

last: Chou

state: Massachusetts

address: 500 Main St

institute: MIT

description: Gene expression data from rat INS-1E cells in the presence and absence of cytokines and/or BRD0476

hyb_protocol: Biotinlyated cRNA targets were normalized, fragmented and hybridized to Affymetrix Rat 230 2.0 arrays (GPL16251) using Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)

data_processing: The data were analyzed with GenePattern (modules ExpressionFileCreator, PreProcessDataset, and GSEA) using robust multi-array (RMA) analysis for background correction, thresholding and normalization.

organism: Rattus norvegicus

source_name: Rat INS-1E cells with no cytokines and DMSO for 12 hours

label_protocol: 500 ng of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688).

growth_protocol: Rat INS-1E cells were grown in RPMI medium with 10% FBS, pen/strep, HEPES, sodium pyruvate and beta-mercaptoethanol.

extract_protocol: Extraction of total RNA was performed using the RNEasy kit according to the manufacturer's instructions.

treatment_protocol: Rat INS-1E cells were treated with 10ng/ml IL-1b, 50ng/ml IFN-g and 25 ng/ml TNF-a for 6 or 12 hours in the presence or absence of 10uM BRD0476.

value: insulinoma cell

tag: agent

value: DMSO

tag: time point

value: 12 hours

tag: tissue

value: pancreatc islets


title: 12hr_BRD0476_Cyto_3

source_name: Rat INS-1E cells with cytokines and BRD0476 for 12 hours

value: cytokines and BRD0476


title: 12hr_DMSO_NoCyto_3


title: 12hr_BRD0476_NoCyto_3

source_name: Rat INS-1E cells with no cytokines and BRD0476 for 12 hours


title: 12hr_BRD0476_NoCyto_1


title: 12hr_DMSO_NoCyto_2


title: chorionic villi sample 46

type: genomic

country: Germany

description: chorionic villi sample

molecule: genomic DNA

source_name: chorionic villi sample 46


title: 6hr_BRD0476_Cyto_3

source_name: Rat INS-1E cells with cytokines and BRD0476 for 6 hours

value: 6 hours


title: 6hr_BRD0476_Cyto_1


title: chorionic villi sample 44

description: chorionic villi sample

source_name: chorionic villi sample 44


title: chorionic villi sample 45

description: chorionic villi sample

source_name: chorionic villi sample 45


title: 6hr_DMSO_Cyto_2

source_name: Rat INS-1E cells with cytokines and DMSO for 6 hours

value: cytokines and DMSO


title: 6hr_DMSO_Cyto_3


title: 6hr_BRD0476_Cyto_2


title: chorionic villi sample 42

description: chorionic villi sample

source_name: chorionic villi sample 42


title: chorionic villi sample 43

description: chorionic villi sample

source_name: chorionic villi sample 43


title: NEB_RA_rep2

city: Los Angeles

first: Kevin

last: Peterson

state: CA

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine

description: Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid for additional 3 days before harvested for total RNA extraction.

hyb_protocol: 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays  were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Data were analyzed with dChip

organism: Mus musculus

source_name: Neuralized embryoid bodies, all trans retinoic acid (500nM), 3 days

label_protocol: Biotinylated cRNA were prepared according to the standard protocol  (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA

growth_protocol: Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.

extract_protocol: Total RNA was isolated with mirVana kit from Ambion

treatment_protocol: Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).

value: Gli1-FLAG ESC-derived neural progenitors

value: all trans retinoic acid (500nM)


title: chorionic villi sample 41 (duplicate of chorionic villi 21)

description: chorionic villi sample


title: 6hr_BRD0476_NoCyto_3

source_name: Rat INS-1E cells with no cytokines and BRD0476 for 6 hours


title: THP-1_PBS_2

city: Utrecht

first: Karlijn

last: van Keulen

address: Heidelberglaan 100, G02.523

department: division heart and lungs

country: Netherlands

institute: University Medical Center Utrecht

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Gene expression values of the chips were normalized in BeadStudio (version 3.2 Illumina)

source_name: THP-1 monocytes, PBS, 24hrs

label_protocol: Illumina TotalPrep RNA Amplification Kits were used for cDNA and cRNA synthesis (Ambion) according the manufacturer’s protocol

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium containing 50mM 2-mercaptoethanol, 100 U/ml penicillin, 100 μg/ml streptomycin, and 5% FBS. Monocytes, in a density of 2*10^6 cells/4 mL were starved O/N prior to stimulation in medium containing 0.1% FCS.

extract_protocol: RNA of stimulated monocytes was isolated using Tripure reagent (Roche) according the manufacturer’s protocol. High quality RNA was obtained with NucleoSpin RNA II kits (Machery-Nagel) inclusive DNase treatment

treatment_protocol: THP-1 cells were stimulated with LPS (100ng/mL) or TGFβ1 (1ng/mL) or LPS and TGFβ1 for 24 hrs and kept in an CO2 injecting incubator. As a control PBS was added to the cells.

value: THP-1 monocytic cell line

tag: agent (stimulus)

value: PBS


title: chorionic villi sample 39

description: chorionic villi sample

source_name: chorionic villi sample 39


title: 6hr_BRD0476_NoCyto_1


title: chorionic villi sample 40

description: chorionic villi sample

source_name: chorionic villi sample 40


title: 6hr_DMSO_Cyto_1


title: chorionic villi sample 37

description: chorionic villi sample

source_name: chorionic villi sample 37


title: 6hr_DMSO_NoCyto_2

source_name: Rat INS-1E cells with no cytokines and DMSO for 6 hours


title: 6hr_BRD0476_NoCyto_2


title: chorionic villi sample 36

description: chorionic villi sample

source_name: chorionic villi sample 36


title: chorionic villi sample 38

description: chorionic villi sample

source_name: chorionic villi sample 38


title: Negative siRNA treated U-2OS

city: Ann Arbor

first: Hiroko

last: Nagao-kitamoto

address: 1150 W Medical Center Dr,

institute: The University of Michigan Medical school

description: Gene expression data from Negative siRNA treating U-2OS

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Osteosarcoma

label_protocol: Second-Strand cDNA (ssDNA) were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: U-2OS cell lines were cultured in DMEM at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from the cell lines and tissue specimens using miR-Vana RNA isolation kits.

treatment_protocol: U-2OS cells were treated with siRNA for 48 hr.

value: Osteosarcoma, bone


title: 6hr_DMSO_NoCyto_1


title: 6hr_DMSO_NoCyto_3


title: chorionic villi sample 33 (duplicate of chorionic villi 26)

description: chorionic villi sample

value: chorionic villi sample


title: chorionic villi sample 35

description: chorionic villi sample

source_name: chorionic villi sample 35


title: NEB_RA_rep1


title: EBTPd12#2

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: CD34+CD43+CD45+ cells differentiated for 12 days in EBs

hyb_protocol: The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes, and then injected into a GeneChip ST cartridge. The arrays were incubated at 45°C for 17 hours ± 1 hour in a rotating oven at 60 rpm. The arrays were then washed and stained according to the GeneChip Expression Wash, Stain and Scan User Manual (P/N702731).

scan_protocol: Fluorescence signals were scanned with the Affymetrix GeneChip Scaner 3000. Affymetrix GeneChip Command Console (AGCC) software was used for acquisition of the initial image of the scanned array.

data_processing: The Affymetrix Expression Console was used to normalize data and determine signal intensity (RMA-Sketch).

source_name: CD34+CD43+CD45+ cells/EBd12

label_protocol: 45 μL of fragmented single-stranded DNA was mixed with 15 μL of master mix containing 5X TdT buffer, TdT and DNA Labeling reagent, and was incubated at 37°C for 60 minutes.

growth_protocol: ES cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM)-F12 (Sigma) supplemented with 1x MEM non-essential amino acids (Gibco-Invitrogen), 1x GlutaMAX-I (Gibco-Invitrogen), 20% knockout serum replacement (KSR) (Gibco-Invitrogen), 0.1 mM 2-mercaptoethanol (2-ME)(Sigma), and 5 ng/mL basic fibroblast growth factor (bFGF)(ReproCELL) either on irradiated MEF as feeder layers.

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

value: CD34+CD43+CD45+ hematopoietic stem/progenitor cells

tag: days of eb differentiation


title: GLI2 siRNA treated U-2OS

description: Gene expression data from GLI2 siRNA treating U-2OS


title: chorionic villi sample 31

description: chorionic villi sample

source_name: chorionic villi sample 31


title: EBSPd12#2

description: CD34+CD43-CD45- cells differentiated for 12 days in EBs

source_name: CD34+CD43-CD45- cells/EBd12

value: CD34+CD43+CD45- hematopoietic stem/progenitor cells


title: chorionic villi sample 32

description: chorionic villi sample

source_name: chorionic villi sample 32


title: EBTPd12#1


title: EBSPd12#1


title: chorionic villi sample 30

description: chorionic villi sample

source_name: chorionic villi sample 30


title: EBTPd08#2

description: CD34+CD43+CD45+ cells differentiated for 8 days in EBs

source_name: CD34+CD43+CD45+ cells/EBd08


title: chorionic villi sample 25

description: chorionic villi sample

source_name: chorionic villi sample 25


title: chorionic villi sample 22

description: chorionic villi sample

source_name: chorionic villi sample 22


title: chorionic villi sample 26

description: chorionic villi sample

source_name: chorionic villi sample 26


title: EBSPd06#2

description: CD34+CD43-CD45- cells differentiated for 6 days in EBs

source_name: CD34+CD43-CD45- cells/EBd06


title: EBSPd08#2

description: CD34+CD43-CD45- cells differentiated for 8 days in EBs

source_name: CD34+CD43-CD45- cells/EBd08


title: chorionic villi sample 29

description: chorionic villi sample

source_name: chorionic villi sample 29


title: chorionic villi sample 24

description: chorionic villi sample

source_name: chorionic villi sample 24


title: chorionic villi sample 21

description: chorionic villi sample

source_name: chorionic villi sample 21


title: chorionic villi sample 28

description: chorionic villi sample

source_name: chorionic villi sample 28


title: EBDPd08#2

description: CD34+CD43+CD45- cells differentiated for 8 days in EBs

source_name: CD34+CD43+CD45- cells/EBd08


title: EBTPd08#1


title: EBDPd08#1


title: chorionic villi sample 27

description: chorionic villi sample

source_name: chorionic villi sample 27


title: chorionic villi sample 20

description: chorionic villi sample

source_name: chorionic villi sample 20


title: EBSPd06#1

value: CD34+CD43-CD45- hematopoietic stem/progenitor cells


title: chorionic villi sample 19

description: chorionic villi sample

source_name: chorionic villi sample 19


title: chorionic villi sample 23

description: chorionic villi sample

source_name: chorionic villi sample 23


title: Sox17TPd08

description: CD34+CD43+CD45low hemogenic endothelium-like cells transduced with a Sox17-ERT retrovirus cocultured with OP9 stromal cells in the presence of 4OH-tamoxifen

tag: transduction


title: EBSPd08#1


title: chorionic villi sample 34

description: chorionic villi sample

source_name: chorionic villi sample 34


title: Sox17TPd12

value: CD34+CD43+CD45low hemogenic endothelium-like cells

value: transduced with a Sox17-ERT retrovirus cocultured with OP9 stromal cells in the presence of 4OH-tamoxifen


title: Sox17SPd06


title: chorionic villi sample 16

description: chorionic villi sample

source_name: chorionic villi sample 16


title: chorionic villi sample 17

description: chorionic villi sample

source_name: chorionic villi sample 17


title: chorionic villi sample 18

description: chorionic villi sample

source_name: chorionic villi sample 18


title: Sox17DPd08


title: Sox17SPd08


title: chorionic villi sample 13

description: chorionic villi sample

source_name: chorionic villi sample 13


title: chorionic villi sample 11

description: chorionic villi sample

source_name: chorionic villi sample 11


title: chorionic villi sample 7

description: chorionic villi sample

source_name: chorionic villi sample 7


title: chorionic villi sample 9

description: chorionic villi sample

source_name: chorionic villi sample 9


title: chorionic villi sample 10

description: chorionic villi sample

source_name: chorionic villi sample 10


title: chorionic villi sample 14

description: chorionic villi sample

source_name: chorionic villi sample 14


title: chorionic villi sample 15

description: chorionic villi sample

source_name: chorionic villi sample 15


title: 0_Human-100_Mouse [83709_6E]

city: Miami

first: Camilo

last: Valdes

state: FL

address: Locator C-213.  1120 NW 14 Street

department: Center for Computational Science

institute: University of Miami

description: Replicate 2

hyb_protocol: Standard illumina hybridization protocol (58 degrees for 16-20 hours).

scan_protocol: Standard illumina scanning protocol

data_processing: Raw expression data was background corrected, quantile normalized, and log2 transformed using the GeneSpring GX software.

label: Biotin

source_name: mouse normal lung tissue

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

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA integrity was determined by analysis on an Agilent 2100 Bioanalyzer following manufacturer's recommendations.

tag: strain

value: NOD scid gamma

tag: proportions

value: human tissue 0%, mouse tissue 100%


title: 25_Human-75_Mouse [83708_6D]

description: Replicate 2

organism:
Homo sapiens
Mus musculus

source_name: human breast carcinoma and mouse normal lung tissue

value: human tissue 25%, mouse tissue 75%


title: chorionic villi sample 6

description: chorionic villi sample

source_name: chorionic villi sample 6


title: 100_Human-0_Mouse [83710_7A]

description: Replicate 3

source_name: human breast carcinoma

value: human tissue 100%, mouse tissue 0%


title: 50_Human-50_Mouse [83707_6C]

description: Replicate 2

value: human tissue 50%, mouse tissue 50%


title: 25_Human-75_Mouse [83713_7D]

description: Replicate 3


title: 75_Human-25_Mouse [83711_7B]

description: Replicate 3

value: human tissue 75%, mouse tissue 25%


title: 75_Human-25_Mouse [83706_6B]

description: Replicate 2


title: chorionic villi sample 8

description: chorionic villi sample

source_name: chorionic villi sample 8


title: 100_Human-0_Mouse [83705_6A]

description: Replicate 2


title: 0_Human-100_Mouse [83704_5E]

description: Replicate 1


title: chorionic villi sample 4

description: chorionic villi sample

source_name: chorionic villi sample 4


title: 50_Human-50_Mouse [83702_5C]

description: Replicate 1


title: chorionic villi sample 12

description: chorionic villi sample

source_name: chorionic villi sample 12


title: chorionic villi sample 2

description: chorionic villi sample

source_name: chorionic villi sample 2


title: chorionic villi sample 5

description: chorionic villi sample

source_name: chorionic villi sample 5


title: 0_Human-100_Mouse [83714_7E]

description: Replicate 3


title: chorionic villi sample 1

description: chorionic villi sample

source_name: chorionic villi sample 1


title: 25_Human-75_Mouse [83703_5D]

description: Replicate 1


title: chorionic villi sample 3

description: chorionic villi sample

source_name: chorionic villi sample 3


title: 75_Human-25_Mouse [83701_5B]

description: Replicate 1


title: amniotic cell sample 15

description: amniotic cell sample

source_name: amniotic cell sample 15

value: amniotic cell sample


title: amniotic cell sample 14

description: amniotic cell sample

source_name: amniotic cell sample 14


title: amniotic cell sample 12

description: amniotic cell sample

source_name: amniotic cell sample 12


title: 75_Human-25_Mouse [83686_2B]

description: Replicate 2


title: amniotic cell sample 13

description: amniotic cell sample

source_name: amniotic cell sample 13


title: 100_Human-0_Mouse [83700_5A]

description: Replicate 1


title: 50_Human-50_Mouse [83692_3C]

description: Replicate 3


title: 25_Human-75_Mouse [83693_3D]

description: Replicate 3


title: amniotic cell sample 16

description: amniotic cell sample

source_name: amniotic cell sample 16


title: 25_Human-75_Mouse [83688_2D]

description: Replicate 2


title: 25_Human-75_Mouse [83683_1D]

description: Replicate 1


title: amniotic cell sample 10

description: amniotic cell sample

source_name: amniotic cell sample 10


title: 50_Human-50_Mouse [83687_2C]

description: Replicate 2


title: amniotic cell sample 9

description: amniotic cell sample

source_name: amniotic cell sample 9


title: third trimester #6

city: Shreveport

first: Yuping

last: Wang

state: LA

address: 1501 Kings Highway

department: Ob/Gyn

institute: LSUHSC-Shreveport

hyb_protocol: Following fragmentation, 1 ug of labeled product was hybridized for 18 hr at 48C on GeneChip miRNA 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 Expression Console 1.2, using RMA + DABG, on a linear scale.

source_name: third trimester

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTag Biotin HSR RNA Labeling Kit, Affymetrix).

extract_protocol: Total RNA was isolated from placental villous tissues with Trizol reagent (Invitrogen, Carlsbad, CA).  RNA quality and quantity was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: placenta


title: third trimester #5


title: third trimester #4


title: third trimester #3


title: ΔplcRa T2g vs WT T2r

city: Guyancourt

first: Eugenie

last: HUILLET

address: La Minière INRA

department: MICA

country: France

institute: INRA institute

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_2_4
WT vs ΔplcRa T2 biological duplo 2 of 2

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, using the extended dynamic range scan mode and 10 micron scan resolution according to the Agilent protocol .

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was analyzed with the Vampire webbased microarray suite.

organism: Bacillus cereus ATCC 14579

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

growth_protocol: The type strain B. cereus ATCC14579, an ∆plcRa isogenic mutant strain and a strain enabling overexpressing of the plcRa gene (Wild-type strain harboring pHT315plcRa vector) were used throughout this study. Strains were grown in LB broth at 37°C, in flasks, with an aeration ratio of 10, on a rotary shaker at 175 rpm. Cultures were inoculated to an OD600 of 0.05 with cells in the vegetative phase in LB broth, and cell cultures were harvested 1h (t1) and 2h after (t2) the onset of stationary phase.

extract_protocol: RNA was extracted using the Trizol method as described by van Schaik et al., 2004

tag: genotype/variation

value: ΔplcRa

tag: developmental stage

value: B. cereus ATCC14579 (plcRa deletion) cells were grown to 2 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)

value: wild type

value: B. cereus ATCC14579 cells were grown to 2 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)


title: 100_Human-0_Mouse [83680_1A]

description: Replicate 1


title: amniotic cell sample 8

description: amniotic cell sample

source_name: amniotic cell sample 8


title: 50_Human-50_Mouse [83712_7C]

description: Replicate 3

source_name: human breast carcinoma and mouse normal lung tissue


title: 50_Human-50_Mouse [83682_1C]

description: Replicate 1


title: amniotic cell sample 7

description: amniotic cell sample

source_name: amniotic cell sample 7


title: 0_Human-100_Mouse [83684_1E]

description: Replicate 1

source_name: mouse normal lung tissue


title: amniotic cell sample 6

description: amniotic cell sample

source_name: amniotic cell sample 6


title: WT T2g vs ΔplcRa T2r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_2_3
WT vs ΔplcRa T2 biological duplo 1 of 2


title: third trimester #2


title: WT T1g vs ΔplcRa T1r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_2_1
WT vs ΔplcRa T1 biological duplo 1 of 2

value: B. cereus ATCC14579 wildtype cells were grown to 1 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)

value: B. cereus ATCC14579 (plcRa deletion) cells were grown to 1 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)


title: third trimester #1


title: ΔplcRa T1g vs WT T1r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_2_2
WT vs ΔplcRa T1 biological duplo 2 of 2


title: amniotic cell sample 5

description: amniotic cell sample

source_name: amniotic cell sample 5


title: OEplcRa T1g vs WT T1r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_1_2
WT vs OEplcRa T1 biological duplo 2 of 2

value: OEplcRa

value: B. cereus ATCC14579 (plcRa overexpression) cells were grown to 1 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)

value: B. cereus ATCC14579 cells were grown to 1 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)


title: amniotic cell sample 3

description: amniotic cell sample

source_name: amniotic cell sample 3


title: 0_Human-100_Mouse [83689_2E]

description: Replicate 2

value: NOD scid gamma


title: 100_Human-0_Mouse [83685_2A]

description: Replicate 2

source_name: human breast carcinoma


title: OEplcRa T2g vs WT T2r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_1_4
WT vs OEplcRa T2 biological duplo 2 of 2

value: B. cereus ATCC14579 (plcRa overexpression) cells were grown to 2 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)


title: amniotic cell sample 4

description: amniotic cell sample

source_name: amniotic cell sample 4


title: first trimester #6

source_name: first trimester


title: first trimester #2


title: first trimester #5


title: WT T2g vs OEplcRa T2r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_1_3
WT vs OEplcRa T2 biological duplo 1 of 2

value: B. cereus ATCC14579 cells were grown to 2 hours after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)


title: 100_Human-0_Mouse [83690_3A]

description: Replicate 3

value: human tissue 100%, mouse tissue 0%


title: amniotic cell sample 2

description: amniotic cell sample

source_name: amniotic cell sample 2


title: first trimester #3


title: first trimester #4


title: WT T1g vs OEplcRa T1r

description:
US22502548_251734310035_S02_Bcereus14579_3rdDesign_1_1
WT vs OEplcRa T1 biological duplo 1 of 2


title: amniotic cell sample 1

description: amniotic cell sample

source_name: amniotic cell sample 1


title: 0_Human-100_Mouse [83694_3E]

description: Replicate 3

value: human tissue 0%, mouse tissue 100%


title: first trimester #1


title: 75_Human-25_Mouse [83681_1B]

description: Replicate 1

value: human tissue 75%, mouse tissue 25%


title: 75_Human-25_Mouse [83691_3B]

description: Replicate 3


title: 3Flag-Sox17-ERT_Promoter 1

description: ChIP-on-chip data from human ES cells-derived CD34+CD43+CD45low cells (hemogenic endothelium-like cells) overexpressing 3xFLAG-Sox17-ERT

hyb_protocol: Agilent mammalian ChIP-on-chip protocol (ver.9.0)

scan_protocol: ChIP-v1_10_Apr08, Agilent DNA Microarray Scanner G2505C, Agilent Scan Control (Ver. A.8.4.1)

data_processing: Scanned images were quantified with Agilent Feature Extraction software under standard conditions. Signals were normalized using rank consistency filter algorithm.

source_name: Input

extract_protocol: ES cells were subjected to ChIP assay using a Rybp antibody. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification as described previously (van Bakel et al., 2008).

treatment_protocol: ES cells were treated with 1 % formaldehyde/PBS for 10 min at room temperature. Cells were washed with PBS, collected and resuspended in swelling buffer [20 mM Hepes (pH 7.8), 1.5 mM MgCl2, 10 mM KCl, 0.1 % NP-40, and 1 mM DTT] by pipetting and then kept on ice for 10 min. After Dounce homogenizing 10-20 times, the cells were centrifuged and then the pellets were resuspended in RIPA buffer [20 mM Tis-HCl (pH 8.0), 1 mM EDTA, 140 mM NaCl, 1 % Triton X-100, 0.1 % SDS, and 0.1 % deoxycholic acid] containing protease inhibitors and sonicated into fragments with an average length of 0.3-0.5 kb. After centrifugation, the supernatants were subjected to IP with specific antibodies as previously described (Orlando et al., 1997)

value: embryonic stem cell

tag: sample type

value: reference

source_name: Flag-IP

tag: antibody

value: anti-FLAG

tag: vendor

value: M2 Monoclonal

tag: catalog/lot#

value: Code F 3165


title: pTH4325_HK_8mer

status: Public on Dec 13 2012

type: protein

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: Oct1_HK design

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector.

tag: dbd

value: Pou,Homeobox

tag: platform_id_id design

value: HK


title: pTH4269_ME_8mer

source_name: Rarg_ME design

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

value: ME


title: pTH3998_ME_8mer

source_name: Tbx3_ME design

value: T-box


title: pTH3973_HK_8mer

source_name: Tbx4_HK design


title: pTH4269_HK_8mer

source_name: Rarg_HK design


title: pTH3998_HK_8mer

source_name: Tbx3_HK design


title: pTH3862_ME_8mer

source_name: Sox6_ME design


title: pTH3991_ME_8mer

source_name: Mzf1_ME design


title: pTH3984_ME_8mer


title: pTH3984_HK_8mer

source_name: Mzf1_HK design


title: pTH3862_HK_8mer

source_name: Sox6_HK design


title: pTH4326_ME_8mer

source_name: Pit1_ME design


title: pTH3866_HK_8mer

source_name: Tcf3_HK design

value: HLH


title: pTH3855_ME_8mer

source_name: Foxp1_ME design


title: pTH3973_ME_8mer

source_name: Tbx4_ME design


title: pTH3991_HK_8mer


title: pTH4325_ME_8mer

source_name: Oct1_ME design


title: pTH4326_HK_8mer

source_name: Pit1_HK design


title: pTH3997_ME_8mer

source_name: Zscan20_ME design


title: pTH3846_ME_8mer

source_name: Foxo1_ME design


title: pTH3855_HK_8mer

source_name: Foxp1_HK design


title: pTH3997_HK_8mer

source_name: Zscan20_HK design


title: pTH3831_HK_8mer

source_name: Dbp_HK design


title: pTH3841_ME_8mer

source_name: Esrrg_ME design


title: pTH3831_ME_8mer

source_name: Dbp_ME design


title: pTH3846_HK_8mer

source_name: Foxo1_HK design


title: pTH3866_ME_8mer

source_name: Tcf3_ME design


title: pTH3822_ME_8mer

source_name: Tbx1_ME design


title: pTH3841_HK_8mer

source_name: Esrrg_HK design


title: amniotic cell sample 11

description: amniotic cell sample

source_name: amniotic cell sample 11

tag: karyotype

tag: cell type

value: amniotic cell sample


title: pTH3822_HK_8mer

source_name: Tbx1_HK design


title: pTH3819_ME_8mer

source_name: Pou3f1_ME design

value: Homeobox


title: pTH3818_ME_8mer

source_name: Pou1f1_ME design


title: pTH3777_ME_8mer

source_name: Tbx20_ME design


title: pTH3775_HK_8mer

source_name: Tbx5_HK design


title: pTH3796_ME_8mer

source_name: Foxc2_ME design


title: pTH3818_HK_8mer

source_name: Pou1f1_HK design


title: pTH3751_HK_8mer

source_name: Tbx2_HK design


title: pTH3749_HK_8mer

source_name: Foxo3_HK design


title: pTH3731_ME_8mer

source_name: Foxo4_ME design


title: pTH3520_HK_8mer

source_name: Sp140_HK design

value: SAND


title: pTH3520_ME_8mer

source_name: Sp140_ME design


title: pTH3775_ME_8mer

source_name: Tbx5_ME design


title: pTH3796_HK_8mer

source_name: Foxc2_HK design


title: pTH3811_HK_8mer

source_name: Nr2f1_HK design


title: pTH3477_HK_8mer

source_name: Foxo6_HK design


title: pTH3777_HK_8mer

source_name: Tbx20_HK design


title: pTH3712_HK_8mer

source_name: Mybl2_HK design


title: pTH3731_HK_8mer

source_name: Foxo4_HK design


title: pTH3510_ME_8mer

source_name: Esr1_ME design


title: pTH3749_ME_8mer

source_name: Foxo3_ME design


title: pTH3751_ME_8mer

source_name: Tbx2_ME design


title: pTH3516_HK_8mer

source_name: Rfx7_HK design


title: pTH3712_ME_8mer

source_name: Mybl2_ME design


title: pTH3811_ME_8mer

source_name: Nr2f1_ME design


title: pTH3477_ME_8mer

source_name: Foxo6_ME design


title: pTH3516_ME_8mer

source_name: Rfx7_ME design


title: pTH3510_HK_8mer

source_name: Esr1_HK design


title: pTH3469_ME_8mer

source_name: Rorb_ME design


title: pTH3469_HK_8mer

source_name: Rorb_HK design


title: pTH3819_HK_8mer

source_name: Pou3f1_HK design


title: pTH3468_HK_8mer

source_name: Nr5a2_HK design


title: pTH3467_ME_8mer

source_name: Nr4a2_ME design


title: pTH3087_HK_8mer

source_name: Sox3_HK design


title: pTH3120_HK_8mer

source_name: Zfp637_HK design


title: pTH3086_ME_8mer

source_name: Klf8_ME design


title: pTH3468_ME_8mer

source_name: Nr5a2_ME design


title: pTH3205_HK_8mer

source_name: Dmrtc2_HK design

value: DM


title: pTH3456_HK_8mer

source_name: P42pop_HK design


title: pTH3087_ME_8mer

source_name: Sox3_ME design


title: pTH3464_HK_8mer

source_name: Rora_HK design


title: pTH3208_HK_8mer

source_name: Cebpb_HK design


title: pTH3091_HK_8mer

source_name: Egr2_HK design


title: pTH3086_HK_8mer

source_name: Klf8_HK design


title: pTH3455_ME_8mer

source_name: Prdm11_ME design


title: pTH3464_ME_8mer

source_name: Rora_ME design


title: pTH3220_HK_8mer

source_name: Zfp3_HK design


title: pTH3208_ME_8mer

source_name: Cebpb_ME design


title: pTH3455_HK_8mer

source_name: Prdm11_HK design


title: pTH3091_ME_8mer

source_name: Egr2_ME design


title: pTH3205_ME_8mer

source_name: Dmrtc2_ME design


title: pTH3120_ME_8mer

source_name: Zfp637_ME design


title: pTH3084_HK_8mer

source_name: Gmeb2_HK design


title: pTH3084_ME_8mer

source_name: Gmeb2_ME design


title: pTH3456_ME_8mer

source_name: P42pop_ME design


title: pTH3467_HK_8mer

source_name: Nr4a2_HK design


title: pTH3220_ME_8mer

source_name: Zfp3_ME design


title: pTH3064_HK_8mer

source_name: Junb_HK design


title: pTH3075_ME_8mer

source_name: Zfp202_ME design


title: pTH3075_HK_8mer

source_name: Zfp202_HK design


title: pTH3064_ME_8mer

source_name: Junb_ME design


title: pTH3046_HK_8mer

source_name: Sdccag8_HK design


title: pTH3046_ME_8mer

source_name: Sdccag8_ME design


title: pTH2933_ME_8mer

source_name: Zfx_ME design


title: pTH2933_HK_8mer

source_name: Zfx_HK design


title: pTH2885_ME_8mer

source_name: Tfec_ME design


title: pTH3054_HK_8mer

source_name: Mecp2_HK design

value: MBD


title: pTH3043_HK_8mer

source_name: Foxj2_HK design


title: pTH3043_ME_8mer

source_name: Foxj2_ME design


title: pTH3054_ME_8mer

source_name: Mecp2_ME design


title: pTH3041_HK_8mer

source_name: Nfil3_HK design


title: pTH3041_ME_8mer

source_name: Nfil3_ME design


title: pTH2936_ME_8mer

source_name: Nr2e1_ME design


title: pTH3037_HK_8mer

source_name: Nhlh2_HK design


title: pTH2882_HK_8mer

source_name: Mlx_HK design


title: pTH2882_ME_8mer

source_name: Mlx_ME design


title: pTH2936_HK_8mer

source_name: Nr2e1_HK design


title: pTH2857_HK_8mer

source_name: Znf740_HK design


title: pTH2852_HK_8mer

source_name: Xbp1_HK design


title: pTH2852_ME_8mer

source_name: Xbp1_ME design


title: pTH2885_HK_8mer

source_name: Tfec_HK design


title: pTH2857_ME_8mer

source_name: Znf740_ME design


title: pTH2846_HK_8mer

source_name: Foxg1_HK design


title: pTH2842_ME_8mer

source_name: Nkx2-9_ME design


title: pTH2846_ME_8mer

source_name: Foxg1_ME design


title: pTH2842_HK_8mer

source_name: Nkx2-9_HK design


title: pTH2835_ME_8mer

source_name: Irf2_ME design

value: IRF


title: pTH2835_HK_8mer

source_name: Irf2_HK design


title: pTH2818_HK_8mer

source_name: Zic5_HK design


title: pTH2818_ME_8mer

source_name: Zic5_ME design


title: pTH2677_ME_8mer

source_name: Sox14_ME design


title: pTH2427_HK_8mer

source_name: Zscan10_HK design


title: pTH2684_HK_8mer

source_name: Atf3_HK design


title: pTH2648_HK_8mer

source_name: Zfp300_HK design


title: pTH2820_HK_8mer

source_name: Egr3_HK design


title: pTH2684_ME_8mer

source_name: Atf3_ME design


title: pTH2682_ME_8mer

source_name: Zfp263_ME design


title: pTH2820_ME_8mer

source_name: Egr3_ME design


title: pTH2682_HK_8mer

source_name: Zfp263_HK design


title: pTH2361_ME_8mer

source_name: Ahctf1_ME design


title: pTH2427_ME_8mer

source_name: Zscan10_ME design


title: pTH2415_ME_8mer


title: pTH2648_ME_8mer

source_name: Zfp300_ME design


title: pTH2340_ME_8mer

source_name: Snai1_ME design


title: pTH2340_HK_8mer

source_name: Snai1_HK design


title: pTH2366_ME_8mer

source_name: Zbtb1_ME design


title: pTH2415_HK_8mer


title: pTH2677_HK_8mer

source_name: Sox14_HK design


title: pTH2311_ME_8mer

source_name: Esrrb_ME design


title: pTH2353_ME_8mer

source_name: Klf9_ME design


title: pTH2353_HK_8mer

source_name: Klf9_HK design


title: pTH2311_HK_8mer

source_name: Esrrb_HK design


title: pTH2361_HK_8mer

source_name: Ahctf1_HK design


title: pTH2283_ME_8mer

source_name: Zkscan5_ME design


title: pTH2366_HK_8mer

source_name: Zbtb1_HK design


title: pTH2283_HK_8mer

source_name: Zkscan5_HK design


title: pTH1739_ME_8mer

source_name: Ar_ME design


title: pTH2280_HK_8mer

source_name: Zkscan1_HK design


title: pTH2193_ME_8mer

source_name: Nr2f6_ME design


title: pTH1729_ME_8mer

source_name: Sox10_ME design


title: pTH2193_HK_8mer

source_name: Nr2f6_HK design


title: pTH1288_ME_8mer

source_name: Foxp2_ME design


title: pTH1739_HK_8mer

source_name: Ar_HK design


title: pTH1288_HK_8mer

source_name: Foxp2_HK design


title: pTH1001_ME_8mer

source_name: Dnajc21_ME design


title: pTH1292_HK_8mer

source_name: Zscan10_HK design


title: pTH1729_HK_8mer

source_name: Sox10_HK design


title: pTH1001_HK_8mer

source_name: Dnajc21_HK design


title: pTH0978_ME_8mer

source_name: Sp1_ME design


title: pTH1292_ME_8mer

source_name: Zscan10_ME design


title: pTH1284_HK_8mer

source_name: Nr2c1_HK design


title: pTH1014_HK_8mer

source_name: Atf4_HK design


title: pTH0977_HK_8mer

source_name: Klf12_HK design


title: pTH1014_ME_8mer

source_name: Atf4_ME design


title: pTH0977_ME_8mer

source_name: Klf12_ME design


title: pTH0914_HK_8mer

source_name: Srebf1_HK design


title: pTH1049_HK_8mer

source_name: Gata4_HK design

value: GATA


title: pTH0978_HK_8mer

source_name: Sp1_HK design


title: pTH1049_ME_8mer

source_name: Gata4_ME design


title: pTH1284_ME_8mer

source_name: Nr2c1_ME design


title: RA, singing 6hr, replicate e

city: Durham

first: Andreas

middle: Robert

last: Pfenning

state: NC

address: Duke University Medical Center, Box 3209, Department of Neurobiology

department: Neurobiology

institute: Duke University

description:
Ra_6_e_3833
Gene expression after singing

hyb_protocol: Labeled cDNA was dried in a speed-vac and resuspended in 25ul of hybridization buffer that contained 16% formamide, and 1X Agilent Blocking buffer. Samples were then denatured at 95 degrees for 3 mins and 18uLs of each samples was loaded to each array. Each micrroarray slide contained 4 arrays (4X44K) that were hybridized using a special A4 clamp to hold Agilent 4 x 44K arrays in Maui A4 mixers. The mixer was held at 55oC for at least 20 hrs, with the humidity chamber positioned over arrays.The following day, slides were rinsed in pre-heated (42C). They were then shaken in Agilent Wash 1 buffer solution at RT X 1min and then Agilent Wash 2 at 37C for 1min. The slides were then slowly removed from the Wash buffer to minimize droplet formation.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000 Microarray Scanner and Agilent's Feature Extraction Software v9.5.1 using one color scan setting for 4x44k array slides (Scan resolution was 5um, Dye channel was set to 532 [Green] and PMT to 520).

data_processing: The data was normalized with variance stabilization for one-color data based on Huber et al 2002 [PMID 12169536].  Microarrays with a low percentage of probes above background and high standard deviation from the median were removed.

organism: Taeniopygia guttata

source_name: RA_singing 6hr

label_protocol: 2.2 ugs of purified cDNA was labeled and fragmented using FL-Ovation Cy3 labeling and fragmentation kit according to the manufacturers instructions (Nugen). 2.2 ugs of purified cDNA was labeled and fragmented using FL-Ovation Cy3 labeling and fragmentation kit according to the manufacturers instructions (Nugen).   Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Animal housing protocol : 54 male zebra finch birds were isolated overnight in sound attenuation chambers on a 12/12 light:dark cycle with ad lib access to food and water.

extract_protocol: RNA was prepared using the Picopure RNA Extraction kit (Molecular Devices, Sunnyvale, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop Wilmington, DE) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). From 1.5-2ng of total RNA, amplified cDNA was prepared using the WT-Ovation Pico System (Nugen, San Carlos, CA) according to the manufacturer's instructions.

treatment_protocol: In the morning before singing or immediately after singing for 0.5, 1, 2, 3, 4, 5, 6, or 7hrs, brains were quickly dissected. For the singing groups, we used birds that sang continuously >25 bouts per 0.5 hours.

tag: gender

value: Male

tag: age

value: >120 days

value: Brain, RA


title: RA, singing 7hr, replicate a

description:
Ra_7_a_3478
Gene expression after singing

source_name: RA_singing 7hr

tag: tissue


title: RA, singing 7hr, replicate b

description:
Ra_7_b_3478
Gene expression after singing


title: pTH0914_ME_8mer

source_name: Srebf1_ME design


title: RA, singing 6hr, replicate c

description:
Ra_6_c_3478
Gene expression after singing


title: RA, singing 7hr, replicate f

description:
Ra_7_f_3833
Gene expression after singing


title: RA, singing 6hr, replicate b

description:
Ra_6_b_3478
Gene expression after singing


title: RA, singing 6hr, replicate f

description:
Ra_6_f_3833
Gene expression after singing


title: RA, singing 5hr, replicate f

description:
Ra_5_f_3833
Gene expression after singing

source_name: RA_singing 5hr


title: RA, singing 5hr, replicate c

description:
Ra_5_c_3478
Gene expression after singing


title: RA, singing 7hr, replicate d

description:
Ra_7_d_3833
Gene expression after singing


title: RA, singing 5hr, replicate a

description:
Ra_5_a_3478
Gene expression after singing


title: RA, singing 5hr, replicate b

description:
Ra_5_b_3478
Gene expression after singing


title: RA, singing 4hr, replicate f

description:
Ra_4_f_3833
Gene expression after singing

source_name: RA_singing 4hr


title: RA, singing 4hr, replicate d

description:
Ra_4_d_3833
Gene expression after singing


title: RA, singing 4hr, replicate e

description:
Ra_4_e_3833
Gene expression after singing


title: RA, singing 4hr, replicate c

description:
Ra_4_c_3478
Gene expression after singing


title: pTH3037_ME_8mer

source_name: Nhlh2_ME design


title: RA, singing 4hr, replicate b

description:
Ra_4_b_3478
Gene expression after singing


title: RA, singing 4hr, replicate a

description:
Ra_4_a_4110
Gene expression after singing


title: RA, singing 3hr, replicate e

description:
Ra_3_e_3833
Gene expression after singing

source_name: RA_singing 3hr


title: RA, singing 3hr, replicate d

description:
Ra_3_d_4280
Gene expression after singing


title: RA, singing 5hr, replicate d

description:
Ra_5_d_3833
Gene expression after singing


title: RA, singing 3hr, replicate c

description:
Ra_3_c_4107
Gene expression after singing


title: RA, singing 2hr, replicate a

description:
Ra_2_a_3478
Gene expression after singing

source_name: RA_singing 2hr


title: RA, singing 0.5hr, replicate f

description:
Ra_0.5_f_3833
Gene expression after singing

source_name: RA_singing 0.5hr


title: RA, singing 0.5hr, replicate c

description:
Ra_0.5_c_3478
Gene expression after singing


title: RA, silent 1hr, replicate h

description:
Ra_0_h_4031
Silent control sample for gene expression after singing

source_name: RA_silent 1hr


title: RA, singing 2hr, replicate b

description:
Ra_2_b_4280
Gene expression after singing


title: RA, singing 3hr, replicate b

description:
Ra_3_b_3478
Gene expression after singing


title: RA, singing 3hr, replicate a

description:
Ra_3_a_4107
Gene expression after singing


title: RA, singing 6hr, replicate a

description:
Ra_6_a_3478
Gene expression after singing


title: RA, singing 2hr, replicate c

description:
Ra_2_c_3478
Gene expression after singing


title: RA, singing 0.5hr, replicate a

description:
Ra_0.5_a_3478
Gene expression after singing


title: RA, singing 1hr, replicate e

description:
Ra_1_e_3833
Gene expression after singing

source_name: RA_singing 1hr


title: RA, singing 1hr, replicate f

description:
Ra_1_f_3833
Gene expression after singing


title: RA, singing 1hr, replicate a

description:
Ra_1_a_3478
Gene expression after singing


title: RA, singing 7hr, replicate c

description:
Ra_7_c_3478
Gene expression after singing


title: RA, singing 0.5hr, replicate e

description:
Ra_0.5_e_3833
Gene expression after singing


title: RA, singing 2hr, replicate d

description:
Ra_2_d_3833
Gene expression after singing


title: RA, singing 0.5hr, replicate b

description:
Ra_0.5_b_3478
Gene expression after singing


title: pTH2280_ME_8mer

source_name: Zkscan1_ME design


title: RA, silent 1hr, replicate e

description:
Ra_0_e_3835
Silent control sample for gene expression after singing


title: RA, silent 1hr, replicate i

description:
Ra_0_i_4031
Silent control sample for gene expression after singing


title: RA, silent 1hr, replicate f

description:
Ra_0_f_3835
Silent control sample for gene expression after singing


title: LMAN, singing 6hr, replicate d

description:
LM_6_d_4107redo
Gene expression after singing

source_name: LMAN_singing 6hr

value: Brain, LMAN


title: RA, silent 1hr, replicate a

description:
Ra_0_a_3843
Silent control sample for gene expression after singing


title: RA, singing 7hr, replicate e

description:
Ra_7_e_3833
Gene expression after singing


title: RA, singing 0.5hr, replicate d

description:
Ra_0.5_d_3833
Gene expression after singing


title: LMAN, singing 6hr, replicate f

description:
LM_6_f_4110
Gene expression after singing


title: RA, silent 1hr, replicate d

description:
Ra_0_d_3835
Silent control sample for gene expression after singing


title: LMAN, singing 5hr, replicate e

description:
LM_5_e_4107redo
Gene expression after singing

source_name: LMAN_singing 5hr


title: RA, silent 1hr, replicate c

description:
Ra_0_c_3843
Silent control sample for gene expression after singing


title: LMAN, singing 6hr, replicate e

description:
LM_6_e_4280
Gene expression after singing


title: LMAN, singing 5hr, replicate d

description:
LM_5_d_3832
Gene expression after singing


title: LMAN, singing 2hr, replicate f

description:
LM_2_f_4280
Gene expression after singing

source_name: LMAN_singing 2hr


title: LMAN, singing 3hr, replicate d

description:
LM_3_d_3832
Gene expression after singing

source_name: LMAN_singing 3hr


title: LMAN, singing 5hr, replicate f

description:
LM_5_f_4107redo
Gene expression after singing


title: LMAN, singing 4hr, replicate f

description:
LM_4_f_4107
Gene expression after singing

source_name: LMAN_singing 4hr


title: LMAN, singing 3hr, replicate f

description:
LM_3_f_3832
Gene expression after singing


title: LMAN, singing 2hr, replicate e

description:
LM_2_e_3832
Gene expression after singing


title: LMAN, singing 1hr, replicate f

description:
LM_1_f_3832
Gene expression after singing

source_name: LMAN_singing 1hr


title: LMAN, singing 1hr, replicate e

description:
LM_1_e_3832
Gene expression after singing


title: LMAN, singing 1hr, replicate d

description:
LM_1_d_3832
Gene expression after singing


title: RA, singing 1hr, replicate d

description:
Ra_1_d_3833
Gene expression after singing


title: LMAN, singing 0.5hr, replicate f

description:
LM_0.5_f_4110
Gene expression after singing

source_name: LMAN_singing 0.5hr


title: LMAN, singing 2hr, replicate d

description:
LM_2_d_3832
Gene expression after singing


title: LMAN, singing 4hr, replicate e

description:
LM_4_e_4107
Gene expression after singing


title: HVC, singing 7hr, replicate e

description:
HVC_7_e_4107redo
Gene expression after singing

source_name: HVC_singing 7hr

value: Brain, HVC


title: HVC, singing 7hr, replicate f

description:
HVC_7_f_4107redo
Gene expression after singing


title: LMAN,silent 1hr, replicate e

description:
LM_0_e_3835
Silent control sample for gene expression after singing

source_name: LMAN_silent 1hr


title: LMAN, silent 1hr, replicate d

description:
LM_0_d_3835
Silent control sample for gene expression after singing


title: LMAN, silent 1hr, replicate i

description:
LM_0_i_4031
Silent control sample for gene expression after singing


title: LMAN, singing 4hr, replicate d

description:
LM_4_d_4107
Gene expression after singing


title: HVC, singing 6hr, replicate e

description:
HVC_6_e_4107redo
Gene expression after singing

source_name: HVC_singing 6hr


title: LMAN, silent 1hr, replicate f

description:
LM_0_f_3835
Silent control sample for gene expression after singing


title: LMAN, singing 0.5hr, replicate e

description:
LM_0.5_e_3832
Gene expression after singing


title: HVC, singing 7hr, replicate b

description:
HVC_7_b_3478
Gene expression after singing


title: HVC, singing 7hr, replicate a

description:
HVC_7_a_3478
Gene expression after singing


title: LMAN, silent 1hr, replicate h

description:
LM_0_h_4031
Silent control sample for gene expression after singing


title: LMAN, singing 3hr, replicate e

description:
LM_3_e_3832
Gene expression after singing


title: HVC, singing 7hr, replicate c

description:
HVC_7_c_4280
Gene expression after singing


title: LMAN, singing 0.5hr, replicate d

description:
LM_0.5_d_3832
Gene expression after singing


title: HVC, singing 6hr, replicate a

description:
HVC_6_a_3478
Gene expression after singing


title: HVC, singing 6hr, replicate d

description:
HVC_6_d_3834
Gene expression after singing


title: HVC, singing 5hr, replicate f

description:
HVC_5_f_4107redo
Gene expression after singing

source_name: HVC_singing 5hr


title: HVC, singing 4hr, replicate f

description:
HVC_4_f_4107
Gene expression after singing

source_name: HVC_singing 4hr


title: HVC, singing 4hr, replicate c

description:
HVC_4_c_3478
Gene expression after singing


title: HVC, singing 4hr, replicate a

description:
HVC_4_a_3478
Gene expression after singing


title: HVC, singing 6hr, replicate c

description:
HVC_6_c_3478
Gene expression after singing


title: HVC, singing 5hr, replicate e

description:
HVC_5_e_4107redo
Gene expression after singing


title: HVC, singing 5hr, replicate a

description:
HVC_5_a_3478
Gene expression after singing


title: HVC, singing 5hr, replicate c

description:
HVC_5_c_3478
Gene expression after singing


title: HVC, singing 4hr, replicate e

description:
HVC_4_e_4107redo
Gene expression after singing


title: RA, singing 6hr, replicate d

description:
Ra_6_d_3833
Gene expression after singing

source_name: RA_singing 6hr


title: HVC, singing 3hr, replicate f

description:
HVC_3_f_3834
Gene expression after singing

source_name: HVC_singing 3hr


title: HVC, singing 6hr, replicate b

description:
HVC_6_b_3478
Gene expression after singing


title: HVC, singing 2hr, replicate f

description:
HVC_2_f_3834
Gene expression after singing

source_name: HVC_singing 2hr


title: HVC, singing 1hr, replicate f

description:
HVC_1_f_3834
Gene expression after singing

source_name: HVC_singing 1hr


title: HVC, singing 3hr, replicate a

description:
HVC_3_a_3478
Gene expression after singing


title: HVC, singing 2hr, replicate a

description:
HVC_2_a_3478
Gene expression after singing


title: HVC, singing 4hr, replicate b

description:
HVC_4_b_3478
Gene expression after singing


title: HVC, singing 2hr, replicate d

description:
HVC_2_d_3834
Gene expression after singing


title: HVC, singing 3hr, replicate b

description:
HVC_3_b_3478
Gene expression after singing


title: HVC, singing 3hr, replicate d

description:
HVC_3_d_3834
Gene expression after singing


title: HVC, singing 1hr, replicate d

description:
HVC_1_d_3834
Gene expression after singing


title: HVC, singing 1hr, replicate e

description:
HVC_1_e_3834
Gene expression after singing


title: HVC, singing 1hr, replicate a

description:
HVC_1_a_3478
Gene expression after singing


title: Candida-specific CD4 T cells, Biological Replicate 3

city: Silver Spring

first: Haitao

last: Hu

state: MD

address: 503 Robert Grant Ave

department: US Military HIV Research Program

institute: Walter Reed Army Institute of Research

description: Gene expression in Candida-specific CD4+ T cells, biological replicate 3

hyb_protocol: Standard hybridization protocol

scan_protocol: Standard scanning protocol

data_processing:
Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.

source_name: WRAIR* RV229

label_protocol: RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).

growth_protocol: PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)

extract_protocol: RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.

value: PBMC

tag: cd4 response to antigens

value: Candida Albicans+

tag: hiv infection status

value: HIV-


title: CMV-specific CD4 T cells, Biological Replicate 1

description: Gene expression in CMV-specific CD4+ T cells, biological replicate 1

value: CMV+


title: Candida-specific CD4 T cells, Biological Replicate 2

description: Gene expression in Candida-specific CD4+ T cells, biological replicate 2


title: CMV-specific CD4 T cells, Biological Replicate 2

description: Gene expression in CMV-specific CD4+ T cells, biological replicate 2


title: HVC, singing 3hr, replicate e

description:
HVC_3_e_3834
Gene expression after singing


title: HVC, singing 5hr, replicate b

description:
HVC_5_b_3478
Gene expression after singing


title: Candida-specific CD4 T cells, Biological Replicate 1

description: Gene expression in Candida-specific CD4+ T cells, biological replicate 1


title: HVC, singing 1hr, replicate b

description:
HVC_1_b_3478
Gene expression after singing


title: HVC, singing 2hr, replicate e

description:
HVC_2_e_3834
Gene expression after singing


title: HVC, singing 0.5hr, replicate f

description:
HVC_0.5_f_3834
Gene expression after singing

source_name: HVC_singing 0.5hr


title: TT-specific CD4 T cells, Biological Replicate 2

description: Gene expression in TT-specific CD4+ T cells, biological replicate 2

value: Tetanus toxoid+


title: HVC, singing 0.5hr, replicate d

description:
HVC_0.5_d_3834
Gene expression after singing


title: HVC, singing 0.5hr, replicate b

description:
HVC_0.5_b_3478
Gene expression after singing


title: CMV-specific CD4 T cells, Biological Replicate 3

description: Gene expression in CMV-specific CD4+ T cells, biological replicate 3


title: TT-specific CD4 T cells, Biological Replicate 1

description: Gene expression in TT-specific CD4+ T cells, biological replicate 1


title: TT-specific CD4 T cells, Biological Replicate 3

description: Gene expression in TT-specific CD4+ T cells, biological replicate 3


title: HVC, singing 0.5hr, replicate e

description:
HVC_0.5_e_3834
Gene expression after singing


title: Jurkat PD-0332991 treated replicate2

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Genespring GX program. No further adjustments were made to the data in the table.

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Grown in RPMI + 10% FCS + 1% Glutamax + 1% Pen/Strep

extract_protocol: Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: Treated with DMSO or 1 uM PD-0332991 for 15 hours prior to RNA extraction

tag: cell line

value: Jurkat

value: T cell acute lymphoblastic leukemia cells (T-ALL)

tag: treated with


title: Jurkat DMSO treated replicate 2

value: DMSO for 15hrs


title: HVC, silent 1hr, replicate c

description:
HVC_0_c_3843
Silent control sample for gene expression after singing

source_name: HVC_silent 1hr


title: HVC, silent 1hr, replicate e

description:
HVC_0_e_3835
Silent control sample for gene expression after singing


title: Jurkat PD-0332991 treated replicate1


title: HVC, singing 0.5hr, replicate a

description:
HVC_0.5_a_3478
Gene expression after singing


title: HVC, silent 1hr, replicate f

description:
HVC_0_f_3835
Silent control sample for gene expression after singing


title: HVC, silent 1hr, replicate i

description:
HVC_0_i_4031
Silent control sample for gene expression after singing


title: Area X, singing 7hr, replicate f

description:
Ax_7_f_3831
Gene expression after singing

source_name: Area X_singing 7hr

value: Brain, Area X


title: HVC, silent 1hr, replicate d

description:
HVC_0_d_3835
Silent control sample for gene expression after singing


title: CUTL1 PD-0332991 treated replicate1


title: CEM DMSO treated replicate 2

value: CEM


title: CEM PD-0332991 treated replicate2


title: Area X, singing 7hr, replicate a

description:
Ax_7_a_3478
Gene expression after singing


title: Area X, singing 6hr, replicate d

description:
Ax_6_d_3831
Gene expression after singing

source_name: Area X_singing 6hr


title: Jurkat DMSO treated replicate 1


title: DND41 PD-0332991 treated replicate1


title: Area X, singing 7hr, replicate e

description:
Ax_7_e_3831
Gene expression after singing


title: CUTL1 DMSO treated replicate 2


title: Area X, singing 6hr, replicate f

description:
Ax_6_f_3831
Gene expression after singing


title: CUTL1 DMSO treated replicate 1


title: Area X, singing 7hr, replicate c

description:
Ax_7_c_3478
Gene expression after singing


title: DND41 DMSO treated replicate 2


title: Area X, singing 7hr, replicate d

description:
Ax_7_d_4107redo
Gene expression after singing


title: HVC, silent 1hr, replicate h

description:
HVC_0_h_4031
Silent control sample for gene expression after singing


title: CUTL1 PD-0332991 treated replicate2


title: DND41 PD-0332991 treated replicate2


title: CEM PD-0332991 treated replicate1


title: Area X, singing 7hr, replicate b

description:
Ax_7_b_3478
Gene expression after singing


title: DND41 DMSO treated replicate 1


title: Area X, singing 5hr, replicate f

description:
Ax_5_f_3831
Gene expression after singing

source_name: Area X_singing 5hr


title: Area X, singing 6hr, replicate c

description:
Ax_6_c_3478
Gene expression after singing


title: Lysate Replicate 2

city: New York

first: Manuel

last: Ascano

state: NY

address: 1230 York Avenue Box 186

department: HHMI/Laboratory of RNA Molecular Biology

institute: The Rockefeller University

hyb_protocol: 3 µg cRNA hybridized to HGU133 Plus 2.0 Arrays for 16 h at 45ºC

scan_protocol: Genechips scanned on Affymetrix Genechip 300 7G scanner

data_processing: R package 'affy' for normalization with the following normalization parameters: 'expresso(fmrRIP, normalize.method=quantiles.robust, bgcorrect.method=rma,pmcorrect.method=pmonly, summary.method=mas)'

source_name: FlpIn T-Rex Human embryonic kidney 293 stable cell line

label_protocol: 2 µg of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay (Affymetrix) according to manufacturer's protocol. Biotinylated cRNA targets were cleaned up, fragmented, and hybridized to Human Genome U133 Plus 2.0 Array (Affymetrix).

growth_protocol: FlpIn T-Rex HEK293 stable cell lines were cultured in DMEM (11995, Invitrogen) supplemented with 10% Fetal bovine serum, 2 mM L-Glutamine, 50 units of Penicillin, 50 µg/ml Streptomycin, 100 µg/ml Hygromycin, and 15 µg/ml Blasticidin

extract_protocol: Total or immunoprecipitated RNA was extracted by phenol-chloroform, followed by ethanol precipitation. Rneasy Mini Kit (Invitrogen) was used according to manufacturer's instructions as a final step.

treatment_protocol: Expression of stable transgenes were induced by incubation with 1 µg/ml doxycyline for 16 h. Cells were then lysed in NP-40 lysis buffer (50 mM HEPES-KOH at pH 7.4, 150 mM KCl, 2 mM EDTA, 0.5 mM DTT, 1 mM NaF, and 0.5% NP-40, EDTA-free protease inhibitor cocktail (Roche)), and centrifuge-clarified supernatants were collected. Total RNA was collected prior to IP and labelled as Lysate. Supernatants were subjected to IP using anti-FLAG M2 monoclonal antibodies conjugated to Protein G-ferromagnetic beads (Dynabeads, Invitrogen). Immunoprecipitates were washed three times using NP-40 lysis buffer (containing 300 mM KCl).

tag: rip antibody


title: Area X, singing 5hr, replicate e

description:
Ax_5_e_3831
Gene expression after singing


title: Area X, singing 5hr, replicate c

description:
Ax_5_c_3478
Gene expression after singing


title: Immunoprecipitate Replicate 2

description:
IP_2
RNA from immunoprecipitated FlagHA FMRP

value: FlpIn T-Rex Human embryonic kidney 293 stable cell line

value: anti-FLAG M2 [Sigma-Aldrich, cat# F1804, lot#101M6216]


title: ZMIZ1_knockdown4

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

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

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

data_processing: PM-only version of Robust Multi-array Average (RMA) algorithm (PMID: 12925520) was used inside the affy bioconductor package implemented in the R-statistical environment version 2.12.2.  This process the .CEL files and results in base-2 logarithms of estimated expression.

source_name: Human T-cell Acute Lymphoblastic Leukemia cell line CEM

label_protocol: Biotinylated amplified RNA targets were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

extract_protocol: Total RNA was extracted from CEM cells using the RNeasy Kit (Qiagen)

tag: transfected agent

value: shRNA against ZMIZ1


title: Area X, singing 6hr, replicate b

description:
Ax_6_b_3478
Gene expression after singing

value: Male

value: >120 days


title: ZMIZ1_knockdown2


title: Area X, singing 5hr, replicate d

description:
Ax_5_d_3831
Gene expression after singing


title: Area X, singing 6hr, replicate a

description:
Ax_6_a_3478
Gene expression after singing


title: control1

value: scrambled shRNA


title: Area X, singing 5hr, replicate b

description:
Ax_5_b_3478
Gene expression after singing


title: Area X, singing 4hr, replicate d

description:
Ax_4_d_3831
Gene expression after singing

source_name: Area X_singing 4hr


title: Immunoprecipitate Replicate 1

description:
IP_1
RNA from immunoprecipitated FlagHA FMRP


title: control3


title: Area X, singing 4hr, replicate a

description:
Ax_4_a_4107redo
Gene expression after singing


title: Area X, singing 4hr, replicate e

description:
Ax_4_e_3831
Gene expression after singing


title: Area X, singing 4hr, replicate b

description:
Ax_4_b_3478
Gene expression after singing


title: ZMIZ1_knockdown3


title: control2


title: ZMIZ1_knockdown1


title: Area X, singing 5hr, replicate a

description:
Ax_5_a_3478
Gene expression after singing


title: Area X, singing 4hr, replicate f

description:
Ax_4_f_3831
Gene expression after singing


title: control4


title: Area X, singing 4hr, replicate c

description:
Ax_4_c_3478
Gene expression after singing


title: CEM DMSO treated replicate 1


title: Area X, singing 3hr, replicate d

description:
Ax_3_d_3831
Gene expression after singing

source_name: Area X_singing 3hr


title: Area X, singing 3hr, replicate f

description:
Ax_3_f_3831
Gene expression after singing


title: Kid_Con_C_s20 [tech reps 1 and 2]

city: Leicester

first: Yuri

middle: E

last: Dubrova

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

description:
Control
Two technical replicates used to generate the data for SAMPLE 52.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization System 4 following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using GenePix Axon 4200 AL scanner, following their standard operating protocol.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).  RMA-normalized, averaged gene-level signals reported in Data table below.
The .txt files represent RMA-normalized, probe-level data generated using the NimbleScan software.

source_name: Group C Control male 20 Kidney

label_protocol: Labeling was performe using the NimbleGen One-Color DNA Labeling Kit.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: Diet low in methionine and lacking choline and folic acid (Diet #518892, Dyets Inc, Bethelhem, USA)

tag: strain

value: BALB/c

tag: treatment

value: Control

tag: time after the end of methyl-deficient diet

value: Kidney


title: Kid_Diet_C_d16 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 53.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 16 Kidney

value: Methyl-deficient diet

value: 6 weeks


title: Liv_Diet_C_d20 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 49.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 20 Liver

value: Liver


title: Kid_Diet_C_d17 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 54.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 17 Kidney


title: Area X, singing 3hr, replicate b

description:
Ax_3_b_4107
Gene expression after singing


title: Liv_Diet_C_d18 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 47.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 18 Liver


title: Kid_Diet_C_d18 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 55.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 18 Kidney


title: Kid_Diet_C_d20 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 57.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 20 Kidney


title: Kid_Con_C_s16 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 50.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Control male 16 Kidney


title: Area X, singing 3hr, replicate c

description:
Ax_3_c_3478
Gene expression after singing


title: Area X, singing 2hr, replicate d

description:
Ax_2_d_3831
Gene expression after singing

source_name: Area X_singing 2hr


title: Liv_Con_C_s20 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 44.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Control male 20 Liver


title: Area X, singing 2hr, replicate f

description:
Ax_2_f_3831
Gene expression after singing


title: Kid_Diet_C_d19 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 56.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 19 Kidney


title: Liv_Diet_C_d19 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 48.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 19 Liver


title: Liv_Diet_C_d17 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 46.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 17 Liver


title: Kid_Con_C_s17 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 51.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Control male 17 Kidney


title: Liv_Con_C_s18 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 43.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Control male 18 Liver


title: Area X, singing 1hr, replicate d

description:
Ax_1_d_4280
Gene expression after singing

source_name: Area X_singing 1hr


title: Area X, singing 2hr, replicate a

description:
Ax_2_a_3478
Gene expression after singing


title: Liv_Diet_C_d16 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 6 weeks of normal diet
Two technical replicates used to generate the data for SAMPLE 45.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Diet male 16 Liver


title: Area X, singing 3hr, replicate a

description:
Ax_3_a_3478
Gene expression after singing

source_name: Area X_singing 3hr


title: Area X, singing 2hr, replicate e

description:
Ax_2_e_3831
Gene expression after singing


title: Area X, singing 3hr, replicate e

description:
Ax_3_e_3831
Gene expression after singing


title: Area X, singing 1hr, replicate f

description:
Ax_1_f_3831
Gene expression after singing


title: Area X, singing 2hr, replicate c

description:
Ax_2_c_3478
Gene expression after singing


title: Liv_Con_C_s16 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 41.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Control male 16 Liver


title: Area X, singing 1hr, replicate a

description:
Ax_1_a_3478
Gene expression after singing


title: Liv_Con_C_s17 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 42.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group C Control male 17 Liver


title: Area X, singing 1hr, replicate b

description:
Ax_1_b_3478
Gene expression after singing


title: Area X, singing 1hr, replicate c

description:
Ax_1_c_3478
Gene expression after singing


title: Kid_Diet_B_d12 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 38.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 12 Kidney

value: 2 weeks


title: Kid_Diet_B_d13 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 39.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 13 Kidney


title: Kid_Con_B_s12 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 34.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 12 Kidney


title: Kid_Diet_B_d14 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 40.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 14 Kidney


title: Kid_Con_B_s13 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 35.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 13 Kidney


title: Area X, silent 1hr, replicate i

description:
Ax_0_i_4031
Silent control sample for gene expression after singing

source_name: Area X_silent 1hr


title: Area X, singing 0.5hr, replicate a

description:
Ax_0.5_a_3478
Gene expression after singing

source_name: Area X_singing 0.5hr


title: Area X, singing 0.5hr, replicate b

description:
Ax_0.5_b_3478
Gene expression after singing


title: Area X, silent 1hr, replicate a

description:
Ax_0_a_3843
Silent control sample for gene expression after singing


title: Area X, silent 1hr, replicate h

description:
Ax_0_h_4031
Silent control sample for gene expression after singing


title: Liv_Diet_B_d13 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 31.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 13 Liver


title: Kid_Con_B_s11 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 33.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 11 Kidney


title: Liv_Diet_B_d14 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 32.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 14 Liver


title: Area X, singing 0.5hr, replicate e

description:
Ax_0.5_e_3831
Gene expression after singing


title: Kid_Con_B_s14 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 36.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 14 Kidney


title: Area X, silent 1hr, replicate d

description:
Ax_0_d_3835
Silent control sample for gene expression after singing


title: Area X, singing 0.5hr, replicate c

description:
Ax_0.5_c_4110
Gene expression after singing


title: Area X,silent 1hr, replicate f

description:
Ax_0_f_3835
Silent control sample for gene expression after singing


title: Area X, singing 0.5hr, replicate d

description:
Ax_0.5_d_3831
Gene expression after singing


title: Liv_Diet_B_d11 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 29.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 11 Liver


title: Liv_Diet_B_d12 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 30.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 12 Liver


title: Area X, silent 1hr, replicate e

description:
Ax_0_e_3835
Silent control sample for gene expression after singing


title: Liv_Con_B_s15 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 28.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 15 Liver


title: Kid_Diet_B_d11 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks + 2 weeks on normal diet
Two technical replicates used to generate the data for SAMPLE 37.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Diet male 11 Kidney


title: Lysate Replicate 1

source_name: FlpIn T-Rex Human embryonic kidney 293 stable cell line


title: Kid_Diet_A_d6 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 22.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 6 Kidney

value: 0 weeks


title: Liv_Con_B_s14 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 27.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 14 Liver


title: Liv_Con_B_s12 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 26.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 12 Liver


title: Kid_Diet_A_d7 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 23.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 7 Kidney


title: Kid_Con_A_s6 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 18.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 6 Kidney


title: Kid_Diet_A_d8 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 24.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 8 Kidney


title: Kid_Con_A_s7 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 19.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 7 Kidney


title: Liv_Con_B_s11 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 25.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group B Control male 11 Liver


title: Kid_Diet_A_d4 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 21.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 4 Kidney


title: Kid_Con_A_s2 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 15.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 2 Kidney


title: Kid_Diet_A_d3 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 20.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 3 Kidney


title: Kid_Con_A_s1 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 14.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 1 Kidney


title: Liv_Diet_A_d4 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 11.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 4 Liver


title: Kid_Con_A_s5 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 17.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 5 Kidney


title: Liv_Diet_A_d6 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 14.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 6 Liver


title: Liv_Diet_A_d3 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 10.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 3 Liver


title: NTG at 4 months, biological rep3

first: sudarsan

last: rajan

address: 3333 Burnet Ave

institute: CCHMC

description:
D7
Gene expression data from left ventricular tissue of 4-month-old NTG mice.

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 utilizing the fluidics protocol FS450-0007.

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

data_processing: CEL files were processed by RMAExpress (http://rmaexpress.bmbolstad.com , http://bioconductor.org) using the default options. RMA data was then loaded into GeneSpring 7.0 software (Silicon Genetics Inc., Redwood City, CA) and analyzed.

source_name: NTG mouse heart at 4 months of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 nanograms of total RNA.

growth_protocol: The mice used for the study were housed in a barrier facility and all animal procedures were conducted in conformance with the "Guiding Principles for Research Involving Animals and Human Beings" of the American Physiological Society.

extract_protocol: Total RNA was prepared using the Trizol method (Invitrogen), followed by purification using the RNeasy Cleanup kit (Qiagen). The quality of the total RNA was analyzed with an Agilent Bioanalyzer 2100 (Hewlett Packard) using the RNA 6000 Nano Assay to ensure that samples prepared for microarray hybridization meet the Affymetrix guidelines.

treatment_protocol: Left ventricular tissue was collected and frozen immediately in liquid nitrogen and the samples were stored in -80oC until the RNA isolation.

tag: strain/background = FVB/N

tag: genotype/variation

value: nontransgenic

value: left ventricle

value: 4 months


title: Tm180/PLB KO at 4 months, biological rep3

description:
D6
Gene expression data from left ventricular tissue of 4-month-old Tm180/PLB KO mice.

source_name: Tm180/PLB KO mouse heart at 4 months of age

value: α-tropomyosin transgenic and phospholamban knockout


title: Liv_Diet_A_d5 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 12.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 5 Liver


title: Tm180 at 4 months, biological rep3

description:
D8
Gene expression data from left ventricular tissue of 4-month-old Tm180 mice.

source_name: Tm180 mouse heart at 4 months of age

value: α-tropomyosin transgenic


title: Liv_Con_A_s7 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 5.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 7 Liver


title: NTG at 4 months, biological rep1

description:
B7
Gene expression data from left ventricular tissue of 4-month-old NTG mice.


title: Tm180 at 4 months, biological rep1

description:
B8
Gene expression data from left ventricular tissue of 4-month-old Tm180 mice.


title: Kid_Con_A_s4 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 16
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 4 Kidney


title: Liv_Diet_A_d2 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 8.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 2 Liver


title: Liv_Con_A_s8 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 6.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 8 Liver


title: Tm180 at 4 months, biological rep2

description:
C8
Gene expression data from left ventricular tissue of 4-month-old Tm180 mice.


title: Tm180/PLB KO at 4 months, biological rep2

description:
C6
Gene expression data from left ventricular tissue of 4-month-old Tm180/PLB KO mice.

source_name: Tm180/PLB KO mouse heart at 12 months of age


title: Liv_Diet_A_d1 [tech reps 1 and 2]

description:
Methyl-deficient diet for 8 weeks
Two technical replicates used to generate the data for SAMPLE 7.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Diet male 1 Liver


title: Liv_Con_A_s6 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 4.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 6 Liver


title: NTG at 4 months, biological rep2

description:
C7
Gene expression data from left ventricular tissue of 4-month-old NTG mice.


title: Tm180/PLB KO at 4 months, biological rep1

description:
B6
Gene expression data from left ventricular tissue of 4-month-old Tm180/PLB KO mice.


title: PLB KO at 4 months, biological rep1

description:
B5
Gene expression data from left ventricular tissue of 4-month-old PLB KO mice.

source_name: PLB KO mouse heart at 4 months of age

value: phospholamban knockout


title: Tm180 at 12 months, biological rep3

description:
D4
Gene expression data from left ventricular tissue of 12-month-old Tm180 mice.

source_name: Tm180 mouse heart at 12 months of age

value: 12 months


title: Tm180 at 12 months, biological rep2

description:
C4
Gene expression data from left ventricular tissue of 12-month-old Tm180 mice.


title: PLB KO at 4 months, biological rep3

description:
D5
Gene expression data from left ventricular tissue of 4-month-old PLB KO mice.


title: Liv_Con_A_s4 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 2.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 4 Liver


title: Liv_Con_A_s5 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 3.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 5 Liver


title: Tm180 at 12 months, biological rep1

description:
B4
Gene expression data from left ventricular tissue of 12-month-old Tm180 mice.


title: PLB KO at 12 months, biological rep1

description:
B1
Gene expression data from left ventricular tissue of 12-month-old PLB KO mice.

source_name: PLB KO mouse heart at 12 months of age


title: NTG at 12 months, biological rep1

description:
B3
Gene expression data from left ventricular tissue of 12-month-old NTG mice.

source_name: NTG mouse heart at 12 months of age


title: NTG at 12 months, biological rep2

description:
C3
Gene expression data from left ventricular tissue of 12-month-old NTG mice.


title: PLB KO at 4 months, biological rep2

description:
C5
Gene expression data from left ventricular tissue of 4-month-old PLB KO mice.


title: Tm180/PLB KO at 12 months, biological rep1

description:
B2
Gene expression data from left ventricular tissue of 12-month-old Tm180/PLB KO mice.


title: NTG at 12 months, biological rep3

description:
D3
Gene expression data from left ventricular tissue of 12-month-old NTG mice.


title: PLB KO at 12 months, biological rep3

description:
D1
Gene expression data from left ventricular tissue of 12-month-old PLB KO mice.


title: Liv_Con_A_s3 [tech reps 1 and 2]

description:
Control
Two technical replicates used to generate the data for SAMPLE 1.
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: Group A Control male 3 Liver


title: Tm180/PLB KO at 12 months, biological rep3

description:
D2
Gene expression data from left ventricular tissue of 12-month-old Tm180/PLB KO mice.


title: ChIP-chip of Rec8-Flag from set1∆ cells at 6 hr in meiosis#1

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

description: Rec8-Flag ChIP chip in set1∆ meiotic cells

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix6.0 software

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then the ratios from replicate #1 and replicate #2 were averaged, and the resulting mean ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

organism: Saccharomyces cerevisiae

source_name: ChIP of Rec8-Flag

label_protocol: two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 6 hr in meiosis

extract_protocol: 10ml (2*108 cells) were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 0.8 µg of monoclonal 9E10 anti-Myc (Santa Cruz) or 2 µg of mouse monoclonal M2 anti-FLAG (Sigma) or 2 µl of monoclonal 8WG16 (Covance) and 30 µl protein G magnetic beads suspension (New England Biolabs)

tag: growth condition

value: at 6 hr in meiosis

tag: chip antibody

value: anti-Flag M2 antibody (F1804, Sigma)

source_name: Whole cell extract

label_protocol: 1/70 of the DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling


title: Tm180/PLB KO at 12 months, biological rep2

description:
C2
Gene expression data from left ventricular tissue of 12-month-old Tm180/PLB KO mice.


title: ChIP-chip anti-Myc no tag control

description: no tag ChIP chip control

source_name: ChIP anti-Myc

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 3 hr in meiosis

value: at 3 hr in meiosis

value: 9E10 anti-Myc (sc-40, Santa Cruz)


title: PLB KO at 12 months, biological rep2

description:
C1
Gene expression data from left ventricular tissue of 12-month-old PLB KO mice.