title: Astrocyte_SBSN IgG_LPS(+)_rep6

source_name: Human astrocyte exposure to SBSN IgG with LPS (1μg/ml) for 24 h

value: SBSN IgG with LPS (1μg/ml) for 24 h


title: Astrocyte_non IgG_LPS(+)_rep2

status: Public on Sep 01 2016

type: RNA

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

country: Japan

institute: Shimane University Faculty of Medicine

hyb_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: We followed manufacturer's protocol, and used GenePix 4400A. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

molecule: total RNA

organism: Homo sapiens

source_name: Human astrocyte exposure to non IgG with LPS (1μg/ml) for 24 h

growth_protocol: Normal human astrocytes (NHAs) isolated from human fetal brains (Clonetics normal human astrocytes; Lonza, Switzerland) were maintained in RPMI 1640 supplemented with 10 % fetal calf serum and seeded into 6-well tissue culture plates to a density of 4 × 10^5 cells 24 hours prior to experimentation.

extract_protocol: RNeasy mini kit (Qiagen, Miami, FL) was used.

tag: cell type

value: astrocytes

tag: treatment

value: non IgG with LPS (1μg/ml) for 24 h


title: rice seedling at 8 day after live S. meliloti1021 (LS) inoculation biological repeat 3

city: Beijing

first: Shihua

last: Shen

address: No.20 Nanxincun, Xiangshan South Rd

department: Institute of Botany,

country: China

institute: the Chinese Academy of Sciences

hyb_protocol: RNA from the three independent replicate samples were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix rice genome arrays.(Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: Chips were then washed and stained in the Affymetrix Fluidics Station 450 and then scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The SAM (Significant Analysis of Microarray) software was applied to identify differentially expressed genes (DEGs) between DS and LS using the two classes unpaired method based on the empirical criterion of more than 1.5-fold change and significant q value (FDR adjusted P value) less than 0.05.

label: biotin

organism: Oryza sativa Japonica Group

source_name: Shoots of rice seedlings_live S. meliloti1021 (LS)_8d

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For gnotobiotic culture, rice (Oryza sativa L. ssp. japonica) seeds were surface disinfected with 75% ethanol for 10 min and washed three times with distilled water. And then surface sterilized with 0.1% HgCl2 for 5 min and washed three times again with distilled water. Surface sterilized seeds were germinated in petri plates with distilled water in the dark for 3 days at 28℃. Then, six germinated seeds were selected and transferred aseptically into sterilized glass bottle, which containing 175 cm3 of sterile vermiculite and 1/4 100 mL of Kimura B solution (Yoshida et al., 1971). Rice plants were cultured hydroponically in growth chamber. The relative humidity was kept at 50%-70%. The light/dark period was 14 h/10 h, and temperatures were 28℃ during daytime and 25℃ at night, respectively.

extract_protocol: Total RNA were extracted using Trizol reagent (Sango Biotech), and then digested with DNase I (TaKaRa) at 37 ℃ for 15 min to remove any contaminating DNA.

treatment_protocol: S. meliloti1021 were cultured for 48 h on TY liquid media at 28°C incubator, collected and then suspended with phosphate-buffered saline (PBS, pH 7.4) to OD600=0.8. After 2 days transferred to sterilized glass bottles,live S. meliloti1021 were carefully inoculated into the treat seedling rhizosphere with 1 mL/plant. The controls were inoculated with 1mL dead rhizobium (DS) for each seedling

tag: tissue

value: shoots of rice seedlings

tag: age

value: 5 days old

tag: inoculated with

value: live S. meliloti1021 (LS)

tag: time points

value: 8 DAI


title: rice seedling at 8 day after live S. meliloti1021 (LS) inoculation biological repeat 2

source_name: Shoots of rice seedlings_live S. meliloti1021 LS)_8d


title: rice seedling at 5 day after dead S. meliloti1021 (DS) inoculation biological repeat 1

source_name: Shoots of rice seedlings_dead S. meliloti1021 (DS)_5d

value: dead S. meliloti1021 (DS)

value: 5 DAI


title: rice seedling at 8 day after dead S. meliloti1021 (DS) inoculation biological repeat 3

source_name: Shoots of rice seedlings_dead S. meliloti1021 (DS)_8d


title: rice seedling at 5 day after live S. meliloti1021 (LS) inoculation biological repeat 2

source_name: Shoots of rice seedlings_live S. meliloti1021 LS)_5d


title: rice seedling at 5 day after live S. meliloti1021 (LS) inoculation biological repeat 3

source_name: Shoots of rice seedlings_live S. meliloti1021 (LS)_5d


title: rice seedling at 5 day after dead S. meliloti1021 (DS) inoculation biological repeat 2


title: rice seedling at 5 day after dead S. meliloti1021 (DS) inoculation biological repeat 3


title: rice seedling at 2 day after live S. meliloti1021 (LS) inoculation biological repeat 2

source_name: Shoots of rice seedlings_live S. meliloti1021 LS)_2d

value: 2 DAI


title: Astrocyte_norm IgG_LPS(-)_rep3

source_name: Human astrocyte exposure to normal IgG for 24 h

label_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

value: normal IgG for 24 h


title: rice seedling at 2 day after dead S. meliloti1021 (DS) inoculation biological repeat 1

source_name: Shoots of rice seedlings_dead S. meliloti1021 (DS)_2d


title: FAIRE Meiosis TC - YPD Replicate 6

type: genomic

city: Chicago

first: Sean

middle: Erik

last: Hanlon

state: IL

address: 920 E. 58th Street – CLSC 515E

department: Department of Human Genetics

country: USA

institute: University of Chicago

description: FAIRE open chromatin dynamics during meiosis timecourse. YPD (logarithmic) growth sample.

hyb_protocol: Four micrograms of fluorescently labeled reference DNA and four micrograms of fluorescently labeled FAIRE DNA were used in the hybridization. Samples were competitively hybridized with the reference at 52C for 16 hours in a Maui hybridization chamber to yeast whole genome 4 x 44k tiling microarrays (Agilent; ~270 bp resolution).

scan_protocol: The arrays were scanned with an Axon 4000B scanner, and data was extracted using GenePix 6.0 software.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, or with a background corrected sum of medians for both channels less than 500, were excluded from analysis (flagged as bad in GenePix). Additionally, those probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (FAIRE/reference) for each probe was converted to a log2 ratio. These log2 ratios (FAIRE/reference) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

molecule: genomic DNA

organism: Saccharomyces cerevisiae SK1

source_name: Genomic DNA common reference

label_protocol: ~100 ng starting material was amplified using the Whole-Genome Amplification kit (Sigma) as described (O'Geen, Nicolet, Blahnik, Green and Farnham 2006). Two micrograms of amplified DNA was labeled with Cy5 conjugated dUTP using the BioPrime Array CGH kit (Invitrogen). DNA concentration and dye incorporation were measured using a Nanodrop spectrometer.

growth_protocol: Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8 and 100 ml of cells were collected. Synchronous meiosis/sporulation was carried out by using YPD overnight cultures to inoculate YPA (1% yeast extract, 2% peptone, 2% potassium acetate) cultures at an OD600 of 0.1. YPA cultures were grown at 30C to an OD600 of 0.8-1.2 (about 16 hours). Cells were collected by centrifugation and washed with SM (2% potassium acetate). The cells were resuspended at an OD600 of 2.0 in SM (~600ml) and incubated in 2L flasks at 30C with shaking at 265 rpm. Cells were collected after 0, 1.5, or 3 hours in SM (50 ml of cells). All samples were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. Samples were then snap frozen in a dry ice/ethanol bath and stored at -80C until FAIRE enrichment was performed.

extract_protocol: 100 ml of UNFIXED vegetative cells (OD600 0.6-0.8) were washed twice with 1X cold PBS. The cells were resuspended in lysis buffer and lysed with glass beads. The chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. The UNFIXED reference samples were phenol-chloroform extracted to remove proteins. The resulting sonicated genomic DNA was precipitated with isopropanol and resuspended in 10 mM Tris-Cl pH 7.4 and the concentration was determined with a spectrophotometer.

tag: strain

value: SK1 yeast strain SHy002

tag: growth condition

value: YPD

tag: molecule

value: Genomic DNA common reference

source_name: FAIRE enriched DNA from YPD

value: FAIRE enriched DNA


title: rice seedling at 8 day after dead S. meliloti1021 (DS) inoculation biological repeat 1


title: rice seedling at 2 day after live S. meliloti1021 (LS) inoculation biological repeat 3

source_name: Shoots of rice seedlings_live S. meliloti1021 (LS)_2d


title: rice seedling at 2 day after dead S. meliloti1021 (DS) inoculation biological repeat 3


title: rice seedling at 2 day after dead S. meliloti1021 (DS) inoculation biological repeat 2


title: rice seedling at 8 day after live S. meliloti1021 (LS) inoculation biological repeat 1


title: rice seedling at 8 day after dead S. meliloti1021 (DS) inoculation biological repeat 2


title: rice seedling at 1 day after live S. meliloti1021 (LS) inoculation biological repeat 3

source_name: Shoots of rice seedlings_live S. meliloti1021 (LS)_1d

value: 1 DAI


title: rice seedling at 2 day after live S. meliloti1021 (LS) inoculation biological repeat 1


title: rice seedling at 5 day after live S. meliloti1021 (LS) inoculation biological repeat 1


title: rice seedling at 1 day after live S. meliloti1021 (LS) inoculation biological repeat 2

source_name: Shoots of rice seedlings_live S. meliloti1021 LS)_1d


title: rice seedling at 1 day after live S. meliloti1021 (LS) inoculation biological repeat 1


title: rice seedling at 1 day after dead S. meliloti1021 (DS) inoculation biological repeat 2

source_name: Shoots of rice seedlings_dead S. meliloti1021 (DS)_1d


title: rice seedling at 1 day after dead S. meliloti1021 (DS) inoculation biological repeat 3


title: PBMC post F42K stimulation [7008]

city: Houston

first: Radvanyi

last: Laszlo

address: 7455 Fannin St

institute: UT MD Anderson Cancer Center

hyb_protocol: cDNA were hybridized on hybridized on to Human GeneChip ST 1.0® (Affymetrix Inc)  GeneChips. Arrays were stained with fluorescence on a Genechip Fluidics Station 450 (Affymetrix) according to the respective manufacturers' instructions

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

data_processing: The data were analyzed with Partek Genomics Suite 6.0 software (Partek Ink) after RMA normalization. One way ANOVA with consider donor diversity and two sample t-tests were performed using Partek software

source_name: PBMC_healthy control_after 24 h of F42K stimulation

label_protocol: 300ng isolated RNA was amplified using WT expression kit and labeled with biotin using Affymetrix labeling kits according to the manufacturer’s instruction

growth_protocol: Fresh  Fresh PBMC from healthy controls  were isolated from buffy coat and culture in RMPI1640

extract_protocol: Total RNA was isolated using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instruction

treatment_protocol: 2x10e6 PBMC from healthy controls were stimulated with 0.4nM WT IL-2 or F42K for 24 hours at 37C and 5% CO2.

tag: subject status

value: healthy donors

tag: donor id

tag: age (yr)

value: Peripheral blood mononuclear cells (PBMC)

tag: stimulated with

value: 0.4nM F42K IL-2 for 24 hr


title: rice seedling at 1 day after dead S. meliloti1021 (DS) inoculation biological repeat 1


title: PBMC post F42K stimulation [8773]


title: PBMC post F42K stimulation [2141]


title: PBMC post IL-15 stimulation [4340]

source_name: PBMC_healthy control_after 24 h of IL-15 stimulation

value: 0.4nM IL-15 for 24 hr


title: PBMC post IL-15 stimulation [8773]


title: PBMC post IL-15 stimulation [7008]


title: PBMC post WT IL-2 stimulation [9307]

description: 9307-WT IL-2

source_name: PBMC_healthy control_after 24 h of WT IL-2 stimulation

value: 0.4nM WT IL-2 for 24 hr


title: hMSC-TERT4 at Day 12 post osteoblast induction

city: Sydney

first: Natalie

last: Twine

address: High Street, Kensington

country: Australia

institute: University of New South Wales

description: hMSC_TERT4 cells at day 12 post osteoblast induction

hyb_protocol: Following fragmentation, 15 μg of labeled cRNA was hybridised for 16 hours at 45C on the HuGene 1.0 ST array. Arrays were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: Arrays  were scanned using an HP Laser scanner.

data_processing: Data was analysed using the Partek Genomics Suite version 6.12.0307, RMA was used to normalise the data

label_protocol: 500ng of total RNA from each sample was used for biotin-labelled cRNA

growth_protocol: hMSC-TERT4 cells were used as a model for primary hMSC. hMSC-TERT cells were routinely cultured in standard media (MEM) with 10% v/v FBS.

extract_protocol: At days 0, 1, 3, 6, 9 and 12 after induction of osteoblast differentiation total RNA was extracted using TRIzol

treatment_protocol: Ex vivo osteoblast differentiation in hMSC-TERT4 cells was performed using osteoblast induction medium containing containing β-glycerophosphate (10mM), L-ascorbic acid-2-phosphate (50µg/ml), dexamathasone (10nM) and calcitriol (10nM) in standard medium (SM). Media were changed every 3 days until day 15.

tag: cell line


title: PBMC post IL-15 stimulation [9307]


title: PBMC post WT IL-2 stimulation [7008]

description: 7008-WT IL-2


title: PBMC post IL-15 stimulation [2141]


title: Un-irradiated vs. 1 day after TBI

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Mus musculus

source_name: UT

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNA was isolated from samples using RNeasy kit (QIAGEN).

value: bone marrow stromal cells

source_name: 1days 9.5Gy


title: Un-irradiated vs. 3 days after TBI

source_name: 3days 9.5Gy


title: PBMC post F42K stimulation [9307]


title: hMSC-TERT4 at Day 6 post osteoblast induction

description: hMSC_TERT4 cells at day 6 post osteoblast induction


title: PBMC post F42K stimulation [4340]


title: hMSC-TERT4 at Day 1 post osteoblast induction

description: hMSC_TERT4 cells at day 1 post osteoblast induction


title: PBMC post WT IL-2 stimulation [8773]

description: 8773-WT IL-2


title: PBMC post WT IL-2 stimulation [4340]

description: 4340-WT IL-2


title: hMSC-TERT4 at Day 0 post osteoblast induction

description: hMSC_TERT4 cells at day 0 post osteoblast induction


title: PBMC post WT IL-2 stimulation [2141]

description: 2141-WT IL-2


title: hMSC-TERT4 at Day 9 post osteoblast induction

description: hMSC_TERT4 cells at day 9 post osteoblast induction


title: hMSC-TERT4 at Day 3 post osteoblast induction

description: hMSC_TERT4 cells at day 3 post osteoblast induction


title: PBMC post F42K stimulation [8768]


title: PBMC post IL-15 stimulation [8156]


title: PBMC post IL-15 stimulation [8768]


title: PBMC post WT IL-2 stimulation [8156]

description: 8156-WT IL-2


title: PBMC post F42K stimulation [7012]


title: PBMC post IL-15 stimulation [7012]


title: PBMC post F42K stimulation [8156]


title: PBMC post WT IL-2 stimulation [7012]

description: 7012-WT IL-2


title: PBMC post WT IL-2 stimulation [8768]

description: 8768-WT IL-2


title: PBMC post IL-15 stimulation [6130]


title: H2009 Scrambled, replicate1

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: Gene expression data from scrambled

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome 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 using Affymetrix Power Tools (APT) with Robust Multiarray Average (RMA) method.

source_name: Cancer Cell Line

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

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

value: control

tag: sample type

value: H2009 cell line, with scrambled shRNA


title: Ctrl-Veh-r1

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

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

scan_protocol: Chips were scanned with a GeneChip scanner 3000 7G (Affymetrix) and images were extracted with the GeneChip operating software (Affymetrix GCOS v1.4). The microarray processing was performed at the DNA Biochip Platform service at CHUQ-CHUL Research Centre (Québec, Canada)

data_processing: Quantified Affymetrix image files (“.CEL” files) for each of the treatment conditions (including two independent replicates per treatment condition) were exported into the statistical software environment R where the microarray analyses were performed using the Bioconductor package OneChannelGUI

source_name: T47D cells transfected with Control siRNAs and treated with vehicle

label_protocol: RNA samples were processed according to the manufacturer’s recommended procedures on GeneChip Whole Transcript (WT) Sense Target Labeling Assay from Affymetrix (http://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_ manual.pdf). The assay was started with 0.2 µg of each T47D cells RNA samples and the protocol is based on the principle of performing one cycle of cDNA synthesis and in vitro transcription (IVT) for target amplification to generate cRNA following by reverse transcription reactions to synthesis the WT cDNA. About 2.7 µg sample of fragmented cDNAs was used to hybridize human oligonucleotide array Gene 1.0 ST (Genechip; Affymetrix)

growth_protocol: T47D cells were obtained from the American Type Culture Collection (ATCC) and were propagated in phenol red-free DME high glucose medium containing 7.5 mg/l bovine insulin (Sigma, Oakville, Ontario, Canada) and 10% fetal bovine serum (Invitrogen). When indicated, FBS was treated overnight at 4oC with 2% dextran-coated charcoal to remove the remaining steroids present in the serum. Cells were incubated at 37oC in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was isolated from T47D cells using Trizol Reagent (Invitogen) in 6-well plates. RNA samples were treated with DNase1, purified using RNeasy Mini Kit column (Qiagen, Mississauga, ON, Canada), and RNA quality was assessed on the Agilent Bioanalyser 2100. Analysis using the RNA 6000 Nano Chip showed good qualities for all RNA samples with the RNA Integrity Numbers (RIN) greater than 8/10 for all the samples. RNA samples for subsequent microarray analyses and reverse transcription quantitative real-time PCR (RT-qPCR) comprised of eight samples composed of two biological repetitions for each of the four treatment conditions.

treatment_protocol: The sense and antisense sequences of three 17β-HSD1 siRNAs were selected and synthesized as previously described6 Scramble siRNA was used as control siRNA. Two days before transfection, T47D cells in T75 flasks were cultured in steroid deprived medium (dextran-coated charcoal-treated medium). On the transfection day, cells in T75 flasks were trypsined and ressuspended in a fresh charcoal-treated medium. 3x105 cells were then reverse-transfected in 6-well plates with 200 nM mixed 17β-HSD1 specific siRNAs or with negative control siRNA using Lipofectamine siRNAMax (Invitrogen), and cells were incubated. Two days (48 hours) after transfection, cell culture media were replaced by fresh charcoal-treated medium containing either the steroid E2 (1 nM) or ethanol as a vehicle control, and cells were incubated for two more days before RNA extraction. The RNA samples included two independent biological replicates, coming from two independent cell culture experiments, for a total of eight RNA samples.


title: siRNA-Veh-r2

source_name: T47D cells transfected with 17β-HSD1 siRNAs and treated with vehicle


title: Ctrl-E2-r2

source_name: T47D cells transfected with Control siRNAs and treated with E2


title: PBMC post WT IL-2 stimulation [6130]

description: 6130-WT IL-2


title: H460 knock-down, replicate3

description: Gene expression data from knock-down

value: PKC-delta KD

value: H460 cell line, with knockdown shRNA


title: H2009 Scrambled, replicate2

description: Gene expression data from scrambled


title: siRNA-Veh-r1


title: siRNA-E2-r1

source_name: T47D cells transfected with 17β-HSD1 siRNAs and treated with E2


title: siRNA-E2-r2


title: H2009 knock-down, replicate1

description: Gene expression data from knock-down

value: H2009 cell line, with knockdown shRNA


title: PBMC post F42K stimulation [6130]


title: Ctrl-Veh-r2


title: H2009 knock-down, replicate3

description: Gene expression data from knock-down


title: H460 knock-down, replicate2

description: Gene expression data from knock-down


title: Ctrl-E2-r1


title: H441 knock-down, replicate2

description: Gene expression data from knock-down

value: H441 cell line, with knockdown shRNA


title: H460 Scrambled, replicate3

description: Gene expression data from scrambled

value: H460 cell line, with scrambled shRNA


title: H2009 Scrambled, replicate3

description: Gene expression data from scrambled


title: H460 Scrambled, replicate1

description: Gene expression data from scrambled


title: H460 Scrambled, replicate2

description: Gene expression data from scrambled


title: H2009 knock-down, replicate2

description: Gene expression data from knock-down


title: H460 knock-down, replicate1

description: Gene expression data from knock-down


title: H441 Scrambled, replicate2

description: Gene expression data from scrambled

value: H441 cell line, with scrambled shRNA


title: A549 knock-down, replicate2

description: Gene expression data from knock-down

value: A549 cell line, with knockdown shRNA


title: H441 Scrambled, replicate3

description: Gene expression data from scrambled


title: A549 knock-down, replicate1

description: Gene expression data from knock-down


title: H441 knock-down, replicate1

description: Gene expression data from knock-down


title: A549 Scrambled, replicate3

description: Gene expression data from scrambled

value: A549 cell line, with scrambled shRNA


title: H441 knock-down, replicate3

description: Gene expression data from knock-down


title: A549 knock-down, replicate3

description: Gene expression data from knock-down


title: H441 Scrambled, replicate1

description: Gene expression data from scrambled


title: A549 Scrambled, replicate1

description: Gene expression data from scrambled


title: kidney-FVB-14

city: New York

first: Ali

last: Gharavi

state: New York

address: 1150 Saint Nicholas Ave., Room 413

department: Medicine/Nephrology

institute: Columbia University

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

source_name: kidney-FVB

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated from 560 µL of saliva supernatant with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

value: kidney

value: FVBN/J

tag: gender

value: F


title: A549 Scrambled, replicate2

description: Gene expression data from scrambled


title: kidney-FVB-17


title: kidney-FVB-19


title: kidney-FVB-15


title: kidney-FVB-12


title: kidney-FVB-9

value: M


title: kidney-FVB-18


title: kidney-FVB-10


title: kidney-FVB-5


title: kidney-FVB-8


title: kidney-FVB-13


title: kidney-CAST-20

source_name: kidney-CAST


title: kidney-FVB-16


title: kidney-CAST-19


title: kidney-FVB-3


title: kidney-FVB-11


title: kidney-FVB-7


title: kidney-FVB-2


title: kidney-FVB-6


title: kidney-CAST-18


title: kidney-FVB-4


title: kidney-FVB-1


title: kidney-CAST-16


title: kidney-CAST-13


title: kidney-CAST-14


title: kidney-CAST-15


title: kidney-CAST-12


title: kidney-CAST-17


title: kidney-CAST-11


title: kidney-CAST-6


title: kidney-CAST-3


title: kidney-CAST-8


title: kidney-CAST-10


title: kidney-CAST-7


title: kidney-CAST-1


title: kidney-CAST-5


title: kidney-CAST-2


title: kidney-CAST-9


title: Vehicle_4 [48hr]

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression data from F1 mice treated with Vehicle

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.

source_name: F1 mice treated with Vehicle, biological replicate 4

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: 10-12 week old C57Bl/6 and B6D2F1 mice were purchased from the Jackson Laboratoires.  To initiate GVHD, splenocytes equaling 4X10^7 T cells were i.v. injected into F1 host mice.

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

treatment_protocol: F1 mice (n=4) were treated i.p. with 15μg/kg TCDD on day 0, or vehicle or 2mg/kg Cl-BBQ on days 0 and 1. Mice were sacrificed on day 2 and alloresponding CD4+ T cells (at least 2 cell divisions based on CFSE dilution) were isolated by pan-CD4 microbeads followed by FACS sorting.

tag: time point

tag: host strain

value: Spleen and lymph node

value: Vehicle treated


title: kidney-CAST-4


title: 245B 51 Replicate 3

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Following fragmentation and terminal labeling, 5.2ug of ss-cDNA were hybridized for 16hr at 45C on GeneChip Human Transcriptome Array 2.0. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneCHip Scanner 3000 System.

data_processing: The data were analyzed with Expression Console Software using RMA analysis.

source_name: EndoC-betaH1 cell line (human beta cell line)

label_protocol: Fragmented and labeled ss-cDNA was prepared according to Affymetrix WT PLUS Reagent Kit  user guide

growth_protocol: EndoC-betaH1 were maintained as previously described (Ravassard et al.,

treatment_protocol: Five non-targeting and four amiRNAs targeting each of 5 TF and 25 lncRNAs were designed using

tag: replicate

value: Replicate 3

tag: lentivirus


title: Vehicle_3 [48hr]

source_name: F1 mice treated with Vehicle, biological replicate 3

tag: tissue

tag: treatment


title: BBQ_3 [48hr]

description: Gene expression data from F1 mice treated with Cl-BBQ

source_name: F1 mice treated with Cl-BBQ, biological replicate 3

value: BBQ treated


title: Vehicle_2 [48hr]

source_name: F1 mice treated with Vehicle, biological replicate 2


title: 245B 50 Replicate 2

value: Replicate 2


title: TCDD_3 [48hr]

description: Gene expression data from F1 mice treated with TCDD

source_name: F1 mice treated with TCDD, biological replicate 3

value: TCDD treated


title: TCDD_4 [48hr]

source_name: F1 mice treated with TCDD, biological replicate 4


title: 245B 49 Replicate 2


title: Vehicle_1 [48hr]

source_name: F1 mice treated with Vehicle, biological replicate 1


title: TCDD_2 [48hr]

source_name: F1 mice treated with TCDD, biological replicate 2


title: 245B 42 Replicate 2


title: TCDD_1 [48hr]

source_name: F1 mice treated with TCDD, biological replicate 1


title: 245B 48 Replicate 2


title: BBQ_4 [48hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 4


title: 245B 37 Replicate 3


title: BBQ_2 [48hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 2


title: Rescue_Ctrl_3

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: A total of 3.75 mg of cDNA from the last step was hybridized to the GeneChip Test3 array (Affymetrix) to test the quality of the labeled target. Nucleic acid samples that passed quality control were then hybridized to the Affymetrix Mouse GeneST 1.0 chip. Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (https://www.einstein.yu.edu/research/shared-facilities/cores/46/genomics/) according to the Affymetrix manual.

scan_protocol: Scanning were performed in the Genomics Core at Einstein (https://www.einstein.yu.edu/research/shared-facilities/cores/46/genomics/) according to the Affymetrix manual

data_processing: Data analysis was performed in the R statistical package. GeneChip data were pre-processed by the ‘oligo’ package (PMID: 20688976), which implements Robust Multichip Average (RMA) algorithm with background correction, quantile normalization and gene level summarization (PMID: 12925520).

source_name: anterior portion of the secondary heart field mesoderm

label_protocol: Biotinylated single-stranded cDNA targets were amplified from 100 nanograms (ng) starting total RNA using the Ovation RNA Amplification System V2 and FLOvation cDNA Biotin Module V2 (NuGEN).

growth_protocol: Embryos at E9.5 (19 - 21 somites pairs) were used for quantitative gene expression studies of microdissected AHFs

extract_protocol: The tissue was homogenized in Buffer RLT (QIAGEN). Total RNA was isolated with the RNeasy Micro Kit according to the manufacturer’s protocol. Quality and quantity of total RNA were determined using an Agilent 2100 Bioanalyzer (Agilent) and an ND-1000 Spectrophotometer (NanoDrop), respectively.

treatment_protocol: The mouse mutant alleles used in this study have been described previously: Tbx1+/- (PMID: 11239417), Tbx1f/+ (flox = f) [PMID: 16452092], β-cateninf/+ and β-cateninE3/+ (PMID: 11262227), Mef2c-AHF-Cre/+ (PMID: 16188249), ROSA26-GFPf/+ (RCE:loxP; 19363146) and Wnt/β-catenin signaling reporter mice (Tg(TCF/Lef1-HIST1H2BB/EGFP)61Hadj/J; TCF/Lef:H2B-GFP; PMID: 21176145). To generate Mef2c-AHF-Cre/+;Tbx1f/- mutant embryos, Mef2c-AHF-Cre/+ transgenic male mice were crossed to Tbx1+/- mice to obtain male Mef2c-AHF-Cre/+;Tbx1+/- mice that were then crossed with Tbx1f/f females. Alternatively, to generate Mef2c-AHF-Cre/+;Tbx1f/f mutant embryos, Mef2c-AHF-Cre/+ transgenic male mice were crossed to Tbx1f/f mice to obtain male Mef2c-AHF-Cre/+;Tbx1f/+ mice, and these were then crossed with Tbx1f/f females. Wild type and Me2fc-AHF-Cre/+;Tbx1f/+ littermates were used as controls for the experiments. Rescued embryos were generated by addition of one copy of β-cateninflox allele to the conditional Tbx1 loss of function embryos. In this case, the females used for the experimental crosses were Tbx1f/f;β-catenin f/f genotype. The reporter ROSA26-GFP f/+ allele was added to the Tbx1f/f and Tbx1f/f;β-catenin f/f lines when visualizing the anterior heart field domain was needed. β-catenin loss of function embryos were generated by crossing Mef2c-AHF-Cre/+;β-cateninf/+ males with β-cateninf/f females.

value: anterior heart field

tag: genotype/variation

value: Rescue control

tag: developmental stage


title: Rescue_Ctrl_2


title: 245B 35 Replicate 2


title: Rescue_Ctrl_1


title: 245B 36 Replicate 2


title: 245B 33 Replicate 2


title: 245B 34 Replicate 2


title: Rescue_KO_2

value: Rescue KO


title: BBQ_1 [48hr]

source_name: F1 mice treated with Cl-BBQ, biological replicate 1


title: Rescue_Ctrl_4


title: Rescue_KO_3


title: Rescue_KO_1


title: Rescue_KO_4


title: Bcat_Ctrl_3

value: Bcat control


title: Bcat_Ctrl_4


title: Bcat_Ctrl_1


title: Bcat_Ctrl_2


title: Bcat_KO_2

value: Bcat KO


title: Bcat_KO_3


title: Tbx1_Ctrl_1

value: Tbx1 control


title: Bcat_KO_4


title: 245B 29 Replicate 2


title: Tbx1_Ctrl_4


title: Bcat_KO_1


title: 245B 31 Replicate 2


title: Tbx1_Ctrl_3


title: 245B 32 Replicate 2


title: 245B 30 Replicate 2


title: 245B 21 Replicate 2


title: Tbx1_KO_2

value: Tbx1 KO


title: 245B 22 Replicate 2


title: 245B 28 Replicate 2


title: Tbx1_Ctrl_2


title: Tbx1_KO_4


title: Tbx1_KO_3


title: ROSA26Foxf1:Tie2-cre lung biological replicate 3

first: Pawel

last: Stankiewicz

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: SAMPLE 5

hyb_protocol: standard Illumina hybridization protocol

scan_protocol: standard illumina scanning protocol

data_processing: The data were normalized by robust spline normalization (RST) using the lumi bioconductor package

source_name: Whole lung

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

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

value: lung

tag: genotype

value: embryonic day 18.5


city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadArray 500GX Reader

data_processing: The data were extracted using BeadStudio without modification, normalized with quantile with limma package from R, log2 transformed and filtered for probes with bad detection p-values in all samples within a comparison.

source_name: Tumor microenvironment from B16-shVEGF at Day 14 D14-V6 D14-V6

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

extract_protocol: Tissues were lysed using Tissue Lyser (Qiagen). RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: age

value: 8 weeks


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 14 D14-V5 D14-V5


title: ROSA26Foxf1:Tie2-cre lung biological replicate 2

description: SAMPLE 3


title: 245B 20 Replicate 2


title: 245B 19 Replicate 2


title: 245B 16 Replicate 2


title: ROSA26Foxf1:Tie2-cre lung biological replicate 1

description: SAMPLE 1


title: 245B 14 Replicate 2


title: 245B 15 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 14 D14-V3 D14-V3


title: 245B 12 Replicate 2

source_name: EndoC-betaH1 cell line (human beta cell line)


title: 245B 17 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 4 D4-V4 D4-V4


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 14 D14-V1 D14-V1


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 14 D14-V2 D14-V2


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 4 D4-V5 D4-V5


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 14 D14-V4 D14-V4


title: 245B 11 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 4 D4-V3 D4-V3


title: 245B 10 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 4 D4-V2 D4-V2


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 14 D14-T5 D14-T5


title: ROSA26-LSL-Foxf1 lung biological replicate 3

description: SAMPLE 6


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 14 D14-T4 D14-T4


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 14 D14-T3 D14-T3


title: 245B 9 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shVEGF at Day 4 D4-V1 D4-V1


title: 245B 7 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 14 D14-T2 D14-T2


title: 245B 8 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 4 D4-T6 D4-T6


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 14 D14-T1 D14-T1


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 4 D4-T4 D4-T4


title: 245B 5 Replicate 2


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 4 D4-T5 D4-T5


title: 245B 6 Replicate 2

source_name: EndoC-betaH1 cell line (human beta cell line)


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 4 D4-T3 D4-T3


description: replicate 5

source_name: Tumor microenvironment  from B16-WT at Day 14 D14-5 D14-5


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 4 D4-T1 D4-T1


description: replicate 3

source_name: Tumor microenvironment  from B16-WT at Day 14 D14-3 D14-3


title: 245B 3 Replicate 2


title: 245B 2 Replicate 2


title: 245B 4 Replicate 2


description: replicate 4

source_name: Tumor microenvironment  from B16-WT at Day 14 D14-4 D14-4


title: Tbx1_KO_1

source_name: anterior portion of the secondary heart field mesoderm


description: replicate 2

source_name: Tumor microenvironment  from B16-WT at Day 14 D14-2 D14-2


description: replicate 5

source_name: Tumor microenvironment from B16-shTGFb at Day 4 D4-T2 D4-T2


description: replicate 1

source_name: Tumor microenvironment  from B16-WT at Day 14 D14-1 D14-1


description: replicate 2

source_name: Tumor microenvironment from B16-WT at Day 4 D4-2 D4-2


description: replicate 3

source_name: Tumor microenvironment from B16-WT at Day 4 D4-3 D4-3


title: Control Tissue  CTRL 3

description: replicate 3

source_name: Control Tissue  CTRL 3 CTRL 3

value: Control Tissue


description: replicate 4

source_name: Tumor microenvironment from B16-WT at Day 4 D4-4 D4-4


title: Control Tissue  CTRL 2

description: replicate 2

source_name: Control Tissue  CTRL 2 CTRL 2


title: Control Tissue  CTRL 4

description: replicate 4

source_name: Control Tissue  CTRL 4 CTRL 4


title: Control Tissue  CTRL 1

description: replicate 1

source_name: Control Tissue  CTRL 1 CTRL 1


title: 245A 43 Replicate 1

source_name: EndoC-betaH1 cell line (human beta cell line)

value: Replicate 1


title: 245A 49 Replicate 1


title: Control Tissue  CTRL 5

description: replicate 5

source_name: Control Tissue  CTRL 5 CTRL 5


title: HPM_replication3-fat

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

department: Animal Science

institute: South China Agricultural University

description:
HPM3-fat
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

hyb_protocol: After labelling, the samples were hybridized to the Affymetrix miRNA array as recommended by the vendor.

scan_protocol: Standard Affymetrix array cassette staining, washing and scanning was performed using the post-hybridization kit (Affymetrix, Santa Clara, CA, USA) and GeneChip Scanner 3000.

data_processing: The 24 miRNA microarray raw data analysis were performed using Partek Genomics SuiteTM (Partek GS), version 6.4

organism: Gallus gallus

source_name: HPM-fat

label_protocol: 1 μg of total RNA was labelled with the FlashTag Biotin RNA Labelling Kit.

growth_protocol: All the birds were raised in floor pens and fed commercial corn-soybean diets that met NRC requirements.

extract_protocol: Total RNA was extracted from each sample using Trizol (Invitrogen) according to manufacturer’s instructions. The concentration and quality of RNA for each sample were measured by the UV absorbance at 260 nm and checked by gel electrophoresis.

treatment_protocol: The tissues were collected for RNA extreaction at the same 7-week old age

tag: breed trait

value: hypertrophic pectoral muscle

value: fat


title: HPM_replication3-muscle

description:
HPM3-muscle
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: HPM-muscle

value: muscle


title: 245A 43REP Replicate 3

value: Replicate 3


title: 245A 51 Replicate 1


title: HPM_replication3-liver

description:
HPM3-liver
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: HPM-liver

value: liver


title: 245A 48 Replicate 1


title: Control Tissue  CTRL 6

description: replicate 6

source_name: Control Tissue  CTRL 6 CTRL 6


title: HPM_replication3-hypothalamus

description:
HPM3-hypothalamus
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: HPM-hypothalamus

value: hypothalamus


title: HPM_replication2-fat

description:
HPM2-fat
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: Control Tissue  CTRL 7

description: replicate 7

source_name: Control Tissue  CTRL 7 CTRL 7


title: 245A 36 Replicate 1


title: 245A 42 Replicate 1


title: HPM_replication2-muscle

description:
HPM2-muscle
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: HPM_replication2-liver

description:
HPM2-liver
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: HPM_replication2-hypothalamus

description:
HPM2-hypothalamus
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: HPM_replication1-fat

description:
HPM1-fat
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: HPM_replication1-muscle

description:
HPM1-muscle
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication3-fat

description:
NPM3-fat
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: NPM-fat

value: normal pectoral muscle


title: HPM_replication1-hypothalamus

description:
HPM1-hypothalamus
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication3-muscle

description:
NPM3-muscle
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: NPM-muscle


title: 245A 35 Replicate 1


title: 245B 1 Replicate 2

value: Replicate 2


title: 245A 32 Replicate 1


title: ROSA26-LSL-Foxf1 lung biological replicate 2

description: SAMPLE 4

source_name: Whole lung


title: HPM_replication1-liver

description:
HPM1-liver
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication3-hypothalamus

description:
NPM3-hypothalamus
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: NPM-hypothalamus


title: 245A 33 Replicate 1


title: NPM_replication2-hypothalamus

description:
NPM2-hypothalamus
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication2-fat

description:
NPM2-fat
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication2-muscle

description:
NPM2-muscle
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication2-liver

description:
NPM2-liver
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle

source_name: NPM-liver


title: NPM_replication1-fat

description:
NPM1-fat
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: 245A 34 Replicate 1


title: NPM_replication3-liver

description:
NPM3-liver
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: 245A 30 Replicate 1


title: 245A 29 Replicate 1


title: NPM_replication1-muscle

description:
NPM1-muscle
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication1-hypothalamus

description:
NPM1-hypothalamus
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: NPM_replication1-liver

description:
NPM1-liver
miRNA expression in different tissue from different breed chickens with hypertrophic pectoral muscle or normal pectoral muscle


title: 245A 31 Replicate 1


title: 245A 22 Replicate 1


title: 245A 28 Replicate 1


title: 245A 20 Replicate 1


description: replicate 1

source_name: Tumor microenvironment from B16-WT at Day 4 D4-1 D4-1


title: 245A 14 Replicate 1


title: 245A 15 Replicate 1


title: 245A 17 Replicate 1


title: 245A 19REP Replicate 3


title: 245A 9 Replicate 1


title: 245A 6 Replicate 1


title: 245A 16 Replicate 1


title: 245A 12 Replicate 1


title: 245A 19 Replicate 1


title: 245A 11 Replicate 1


title: 245A 7 Replicate 1


title: 245A 10 Replicate 1


title: 245A 4 Replicate 1


title: 245A 8 Replicate 1


title: 245A 2 Replicate 1


title: 245A 5 Replicate 1


title: 245A 3 Replicate 1


title: 245A 21 Replicate 1


title: 242A 16 Replicate 3


title: 242A 39 Replicate 3


title: 242A 38 Replicate 3


title: ROSA26-LSL-Foxf1 lung biological replicate 1

description: SAMPLE 2


title: 242A 1 Replicate 3


title: 245 UNT1 Replicate 1

value: Untreatedcells


title: 242A 4 Replicate 3


title: 245A 1 Replicate 1


title: 242A 17 Replicate 3


title: Dose 1000, WT, PP, biological replicate 6

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_117_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

hyb_protocol: 1.6ug of labeled cDNA was added to Gene Titan Hybridization Cocktail formulation for 3’ Array plates (Affymetrix, Santa Clara, CA) as described in appendix VI of the Ovation® PicoSL WTA system V2 user manual (Nugen, San Carlos, CA).  Finally, the samples were hybridized onto a HT RG-230 PM Array Plate (96 or 16 plate, Affymetrix) and analyzed using the Gene Titan microarray system (Affymetrix) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6

organism: Rattus norvegicus

source_name: Dose 1000, WT, PP

label_protocol: The RNA was amplified to cDNA using the Ovation Pico WTA system V2 (Nugen, San Carlos, CA) and purified using a QIAquick PCR Purification kit (Qiagen) according to the manufacturer’s protocol.  The cDNA was quantified using a nanodrop (model ND-1000, ThermoFisher Scientific, Waltham, MA).  5ug of each sample was biotin-labeled using the Encore Biotin Module (Nugen) according to the manufacturer’s protocol.

growth_protocol: Adult male Sprague-Dawley rats purchased from Charles Rivers Laboratories, Inc (Raleigh, NC).  Animals kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 68-79°F with a relative humidity of approximately 30-70%. All animals allowed access to NIH-07 standard diet and reverse osmosis water ad libitum.

extract_protocol: A 4 mm by 10 mm section from the center of the left liver lobe will be collected,preserved in O.C.T. compound, frozen on dry ice and stored at -80°C.  12micron thick slices were sectioned from the preserved tissue using a cryostat and placed onto membrane slides.  The sections were immediately fixed and stained using the following steps

treatment_protocol: Animals 1 – 56 will be weighed and vehicle or chemical treatment will be administered by oral gavage for 4 days.  No other procedures will be performed on these animals until day 5.  On day 5 (24 hr after the final dose), animals will be euthanized by isoflurane anesthesia and exsanguination.  Doses

value: Sprague-Dawley

tag: cell type

value: Periportal (PP) Hepatocyte

value: Wild type (WT)

tag: agent

value: TCDD

tag: dose

value: 1000 ng/kg/day

tag: exposure time

value: 28 days

tag: animal id


title: 245 UNT2 Replicate 1

tag: cell line


title: Dose 1000, WT, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_112n_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_96_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 300, WT, PP

value: 300 ng/kg/day


title: Dose 1000, WT, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_114_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, WT, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_118_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, WT, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_113_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, WT, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_119_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, WT, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_116_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: 242A 43 Replicate 3

value: CDS HNF1A_sh4


title: 242A 12 Replicate 3


title: 242A 3 Replicate 3


title: Dose 300, WT, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_94_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, WT, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_111_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_99_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: 242A 5 Replicate 3


title: Dose 300, WT, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_97_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: 242A 2 Replicate 3


title: Dose 300, WT, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_93n_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_92_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_77_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 100, WT, PP

value: 100 ng/kg/day


title: Dose 100, WT, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_75_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_78_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_91_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_73_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_72_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_59n_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 22, WT, PP

value: 22 ng/kg/day


title: Dose 22, WT, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_56_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_54_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_71_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_58_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_57_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_39n_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 3, WT, PP

value: 3 ng/kg/day


title: Dose 300, WT, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_98_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_76_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_52_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_36_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_34_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_38_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_51_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_37_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_79_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_33_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_53_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_17_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 0, WT, PP

value: control

value: 0 ng/kg/day


title: Dose 3, WT, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_32_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_31_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_19_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_18_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_16_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_14_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_11_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_13_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, KO, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_314_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 1000, KO, PP

value: AHR-Knock-out (KO)


title: Dose 1000, KO, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_313_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_299_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 300, KO, PP


title: Dose 1000, KO, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_317_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_298_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_12_WT_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, KO, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_312_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_297_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_296_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, KO, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_318_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_294_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, KO, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_316_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 1000, KO, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_311_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_291_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, KO, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_282_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, KO, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_274_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 100, KO, PP


title: Dose 100, KO, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_278_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, KO, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_279_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, KO, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_277_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).