title: NOOT_TNKS07_2 with array type Medicago from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: Legume plants establish a symbiotic interaction with soil bacteria called rhizobia. A complex molecular dialogue between the two partners is necessary for the successful infection and organogenesis processes that will ultimately result in the formation of a nitrogen fixing nodule. During a M. truncatula Tnt1 mutant screen, a new class of symbiotic mutant called noot (nodule root) was identified. This original single recessive mutant develops a root in apical position of nodules that are colonized by bacteria and functional for nitrogen fixation. This conversion suggests that the legume nodule morphogenetic pathway may be derived from a root program. We cloned the NOOT gene and showed that it corresponds to Pisum sativum COCH (Ferguson and Reid, 2005, Plant Cell Physiol 46, 1583-1589). The goal of this project is to compare the transcriptomes from wild type nodules and roots to the noot nodule one. This will allow us to unravel the similarity and differences between the wild type and mutant nodule transcriptomes but also to know which developmental pathway is under the control of the NOOT gene.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: roots - in vitro growth condition on BNM (nitrogen poor medium) plates. - 16h light - 24°C -

treatment_protocol: Name:21days  - induction - infection with symbiotic bacteria,sinorhizobium meliloti

value: nodules

tag: genotype/variation

value: noot mutant Tnk507

tag: developmental stage (boyes et al. plant cell 2001)

value: root nodules from 21 days seedling


title: R108R_10 with array type Medicago from Affymetrix

status: Public on Jun 01 2012

type: RNA

label: Biotin

molecule: total RNA

growth_protocol: roots - - in vitro growth condition on BNM (nitrogen poor medium) plates. - 16h light - 24°C

treatment_protocol: Name:20days  - induction - infection with symbiotic bacteria,sinorhizobium meliloti

tag: tissue

value: roots

value: wild type

value: roots from 20 days seedling


title: R108N_1 with array type Medicago from Affymetrix

value: root nodules from 20 days old seedling


title: NOOT_TNKS07_1 with array type Medicago from Affymetrix

growth_protocol: roots - in vitro growth condition on BNM (nitrogen poor medium) plates. - 16h light - 24°C


title: Myeloma cells resistant to the drug at start point sample 2

city: Chicago

first: Samuel

last: McBrayer

address: 303 E Superior

country: USA

institute: Northwestern University

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Quantile normalization with variance stabilizing transformation using 'lumi' R package.

organism: Homo sapiens

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: cell type

value: Myeloma

tag: cell line


title: FTC005

city: Brussels

first: Gil

last: Tomas

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: follicular thyroid carcinoma

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalized with RMA using the affy Bioconductor package

source_name: tumor

label_protocol: standard Affymetrix protocol

extract_protocol: All patients undergoing thyroid surgery by one of the authors (TJF) had thyroid tumor samples collected at the time of surgery. Tumor tissue was dissected by a pathologist and snap frozen in liquid nitrigen and stored at -80C. RNA was extracted, following the manufacturer's protocol, from each sample after homogeneization in TRIzol reagent and RNA clean-up was performed using RNeasy MiniKit.

tag: clinical description

value: follicular thyroid carcinoma


title: NOOT_NF2717_2 with array type Medicago from Affymetrix

value: noot mutant NF2717


title: FA012

description: follicular adenoma

value: follicular adenoma


title: FA013

description: follicular adenoma


title: FA008

description: follicular adenoma


title: FA009

description: follicular adenoma


title: Myeloma cells sensitive to the drug at 17 hrs sample 3


title: FA005

description: follicular adenoma


title: FA006

description: follicular adenoma


title: FA011

description: follicular adenoma


title: Myeloma cells sensitive to the drug at 17 hrs sample 2


title: FA010

description: follicular adenoma


title: Myeloma cells sensitive to the drug at 17 hrs sample 1


title: FA007

description: follicular adenoma


title: FA003

description: follicular adenoma


title: FA004

description: follicular adenoma


title: WT 30mM AcH 2

city: Valencia

first: Guillem

last: Hueso

address: Avenido de los Naranjos

country: Spain

institute: IBMCP

hyb_protocol: Slides were hybridized using manual chambers according to the manufacturer. Briefly, slides were prehybridized in 5x SSC, 0.1% SDS, and 0.1mg/ml BSA for 45m, and rinsed in 0.1 x SSC two times before drying. Both samples were resuspended in 50% formamide, 5 x SSC, 0.1% SDS, and 0.1mg/ml of sonicated salmon sperm DNA, denatured for 5m and injected between slide and coverslip (Lifterslips). Hybridization was performed overnight at 42ºC. Washes: a) Arrays were immersed in 2x SSC, 0.1% SDS at 42ºC until the coverslip moved freely away from the slide. b) Transferred to 2 x SSC, 0.1% SDS at 42ºC for 5 minutes. c) Transferred to 0.1 x SSC, 0.1% SDS at room temperature for 5 minutes. Repeated step. d) Transferred to 0.1 x SSC at room temperature for 1 minute. Repeated 4 times.e) Rinsed in 0.01 x SSC for 10 seconds. Dried by centrifugation at 1600 x g for 2 minutes.

scan_protocol: Slides were scanned at 10um resolution using a 4200B Molecular Devices scanner, adjusting PMT values so that the ratio Cy5/Cy3 total intensity was close to 1. Image analysis was performed using GenePix 6.0 software.

data_processing: Local background was used for background subtraction. Background-subtracted signals were used for ratio calculations. Data were normalized by global-median and print-tip loess. Features whose background-subtracted intensity do not reach two times background intensity were flagged as bad and rejected for further analysis (Value=null). Same for features affected by hybridization and washing  artifacts, if any. Original value data are log ratios of lowess-normalized Cy5/Cy3 signals.

organism: Saccharomyces cerevisiae

source_name: WT, 30mM AcH

label_protocol: Indirect labelling.

growth_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=0.6.

extract_protocol: Standard protocol (acid-phenol extraction).

treatment_protocol: 50ml of yeast culture was treated with 30mM acetic acid (AcH) for 2 hours. Cells were harvested by centrifugation and washed with water. Dried cell pellet was kept at-80 until RNA purification.

tag: strain

tag: genotype

value: MATa, his3Δ1, leu2Δ0, LYS2, met15Δ0, ura3Δ3

tag: treatment

value: acetic acid

tag: treatment duration

value: 2 hrs

source_name: WT


title: R108N_2 with array type Medicago from Affymetrix

treatment_protocol: Name:18 days  - induction - infection with symbiotic bacteria,sinorhizobium meliloti

value: root nodules from 18 days seedling


title: R108N_3 with array type Medicago from Affymetrix

value: root nodules from 20 days seedling


title: FA001

description: follicular adenoma


title: R108R_1 with array type Medicago from Affymetrix

value: roots from 18 days seedling


title: FA002

description: follicular adenoma


title: PRC+ERRalpha-rep2

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

description:
raw data file (please see Series record): RO82_W1_PRC+ERRalpha_rep2.txt
Biological replicate 2 of 2. Cells treated with both PRC and ERRalpha plasmids

hyb_protocol: Agilent hybridization protocol was used

scan_protocol: Agilent scanner

data_processing: Two-channel hybridizations were analyzed as single-channel. The hierarchical gene clustering was computed on median-gene-centered and log-transformed data using average linkage and uncentered correlation distances. Computations and visualization were performed using Cluster and TreeView software (Eisen et al., 1998). The Expression Analysis Systematic Explorer (EASE) and Gene Set analysis were used to determine the statistical over represented and differentially expressed genes (Tusher et al., 2001). The data matrix contains 13 K out of 45K when normalized, filtered and selected for relevant signal intensities (different from background).

label_protocol: RNA amplification and cDNA labeling using Cy3/Cy5 dyes according to manufacturer’s recommendations (Agilent)

growth_protocol: RO82_W1 cells were grown in a mixed 60:30 DMEM-F12/endothelial basal medium supplemented with 10% fetal bovine serum, 1% L-glutamine, and an antibiotic cocktail

extract_protocol: Total RNA was isolated from cultured cells using the RNeasy kit . The integrity of RNA was determined using a Bio-Analyzer 2100

treatment_protocol: Cells were treated with 0.05 µg  of either PGl3, PRC and ERRalpha plasmid or with 0.05 µg of both PRC+ERRalpha plasmids

value: cancer thyroid cell line

value: PRC+ERRalpha transfected cells


title: Myeloma cells sensitive to the drug at 5 hrs sample 4


title: R108R_2 with array type Medicago from Affymetrix


title: NOOT_NF2717_1 with array type Medicago from Affymetrix

value: nodules

value: root nodules from 21 days seeding


title: Myeloma cells sensitive to the drug at 5 hrs sample 3


title: Myeloma cells sensitive to the drug at 5 hrs sample 2


title: Myeloma cells sensitive to the drug at start point sample 4


title: Myeloma cells sensitive to the drug at 5 hrs sample 1


title: PRC+ERRalpha-rep1

description:
raw data file (please see Series record): RO82_W1_PRC+ERRalpha_rep1.txt
Biological replicate 1 of 2. Cells treated with both PRC and ERRalpha plasmids


title: WT 1

value: MATa, his3Δ1, leu2Δ0, LYS2, met15Δ0, ura3Δ0


title: WT 30mM AcH 1

value: MATa, his3Δ1, leu2Δ0, LYS2, met15Δ0, ura3Δ1


title: WT 2

value: MATa, his3Δ1, leu2Δ0, LYS2, met15Δ0, ura3Δ2


title: control-rep2

description:
raw data file (please see Series record): RO82_W1_PGl3_control_rep2.txt
Biological replicate 2 of 2. Control cells, PGl3 plasmid

value: control cells


title: ERRalpha-rep2

description:
raw data file (please see Series record): RO82_W1_ERRalpha_rep2.txt
Biological replicate 2 of 2. Cells treated with ERRalpha plasmid

value: ERRalpha transfected cells


title: ERRalpha-rep1

description:
raw data file (please see Series record): RO82_W1_ERRalpha_rep1.txt
Biological replicate 1 of 2. Cells treated with ERRalpha plasmid


title: 754

city: brisbane

first: santiyagu

middle: mary

last: savarimuthu francis

address: lvl 1, clinical sciences building, rode road, chermside

department: Thoracic Medicine

country: Australia

institute: The Prince Charles Hospital

description: microRNA expression

hyb_protocol: 100ng of total RNA from lung tissue was dephosphorylated using calf intestine alkaline phosphotase to create sticky ends for ligation of the fluorescent dye pCp-Cy3 and T4 RNA ligase (GE Healthcare, Little Chalfont, England). The resulting labeled RNA was purified using Micro-bio spin 6 columns (Bio-Rad, Hercules, CA, USA) to remove unlabeled dye and then hybridized to the Agilent microarray slide for 20hrs at 55⁰C

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

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

source_name: Normal Lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Macroscipcally uninvolved lung tissues were obtained by histopathologists from patients undergoing curative resection for lung cancer. The lung tissues were snap frozen in liquid nitrogen and stored at -80C until use.

extract_protocol: Total RNA was extracted and cleaned using Trizol and DNeasy mini kit following manufacturer's instructions.

tag: age

tag: Sex

value: M

tag: kco% predicted

tag: pack years

tag: age quit smoking

tag: copd status

value: mild


title: 759

description: microRNA expression

value: moderate


title: PRC-rep1

description:
raw data file (please see Series record): RO82_W1_PRC_rep1.txt
Biological replicate 1 of 2. Cells treated with PRC plasmid

value: PRC transfected cells


title: PRC-rep2

description:
raw data file (please see Series record): RO82_W1_PRC_rep2.txt
Biological replicate 2 of 2. Cells treated with PRC plasmid


title: 679

description: microRNA expression

value: F


title: Myeloma cells sensitive to the drug at start point sample 2

value: Myeloma


title: GATA1 KD CMK-5b-2

city: Detroit

first: Yubin

last: Ge

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

hyb_protocol: Whole human genome oligonucleotide microarrays (Agilent Technologies, catalog no. G4112A) were hybridized using 0.75 ug of Alexa 555 labeled aRNA and 0.75 ug of Alexa 647 labeled aRNA. Agilent's SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 h at 60 °C. After hybridization, the slides were washed per Agilent's SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner with extended dynamic range (XDR) at 5 micron resolution.

data_processing: Tiff images were analyzed with Agilent's feature extraction software (v9.5.3.1) using protocol GE2_v5_95_Feb07. Linear and LOWESS normalization were performed.

label: Alexa 555

source_name: CMK-5b GATA1 shRNA infected cells

label_protocol: Alexa555 and Alexa 647 labeled aRNA was prepared from 500ng total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Alexa Dye (Invitrogen/Molecular Probes, Eugen OR) incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The parental CMK cells and the shRNA stable clones were cultured in RPMI 1640 with 10% fetal bovine serum (Hyclone, Logan, UT) and 2 mM L-glutamine plus 100 U/ml penicillin and 100 µg/ml streptomycin, in a 37 °C humidified atmosphere containing 5% CO2/95% air.

extract_protocol: Total RNAs were extracted from the CMK shRNA stable clones using TRIzol reagent (Invitrogen, Carlsbad, CA). The quality and quantify of the extracted total RNAs were determined on a NanoDrop analyzer.

treatment_protocol: Knockdown of GATA1 in the CMK cells was performed using shRNA lentivirus. Two clones designated CMK-5a and CMK-5b were used. A pool of cells from a negative control infection (lentivirus expressing a shRNA with limited homology to any known human genes) was used as the negative control (designated CMK-neg).

tag: transfection

value: GATA1 shRNA

tag: clone

tag: parental cell line

value: CMK

label: Alexa 647

source_name: CMK neg control cells

value: negative control

value: CMK-neg


title: Myeloma cells sensitive to the drug at start point sample 1


title: 712

description: microRNA expression


title: 706

description: microRNA expression


title: Array2_Diabetes7

city: Brisbane

first: Katharine

last: Irvine

address: Translational Research Institute

institute: Mater Research Institute UQ

hyb_protocol: Standard Illumina bead array protocol

scan_protocol: Illumina iScan, standard Illumina protocol

data_processing: Raw data were exported from Beadstudio (Illumina), followed by filtering and normalization (variance stabilization and quantile normalization) using the Bioconductor Lumi package in R. For each array, detected probes were required to have an Illumina Detection Score of 1 in at least 1 sample.

source_name: CD14+ Monocyte

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

extract_protocol: CD14+ monocytes were purified from ficoll-separated PBMC by positive selection using CD14 MACS magnetic beads (Miltenyi). Total RNA was purified using Qiagen Rneasy columns with on-column DNase digestion.

tag: array

tag: group

value: Diabetes Group A

tag: age at diagnosis

tag: gender

tag: hba1c 3months post diagnosis

tag: insulin dose (u/kg/day) 3months post diagnosis

tag: hba1c 6months post diagnosis

tag: insulin dose (u/kg/day) 6months post diagnosis

tag: hba1c 9months post diagnosis

tag: insulin dose (u/kg/day) 9months post diagnosis

value: no visit

tag: hba1c 12months post diagnosis

tag: insulin dose (u/kg/day) 12months post diagnosis


title: GATA1 KD CMK-5b-1


title: Array2_Diabetes8

value: Diabetes Group B

value: not available


title: 652

description: microRNA expression

tag: age

tag: Sex

tag: kco% predicted

tag: pack years

tag: age quit smoking


title: GATA1 KD CMK-5a-2

source_name: CMK-5a GATA1 shRNA infected cells

tag: transfection

tag: clone

tag: parental cell line


title: 649

description: microRNA expression

tag: copd status


title: Myeloma cells sensitive to the drug at start point sample 3

tag: cell type

tag: cell line


title: GATA1 KD CMK-5a-1


title: Array2_Diabetes6

tag: array

tag: group

tag: age at diagnosis

tag: gender

tag: hba1c 3months post diagnosis

tag: insulin dose (u/kg/day) 3months post diagnosis

tag: hba1c 6months post diagnosis


title: control-rep1

description:
raw data file (please see Series record): RO82_W1_PGl3_control_rep1.txt
Biological replicate 1 of 2. Control cells, PGl3 plasmid

value: cancer thyroid cell line

tag: treatment


title: 638

description: microRNA expression

tag: age

tag: Sex

tag: kco% predicted


title: 585

description: microRNA expression

tag: pack years

tag: age quit smoking


title: embryo at HH8_NP_rep4

city: Bethesda

first: Yukinori

last: Endo

state: MD

address: 30 Convent Drive, MSC 4370, Room 402

department: Laboratory of Cell and Developmental Biology

institute: NIDCR, NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken 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 with Affymetrix GeneChip Operating System (GCOS) 1.x using Affymetrix MSA5 default analysis settings and global scaling as normalization method.

label: biotin

organism: Gallus gallus

source_name: cranial neural plate, HH8

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

growth_protocol: Fertile chicken eggs were incubated at 38C in a humidified incubator.

extract_protocol: The isolated tissues were dissolved in TRIzol (Invitrogen), snap frozen in dry ice/ethanol, and then stored at -80C overnight. Total RNA were isolated according to the manufacturer's protocol.

treatment_protocol: Cranial neural folds and neural plates were dissected from HH stage 8 embryos using tungsten needles in ice-cold Hank's balanced salt solution with supplemented with 1 mM MgCl2, 1 mM CaCl2, and 1 mM HEPES at pH 7.5.

tag: embryo stage

tag: tissue

value: cranial neural plate (NP)


title: 510

description: microRNA expression

tag: copd status


title: 523

description: microRNA expression


title: 623

description: microRNA expression


title: embryo at HH8_NP_rep3


title: 554

description: microRNA expression


title: embryo at HH8_NP_rep2


title: FA014

description: follicular adenoma

tag: clinical description

value: follicular adenoma


title: Array2_Diabetes1

tag: array

tag: hba1c 9months post diagnosis

tag: hba1c 12months post diagnosis

tag: insulin dose (u/kg/day) 12months post diagnosis


title: Array2_Healthy3

tag: group

value: Healthy

tag: age at diagnosis

value: adult

tag: gender

value: M

tag: hba1c 3months post diagnosis

value: not applicable

tag: insulin dose (u/kg/day) 6months post diagnosis

tag: insulin dose (u/kg/day) 9months post diagnosis


title: 483

description: microRNA expression

tag: age

tag: Sex

value: F

tag: kco% predicted

value: moderate


title: Array2_Diabetes4

tag: insulin dose (u/kg/day) 3months post diagnosis

tag: hba1c 6months post diagnosis


title: 486

description: microRNA expression

tag: pack years

tag: age quit smoking

tag: copd status


title: FTC004

description: follicular thyroid carcinoma

tag: clinical description

value: follicular thyroid carcinoma


title: 567

description: microRNA expression

value: mild


title: 509

description: microRNA expression


title: embryo at HH8_NP_rep1

tag: embryo stage

tag: tissue


title: Array2_Diabetes3

tag: array

tag: group

tag: hba1c 9months post diagnosis

tag: hba1c 12months post diagnosis

tag: insulin dose (u/kg/day) 12months post diagnosis


title: Array2_Diabetes2

tag: age at diagnosis

tag: gender

tag: hba1c 3months post diagnosis

tag: insulin dose (u/kg/day) 6months post diagnosis

tag: insulin dose (u/kg/day) 9months post diagnosis


title: embryo at HH8_NF_rep4

source_name: cranial neural fold, HH8

value: cranial neural fold (NF)


title: 567_2

description: microRNA expression

tag: age

tag: Sex

tag: kco% predicted


title: Array2_Healthy4

tag: insulin dose (u/kg/day) 3months post diagnosis

tag: hba1c 6months post diagnosis


title: Array2_Diabetes5


title: embryo at HH8_NF_rep3

tag: embryo stage


title: embryo at HH8_NF_rep2

tag: tissue


title: 484

description: microRNA expression

tag: pack years

tag: age quit smoking

tag: copd status


title: 479

description: microRNA expression


title: 467

description: microRNA expression


title: 406

description: microRNA expression


title: 365

description: microRNA expression


title: 368

description: microRNA expression


title: 473

description: microRNA expression


title: 534

description: microRNA expression


title: embryo at HH8_NF_rep1


title: 368_2

description: microRNA expression


title: 347

description: microRNA expression


title: 26

description: microRNA expression


title: Array1_Diabetes8

tag: array

tag: group

tag: hba1c 9months post diagnosis

tag: hba1c 12months post diagnosis


title: Array2_Healthy1

tag: age at diagnosis

tag: gender

tag: hba1c 3months post diagnosis

tag: insulin dose (u/kg/day) 12months post diagnosis


title: Array2_Healthy2

tag: insulin dose (u/kg/day) 6months post diagnosis

tag: insulin dose (u/kg/day) 9months post diagnosis


title: Epithelial Live N. meningitidis PilE- 7h rep4

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

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

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

description: Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX7.3 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 50th percentile.

source_name: 16HBE14 human bronchial epithelial cells,7h,Live N. meningitidis PilE-

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification 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 NanoDrop 1000 instrument.

tag: cell type

tag: infection status

value: Live N. meningitidis PilE-

tag: time (hours)


title: Array1_Diabetes6

tag: insulin dose (u/kg/day) 3months post diagnosis

tag: hba1c 6months post diagnosis


title: 111

description: microRNA expression

tag: age

tag: Sex

tag: kco% predicted

tag: pack years

tag: age quit smoking


title: 322

description: microRNA expression

tag: copd status


title: Epithelial Live N. meningitidis PilE- 7h rep3

description: Replicate 3

value: 16HBE14 human bronchial epithelial cells


title: Epithelial Live N. meningitidis PilE- 6h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,6h,Live N. meningitidis PilE-


title: Epithelial Live N. meningitidis PilE- 7h rep2

description: Replicate 2


title: Epithelial Live N. meningitidis PilE- 7h rep1

description: Replicate 1


title: Array1_Diabetes5

tag: array

tag: group

value: Diabetes Group A

tag: age at diagnosis

value: no visit

tag: hba1c 9months post diagnosis

tag: hba1c 12months post diagnosis


title: Array1_Diabetes4

value: Diabetes Group B

tag: gender

tag: hba1c 3months post diagnosis

tag: insulin dose (u/kg/day) 6months post diagnosis

tag: insulin dose (u/kg/day) 9months post diagnosis

tag: insulin dose (u/kg/day) 12months post diagnosis


title: non-degenerative disc, rep2

city: Taoyuan

first: Tsung-Ting

last: Tsai

address: No.5 Fushing St., Kweishan Township

department: Department of Orthopaedic Surgery

country: Taiwan

institute: Chang Gung Memorial Hospital

hyb_protocol: 10 μg fragmented and labeled cDNA were hybridized for 16 hr at 45°C in GeneChip® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using Robust Multichip Average (RMA) for normalization and MATLAB for log ratio.

source_name: non-degenerative disc

label_protocol: One-cycle cDNA synthesis was performed from 6 μg total RNA according to the standard Affymetrix protocol in GeneChip® Expression Analysis Technical Manual.

growth_protocol: The disc tissues were cultured as explants in DMEM supplemented with 10% FBS and antibiotics at 37°C in a 5% CO2 humidified incubator. When nucleus pulposus cells reached confluence, they were lifted using a trypsin-EDTA acid solution (0.25%, 1 mM) and subcultured in 10-cm dishes.

extract_protocol: TRIzol extraction procedure of total RNA from nucleus pulposus cells was performed according phenol-chloroform method.

treatment_protocol: No special treatment was applied on nucleus pulposus cells.

tag: tissue

value: human intervertebral disc from young patient

tag: diagnosis

value: adolescent idiopathic scoliosis


title: non-degenerative disc, rep3

tag: age


title: Epithelial Live N. meningitidis PilE- 6h rep3

description: Replicate 3

tag: cell type

tag: infection status

tag: time (hours)


title: degenerative disc, rep3

source_name: degenerative disc

value: human intervertebral disc from elderly patient

value: degenerative disc disease


title: degenerative disc, rep2


title: Array1_Diabetes3

tag: insulin dose (u/kg/day) 3months post diagnosis

tag: hba1c 6months post diagnosis


title: Epithelial Live N. meningitidis PilE- 6h rep1

description: Replicate 1


title: Array1_Diabetes7

tag: array

tag: group


title: Epithelial Live N. meningitidis PilE- 6h rep2

description: Replicate 2


title: non-degenerative disc, rep1


title: degenerative disc, rep1


title: Array1_Diabetes2

tag: age at diagnosis

tag: hba1c 9months post diagnosis


title: propylene glycol 3

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

hyb_protocol: Array hybridization were performed as recommended by Affymetrix standard protocol.

scan_protocol: GeneChips were scanned using the Gene Chip GCS3000 high-resolution scanner with auto-loading carousel.

data_processing: Raw CEL files were analyzed using robust multi-array average for normalization and calculation of probe intensities.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655_2g/L propylene glycol

label_protocol: End-terminus biotin labeling using Affymetrix GeneChip Labeling Kit.

growth_protocol: Propylene glycol-evolved E. coli K12 MG1655 was cultivated in 2g/L propylene glycol or 2g/L glycerol M9 minimal media at 37 degree and cells were harvested at mid-log phase (OD600 ~ 0.3) for total RNA isolation.

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) with DNaseI treatment in accordance with manufacturer’s instruction.

treatment_protocol: For RNA integrity and purity the cells were treated by 2 vol of RNAprotect Bacteria Reagent (Qiagen).

tag: genotype/variation

value: Propylene glycol-evolved E. coli K12 MG1655 to metabolize propylene glycol under aerobic condition

tag: m9 minimal media supplemented with

value: 2g/L propylene glycol


title: glycerol 3

source_name: E. coli K12 MG1655_2g/L glycerol

value: 2g/L glycerol


title: propylene glycol 2


title: propylene glycol 1


title: glycerol 1


title: glycerol 2


title: Array1_Healthy2

value: Healthy

value: adult

tag: gender

value: M

tag: hba1c 3months post diagnosis

value: not applicable

tag: insulin dose (u/kg/day) 6months post diagnosis

tag: hba1c 12months post diagnosis


title: Array1_Diabetes1

tag: insulin dose (u/kg/day) 9months post diagnosis

tag: insulin dose (u/kg/day) 12months post diagnosis

value: not available


title: Array1_Healthy1


title: Epithelial Live N. meningitidis PilE- 5h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,5h,Live N. meningitidis PilE-

tag: cell type

value: Live N. meningitidis PilE-


title: BEAS-2B-miR34c transfected_replicate

description: Replicate

data_processing: The data were normalised to the 75th percentile using quantile normalisation with IlluminaGUI in R

source_name: Lung Epithelium

growth_protocol: BEAS-2B (CRL-9609) was cultured in RPMI supplemented with 10% Fetal Bovine Serum and antibiotics. HFL 1 (CCL-153) was cultured in DMEM supplemented with 10% Fetal Bovine Serum

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.

treatment_protocol: Human miR-34c-5p expression was increased in BEAS-2B and HFL 1 cell lines using 50nM of miR-34c synthetic premiR obtained from Ambion following manufacturers instructions

tag: cell line

tag: transfection

value: miR34c transfected


title: Epithelial Live N. meningitidis PilE- 5h rep2

description: Replicate 2

value: 16HBE14 human bronchial epithelial cells

tag: infection status

tag: time (hours)


title: BEAS-2B-Scrambled transfected

value: Scrambled transfected


title: Epithelial Live N. meningitidis PilE- 5h rep1

description: Replicate 1


title: Epithelial Live N. meningitidis PilE- 4h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,4h,Live N. meningitidis PilE-


title: ABI3:GR DEX induced 1

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

country: Germany

institute: IPK

description: gene expression after 4h treatment with DEX

hyb_protocol: 1.65 µg of Cy3 labelled cRNA was fragmented according to the manufacturer's instruction. 1.425 µg of fragmented cRNA (conc:15 ng/µl) was hybridized at 65°C, 10 rpm, 17 h in an Agilent hybridization oven

scan_protocol: Scanning was performed using an Agilent DNA Microarray Scanner (Model G2505C) and Scan Control Software (version A.8.3.1) of Agilent

data_processing: Primary data analysis was performed using Agilent's Feature Extraction Software (version 10.7.3.1)

organism: Arabidopsis thaliana

source_name: whole seedling

label_protocol: Cyanin 3 labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit, One color (#5190-2305) of Agilent Technologies according to the manufacturers instructions

growth_protocol: Seedlings were grown on MS-agar plates, supplemented with selective antibiotic, 16 h light/ 8h dark

extract_protocol: Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: Two weeks old seedlings of wildtype (WT, Col-0) and ABI3:GR transgenics were incubated in liquid MS media supplemented with either Abscisic acid (ABA;10 µM) or Dexamethasone (DEX; 30 µM) or both; an identical volume of ethanol used as solute for ABA and DEX was added in the mock treatment

tag: developmental stage according to boyes et. al 2001

tag: treatment

value: 4h treatment with DEX


title: Epithelial Live N. meningitidis PilE- 4h rep3

description: Replicate 3


title: ABI3:GR ABA+DEX induced 2

description: gene expression after 4h treatment with ABA and DEX

value: 4h treatment with ABA and DEX


title: ABI3:GR ABA induced 2

description: gene expression after 4h treatment with ABA

value: 4h treatment with ABA


title: HFL 1-Scrambled transfected_replicate

description: Replicate

source_name: Lung Fibroblast

value: HFL 1


title: BEAS-2B-miR34c transfected


title: HFL 1-Scrambled transfected


title: ABI3:GR uninduced 2

description: gene expression after 4h mock treatment

value: 4h mock treatment


title: WT ABA+DEX induced 2

value: WT, Col-0


title: ABI3:GR uninduced 1

description: gene expression after 4h mock treatment


title: ABI3 ChIP-chip_bio2_array 1

type: genomic

description:
ABI3_bio2_array 1
biological replicate 2
Agilent Feature Extraction file:
US81403230_251479810018_S01_ChIP_105_Dec08.txt

hyb_protocol: 5 µg of both labeled samples were combined and mixed with Agilent-Blocking and -Hybridization buffer and 50 µg Cot-1DNA, f.v. 520 µl. After incubation for 3 min at 95°C and 30 min at 37°C, followed by centrifugation (1 min, 17,900g), 460 µl of the supernatant were used for hybridisation with each of the two 244K arrays in an Agilent-Hybrdization oven at 65°C (20rpm, 40 h), followed by sequential washing steps (performed by ATLAS GmbH Berlin).

data_processing: For primary data processing Agilent Feature Extraction Software (Version 10.5.1.1) was used.

molecule: genomic DNA

source_name: Control (input) non-immunoprecipitated chromatin fragments, seeds

label_protocol: DNA fragments were labeled  with Cy3-dUTP(ChIP sample) and Cy5-dUTP (control) using the Agilent Genomic DNA labelling Kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Arabidopsis plants were grown on soil, with a 16 h light/ 8 h dark cycle

extract_protocol: Chromatin was isolated from unripe seeds of Arabidopsis thaliana Col-0, harvested 11-13 days after pollination. Cross-linking was done with 1% formaldehyde  for 20 min under vacuum, terminated by addition of glycine with a final concentration of 125 mM. Seeds were Potter-homogenized, filtered and the nuclei collected by centrifugation. Nuclear membranes were dissolved with detergents and  the chromatin was collected by high speed centrifugation. Chromatin was fragmented to an average size of 500 bp by ultra sonic treatment.   10 µg chromatin were combined with 2 µg anti-ABI3 antibody. The antibody-chromatin complex was captured by protein A coated magnetic beads (Invitrogen). After different washings the TF-DNA complex was eluted from the beads at 65°C for 15 min using 1% SDS. Eluates were incubated overnight at 65°C to reverse the cross-links. DNA  fragments were purified using a QIAquick PCR Purification Kit (Qiagen) and their concentration was determined with a NanoDrop 3300 (Thermo Fisher Scientific) fluorescence spectrophotometer. An aliquot (0.5 µg) of non-immunoprecipitated chromatin served as input control.   DNA fragments were blunted and ligated  with the  adapters oJW102  and oJW103 (Young lab:jura.wi.mit.edu/young_public/hESregulation/ChIP.html).  Adapter-ligated fragments were amplified using oJW102 as sole primer.

tag: ecotype

tag: tissue

value: seed

tag: days after pollination

source_name: Chromatin fragments precipitated with anti-ABI3 antibody, seeds

tag: chip antibody

value: anti-ABI3 (raised against amino acid 2-237 of ABI3 in rabbits; selfmade)


title: Epithelial Live N. meningitidis PilE- 5h rep3

description: Replicate 3


title: Epithelial Live N. meningitidis PilE- 3h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,3h,Live N. meningitidis PilE-


title: Epithelial Live N. meningitidis PilE- 4h rep1

description: Replicate 1


title: WT DEX induced 2

tag: genotype/variation


title: ABI3:GR ABA induced 1


title: ABI3:GR ABA+DEX induced 1


title: Epithelial Live N. meningitidis PilE- 4h rep2

description: Replicate 2


title: WT ABA+DEX induced 1


title: ABI3 ChIP-chip_bio1_array 1

description:
ABI3_bio1_array 1
biological replicate 1
Agilent Feature Extraction file:
US81403230_251479810017_S01_ChIP_105_Dec08.txt


title: WT ABA induced 2


title: HFL 1-miR34c transfected


title: Epithelial Live N. meningitidis PilE- 3h rep1

description: Replicate 1


title: WT ABA induced 1


title: Patient 26 (non small cell lung carcinoma)

city: Stanford

first: Olivier

last: Gevaert

address: 1265 Welch Road

department: Medicine

institute: Stanford University

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: Normalization was done by log2 transformation and quantile normalization. Probe selection was done using significat detection-pvalues in at least 60% of the samples at a p-value threshold of 0.05

source_name: tumor

label_protocol: According to Illumina protocol.

extract_protocol: Qiagen RNA isolation kit

value: non small cell lung carcinoma

tag: histology

value: adeno


title: V4.LiC.042Tla

city: Daejeon

first: Sang-Yeop

last: Lee

address: 125 Gwahangno, Yuseong-gu

country: South Korea

institute: KRIBB

description: To export to gene expression data based on unique gene, we use Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using quantile normalization and log2 transformation.

source_name: Undifferentiated HCC (GIII/IV) tissues

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to the Illumina recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer's protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide.

tag: grade

value: GIII/IV


title: V4.LiC.041Tla


title: HFL 1-miR34c transfected_replicate

description: Replicate


title: Epithelial Live N. meningitidis PilE- 3h rep2

description: Replicate 2


title: Epithelial Live N. meningitidis PilE- 0h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,0h,Live N. meningitidis PilE-


title: Patient 25 (non small cell lung carcinoma)


title: WT uninduced 2

description: gene expression after 4h mock treatment


title: V4.LiC.040Tla


title: V4.LiC.039Tla


title: ABI3:GR DEX induced 2


title: WT DEX induced 1


title: WT uninduced 1

description: gene expression after 4h mock treatment


title: Patient 24 (non small cell lung carcinoma)

value: squamous


title: Epithelial Live N. meningitidis PilE- 0h rep3

description: Replicate 3


title: V4.LiC.037Tla


title: Patient 23 (non small cell lung carcinoma)


title: V4.LiC.036Tla


title: Epithelial Live N. meningitidis PilE- 0h rep2

description: Replicate 2


title: Epithelial Live N. meningitidis PilE- 3h rep3

description: Replicate 3


title: Epithelial Live N. meningitidis PilE- 0h rep1

description: Replicate 1


title: V4.LiC.038Tla


title: Patient 22 (non small cell lung carcinoma)


title: V4.LiC.035Tla


title: Patient 21 (non small cell lung carcinoma)


title: Epithelial Live N. meningitidis cap- 7h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,7h,Live N. meningitidis cap-

value: Live N. meningitidis cap-


title: V4.LiC.033Tea

source_name: Differentiated HCC (GI/II) tissues

value: differentiated hepatocellular carcinoma

value: GI/II


title: V4.LiC.030Tea


title: V4.LiC.029Tea


title: V4.LiC.031Tea


title: Epithelial Live N. meningitidis cap- 7h rep2

description: Replicate 2

value: 16HBE14 human bronchial epithelial cells


title: V4.LiC.034Tla


title: Epithelial Live N. meningitidis cap- 7h rep4

description: Replicate 4


title: Epithelial Live N. meningitidis cap- 6h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,6h,Live N. meningitidis cap-


title: V4.LiC.028Tea


title: V4.LiC.032Tea


title: Patient 18 (non small cell lung carcinoma)


title: V4.LiC.027Tea


title: V4.LiC.023Tla


title: Epithelial Live N. meningitidis cap- 6h rep2

description: Replicate 2


title: Epithelial Live N. meningitidis cap- 7h rep1

description: Replicate 1


title: V4.LiC.020Tla


title: Patient 15 (non small cell lung carcinoma)


title: Patient 17 (non small cell lung carcinoma)


title: Patient 19 (non small cell lung carcinoma)


title: Epithelial Live N. meningitidis cap- 6h rep3

description: Replicate 3


title: V4.LiC.026Tea


title: V4.LiC.021Tla


title: Patient 16 (non small cell lung carcinoma)


title: Patient 20 (non small cell lung carcinoma)


title: Patient 14 (non small cell lung carcinoma)


title: V4.LiC.022Tla


title: V4.LiC.024Tla


title: V4.LiC.019Tla


title: V4.LiC.025Tea


title: Epithelial Live N. meningitidis cap- 6h rep1

description: Replicate 1


title: Epithelial Live N. meningitidis cap- 5h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,5h,Live N. meningitidis cap-


title: BEAS-2B-Scrambled transfected_replicate

description: Replicate

value: Scrambled transfected


title: V4.LiC.018Tla


title: Epithelial Live N. meningitidis cap- 5h rep3

description: Replicate 3


title: Patient 13 (non small cell lung carcinoma)


title: Patient 12 (non small cell lung carcinoma)


title: Patient 11 (non small cell lung carcinoma)


title: V4.LiC.012Tea


title: Epithelial Live N. meningitidis cap- 5h rep2

description: Replicate 2


title: V4.LiC.013Tla


title: Epithelial Live N. meningitidis cap- 5h rep1

description: Replicate 1


title: V4.LiC.014Tla


title: V4.LiC.016Tla


title: V4.LiC.017Tla


title: V4.LiC.011Tea


title: Epithelial Live N. meningitidis cap- 4h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,4h,Live N. meningitidis cap-


title: Patient 8 (non small cell lung carcinoma)


title: V4.LiC.015Tla


title: V4.LiC.007Tea


title: Patient 9 (non small cell lung carcinoma)


title: NNK+SECY 3

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description: NNK injected and selenocystine in diet

hyb_protocol: Agilent two-color GE hyb/wash protocol

scan_protocol: Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802

data_processing: Feature extraction and processing - Agilent FE8.1.1.1 protocol, lowess normaliztion and background subtracted

organism: Mus musculus

source_name: mouse lung

label_protocol: Agilent two-color LRILAK labeling protocol

growth_protocol: Animals were housed on hardwood bedding in a temperature and humidity controlled environment on a 12 hr light/dark cycle and given free access to food and water. Animals were stabilized on an unsupplemented AIN-76 diet for one week prior to the start of the experiment.

extract_protocol: Animals were sacrificed thirteen days after NNK administration. Lung tissue was harvested, immediately homogenized in Trizol and frozen. RNA was purified by the Trizol protocol followed by Qiagen RNeasy clean-up and then quantified on a Nanodrop ND-1000 spectrophotometer. The quality of the RNA samples collected was determined using the Experion Automated Electrophoresis Station (Biorad) with the RNA StdSens Analysis Kit. All samples displayed RNA Quality Index (RQI) levels greater than 9.

treatment_protocol: Animals were either injected with NNK (single IP injection with 10 uM NNK in 0.2 mL saline), supplemented with 15 ppm selenocystine in their diet, or given both treatments.

tag: strain

value: A/J

tag: gender

value: female

tag: treatment group

value: NNK+SECY

value: NNK+selenocytine biological replicate

source_name: mouse lung control

tag: reference

value: equal mix of untreated 1-4


title: Patient 7 (non small cell lung carcinoma)

tag: cell type


title: NNK+SECY 4

description: NNK injected and selenocystine in diet


title: Epithelial Live N. meningitidis cap- 4h rep4

description: Replicate 4


title: V4.LiC.010Tea


title: V4.LiC.008Tea


title: Patient 10 (non small cell lung carcinoma)


title: V4.LiC.009Tea


title: Epithelial Live N. meningitidis cap- 4h rep1

description: Replicate 1


title: NNK+SECY 2

description: NNK injected and selenocystine in diet


title: V4.LiC.006Tea


title: Patient 6 (non small cell lung carcinoma)


title: Epithelial Live N. meningitidis cap- 3h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,3h,Live N. meningitidis cap-


title: V4.LiC.005Tea


title: Epithelial Live N. meningitidis cap- 3h rep3

description: Replicate 3


title: Patient 5 (non small cell lung carcinoma)


title: Patient 1 (non small cell lung carcinoma)


title: Epithelial Live N. meningitidis cap- 3h rep1

description: Replicate 1


title: Epithelial Live N. meningitidis cap- 3h rep2

description: Replicate 2


title: V4.LiC.004Tea


title: SECY 1

description: selenocystine in diet

value: SECY

value: selenocytine (15 ppm in diet) treated


title: Epithelial Live N. meningitidis cap- 0h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,0h,Live N. meningitidis cap-


title: SECY 3

description: selenocystine in diet

value: selenocytine biological replicate


title: Patient 2 (non small cell lung carcinoma)

value: non small cell lung carcinoma


title: V4.LiC.020NT

source_name: Liver cirrhosis tissues

value: cirrhotic liver


title: Patient 3 (non small cell lung carcinoma)

value: adeno


title: Patient 4 (non small cell lung carcinoma)


title: NNK 4

description: NNK injected mice

value: NNK

value: NNK biological replicate


title: V4.LiC.021NT


title: Epithelial Live N. meningitidis cap- 0h rep3

description: Replicate 3

value: Live N. meningitidis cap-


title: V4.LiC.001Tea

value: differentiated hepatocellular carcinoma

value: GI/II


title: NNK+SECY 1

description: NNK injected and selenocystine in diet

value: NNK+selenocytine treated


title: Epithelial Live N. meningitidis cap- 0h rep2

description: Replicate 2

value: 16HBE14 human bronchial epithelial cells


title: V4.LiC.003Tea


title: NNK 2

description: NNK injected mice

value: A/J

value: female


title: V4.LiC.019NT


title: Epithelial Live N. meningitidis cap- 0h rep1

description: Replicate 1


title: NNK 3

description: NNK injected mice


title: SECY 2

description: selenocystine in diet


title: SECY 4

description: selenocystine in diet


title: V4.LiC.002Tea


title: NNK 1

description: NNK injected mice

value: NNK (10 uM in 200 ul) treated


title: Epithelial Live WT N. meningitidis 7h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,7h,Live WT N. meningitidis

value: Live WT N. meningitidis


title: V4.LiC.016NT


title: V4.LiC.017NT


title: Epithelial Live WT N. meningitidis 7h rep1

description: Replicate 1


title: Untreated 4

description: untreated control

value: Untreated

value: control biological replicate

value: equal mix of untreated 1-4


title: Epithelial Live WT N. meningitidis 7h rep3

description: Replicate 3


title: V4.LiC.015NT


title: V4.LiC.018NT


title: Epithelial Live WT N. meningitidis 7h rep2

description: Replicate 2


title: Epithelial Live WT N. meningitidis 6h rep2

description: Replicate 2

source_name: 16HBE14 human bronchial epithelial cells,6h,Live WT N. meningitidis


title: Untreated 2

description: untreated control


title: Epithelial Live WT N. meningitidis 6h rep3

description: Replicate 3


title: Epithelial Live WT N. meningitidis 6h rep1

description: Replicate 1


title: V4.LiC.010NT


title: V4.LiC.013NT


title: V4.LiC.014NT


title: V4.LiC.011NT


title: Imbibed 35S-GSH1 seeds_4˚C_24hr_rep1

city: Kaga-gun

first: Aya

last: Hatano-Iwasaki

state: Okayama

address: 7549-1 Yoshikawa, Kibichuo-cho

country: Japan

institute: Okayama Prefectural Technology Center for  Agriculture, Forestry and Fisheries, Research Institute for Biological Sciences

description: Gene expression data from seeds imbibed with vernalization of 35S-GSH1

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on  Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS) 1.4 using default analysis settings

source_name: Seeds of 35S-GSH1 imbibed at 4˚C for 24hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Affymetrix_Genechip_Expression Analysis Technical Manual; http://www.affymetrix.com).

extract_protocol: Total RNA extraction from seeds was performed using a CTAB-based method according to Mukai Y, Yamamoto N (1997) DNA and RNA isolation method of woody plants. In: PCR Experimental Protocols for Plant (eds. Shimamoto K, Sasaki T), pp. 57-62. Shujunsha Co. Ltd, Tokyo.

treatment_protocol: Seeds were imbibed at 22˚C or 4˚C for 24 hour.

tag: ecotype background

value: Columbia (Col-0)

value: 35S-GSH1 (GSH1 overexpression)

value: seeds


title: Untreated 1

description: untreated control

value: control


title: Untreated 3

description: untreated control


title: Epithelial Live WT N. meningitidis 6h rep4

description: Replicate 4

tag: infection status


title: Imbibed 35S-GSH1 seeds_22˚C_24hr_rep2

description: Gene expression data from seeds imbibed without vernalization of 35S-GSH1

source_name: Seeds of 35S-GSH1 imbibed at 22˚C for 24hr


title: Imbibed Col-0 seeds_4˚C_24hr_rep2

description: Gene expression data from seeds imbibed with vernalization of Col-0

source_name: Seeds of Col-0 imbibed at 4˚C for 24hr

value: wildtype


title: Imbibed 35S-GSH1 seeds_4˚C_24hr_rep2


title: V4.LiC.012NT

value: cirrhotic liver


title: V4.LiC.009NT


title: Epithelial Live WT N. meningitidis 5h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,5h,Live WT N. meningitidis

tag: time (hours)


title: Imbibed Col-0 seeds_4˚C_24hr_rep1


title: Imbibed 35S-GSH1 seeds_22˚C_24hr_rep1


title: Imbibed Col-0 seeds_22˚C_24hr_rep2

description: Gene expression data from seeds imbibed without vernalization of Col-0

source_name: Seeds of Col-0 imbibed at 22˚C for 24hr


title: Epithelial Live WT N. meningitidis 5h rep2

description: Replicate 2


title: Imbibed Col-0 seeds_22˚C_24hr_rep1


title: Epithelial Live WT N. meningitidis 5h rep3

description: Replicate 3


title: Epithelial Live WT N. meningitidis 4h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,4h,Live WT N. meningitidis


title: Epithelial Live WT N. meningitidis 4h rep4

description: Replicate 4


title: Epithelial Live WT N. meningitidis 4h rep1

description: Replicate 1


title: Epithelial Live WT N. meningitidis 5h rep1

description: Replicate 1


title: V4.LiC.006NT


title: Liver_Dox_CT44

city: Philadelphia

first: Michael

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

institute: UPenn

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing:
Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features.
Signal was calculated by RMA implemented in Affymetrix Expression Console.

Exons used in analysis: core

source_name: liver, Clock rescue

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Mice were housed in light-tight chambers and entrained to a 12 hours light, 12 hours dark environment before being released into constant darkness.

extract_protocol: Mice were euthanized in the dark, and liver samples were quickly excised.

treatment_protocol: Three days before the final lights off (at ZT12), experimental animals were treated with either water or doxycycline (30ug/ml; Sigma-Aldrich) supplied in the drinking water. Starting at CT48, four WT mice (two females and two males) and Clock–rescue mice (one female and one male) were sacrificed in the dark every two hours.

tag: strain/background

tag: genotype

value: Scg2::tTA; tetO::Clockwt; ClockD19/D65

value: doxycycline

value: liver

value: male and female

tag: sampling time


title: Liver_Dox_CT46

value: Scg2::tTA; tetO::Clockwt; ClockD19/D66

tag: treatment

tag: tissue


title: Epithelial Live WT N. meningitidis 4h rep2

description: Replicate 2

value: 16HBE14 human bronchial epithelial cells


title: Liver_Dox_CT38

value: Scg2::tTA; tetO::Clockwt; ClockD19/D62


title: V4.LiC.002NT


title: V4.LiC.004NT


title: V4.LiC.003NT


title: Epithelial Live WT N. meningitidis 3h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,3h,Live WT N. meningitidis

value: Live WT N. meningitidis


title: V4.LiC.001NT


title: V4.LiC.007NT


title: V4.Li.021N

source_name: Normal liver tissue

value: normal liver


title: V4.LiC.005NT


title: Liver_Dox_CT42

value: Scg2::tTA; tetO::Clockwt; ClockD19/D64


title: Epithelial Live WT N. meningitidis 3h rep4

description: Replicate 4


title: Liver_Dox_CT36

value: Scg2::tTA; tetO::Clockwt; ClockD19/D61


title: Epithelial Live WT N. meningitidis 3h rep2

description: Replicate 2


title: V4.LiC.008NT


title: Liver_Dox_CT34

value: Scg2::tTA; tetO::Clockwt; ClockD19/D60


title: Liver_Dox_CT40

value: Scg2::tTA; tetO::Clockwt; ClockD19/D63


title: V4.Li.019N


title: Epithelial Live WT N. meningitidis 3h rep1

description: Replicate 1


title: V4.Li.018N


title: Liver_Dox_CT30

value: Scg2::tTA; tetO::Clockwt; ClockD19/D58


title: Epithelial Live WT N. meningitidis 0h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,0h,Live WT N. meningitidis


title: Epithelial Live N. meningitidis cap- 4h rep2

description: Replicate 2

source_name: 16HBE14 human bronchial epithelial cells,4h,Live N. meningitidis cap-

value: Live N. meningitidis cap-


title: Liver_Dox_CT26

value: Scg2::tTA; tetO::Clockwt; ClockD19/D56


title: V4.Li.020N


title: V4.Li.017N


title: Liver_Dox_CT24

value: Scg2::tTA; tetO::Clockwt; ClockD19/D55


title: V4.Li.015N


title: Epithelial Killed WT N. meningitidis 7h rep2

description: Replicate 2

source_name: 16HBE14 human bronchial epithelial cells,7h,Killed WT N. meningitidis

value: Killed WT N. meningitidis


title: Epithelial Killed WT N. meningitidis 7h rep3

description: Replicate 3


title: Liver_Dox_CT22

value: Scg2::tTA; tetO::Clockwt; ClockD19/D54

value: doxycycline


title: V4.Li.016N


title: Liver_Dox_CT16

value: Scg2::tTA; tetO::Clockwt; ClockD19/D51

value: liver

value: male and female


title: Epithelial Live WT N. meningitidis 0h rep1

description: Replicate 1

value: 16HBE14 human bronchial epithelial cells


title: Liver_Dox_CT20

value: Scg2::tTA; tetO::Clockwt; ClockD19/D53


title: V4.Li.013N

value: normal liver


title: Epithelial Killed WT N. meningitidis 7h rep4

description: Replicate 4


title: Epithelial Live WT N. meningitidis 0h rep3

description: Replicate 3

value: Live WT N. meningitidis


title: V4.Li.014N


title: Epithelial Killed WT N. meningitidis 7h rep1

description: Replicate 1


title: Epithelial Killed WT N. meningitidis 6h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,6h,Killed WT N. meningitidis


title: Liver_Dox_CT18

value: Scg2::tTA; tetO::Clockwt; ClockD19/D52


title: V4.Li.012N


title: V4.Li.010N


title: Liver_Dox_CT14

value: Scg2::tTA; tetO::Clockwt; ClockD19/D50


title: V4.Li.011N


title: Epithelial Killed WT N. meningitidis 6h rep2

description: Replicate 2


title: Epithelial Killed WT N. meningitidis 6h rep3

description: Replicate 3


title: Liver_Dox_CT10

value: Scg2::tTA; tetO::Clockwt; ClockD19/D48


title: Liver_Dox_CT8

value: Scg2::tTA; tetO::Clockwt; ClockD19/D47


title: Liver_Dox_CT12

value: Scg2::tTA; tetO::Clockwt; ClockD19/D49


title: V4.Li.009N


title: Epithelial Killed WT N. meningitidis 6h rep1

description: Replicate 1


title: V4.Li.008N


title: Liver_Dox_CT6

value: Scg2::tTA; tetO::Clockwt; ClockD19/D46


title: Epithelial Killed WT N. meningitidis 5h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,5h,Killed WT N. meningitidis


title: V4.Li.007N


title: Epithelial Killed WT N. meningitidis 5h rep3

description: Replicate 3


title: V4.Li.005N


title: Epithelial Killed WT N. meningitidis 5h rep2

description: Replicate 2


title: V4.Li.003N


title: Epithelial Killed WT N. meningitidis 4h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,4h,Killed WT N. meningitidis


title: Liver_H2O_CT46

source_name: liver, Clock mutant

value: Scg2::tTA; tetO::Clockwt; ClockD19/D42

value: water


title: V4.Li.006N


title: V4.Li.002N


title: Epithelial Killed WT N. meningitidis 5h rep1

description: Replicate 1

value: Killed WT N. meningitidis


title: Liver_Dox_CT2

value: Scg2::tTA; tetO::Clockwt; ClockD19/D44

value: doxycycline


title: Liver_Dox_CT0

value: Scg2::tTA; tetO::Clockwt; ClockD19/D43

value: liver


title: Liver_Dox_CT4

value: Scg2::tTA; tetO::Clockwt; ClockD19/D45

value: male and female


title: Liver_H2O_CT40

value: Scg2::tTA; tetO::Clockwt; ClockD19/D39


title: Liver_H2O_CT42

value: Scg2::tTA; tetO::Clockwt; ClockD19/D40


title: Epithelial Killed WT N. meningitidis 4h rep3

description: Replicate 3

value: 16HBE14 human bronchial epithelial cells


title: V4.Li.001N

value: normal liver


title: Epithelial Killed WT N. meningitidis 4h rep2

description: Replicate 2


title: Liver_Dox_CT28

value: Scg2::tTA; tetO::Clockwt; ClockD19/D57


title: Epithelial Killed WT N. meningitidis 4h rep1

description: Replicate 1


title: Epithelial Killed WT N. meningitidis 3h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,3h,Killed WT N. meningitidis


title: Liver_H2O_CT44

value: Scg2::tTA; tetO::Clockwt; ClockD19/D41


title: Liver_H2O_CT38

value: Scg2::tTA; tetO::Clockwt; ClockD19/D38


title: V4.Li.004N


title: Liver_H2O_CT36

value: Scg2::tTA; tetO::Clockwt; ClockD19/D37


title: Epithelial Killed WT N. meningitidis 3h rep1

description: Replicate 1


title: Epithelial Killed WT N. meningitidis 3h rep2

description: Replicate 2


title: Epithelial Killed WT N. meningitidis 3h rep4

description: Replicate 4


title: Epithelial Killed WT N. meningitidis 0h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,0h,Killed WT N. meningitidis


title: Epithelial Killed WT N. meningitidis 0h rep3

description: Replicate 3


title: Liver_H2O_CT28

value: Scg2::tTA; tetO::Clockwt; ClockD19/D33


title: Epithelial Killed WT N. meningitidis 0h rep1

description: Replicate 1


title: Liver_H2O_CT30

value: Scg2::tTA; tetO::Clockwt; ClockD19/D34

value: water


title: Liver_H2O_CT24

value: Scg2::tTA; tetO::Clockwt; ClockD19/D31


title: Epithelial Killed WT N. meningitidis 0h rep2

description: Replicate 2

value: Killed WT N. meningitidis


title: Liver_H2O_CT34

value: Scg2::tTA; tetO::Clockwt; ClockD19/D36


title: Epithelial Live WT N. lactamica 7h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,7h,Live WT N. lactamica

value: Live WT N. lactamica


title: Liver_H2O_CT22

value: Scg2::tTA; tetO::Clockwt; ClockD19/D30

value: liver


title: Epithelial Live WT N. lactamica 7h rep3

description: Replicate 3


title: Liver_H2O_CT20

value: Scg2::tTA; tetO::Clockwt; ClockD19/D29

value: male and female


title: Epithelial Live WT N. lactamica 6h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,6h,Live WT N. lactamica


title: Epithelial Live WT N. lactamica 6h rep4

description: Replicate 4

value: 16HBE14 human bronchial epithelial cells


title: Liver_H2O_CT26

value: Scg2::tTA; tetO::Clockwt; ClockD19/D32


title: Liver_H2O_CT16

value: Scg2::tTA; tetO::Clockwt; ClockD19/D27


title: Epithelial Live WT N. lactamica 7h rep1

description: Replicate 1


title: Liver_H2O_CT14

value: Scg2::tTA; tetO::Clockwt; ClockD19/D26


title: Epithelial Live WT N. lactamica 7h rep2

description: Replicate 2


title: Epithelial Live WT N. lactamica 6h rep2

description: Replicate 2


title: Liver_H2O_CT10

value: Scg2::tTA; tetO::Clockwt; ClockD19/D24


title: Liver_H2O_CT8

value: Scg2::tTA; tetO::Clockwt; ClockD19/D23


title: Liver_H2O_CT12

value: Scg2::tTA; tetO::Clockwt; ClockD19/D25


title: Liver_Dox_CT32

value: Scg2::tTA; tetO::Clockwt; ClockD19/D59

value: doxycycline


title: Epithelial Live WT N. meningitidis 0h rep2

description: Replicate 2

value: Live WT N. meningitidis


title: Epithelial Live WT N. lactamica 6h rep1

description: Replicate 1


title: Epithelial Live WT N. lactamica 5h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,5h,Live WT N. lactamica


title: Liver_H2O_CT18

value: Scg2::tTA; tetO::Clockwt; ClockD19/D28

value: water


title: SC24 VS SC48 [dye swap]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: dye-swap

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Neurospora crassa

source_name: perithecia

label_protocol: 2 µg of mRNA were primed with .5 µl of 10 µM MTP or Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 40 U SuperScript II RTase (Invitrogen), and .8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: Synthetic Crossing Meidum (SCM) or Carrot Agar (CA) room temperature

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

treatment_protocol: constant light, crossing between Mat A protoperithecia and Mat a conidia

tag: growth medium

value: CA

tag: time


title: SS72 VS SC72 [dye swap]

description: dye-swap

value: SCM


title: SS96 VS SS120 [dye swap]

description: dye-swap


title: Liver_H2O_CT6

value: Scg2::tTA; tetO::Clockwt; ClockD19/D22

value: liver


title: Epithelial Live WT N. lactamica 5h rep1

description: Replicate 1

value: Live WT N. lactamica


title: Epithelial Live WT N. lactamica 5h rep2

description: Replicate 2

value: 16HBE14 human bronchial epithelial cells


title: SC24 VS SC48

description: dye-swap


title: Epithelial Live WT N. lactamica 5h rep3

description: Replicate 3


title: Liver_H2O_CT0

value: Scg2::tTA; tetO::Clockwt; ClockD19/D19

value: male and female


title: SS48 vs SC48 [dye swap]

description: dye-swap


title: SS120 VS SS96

description: dye-swap


title: Liver_WT_CT42

source_name: liver, WT

value: wildtype


title: Liver_H2O_CT4

value: Scg2::tTA; tetO::Clockwt; ClockD19/D21


title: SC72 VS SS72

description: dye-swap


title: Liver_H2O_CT2

value: Scg2::tTA; tetO::Clockwt; ClockD19/D20


title: Epithelial Live WT N. lactamica 4h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,4h,Live WT N. lactamica


title: SC96 vs SC120 [dye swap]

description: dye-swap


title: THP1 H3K4me3

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description:
H3K4me3_THP1
H3K4me3 profile with THP1 cells.

hyb_protocol: According to the NimbleGen kit.

scan_protocol: NimbleScan's default procedures using an Agilent Scanner.

data_processing: Mean-centered log2 ratios (Cy5/Cy3) (NimbleScan).

source_name: H3K4me3 ChIP with THP1 cells

label_protocol: According to the standard NimbleGen protocol.

growth_protocol: RPMI medium

extract_protocol: Peripheral blood monocytes were freshly isolated from normal and T1D subjects and then crosslinked in 1% formaldehyde, sonicated to shear DNA, and immunoprecipitated with antibodies to histone PTMs. IP with no antibody was used as the Input control.

treatment_protocol: None.

tag: cell line

tag: chip antibody

tag: antibody vendor

value: Millipore

tag: antibody catalog #

source_name: THP1, no antibody control


title: Epithelial Live WT N. lactamica 4h rep3

description: Replicate 3


title: Epithelial Live WT N. lactamica 4h rep2

description: Replicate 2


title: Liver_WT_CT44

tag: gender


title: Epithelial Live WT N. lactamica 4h rep1

description: Replicate 1


title: Liver_WT_CT46


title: SS0 vs SS144 [dye swap]

description: dye-swap

value: SCm


title: SC48 vs SS48

description: dye-swap


title: Epithelial Live WT N. lactamica 3h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,3h,Live WT N. lactamica


title: Liver_WT_CT40


title: THP1 p300

description:
p300_THP1
p300 profile with THP1 cells.

source_name: p300 ChIP with THP1 cells

value: Abcam


title: THP1 H3K4me1

description:
H3K4me1_THP1
H3K4me1 profile with THP1 cells.

source_name: H3K4me1 ChIP with THP1 cells


title: Epithelial Live WT N. lactamica 3h rep3

description: Replicate 3


title: Liver_WT_CT36


title: Normal monocytes H4K16Ac

description:
H4K16ac_NORMAL
H4K16Ac profile with pooled normal samples.

source_name: H4K16Ac ChIP with pooled normal samples

value: peripheral blood monocytes

tag: disease status

value: healthy, non-diabetic

source_name: monocyte, no antibody control


title: Normal monocytes H3K9me2

description:
H3K9me2_NORMAL
H3K9me2 profile with pooled normal samples.

source_name: H3K9me2 ChIP with pooled normal samples

tag: cell type


title: T1D monocytes H3K9me2

description:
H3K9me2_T1D
H3K9me2 profile with pooled type 1 diabetes samples.

source_name: H3K9me2 ChIP with pooled type 1 diabetes samples

value: type 1 diabetes


title: T1D monocytes H3K4me3

description:
H3K4me3_T1D
H3K4me3 profile with pooled type 1 diabetes samples.

source_name: H3K4me3 ChIP with pooled type 1 diabetes samples


title: SC120 vs SC144 [dye swap]

description: dye-swap

value: CA


title: T1D monocytes H4k16Ac

description:
H4K16ac_T1D
H4K16Ac profile with pooled type 1 diabetes samples.

source_name: H4K16Ac ChIP with pooled type 1 diabetes samples


title: Liver_WT_CT38

value: water


title: SS144 vs SS0

description: dye-swap

value: SCM


title: Epithelial Live WT N. lactamica 3h rep2

description: Replicate 2


title: Liver_WT_CT32

value: liver


title: Epithelial Live WT N. lactamica 3h rep1

description: Replicate 1

value: Live WT N. lactamica


title: Liver_WT_CT30


title: Normal monocytes H3K4me3

description:
H3K4me3_NORMAL
H3K4me3 profile with pooled normal samples.

source_name: H3K4me3 ChIP with pooled normal samples


title: SS72 vs SS96 [dye swap]

description: dye-swap


title: SS120 vs SC120 [dye swap]

description: dye-swap


title: Epithelial Live WT N. lactamica 0h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,0h,Live WT N. lactamica


title: Liver_WT_CT26


title: Epithelial Live WT N. lactamica 0h rep4

description: Replicate 4

value: 16HBE14 human bronchial epithelial cells


title: Liver_WT_CT28


title: Epithelial Live WT N. lactamica 0h rep2

description: Replicate 2


title: SC72 vs SC96 [dye swap]

description: dye-swap


title: TPA treated 168h

type: mixed

city: madison

first: James

last: Thomson

state: Wisconsin

address: 425 Henry Mall

department: Regenerative Biology

institute: Mogridge Institute for Research

description: the second channel (genomic DNA) serve as common reference across the experiments

hyb_protocol: Array hybridization, wash were performed according to NimbleGen’s recommended protocol

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and the PMT settings were followed by NimbleGen array manual

data_processing: 1. Image extraction: NimbleScan provided by NimbleGen is used to extract signal data from image files (*.TFF). Signal meansurements were saved in .pair files.  2. Normalization: Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.

source_name: TPA treated 168h

label_protocol: Amino Allyl labeling method

growth_protocol: Human ES cells (H9 cell line) were cultured in human ES cell culture medium preconditioned with irradiated mouse embryonic fibroblasts (MEF) on Matrigel (BD Biosciences, Bedford, MA) as described (Xu C, Inokuma MS, Denham J, et al. Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol. 2001;19:971-974). For routine maintenance, cells were passaged with 1mg/ml Collagenase (Invitrogen Corporation, Carlsbad, CA). For the TPA treatment time course experiment, cells were individualized with 0.05% Trypsin-EDTA, and seeded at 2 X 106 cells per 10 cm tissue culture dish. Twenty-four hours later, the cells formed small colonies with relatively uniform size (20-30 cells per colony).

extract_protocol: Total RNA was prepared with RNeasy Mini Kit (Qiagen, Inc., Valencia, CA) and subjected to on-column DNase treatment.

treatment_protocol: Cells were exposed to TPA at 50nM and were harvested at 0, 1, 3, 6, 12 18, 24, 30, 36, 42, 48, 72, 96, 168 hours after TPA treatment for RNA purification.

value: embryonic stem (ES)

source_name: undifferentiated H9 (common reference)


title: TPA treated 48h

source_name: TPA treated 48h


title: TPA treated 72h

source_name: TPA treated 72h


title: TPA treated 120h

source_name: TPA treated 120h


title: T1D monocytes H3K9Ac

description:
H3K9ac_T1D
H3K9Ac profile with pooled type 1 diabetes samples.

source_name: H3K9Ac ChIP with pooled type 1 diabetes samples


title: Normal monocytes H3K9Ac

description:
H3K9ac_NORMAL
H3K9Ac profile with pooled normal samples.

source_name: H3K9Ac ChIP with pooled normal samples


title: SC120 vs SS120

description: dye-swap

source_name: perithecia


title: Liver_WT_CT24

source_name: liver, WT

value: male and female


title: SS96 vs SS72

description: dye-swap


title: Epithelial Live WT N. lactamica 0h rep1

description: Replicate 1


title: Liver_WT_CT22

value: wildtype


title: SS120 vs SS144 [dye swap]

description: dye-swap


title: Epithelial Killed WT N. lactamica 7h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,7h,Killed WT N. lactamica

value: Killed WT N. lactamica


title: Epithelial Killed WT N. lactamica 7h rep3

description: Replicate 3


title: TPA treated 42h

source_name: TPA treated 42h


title: Liver_WT_CT16


title: Epithelial Killed WT N. lactamica 7h rep1

description: Replicate 1


title: Liver_WT_CT18


title: TPA treated 24h

source_name: TPA treated 24h


title: Liver_WT_CT14


title: SS24 vs SC24 [dye swap]

description: dye-swap


title: Epithelial Killed WT N. lactamica 6h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,6h,Killed WT N. lactamica


title: SC24 vs SS24

description: dye-swap


title: TPA treated 36h

source_name: TPA treated 36h


title: TPA treated 30h

source_name: TPA treated 30h


title: Liver_WT_CT20


title: SC48 vs SC72 [dye swap]

description: dye-swap


title: TPA treated 12h

source_name: TPA treated 12h


title: Epithelial Killed WT N. lactamica 6h rep2

description: Replicate 2


title: Epithelial Killed WT N. lactamica 7h rep2

description: Replicate 2


title: SC96 vs SC120

description: dye-swap


title: SS120 vs SS144

description: dye-swap


title: Epithelial Killed WT N. lactamica 6h rep3

description: Replicate 3


title: TPA treated 18h

source_name: TPA treated 18h


title: TPA treated 3h

source_name: TPA treated 3h


title: TPA treated 6h

source_name: TPA treated 6h

source_name: undifferentiated H9 (common reference)


title: Liver_WT_CT8


title: Liver_WT_CT12


title: Liver_WT_CT10


title: Epithelial Killed WT N. lactamica 6h rep1

description: Replicate 1


title: SC2 vs SC0 [dye swap]

description: dye-swap


title: Liver_WT_CT6


title: Epithelial Killed WT N. lactamica 5h rep3

description: Replicate 3

source_name: 16HBE14 human bronchial epithelial cells,5h,Killed WT N. lactamica


title: SC0 vs SC144 [dye swap]

description: dye-swap


title: Liver_WT_CT2


title: Liver_H2O_CT32

source_name: liver, Clock mutant

value: Scg2::tTA; tetO::Clockwt; ClockD19/D35


title: SS0 vs SC0 [dye swap]

description: dye-swap


title: ES control 0hr replicate 2

source_name: ES control 0hr


title: SS72 vs SS48

description: dye-swap


title: North Moutain_soil_C

city: Rio de Janeiro

first: Lia

last: Teixeira

state: RJ

address: Av. Carlos Chagas Filho, 373

country: Brazil

institute: Universidade Federal do Rio de Janeiro

hyb_protocol: Slides were pre-hybridized for 1 h at 37°C with a DIG easy hybridization solution (Roche Applied Science, Laval, QC, Canada) containing 5% BSA. Samples were then assigned randomly to a sub-array and hybridization was carried out for approximately 20 h at 37°C on a Slide Booster apparatus (Implen, Calabasas, CA). Slides were washed three times for 5 minutes at 37°C in 0.1X SSC / 0.1% SDS followed by a single wash for 5 minutes at 37°C in 0.1X SSC.

scan_protocol: Slides were scanned in a ScanArray GX PLUS Microarray Scanner (Perkin-Elmer, Boston, MA) at a resolution of 10 µm.

data_processing:
Images were transferred to QuantArray (Perkin-Elmer) where each spot was identified and quantified. Data was then exported to Excel where net spot intensity was calculated by subtracting the background signal from the target spot intensity.
A spot was scored as “present” if its net intensity was at least 3 times higher than the median net intensity of all spots. For a taxon to be scored as present, all of its triplicate spots had to be scored as present. The results from the 16S rRNA gene microarray were only used in the binary form (presence/absence of taxa).

organism: Bacteria

source_name: Admiralty Bay, King George Island, Antarctic

label_protocol: For the microarray assays all the triplicate rhizosphere and bulk soil samples from the six sample sites were used (47 samples). A 16S rRNA gene fragment was amplified using the universal primers F1-R13 (Lane 1991). The PCR mixture comprised 1 µl of template DNA (10 - 20 ng), 20 pmol of universal primers, 5 µl of 10 x PCR  buffer (Fermentas, Burlington, Ontario, CA), 1.5 mM MgCl2, 2.5 U of Taq DNA polymerase (Fermentas), 0.2 mM of each dNTP and sterile filtered water to a final volume of 50 µl. The temperature profile included an initial denaturation step at 94°C for 5 min, 35 cycles of a denaturation step at 94°C for 30s, a primer annealing step at 50°C for 30s and an extension step at 72°C for 45s, followed by a final step of 7 min at 72°C. PCR products were purified using the PureLink TM PCR purification Kit (Invitrogen Canada, Burlington, Ontario, CA).

growth_protocol: The study used a non culturable method to access the bacterial communities in soils and rhizospheres

extract_protocol: The DNA extractions were made using the Fast DNA Spin Kit for soil (QBIOgene, Carlsbad, CA) following the manufacturer’s instructions.

treatment_protocol: To assess the bacterial communities associated with the rhizospheres of both vascular plants, 5 g of the roots with aggregated soil was shaken in a saline solution (NaCl 0.85%) for 2 hours. Then 50 mL of the supernatant was centrifuged for 10 minutes at 9,000 rpm, and 0.5 g of the pelleted soil was used for DNA extraction. For the bulk soil, 0.5g of each sample was used for the extractions

tag: source

value: Bulk soil


title: Liver_WT_CT4


title: Epithelial Killed WT N. lactamica 5h rep4

description: Replicate 4

tag: infection status


title: ES control 0hr replicate 3


title: SS48 vs SS72 [dye swap]

description: dye-swap

source_name: perithecia


title: SC0 vs SS0

description: dye-swap


title: Liver_WT_CT0

source_name: liver, WT


title: ES control 0hr replicate 1


title: TPA treated 1h

source_name: TPA treated 1h


title: Epithelial Killed WT N. lactamica 5h rep1

description: Replicate 1

tag: time (hours)


title: Epithelial Killed WT N. lactamica 5h rep2

description: Replicate 2


title: North Moutain_soil_B


title: Epithelial Killed WT N. lactamica 4h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,4h,Killed WT N. lactamica


title: Liver_WT_CT34

tag: strain/background


title: North Moutain_soil_A


title: SC0 vs SC144

description: dye-swap


title: North Moutain_deschampsia_B

value: Rhizosphere from Deschampsia antarctica


title: SS24 vs SS48 [dye swap]

description: dye-swap


title: North Moutain_deschampsia_A


title: SS2 vs SC2 [dye swap]

description: dye-swap


title: SC0 vs SC2

description: dye-swap


title: SC2 vs SS2

description: dye-swap


title: Epithelial Killed WT N. lactamica 4h rep3

description: Replicate 3


title: SC48 vs SC72

description: dye-swap


title: SS48 vs SS24

description: dye-swap


title: Copacabana_soil_C


title: Copacabana_soil_B


title: GhHD-1 over-expression 0 dpa ovule, biological replicate 1

city: Canberra

first: Sally

middle: Ann

last: Walford

state: ACT

address: Clunies Ross street

department: Plant Industry

institute: CSIRO

description: Gene expression data from 0 dpa GhHD-1 over-expression transgenic cotton ovules; i.e. cotton fibre initiation stage

hyb_protocol: Samples were prepared for hybridisation to the GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul is prepared for each sample and 200ul loaded into a GeneChip.  The chip is hybridised at at 45°C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation, the chip is washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: The chips are then scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL and CHP files for analysis.

data_processing: Microarray analyses were performed on 2 biological replicates of each sample and the data was analysed in R (V2.7.1) using packages from Bioconductor. Robust multichip averaging (RMA) was performed with the EXPRESSO function using quantile normalization, background correction and the median polish method. Differentially expressed genes were identified across the normalised microarray datasets for biological replicates using linear modelling in limma in R. Each experimental sample was compared with the null sample.

organism: Gossypium hirsutum

source_name: GhHD-1 over-expression_0 dpa ovule

label_protocol: Total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  1-3ug of total RNA was labelled using a cDNA synthesis kit GeneChip. Eukaryotic poly-A RNA spikes (Millenium Sciences cat no. 900433) were added to the reaction to determine the labelling efficiency.  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: All the cotton lines were grown in a glasshouse with a temperature of 30°C/22°C (day/night).

extract_protocol: A total 200mg of ovules was initially ground in 1 ml of extraction buffer (30mM EGTA; 1%(w/v) SDS;  1%(w/v) Sodium deoxycholate; 2%(w/v) PVP (40000 mw); 0.5% Nonidet-40 (NP-40)) at  80C together with 60uL 25 mg/mL proteinase K. An additional 2 mL of extraction Buffer was added with further gentle grinding. The sample was then furthervprocessed using the qiagen RNAeasy Plant Mini kit (Cat no 74904) according to the manufacturers specifications.

treatment_protocol: Developing ovules were excised from developing flower buds on the day of anthesis (0 dpa) and stored in RNAlater at -20°C. Ovules were always collected at a similar time each day (10 am–11 am.) and samples to be compared on a microarray were only used when they were collected on the same date and from the same glasshouse to minimize between time or location variability.

tag: genotype/variation

value: GhHD-1 over-expression

value: whole 0 dpa cotton ovules

tag: developmental stage

value: cotton fibre initiation stage


title: Epithelial Killed WT N. lactamica 3h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,3h,Killed WT N. lactamica


title: GhHD-1 over-expression 0 dpa ovule, biological replicate 3


title: GhHD-1 over-expression 0 dpa ovule, biological replicate 2


title: GhHD-1 silenced 0 dpa ovule, biological replicate 1

description: Gene expression data from 0 dpa GhHD-1 silenced transgenic cotton ovules; i.e. cotton fibre initiation stage

source_name: GhHD-1 silenced_0 dpa ovule

value: GhHD-1 silenced


title: Wild-type 0 dpa ovule, biological replicate 2

description: Gene expression data from 0 dpa wild-type cotton ovules; i.e. cotton fibre initiation stage

source_name: Wild-type_0 dpa ovule

value: wild type


title: GhHD-1 silenced 0 dpa ovule, biological replicate 2


title: Copacabana_soil_A


title: North Moutain_deschampsia_C


title: Epithelial Killed WT N. lactamica 4h rep1

description: Replicate 1


title: Wild-type 0 dpa ovule, biological replicate 1


title: Epithelial Killed WT N. lactamica 3h rep1

description: Replicate 1


title: Epithelial Killed WT N. lactamica 3h rep2

description: Replicate 2


title: Epithelial Killed WT N. lactamica 4h rep2

description: Replicate 2


title: Copacabana_deschampsia_C


title: SS0 vs SS2 [dye swap]

description: dye-swap


title: irma_21j_4 with array type Cotton from Affymetrix

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

institute: INRA

description: Genes involved in somatic embryogenesis?

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Gossypium

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: see supplementary file on the Series record

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_21j_4:1ug.

treatment_protocol: no treatment

tag: variety

value: irma from NEmb

tag: age


title: Epithelial Killed WT N. lactamica 0h rep4

description: Replicate 4

data_processing: The data were analysed in Genespring GX7.3 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 50th percentile.

source_name: 16HBE14 human bronchial epithelial cells,0h,Killed WT N. lactamica

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 NanoDrop 1000 instrument.


title: Epithelial Killed WT N. lactamica 3h rep3

description: Replicate 3


title: SC120 vs SC144

description: dye-swap

tag: growth medium

value: CA


title: irma_21j_3 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_21j_3:1ug.


title: Epithelial Killed WT N. lactamica 0h rep3

description: Replicate 3


title: Copacabana_deschampsia_B


title: Quimica_soil_C


title: Copacabana_deschampsia_A


title: Quimica_soil_B


title: SS144 vs SC144

description: dye-swap

value: SCM

tag: time


title: Epithelial Mock 7h rep8

description: Replicate 8

source_name: 16HBE14 human bronchial epithelial cells,7h,mock-infected

value: Mock-infected


title: Quimica_soil_A


title: b2_21j_3 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_21j_3:1ug.

value: B2 batch of seeds from Coker310


title: Epithelial Killed WT N. lactamica 0h rep2

description: Replicate 2

value: 16HBE14 human bronchial epithelial cells


title: Quimica_colobanthus_9

value: Rhizosphere from Colobanthus quitensis


title: SC2 vs SC24 [dye swap]

description: dye-swap


title: b2_21j_4 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_21j_4:1ug.


title: Quimica_colobanthus_8


title: 1a_21j_4 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_21j_4:1ug.

value: 1a batch of seeds from Coker310


title: SC144 vs SS144

description: dye-swap


title: Quimica_colobanthus_7


title: SS96 vs SC96 [dye swap]

description: dye-swap


title: SS0 vs SS2

description: dye-swap


title: Epithelial Mock 7h rep6

description: Replicate 6


title: 1a_21j_2 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_21j_2:1ug.


title: SC2 vs SC24

description: dye-swap


title: SS2 vs SS24

description: dye-swap


title: 1a_21j_3 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_21j_3:1ug.


title: Epithelial Mock 7h rep7

description: Replicate 7


title: Epithelial Mock 7h rep5

description: Replicate 5


title: Epithelial Killed WT N. lactamica 0h rep1

description: Replicate 1

value: Killed WT N. lactamica


title: 1a_64j_2 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_64j_2:1ug.


title: SS24 vs SS2

description: dye-swap


title: Epithelial Mock 7h rep4

description: Replicate 4


title: 1a_64j_1 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_64j_1:1ug.


title: SC72 vs SC96

description: dye-swap


title: 1a_21j_1 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_21j_1:1ug.


title: Quimica_deschampsia_9


title: Demay_soil_B


title: Quimica_deschampsia_7


title: Demay_soil_C


title: SC96 vs SS96

description: dye-swap


title: Demay_soil_A


title: irma_64j_2 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_64j_2:1ug.


title: Epithelial Mock 7h rep1

description: Replicate 1


title: Epithelial Mock 7h rep2

description: Replicate 2


title: Demay_deschampsia_C


title: Epithelial Mock 7h rep3

description: Replicate 3


title: b2_21j_2 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_21j_2:1ug.


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 8

city: East Lansing

first: Kelly

middle: R

last: Sporer

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 4 (dye swap), replicate 8 of 8.

hyb_protocol: Fragmented, Cy3-coupled aRNA was mixed with its Cy5-coupled partner, and the mixtures were brought to 110 μL with 68°C SlideHyb 1 (Ambion, Inc.) and incubated at 68°C for 5 min.  These dye-coupled mixtures were then hybridized to oligonucleotide microarrays (described previously) for 18 h in a GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI) using the following conditions: 54°C for 18 h, followed by a medium-stringency wash at 42°C (2X SSC, 0.1% SDS), a high-stringency wash (0.2X SSC, 0.1% SDS) at 22°C, and a wash with postwash buffer (0.2X SSC) at 22°C.  Arrays were then rinsed in 2X SSC and Nanopure H2O, dried by centrifugation at 500 × g for 5 min.

scan_protocol: Scanned with a GenePix 4000B (Molecular Devices, Sunnyvale, CA) scanner. Image analysis was performed using GenePix Pro 6.0, and spot intensities were exported as GPR files.

data_processing: Fluorescence intensity data was normalized for dye intensity bias using the LOESS procedure of the normalizeWithinArray function of the Bioconductor R software LIMMA (Smyth 2004).

organism: Meleagris gallopavo

source_name: Total RNA from turkey muscle satellite cell

label_protocol: Total RNA for use in microarrays was amplified using two rounds of amplification with the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) per manufacturer instructions.  Briefly, 1 μg total RNA was incubated with T7 Oligo(dT) primer for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h.  Second strand synthesis was performed at 16°C for 2 h.  Double-stranded cDNA was then purified, and in vitro transcription was performed at 37°C for 6 h.  The resulting aRNA was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).  For the dye coupling procedure, 15 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine.  Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

growth_protocol: Satellite cells were isolated from the pectoralis major muscle of 7-week-old male RBC2 line turkeys and plated in 24-well gelatin-coated cell culture plates in antibiotic free plating media.  Satellite cell cultures were transfected cells with the appropriate siRNA or mock-transfected to a final concentration of 20 pM of each siRNA and 1.5 µL lipofectamine 2000 (Invitrogen) contained in 100 µL Opti-MEM I Reduced Serum medium (Invitrogen) per well.  The transfection mixture was added to the cells and incubated for 5 hours at 37 °C in a 95% air/5% CO2 incubator.  After incubation, the medium was replaced with growth medium containing McCoy’s 5A (Sigma-Aldrich, St. Louis, MO) containing 10% chicken serum (Gemini BioProducts, West Sacramento, CA), and 5% horse serum (Gemini BioProducts) with 0.1% antibiotic/antimycotic (Gemini BioProducts).  The growth medium was changed every 24 hours until the cells reached 60-65% confluency.  Differentiation was induced by changing the medium to Dulbecco’s Modified Eagle Medium (DMEM; Sigma-Aldrich) containing 3% horse serum, 0.1 mg/mL porcine gelatin (Sigma-Aldrich), and 1.0 mg/mL BSA (Sigma-Aldrich) with 10 µg/mL gentamicin (Invitrogen), and 0.1% antibiotic/antimycotic.  The differentiation medium was changed daily.  After 48 h of differentiation, the plates were removed, washed with PBS, and stored at -70 °C until analysis.

extract_protocol: Total RNA was extracted from cell culture plates (n = 4) using TRIReagent (Molecular Research Center, Cincinnati, OH) following manufacturer's instructions.  RNA integrity and concentration was determined using an Agilent 2100 Bioanlyzer (Santa Clara, CA).

treatment_protocol: The si RNA sequences were designed using Invitrogen’s BLOCK-iT RNAi designer.  The primer sequences targeting versican corresponding to the coding region 7278 to 7296 were 5’-GCUCAUCAGUGAUCCAUUA-3’ (sense) and 5’-UAAUGGAUCACUGAUGAGC-3’ (antisense).  The siRNAs were purchased from Invitrogen in the desalted, pre-annealed duplex form.  The transfection of the siRNAs into the satellite cells were done using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s recommended conditions.

tag: transfection

value: Control

tag: cell growth stage

value: 48h Differentiation

value: muscle satellite cell

value: VCAN-siRNA


title: Epithelial Mock 6h rep7

description: Replicate 7

hyb_protocol: Standard Illumina hybridization protocol

source_name: 16HBE14 human bronchial epithelial cells,6h,mock-infected

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays


title: Quimica_deschampsia_8

value: Rhizosphere from Deschampsia antarctica


title: b2_64j_2 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_64j_2:1ug.


title: irma_21j_2 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_21j_2:1ug.


title: Epithelial Mock 6h rep8

description: Replicate 8


title: Epithelial Mock 6h rep6

description: Replicate 6


title: irma_21j_1 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_21j_1:1ug.


title: b2_64j_1 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_64j_1:1ug.


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 6

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 3 (dye swap), replicate 6 of 8.


title: Epithelial Mock 6h rep3

description: Replicate 3

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 NanoDrop 1000 instrument.


title: Demay_deschampsia_B

extract_protocol: The DNA extractions were made using the Fast DNA Spin Kit for soil (QBIOgene, Carlsbad, CA) following the manufacturer’s instructions.


title: b2_21j_1 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_21j_1:1ug.


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 5

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 3, replicate 5 of 8.


title: Demay_deschampsia_A


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 7

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 4, replicate 7 of 8.


title: Demay_colobanthus_C


title: Demay_colobanthus_A


title: Demay_colobanthus_B


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 4

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 2 (dye swap), replicate 4 of 8.


title: Arctowski_soil_B

value: Bulk soil


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 3

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 2, replicate 3 of 8.


title: irma_64j_1 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_64j_1:1ug.


title: Epithelial Mock 6h rep1

description: Replicate 1


title: b2_64j_4 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_64j_4:1ug.


title: b2_64j_3 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; b2_64j_3:1ug.