title: ABN+Rarg+Nr5a2 iN cells

description:
Total RNA was extracted from ABN+Rarg+Nr5a2 infected MEFs at 12 days after infection.
Cultured in vitro cells.

source_name: induced neurons from MEFs by Ascl1+Brn2+Ngn2+Rarg+Nr5a2

value: induced neurons


title: breast_invasive ductal carcinoma_8050

status: Public on Dec 05 2013

type: RNA

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Raw Green (ch1, sample) and Red (ch2, reference) expression levels were quantified using Agilent Feature Extraction software (version 9.5) based on MedianSignal output.  Expression levels were normalized by lowess normalization using standard Feature expression software settings (see manual for details at http://www.chem.agilent.com/Library/usermanuals/Public/ReferenceGuide_050416.pdf).

molecule: total RNA

organism: Homo sapiens

source_name: breast_invasive ductal carcinoma_8050

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
A reference sample was made by processing of a breast cancer reference pool (BRP) (previously generated by pooling breast tumor RNAs [Glas et al, BMC Genomics 2006]) similarly as the testsamples.

tag: gender

value: female

tag: age at diagnosis

tag: menopausal status at start therapy

value: post

tag: tissue

value: breast

tag: tumor type

value: invasive ductal carcinoma

tag: location

tag: grade

tag: er status

value: positive

tag: pr status

tag: her2 status

value: negative

tag: pik3ca status

value: wildtype

source_name: common breast cancer reference pool (BRP)

tag: sample type

value: reference


title: DS_DAP_OS_Rep1

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Five Medicago truncatula plants were grown at controlled light/temperature conditions: 20/18°C 16 h light/dark in osmotic conditions (-0.1 Mpa) from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 12 DAP to Abscission. Dry seeds (DS) was the last analysed stage of development, seeds were let at the same environmental conditions for one week after abscission

extract_protocol: For each data point of seed development and for each repetition, 50 seeds were collected and the total RNA was extracted with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommendations

treatment_protocol: Medicago truncatula seeds developed at 20/18°C 16 h light/dark, -0.1MPa from 1 DAP to DS stage

tag: tissus

value: seed

tag: genetic background

tag: developmental stage

value: DS

tag: phenotype

value: Wild-type

tag: treatment

value: Seeds developed at 20-18°C 16h -0.1MPa

tag: age

tag: harvest date


title: Primary neurons

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description:
Total RNA was extracted from primary neurons which cultured in vitro within one week.
Cultured in vitro cells.

hyb_protocol: MOA v2.0 arrays were pre-heated at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (at 100% laser power, 635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity by GenePix Pro software (4.1.1.44).

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). Intensity normalized by median scaling method performed on data set without flagged (probes that flag<0 within all arrays) and control data. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

organism: Mus musculus

source_name: from postnatal day 0 hippocampus neurons

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: The mouse embryonic fibroblasts were cultured in fibroblast medium (high glucose DMEM, 10% FBS, 2 mM Glutamax). Induced neurons and primary neurons were cultured in neural medium (Neural Basal/DMEM-F12 1:1, 1×B-27, 5 ng/ml BDNF).

extract_protocol: RNA extraction by Trizol Reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6.5).

treatment_protocol: MEFs were used between passages 2 and 4, and primary neurons were cultured within one week. Induced neurons were induced from MEFs by ABN+Rarg+Nr5a2 through adenovirus. Induced neurons for the array experiment were the total final cells population including converted iN cells and non-converted cells and formed a mixed population.

value: postnatal day 0

value: hippocampus

tag: cell type

value: primary neurons


title: breast_invasive ductal carcinoma_8009

source_name: breast_invasive ductal carcinoma_8009

tag: gender

tag: age at diagnosis

tag: tissue


title: 12_DAP_OS_Rep3

value: 12_DAP maturation

value: 12 days after flowering


title: DS_DAP_OS_Rep2


title: 20_DAP_OS_Rep1

value: 20_DAP maturation

value: 20 days after flowering


title: 12_DAP_OS_Rep4


title: Abs_DAP_OS_Rep1

value: Abscission


title: 25_DAP_OS_Rep1

value: 25_DAP maturation

value: 25 days after flowering


title: 25_DAP_OS_Rep2


title: 20_DAP_OS_Rep2


title: 15_DAP_OS_Rep1

value: 15_DAP maturation

value: 15 days after flowering


title: 30_DAP_OS_Rep1

value: 30_DAP maturation

value: 30 days after flowering


title: 15_DAP_OS_Rep2

value: seed


title: 12_DAP_OS_Rep2

value: Wild-type


title: 12_DAP_OS_Rep1

value: Seeds developed at 20-18°C 16h -0.1MPa


title: DS_DAP_GH_Rep1

growth_protocol: Five Medicago truncatula plants were grown at variable light and temperature conditions, under greenhouse environment (period March-June): from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 16 DAP to Abscission. Dry seeds (DS) was the last analysed stage of development, seeds were let at the same environmental conditions for one week after abscission

treatment_protocol: Medicago truncatula seeds developed in greenhouse from 1 DAP to DS stage

value: DS

value: Seeds developed under greenhouse conditions


title: DS_DAP_GH_Rep2


title: 30_DAP_OS_Rep2


title: Abs_DAP_OS_Rep2


title: 16_DAP_GH_Rep3

value: 16_DAP maturation

value: 16 days after flowering


title: Abs_DAP_GH_Rep2


title: 16_DAP_GH_Rep4


title: Abs_DAP_GH_Rep1


title: 40_DAP_GH_Rep1

value: 40_DAP maturation

value: 40 days after flowering


title: 36_DAP_GH_Rep2

value: 36_DAP maturation

value: 36 days after flowering


title: 36_DAP_GH_Rep1


title: 32_DAP_GH_Rep2

value: 32_DAP maturation

value: 32 days after flowering


title: 28_DAP_GH_Rep2

value: 28_DAP maturation

value: 28 days after flowering


title: 28_DAP_GH_Rep1


title: 32_DAP_GH_Rep1


title: 20_DAP_GH_Rep1

value: 20_DAP maturation

value: 20 days after flowering


title: 20_DAP_GH_Rep2

value: seed


title: 24_DAP_GH_Rep1

value: 24_DAP maturation

value: Wild-type

value: 24 days after flowering


title: DS_DAP_26C_Rep2

growth_protocol: Five Medicago truncatula plants were grown at controlled light/temperature conditions: 26/24°C 16 h light/dark  from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 7 DAP to Abscission. Dry seeds (DS) was the last analysed stage of development, seeds were let at the same environmental conditions for one week after abscission

treatment_protocol: Medicago truncatula seeds developed at 26/24°C 16 h light/dark from 1 DAP to DS stage

value: DS

value: Seeds developed at 21-19°C 16h


title: 24_DAP_GH_Rep2

value: Seeds developed under greenhouse conditions


title: Abs_DAP_26C_Rep2

value: Abscission


title: 17_DAP_26C_Rep1

value: 17_DAP maturation

value: 17 days after flowering


title: 16_DAP_GH_Rep2

value: 16_DAP maturation

value: 16 days after flowering


title: 14_DAP_26C_Rep2

value: 14_DAP maturation

value: 14 days after flowering


title: 20_DAP_26C_Rep2


title: 20_DAP_26C_Rep1


title: Abs_DAP_26C_Rep1


title: DS_DAP_26C_Rep1


title: 14_DAP_26C_Rep1


title: HepG2 exposed to PBS for 48h, biological rep 3

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls

label: biotin

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either 7µM of cisplatin or solvent ( 0.5% PBS)

tag: cell line

tag: time


title: 9_DAP_26C_Rep1

value: 9_DAP maturation

value: 9 days after flowering


title: 7_DAP_26C_Rep1

value: 7_DAP maturation

value: 7 days after flowering


title: 40_DAP_GH_Rep2

value: seed

value: 40_DAP maturation

value: 40 days after flowering


title: 11_DAP_26C_Rep2

value: 11_DAP maturation

value: Wild-type

value: 11 days after flowering


title: 9_DAP_26C_Rep2

value: Seeds developed at 21-19°C 16h


title: 11_DAP_26C_Rep1


title: HepG2 exposed to PBS for 48h, biological rep 1


title: 16_DAP_GH_Rep1

value: Seeds developed under greenhouse conditions


title: 17_DAP_26C_Rep2

value: 17_DAP maturation

value: 17 days after flowering


title: HepG2 exposed to PBS for 48h, biological rep 2


title: 7_DAP_26C_Rep2


title: HepG2 exposed to PBS for 24h, biological rep 1


title: HepG2 exposed to PBS for 24h, biological rep 2


title: HepG2 exposed to PBS for 24h, biological rep 3


title: SDY2

city: Montreal

first: Bernard

last: Robaire

address: 3655 Sir William Osler

country: Canada

institute: McGill University

description: Gene expression in young CD9-positive testis cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 12.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: CD9-positive cells from 4 month old rat testes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 18 ng 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-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit

treatment_protocol: CD9-positive cells were isolated from transgenic germ cell-specific GFP Sprague Dawley rats of 4 months and 21 months of age using FACS sorting in combination with a CD9 antibody

value: 4 m

value: CD9-positive testis cells, young

tag: strain

value: Sprague-Dawley


title: SDA3

description: Gene expression in aged CD9-positive testis cells

source_name: CD9-positive cells from 21 month old rat testes

value: CD9-positive testis cells, aged


title: HepG2 exposed to CisPl for 48h, biological rep 2

value: CisPl,  7µM


title: SDY3


title: SDA4


title: HepG2 exposed to CisPl for 48h, biological rep 3


title: SDY4


title: HepG2 exposed to PBS for 12h, biological rep 1


title: HepG2 exposed to PBS for 12h, biological rep 2


title: HepG2 exposed to CisPl for 24h, biological rep 3


title: SDA1


title: Corr PQ/MB 3

city: Guelph

first: Scott

last: Ryan

state: ON

address: 50 Stone Rd E

institute: University of Guelph

hyb_protocol: The slides were hybridized at 65ºC for at least 17 hr according to manufacturer's protocol.

scan_protocol: The slides were subsequently washed and scanned with an Illumina DNA Microarray Scanner according to manufacturer's protocol.

data_processing: After scanning, the intensities of the spots were extracted using Feature Extraction Version 10.1.1.For each sample, raw median probe intensity data were normalized using GeneSpring GX Version 10.0 (Agilent Technologies), first by scaling probe signals within each microarray by the quantiles method, then by eliminating probes with no or marginal signal in all samples, and finally by averaging the normalized signal among replicate samples.

source_name: hiPSCs driven to DA neurons, genetically corrected, paraquat and maneb

label_protocol: 500 ng of RNA was labeled and used for each microarray according to manufacturer's protocol.

growth_protocol: hiPSC colonies were dissociated into a single cell suspension using accutase. To purify PSCs and remove fibroblast feeders, medium containing dissociated fibroblasts and PSCs was placed in gelatin-coated dishes. After adherence of the dissociated fibroblasts, supernatant containing purified PSCs was collected and re-plated at 4x104 cells/cm2 on Matrigel (BD)-coated tissue culture dishes for differentiation. Floor-plate induction was carried out using medium containing knockout serum replacement (KSR), LDN193189 (100 nM), SB431542 (10 μM), Sonic Hedgehog (SHH) C25II (100 ng/ml), Purmorphamine (2 μM), Fibroblast growth factor 8 (FGF8; 100 ng ml−1), and CHIR99021 (3 μM). On day 5 of differentiation, KSR medium was incrementally shifted to N2 medium (25%, 50%, 75%) every 2 days. On day 11, the medium was changed to Neurobasal/B27/Glutamax supplemented with CHIR. On day 13, CHIR was replaced with Brain Derived Neurotrophic Factor (BDNF; 20 ng ml−1), ascorbic acid (0.2 mM), Glial Derived Neurotrophic Factor (GDNF; 20 ng ml−1), transforming growth factor beta 3 (TGFβ3; 1 ng ml−1), dibutyryl cAMP (db cAMP; 0.5 mM), and DAPT (10 μM) for 9 days. On day 20, cells were dissociated using accutase and re-plated under high cell density 400x103 cells/cm2 in terminal differentiation medium (NB/B27 + BDNF, ascorbic acid, GDNF, db cAMP, TGFβ3 and DAPT) or DAN Medium (DA Neuron) on dishes pre-coated with poly-ornithine(15 μg/ml)/laminin (1 μg ml−1)/fibronectin (2 μg ml−1).

extract_protocol: RNA was harvested from A53T mutant and corrected hNs (n = 3 experiments) using the ZR RNA Prep kit (Zymo Research) according to manufacturer's protocol.

treatment_protocol: Exposure to either 2.8uM paraquat in combination with 1uM maneb for 24h or PBS vehicle control.

value: DA neurons

tag: genotype/variation

value: genetically corrected

value: paraquat and maneb


title: A53T PQ/MB 3

source_name: hiPSCs driven to DA neurons, A53T mutant, paraquat and maneb

value: A53T mutation


title: resistant sample 2

status: Public on Dec 06 2013

type: genomic

city: La Jolla

last: Mischel

state: California

address: 9500 Gilman Drive, CMME, room 2021

department: Pathology

country: USA

institute: LICR, UCSD

hyb_protocol: As per standard Affymetrix SNP6.0 array protocol.

data_processing:
The Affymetrix SNP6.0 array data were analysed for copy number variation using 200kb filter and 50 markers as described in the matrix tables attached.
Chromosomal copy number gain and loss were identified in control and CC214-2 resistant samples.

molecule: genomic DNA

source_name: GBM39 xenograft

growth_protocol: GBM39 primary neurospheres were cultured in standard cancer stem cell medium conditions and then were injected in the mice flanks to generate xenograft tissues.

extract_protocol: Genomic DNA was extracted from GBM39 control and CC214-2 resistant xenografts using the Qiagen QIAamp DNA Mini kit protocol. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Mice carrying CC214-2 resistant xenografts were treated with a solution of CC214-2 once every two days, by gavage, for 40 days; control samples were left un-treated.

value: primary GBM sample

value: GBM39 xenograft

value: CC214-2 resistant


title: HepG2 exposed to PBS for 12h, biological rep 3


title: HepG2 exposed to CisPl for 48h, biological rep 1


title: A53T PQ/MB 2


title: control sample 2

scan_protocol: As per standard Affymetrix SNP6.0 array protocol.

value: control


title: Corr PQ/MB 2


title: SDY1


title: A53T PQ/MB 1


title: Corr PQ/MB 1


title: A53T 3

source_name: hiPSCs driven to DA neurons, A53T mutant, PBS vehicle control

value: PBS vehicle


title: HepG2 exposed to CisPl for 12h, biological rep 3


title: control sample 1

label_protocol: As per standard Affymetrix SNP6.0 array protocol.


title: HepG2 exposed to CisPl for 12h, biological rep 2


title: HepG2 exposed to CisPl for 24h, biological rep 2


title: Corr 3

source_name: hiPSCs driven to DA neurons, genetically corrected, PBS vehicle control


title: BS2011051062

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

description: Gene expression data of gastrocnemius muscle mRNA from old (24 month old) knock-out mice

hyb_protocol: standard Affymetrix procedure.

scan_protocol: standard Affymetrix procedure.

data_processing: The data were analyzed with RMA (log2) normalized data using the just.rma function in the affy package in Biocinductor

source_name: Gastrocnemius muscle mRNA from old (24 month old) knock-out mice

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

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

value: Gastrocnemius muscle

tag: genotype

value: KO

value: OLD


title: HepG2 exposed to CisPl for 12h, biological rep 1


title: BS2011051063


title: Corr 1


title: A53T 1


title: A53T 2


title: Corr 2


title: SDA2


title: PS-40min-3B

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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: RMA by software Partek

organism: Escherichia coli

growth_protocol: All E. Coli studies were approved by the NIDDK/NIH Animal Care and Use Committee.

treatment_protocol: Cell culture were maintained in a pathogen-free facility.  E. coli Cell culture extraction protocal  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: treatment group


title: PS-60min-4A


title: PS-40min-3C


title: BS2011051061

description: Gene expression data of gastrocnemius muscle mRNA from old (24 month old) wild-type mice

source_name: Gastrocnemius muscle mRNA from old (24 month old) wild-type mice

value: WT


title: BS2011051060


title: PS-40min-3A


title: BS2011051064


title: fzo1D/D 5

city: Delhi

first: Sneh

middle: Lata

last: Panwar

state: Delhi

address: New Mehrauli Road

department: Scholo of Life Sciences

country: India

institute: Jawaharlal Nehru University

description:
Mutant/Treated
Cells harbor aberrant mitochondria.

hyb_protocol: 600 ng  Cy3 labeled samples for 8x15 arrays were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner at 5 micron resolution

data_processing: Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1  and 75th percentile shift Normalization of the data was done in GeneSpring GX V 11.

organism: Candida albicans

source_name: fzo1D/D mutant

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: The wild type and mutant were grown in Yeast Nitrogen Base-Glucose (2%) till log phase at 30°C/220 rpm shaking.

extract_protocol: RNA was extracted by Qiagen RNeasy Mini Kit according to manufacturers protocol

treatment_protocol: Cultures were centrifuged at 10,000 rpm for 5 min, washed with DEPC-treated water and proceeded for RNA extraction


title: PS-60min-4C


title: resistant sample 1


title: HepG2 exposed to CisPl for 24h, biological rep 1


title: PS-60min-4B


title: fzo1D/D 1


title: PS-20min-2B


title: PS-20min-2C


title: fzo1D/D 3


title: BS2011051059


title: Wildtype 5

description: Control

source_name: Wildtype

value: laboratory strain

value: wild-type


title: BS2011051057

description: Gene expression data of gastrocnemius muscle mRNA from young (10 week old) knock-out mice

source_name: Gastrocnemius muscle mRNA from young (10 week old) knock-out mice

value: YOUNG


title: PA-1B

source_name: PA

value: PA


title: Wildtype 4

description: Control


title: PA-1A


title: BS2011051058


title: Wildtype 2

description: Control


title: PA-1C


title: BS2011051055

description: Gene expression data of gastrocnemius muscle mRNA from young (10 week old) wild-type mice

source_name: Gastrocnemius muscle mRNA from young (10 week old) wild-type mice


title: PS-20min-2A


title: HepaRG reprogramming, 48h, replicate 3

city: Rennes

first: Hélène

last: Dubois-Pot-Schneider

address: Hopital Pontchaillou, rue Henri Le Guilloux

institute: INSERM UMR 991

description: Gene expression data from hepatocytes-HepaRG after 48h of low density seeding

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Hepatocytes-HepaRG after 48h of low density seeding

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit).

growth_protocol: HepaRG cells were grown in William's E medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 μg/ml insulin, and 50 μM hydrocortisone hemisuccinate. After 2 weeks, medium was supplemented with 2% DMSO and the cells cultured for 2 more weeks.

extract_protocol: RNA extractions were performed with RNeasy mini kit (Qiagen)  following the manufacturer's recommendations.

treatment_protocol: Hepatocytes-HepaRG were selectively detached (gentle trypsinization) and seeded at low density to induce reprogramming. Cells were then collected after 0, 1, 4, 8, 12, 16, 24 and 48 hours.

value: HepaRG


title: HepaRG reprogramming, 48h, replicate 2


title: BS2011051056


title: HepaRG reprogramming, 24h, replicate 3

description: Gene expression data from hepatocytes-HepaRG after 24h of low density seeding

source_name: Hepatocytes-HepaRG after 24h of low density seeding


title: HepaRG reprogramming, 48h, replicate 1


title: HepaRG reprogramming, 24h, replicate 2


title: HepaRG reprogramming, 16h, replicate 2

description: Gene expression data from hepatocytes-HepaRG after 16h of low density seeding

source_name: Hepatocytes-HepaRG after 16h of low density seeding


title: BS2011051054_2


title: HepaRG reprogramming, 24h, replicate 1


title: BS2011051053


title: HepaRG reprogramming, 12h, replicate 3

description: Gene expression data from hepatocytes-HepaRG after 12h of low density seeding

source_name: Hepatocytes-HepaRG after 12h of low density seeding


title: HepaRG reprogramming, 16h, replicate 3


title: HepaRG reprogramming, 16h, replicate 1


title: wild-type 5

city: Bundoora, Melbourne

first: Song

middle: F

last: Li

state: VIC

address: Kingsbury Dr

department: Botany

country: Australia

institute: La Trobe University

description: SAMPLE 5

hyb_protocol: samples were hybridized to Affymetrix Arabidopsis  ATH1 genome arrays, washed using a Genechip fluidics station, and  scanned using the Genechip Scanner 3000

scan_protocol: scanned using the Genechip Scanner 3000

data_processing: Microarray data were processed using the ArrayAssist 5.5.1 software provided by Stratagene.  and Strand Life Sciences.

organism: Arabidopsis thaliana

source_name: wild-type

label_protocol: biotin labeling of cRNA.

growth_protocol: Approximately 1000 anthers at stages 5 to 8 were dissected from the wild  type and the myb80 mutant for each  biological replicate for subsequent RNA isolation

extract_protocol: The RNeasy plant kit was used for RNA exraction.

treatment_protocol: myb80 mutant vs wild-type

value: wild type

value: anther


title: cow8609_not challenged 24h

city: Ithaca

first: Anja

last: Sipka

state: NY

address: S3 114 Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University College of Veterinary Medicine

hyb_protocol: Following fragmentation 15 µg aRNA was hybridized to a GeneChip® Bovine Genome Array for 16 h at 45°C in a rotating Affymetrix hybridization oven. After hybridization the array was washed and stained using the GeneChip ® Hybridization Wash and Stain Kit

scan_protocol: Slides were scanned immediately after washing on the Affymetrix GeneChip® Scanner 7G Plus, according to the manufacturer’s protocol.

data_processing: The raw data was analyzed using Bioconductor in R. Normalization of expression values was performed using the Robust Multiarray Average (RMA) algorithm as implemented in the Affy package. Differential expression of each gene was assessed using empirical Bayes models which were implemented in the R package Limma

organism: Bos taurus

source_name: mammary gland tissue, right front quarter, cisternal region, 24h

label_protocol: Total RNA was amplified and biotin labeled (aRNA) with the MessageAmpTM Premier RNA Amplification Kit (Ambion®, Life Technologies, Carlsbad, CA). The obtained aRNA (15 µg per sample) was fragmented at 94°C for 35 min in a reaction volume of 30 µl containing 6 µl 5x array fragmentation buffer and nuclease free water following the manufacturer’s instructions.

extract_protocol: Tissue was disrupted in lysis buffer using eppendorf pestles and RNA was extracted using the RNeasy kit (QIAGen, Gaithersburg, MD) as to the manufacturer’s instructions. Purity and integrity of the RNA was assessed using microfluidics analysis (2100 Bioanalyzer, Agilent). Only samples with an RNA integrity number > 8.0 were used for further analysis.

treatment_protocol: Five midlactating HF cows were challenged with 100 CFU in 3 quarters and treated with Cefapirin only and the combination of Cefaprirn and Prednisolne in another quarter at 4, 12, 24 and 36h post challenge. After 24h (n=3) or 48h (n=3) post challenge cows were sacrificed and  mammary gland tissue was collected from each quarter and total RNA was subjected to microarray analysis. Microarray data was analyzed seperately for the two different sample time points.

tag: breed

value: Holstein Friesian

tag: time point

tag: challenge

value: no challenge

value: no treatment


title: cow8609 challenged not treated 24h

source_name: mammary gland tissue, left front quarter, cisternal region, 24h

value: 100 CFU E. coli


title: HepaRG reprogramming, 8h, replicate 3

description: Gene expression data from hepatocytes-HepaRG after 8h of low density seeding

source_name: Hepatocytes-HepaRG after 8h of low density seeding


title: HepaRG reprogramming, 12h, replicate 2


title: PMH exposed to PBS for 48h, biological rep 3

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Mouse Genome 430 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 16,395 probe sets represent 16,331 unique genes and 64 internal controls

source_name: primary hepatocytes

growth_protocol: Primary mouse hepatocytes were isolated from adult male C57BL/6 mice using a perfusion method and cultured between a collagen-collagen sandwich formation in two six wells plates

treatment_protocol: After a recovery period of 40-42h, the Dulbecco's Modified Eagle's culture medium was replaced by culture medium containing cisplatin or a vehicle control (0.5% of PBS).

value: PMH


title: wild-type 6

description: SAMPLE 6


title: cow8609 challenged Cefapirin + Prednisolone 24h

source_name: mammary gland tissue, left rear quarter, cisternal region, 24h

value: 300mg Cefapirin + 20mg Prednisolopne intramammary


title: PMH exposed to PBS for 48h, biological rep 2


title: mutant 5-2

description: SAMPLE 3

source_name: mutant

value: myb80 mutant


title: wild-type 2

description: SAMPLE 4


title: HepaRG reprogramming, 8h, replicate 1


title: cow8507 challenged Cefapirin 48h

source_name: mammary gland tissue, left rear quarter, cisternal region, 48h

value: 300mg Cefapirin, intramammary


title: mutant 4

description: SAMPLE 2


title: HepaRG reprogramming, 8h, replicate 2


title: PMH exposed to PBS for 48h, biological rep 1


title: HepaRG reprogramming, 12h, replicate 1


title: mutant 1

description: SAMPLE 1


title: cow8609 challenged Cefapirin 24h

source_name: mammary gland tissue, right rear quarter, cisternal region, 24h


title: PMH exposed to CisPl for 48h, biological rep 3

value: CisPl,  7µM


title: HepaRG reprogramming, 4h, replicate 2

description: Gene expression data from hepatocytes-HepaRG after 4h of low density seeding

source_name: Hepatocytes-HepaRG after 4h of low density seeding


title: PMH exposed to CisPl for 48h, biological rep 2


title: HepaRG reprogramming, 4h, replicate 1


title: PMH exposed to CisPl for 48h, biological rep 1


title: PMH exposed to PBS for 24h, biological rep 3


title: HepaRG reprogramming, 1h, replicate 3

description: Gene expression data from hepatocytes-HepaRG after 1h of low density seeding

source_name: Hepatocytes-HepaRG after 1h of low density seeding


title: cow8452 challenged Cefapirin + Prednisolone 48h


title: HepaRG reprogramming, 0h, replicate 3

description: Gene expression data from hepatocytes-HepaRG

source_name: Hepatocytes HepaRG


title: HepaRG reprogramming, 1h, replicate 1


title: cow8452 challenged not treated 48h

source_name: mammary gland tissue, left front quarter, cisternal region, 48h


title: Gemin2 MO replicate 7

city: Philadelphia

first: Kelvin

last: See

state: PA

address: 3400 Civic Center Blvd, Smilow Center for Translational Research

department: Medicine

institute: University of Pennsylvania

description: Biological replicate 7 of 7

hyb_protocol: Hybridisation was performed at 42°C overnight  in MAUI hybridisation station (BioMicro)

scan_protocol: Scanning of the arrays was performed using GenePix Pro 4.0 image analysis software on a GenePix 4000B microarray scanner (Axon Instruments, California, US).

data_processing: Genespring v10 software was used to generate LOWESS normalized data from log ratio of processed Cy5 signal/processed Cy3 signal.

organism: Danio rerio

source_name: Gemin2 MO injected

label_protocol: To fluorescently label cDNA, 10μg of total RNA per experimental sample and per control sample was reverse transcribed in the presence of Cy5 and Cy3 dye (Amersham Inc.) respectively. Labelled cDNAs were pooled, concentrated and purified using QIAquick columns before being resuspended in DIG EasyHyb (Roche) for hybridisation.

growth_protocol: Zebrafish embryos reared at temperature of 28°C in embryo media

extract_protocol: Total RNA was extracted after homogenisation and Phenol Chlorofoam extraction, DNase I digestion followed by second round of Phenol-Chlorofoam extraction

treatment_protocol: Embryos were injected with either SMN MO, Gemin2 MO, or control MO at one - two cell stage

value: whole embryo

tag: Stage

source_name: Control MO injected


title: cow8507_not challenged 48h

source_name: mammary gland tissue, right front quarter, cisternal region, 48h

tag: treatment


title: cow8507 challenged not treated 48h


title: HepaRG reprogramming, 4h, replicate 3


title: cow8452_not challenged 48h


title: cow8507 challenged Cefapirin + Prednisolone 48h

source_name: mammary gland tissue, right rear quarter, cisternal region, 48h


title: PMH exposed to PBS for 24h, biological rep 2


title: HepaRG reprogramming, 1h, replicate 2


title: HepaRG reprogramming, 0h, replicate 2


title: cow8620 challenged Cefapirin + Prednisolone 24h


title: Gemin2 MO replicate 4

description: Biological replicate 4 of 7


title: Gemin2 MO replicate 6

description: Biological replicate 6 of 7


title: cow8452 challenged Cefapirin 48h


title: cow8620 challenged not treated 24h


title: Gemin2 MO replicate 3

description: Biological replicate 3 of 7


title: cow8620 challenged Cefapirin 24h


title: HepaRG reprogramming, 0h, replicate 1


title: PMH exposed to CisPl for 24h, biological rep 3


title: PMH exposed to PBS for 24h, biological rep 1


title: cow8620_not challenged 24h


title: PMH exposed to CisPl for 24h, biological rep 2


title: Gemin2 MO replicate 5

description: Biological replicate 5 of 7


title: PMH exposed to CisPl for 24h, biological rep 1


title: Gemin2 MO replicate 2

description: Biological replicate 2 of 7


title: SMN MO replicate 6

description: Biological replicate 6 of 6

source_name: SMN MO injected


title: cow8605 challenged Cefapirin 48h


title: line E hiPSC-derived neuron 11_28

status: Public on Dec 04 2013

city: Charlottesville

first: Michael

middle: J

last: McConnell

state: VA

address: 1340 Jefferson Park Ave

institute: University of Virginia

description: single cell genome was subjected to multiple displacement amplification prior to hybridization

hyb_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

data_processing:
Partek Genomics Suite Software (version 6.6 beta, Partek, St. Louis, MO) was used to calculate predicted copy numbers for each probe set intensity. A custom copy number model composed of 161 MDA single cell experiments (from this and other studies) was generated to perform quantile normalization of the calculated copy numbers. The background-adjusted values were then subjected to GC correction in windows of 10 Mb, and artifact-prone probes were removed according to Pugh et al. (Nuleic Acids Research, 2008) We then performed smoothing by taking the median copy number value in non-overlapping genomic windows composed of 100 probes. On average, each 100-probe bin corresponds to 666 Kb of genome sequence. At this stage we also excluded 6 of 107 samples that had excessively "noisy" copy number profiles, defined as having a median absolute deviation (MAD) greater than 0.7. To detect CNVs, we used the circularly binary segmentation (CBS) algorithm from the DNAcopy package in R, with the following parameters: alpha=0.001, undo.splits="sdundo", undo.SD=1. We defined CNVs as segments composed of 10 or more contiguous genomic windows whose copy number value differed from the dataset's median copy number by at least 1 MAD. We did not attempt to detect CNVs on the Y chromosome.
Single cell genomes, amplified by mulitple displacement amplification, were analyzed on Affy 250K_NSP arrays.

source_name: hiPSC-derived neuron

growth_protocol: cells were grown according to standard conditions (Brennand, et al. Nature 2011)

extract_protocol: Single cells were transferred to a 200uL PCR tube containing 1.5 uL lysis buffer alkaline lysis buffer.  Mulieple Displacement amplification was perfomred according to manufacturers instructions (Genomiphi V2, GE Helthsciences).MDA products (5 ng) were examined for even amplification (e.g., +/- 5% of the Ct for 5 ng bulk genomic DNA) using qPCR (Applied Biosystems, San Diego, CA). To test for even amplification, we used a 10 locus subset of the 47 single copy loci used in Hosono et al. (Genome Research, 2009) (Chr1p, Chr2p, Chr3q, Chr7p, Chr10p, Chr11p, Chr14q, Chr17q, Chr19p, and Chr21q).

value: hiPSC-derived neuron

value: female


title: line E hiPSC-derived neuron 9_28

scan_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual


title: SMN MO replicate 1

description: Biological replicate 1 of 6


title: line E hiPSC-derived neuron 7_28

label_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual


title: SMN MO replicate 4

description: Biological replicate 4 of 6


title: line E hiPSC-derived neuron 6_28


title: line E hiPSC-derived neuron 7


title: Control WT sample C vs Paraxis-/- sample B

city: Tempe

first: Megan

last: Rowton

state: AZ

department: School of Life Sciences

institute: Arizona State University

description:
Third WT biological replicate (C) tissue pool compared with second Paraxis-/- biological replicate (B) tissue pool.
WT C vs Paraxis-/- B

hyb_protocol: A Cy5-labeled sample (WT or Paraxis-/-) was hybridized to an array along with a Cy3-labeled sample of the other genotype according to manufacturer's protocols.

scan_protocol: Array slides were washed and scanned at 5uM using an Agilent Microarray Scanner (model G2505B) in an ozone controlled environment.

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

source_name: E9.5 WT presomitic mesoderm and somites I-IV

label_protocol: 250 ng total RNA was reverse transcribed with M-MLV reverse transcriptase and either Cy5 or Cy3 dyes.

growth_protocol: WT and Paraxis-/- embryos were harvested at E9.5.

extract_protocol: 5 tissue samples of each genotype were combined to create a biological replicate. 3 replicates for each genotype were collected. Tissue was sonicated with a Covaris S-2 tissue disrupter, and total RNA was extracted using a Qiagen RNeasy Micro Kit. RNA integrity was validated with an Agilent 2100 Bioanalyzer, and RNA with a minimum RNA integrity number of 7.9 was used for cRNA probes.

treatment_protocol: Anterior presomitic mesoderm and somites I-IV were dissected and flash frozen in individual tubes until genotyping could be completed.

tag: age

value: anterior PSM and somites I-IV

value: WT

source_name: E9.5 Paraxis-/- presomitic mesoderm and somites I-IV

value: Paraxis-/-


title: line E hiPSC-derived neuron 5_28


title: 2ΔIcln_vs_2WT

city: Montpellier

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

institute: CNRS

hyb_protocol: Approximately 6μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

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

data_processing: Data were processed with the TAS software with the following settings: Scale to target intensity 100; Signal scale Log2; p-value scale -10Log10; Bandwidth 40; Two sided test type; PM/MM intensities.Data were analyzed by two sample comparison, normalized using quantile normalization plus scaling. Both control and treatment groups were normalized together.

organism: Schizosaccharomyces pombe

source_name: deltaICln mutant

label_protocol: Labelling was done according to the Affymetrix tiling array manufacturer instructions starting from 10μg of total RNA.

growth_protocol: Both wild type and mutant strains were grown at 25°C in YES medium

extract_protocol: Total RNA were purified with Tri-Reagent (Sigma) and treated with RQ1 RNAse-free DNAse.

tag: mating type

value: h-

value: ΔIcln mutant

source_name: wild type strain

value: wild type


title: line E hiPSC-derived neuron 4_28

tag: cell type


title: line E hiPSC-derived neuron 4_16

tag: gender


title: RKO-sh-Luci

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

description: Gene expression data after BCLAF1-L inhibition in RKO cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

source_name: RKO-sh-Luci

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Human colon cancer RKO cells were cultured in Dulbecco’s modified eagle medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 g/mL streptomycin, incubated at 37°C in a humidified atmosphere containing 5% CO2.

treatment_protocol: After infected by retrovirus targetting control(sh-Luci) or BCLALAF1-L(sh-BCLAF1-L#), stable RKO cell lines were generated by puromycin selection.

value: RKO

value: human colon cancer


title: SMN MO replicate 3

description: Biological replicate 3 of 6


title: cow8605 challenged Cefapirin + Prednisolone 48h

value: Holstein Friesian

value: 100 CFU E. coli


title: cow8605 challenged not treated 48h

value: no treatment


title: line E hiPSC-derived neuron 12_28


title: SMN MO replicate 2

description: Biological replicate 2 of 6


title: RKO-sh-BCLAF1-L


title: line E hiPSC-derived neuron 4


title: SMN MO replicate 5

description: Biological replicate 5 of 6


title: Dye swap: Paraxis-/- sample A vs control WT sample A

description:
First Paraxis-/- biological replicate (A) tissue pool compared with first WT biological replicate (A) tissue pool. This is a dye-swap of the first sample (Control WT sample A vs Paraxis-/- sample A).
Paraxis-/-A vs WT A


title: Dye swap: Paraxis-/- sample B vs control WT sample C

description:
Second WT biological replicate (B) tissue pool compared with third Paraxis-/- biological replicate (C) tissue pool. This is a dye-swap of the third sample (Control WT sample C vs Paraxis-/- sample B).
Paraxis-/- B vs WT C


title: Control WT sample B vs Paraxis-/- sample C

description:
Second WT biological replicate (B) tissue pool compared with third Paraxis-/- biological replicate (C) tissue pool.
WT B vs Paraxis-/- C


title: line E hiPSC-derived neuron 2_16


title: Dye swap: Paraxis-/- sample C vs control WT sample B

description:
Third WT biological replicate (C) tissue pool compared with second Paraxis-/- biological replicate (B) tissue pool. This is a dye-swap of the third sample (Control WT sample B vs Paraxis-/- sample C).
Paraxis-/-C vs WT B


title: line E hiPSC-derived neuron 3_16


title: line E hiPSC-derived neuron 18_28


title: line D hiPSC-derived NPC 6-1_23

source_name: hiPSC-derived NPC

value: hiPSC-derived NPC


title: line D hiPSC-derived NPC 27


title: line D hiPSC-derived NPC 26


title: cow8605_not challenged 48h

value: no challenge


title: line D hiPSC-derived NPC 22


title: line D hiPSC-derived NPC 25


title: line D hiPSC-derived NPC 18-1_23


title: Gemin2 MO replicate 1

description: Biological replicate 1 of 7


title: line D hiPSC-derived neuron 5


title: line D clone G8 fibroblast 19

source_name: fibroblast

value: fibroblast


title: line D hiPSC-derived neuron 7


title: line D hiPSC-derived NPC 14-1_23


title: line D hiPSC-derived neuron 4


title: line D hiPSC-derived NPC 11-1_23


title: line D clone G8 fibroblast 20


title: line D clone G8 fibroblast 15


title: Control WT sample A vs Paraxis-/- sample A

description:
First WT biological replicate (A) tissue pool compared with first Paraxis-/- biological replicate (A) tissue pool.
WT A vs Paraxis-/- A


title: line D hiPSC-derived neuron 1


title: line D hiPSC-derived neuron 2


title: line D hiPSC-derived NPC 16-1_23


title: line D hiPSC-derived NPC 15-1_23


title: line D clone G6 fibroblast 9


title: line D clone G8 fibroblast 14


title: line D clone G6 fibroblast 11


title: line D clone G2 fibroblast 6


title: line D clone G2 fibroblast 5


title: line D clone G2 fibroblast j4


title: line D clone G2 fibroblast 4


title: line D hiPSC-derived neuron 8


title: line D fibroblast 9


title: line D fibroblast 6_21


title: line D fibroblast 7


title: line D fibroblast 7_16


title: line D fibroblast 4_21


title: line D fibroblast 5_21


title: line D clone G8 fibroblast 18


title: line D fibroblast 3_16


title: line D fibroblast 22_28


title: line D fibroblast 21_21


title: line D fibroblast 2_21


title: line D fibroblast 22_21


title: line D fibroblast 2_16


title: line D fibroblast 18_28


title: line D fibroblast 2


title: line D fibroblast 14


title: line D fibroblast 14_21


title: line D fibroblast 25_21


title: line D fibroblast 11_21


title: line D fibroblast 10


title: line D clone G6 fibroblast 10


title: line C hiPSC-derived NPC 8-2_23


title: line C hiPSC-derived NPC 7-2_21


title: line D clone G2 fibroblast j2


title: line C hiPSC-derived NPC 3-1_21


title: line C hiPSC-derived NPC 14_21


title: line C hiPSC-derived NPC 3_21


title: line C hiPSC-derived NPC 17_21


title: line C hiPSC-derived NPC 13-1_21


title: line D fibroblast 16_21


title: line C hiPSC-derived neuron 6_8


title: line C hiPSC-derived neuron 8_8


title: line C hiPSC-derived neuron 7-1_23


title: line C hiPSC-derived neuron 6-1_23


title: line C hiPSC-derived NPC 13-2_23


title: line C hiPSC-derived NPC 16-2_23


title: line C hiPSC-derived neuron 5_8


title: line C hiPSC-derived neuron 2


title: line C hiPSC-derived neuron 53


title: line C hiPSC-derived neuron 11_8


title: line C hiPSC-derived neuron 4-2_23


title: line C hiPSC-derived neuron 12-1_23


title: line C hiPSC-derived neuron 32


title: line C hiPSC-derived neuron 52


title: line C hiPSC-derived neuron 17-1_23


title: line C hiPSC-derived neuron 1_8


title: line C hiPSC-derived neuron 15_8


title: line C hiPSC-derived neuron 10


title: line C fibroblast 8-2


title: line C fibroblast 9


title: line C fibroblast 8-1


title: line C hiPSC-derived neuron 9_8


title: line C fibroblast 6_29


title: line C fibroblast 13_29


title: line C fibroblast 13


title: line C fibroblast 12_29


title: line C fibroblast 12


title: line C hiPSC-derived neuron 2-1_23


title: line C hiPSC-derived neuron 2-2_23


title: line C hiPSC-derived neuron 14-1_23


title: line C hiPSC-derived neuron 1


title: line C fibroblast 6-2


title: controlclock_rescue_56h_rep2

city: Cambridge

first: Joseph

middle: Scott

last: Markson

state: MA

address: 52 Oxford St, Room 445

department: Molecular and Cellular Biology

institute: Harvard Univ / Howard Hughes Medical Institut

hyb_protocol: Hybridization was performed as described previously (Vijayan et al 2009).  Specifically, each array was hybridized with 300 ng Cy3- and 300 ng Cy5-labeled cDNA and rotated (5 rotations min-1) at 60º C for 17 hours in SureHyb chambers (Agilent). Arrays were subsequently washed in 6.7X SSPE and 0.005% N-lauryl sarcosine buffer for at least 1 minute, 0.67X SSPE and 0.005% N-lauryl sarcosine buffer for 1 minute, and then Agilent drying and ozone protection wash for 30 seconds at room temperature (1X SSPE = 0.15 M NaCl, 10 μM sodium phosphate, 1 mM EDTA, pH 7.4).

scan_protocol: The arrays were immediately scanned using an Axon 4000B (Molecular Devices) scanner at 5 μm resolution with GenePix software (Molecular Devices)

data_processing: Data was processed as described previously (Vijayan et al 2009).  Specifically, the median intensity of the Cy3 and Cy5 florescence at each spot was extracted using GenePix software (Molecular Devices) and loaded into MATLAB (Mathworks). Loess and quantile normalization were performed using the MATLAB bioinformatics toolbox.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: control clock rescue, 56 h, replicate 2

label_protocol: Labeling was performed as described previously (Vijayan et al 2009).  Specifcally, for each strain, cDNA was prepared for each individual timepoint (channel 1, foreground) as well as for a pool of all timepoints (channel 2, background) as follows: Spike-in RNA (Ambion) was introduced to the total RNA at different concentrations prior to reverse transcription in order to verify proper ratio detection in a wide dynamic range. For each sample, 5 μg total RNA (plus spike-ins) was reverse-transcribed with random 15-mer primers (Operon) and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma) using SuperScript III reverse-transcriptase (Invitrogen) without amplification. RNA was hydrolyzed by alkaline hydrolysis and cDNA was purified by concentration and dilution using Microcon 30 spin column (Millipore). cDNA was labeled with N-Hydroxysuccinimide-ester Cyanine 3 (Cy3, foreground) or Cyanine 5 (Cy5, background) (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 6 hours. Labeled cDNA was purified by concentration and dilution (Microcon 30, Millipore) in preparation for hybridization.

growth_protocol: Cultures were grown in BG-11M media in tissue culture flasks illuminated with 100 µE m-2 s-1 (µmoles photons m-2 s-1) of cool fluorescent light and bubbled continuously with 1% CO2 in air, with the OD750 maintained near 0.3 by diluting the cultures every four hours with fresh medium. Medium was supplemented with 10 mM HEPES-KOH pH 8.0 maintain the pH. Cultures were grown initially in the absence of IPTG, treated with two 12-h dark pulses separated by 12 h of light, and released to constant light concomitant with addition of IPTG to a final concentration of 6 µM.

extract_protocol: Extraction was prepared as described previously (Vijayan et al 2009).  Specifically, RNA was extracted from frozen cells in two steps. First, cells were lysed in 65° C phenol/SDS by vortexing and the total RNA was purified by phenol/chloroform extraction and isopropanol precipitation. Second, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. Total RNA was analyzed on an agarose gel to assess integrity.

treatment_protocol: Cells were collected at designated times by vacuum filtration onto nitrocellulose filters.  The filters were placed in a 50-ml conical tubes, flash-frozen in liquid nitrogen, and stored in -80º C prior to extraction

value: kaiBC::CmR Ptrc::kaiBC (EOC72)

source_name: control clock rescue, pool of samples 24 - 68 h, replicate 2

value: pool of samples 24 h through 68 h


title: controlclock_rescue_60h_rep2

source_name: control clock rescue, 60 h, replicate 2


title: controlclock_rescue_52h_rep2

source_name: control clock rescue, 52 h, replicate 2


title: controlclock_rescue_68h_rep2

source_name: control clock rescue, 68 h, replicate 2


title: controlclock_rescue_24h_rep2

source_name: control clock rescue, 24 h, replicate 2


title: controlclock_rescue_28h_rep2

source_name: control clock rescue, 28 h, replicate 2


title: controlclock_rescue_32h_rep2

source_name: control clock rescue, 32 h, replicate 2


title: controlclock_rescue_44h_rep1

source_name: control clock rescue, 44 h, replicate 1

source_name: control clock rescue, pool of samples 24 - 68 h, replicate 1


title: controlclock_rescue_48h_rep1

source_name: control clock rescue, 48 h, replicate 1


title: controlclock_rescue_64h_rep2

source_name: control clock rescue, 64 h, replicate 2


title: controlclock_rescue_40h_rep1

source_name: control clock rescue, 40 h, replicate 1


title: controlclock_rescue_40h_rep2

source_name: control clock rescue, 40 h, replicate 2


title: controlclock_rescue_36h_rep2

source_name: control clock rescue, 36 h, replicate 2


title: controlclock_rescue_44h_rep2

source_name: control clock rescue, 44 h, replicate 2


title: controlclock_rescue_pool_vs_rpaA-clock_rescue_pool_rep1

data_processing: Data was processed as described previously (Vijayan et al 2009).  Specifically, the median intensity of the Cy3 and Cy5 florescence at each spot was extracted using GenePix software (Molecular Devices) and loaded into MATLAB (Mathworks). Loess and quantile normalization were performed using the MATLAB bioinformatics toolbox, except for the controlclock_rescue_vs_rpaA-clock_rescue_rep1 array, for which only Loess normalization was performed (no quantile normalization)

source_name: ΔrpaA clock rescue, pool of samples 24 - 68 h, replicate 1

value: rpaA::CmR kaiBC::GmR Ptrc::kaiBC (EOC101)


title: controlclock_rescue_48h_rep2

source_name: control clock rescue, 48 h, replicate 2


title: rpaA-clock_rescue_68h_rep2

source_name: ΔrpaA clock rescue, 68 h, replicate 2

source_name: ΔrpaA clock rescue, pool of samples 24 - 68 h, replicate 2


title: controlclock_rescue_52h_rep1

source_name: control clock rescue, 52 h, replicate 1


title: controlclock_rescue_36h_rep1

source_name: control clock rescue, 36 h, replicate 1


title: controlclock_rescue_60h_rep1

source_name: control clock rescue, 60 h, replicate 1


title: controlclock_rescue_64h_rep1

source_name: control clock rescue, 64 h, replicate 1


title: controlclock_rescue_32h_rep1

source_name: control clock rescue, 32 h, replicate 1


title: controlclock_rescue_28h_rep1

source_name: control clock rescue, 28 h, replicate 1


title: controlclock_rescue_68h_rep1

source_name: control clock rescue, 68 h, replicate 1

source_name: control clock rescue, pool of samples 24 - 68 h, replicate 1


title: controlclock_rescue_56h_rep1

source_name: control clock rescue, 56 h, replicate 1


title: rpaA-clock_rescue_64h_rep2

source_name: ΔrpaA clock rescue, 64 h, replicate 2


title: rpaA-clock_rescue_56h_rep2

source_name: ΔrpaA clock rescue, 56 h, replicate 2


title: rpaA-clock_rescue_60h_rep2

source_name: ΔrpaA clock rescue, 60 h, replicate 2


title: rpaA-clock_rescue_52h_rep2

source_name: ΔrpaA clock rescue, 52 h, replicate 2


title: rpaA-clock_rescue_48h_rep2

source_name: ΔrpaA clock rescue, 48 h, replicate 2


title: rpaA-clock_rescue_24h_rep2

source_name: ΔrpaA clock rescue, 24 h, replicate 2


title: rpaA-clock_rescue_40h_rep2

source_name: ΔrpaA clock rescue, 40 h, replicate 2


title: rpaA-clock_rescue_44h_rep2

source_name: ΔrpaA clock rescue, 44 h, replicate 2

source_name: ΔrpaA clock rescue, pool of samples 24 - 68 h, replicate 2


title: rpaA-clock_rescue_40h_rep1

source_name: ΔrpaA clock rescue, 40 h, replicate 1

source_name: ΔrpaA clock rescue, pool of samples 24 - 68 h, replicate 1


title: rpaA-clock_rescue_48h_rep1

source_name: ΔrpaA clock rescue, 48 h, replicate 1


title: rpaA-clock_rescue_52h_rep1

source_name: ΔrpaA clock rescue, 52 h, replicate 1


title: rpaA-clock_rescue_32h_rep1

source_name: ΔrpaA clock rescue, 32 h, replicate 1


title: rpaA-clock_rescue_28h_rep1

source_name: ΔrpaA clock rescue, 28 h, replicate 1


title: rpaA-clock_rescue_56h_rep1

source_name: ΔrpaA clock rescue, 56 h, replicate 1


title: rpaA-clock_rescue_36h_rep2

source_name: ΔrpaA clock rescue, 36 h, replicate 2


title: rpaA-clock_rescue_64h_rep1

source_name: ΔrpaA clock rescue, 64 h, replicate 1


title: controlclock_rescue_24h_rep1

source_name: control clock rescue, 24 h, replicate 1

source_name: control clock rescue, pool of samples 24 - 68 h, replicate 1


title: rpaA-clock_rescue_32h_rep2

source_name: ΔrpaA clock rescue, 32 h, replicate 2


title: rpaA-clock_rescue_44h_rep1

source_name: ΔrpaA clock rescue, 44 h, replicate 1


title: rpaA-clock_rescue_68h_rep1

source_name: ΔrpaA clock rescue, 68 h, replicate 1


title: rpaA-clock_rescue_24h_rep1

source_name: ΔrpaA clock rescue, 24 h, replicate 1


title: rpaA-clock_rescue_28h_rep2

source_name: ΔrpaA clock rescue, 28 h, replicate 2


title: rpaA-_LL_72h_rep1

source_name: rpaA- strain, LL, 72 h

label_protocol: Labeling was performed as described previously (Vijayan et al 2009).  Specifcally, cDNA was prepared for each individual timepoint (channel 1, foreground) as well as for a pool of all timepoints (channel 2, background) as follows: Spike-in RNA (Ambion) was introduced at different concentrations and ratios to the foreground and background channels prior to reverse transcription in order to ensure proper ratio detection in a wide dynamic range. For each sample, 1 μg total RNA (plus spike-ins) was reverse-transcribed with random 15-mer primers (Operon) and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma) using SuperScript III reverse-transcriptase (Invitrogen) without amplification. RNA was hydrolyzed by alkaline hydrolysis and cDNA was purified by concentration and dilution using Microcon 30 spin column (Millipore). cDNA was labeled with N-Hydroxysuccinimide-ester Cyanine 3 (Cy3, foreground) or Cyanine 5 (Cy5, background) (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 6 hours. Labeled cDNA was purified by concentration and dilution (Microcon 30, Millipore) in preparation for hybridization.

growth_protocol: Cells were grown in a custom-made turbidostat described previously (Vijayan, V., et al. (2009). Proc Natl Acad Sci U S A 106, 22564-22568).  The kanamycin-resistant ΔrpaA strain (EOC 66) was grown in a 6 liter cylindrical spinner flask (Corning) at a volume of 4.5 liters. Cells were grown in the modified BG-11 medium described in Vijayan et al 2009. Cells were initially inoculated in the presence of antibiotics (5 µg/ml spectinomycin and 5 µg/ml chloramphenicol), and subsequently diluted with modified BG-11 only. Cells were exposed to surface flux of ~25 µmol photons m-2 s-1 white light, bubbled with 500 ml min-1 1% CO2 in air, maintained at 30º C, and stirred at 0.5-1 rotation per second. The initial OD750 (optical density at 750 nm) was 0.06 and was allowed to increase to 0.15, after which it was maintained at a constant level of 0.15.   Entrainment (see treatment protocol) was begun after OD750 of 0.15 was reached.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light, collected at designated times by vacuum filtration onto nitrocellulose filters, placed in a 50-ml conical tube, flash frozen in liquid nitrogen, and stored in -80º C.

value: rpaA::KmR (EOC 66)

tag: time in ll

source_name: rpaA- strain, LL, pool of samples 24 h through 72 h

tag: reference pool composition

value: pool of samples 24 h through 72 h

tag: reference pool construction

value: Equal mass quantities of each time point were mixed to prepare this background pool


title: WT/rpaA_pool_rep1

description: WT / rpaA-

hyb_protocol: Hybridization was performed as described previously (Vijayan et al 2009).  Specifically, each array was hybridized with 200 ng Cy3- and 200 ng Cy5-labeled cDNA and rotated (5 rotations min-1) at 60º C for 17 hours in SureHyb chambers (Agilent). Arrays were subsequently washed in 6.7X SSPE and 0.005% N-lauryl sarcosine buffer for at least 1 minute, 0.67X SSPE and 0.005% N-lauryl sarcosine buffer for 1 minute, and then Agilent drying and ozone protection wash for 30 seconds at room temperature (1X SSPE = 0.15 M NaCl, 10 μM sodium phosphate, 1 mM EDTA, pH 7.4).

scan_protocol: The arrays were scanned using an Axon 4000B (Molecular Devices) scanner at 5 μm resolution with GenePix software (Molecular Devices)

data_processing: The median intensity of the Cy3 and Cy5 florescence at each spot was extracted using GenePix software (Molecular Devices) and loaded into MATLAB (Mathworks). Loess normalization were performed using the MATLAB bioinformatics toolbox. Quantile normalization was NOT performed.

source_name: wild-type strain, 20 h pool in LL

label_protocol: Labeling was performed as described previously (Vijayan et al 2009).  Specifcally, cDNA was prepared by first pooling equal mass quantities of total RNA from each timepoint (24 h, 28 h, 32 h, 36 h, 40 h, 44 h) of either the wild-type or ΔrpaA culture.  Spike-in RNA (Ambion) was introduced at different concentrations to ensure proper ratio detection in a wide dynamic range. For each sample, 5 μg total RNA (not including spike-ins) was reverse-transcribed with random 15-mer primers (Operon) and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma) using SuperScript III reverse-transcriptase (Invitrogen) without amplification. RNA was hydrolyzed by alkaline hydrolysis and cDNA was purified by concentration and dilution using Microcon 30 spin column (Millipore). cDNA was labeled with N-Hydroxysuccinimide-ester Cyanine 3 (Cy3, foreground) or Cyanine 5 (Cy5, background) (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 6 hours. Labeled cDNA was purified by concentration and dilution (Microcon 30, Millipore) in preparation for hybridization.

growth_protocol: Cells were grown in a custom-made turbidostat described previously (Vijayan, V., et al. (2009). Proc Natl Acad Sci U S A 106, 22564-22568).  Either wild-type (AMC408) or kanamycin-resistant ΔrpaA (EOC 66) culture was grown in a 6 liter cylindrical spinner flask (Corning) at a volume of 4.5 liters. Cells were grown in the modified BG-11 medium described in Vijayan et al 2009. Cells were initially inoculated in the presence of antibiotics (5 µg/ml spectinomycin and 5 µg/ml chloramphenicol), and subsequently diluted with modified BG-11 lacking antibiotics. Cells were exposed to surface flux of ~25 µmol photons m-2 s-1 white light, bubbled with 500 ml min-1 1% CO2 in air, maintained at 30º C, and stirred at 0.5-1 rotation per second. Opitcal density at 750 nm (OD750) was maintained at a constant level of 0.15.   Entrainment is described in treatment protocol.

treatment_protocol: Cells were exposed to two light/dark cycles (i.e., cells were exposed to 12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light, collected at designated times by vacuum filtration onto nitrocellulose filters, placed in a 50-ml conical tube, flash frozen in liquid nitrogen, and stored in -80º C.

tag: time

source_name: rpaA- strain, 20 h pool in LL


title: rpaA-_LL_44h_rep1

source_name: rpaA- strain, LL, 44 h

tag: strain


title: rpaA-_LL_56h_rep1

source_name: rpaA- strain, LL, 56 h


title: rpaA/WT_pool_rep1

description: rpaA- / WT


title: rpaA-_LL_52h_rep1

source_name: rpaA- strain, LL, 52 h


title: rpaA-_LL_28h_rep1

source_name: rpaA- strain, LL, 28 h


title: rpaA-_LL_60h_rep1

source_name: rpaA- strain, LL, 60 h


title: rpaA-_LL_24h_rep1

source_name: rpaA- strain, LL, 24 h


title: rpaA-_LL_68h_rep1

source_name: rpaA- strain, LL, 68 h


title: rpaA-_LL_36h_rep1

source_name: rpaA- strain, LL, 36 h


title: rpaA-_LL_40h_rep1

source_name: rpaA- strain, LL, 40 h


title: rpaA-_LL_32h_rep1

source_name: rpaA- strain, LL, 32 h


title: rpaA-clock_rescue_36h_rep1

source_name: ΔrpaA clock rescue, 36 h, replicate 1

source_name: ΔrpaA clock rescue, pool of samples 24 - 68 h, replicate 1


title: Endothelial cell at T1, patient 9

city: New York

first: Ryan

middle: T

last: Demmer

department: Epidemiology

institute: Columbia University

hyb_protocol: According to manufacturer's protocol

scan_protocol: Arrays were washed, stained and scanned by GeneChip Scanner 300 7G according to the Affymetrix Expression Analysis technical manual. Affymetrix GCOS 1.4 was used as the image acquisition software. The signal, which represents the intensity of each gene, was extracted from the image. The target intensity value from each chip was scaled to 500.

data_processing: Affymetrix GCOS 1.4 was used as the image acquisition software. Normalization was performed using RMA with default settings.

source_name: Human venous endothelial cell after experimental venous hypertension

label_protocol: Biotin labeling of 10 micrograms of amplified RNA was performed using the TrueLabeling Kit (SuperArray Bioscience, Frederick, MD) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated with RNAqueous Micro Kit (Ambion Life Technologies, Grand Island, NY).

value: Venous Endothelial

value: experimental acute venous hypertension

tag: individual

value: patient 9


title: Endothelial cell at T0, patient 9

source_name: Human venous endothelial cell before experimental venous hypertension

value: baseline


title: Endothelial cell at T0, patient 7

value: patient 7


title: rpaA-_LL_48h_rep1

source_name: rpaA- strain, LL, 48 h

source_name: rpaA- strain, LL, pool of samples 24 h through 72 h


title: Endothelial cell at T0, patient 10

value: patient 10


title: Endothelial cell at T1, patient 11

value: patient 11


title: Endothelial cell at T1, patient 8

value: patient 8


title: Endothelial cell at T0, patient 6

value: patient 6


title: Endothelial cell at T1, patient 6


title: Endothelial cell at T1, patient 5

value: patient 5


title: Endothelial cell at T1, patient 7


title: Endothelial cell at T1, patient 10


title: Endothelial cell at T0, patient 12

value: patient 12


title: Endothelial cell at T0, patient 4

value: patient 4


title: Endothelial cell at T0, patient 8


title: Endothelial cell at T1, patient 1

value: patient 1


title: Endothelial cell at T0, patient 11


title: Endothelial cell at T1, patient 2

value: patient 2


title: Endothelial cell at T1, patient 4


title: Endothelial cell at T1, patient 12


title: Endothelial cell at T0, patient 1


title: Endothelial cell at T0, patient 3

value: patient 3


title: rpaA-clock_rescue_60h_rep1

source_name: ΔrpaA clock rescue, 60 h, replicate 1

value: rpaA::CmR kaiBC::GmR Ptrc::kaiBC (EOC101)

value: pool of samples 24 h through 68 h


title: Endothelial cell at T1, patient 3

value: Venous Endothelial


title: Endothelial cell at T0, patient 2


title: Endothelial cell at T0, patient 5


title: PIP Day 11  biological rep 1of3

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
H52
Gene expression data from day 11 of Placode differentiation

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first (nonorm_nobkgd.txt), then quantile normalization and background correction are done.

source_name: H9 hESCs_day 11 of Placode differentiation

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

tag: source cell line

tag: source cell type

value: human embryonic stem cells (hESCs)

value: day 11 of Placode differentiation


title: PIP Day 11 biological rep 2of3

description:
H53
Gene expression data from day 11 of Placode differentiation


title: PIP Day 11 biological rep 3of3

description:
H54
Gene expression data from day 11 of Placode differentiation


title: NSB Day 11  biological rep 1of3

description:
H43
Gene expression data from day 11 of NSB differentiation

source_name: H9 hESCs_day 11 of NSB differentiation

value: day 11 of NSB differentiation


title: PIP Day 9 biological rep 2of3

description:
H38
Gene expression data from day 9 of Placode differentiation

source_name: H9 hESCs_day 9 of Placode differentiation

value: day 9 of Placode differentiation


title: NSB Day 9 biological rep 3of3

description:
H33
Gene expression data from day 9 of NSB differentiation

source_name: H9 hESCs_day 9 of NSB differentiation

value: day 9 of NSB differentiation


title: NSB Day 7  biological rep 1of3

description:
H19
Gene expression data from day 7 of NSB differentiation

source_name: H9 hESCs_day 7 of NSB differentiation

value: day 7 of NSB differentiation


title: PIP Day 7  biological rep 1of3

description:
H25
Gene expression data from day 7 of Placode differentiation

source_name: H9 hESCs_day 7 of Placode differentiation

value: day 7 of Placode differentiation


title: NSB Day 9 biological rep 2of3

description:
H32
Gene expression data from day 9 of NSB differentiation


title: PIP Day 9  biological rep 1of3

description:
H37
Gene expression data from day 9 of Placode differentiation


title: NSB Day 7 biological rep 2of3

description:
H20
Gene expression data from day 7 of NSB differentiation


title: NSB Day 7 biological rep 3of3

description:
H21
Gene expression data from day 7 of NSB differentiation


title: NSB Day 5 biological rep 3of3

description:
H11_H12
Gene expression data from day 5 of NSB differentiation

source_name: H9 hESCs_day 5 of NSB differentiation

value: day 5 of NSB differentiation


title: PIP Day 7 biological rep 3of3

description:
H27
Gene expression data from day 7 of Placode differentiation


title: PIP Day 5  biological rep 1of3

description:
H13_H14
Gene expression data from day 5 of Placode differentiation

source_name: H9 hESCs_day 5 of Placode differentiation

value: day 5 of Placode differentiation


title: NSB Day 11 biological rep 3of3

description:
H45
Gene expression data from day 11 of NSB differentiation


title: PIP Day 9 biological rep 3of3

description:
H39
Gene expression data from day 9 of Placode differentiation


title: NSB Day 9  biological rep 1of3

description:
H31
Gene expression data from day 9 of NSB differentiation


title: PIP Day 7 biological rep 2of3

description:
H26
Gene expression data from day 7 of Placode differentiation


title: PIP Day 5 biological rep 3of3

description:
H17_H18
Gene expression data from day 5 of Placode differentiation


title: PIP Day 5 biological rep 2of3

description:
H15_H16
Gene expression data from day 5 of Placode differentiation


title: NSB Day 5  biological rep 1of3

description:
H7_H8
Gene expression data from day 5 of NSB differentiation


title: NSB Day 5 biological rep 2of3

description:
H9_H10
Gene expression data from day 5 of NSB differentiation


title: NSB Day 11 biological rep 2of3

description:
H44
Gene expression data from day 11 of NSB differentiation


title: Day 3 biological rep 3of3

description:
H5_H6
Gene expression data from day 3 of differentiation

source_name: H9 hESCs_day 3 of differentiation

value: day 3 of differentiation


title: hht2-pm-N108A-2-b

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
genes, no bg corr, dye corr
limma

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0

source_name: refpool

value: wild type


title: hht2-pm-R40A-2-a


title: Dm_ovary_PiwiNT/Piwi2_rep2

city: Moscow

first: Sergey

middle: A

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

country: Russia

institute: IMG

description: Comparison of gene expression levels in PiwiNT/Piwi2 ovaries and in ovaries of mix of heterozygotes PiwiNT/CyO and Piwi2/CyO

hyb_protocol: Equal amounts (10 mkg) of Cy3-coupled aRNA from flies of genotype piwiNT/Piwi2 and Cy5-coupled aRNA from flies PiwiNT/CyO; Piwi2/CyO (or vice versae for dye-swap) were mixed together and concentrated on speedvac to app. 10 mkl. For hybridization, 70 mkl of Dig EasyHyb (Roche) solution containing yeast tRNA (0.5 mkg/mkl) and DTT (0.1 mM) was added to aRNA mix and denatured at 65C fo 10'.  80 mkl of hybridization mix was applied to microarray slide (CDMC) pretreated according to manufacturer recommendations. Slides were covered by plastic Hybrislips (Corning) and hybridized overnight at 37C in moist chamber.  Washings were:  1xSSC, 0.1%SDS, 0.1 mM DTT at 37C. Remove coverslips.  3x15' in 1xSSC, 0.1%SDS, 0.1 mM DTT at 37С  1xSSC, 0.1 mM DTT ≤1' at room temperature  0.1xSSC, 0.1 mM DTT for ≤15sec  After washing, slides were centrifugated 5' at 500G in swinging rotor to remove drops and scanned.

scan_protocol: Microarray slides were scanned at 10µm resolution in PE ScanArray Express Microarray Scanner, using both green and red lasers (PMT75 for Cy5 and PMT90 for Cy3). The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: TIF images were processed in GenePix 6 software. Spots with percent of saturated pixels >3 and damaged or having abnormal appearance were flagged as bad, spots which fall below background threshold criteria:    (([% > B635+1SD] < 50 And [% > B532+1SD] < 50) Or ([SNR 635] < 2 And [SNR 532] < 2) Or (([F635 Median - B635]/[B635] < 1) And ([F532 Median - B532]/[B532] < 1))  flagged as Not found  Resulting .gpr files were exported into FlexArray 1.6.1.1 software, where raw data were background-corrected (normexp algorithm, saddle-point approximation to maximum likelihood without offset) and normalized using loess MA normalizaton (by print tip). Tables for submission were prepared in Excel

organism: Drosophila melanogaster

source_name: Ovaries from heterozygotes mix Piwi2/CyO; PiwiNT/CyO

label_protocol: 3 mkg of total RNA was reverse-transcribed using SuperScript II (Invirtogen) and 0.4 mkg of T7-oligo(dT)21 primer (5’–GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG –(dT)21–3’) in 20 mkl at 45C for 1 h 40'. Reaction was transferred into ice, then to 16C and 124 mkl cooled second strand synthesis mix (Enzymes from Invitrogen) added:   DEPC-treated water 91 mkl  5X Second-Strand Reaction Buffer 30 mkl  10 mM dNTP mix 3 mkl  E. coli DNA Ligase (10 U/μl) 1 mkl  E. coli DNA Polymerase I (10 U/μl) 4 mkl  E. coli RNase H (2 U/μl) 1 mkl  After incubation for 2 h 20' at 16C, 2 µl (10U) of T4 DNA Polymerase was added and the reaction was additionally incubated 5' at 16C, then placed on ice and 10 μl of 0.5 M EDTA added.  RNA in second strand synthesis reaction was hydrolyzed by NaOH (10М NaOH was added to 0.2 М, reaction incubated 15' at 70C and neutralized by 50 mkl of 1М Tris-HCl pH 8), ds cDNA then purified on Millipore Microcon 30 columns according to manufacturer instructions.  IVT and aminoallyl incorporation was carried using Ambion T7 MegaScript kit and T7-bearing ds cDNA from previous step. IVT was performed in the presence of aminoallyl-UTP (1:1,16 unmodified UTP)) for 5 h 30', aRNA from reaction mixture was purified using Qiagen RNAeasy MinElute kit according to manufacturer instruction.  Aminoallyl-aRNA (10-25 mkg) was dye-coupled to succinimide ester of either Cy3 or Cy5 in NaHCO3 -buffer at pH 8.7 for 1 h at room temperature, then purified on Millipore Microcon 30.

growth_protocol: Flies were crossed and propagated at 25 degrees Celsius on standard medium. 2-3 days old adult females were picked for ovary dissection.

extract_protocol: Ovaries were dissected from adult females in PBT (phosphate buffer saline + 0.1% Tween-20). Dissection time - 1-2 h at room temperature. Total RNA was extracted from 30-50 pairs of ovaries using Qiagen RNAeasy Mini kit and columns according to manufacturer instructions. Result of extraction - 30-40 mkg of RNA in sterile water. RNA was immediately used in indirect labeling reaction.

treatment_protocol: Females of PiwiNT/Piwi2 genotype were selected from the progeny of cross, PiwiNT/CyO x Piwi2/CyO, used also to produce mix of heterozygotes, PiwiNT/CyO; Piwi2/CyO

tag: genotype

value: Piwi2/CyO; PiwiNT/CyO

source_name: Ovaries from PiwiNT/Piwi2 flies


title: Day 1 biological rep 3of3

description:
H57
Gene expression data from day 1 of differentiation

source_name: H9 hESCs_day 1 of differentiation

tag: time point

value: day 1 of differentiation


title: hht2-pm-R53A-1-b


title: Day 3  biological rep 1of3

description:
H1_H2
Gene expression data from day 3 of differentiation


title: hht2-pm-N108A-2-a


title: hht2-pm-R53A-1-a


title: Day 3 biological rep 2of3

description:
H3_H4
Gene expression data from day 3 of differentiation


title: hht2-pm-R40A-2-b


title: rpaA-_LL_64h_rep1

source_name: rpaA- strain, LL, 64 h

value: rpaA::KmR (EOC 66)

value: pool of samples 24 h through 72 h

value: Equal mass quantities of each time point were mixed to prepare this background pool


title: hht2-pm-L109A-1-b


title: LSS_liver_Skamania_rep6

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description: Gene expression profiling of wild largescale sucker from three sites in the Columbia River

hyb_protocol: 600 ng of Cy3-labelled cRNA (average specific activity =9.27 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto  custom-designed fathead minnow (15K oligonulceotide) arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 min with GE Wash Buffer 1 (Agilent), GE Wash buffer 2 (Agilent) kept at 37°C , then 30 sec in Stabilization and Drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 035137_D_F_20110628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw intensity data were log2 transformed.

organism: Catostomus macrocheilus

source_name: liver, wild fish, Skamania, replicate 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit from Agilent according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Cy3 dye incorporation and cRNA yield were measured using the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using STAT-60 (Tel-Test) following the manufacturer's instructions and RNA was resuspended in RNA secure (Ambion) to remove RNAse contamination. RNA was treated with TURBO DNA-free (Ambion) to remove DNA contamination and purified using RNeasy wcolumns (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: tissue

value: liver

value: reproductive adults

tag: collection site

value: Skamania


title: Dm_ovary_PiwiNT/Piwi2_rep1


title: Dm_ovary_PiwiNT/Piwi2_rep3


title: LSS_liver_Longview_rep7

source_name: liver, wild fish, Longview, replicate 7

tag: Stage

value: Longview


title: LSS_liver_Skamania_rep8

source_name: liver, wild fish, Skamania, replicate 8


title: LSS_liver_Skamania_rep7

source_name: liver, wild fish, Skamania, replicate 7


title: LSS_liver_Longview_rep2

source_name: liver, wild fish, Longview, replicate 2


title: LSS_liver_Longview_rep4

source_name: liver, wild fish, Longview, replicate 4


title: LSS_liver_Skamania_rep3

source_name: liver, wild fish, Skamania, replicate 3


title: LSS_liver_Skamania_rep4

source_name: liver, wild fish, Skamania, replicate 4


title: hht2-wt-1-a


title: hht2-pm-Q5A-2-a


title: LSS_liver_Skamania_rep1

source_name: liver, wild fish, Skamania, replicate 1


title: LSS_liver_Skamania_rep2

source_name: liver, wild fish, Skamania, replicate 2


title: LSS_liver_Longview_rep6

source_name: liver, wild fish, Longview, replicate 6


title: LSS_liver_Longview_rep5

source_name: liver, wild fish, Longview, replicate 5


title: Day 1 biological rep 1of3

description:
H55
Gene expression data from day 1 of differentiation

value: human embryonic stem cells (hESCs)


title: Day 1 biological rep 2of3

description:
H56
Gene expression data from day 1 of differentiation


title: hht2-pm-Q5A-2-b

source_name: refpool


title: LSS_liver_Longview_rep3

source_name: liver, wild fish, Longview, replicate 3


title: hht2-wt-1-b


title: hht2-pm-G44A-2-b


title: hht2-pm-G44A-2-a


title: LSS_liver_Longview_rep1

source_name: liver, wild fish, Longview, replicate 1


title: LSS_liver_Skamania_rep5

source_name: liver, wild fish, Skamania, replicate 5


title: hht2-pm-L109A-1-a


title: hhf2-wt-1-b


title: LSS_liver_ColumbiaCity_rep6

source_name: liver, wild fish, Columbia City, replicate 6

value: Columbia City


title: LSS_liver_ColumbiaCity_rep3

source_name: liver, wild fish, Columbia City, replicate 3


title: hhf2-wt-1-a


title: LSS_liver_ColumbiaCity_rep4

source_name: liver, wild fish, Columbia City, replicate 4


title: LSS_liver_ColumbiaCity_rep1

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 035137_D_F_20110628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw intensity data were log2 transformed. Raw intensity data were log2 transformed.

source_name: liver, wild fish, Columbia City, replicate 1


title: LSS_liver_ColumbiaCity_rep5

source_name: liver, wild fish, Columbia City, replicate 5


title: hhf2-pm-V81A-2-a


title: hhf2-pm-Y98A-1-b


title: hhf2-pm-K44A-2-b


title: LSS_liver_ColumbiaCity_rep2

source_name: liver, wild fish, Columbia City, replicate 2


title: hhf2-pm-V81A-2-b


title: hhf2-pm-Y98A-1-a


title: BL6_T5-115_10d_heart

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: BL6_T5-113_10d_heart_miRNA_Hy3_v_BL6_T5-115_10d_heart_miRNA_Hy5.csv

hyb_protocol: Labeled samples were hybridized to Exiqon 5th generation miRCURY LNA microRNA array according to the manufacturer's protocol.

scan_protocol: After hybridization, the slides were washed and scanned with a scanner from Agilent (Santa Clara, CA).

data_processing: Scanned data was processed using AnalyzerDG software. For the preprocessing of two-channel microarray data in each experimental group,  Hy3 and Hy5 (high energy scanned) intensities were concatenated, normalized using LOWESS (within-array normalization) and normalized using the quantile method (between-array normalization).

source_name: Stressed_heart_tissue, T5R10

label_protocol: Total RNA from the heart tissue was labeled with either Hy3 or Hy5 dye with labeling kits from Exiqon then hybridized at 56°C for 16 h.

extract_protocol: Total RNA was isolated from individual mouse heart samples by homogenization in TRIzol reagent per the manufacturer’s protocol (Invitrogen, Gran Island, NY). The quality and quantity of the RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA).

treatment_protocol: The experimental animals were kept in a wire mesh box inside the aggressor´s cage for 6 hours a day for either 5 or 10 consecutive days.  Animals were randomly assigned to aggressors cages.  Each subject mouse was randomly placed 3-5 times within the home cage of an aggressor mouse and received bites/attacks for up to 2 min (or until 10 attacks/bites occurred, whichever came first.  Each day the stress procedure occurred at different times and different resident mice were used for each aggressor.  Body weight and temperature of the experimental mice were measured every day prior the beginning of the social defeat period and the return to their home cages.   Control mice were kept inside of the wired mesh boxes inside of a large cage without any aggressor.

value: Stressed_heart_tissue, T5R10


title: BL6_T5-113_10d_heart


title: BL6_T5-114_10d_heart

description: BL6_T5-112_10d_heart_miRNA_Hy3_v_BL6_T5-114_10d_heart_miRNA_Hy5.csv


title: BL6_T5-138_1d_heart

description: BL6_T5-136_1d_heart_miRNA_Hy3_v_BL6_T5-138_1d_heart_miRNA_Hy5.csv

source_name: Stressed_heart_tissue, T5R1

value: Stressed_heart_tissue, T5R1


title: BL6_T5-137_1d_heart

description: BL6_T5-135_1d_heart_miRNA_Hy3_v_BL6_T5-137_1d_heart_miRNA_Hy5.csv


title: BL6_T5-135_1d_heart


title: BL6_T5-136_1d_heart


title: hhf2-pm-K44A-2-a


title: BL6_T10-63_42d_heart

description: BL6_T10-59_42d_heart_miRNA_Hy3_v_BL6_T10-63_42d_heart_miRNA_Hy5.csv

source_name: Stressed_heart_tissue, T10R42

value: Stressed_heart_tissue, T10R42


title: BL6_T5-112_10d_heart


title: BL6_T10-59_42d_heart


title: Treated-2dayStress-1dayRest [BL6_T2-735_1d_heart]

description: Gene expression after 2day-stress and 1day-rest, treated mouse heart tissue

hyb_protocol: The labeled antisense cRNAs were purified and hybridized to microarrays. The hybridization was carried out for 16 h at 45°C.

scan_protocol: The arrays were washed and scanned using an Agilent scanner.

data_processing: The scanned images of the arrays were converted and imported into the Institute for Systems Biology’s Systems Biology Experiment Analysis System (SBEAMS) for array data normalization and further analyses.

source_name: Heart tissue, 2day-stress, 1day-rest, rep2

label_protocol: Total RNA was reverse transcribed and followed by generation of cDNAs. The resulting cDNAs were transcribed and labeled with cyanine 3-CTP.

value: heart tissue


title: Treated-3dayStress-1dayRest [BL6_T3-702_1d_heart]

description: Gene expression after 3day-stress and 1day-rest, treated mouse heart tissue

source_name: Heart tissue, 3day-stress, 1day-rest, rep2


title: Treated-3dayStress-1dayRest [BL6_T3-701_1d_heart]

source_name: Heart tissue, 3day-stress, 1day-rest, rep1


title: BL6_T10-60_42d_heart

description: BL6_T10-57_42d_heart_miRNA_Hy3_v_BL6_T10-60_42d_heart_miRNA_Hy5.csv


title: BL6_T10-57_42d_heart


title: BL6_C10-96_1d_heart

description: BL6_T10-108_1d_heart_miRNA_Hy3_v_BL6_C10-96_1d_heart_miRNA_Hy5.csv

source_name: Control_heart_tissue, C10R1

value: Control_heart_tissue, C10R1


title: Treated-3dayStress-1dayRest [BL6_T3-704_1d_heart]

source_name: Heart tissue, 3day-stress, 1day-rest, rep4


title: Treated-3dayStress-1dayRest [BL6_T3-703_1d_heart]

source_name: Heart tissue, 3day-stress, 1day-rest, rep3


title: Treated-2dayStress-1dayRest [BL6_T2-734_1d_heart]

source_name: Heart tissue, 2day-stress, 1day-rest, rep1


title: Treated-2dayStress-1dayRest [BL6_T2-736_1d_heart]

source_name: Heart tissue, 2day-stress, 1day-rest, rep3


title: BL6_C5-134_10d_heart

description: BL6_C5-134_10d_heart_miRNA_Hy3_v_BL6_C5-126_10d_heart_miRNA_Hy5.csv

source_name: Control_heart_tissue, C5R10

value: Control_heart_tissue, C5R10


title: Control [BL6_C2-688_1d_heart]

description: Gene expression after 2day-stress and 1day-rest, control mouse heart tissue


title: Treated-1dayStress-1dayRest [BL6_T1-740_1d_heart]

description: Gene expression after 1day-stress and 1day-rest, treated mouse heart tissue

source_name: Heart tissue, 1day-stress, 1day-rest, rep2


title: BL6_C5-126_10d_heart


title: Treated-1dayStress-1dayRest [BL6_T1-739_1d_heart]

source_name: Heart tissue, 1day-stress, 1day-rest, rep1


title: Treated-1dayStress-1dayRest [BL6_T1-742_1d_heart]

source_name: Heart tissue, 1day-stress, 1day-rest, rep4


title: BL6_T10-107_1d_heart

description: BL6_T10-107_1d_heart_miRNA_Hy3_v_BL6_C10-95_1d_heart_miRNA_Hy5.csv

source_name: Stressed_heart_tissue, T10R1

value: Stressed_heart_tissue, T10R1


title: BL6_T10-108_1d_heart


title: BL6_C5-133_10d_heart

description: BL6_C5-133_10d_heart_miRNA_Hy3_v_BL6_C5-125_10d_heart_miRNA_Hy5.csv


title: BL6_C10-95_1d_heart


title: Control [BL6_C2-687_1d_heart]


title: BL6_C5-130_1d_heart

description: BL6_C5-128_1d_heart_miRNA_Hy3_v_BL6_C5-130_1d_heart_miRNA_Hy5.csv

source_name: Control_heart_tissue, C5R1

value: Control_heart_tissue, C5R1


title: Treated-2dayStress-1dayRest [BL6_T2-737_1d_heart]

source_name: Heart tissue, 2day-stress, 1day-rest, rep4


title: Control [BL6_C2-686_1d_heart]


title: BL6_C5-128_1d_heart


title: Control [BL6_C2-689_1d_heart]


title: Treated-1dayStress-1dayRest [BL6_T1-741_1d_heart]

source_name: Heart tissue, 1day-stress, 1day-rest, rep3


title: BL6_C5-127_1d_heart

description: BL6_C5-127_1d_heart_miRNA_Hy3_v_BL6_C5-129_1d_heart_miRNA_Hy5.csv


title: BL6_C5-125_10d_heart


title: BL6_T10-110_1d_heart

description: BL6_C10-94_1d_heart_miRNA_Hy3_v_BL6_T10-110_1d_heart_miRNA_Hy5.csv


title: BL6_C10-94_1d_heart


title: BL6_C10-93_1d_heart

description: BL6_C10-93_1d_heart_miRNA_Hy3_v_BL6_T10-109_1d_heart_miRNA_Hy5.csv


title: Treated-5dayStress-1dayRest [BL6_T5-136_1d_heart]

description: Gene expression after 5day-stress and 1day-rest, treated mouse heart tissue

source_name: Heart tissue, 5day-stress, 1day-rest, rep2


title: BL6_T10-109_1d_heart


title: Treated-5dayStress-1dayRest [BL6_T5-138_1d_heart]

source_name: Heart tissue, 5day-stress, 1day-rest, rep4


title: BL6_C10-50_42d_heart

description: BL6_C10-48_42d_heart_miRNA_Hy3_v_BL6_C10-50_42d_heart_miRNA_Hy5.csv

source_name: Control_heart_tissue, C10R42

value: Control_heart_tissue, C10R42


title: BL6_C10-48_42d_heart


title: Treated-5dayStress-1dayRest [BL6_T5-137_1d_heart]

source_name: Heart tissue, 5day-stress, 1day-rest, rep3


title: BL6_C10-49_42d_heart

description: BL6_C10-46_42d_heart_miRNA_Hy3_v_BL6_C10-49_42d_heart_miRNA_Hy5.csv


title: Treated-5dayStress-10dayRest [BL6_T5-114_10d_heart]

description: Gene expression after 5day-stress and 10day-rest, treated mouse heart tissue

source_name: Heart tissue, 5day-stress, 10day-rest, rep3


title: Treated-5dayStress-1dayRest [BL6_T5-135_1d_heart]

source_name: Heart tissue, 5day-stress, 1day-rest, rep1


title: Treated-5dayStress-10dayRest [BL6_T5-115_10d_heart]

source_name: Heart tissue, 5day-stress, 10day-rest, rep4


title: Treated-10dayStress-42dayRest [BL6_T10-59_42d_heart]

description: Gene expression after 10day-stress and 42day-rest, treated mouse heart tissue

source_name: Heart tissue, 10day-stress, 42day-rest, rep2


title: T2R1_rep4

data_processing: Scanned data was processed using Agilent Feature Extraction. For the preprocessing of two-channel microarray data,  gProcessedSignal and rProcessedSignal intensities were concatenated and they were normalized using quantile method.


title: Treated-5dayStress-10dayRest [BL6_T5-113_10d_heart]

source_name: Heart tissue, 5day-stress, 10day-rest, rep2


title: Treated-10dayStress-1dayRest [BL6_T10-109_1d_heart]

description: Gene expression after 10day-stress and 1day-rest, treated mouse heart tissue

source_name: Heart tissue, 10day-stress, 1day-rest, rep3


title: Treated-10dayStress-42dayRest [BL6_T10-63_42d_heart]

source_name: Heart tissue, 10day-stress, 42day-rest, rep4


title: T2R1_rep3


title: T2R1_rep2


title: Treated-10dayStress-1dayRest [BL6_T10-110_1d_heart]

source_name: Heart tissue, 10day-stress, 1day-rest, rep4


title: Treated-5dayStress-10dayRest [BL6_T5-112_10d_heart]

source_name: Heart tissue, 5day-stress, 10day-rest, rep1


title: Treated-10dayStress-1dayRest [BL6_T10-107_1d_heart]

source_name: Heart tissue, 10day-stress, 1day-rest, rep1


title: Treated-10dayStress-42dayRest [BL6_T10-60_42d_heart]

source_name: Heart tissue, 10day-stress, 42day-rest, rep3


title: BL6_C10-46_42d_heart


title: Treated-10dayStress-1dayRest [BL6_T10-108_1d_heart]

source_name: Heart tissue, 10day-stress, 1day-rest, rep2


title: Treated-10dayStress-42dayRest [BL6_T10-57_42d_heart]

source_name: Heart tissue, 10day-stress, 42day-rest, rep1


title: T2R1_rep1


title: T1R1_rep3


title: T1R1_rep2


title: T3R1_rep4


title: Control-5dayStress-1dayRest [BL6_C5-129_1d_Heart]

description: Gene expression after 5day-stress and 1day-rest, control mouse heart tissue


title: T1R1_rep4


title: Control-5dayStress-1dayRest [BL6_C5-130_1d_Heart]


title: Control-5dayStress-1dayRest [BL6_C5-127_1d_Heart]


title: Control-5dayStress-1dayRest [BL6_C5-128_1d_Heart]

source_name: Heart tissue, 5day-stress, 1day-rest, rep2


title: Control-5dayStress-10dayRest [BL6_C5-134_10d_Heart]

description: Gene expression after 5day-stress and 10day-rest, control mouse heart tissue


title: T3R1_rep3


title: Control-10dayStress-42dayRest [BL6_C10-50_42d_Heart]

description: Gene expression after 10day-stress and 42day-rest, control mouse heart tissue


title: T3R1_rep2


title: Control-5dayStress-10dayRest [BL6_C5-125_10d_Heart]


title: T1R1_rep1


title: Control-10dayStress-42dayRest [BL6_C10-49_42d_Heart]


title: C2R1_rep2


title: Control-5dayStress-10dayRest [BL6_C5-133_10d_Heart]


title: C2R1_rep1


title: C2R1_rep3


title: C2R1_rep4


title: Control-5dayStress-10dayRest [BL6_C5-126_10d_Heart]


title: T3R1_rep1


title: Control-10dayStress-42dayRest [BL6_C10-46_42d_Heart]


title: Control-10dayStress-1dayRest [BL6_C10-96_1d_heart]

description: Gene expression after 10day-stress and 1day-rest, control mouse heart tissue


title: Control-10dayStress-1dayRest [BL6_C10-93_1d_heart]


title: Control-10dayStress-42dayRest [BL6_C10-48_42d_Heart]