title: 18 XY vs 18 XX (22K-2)

status: Public on Mar 31 2010

city: Bunkyo-ku

first: Shin

last: Kobayashi

state: Tokyo

address: 1-5-45 yushima

department: Medical Research Institute

institute: Tokyo Mdical & Dental University

description: Total RNAs were extracted from over 200 male or female sex-separated blastocysts using an ISOGEN in the presence of 1µg of yeast tRNA as a carrier.

hyb_protocol: Hybridization was carried out for 17 hours using an Agilent’s in situ Hybridization Kit Plus.

scan_protocol: All microarray experiments were carried out following the Agilent’s standard methodology. All experimental procedures can be obtained from the Agilent’s web site (http://www.chem.agilent.com/scripts/generic.asp? lpage=11617&indcol=N&prodcol=Y).

data_processing: Hybridized slides were scanned using the Agilen’ts microarray scanner.

source_name: E3.5 blastocyst 18 XY

label_protocol: Total RNA was labeled using a Low Input Fluorescent Linear Amplification kit (Agilent) following the manufacturer’s instruction.

growth_protocol: B6C3F1 female mice of 8 weeks in age, were superovulated with 5 IU of pregnant mare serum gonadotropin (PMS) followed by 5 IU of human chorionic gonadotropin (hCG) 48 hr later, and were mated with XGFPY male mice. Four-cell stage embryos were collected from the oviducts 55 hr after the hCG injection and placed in kSOM and incubated in a humidified atmosphere of 5% CO2 in air at 37 ºC for an additional 38 hr.

extract_protocol: RNA was obtained using ISOGEN (NIPPON GENE Inc., Japan) which is based on the acid guanidine thiocyanate-phenol-chloroform extraction method.

treatment_protocol: No treatment

tag: sex

value: male (GFP negative)

value: whole embryo

source_name: E3.5 blastocyst 18 XX

value: female (GFP positive)


title: 23 XX vs 23 XY (22K-2)

type: RNA

country: Japan

molecule: total RNA

organism: Mus musculus

source_name: E3.5 blastocyst 23 XX

tag: strain

tag: age

tag: tissue

source_name: E3.5 blastocyst 23 XY


title: 19 XY vs 19 XX (22K-2)

source_name: E3.5 blastocyst 19 XY

source_name: E3.5 blastocyst 19 XX


title: 19 XX vs 19 XY (22K-2)


title: 18 XX vs 18 XY (22K-2)


title: Mouse spleen control BXD98

city: Knoxville

first: Rachel

last: Lynch

state: TN

address: 2640 Morgan Circle Drive, 51f McCord Hall

department: Life Sciences

country: USA

institute: University of Tennessee

description: Pool of equal amounts of RNA from 2 individuals from same sex/strain

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were background corrected (force positive) and then normalized using Variance Stabilizing Transformation (VST) followed by Robust Spline Normalization (RSN) using the lumi package in Bioconductor.

source_name: Mouse spleen BXD98

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit (Ambion Catalog # IL1791)

extract_protocol: Spleens were stabilized in RNAlater and total RNA was extracted using RNeasy Mini Kits (Qiagen, Valencia, CA), and RNA concentration and quality was assessed using the Experion RNA StdSens Chips on the Experion system (Bio-Rad, Hercules, CA).

value: Male

value: spleen


title: 23 XY vs 23 XX (22K-2)


title: E10.5 Magoh mutant cortex, biological rep 2

status: Public on Apr 04 2010

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

hyb_protocol: Labelled and fragmented cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST chips overnight. The chips were washed and stained by the Affymetrix Fluidics Station.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were caluculated using Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software. RMA normalziation was performed to generate the CHP files. Genesifter software and Pairwise comparisons were perfomed with Benjamini and Hochberg correction.

label: biotin

source_name: Magoh-Mos2 heterozygous E10.5 cortices

label_protocol: Per RNA labeling, 300 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 1.0 ST chip

growth_protocol: E10.5 embyros were harvested from pregnant females and cortices (pair per embyro) were carefully dissected and placed on ice

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

treatment_protocol: Lysates were gently homogenized in cold PBS and then Trizol and frozen at -80C

value: embryonic brain cortex

tag: genotype

value: Magoh

tag: genetic background


title: Mouse spleen control BXD83

source_name: Mouse spleen BXD83


title: Mouse spleen control BXD96

source_name: Mouse spleen BXD96

value: Female


title: Mouse spleen control BXD73

source_name: Mouse spleen BXD73


title: Mouse spleen control BXD65

source_name: Mouse spleen BXD65


title: Mouse spleen control BXD68

source_name: Mouse spleen BXD68


title: Mouse spleen control BXD70

source_name: Mouse spleen BXD70


title: Mouse spleen control BXD87

source_name: Mouse spleen BXD87


title: Mouse spleen control BXD50

source_name: Mouse spleen BXD50


title: Mouse spleen control BXD62

source_name: Mouse spleen BXD62


title: Mouse spleen control BXD44

source_name: Mouse spleen BXD44


title: Mouse spleen control BXD51

source_name: Mouse spleen BXD51


title: Mouse spleen control BXD42

source_name: Mouse spleen BXD42


title: Mouse spleen control BXD69

source_name: Mouse spleen BXD69


title: Cdr2 siRNA-HeLa-3

status: Public on Apr 07 2010

city: New York

first: Kevin

middle: J

last: O'Donovan

state: NY

address: 1230 York Avenue

institute: Rockefeller Univeristy

description: Gene expresion data from cdr2 siRNA siRNA-treated HeLa cells 3 hours following release from mitotic (nocodazole) block

hyb_protocol: The biotinylated cRNA targets are were cleaned up, fragmented, and hybridized to GeneChip expression arrays according to standard Affymetrix protocols

scan_protocol: Gene chips were scanned using the GeneArray® Scanner from Affymetrix

data_processing: The data were normalized using MAS5.0 and analyzed using GenespringGX 4.0

organism: Homo sapiens

source_name: cdr2 siRNA-treated HeLa cells 3 hours following release from mitotic (nocodazole) block

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion protocol from 6 ug total RNA (MessageAmp RNA Amplification Kits)

growth_protocol: Cells were grown in DMEM/10% FBS/Pen-Strep

extract_protocol: HeLa cells were washed twice with PBS and RNA was harvested directly using the RLT buffer from the Rneasy kit from Qiagen

treatment_protocol: Cells were treated with cdr2 or control siRNAs 48 hours prior to synchronization in mitosis. Cells were synchronized by incubating in 2mM thymidine for 18 hours followed by washout for 3 hours then addition of 0.8uM nocodazole for 12 hours. RNA was harvested 3 hours after release from a mitotic block.

tag: cell line

value: HeLa cell-cervical carcinoma

tag: protocol

value: siRNA-mediated cdr2 knockdown


title: Mouse spleen control BXD40

source_name: Mouse spleen BXD40


title: Mouse spleen control BXD48

source_name: Mouse spleen BXD48


title: HeLa_Pol3ChIParray_rep1 Slide 10

status: Public on Apr 14 2010

type: genomic

first: Andrew

last: Oler

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

description: Pol3 ChIP-chip, Santa Cruz Biotechnologies sc-21754 RPC32 antibody, whole nonrepeat genome array slide 10 of 10

hyb_protocol: ChIP array hybridization and wash were carried out according the Agilent Technologies Mammalian ChIP-on-chip protocol version 10.0 (www.Agilent.com).

scan_protocol: Arrays were scanned with Agilent Technologies’ Scanner C (Cat. G2505C).

data_processing: Feature Extraction was performed with Agilent Technologies FE version 10.1.1.22 using the default ChIP settings.  Arrays were analyzed using DNA Analytics’ ChIP-chip analysis module (Agilent) and bound regions for all ten arrays were determined using the default analysis settings.  Briefly, default Feature Extraction (FE) output was used for normalization and the FE Error Model was used for Error Modeling.  Enriched regions were determined using the Whitehead Per Array Neighbourhood Model.  A probe is considered bound based on the average intensity of itself and 2 of its neighbors.  In this model, the average must pass a p-value cutoff of 0.0001 and either the central probe and a neighbor must pass p-value cutoffs of  0.0001 and 0.01, respectively, or a single neighbor has to pass a p-value cutoff of 0.005.

molecule: genomic DNA

source_name: HeLa S3

label_protocol: ChIP, amplification and labeling were carried out according the Agilent Technologies Mammalian ChIP-on-chip protocol version 10.0 (www.Agilent.com).

growth_protocol: HeLa S3 cells were cultured and harvested by Biovest International according to standard protocols.  Briefly, cells were grown in Joklik's modified MEM in suspension flasks with 5% newborn calf serum and harvested at mid log phase (about 0.5-0.65 x 10^6/ml).

extract_protocol: Crosslinked Hela cells (Biovest International), were used to perform Chromatin Immunoprecipitation for RPC32 (Santa Cruz Biotechnology cat # SC-21754).

value: HeLa S3, ATCC CCL-2.2

tag: chip antibody

value: RPC32 (Pol III), sc-21754


title: Mouse spleen control BXD66

source_name: Mouse spleen BXD66


title: Mouse spleen control BXD61

source_name: Mouse spleen BXD61


title: Mouse spleen control BXD75

source_name: Mouse spleen BXD75


title: Mouse spleen control BXD38

source_name: Mouse spleen BXD38


title: Mouse spleen control BXD43

source_name: Mouse spleen BXD43


title: Mouse spleen control BXD45

source_name: Mouse spleen BXD45


title: Mouse spleen control BXD33

source_name: Mouse spleen BXD33


title: Mouse spleen control BXD34

source_name: Mouse spleen BXD34


title: Mouse spleen control BXD28

source_name: Mouse spleen BXD28


title: Mouse spleen control BXD29

source_name: Mouse spleen BXD29


title: Mouse spleen control BXD21

source_name: Mouse spleen BXD21


title: Mouse spleen control BXD24

source_name: Mouse spleen BXD24


title: Mouse spleen control BXD36

source_name: Mouse spleen BXD36


title: Mouse spleen control BXD32

source_name: Mouse spleen BXD32


title: Mouse spleen control BXD16

source_name: Mouse spleen BXD16


title: Mouse spleen control BXD27

source_name: Mouse spleen BXD27


title: Mouse spleen control BXD18

source_name: Mouse spleen BXD18


title: Mouse spleen control BXD19

source_name: Mouse spleen BXD19


title: miRNA_neutrophils_before exercise_09

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

description: gene expression before-exercise

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: The results were analyzed using GeneSpring GX 10.0.2 Software (Agilent Technologies, Inc).

source_name: Human netrophils before exercise

label_protocol: One hundred ng of total RNA was labeled with the fluorescent dye Cyanine 3-pCp (Cy3) using the miRNA Labeling Reagent and Hybridization Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

extract_protocol: Neutrophils were isolated from EDTA treated peripheral blood using OptiPrep Density Gradient Medium (SIGMA). Using Wright-Giemsa stain, we determined that this approach to neutrophil isolation consistently yielded ≥ 98% purification. Total RNA was extracted using TRIzol® (Gibco BRL Life Technologies, Rockville, MD).

treatment_protocol: Blood sample was drawn before and immediately after 20 min of exercise.

tag: cell type

value: neutrophils


title: miRNA_neutrophils_before exercise_10

description: gene expression before-exercise


title: gnl2-vs-wt-1

city: Utrecht

first: Judith

last: Paridaen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: The arrays were scanned using a G2505C Agilent DNA microarray scanner

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Danio rerio

label_protocol: Control targets and hybridization buffer (Gene Expression Hybridization Kit (5188-5242, Agilent) were added and samples were hybridized for 17 hours at 60 °C  to a 22K zebrafish expression array (G2518a option 001; Agilent). Subsequently, arrays were washed according to manufacturer's instructions.

growth_protocol: Zebrafish embryos (progeny of two gnl2 heterozygous carriers or wild-type TL zebrafish) were cultured at 28.5 °C in standard embryo medium until collection at 22 hpf based on morphological characteristics. Half of the collected embryos were used for genotyping to confirm mutant genotype.

extract_protocol: 500 ng total RNA was reverse transcribed and labelled cRNA was synthesized using the two color Quick-Amp Labeling Kit (5190-0444, Agilent) incorporating cy3 or cy5. Samples were purified using the RNeasy Mini kit (Qiagen) and concentration and dye incorporation were determined using a Nanodrop spectrophotometer.

treatment_protocol: Total RNA from 40 mutant or wild-type embryos was extracted using Trizol reagent following manufacturer's instructions followed by RNA cleanup using Qiagen RNeasy kit according to manufacturer's instructions

value: Gnl2 (bw41c) homozygous

value: 22 hpf

source_name: WT

value: Wild-type (TL)


title: wt-vs-gnl2-1

value: WT (TL)


title: miRNA_neutrophils_after exercise_09

description: gene expression after-exercise

source_name: Human netrophils after 20 min bout of exercise


title: miRNA_neutrophils_after exercise_08

description: gene expression after-exercise


title: Mouse spleen control BXD11

source_name: Mouse spleen BXD11


title: miRNA_neutrophils_after exercise_11

description: gene expression after-exercise


title: miRNA_neutrophils_before exercise_08

description: gene expression before-exercise


title: miRNA_neutrophils_after exercise_10

description: gene expression after-exercise


title: Mouse spleen control BXD14

source_name: Mouse spleen BXD14


title: Mouse spleen control BXD12

source_name: Mouse spleen BXD12


title: miRNA_neutrophils_before exercise_05

description: gene expression before-exercise


title: Mouse spleen control BXD6

source_name: Mouse spleen BXD6


title: miRNA_neutrophils_after exercise_06

description: gene expression after-exercise


title: miRNA_neutrophils_before exercise_11

description: gene expression before-exercise


title: miRNA_neutrophils_after exercise_05

description: gene expression after-exercise


title: miRNA_neutrophils_before exercise_04

description: gene expression before-exercise


title: miRNA_neutrophils_before exercise_06

description: gene expression before-exercise


title: miRNA_neutrophils_after exercise_04

description: gene expression after-exercise


title: miRNA_neutrophils_after exercise_07

description: gene expression after-exercise


title: miRNA_neutrophils_after exercise_02

description: gene expression after-exercise


title: miRNA_neutrophils_after exercise_03

description: gene expression after-exercise


title: miRNA_neutrophils_before exercise_02

description: gene expression before-exercise


title: miRNA_neutrophils_before exercise_03

description: gene expression before-exercise


title: miRNA_neutrophils_before exercise_01

description: gene expression before-exercise


title: miRNA_neutrophils_after exercise_01

description: gene expression after-exercise


title: Male, hUSF1, Replicate 1

city: Los Angeles

first: Sulin

last: Wu

address: 675 Charles Young E. Dr,

department: Human Genetics

institute: UCLA

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Lumi (Bioconductor) in R

label: Biotin

source_name: Male, hUSF1

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

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

value: 4 months

value: liver


title: Female, hUSF1, Replicate 2

description: Replicate 2

source_name: Female, hUSF1


title: Male, hUSF1, Replicate 2

description: Replicate 2


title: Female, eGFP, Replicate 3

description: Replicate 3

source_name: Female, eGFP


title: Female, eGFP, Replicate 2

description: Replicate 2


title: Male, hUSF1, Replicate 3

description: Replicate 3


title: Female, hUSF1, Replicate 3

description: Replicate 3


title: Male, eGFP, Replicate 1

description: Replicate 1

source_name: Male, eGFP


title: Male, eGFP, Replicate 3

description: Replicate 3


title: Male, eGFP, Replicate 2

description: Replicate 2


title: Female, hUSF1, Replicate 1

description: Replicate 1


title: miRNA_neutrophils_before exercise_07

description: gene expression before-exercise


title: EP4KO (KO or Tg) #3 - low EF

city: Detroit

first: Margot

middle: C

last: LaPointe

state: MI

address: 2799 W. Grand Blvd.

department: Internal Medicine

institute: Henry Ford Hospital

scan_protocol: Standard Illumina scanning protocol with BeadStation 500 GX with scan settings at the default settings for Direct Hybridization.

data_processing: Raw expression data of the 24 mice from the Illumina BeadStudio software were processed using the lumi program (version 1.6.3), which is an implemented package designed for processing Illumina microarrays in R (version 2.8.0) [http://www.R-project.org.], the open source environment of statistical analysis. The raw intensities from each mouse sample were transformed using variance stabilization transformation (VST), which takes advantage of the multiple replicates available on the Illumina arrays.

source_name: left ventricle

label_protocol: Biotinylated cRNAs were prepared with the Illumina TotalPrep RNA amplification kit.

extract_protocol: RNA was extracted using an RNAeasy fibrous tissue mini kit (Qiagen), followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

value: mixed genetic background

tag: age (weeks)

tag: ef%

value: male

value: left ventricle


title: EP4KO (KO or Tg) #5 - low EF


title: Female, eGFP, Replicate 1

description: Replicate 1


title: EP4KO (KO or Tg) #11 - high EF


title: EP4KO (KO or Tg) #10 - high EF


title: EP4KO (KO or Tg) #8 - high EF


title: EP4KO (KO or Tg) #7 - high EF


title: EP4KO (KO or Tg) #9 - high EF


title: EP4KO (KO or Tg) #12 - high EF


title: EP4KO (KO or Tg) #6- low EF


title: EP4KO (KO or Tg) #1 - low EF


title: Wildtype (WT) or Cont sample 10


title: Wildtype (WT) or Cont sample 11


title: EP4KO (KO or Tg) #2 - low EF


title: EP4KO (KO or Tg) #4 - low EF


title: EP4KO (KO or Tg) #13 - high EF


title: Wildtype (WT) or Cont sample 7


title: Wildtype (WT) or Cont sample 4


title: U937_untreated_rep1

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: gender: male

hyb_protocol: Samples were hybridized according to the manufacture's instruction. 1.65 µg labeled cRNA was supplemented with 11 µl Agilent 10x blocking agent, 2.2 µl Agilent 25x fragmentation buffer and nuclease-free water up to 55 µl final volumen. The sample was incubated at 60°C for 30 minutes, supplemented with 55 µl 2x hybridisation buffer and 100 µl of the mix was hybridisized for 16h at 65°C using an SureHyb chamber and an Agilent hybridization oven. Arrays were disassembled and washed for 1 minute in Agilent gene Expression (GE)  wash buffer 1 followed by washing 1 minute in prewarmed (37°C) GE wash buffer 2.

scan_protocol: Images were scanned immediately after washing using a DNA microarray scanner (Agilent) at 5 µm resolution.

data_processing: Data was processed using Feature Extraction Software (Agilent) and further analyzed using GeneSpring GX software version 10. Raw data was normalized by a 75 percentile shift, log2-transformed and shifted to values above one.

source_name: cell culture, myeloid leukemia cell line

label_protocol: Labeling and hybridization were performed using the Agilent Gene Expression system according to the manufacturer’s instructions. In brief, 200 ng to 1000 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low RNA Input Linear Amplification Kit (Agilent). Labeling efficiency was controlled using the NanoDrop spectrophotometer.

growth_protocol: Sorted CD34+ progenitor cells from two healthy male donors were purchased from Lonza Cologne AG, Cologne, Germany. The human myeloid leukemia cell line U937 was grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany).

extract_protocol: Total cellular RNA of the different cell types was isolated using the RNeasy Kit (Qiagen). RNA concentration was measured with a ND-1000 Spectrophotometer (NanoDrop, Thermo Fisher Scientific) and quality was controlled on agarose gels or using the Agilent Bioanalyzer.

tag: gender

value: luekemic myelid


title: Wildtype (WT) or Cont sample 3


title: Wildtype (WT) or Cont sample 6


title: Wildtype (WT) or Cont sample 2


title: Wildtype (WT) or Cont sample 5


title: Wildtype (WT) or Cont sample 8


title: Wildtype (WT) or Cont sample 9


title: CD34+progenitor_sorted_rep2

description: gender: male

source_name: whole blood, donor5

value: CD34+ hematopoietic progenitor cells


title: Wildtype (WT) or Cont sample 1


title: CD14+monocytes_sorted_rep3

description: gender: male

source_name: whole blood, donor3

value: CD14+ peripheral blood monocytes


title: CD34+progenitor_sorted_rep1

description: gender: male

source_name: whole blood, donor4


title: CD14+monocytes_sorted_rep2

description: gender: male

source_name: whole blood, donor2


title: OFTu + OV-IA82 at 4 hpi

city: Urbana

first: Diego

middle: G.

last: Diel

state: IL

address: 2001, S Lincoln Ave

department: Pathobiology

institute: University of Illinois

description: Gene  expression data from OFTu cells infectec with Wild Type ORFV OV-IA82 and harvested for RNA extraction at 4 hpi

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Bovine Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages using these 4 arrays plus 14 other arrays from additional mutants and time points (not released at this time). Additionally, Affymetrix's Call Detection algorithm was used to exclude probesets that were not called Present on at least one array or Marginal on two arrays from the fold-change calculation.

organism: Ovis aries

source_name: Primary ovine fetal turbinate cells infected with ORFV strain OV-IA82 at 4hpi

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: OFTu cells were cultured in MEM supplemented with 10% of fetal bovine serum, 2 mM L-Glutamine, 50µg/mL of gentamicin, 100U/mL of Penicilin and 100µg/mL of streptomicin. Cells were cultured at 37° for 16 h with 5% of CO2.

extract_protocol: Total RNA was extracted wirh TRIZOL reagent according to manufacturer's instructions. Samples were treated with DNAase for 10 min at 37° followed by clean up using the RNeasy Kit from Qiagen following the recommended protocol.

treatment_protocol: OFTu cells were cultured in 35 mm dishes (7 X 10^5 cells/dish) for 16 hours and inoculated with 10 m.o.i of the Wild type virus (OV-IA82) or deletion mutant virus (OV-IA82Δ024). Cells were harvested and total RNA was extracted at 2 and 4 hours post-infection.

value: primary ovine fetal turbinate cells

tag: passage number

tag: time of culture before infection

tag: time post-infection

value: 4 h


title: OFTu + OV-IA82 at 2 hpi

description: Gene  expression data from OFTu cells infectec with Wild Type ORFV OV-IA82 and harvested for RNA extraction at 2 hpi

source_name: Primary ovine fetal turbinate cells infected with ORFV strain OV-IA82 at 2hpi

value: 2 h


title: OFTu + OV-IA82Δ024 at 4 hpi

description: Gene  expression data from OFTu cells infectec with deletion mutant ORFV OV-IA82Δ024 and harvested for RNA extraction at 2 hpi

source_name: Primary ovine fetal turbinate cells infected with ORFV strain OV-IA82Δ024 at 4hpi


title: OFTu + OV-IA82Δ024 at 2 hpi


title: CD14+monocytes_sorted_rep1

description: gender: male

source_name: whole blood, donor1


title: A114_16_10b_wt_beta_T0901317

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: To study the importance of each of the receptor subtypes, myotube cultures derived from wild type (WT), LXRa and LXRb knockout (KO) mice were established.

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA v2.10.0, applying the Emperical Bayes (EB) estimate to estimate background levels.

source_name: primary myotubes derived from WT

label_protocol: Affymetrix One-cycle Target Labeling Assay was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix. A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: The hindlimbs were removed from 5-6 weeks old female LXRα and LXRβ KO mice and the bones were dissected away. The remaining muscle mass was minced to a slurry with razor blades. The tissue was then incubated in 2 % collagenase II at 37 °C for 90 minutes to enzymatically dissociate the cells. Trituration was performed to separate myofibres. Satellite cells were liberated by further digestion with Blendzyme 0.038 WU/ml at 37 °C for 30 minutes and then passed through 70 µm nylon mesh. To sediment the dissociated cells, the filtrate was spun at 1000 g. The pellet was resuspended in growth medium and seeded out on collagen II coated flasks. To enrich myoblasts, cells were split using HBSS with no trypsin or EDTA. Further enrichment of myoblasts was obtained by preplating. When fibroblasts were no longer visible in the culture, a cell-bank was established. The cells were grown at 37 °C in a humidified 5 % CO2 atmosphere. Growth medium for myoblasts was composed of Ham’s F-10 nutrient mixture supplemented with 20 % FBS and 5 ng/ml bFGF, whereas DMEM supplemented with 2 % horse serum was used as differential medium. Culturing of cells was performed in flasks and wells coated with Matrigel (BD Biosciences) diluted 1:50 in DMEM.

extract_protocol: Total RNA was prepared from primary myotubes from three mice per group using Agilent Total RNA isolation kit according to the supplier’s protocol (Agilent Technologies, Santa Clara, CA, USA). RNA was used individually and RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mouse myoblasts were grown to confluence, allowed to differentiate for two days, and then exposed to either 1 µM T0901317 or vehicle (DMSO) for another two days before experiments were performed.

tag: Backgroud:C57/BL6, Gender:female, Age:5-6 weeks


title: A114_21_6b_ko_LXRbeta_ctr

source_name: primary myotubes derived from LXRb knockout mice


title: A114_24_9b_ko_LXRbeta_T0901317


title: A114_13_5b_wt_beta_ctr


title: A114_08_2a_ko_LXRalpha_T0901317

source_name: primary myotubes derived from LXRa knockout mice


title: A114_22_6b_ko_LXRbeta_T0901317

source_name: primary myotube derived from LXRb knockout mice


title: A114_15_10b_wt_beta_ctr


title: A114_07_2a_ko_LXRalpha_ctr


title: A114_12_11a_ko_LXRalpha_T0901317


title: A114_14_5b_wt_beta_T0901317


title: Acute myeloid leukemia (AML), first diagnosis, before treatment L81

hyb_protocol: Comparative MCIp hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the recommended, stringent protocol (Agilent).

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were analysed and data extracted using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data were obtained from log10 transformed, processed Red signal/processed Green signal values derived from image analysis with Agilent Feature Extraction Software (version 9.5.1).  Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis.

label: Alexa Fluor 5–dCTP

source_name: acute leukemia

label_protocol: Enriched methylated DNA fragments of the high-salt MCIp fractions were labeled with Alexa Fluor 5–dCTP (cancer cells) and Alexa Fluor 3–dCTP (normal cells) using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Leukemic blasts and bone marrow cells from AML patients were collected during routine diagnostic bone marrow aspirations. Patients had given informed consent to additional sample collection and analyses according to a protocol approved by the local ethical committee. DNA was prepared after Ficoll gradient centrifugation using Qiagen Blood & Cell Culture DNA Kit. DNA concentration was determined with the NanoDrop spectrophotometer and quality was assessed by agarose gel electrophoresis.

extract_protocol: MCIp enrichment of methylated DNA was performed essentially as described (Gebhard et al. 2006, Cancer Research). In brief, genomic DNA was sonicated to a mean fragment size of 350-400 bp. Two µg of each sample were incubated with 150 µl Protein A-Sepharose 4 Fast Flow beads (GE Healthcare) coated with 60 µg purified MBD-Fc protein in 2 ml Ultrafree-MC centrifugal filter devices (Amicon/Millipore) for 3 h at 4°C in buffer containing 300 mM NaCl. Beads were centrifuged to recover unbound DNA fragments (300 mM fraction) and subsequently washed with buffers containing increasing NaCl concentrations (400, 500, 550 mM). Densely CpG-methylated DNA was eluted with a high-salt buffer (1000 mM NaCl) and all fractions were desalted using the MinElute PCR purification kit (Qiagen). The separation of CpG methylation densities of individual MCIp fractions was controlled by qPCR using primers covering the imprinted SNRPN

tag: sample

value: human acute myeloid leukemia (AML), first diagnosis, before treatment

value: MCIp enrichment

tag: disease state

value: AML

label: Alexa Fluor 3–dCTP

source_name: peripheral blood monocytes

value: peripheral blood monocytes

value: mixture of three young (age 20-30) and healthy donors

value: normal


title: A114_11_11a_ko_LXRalpha_ctr


title: Acute myeloid leukemia (AML), first diagnosis, before treatment L79

value: female

tag: age


title: Acute myeloid leukemia (AML-M4), first diagnosis, before treatment L83

value: human acute myeloid leukemia (AML-M4), first diagnosis, before treatment


title: A114_05_12a_wt_alpha_ctr


title: Acute myeloid leukemia (AML-M4), first diagnosis, before treatment L67


title: Acute myeloid leukemia (AML-M1), first diagnosis, before treatment L69

value: human acute myeloid leukemia (AML-M1), first diagnosis, before treatment


title: Acute myeloid leukemia (AML-M3), first diagnosis, before treatment L77

value: male

value: human acute myeloid leukemia (AML-M3), first diagnosis, before treatment


title: Acute lymphatic leukemia (T-ALL), first diagnosis, before treatment L75

value: human acute lymphatic leukemia (T-ALL), first diagnosis, before treatment

value: T-ALL


title: A114_04_3a_wt_alpha_T0901317


title: A114_03_3a_wt_alpha_ctr


title: Dwarf - control population (D38-Cy3)

city: Québec

first: Jérôme

last: St-Cyr

state: Québec

address: 1030, Avenue de la Médecine

department: Biologie

country: Canada

institute: Université Laval

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed in Roberge et al. (2006)

scan_protocol: Transcription profiles from dwarf and normal population samples were measured using the Scanarray laser instrument (Packard Bioscience). Pictures were analysed and gene expression levels quantified using the Quantarray software with the histogram quantification method.

data_processing: Data from the two individuals were exported in text format and were analysed using a mixed model ANOVA and the R/MAANOVA package (Kerr and Churchill 2000; Wu et al. 2002)

organism: Coregonus clupeaformis

source_name: Dwarf - control population_SAMPLE 48

label_protocol: Messenger RNA from each sample was reverse-transcribed and labelled using the Genisphere 3DNA Array 50 kit provided by Invitrogen, using the Superscript II retro-transcriptase enzyme and Cy3/Cy5 dyes (Genisphere), according to the manufacturer’s recommendations (Invitrogen protocol: http://web.uvic.ca/cbr/grasp/).

extract_protocol: Liver tissues were frozen immediately after sampling in liquid nitrogen, and stored at –80 °C. Samples were treated with DNAse enzyme prior to labeling.  All RNA extractions were performed on ice (4°C) and following the same protocol to reduce technical biases in genes expression measures. Total RNA was extracted from 100 mg of liver tissue from individual samples using the Trizol Reagent extraction protocol (Gibco BRL), according to the manufacturer’s recommendations. Subsequently, RNA integrity and quantity was controlled using a 2100 Bioanalyzer (Agilent)

tag: tissue

value: liver

tag: ecotype

value: Dwarf

tag: growth protocol (environment)

value: control population


title: Normal - control population (N39-Al)

source_name: Normal - control population_SAMPLE 45

value: Normal


title: Normal - control population (N37-Cy3)

source_name: Normal - control population_SAMPLE 42


title: Normal - control population (N38-Cy3)

source_name: Normal - control population_SAMPLE 44


title: Acute lymphatic leukemia (cB-ALL), first diagnosis, before treatment L73

value: human acute lymphatic leukemia (cB-ALL), first diagnosis, before treatment

value: cB-ALL


title: Normal - control population (N40-Al)

source_name: Normal - control population_SAMPLE 47


title: Dwarf - control population (D39-Cy3)

source_name: Dwarf - control population_SAMPLE 46


title: Dwarf - control population (D37-Al)

source_name: Dwarf - control population_SAMPLE 41


title: Dwarf - control population (D40-Al)

source_name: Dwarf - control population_SAMPLE 43


title: Comparative MCIp-on-Chip for THP1 and human blood monocytes; Replicate 2

description: Biological replicate 2 of 3;

source_name: THP-1 cell line

growth_protocol: The human histiocytic lymphoma cell line U937 and the human acute monocytic leukemia THP-1 were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (Gibco BRL, Eggenstein, Germany). Human peripheral blood monocytes of healthy male donors were purified from blood mononuclear cells after Ficoll gradient centrifugation and subsequent elutriation.

tag: cell line description

value: human acute monocytic leukemia

tag: cell line

tag: enrichment

value: MCIp

value: peripheral blood monocytes; mixture of three young (age 20-30) and healthy donors


title: ChIP-on-Chip for YY1 in human blood monocytes Replicate 1

description: Biological replicate 1 of 2;

hyb_protocol: ChIP-versus-input hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the recommended, stringent protocol (Agilent).

source_name: peripheral blood monocytes, donor 1

label_protocol: Amplified ChIP material was labeled with Alexa Fluor 5–dCTP and the genomic input with Alexa Fluor 3–dCTP using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Human peripheral blood monocytes were purified from blood mononuclear cells after Ficoll gradient centrifugation and subsequent elutriation.

extract_protocol: ChIP analysis of purified peripheral blood monocytes was performed essentially as described (Metivier et al. 2003). Precipitation of pre-cleared chromatin from 10x10E6 cells was done overnight at 4 °C using 5 µg anti-YY1 (Santa Cruz, sc-1703), anti-NRF1 (Abcam ab34682), anti-Sp1 (Upstate, 07645) and anti-rabbit IgG (Upstate). After reversion of crosslinks, enriched DNA fragments were recovered using the Qiaquick PCR-purification kit (Qiagen). The quality of each ChIP was controlled at known target sites by qPCR. For ChIP-on-Chip analysis, all samples as well as an aliquot of equally treated input DNA were amplified by LM-PCR for subsequent labelling as follows. ChIP and input DNA were blunted and phosphorylated for 30 minutes at 20°C in 50 µl reactions containing 10x T4 DNA ligase buffer, 2 µl dNTP mix (10 mM each), 3 U T4 DNA polymerase, 10 U T4 polynucleotide kinase and 1 U Klenow DNA polymerase. Purification using the Qiaquick PCR purification kit (Qiagen) was followed by the addition of Adenine to 3’-ends using Klenow fragment (3’ to 5’ exo minus), and dATP (1 mM) for 30 minutes at 37 °C. After clean-up using the MinElute kit (Qiagen), DNA fragments were ligated to linker DNA (60 µM pre-annealed JW102s 5'-GCG GTG ACC CGG GAG ATC TGA ATT CT-3' and JW103 5'-GAA TTC AGA TC-3') with 4 µl DNA Quick-Ligase (NEB) in a 30 µl reaction for 15 minutes at RT. Samples were cleaned-up (Qiaquick PCR purification kit (Qiagen)) and amplified using Phusion Polymerase and JW102s oligonucleotide for 15 cycles in the presence of 1.5M betaine (Sigma). The product of the first amplification was diluted 1/20 with ddH2O and 5 µl of the dilution were used for a second round of amplification (15 cycles) using Phusion Polymerase HOT START and JW102s oligonucleotide in the presence of 1.5M betaine (Sigma). The amplified ChIP and input material were purified using Qiaquick PCR purification kit (Qiagen).

tag: cell type

value: peripheral blood monocytes

tag: chip antibody

tag: fraction

value: genomic input material


title: ChIP-on-Chip for YY1 in human blood monocytes Replicate 2

description: Biological replicate 2 of 2;

source_name: peripheral blood monocytes, donor 2

tag: gender


title: ChIP-on-Chip for NRF1 in human blood monocytes Replicate 2

description: Biological replicate 2 of 2;


title: ChIP-on-Chip for SP1 in human blood monocytes Replicate 2

description: Biological replicate 2 of 2;

source_name: peripheral blood monocytes, donor 3


title: Dwarf - control population (D36-Cy3)

source_name: Dwarf - control population_SAMPLE 40


title: Comparative MCIp-on-Chip for U937 and human blood monocytes; Replicate 2

description: Biological replicate 2 of 3;

source_name: U937 cell line

value: human histiocytic lymphoma


title: Normal - control population (N36-Al)

source_name: Normal - control population_SAMPLE 39


title: ChIP-on-Chip for SP1 in human blood monocytes Replicate 1

description: Biological replicate 1 of 2;


title: ChIP-on-Chip for NRF1 in human blood monocytes Replicate 1

description: Biological replicate 1 of 2;


title: Dwarf - control population (D35-Cy3)

source_name: Dwarf - control population_SAMPLE 38


title: Normal - control population (N35-Al)

source_name: Normal - control population_SAMPLE 37


title: Comparative MCIp-on-Chip for THP1 and human blood monocytes; Replicate 1

description: Biological replicate 1 of 3;

source_name: peripheral blood monocytes


title: A114_23_9b_ko_LXRbeta_ctr

source_name: primary myotube derived from LXRb knockout mice


title: Comparative MCIp-on-Chip for U937 and human blood monocytes; Replicate 3

description: Biological replicate 3 of 3;


title: Normal - control population (N33-Cy3)

source_name: Normal - control population_SAMPLE 34


title: Dwarf - control population (D33-Al)

source_name: Dwarf - control population_SAMPLE 33


title: Comparative MCIp-on-Chip for U937 and human blood monocytes; Replicate 1

description: Biological replicate 1 of 3;


title: Normal - control population (N34-Cy3)

source_name: Normal - control population_SAMPLE 36


title: Dwarf - Lake 2 (D24-Cy3)

source_name: Dwarf - Lake 2_SAMPLE 32

value: Lake 2


title: Dwarf - control population (D34-Al)

source_name: Dwarf - control population_SAMPLE 35


title: 18 XX vs 18 XY (22K-1)

source_name: E3.5 blastocyst 18 XX

tag: strain

tag: sex

value: female (GFP positive)

value: whole embryo

source_name: E3.5 blastocyst 18 XY

value: male (GFP negative)


title: Normal - Lake 2 (N24-Al)

source_name: Normal - Lake 2_SAMPLE 31


title: Normal - Lake 2 (N23-Al)

source_name: Normal - Lake 2_SAMPLE 29


title: 23 XY vs 23 XX (22K-1)

source_name: E3.5 blastocyst 23 XY

source_name: E3.5 blastocyst 23 XX


title: Dwarf - Lake 2 (D23-Cy3)

source_name: Dwarf - Lake 2_SAMPLE 30


title: 23 XX vs 23 XY (22K-1)


title: Normal - Lake 2 (N22-Cy3)

source_name: Normal - Lake 2_SAMPLE 28


title: 19 XY vs 19 XY (22K-1)

source_name: E3.5 blastocyst 19 XY

source_name: E3.5 blastocyst 19 XX


title: Dwarf - Lake 2 (D17-Al)

source_name: Dwarf - Lake 2_SAMPLE 27


title: Normal - Lake 2 (N21-Cy3)

source_name: Normal - Lake 2_SAMPLE 26


title: cryko-LL60-2

city: Hanover

first: Chen-Hui

last: Chen

state: NH

address: 702 Remsen

department: Genetics

institute: Dartmouth College

description: reference RNA design

hyb_protocol: Before prehybridization, microarray slides were pre-treated with 600 mJ UV and Pronto Background Reduction kit (Corning) according to the manufacturer’s protocol. Slides were prehybridized at 42˚C for 45 min with prehybridization buffer (5X SSC, 0.1% SDS and 1% BSA) and then spun dry for one min at 1000 RPM. The dried cDNA sample was rehydrated in 31.5 ul hybridization buffer (25% formamide, 5X SSC, 0.1 SDS) for several minutes before adding 3.5 ul 10X blocker (1µg/µl ssDNA and 2µg/µl tRNA in water, Sigma). The mixture was heated at 95 ˚C for 3 min, cooled down on ice for 30 seconds and then quickly spun before pipetting onto the slide under a Lifter slip (VWR). The slide was placed in the oven (Boekel InSlide Out Model 241000 hybridization oven) for hybridization overnight at 42˚C. To maintain humidity in the hybridization cassette, 2 ml of hybridization buffer containing 25% formamide were pipetted onto 4 Whatman 42.5 mm filter paper circles within the cassette. To wash the slides, 2X SSC/ 0.1% SDS was used for the first incubation at 42˚C for 5 min and then followed by 0.1X SSC/ 0.1% SDS at RT for 10 min. The final wash was performed twice using 0.1X SSC only at RT for 5 min. Slides were spun dry before scanning.

scan_protocol: The slides were scanned with a GMS 418 microarray scanner (Affymetrix). After griding with ScanAlyze 2.51, the raw data were uploaded and normalized with GeneTraffic software (Stratagene).

data_processing: Spots of insufficient quality were flagged by visual inspection and signal to background noise ratio. The following steps were performed using BRB-Array tools. Spots were excluded if both intensities are below the minimum fluorescent intensity (100 in sample channel and 200 in reference channel).  After normalizing the data using lowess smoother, genes missing more than 20% of their measurements were all excluded before further analysis.

label: Alexa Fluor 647

organism: Neurospora crassa

source_name: cryko, light exposure for 60 min

label_protocol: 5 μg anchored oligo(dT) 20mer (2.5µg/µl, Invitrogen) was mixed with the RNA sample in a total of 18.4 μl. After incubation at 70 ˚C for 10 min, the mixture was cooled on ice for another 10 min. Reverse transcription was performed using 400 U Superscript II Reverse Transcriptase (200 U/μl, Invitrogen) with amino-allyl-dUPT/dNTP (aadUPT: 15 mM, dTTP: 10 mM, dATP: 25 mM, dCTP: 25 mM, dGTP: 25 mM) at 42 ˚C for 2 hours in a 30 µl reaction volume. The RNA was then hydrolyzed by adding 10 µl 1 M NaOH and 10 µl 0.5 M EDTA. After incubation at 65 ˚C for 15 min, 25 µl 1 M Tris pH 7.4 buffer was added to neutralize the reaction. The cDNA was then cleaned up with YM 30 column (Millipore). The eluted cDNA was dried in speed vacuum without heat for about 1-1.5 hour and then resuspend in 5 µl H2O at RT for 15 min. 3 µl 25 mg/ml sodium bicarbonate buffer (Sigma) and 2 µl Alexa dye (Invitrogen) was added. The coupling reaction was incubated for 1 hour in the dark at RT and then inactivated by adding 4.5 µl 4 M hydroxylamine. After15 min in the dark at RT, the labeled cDNA was cleaned up using CyScribe GFX Purification Kit (Amersham) following the manufacturer’s protocol. cDNA was dried in speed vacuum without heat for another 1-1.5 hour. Alexa Fluor 555 was consistently used to label cDNA synthesized from reference RNA, which is a mixture containing equal amounts of RNA samples harvested from different circadian time points and light treatment durations. The same batch of pooled RNA was used as a reference for each array experiment. Alexa Fluor 647 was used exclusively to label cDNA representing sample RNA.

growth_protocol: Frozen conidia were inoculated onto a regular minimal slant one week in advance to generate fresh conidia. On day 0, conidia were suspended in sterile water for quantification. To form a mycelial layer, 1 x 107 of conidia or similar amount of mass (for knockout strain of NCU02713.2) were inoculated into a 10 cm Petri dish with 20 ml Bird medium containing 2% glucose. After 24 hours of incubation in darkness at 25˚C, a mycelial plug was cut with a size No.4 cork borer (8 mm diameter) and transferred into a 125 ml flask with 50 ml Bird medium containing 2% glucose. All procedures were performed under low red light environment to avoid any possible light-stimulating effects.

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen) with a homogenizer (Tissuelyzer, Qiagen) containing stainless beads for pulverizing. Total RNA was then subjected to an additional purification step using RNeasy spin columns (Qiagen). After quantification by spectrophototmeter, 20 μg RNA from each time point was used for cDNA synthesis.

treatment_protocol: After another 24 hours of culture with constant shaking (125 rpm) in darkness at 25 ˚C, the flasks were moved to a shaker in LL at 25 ˚C with a continuous white light stimulus, covering wide-range of spectrum from 400 nm to 700 nm (cool white fluorescent light bulb, General Electric F20T12-CW, 40-50 μmole photons/m2/s) and then harvested samples before (DD) and afte 60minutes (LL60) of white light treatment. Using vacuum filtration, dried mycelia tissues were immediately frozen in liquid nitrogen and stored at -80˚C until RNA extraction.

tag: mycelia from liquid culture

label: Alexa Fluor 555

source_name: pooled RNA from 74A


title: cryko-LL60-3

description: reference RNA design


title: Normal - Lake 2 (N20-Al)

source_name: Normal - Lake 2_SAMPLE 23


title: WT-LL60-3

description: reference RNA design

source_name: 74A(wild-type), light exposure for 60 min


title: Dwarf - Lake 2 (D20-Cy3)

source_name: Dwarf - Lake 2_SAMPLE 24


title: Dwarf - Lake 2 (D21-Al)

source_name: Dwarf - Lake 2_SAMPLE 25


title: Dwarf - Lake 2 (D18-Cy3)

source_name: Dwarf - Lake 2_SAMPLE 20


title: Normal - Lake 2 (N19-Cy3)

source_name: Normal - Lake 2_SAMPLE 22


title: Dwarf - Lake 2 (D19-Al)

source_name: Dwarf - Lake 2_SAMPLE 21


title: Dwarf - Lake 2 (D22-Al)

source_name: Dwarf - Lake 2_SAMPLE 17


title: Normal - Lake 1 (N8-Cy3)

source_name: Normal - Lake 1_SAMPLE 16

value: Lake 1


title: 18 XY vs 18 XX (22K-1)

data_processing: Hybridized slides were scanned using the Agilen’ts microarray scanner

source_name: E3.5 blastocyst 18 XY

source_name: E3.5 blastocyst 18 XX


title: 19 XX vs 19 XY (22K-1)

source_name: E3.5 blastocyst 19 XY


title: Normal - Lake 2 (N17-Cy3)

source_name: Normal - Lake 2_SAMPLE 18

value: liver


title: Normal - Lake 2 (N18-Al)

source_name: Normal - Lake 2_SAMPLE 19


title: WT-LL60-1

description: reference RNA design


title: cryko-LL60-1

description: reference RNA design


title: cryko-DD-2

description: reference RNA design

source_name: cryko in constant darkness


title: Dwarf - Lake 1 (D6-Cy3)

source_name: Dwarf - Lake 1_SAMPLE 14

value: Dwarf


title: cryko-DD-3

description: reference RNA design

source_name: pooled RNA from 74A


title: Normal - Lake 1 (N7-Al)

source_name: Normal - Lake 1_SAMPLE 13


title: Normal - Lake 1 (N6-Al)

source_name: Normal - Lake 1_SAMPLE 11


title: Normal - Lake 1 (N5-Cy3)

source_name: Normal - Lake 1_SAMPLE 10


title: WT-LL60-2

description: reference RNA design

source_name: 74A(wild-type), light exposure for 60 min


title: Dwarf - Lake 1 (D8-Cy3)

source_name: Dwarf - Lake 1_SAMPLE 12


title: Dwarf - Lake 1 (D7-Al)

source_name: Dwarf - Lake 1_SAMPLE 15


title: Dwarf - Lake 1 (D5-Al)

source_name: Dwarf - Lake 1_SAMPLE 9


title: cryko-DD-1

description: reference RNA design


title: WT-DD-3

description: reference RNA design

source_name: 74A(wild-type) in constant darkness


title: Dwarf - Lake 1 (D3-Cy3)

source_name: Dwarf - Lake 1_SAMPLE 6


title: Normal - Lake 1 (N1-Cy3)

source_name: Normal – Lake 1_SAMPLE 2


title: Normal - Lake 1 (N4-Al)

source_name: Normal - Lake 1_SAMPLE 7


title: Dwarf - Lake 1 (D4-Cy3)

source_name: Dwarf - Lake 1_SAMPLE 8


title: Dwarf - Lake 1 (D2-Al)

source_name: Dwarf - Lake 1_SAMPLE 3


title: Normal - Lake 1 (N2-Cy3)

source_name: Normal - Lake 1_SAMPLE 4


title: WT-DD-1

description: reference RNA design


title: WT-DD-2

description: reference RNA design


title: A114_06_12a_wt_alpha_T0901317

source_name: primary myotubes derived from WT

tag: Backgroud:C57/BL6, Gender:female, Age:5-6 weeks


title: Dwarf - Lake 1 (D1-Al)

source_name: Dwarf – Lake 1_SAMPLE 1


title: Normal - Lake 1 (N3-Al)

source_name: Normal - Lake 1_SAMPLE 5


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 7, biological rep2

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

description: Gene expression data from ferret lung on Day 7 after infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using Expression Console Version 1.1 (Affymetrix) default analysis settings.

organism: Mustela putorius furo

source_name: Ferret

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

treatment_protocol: Intranasal infection of ferrets with 10^6 EID50 A/California/07/2009 (H1N1) for the first experiment and 10^6 EID50 A/Brisbane/59/2007 (H1N1) for the second experiment.  On Day 0 (before infection), Day 3 (post infection for the first experiment) or Day 2 (post infection for the second experiment), and Day 5, Day 7 and Day 14 (post infection for both experiments), ferrets were euthanized and lung tissue was excised and put in RNAlater (Ambion, Austin, TX) immediately.

value: lung

tag: virus strain


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 2, biological rep3

description: Gene expression data from ferret lung on Day 2 after infection


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 2, biological rep1


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 2, biological rep2


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 14, biological rep3

description: Gene expression data from ferret lung on Day 14 after infection


title: Ferret lung, uninfected, on Day 0, biological rep1 exp2

description: Gene expression data from ferret lung before infection

value: N/A; Uninfected


title: Ferret lung, uninfected, on Day 0, biological rep2 exp2


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 5, biological rep1

description: Gene expression data from ferret lung on Day 5 after infection


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 7, biological rep3


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 14, biological rep2


title: Comparative MCIp-on-Chip for THP1 and human blood monocytes; Replicate 3

description: Biological replicate 3 of 3;

source_name: THP-1 cell line

value: male

source_name: peripheral blood monocytes


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 7, biological rep1


title: Ferret lung, uninfected, on Day 0, biological rep3 exp2


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 14, biological rep1


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 5, biological rep2


title: Ferret lung with A/Brisbane/59/2007 (H1N1) on Day 5, biological rep3


title: Ferret lung with A/California/07/2009 (H1N1) on Day 5, biological rep2

value: A/California/07/2009 (H1N1)


title: Ferret lung with A/California/07/2009 (H1N1) on Day 7, biological rep3


title: Ferret lung with A/California/07/2009 (H1N1) on Day 7, biological rep1


title: Ferret lung with A/California/07/2009 (H1N1) on Day 14, biological rep1


title: Ferret lung with A/California/07/2009 (H1N1) on Day 14, biological rep2


title: Ferret lung with A/California/07/2009 (H1N1) on Day 3, biological rep1

description: Gene expression data from ferret lung on Day 3 after infection


title: Ferret lung with A/California/07/2009 (H1N1) on Day 5, biological rep1


title: Ferret lung with A/California/07/2009 (H1N1) on Day 3, biological rep2


title: Ferret lung with A/California/07/2009 (H1N1) on Day 3, biological rep3


title: Ferret lung with A/California/07/2009 (H1N1) on Day 14, biological rep3


title: Ferret lung, uninfected, on Day 0, biological rep1


title: Preincubated with ALL1 and activated by activated T cell membranes rep 1

city: Tel-Aviv

first: Dana

last: Baram

country: Israel

institute: Tel-Aviv University

description: Gene expression data from HMC-1 cells

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned at the Weizmann Institute Microarray Core Facility using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The probe set data were generated using Remote Analysis Computation for gene Expression (RACE) via the web interface. The processing algorithm used was gcRMA.

source_name: Human mast cells HMC-1 preincubated with ALL1 and activated by activated T cell membranes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human mast cell line HMC-1 were maintained in suspension in supplemented RPMI under standard conditions.

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen Inc. Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cells were activated for 3 hours via two different activation pathways: A3R activation by Cl-IBMECA, and incubation with activated T cell membranes, with or without 1 hour pretreatment with the peptide ALL1.


title: Ferret lung, uninfected, on Day 0, biological rep2


title: Ferret lung with A/California/07/2009 (H1N1) on Day 7, biological rep2


title: MSC_untreated_cultured-14days_vc_rep3

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

description: Any comment

hyb_protocol: Hybridization was performed with Human Gene 1.0 ST arrays (Affymetrix, Inc, Santa Clara, CA). Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

data_processing: As described earlier [23], to remove variation of a non-biological origin, densitometry values among arrays were normalised using the RMA function and further transformed to the logarithmic 2 (log2) scale. Probes with a known GenBank accession ID correspondence were selected for functional analysis.

source_name: Mesenchymal stem cell untreated and cultured, t=14 days with vector control

label_protocol: Briefly, 100 ng of total RNA from each sample were reverse transcribed to cDNA, followed by overnight in vitro transcription to generate cRNA, which was reverse transcribed, and the 5.5 ug of sense cDNA were fragmented and labeled. The quality of cDNA and fragmented cDNA was assessed in the Agilent bioanalyzer.

extract_protocol: Total RNA from all cell cultures was purified using the Qiagen RNeasy Plus Mini kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions.

value: Bone marrow-derived MSC (Cambrex Biosciences, East Rutherford, NJ)


title: MSC_treated_cultured-14days_rep1

description: Any comment

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

source_name: MSC treated with 1mM 8-Br-cAMP for 14 days


title: MSC_untreated_uncultured_t=0_rep3

description: Any comment

source_name: Mesenchymal stem cell untreated and uncultured, t=0


title: MSC_untreated_cultured-14days_vc_rep2

description: Any comment


title: Ferret lung, uninfected, on Day 0, biological rep3


title: MSC_untreated_uncultured_t=0_rep1

description: Any comment


title: Preincubated with ALL1 and activated by activated T cell membranes rep 2

description: Gene expression data from HMC-1 cells


title: MSC_treated_cultured-14days_rep2

description: Any comment


title: MSC_treated_cultured-14days_rep3

description: Any comment


title: Activated by activated T cell membranes rep 1

description: Gene expression data from HMC-1 cells

source_name: Human mast cells HMC-1 activated by activated T cell membranes


title: Activated by activated T cell membranes rep 2

description: Gene expression data from HMC-1 cells


title: Largest follicle_3

city: Tsukuba

first: KENGO

last: HAYASHI

institute: National Institute of Agrobiological Sciences

hyb_protocol: Labeled cRNA probes (750 ng each) were hybridized to the customized microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 60°C for 17 h. After incubation, the arrays were washed with 6×SSC, 0.005% Triton X-102 at room temperature for 10 min, followed by 5-min washes in 0.1×SSC, 0.005% Triton X-102 at 4°C. Hybridized arrays were blow dried with N2 gas.

scan_protocol: After hybridization, the arrays were scanned using an Agilent Microarray Scanner (Agilent Technology), and Feature Extraction ver. 9.1 (Agilent Technology) was used for image analysis and data extraction.

data_processing: Gene expression datasets were normalized using median of the signal intensity for one hundred GAPDH genes on microarray platform as internal control.

organism: Bos taurus

source_name: Largest follicle_3

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 150–300 ng of total RNA of each follicle using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the whole of individual follicles using ISOGEN (NipponGene, Tokyo, Japan) according to the manufacturer's instructions.

treatment_protocol: Paired ovaries were obtained from four pregnant Japanese Black cows in the institute ranch. Both largest and second largest follicles were dissected from the ovaries, then, surrounding stroma and theca externa were removed from the follicular walls. The follicles were snap-frozen and stored at -80°C until RNA extraction.

value: ovarian follicle


title: Activated by the A3 receptor rep 1

description: Gene expression data from HMC-1 cells

source_name: Human mast cells HMC-1 activated by the A3 receptor


title: Preincubated with ALL1 and activated by the A3 receptor rep 2

description: Gene expression data from HMC-1 cells

source_name: Human mast cells HMC-1 preincubated with ALL1 and activated by the A3 receptor


title: MSC_untreated_cultured-14days_vc_rep1

description: Any comment


title: Incubated with ALL1 rep 2

description: Gene expression data from HMC-1 cells

source_name: Human mast cells HMC-1 incubated with ALL1


title: Second largest follicle_2

source_name: Second largest follicle_2


title: Untreated rep 2

description: Gene expression data from HMC-1 cells

source_name: Human mast cells HMC-1 untreated


title: Incubated with ALL1 rep 1

description: Gene expression data from HMC-1 cells


title: Preincubated with ALL1 and activated by the A3 receptor rep 1

description: Gene expression data from HMC-1 cells


title: Activated by the A3 receptor rep 2

description: Gene expression data from HMC-1 cells


title: Ferret lung with A/California/07/2009 (H1N1) on Day 5, biological rep3


title: MSC_untreated_uncultured_t=0_rep2

description: Any comment


title: Untreated rep 1

description: Gene expression data from HMC-1 cells


title: Largest follicle_2

source_name: Largest follicle_2


title: Second largest follicle_1

source_name: Second largest follicle_1


title: liver_HCC_286-1

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: HCC sample hybridized with control pool sample

hyb_protocol: Hybridisation was performed according to the manufacturer's instuctions (Agilent) at 65°C for 40 hours on a 4x44K microarray (Agilent).

scan_protocol: Scan was performed using a Agilant Scanner Control software v 7.0, with a Agilent G2565B Scanner system

data_processing: Data extraction was performed by using feature extraction software (Agilent) - and the Partek software.

source_name: liver tissue

label_protocol: Cy3 or Cy5 labeling of genomic DNA was performed according to manufacturer's instructions (Agilent oligonucelotide array-based CGH for genomic DNA analysis (for FFPE samples)

extract_protocol: Genomic DNA was isolated using Qiagen genomic DNA separation columns according to the manufacturer's instuctions (Agilent and Qiagen) - DNA was heat fragmented.

value: 31 weeks

tag: genotype

tag: disease state

value: tumor

source_name: liver tissue pool

value: 3 months

value: wildtype

value: healthy


title: liver_HCC_58B-1

tag: age

value: 26 weeks


title: liver_HCC_258

value: 19 weeks


title: liver_HCC_58A-1


title: Largest follicle_1

source_name: Largest follicle_1

tag: tissue


title: liver_HCC_357-2

value: 23 weeks


title: liver_HCC_285-1


title: liver_HCC_357-1


title: liver_HCC_354-3


title: liver_HCC_144-1

value: 20 weeks


title: liver_HCC_144-2


title: liver_HCC_27-1

value: 28 weeks


title: liver_HCC_354-1


title: liver_HCC_272-3

value: 30 weeks


title: Myocardial Infarction + Stem Cells, rep4

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: Gene expression following Myocardial Infarction with stem cell transplantation.

hyb_protocol: Hybridization cocktail for single standard probe array (Porcine Genome Array, Affymetrix) was made by mixing 15 µg of fragmented cRNA with control oligonucleotide B2, 20x eukaryotic hybridization controls, herring sperm DNA (10 mg/ml), acetylated BSA (50 mg/ml) 2x hybridization buffer, and RNase-free water.

scan_protocol: Affymetrix scanner

data_processing: Array data was normalized using GC-RMA method using genedata refiner software.

organism: Sus scrofa

source_name: Myocardial drill biopsy, stem cells

label_protocol: In vitro transcription-synthesis of biotin-labeled cRNA Biotin-labeled RNA targets were obtained by using the Enzo BioArray High Yield RNA Transcript Labeling Kit via in vitro transcription from bacteriophage T7 RNA polymerase promoters according to the manufacturer’s directions (Enzo). The cRNA was then fragmented according to the Affymetrix protocol. Quality and fragmentation of cRNA was confirmed with gel electrophoresis.

growth_protocol: Briefly, female Sinclair miniswine (3 months age, ~10 kg) were anesthetized with pentobarbital (30 mg/kg iv), intubated and ventilated with a respirator with supplemental oxygen.  A left thoracotomy was performed, and the 1st and 2nd diagonal branches of the left anterior descending artery were dissected free and permanently occluded with a ligature. Myocardial drill biopsies were obtained four months following procedure.

extract_protocol: Tissue was placed in TRIzol reagent and homogenized using a rotor-stator homogenizer. Homogenates were transferred to a Phase Lock Gel (PLG) Heavy tube (Eppendorf), chloroform was added, and the mixture was centrifuged. Supernatants were collected, and isopropanol was added to precipitate the RNA. The RNA pellet was washed with 80% ethanol, then air-dried before dissolving in 100 µl of RNase-free H2O. RNA was further purified using the RNeasy Mini protocol according to the manufacturer’s directions (Qiagen). The integrity of each RNA sample was validated using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA) to measure the ratio of 28s/18s ribosomal RNA.

treatment_protocol: MPCs were injected directly into 5 regions of the peri-infarct border zone (BZ) (10 million cells per location; 50 million total diluted in 2 ml saline). Injection sites were marked with a stitch to allow identification of the areas for histological studies. Animals in the placebo group received 2 ml saline in 5 injections at similar BZ injection sites.

tag: breed

value: Sinclair Miniswine (Sinclair Research Center, MO)

value: heart

value: female

tag: treatment

value: stem cells


title: Myocardial Infarction + Stem Cells, rep7


title: Myocardial Infarction + Stem Cells, rep6


title: liver_HCC_272-1


title: liver_HCC_273-4


title: liver_HCC_272-2


title: liver_wt-6w


title: Bc14579 PAA10µg/ml t0_t10

first: Mara

last: Ceragioli

address: Bomenweg

department: Food Microbiology LAb

institute: WUR

description: No extra description.

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

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

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

organism: Bacillus cereus ATCC 14579

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

extract_protocol: RNA was extracted as described by van Schaik et al., 2004

value: OD600 0.5 exposed to Peracetic acid 10µg/ml for 0 min


title: Myocardial Infarction + Stem Cells, rep5


title: Bc14579 PAA10µg/ml t0_t30

description: No extra description.

value: OD600 0.5 exposed to Peracetic acid 10µg/ml for 30 min


title: Bc14579 HP0.05mM t30_t0

description: No extra description.

value: OD600 0.5 exposed to Hydrogen peroxide 0.05mM for 30 min

value: OD600 0.5 exposed to Hydrogen peroxide 0.05mM for 0 min


title: Bc14579 PAA10µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Peracetic acid 10µg/ml for 10 min


title: Bc14579 PAA10µg/ml t30_t0

description: No extra description.


title: liver_HCC_273-1

value: tumor

value: 3 months

value: wildtype


title: Myocardial Infarction + Stem Cells, rep3


title: liver_HCC_273-3

value: healthy


title: Myocardial Infarction, rep6

description: Gene expression following Myocardial Infarction without stem cell transplantation.

source_name: Myocardial drill biopsy, saline

value: saline


title: liver_HCC_273-2


title: BatchCulture_LBTbroth_StationaryPhase_Replicate4

city: Dunedin

first: Anja

last: Huempel

address: 720 Cumberland St

department: Microbiology & Immunology

country: New Zealand

institute: University of Otago

description: Stationary Phase: Biological Replicate 4

hyb_protocol: Hybrization was performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Slides were scanned using an Axon GenePix4000B microarray scanner

data_processing: Tiff images were quantified with Spotfinder software (TIGR), data normalization using total array intensity and LOWESS algorithm with  MIDAS software (TIGR)

organism: Mycolicibacterium smegmatis

source_name: in vitro batch culture

label_protocol: 5 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: Batch cultures were routinely grown in Luria Bertani broth supplemented with 0.05 % (w/v) Tween 80 (LBT) at 37 °C on a rotary shaker.

extract_protocol: Samples were harvested using ice-cold glycerol-saline, cells were disrupted by bead-beating and total RNAwas extracted with TRIzol following manufacturer's instructions

treatment_protocol: Starter cultures were grown to OD600 = 0.5 ± 0.2, samples for microarray analysis were grown in 100 ml LBT in 1 l flasks from initial OD600 = 0.005 at 37 °C on a rotary shaker till point of harvest

value: mc2155 wild type

tag: growth stage

value: stationary phase (μ = 0.07 ± 0.01 h-1)

value: mc2155 ΔsigF


title: Myocardial Infarction + Stem Cells, rep2

value: Sinclair Miniswine (Sinclair Research Center, MO)


title: Bc14579 HP0.05mM t10_t0

description: No extra description.

value: OD600 0.5 exposed to Hydrogen peroxide 0.05mM for 10 min


title: BatchCulture_LBTbroth_StationaryPhase_Replicate3

description: Stationary Phase: Biological Replicate 3


title: Myocardial Infarction + Stem Cells, rep1

value: heart

value: female


title: Bc14579 HP0.05mM t0_t10

description: No extra description.


title: Myocardial Infarction, rep5


title: Bc14579 HP0.2mM t10_t0

description: No extra description.

value: OD600 0.5 exposed to Hydrogen peroxide 0.2mM for 10 min

value: OD600 0.5 exposed to Hydrogen peroxide 0.2mM for 0 min


title: Bc14579 HP0.05mM t0_t30

description: No extra description.

value: OD600 0.5 exposed to Hydrogen peroxide 0.05mM for 30 min


title: Bc14579 HP0.2mM t30_t0

description: No extra description.

value: OD600 0.5 exposed to Hydrogen peroxide 0.2mM for 30 min


title: Myocardial Infarction, rep3


title: Myocardial Infarction, rep4


title: Myocardial Infarction, rep2


title: Bc14579 HP0.2mM t0_t10

description: No extra description.


title: Bc14579 HP0.2mM t0_t30

description: No extra description.


title: BatchCulture_LBTbroth_StationaryPhase_Replicate2

description: Stationary Phase: Biological Replicate 2


title: Bc14579 BC5µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Benzalkonium chloride 5 µg/ml for 10 min

value: OD600 0.5 exposed to Benzalkonium chloride 5 µg/ml for 0 min


title: Myocardial Infarction, rep1


title: Bc14579 BC5µg/ml t30_t0

description: No extra description.

value: OD600 0.5 exposed to Benzalkonium chloride 5 µg/ml for 30 min


title: Bc14579 BC5µg/ml t0_t30

description: No extra description.

value: OD600 0.5 exposed to Benzalkonium chloride 1 µg/ml for 30 min


title: BatchCulture_LBTbroth_ExponentialPhase_Replicate4

description: Exponential Phase: Biological Replicate 4

value: exponential phase (μ = 0.26 ± 0.04 h-1)


title: BatchCulture_LBTbroth_StationaryPhase_Replicate1

description: Stationary Phase: Biological Replicate 1


title: Bc14579 BC2µg/ml t30_t0

description: No extra description.

value: OD600 0.5 exposed to Benzalkonium chloride 2 µg/ml for 0 min

value: OD600 0.5 exposed to Benzalkonium chloride 2 µg/ml for 30 min


title: BatchCulture_LBTbroth_ExponentialPhase_Replicate2

description: Exponential Phase: Biological Replicate 2

value: mc2155 wild type


title: BatchCulture_LBTbroth_ExponentialPhase_Replicate3

description: Exponential Phase: Biological Replicate 3

value: mc2155 ΔsigF


title: Bc14579 BC5µg/ml t0_t10

description: No extra description.


title: Bc14579 BC2µg/ml t0_t30

description: No extra description.


title: BatchCulture_LBTbroth_ExponentialPhase_Replicate1

description: Exponential Phase: Biological Replicate 1


title: Bc14579 BC1µg/ml t0_t30

description: No extra description.

value: OD600 0.5 exposed to Benzalkonium chloride 1 µg/ml for 0 min


title: ST-treated_6h replicate 3

city: Galveston

first: Ashok

middle: K

last: Chopra

state: TX

address: 301 University Blvd.

institute: University of Texas Medical Branch

scan_protocol: Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.

data_processing: Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).

source_name: THP-1 cells

growth_protocol: The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.

extract_protocol: Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).

treatment_protocol: Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with Stx1 (400 ng/ml) in RPMI-1640 + 0.5% FBS for 6h

value: Human myelogenous leukemia (macrophage-like) cells

tag: cell line


title: Bc14579 BC2µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Benzalkonium chloride 1 µg/ml for 10 min


title: kidney_R06283_HG-U133_Plus_2_HSF1

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: R06283_HG-U133_Plus_2_HSF1 regulation: Assay human embryonic kidney cells (HEK293T) for expression of cDNAs before designing siRNAs

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

source_name: total RNA from human embryonic kidney TC cells

label_protocol: standard Affymetrix protocol

growth_protocol: Growth Media: DMEM, Amount of Media: 3, Units of Media: ml, Growth Conditions: DMEM, 10%FBS(HI), Pen/Strep/GlutaMax

extract_protocol: Extraction Method: RNeasy

tag: array type

tag: amount to core

tag: units of amount

value: ug

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: genetic modifications

value: temperature sensitive gene for SV40 T-antigen was inserted

value: kidney

tag: atcc number

tag: number of cells seeded

value: 750K /6 well dish

tag: separation type

value: Scrape in Lysis buffer

tag: harvest time point

tag: units of harvest time point

value: h past seeding


title: ST-treated_6h replicate 1

description: Performed by UTMB microarray core per manufacturer's instructions

tag: cell type


title: ST-treated_6h replicate 2

hyb_protocol: Performed by UTMB microarray core per manufacturer's instructions


title: LPS-treated_6h replicate 2

label_protocol: Performed by UTMB microarray core per manufacturer's instructions

treatment_protocol: Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with LPS (200 ng/ml) in RPMI-1640 + 0.5% FBS for 6h


title: Bc14579 BC1µg/ml t10_t0

description: No extra description.


title: Bc14579 BC1µg/ml t30_t0

description: No extra description.


title: LPS-treated_6h replicate 3


title: kidney_R06282_HG-U133_Plus_2_HSF1

description: R06282_HG-U133_Plus_2_HSF1 regulation: Assay human embryonic kidney cells (HEK293T) for expression of cDNAs before designing siRNAs

tag: tissue

value: 375K /6 well dish


title: Bc14579 BC2µg/ml t0_t10

description: No extra description.


title: LPS-treated_6h replicate 1

tag: cell line


title: Bc14579 SH500µg/ml t30_t0

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 30 min

value: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 0 min


title: Bc14579 BC1µg/ml t0_t10

description: No extra description.


title: Untreated replicate 1

description: The results visualized with a Gene Array scanner using Affymetrix software.

data_processing: RMA normalization was performed using GeneSifter (VizX Labs, Seattle, WA).

treatment_protocol: Untreated


title: p53-dominant negative mutation (arg175His) 10B_DN (A)

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 8.5.1). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA. After normalization, the separate intensity channels were extracted from the ratio measurements

label_protocol: 500ng of RNA was linearly amplified and fluorescently labeled with either Cy3-CTP or Cy5-CTP with the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Amstelveen, The Netherlands).

growth_protocol: SV40 ts-LTA-hTERT oral keratinocytes were maintained in Keratinocyte-SFM supplemented with bovine pituitary extract (25 mg/ 500 ml) human recombinant EGF (2.5 ug/500 ml medium)

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured at 39C for three weeks prior to RNA extraction.

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53-dominant negative mutation (arg175His)


title: HPV16_E6 10B_E6 (A)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16_E6


title: Untreated replicate 3


title: Human CD21hi transitional B cells unstimulated, rep2

city: Sydney

first: Santi

last: Suryani

state: NSW

address: 384 Victoria Street, Darlinghurst

department: Immunology and Inflammation

country: Australia

institute: Garvan Institute of Medical Research

description: Sample pooled from 2 healthy blood donors.

hyb_protocol: According to Affymetrix Hu133Plus2 hybridisation protocol

scan_protocol: According to Affymetrix GCOS version 1.4

data_processing:
Analysed in GeneSpring Software version 7.3.1.
Normalisation:
1. Per Gene: normalised to media with cut off value 5 in raw signal.

source_name: CD21hi transitional B cells

label_protocol: According to Affymetrix Hu133Plus2 labelling protocol

extract_protocol: RNA extracted as per Trizol protocol

value: blood

value: PBMC

tag: b-cell subset


title: Bc14579 SH500µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 10 min


title: p53shRNA 10B_SH (A)

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: Total RNA was isolated with Trizol (Invitrogen, breda, The Netherlands), according to the manufacturer's instructions. Total RNA was further analyzed on the bioanalyzer (Agilent) and only RIN values of 8 or above were included.

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53shRNA


title: Untreated replicate 2


title: Human naive B cells unstimulated, rep2

source_name: naive B cell


title: HPV16_E6 19B_E6 (A)


title: p53-dominant negative mutation (arg175His) 19B_DN (A)


title: Bc14579 SH400µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 400µg/ml for 10 min

value: OD600 0.5 exposed to Sodium hypochlorite 400µg/ml for 0 min


title: Human CD21lo transitional B cells unstimulated, rep2

source_name: CD21lo transitional B cells


title: p53shRNA 19B_SH ( A )

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53 specific shRNA


title: miR-372 19B_MI (A)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by miR-372


title: Human memory B cells unstimulated, rep2

source_name: memory B cell


title: Cord blood CD21hi transitional B cells, rep2

description: Sample pooled from 3 cord blood donors.

source_name: Cord blood CD21hi transitional B cells

value: cord blood


title: Bc14579 SH500µg/ml t0_t10

description: No extra description.

value: OD600 0.5 exposed to Sodium Hypochlorite 500µg/ml for 0 min

value: OD600 0.5 exposed to Sodium Hypochlorite 500µg/ml for 10 min


title: Bc14579 SH400µg/ml t0_t30

description: No extra description.

value: OD600 0.5 exposed to Sodium Hypochlorite 400µg/ml for 0 min

value: OD600 0.5 exposed to Sodium Hypochlorite 400µg/ml for 30 min


title: Bc14579 SH300µg/ml t30_t0

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 300µg/ml for 30 min

value: OD600 0.5 exposed to Sodium hypochlorite 300µg/ml for 0 min


title: Bc14579 SH400µg/ml t0_t10

description: No extra description.


title: Bc14579 SH400µg/ml t30_t0

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 400µg/ml for 30 min


title: miR-372 10B_MI (A)


title: Cord blood CD21lo transitional B cells, rep2

description: Sample pooled from 3 cord blood donors.

source_name: Cord blood CD21lo transitional B cells


title: Cord blood CD21hi transitional B cells

description: Sample pooled from 2 cord blood donors.


title: Cord blood naive B cells, rep2

description: Sample pooled from 3 cord blood donors.

source_name: Cord blood naive B cells


title: Cord blood CD21lo transitional B cells

description: Sample pooled from 2 cord blood donors.


title: p53-dominant negative mutation (arg175His) 19A_DN (A)


title: HPV16_E6 19A_E6 (A)


title: Bc14579 SH300µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 300µg/ml for 10 min


title: Cord blood naive B cells

description: Sample pooled from 2 cord blood donors.


title: HPV16-E6 10A_E6 (A)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16-E6


title: Bc14579 PAA100µg/ml t30_t0

description: No extra description.

value: OD600 0.5 exposed to Peracetic acid 100µg/ml for 30 min

value: OD600 0.5 exposed to Peracetic acid 100µg/ml for 0 min


title: Human memory B cells unstimulated, rep1

description:
Majority of human memory B cells is CD27+ and CD10- and thus the gating strategy is to isolate CD10- and CD27+ B cells.
CD20+CD10-CD27+ cells FACS sorted.
Sample taken from healthy donor.


title: miR-372 19A_MI (A)


title: p53-dominant negative mutation (arg175His) 10A_DN  (A)


title: Human CD21lo transitional B cells unstimulated, rep1

description: Sample taken from healthy donor.


title: p53shRNA 19A_SH (A)


title: miR-372 10A_MI (A)

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 °C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).


title: Human naive B cells unstimulated, rep1

description: Sample taken from healthy donor.


title: Bc14579 SH300µg/ml t0_t30

description: No extra description.


title: Bc14579 SH300µg/ml t0_t10

description: No extra description.


title: Bc14579 PAA100µg/ml t10_t0

description: No extra description.

value: OD600 0.5 exposed to Peracetic acid 100µg/ml for 10 min


title: Bc14579 PAA100µg/ml t0_t30

description: No extra description.


title: Bc14579 PAA100µg/ml t0_t10

description: No extra description.


title: Human CD21hi transitional B cells unstimulated, rep1

description: Sample taken from healthy donor.

value: blood


title: p53shRNA 10A_SH (A)

treatment_protocol: Cells were cultured at 39 °C for three weeks prior RNA extraction.


title: kidney_R06173_HG-U133_Plus_2_HSF1

description: R06173_HG-U133_Plus_2_HSF1 regulation: Assay human embryonic kidney cells (HEK293T) for expression of cDNAs before designing siRNAs

tag: array type

tag: amount to core

tag: units of amount

value: ug

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: temperature sensitive gene for SV40 T-antigen was inserted

value: kidney

value: 1 Mio/6 well dish

value: Scrape in Lysis buffer

value: h past seeding


title: erStress_twins_Cauc_1740twin2_500nM_thapsigargin_4h

status: Public on Mar 30 2010

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

institute: HHMI, University of Pennsylvania

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1740:2 treated with 500nM thapsigargin.

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

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

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

source_name: Lymphoblastoid cell lines derived from family 1740, member 2

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

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

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

treatment_protocol: 500nM thapsigargin 4 hours

value: lymphoblastoid cell line

tag: family id

tag: coriell cell line repository identifier

tag: individual

value: Twin number 2

tag: agent

value: thapsigargin

tag: dose

tag: time

value: 4 hours


title: erStress_twins_Cauc_1756twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1756:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1756, member 2

tag: cell line


title: erStress_twins_Cauc_1752twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1752:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1752, member 2


title: erStress_twins_Cauc_1740twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1740:2 treated with DMSO.

treatment_protocol: DMSO 4 hours

value: DMSO


title: erStress_twins_Cauc_1756twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1756:2 treated with DMSO.


title: erStress_twins_Cauc_1752twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1752:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1752, member 1

value: Twin number 1


title: erStress_twins_Cauc_1716twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1716:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1716, member 2


title: erStress_twins_Cauc_1726twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1726:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1726, member 2


title: erStress_twins_Cauc_1735twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1735:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1735, member 2


title: erStress_twins_Cauc_1740twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1740:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1740, member 1


title: erStress_twins_Cauc_1752twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1752:1 treated with DMSO.


title: erStress_twins_Cauc_1721twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1721:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1721, member 1


title: Bc14579 SH500µg/ml t0_t30

description: No extra description.

value: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 0 min

value: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 30 min


title: erStress_twins_Cauc_1726twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1726:2 treated with DMSO.


title: erStress_twins_Cauc_1752twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1752:2 treated with DMSO.


title: erStress_twins_Cauc_1716twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1716:2 treated with DMSO.


title: erStress_twins_Cauc_1740twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1740:1 treated with DMSO.


title: erStress_twins_Cauc_1756twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1756:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1756, member 1


title: erStress_twins_Cauc_1756twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1756:1 treated with DMSO.


title: erStress_twins_Cauc_1721twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1721:1 treated with 500nM thapsigargin.


title: erStress_twins_Cauc_1735twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1735:1 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1735, member 1


title: erStress_twins_Cauc_1721twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1721:2 treated with DMSO.

source_name: Lymphoblastoid cell lines derived from family 1721, member 2


title: erStress_twins_Cauc_1726twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1726:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1726, member 1


title: erStress_twins_Cauc_1726twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1726:1 treated with DMSO.


title: erStress_twins_Cauc_1735twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1735:1 treated with 500nM thapsigargin.


title: erStress_twins_Cauc_1721twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1721:2 treated with 500nM thapsigargin.


title: erStress_twins_Cauc_1735twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1735:2 treated with DMSO.


title: erStress_twins_Cauc_1716twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1716:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1716, member 1


title: erStress_twins_Cauc_1715twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1715:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1715, member 2


title: erStress_twins_Cauc_1715twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1715:2 treated with DMSO.


title: erStress_twins_Cauc_1705twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1705:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1705, member 1


title: erStress_twins_Cauc_1706twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1706:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1706, member 1


title: erStress_twins_Cauc_1705twin1_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1705:1 treated with DMSO.


title: erStress_twins_Cauc_1706twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1706:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1706, member 2


title: erStress_twins_Cauc_1705twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1705:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1705, member 2


title: erStress_twins_Cauc_1704twin2_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1704:2 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1704, member 2


title: erStress_twins_Cauc_1710twin1_500nM_thapsigargin_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1710:1 treated with 500nM thapsigargin.

source_name: Lymphoblastoid cell lines derived from family 1710, member 1


title: erStress_twins_Cauc_1705twin2_DMSO_4h

description: Gene expression data under ER stress from lymphoblastoid cells of twin 1705:2 treated with DMSO.