title: F344_Day01h_ductus arteriosus_rep2

description: F344 DA replicate 2

source_name: F344_Day01h_ductus arteriosus

value: ductus arteriosus


title: S1

status: Public on Aug 30 2015

type: RNA

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

hyb_protocol: High quality RNA was reverse transcribed and hybridized on the Illumina HumanWG-6 v3 Expression BeadChip

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalisation using Bioconductor

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: memory CD4+ T-cell subsets were isolated by FACS

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

extract_protocol: Total RNA was isolated using RNeasy columns kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: immobilized CD3 and soluble CD28 (1µg/ml) for 3 days

tag: donor

tag: cell type

value: PBMC

tag: cell population


title: BN_Day01h_ductus arteriosus_rep2

status: Public on Aug 29 2015

city: Tokyo

first: Yi-Ting

middle: Emma

last: Hsieh

address: 2-2Wakamatsu-cho, Shinjuku

country: Japan

institute: Waseda University

description: BN DA replicate 2

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hrs at 45℃ on Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner.

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® Software (AGCC v.2.0) and processed by RMA.

organism: Rattus norvegicus

source_name: BN_Day01h_ductus arteriosus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

extract_protocol: Total RNA was extracted from pooled tissues using TRIzol reagent (Invitrogen, La Jolla, CA) as recommended by the manufacturer.

tag: strain

value: Brown-Norway

tag: age

value: 1hr after birth (Day0, full-term)

tag: tissue


title: Healthy Meninge 3

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

country: Spain

institute: Hospital Universitari Germans Trias i Pujol

hyb_protocol: Hybridization, washing, staining and scanning of Affymetrix Human Gene ST 1.0 arrays were performed following the manufacturer's recommendations

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
RMA signal log2 converted from Expression Console Software 1.1.2800.29167. As samples were processes in three batches, ComBat method was used to remove batch effect.

source_name: Meningeal Control

label_protocol: library preparation and amplification were performed following the distributor’s (Sigma-Aldrich) recommendations for whole transcriptome amplification (WTA2). Amplification was performed for 17 cycles, and amplified cDNA was purified and quantified on a NanoDrop ND-1000 spectrophotometer (Thermo-Fischer). Some 8 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from a GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

extract_protocol: RNA was isolated using RNeasy® Mini Kit (QIAGEN) following instructions. Rnase-Free Dnase Set  (QIAGEN) was used to eliminate DNA contamitations.

treatment_protocol: Samples were frozen in liquid Nitrogen immediately after surgical resection, and then conserved at -80ºC until extraction

tag: sample group

value: Control

tag: tissue subtype

value: Meningeal Control

tag: batch

tag: control source

value: BioChain RNA commercial sample

tag: reference cat. #

tag: reference lot #


title: F344_Day01h_aorta_rep1

description: F344 AO replicate 1

value: aorta


title: Healthy Meninge 1


title: BN_Day01h_ductus arteriosus_rep1

description: BN DA replicate 1


title: F344_Day01h_aorta_rep2

description: F344 AO replicate 2


title: PDAC59

status: Public on Aug 28 2015

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

country: USA

institute: Moffitt Cancer Center

description: frozen pancreatic tissue

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Expression values were calculated using the robust multi-array average (RMA) algorithm

source_name: frozen pancreatic tissue

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: overall survival (month)

value: ALIVE

tag: Stage


title: PDAC57

description: frozen pancreatic tissue


title: PDAC56

description: frozen pancreatic tissue

value: DEAD


title: PDAC51

description: frozen pancreatic tissue


title: PDAC55

description: frozen pancreatic tissue


title: HPMEC Consi 3D vs.  HPMEC HSP27si 3d

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

description: Pooled biological replicates

hyb_protocol: The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization. The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

source_name: 5 HPMEC Consi 3D

label_protocol: For control and test RNAs, the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology, USA) according to the manufacturer’s instructions.

growth_protocol: HPMECs were cultured in Endothelial Cell Growth Medium MV and used in nine passage

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

treatment_protocol: SiRNAs against HSPB1 and a control siRNA were transfected into cells. after 3days, cells were harvested.

tag: cell line

value: HPMEC

source_name: 6 HPMEC HSP27si 3d

tag: cell

value: 3 days


title: PDAC62

description: frozen pancreatic tissue


title: PDAC63

description: frozen pancreatic tissue


title: PDAC61

description: frozen pancreatic tissue


title: PDAC47

description: frozen pancreatic tissue


title: PDAC54

description: frozen pancreatic tissue


title: PDAC52

description: frozen pancreatic tissue


title: PDAC50

description: frozen pancreatic tissue


title: PDAC43

description: frozen pancreatic tissue


title: PDAC45

description: frozen pancreatic tissue


title: PDAC58

description: frozen pancreatic tissue


title: PDAC38

description: frozen pancreatic tissue


title: PDAC44

description: frozen pancreatic tissue


title: PDAC39

description: frozen pancreatic tissue


title: PDAC49

description: frozen pancreatic tissue


title: PDAC36

description: frozen pancreatic tissue


title: PDAC53

description: frozen pancreatic tissue


title: PDAC42

description: frozen pancreatic tissue


title: PDAC48

description: frozen pancreatic tissue


title: PDAC60

description: frozen pancreatic tissue


title: PDAC40

description: frozen pancreatic tissue


title: PDAC46

description: frozen pancreatic tissue


title: PDAC41

description: frozen pancreatic tissue


title: PDAC37

description: frozen pancreatic tissue


title: PDAC35

description: frozen pancreatic tissue


title: PDAC34

description: frozen pancreatic tissue


title: PDAC30

description: frozen pancreatic tissue


title: PDAC33

description: frozen pancreatic tissue


title: PDAC26

description: frozen pancreatic tissue


title: PDAC32

description: frozen pancreatic tissue


title: PDAC24

description: frozen pancreatic tissue


title: PDAC29

description: frozen pancreatic tissue


title: PDAC27

description: frozen pancreatic tissue


title: PDAC14

description: frozen pancreatic tissue


title: PDAC10

description: frozen pancreatic tissue


title: PDAC11

description: frozen pancreatic tissue


title: PDAC22

description: frozen pancreatic tissue


title: PDAC21

description: frozen pancreatic tissue


title: PDAC13

description: frozen pancreatic tissue


title: PDAC19

description: frozen pancreatic tissue


title: PDAC31

description: frozen pancreatic tissue


title: PDAC17

description: frozen pancreatic tissue


title: PDAC16

description: frozen pancreatic tissue


title: PDAC15

description: frozen pancreatic tissue


title: PDAC8

description: frozen pancreatic tissue


title: PDAC18

description: frozen pancreatic tissue


title: PDAC28

description: frozen pancreatic tissue


title: PDAC7

description: frozen pancreatic tissue


title: PDAC12

description: frozen pancreatic tissue


title: PDAC25

description: frozen pancreatic tissue


title: PDAC23

description: frozen pancreatic tissue


title: PDAC20

description: frozen pancreatic tissue


title: PDAC2

description: frozen pancreatic tissue


title: PDAC5

description: frozen pancreatic tissue


title: PDAC6

description: frozen pancreatic tissue


title: PDAC1

description: frozen pancreatic tissue


title: PDAC4

description: frozen pancreatic tissue


title: CD4_CPT_rep3

city: St. John's

first: Tomasz

middle: I

last: Michalak

state: NL

address: 300 Prince Philip Dr.

department: Division of BioMedical Sciences

institute: Memorial University of Newfoundland and Labrador

hyb_protocol: For hybridization, a hybridization cocktail is prepared and added to the labeled cDNA target using the Hybridization, Wash and Stain kit (Affymetrix Cat. #900720), applied to arrays, and incubated at 45°C for 18 hours. Following hybridization, arrays are washed and stained using standard Affymetrix procedures.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, and data extraction was performed using Affymetrix Expression Console software.

data_processing: The data were analyzed with Affymetrix Expression Console software. Algorithm: MAS 5.0 (ExpressionStat 5.0). To detect differentially expressed probsets, a two-Group comparison with permutation analysis for differential expression (PADE) was performed by Expression Analysis, Inc. according to their technical documents. This two-group comparison analysis detects and estimates changes in expression between two experimental groups that are each represented by multiple specimens per group and incorporates a permutation analysis for differential expression (PADE™). This analysis helps to mitigate false positives, a very important consideration when analyzing whole genome chips where potentially tens of thousands of statistical tests are examined in parallel.

source_name: positively selected CD4+ T cells purified from peripheral blood mononuclear cells isolated using BD vacutainer cell preparation tube

label_protocol: Total RNA samples are converted to amplified cDNA using the Ovation RNA Amplification System V2 (NuGEN Cat. #3100), and subsequently labeled using the Encore Biotin Module (NuGEN Cat. #4200) for hybridization onto Affymetrix GeneChips. Starting with 50ng of total RNA, first strand cDNA is reverse transcribed from polyadenylated RNA (primarily mRNA) using a DNA/RNA chimeric primer. Second strand synthesis is carried out to generate double-stranded cDNA with a unique DNA/RNA heteroduplex at one end. SPIA® amplification is then performed using a DNA/RNA chimeric primer, DNA polymerase, and RNase H in an isothermal reaction. To generate labeled cDNA target, 3.75 µg of purified SPIA® amplified cDNA is fragmented in a combined chemical and enzymatic fragmentation process. The fragmented product is labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3-hydroxyl end of the fragmented cDNA.

extract_protocol: RNA extraction was performed using the AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer’s instruction.

treatment_protocol: PBMC were isolated from whole blood with Ficoll or BD Vacutainer CPT. Immune subsets were positively selected from the purifed PBMC using Miltenyi Biotec MicoBeads.

value: CD4+ T cells (purified from PBMCs)

tag: pbmc isolation method

value: BD vacutainer cell preparation tube


title: PDAC3

description: frozen pancreatic tissue


title: CD4_CPT_rep1

value: BD vacainer cell preparation tube


title: CD14_CPT_rep2

source_name: positively selected CD14+ monocytes purified from peripheral blood mononuclear cells isolated using BD vacutainer cell preparation tube

value: CD14+ monocytes (purified from PBMCs)


title: CD4_Ficoll_rep2

source_name: positively selected CD4+ T cells purified from peripheral blood mononuclear cells isolated using Ficoll

value: Ficoll


title: ET3X2_rat_low_salt_diet_39807_kidney_RNA_RAE230A

city: Toledo

first: Andrew

middle: John

last: McSweeny

state: OH

address: 3000 Arlington Avenue Room # 209, Mail Stop #1008

department: Physiology & Pharmacology: CVMD Track

institute: University of Toledo College of Medicine

description: Gene expression data from S.R(ET3x2) rat 39807 left kidney, low salt diet

hyb_protocol: Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual with quality assessed by hybridization of a 5 g aliquot to a test chip (TestChip3, Affymetrix). Fragmented cRNA probe (5 g) was then hybridized to each of a set of 2 rat GeneChips (RAE230A and RAE230B; Affymetrix).

scan_protocol: Scanning was performed at the University of Toledo Health Science Campus Genomics Core Facility according to the manufacturer's (Affymetrix) instructions.

data_processing: Probe set expression measures were calculated from probe-level data using RMAExpress v0.5 software with background adjustment, quantile normalization and log 2 transformation

source_name: ET3x2 rat 39807 left kidney

label_protocol: Oligonucleotide microarray analysis was performed essentially as described in Lee et al. (2005) using the Affymetrix Rat Genome RAE230 array set (GeneChips 230A and 230B) according to the manufacturer’s protocol.  Double-stranded cDNA was synthesized from 15 microgram total RNA from each rat kidney RNA preparation using reverse transcriptase (SuperScript II, InVitrogen, Carlsbad, CA) and T7-(dT)24 as the oligonucleotide primer. Biotinylated cRNA was synthesized using a kit (Enzo Bioarray High Yield RNA transcript Labeling Kit, Enzo Diagnostics, Farmingdale, NY) and cRNAs were purified on columns (RNeasy mini kit, Qiagen).

extract_protocol: A single rat kidney RNA sample was used for each of 26 RAE230A/B chipsets [10 S-rat samples, 8 S.R(ET3x1) samples, and 8 S.R(ET3x2) samples].  Total RNA was isolated from the kidneys of each rat separately, essentially as described (Lee et al 2003). Briefly, kidneys were homogenized in a guanidine thiocyanate/phenol solution (Ultraspec, Biotecx Laboratories, Houston, TX), extracted with chloroform and isolated using RNA Tack Resin (Biotecx Laboratories). Total RNA was further purified by ethanol precipitation and absorption to a column (RNeasy, Qiagen, Valencia, CA) following the manufacturer's instructions. Kidney RNA integrity was assessed by 1) electrophoretic size-fractionation on 1% agarose gels under denaturing conditions and 2) hybridization of newly made cRNA probes to TestChips (Affymetrix).

treatment_protocol: Age-matched male S (n=10), S.R(ET3x1) (n=8), and S.R(ET3x2) (n=8) rats were bred, housed, and studied concomitantly to minimize envi¬ronmental effects. Rats were weaned at 30 days of age onto a low salt diet (0.4% NaCl, Harlan Teklad diet TD7034) and water ad libitum. At 39-41 days of age one-half of rats from each strain group were switched to a 4% NaCl diet (Harlan Teklad diet TD83033) and water ad libitum for 24 hours.  All rats were then killed by pentobarbital overdose.  Kidneys were removed, decapsulated, blotted dry, and weighed. The kidneys of each rat were then processed separately for isolation of total RNA.

value: S.R(ET3x2), diet:low salt (Harlan Teklad TD7034, 0.4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: ET3X2_rat_low_salt_diet_39806_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39806 left kidney, low salt diet

source_name: ET3x2 rat 39806 left kidney


title: ET3X2_rat_high_salt_diet_39799_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39799 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39799 left kidney

value: S.R(ET3x2), diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: ET3X2_rat_high_salt_diet_39801_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39801 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39801 left kidney


title: ET3X2_rat_low_salt_diet_39820_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39820 left kidney, low salt diet

source_name: ET3x2 rat 39820 left kidney


title: ET3X1_rat_low_salt_diet_39855_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39855 left kidney, low salt diet

source_name: ET3x1 rat 39855 left kidney

value: S.R(ET3x1), diet:low salt (Harlan Teklad TD7034, 0.4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: ET3X2_rat_high_salt_diet_39802_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39802 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39802 left kidney


title: ET3X2_rat_high_salt_diet_39797_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39797 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39797 left kidney


title: CD14_Ficoll_rep3

source_name: positively selected CD14+ monocytes purified from peripheral blood mononuclear cells isolated using Ficoll


title: CD14_CPT_rep3


title: CD4_Ficoll_rep3


title: CD4_Ficoll_rep1


title: ET3X2_rat_low_salt_diet_39805_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x2) rat 39805 left kidney, low salt diet

source_name: ET3x2 rat 39805 left kidney


title: CD8_CPT_rep3

source_name: positively selected CD8+ T cells purified from peripheral blood mononuclear cells isolated using BD vacutainer cell preparation tube

value: CD8+ T cells (purified from PBMCs)


title: CD14_CPT_rep1


title: PDAC9

description: frozen pancreatic tissue

source_name: frozen pancreatic tissue


title: CD14_Ficoll_rep1


title: CD14_Ficoll_rep2


title: ET3X1_rat_low_salt_diet_39851_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39851 left kidney, low salt diet

source_name: ET3x1 rat 39851 left kidney


title: ET3X1_rat_low_salt_diet_39854_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39854 left kidney, low salt diet

source_name: ET3x1 rat 39854 left kidney


title: ET3X1_rat_low_salt_diet_39850_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39850 left kidney, low salt diet

source_name: ET3x1 rat 39850 left kidney


title: low parasitemia Patient Sample 4

city: Bangalore

first: Sanjeev

last: Kumar

state: Karnataka

address: 526/A,19th Main,3-sect,Ganesh Complex (2nd Floor) HSR Layout

department: R&D

country: India

institute: BioCOS Life Sciences Pvt Ltd

description: Gene expression data from pheripheral blood of mild malaria patient

hyb_protocol: Labeled cRNA was fragmented for 35min at 94C according to 49/64 array format and hybridized on Plasmodium/Anopheles Genome Array for 16h at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix gene chip scanner 3000 using GCOS version 1.4 (FS450_0004)

data_processing: First the probe level raw data (CEL files) from HP and LP group of samples were read separately for each sample and only the probes and the corresponding expression data of plasmodium Falciparum (PF) were selected for normalization using in house R and Perl scripts. Then the normalization of the data was done using widely used normalization technique, RMA ( Robust Multi-Array Average), an algorithm used to create an expression matrix from Affymetrix data using R/Bioconductor Affy library.Then using the limma package of R/Bioconductor and with threshold setting of 1.5 and 0.05 on fold change(FC) and p value respectively, the differentially expressed genes were obtained.

source_name: P.falciparum peripheral blood ring stages

label_protocol: Biotinylated cRNA were prepared and purified using RNA binding beads according to the standard Affymetrix protocol from 500ng of total RNA (3' IVT express kit, affymetrix).

growth_protocol: 3D7 strain of Plasmodium falciparum was maintained in continuous culture and synchronized to ring stages using sorbitol and collected into PAX gene blood RNA tubes for RNA extraction    3D7 strain of Plasmodium falciparum was maintained in continuous culture and synchronized to ring stages using sorbitol

extract_protocol: total RNA was isolated using PAXgene blood RNA kit according to manufacturer’s instructions

treatment_protocol: Whole blood samples from malaria infected patients were collected into PAX gene blood RNA tubes for RNA extraction

value: Red blood cells

tag: agent

value: Plasmodium falciparum 3D7


title: Control-2: invitro rings

description: Gene expression data from in vitro ring stages

source_name: P.falciparum invitro ring stages


title: low parasitemia Patient Sample 2


title: low parasitemia Patient Sample 3


title: Control-1: invitro rings


title: Control-3: invitro rings


title: high parasitemia Patient sample 11

description: Gene expression data from pheripheral blood of severe malaria patient

data_processing: First the probe level raw data (CEL files) from HP and LP group of samples were read separately for each sample and only the probes and the corresponding expression data of plasmodium Falciparum (PF) were selected for normalization using in house R and Perl scripts. Then the normalization of the data was done using widely used normalization technique, RMA ( Robust Multi-Array Average), an algorithm used to create an expression matrix from Affymetrix data using R/Bioconductor Affy library. Then using the limma package of R/Bioconductor and with threshold setting of 1.5 and 0.05 on fold change(FC) and p value respectively, the differentially expressed genes were obtained.


title: CD8_CPT_rep2

tag: cell type


title: CD8_Ficoll_rep3

source_name: positively selected CD8+ T cells purified from peripheral blood mononuclear cells isolated using Ficoll


title: Control-4: invitro rings


title: CD8_CPT_rep1


title: low parasitemia Patient Sample 1


title: F344_Day01h_ductus arteriosus_rep1

description: F344 DA replicate 1

source_name: F344_Day01h_ductus arteriosus

value: 1hr after birth (Day0, full-term)

value: ductus arteriosus


title: CD8_Ficoll_rep1


title: ET3X1_rat_high_salt_diet_39848_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39848 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39848 left kidney

value: S.R(ET3x1), diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: high parasitemia Patient sample 8


title: ET3X1_rat_high_salt_diet_39849_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39849 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39849 left kidney


title: high parasitemia Patient sample 9


title: CD8_Ficoll_rep2


title: S_rat_low_salt_diet_S7436_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7436 left kidney, low salt diet

source_name: S rat S7436 left kidney

value: SS/jr, diet:low salt (Harlan Teklad TD7034, 0.4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: CD19_CPT_rep3

source_name: positively selected CD19+ B cells purified from peripheral blood mononuclear cells isolated using BD vacutainer cell preparation tube

value: CD19+ B cells (purified from PBMCs)


title: ET3X1_rat_high_salt_diet_39847_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39847 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39847 left kidney


title: high parasitemia Patient sample 10


title: ET3X1_rat_high_salt_diet_39845_kidney_RNA_RAE230A

description: Gene expression data from S.R(ET3x1) rat 39845 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39845 left kidney


title: CD19_CPT_rep2


title: high parasitemia Patient sample 7


title: high parasitemia Patient sample 6


title: high parasitemia Patient sample 5


title: high parasitemia Patient sample 4


title: high parasitemia Patient sample 3


title: high parasitemia Patient sample 2


title: CD19_CPT_rep1


title: high parasitemia Patient sample 1


title: S_rat_low_salt_diet_S7429_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7429 left kidney, low salt diet

source_name: S rat S7429 left kidney


title: Control-4: invitro rings


title: S_rat_low_salt_diet_S7426_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7426 left kidney, low salt diet

source_name: S rat S7426 left kidney


title: Control-3: invitro rings


title: S_rat_low_salt_diet_S7427_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7427 left kidney, low salt diet

source_name: S rat S7427 left kidney


title: Control-2: invitro rings


title: CD19_Ficoll_rep3

source_name: positively selected CD19+ B cells purified from peripheral blood mononuclear cells isolated using Ficoll


title: S_rat_high_salt_diet_S7435_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7435 left kidney after 24 hours on high salt diet

source_name: S rat S7435 left kidney

value: SS/jr, diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: Control-1: invitro rings


title: S_rat_low_salt_diet_S7428_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7428 left kidney, low salt diet

source_name: S rat S7428 left kidney


title: CD4_CPT_rep2

source_name: positively selected CD4+ T cells purified from peripheral blood mononuclear cells isolated using BD vacutainer cell preparation tube

value: CD4+ T cells (purified from PBMCs)


title: PBMC_CPT_rep3

source_name: peripheral blood mononuclear cells isolated using BD Vacutainer cell preparation tube

value: peripheral blood mononuclear cells

value: BD vacutainer cell preparation tube


title: CD19_Ficoll_rep1


title: S_rat_high_salt_diet_S7416_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7416 left kidney, high salt diet

source_name: S rat S7416 left kidney


title: PBMC_CPT_rep2


title: PBMC_CPT_rep1


title: S_rat_high_salt_diet_S7419_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7419 left kidney after 24 hours on high salt diet

source_name: S rat S7419 left kidney


title: S_rat_high_salt_diet_S7417_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7417 left kidney after 24 hours on high salt diet

source_name: S rat S7417 left kidney


title: S_rat_high_salt_diet_S7418_kidney_RNA_RAE230A

description: Gene expression data from SS/jr rat S7418 left kidney after 24 hours on high salt diet

source_name: S rat S7418 left kidney


title: PBMC_Ficoll_rep2

source_name: peripheral blood mononuclear cells isolated using Ficoll


title: CD19_Ficoll_rep2


title: PBMC_Ficoll_rep1


title: ET3x2_rat_kidney_RNA_pool_I_RAE230A

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool I (rats 39826, 39832 and 39823)

hyb_protocol: Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual with quality assessed by hybridization of a 5 μg aliquot to a test chip (TestChip3, Affymetrix). Fragmented cRNA probe (5 μg) was then hybridized to each of a set of 2 rat GeneChips (RAE230A and RAE230B; Affymetrix).  Hybridization, washing, and staining with streptavidin-phycoerythrin was performed at the University of Toledo Health Science Campus Genomics Core Facility according to the manufacturer's (Affymetrix) instructions.

source_name: ET3x2 rat left kidney

label_protocol: Biotinylated cRNA was synthesized using a kit (Enzo Bioarray High Yield RNA transcript Labeling Kit, Enzo Diagnostics, Farmingdale, NY) and cRNAs were purified on columns (RNeasy mini kit, Qiagen).

extract_protocol: The left kidneys from each rat were homogenized separately in a guanidine thiocyanate/phenol solution (Ultraspec, Biotecx Laboratories, Houston, TX), extracted with chloroform and isolated using RNA Tack Resin (Biotecx Laboratories). Total RNA was further purified by ethanol precipitation and absorption to a column (RNeasy, Qiagen, Valencia, CA) facording to the manufacturer's instructions. RNA integrity was assessed by 1) electrophoretic size-fractionation on 1% agarose gels under denaturing conditions and 2) hybridization of newly made cRNA probes to TestChips (Affymetrix).  Double-stranded cDNA was synthesized (separately) from 15 μg total RNA from each pool of kidney RNA (four pools/strain) using reverse transcriptase (SuperScript II, InVitrogen, Carlsbad, CA) and T7-(dT)24 as the oligonucleotide primer.

treatment_protocol: Male SS/jr (S) rats, S.R(ET3x1) substrain rats and S.R(ET3x2) substrain rats were maintained on a low salt (0.4% NaCl Harlan Teklad diet TD7034) diet until 39-41 days of age and then fed an intermediate (2% NaCl Harlan Teklad diet TD94217) salt diet for 28 days.

value: S.R(ET3x2), age:67-69 days, gender:male, tissue:left kidney


title: ET3x1_rat_kidney_RNA_pool_H_RAE230A

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool H (rats 39864, 39857 and 39865)

source_name: ET3x1 rat left kidney

value: S.R(ET3x1), age:67-69 days, gender:male, tissue:left kidney


title: ET3x2_rat_kidney_RNA_pool_J_RAE230A

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool J (rats 39824, 39829, 39833)


title: ET3x2_rat_kidney_RNA_pool_K_RAE230A

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool K (rats 39830, 39831 and 39822)


title: ET3x1_rat_kidney_RNA_pool_E_RAE230A

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool E (rats 39859, 39836 and 39841)


title: ET3x1_rat_kidney_RNA_pool_F_RAE230A

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool F (rats 39861, 39842 and 39860)


title: S_rat_kidney_RNA_pool_D_RAE230A

description: Gene expression data from S rat left kidney RNA pool D (rats S7447 and S7471)

source_name: S rat left kidney

value: SS/jr, age:67-69 days, gender:male, tissue:left kidney


title: Mature zone Severe drought stress replicate 2

city: Antwerpen

first: Gerrit

middle: TS

last: Beemster

state: Antwerpen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

description: Biological replicate 2 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress

hyb_protocol: Hybridization was  performed as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol.

scan_protocol: Microarrays were scanned using a Genepix Personal 4100A confocal scanner (Axon Instruments), at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm. All spots were identified and quantified by GenePix Pro 6.0 software (Axon Instruments).

data_processing: The R packages array Quality Metrics and array Quality were used to perform a quality control: Spot filtering was done for each array, and spots that did not pass the criteria of FG >BG + 2SD (FG: foreground, BG= background, SD= standard deviation on the local backgrounds of the entire array) were excluded from the analysis. A variance stabilization, which is a between-array normalization was used, following the function normalize Between Arrays (x, method=vsn, lts.quantile=0.5), contained in the package limma.

organism: Zea mays

source_name: Mature tissue Severe drought stress

label_protocol: Samples were labeled using the Quick Amp Labeling Kit (Two Color, Agilent). The labeled samples were purified (by RNeasy Mini Kit), and cRNA yield and relative amount of incorporated labeled dCTPs were determined on a NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Scientific, USA).

growth_protocol: Maize seedlings were grown in a growth chamber under controlled conditions (16h day/8h night, 25°C/18°C day/night [d/n], 300mE.m-2 s-1Photosynthetically Active Radiation).

extract_protocol: The total RNA was extracted using the TRIZOL reagent (Invitrogen) and purified using the RNeasy Plant Mini Kit (Qiagen, Netherlands), following manufacturer's instructions.

treatment_protocol: For control plants the pots were re-watered daily to a Relative Soil Water Content (RSWC) of 54%. For drought treatments water contents were allowed to drop after sowing to43% RSWC (mild stress, no wilting), and 34% RSWC (severe stress, leaves are wilting during the day), respectively, where they were maintained. Three days after emergence of the fifth leaf, the plants were harvested and the growth zone (the first 10 cm from the leaf basis) of leaf 5 of each plant was cut in 10 segments of 1 cm and the samples were stored at -80°C. Total RNA was extracted from segment 1 (meristem) for the three conditions, segment 3 (elongation zone_severe stress), segment 4 (elongation zone_mild stress), segment 5 (elongation_control), and segment 10 (mature zone) for the three conditions. For each sample segments of 4 plants were pooled.

tag: developmental stage

value: mature

tag: treatment

value: severe drought stress

value: leaf


title: S_rat_kidney_RNA_pool_C_RAE230A

description: Gene expression data from S rat left kidney RNA pool C (rats S7446 and S7449)

tag: strain


title: Mature zone Control replicate 3

description: Biological replicate 3 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants

source_name: Mature tissue Control

value: control

tag: tissue


title: ET3x1_rat_kidney_RNA_pool_G_RAE230A

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool G (rats 39856, 39862 and 39843)


title: ET3x2_rat_kidney_RNA_pool_L_RAE230A

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool L (rats 39834, 39828 and 39825)


title: PBMC_Ficoll_rep3

value: Ficoll


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (8420)

city: College Station

first: Robert

middle: Neil

last: Vaughn

state: TX

address: 0965 Agronomy

department: Soil and Crop Sciences

institute: Texas A&M University

description:
Bos taurus x Bos indicus F2
Biological replicate 47 of 47: high v low residual shear force

hyb_protocol: RNA was hybridized to Agilent bovine 4x44K slides according to the hybridization procedures in the QuickAmp Labeling kit manual.  Hybridized slides were also washed and dried according to that protocol.

scan_protocol: Slides were scanned on Agilent Technologies Scanner G2505C US85003609.

data_processing: Agilent GeneSpring software (v 11.0.02) embedded functions were used for data normalization (quantile) and intepretation.  Normalized to baseline median expression across all arrays, minimum threshold 1.0.

organism: Bos indicus x Bos taurus

source_name: Muscle tissue collected < 1hr post-mortem before electrical-stimulation

label_protocol: Samples were labeled according to Agilent One-Color microarray-based gene expression analysis; low input Quick amp labeling protocol (v.6)

extract_protocol:
1.  RNA was extracted from aprx. 100-200 mg muscle sample using TRI Reagent and BCP (Molecular Research Center)
2.  RNA was tested for quality using Agilent 2100 Series Bioanalyzer
3.  RNA with RIN > 8.0 were treated with DNase (Invitrogen) and column purified using RNeasy mini-kit (Qiagen)

tag: residual shear force (es)

value: HIGH

value: Longissimus cervicis

tag: gender

value: Steer

tag: age

value: aprx. 18month


title: S_rat_kidney_RNA_pool_B_RAE230A

description: Gene expression data from S rat left kidney RNA pool B (rats S7439 and S7448)


title: Mature zone Severe drought stress replicate 4

description: Biological replicate 4 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (8419)

description:
Bos taurus x Bos indicus F2
Biological replicate 46 of 47: high v low residual shear force

value: LOW


title: Mature zone Mild drought stress replicate 2

description: Biological replicate 2 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress

source_name: Mature tissue Mild drought stress

value: mild drought stress


title: Mature zone Control replicate 2

description: Biological replicate 2 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: S_rat_kidney_RNA_pool_A_RAE230A

description: Gene expression data from S rat left kidney RNA pool A (rats S7437 and S7462)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8328)

description:
Bos taurus x Bos indicus F2
Biological replicate 45 of 47: high v low residual shear force

tag: residual shear force (nes)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8303)

description:
Bos taurus x Bos indicus F2
Biological replicate 42 of 47: high v low residual shear force


title: Mature zone Control replicate 1

description: Biological replicate 1 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8306)

description:
Bos taurus x Bos indicus F2
Biological replicate 43 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8314)

description:
Bos taurus x Bos indicus F2
Biological replicate 44 of 47: high v low residual shear force


title: Mature zone Control replicate 4

description: Biological replicate 4 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8208)

description:
Bos taurus x Bos indicus F2
Biological replicate 41 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (8157)

description:
Bos taurus x Bos indicus F2
Biological replicate 39 of 47: high v low residual shear force


title: ET3x2_rat_kidney_RNA_pool_K_RAE230B

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool K (rats 39830, 39831 and 39822)

hyb_protocol: Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual with quality assessed by hybridization of a 5 μg aliquot to a test chip (TestChip3, Affymetrix). Fragmented cRNA probe (5 μg) was then hybridized to each of a set of 2 rat GeneChips (RAE230B and RAE230B; Affymetrix).  Hybridization, washing, and staining with streptavidin-phycoerythrin was performed at the University of Toledo Health Science Campus Genomics Core Facility according to the manufacturer's (Affymetrix) instructions.


title: Elongation zone Severe drought stress replicate 2

description: Biological replicate 2 of 4. Segment 3 (3rd centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress

source_name: Expanding tissue Severe drought stress

value: elongation


title: ET3x2_rat_kidney_RNA_pool_L_RAE230B

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool L (rats 39834, 39828 and 39825)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8156)

description:
Bos taurus x Bos indicus F2
Biological replicate 38 of 47: high v low residual shear force


title: Elongation zone Mild drought stress replicate 3

description: Biological replicate 3 of 4. Segment 4 (4th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress

source_name: Expanding tissue Mild drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (8159)

description:
Bos taurus x Bos indicus F2
Biological replicate 40 of 47: high v low residual shear force


title: ET3x2_rat_kidney_RNA_pool_J_RAE230B

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool J (rats 39824, 39829, 39833)


title: ET3x2_rat_kidney_RNA_pool_I_RAE230B

description: Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool I (rats 39826, 39832 and 39823)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (8148)

description:
Bos taurus x Bos indicus F2
Biological replicate 37 of 47: high v low residual shear force


title: ET3x1_rat_kidney_RNA_pool_H_RAE230B

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool H (rats 39864, 39857 and 39865)


title: Elongation zone Mild drought stress replicate 2

description: Biological replicate 2 of 4. Segment 4 (4th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (8050)

description:
Bos taurus x Bos indicus F2
Biological replicate 30 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (8125)

description:
Bos taurus x Bos indicus F2
Biological replicate 34 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (8146)

description:
Bos taurus x Bos indicus F2
Biological replicate 36 of 47: high v low residual shear force


title: ET3x1_rat_kidney_RNA_pool_G_RAE230B

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool G (rats 39856, 39862 and 39843)


title: Mature zone Mild drought stress replicate 3

description: Biological replicate 3 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (8115)

description:
Bos taurus x Bos indicus F2
Biological replicate 33 of 47: high v low residual shear force


title: Elongation zone Severe drought stress replicate 3

description: Biological replicate 3 of 4.Segment 3 (3rd centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (8113)

description:
Bos taurus x Bos indicus F2
Biological replicate 32 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (8133)

description:
Bos taurus x Bos indicus F2
Biological replicate 35 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (8053)

description:
Bos taurus x Bos indicus F2
Biological replicate 31 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (8035)

description:
Bos taurus x Bos indicus F2
Biological replicate 29 of 47: high v low residual shear force


title: ET3x1_rat_kidney_RNA_pool_F_RAE230B

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool F (rats 39861, 39842 and 39860)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (8019)

description:
Bos taurus x Bos indicus F2
Biological replicate 28 of 47: high v low residual shear force


title: ET3x1_rat_kidney_RNA_pool_E_RAE230B

description: Gene expression data from S.R(ET3x1) congenic rat left kidney RNA pool E (rats 39859, 39836 and 39841)


title: Elongation zone Mild drought stress replicate 1

description: Biological replicate 1 of 4. Segment 4 (4th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7742)

description:
Bos taurus x Bos indicus F2
Biological replicate 25 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (8010)

description:
Bos taurus x Bos indicus F2
Biological replicate 27 of 47: high v low residual shear force


title: Elongation zone Control replicate 4

description: Biological replicate 4 of 4. Segment 5 (5th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants

source_name: Expanding tissue Control


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (7732)

description:
Bos taurus x Bos indicus F2
Biological replicate 22 of 47: high v low residual shear force


title: S_rat_kidney_RNA_pool_B_RAE230B

description: Gene expression data from S rat left kidney RNA pool B (rats S7439 and S7448)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (7738)

description:
Bos taurus x Bos indicus F2
Biological replicate 24 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (8004)

description:
Bos taurus x Bos indicus F2
Biological replicate 26 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (7730)

description:
Bos taurus x Bos indicus F2
Biological replicate 20 of 47: high v low residual shear force


title: Elongation zone Control replicate 3

description: Biological replicate 3 of 4. Segment 5 (5th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (7736)

description:
Bos taurus x Bos indicus F2
Biological replicate 23 of 47: high v low residual shear force


title: S_rat_kidney_RNA_pool_D_RAE230B

description: Gene expression data from S rat left kidney RNA pool D (rats S7447 and S7471)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7728)

description:
Bos taurus x Bos indicus F2
Biological replicate 19 of 47: high v low residual shear force


title: Elongation zone Control replicate 2

description: Biological replicate 2 of 4. Segment 5 (5th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: S_rat_kidney_RNA_pool_C_RAE230B

description: Gene expression data from S rat left kidney RNA pool C (rats S7446 and S7449)


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (7715)

description:
Bos taurus x Bos indicus F2
Biological replicate 18 of 47: high v low residual shear force


title: Mature zone Severe drought stress replicate 1

description: Biological replicate 1 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7731)

description:
Bos taurus x Bos indicus F2
Biological replicate 21 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7215)

description:
Bos taurus x Bos indicus F2
Biological replicate 12 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (7232)

description:
Bos taurus x Bos indicus F2
Biological replicate 14 of 47: high v low residual shear force


title: Elongation zone Severe drought stress replicate 4

description: Biological replicate 4 of 4. Segment 3 (3rd centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: Elongation zone Control replicate 1

description: Biological replicate 1 of 4. Segment 5 (5th centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: Elongation zone Mild drought stress replicate 4

description: Biological replicate 4 of 4. Segment 4 (4th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7127)

description:
Bos taurus x Bos indicus F2
Biological replicate 9 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7606)

description:
Bos taurus x Bos indicus F2
Biological replicate 17 of 47: high v low residual shear force


title: S_rat_kidney_RNA_pool_A_RAE230B

description: Gene expression data from S rat left kidney RNA pool A (rats S7437 and S7462)


title: Elongation zone Severe drought stress replicate 1

description: Biological replicate 1 of 4. Segment 3 (3rd centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: ET3X2_rat_low_salt_diet_39820_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39820 left kidney, low salt diet

source_name: ET3x2 rat 39820 left kidney

value: S.R(ET3x2), diet:low salt (Harlan Teklad TD7034, 0.4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (7126)

description:
Bos taurus x Bos indicus F2
Biological replicate 8 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7151)

description:
Bos taurus x Bos indicus F2
Biological replicate 11 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (7518)

description:
Bos taurus x Bos indicus F2
Biological replicate 16 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7227)

description:
Bos taurus x Bos indicus F2
Biological replicate 13 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7142)

description:
Bos taurus x Bos indicus F2
Biological replicate 10 of 47: high v low residual shear force


title: ET3X2_rat_low_salt_diet_39806_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39806 left kidney, low salt diet

source_name: ET3x2 rat 39806 left kidney


title: Mature zone Mild drought stress replicate 1

description: Biological replicate 1 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: ET3X2_rat_low_salt_diet_39805_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39805 left kidney, low salt diet

source_name: ET3x2 rat 39805 left kidney


title: ET3X2_rat_high_salt_diet_39801_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39801 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39801 left kidney

value: S.R(ET3x2), diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: E13-F3V3 / E13-F3C3

type: genomic

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Vinclozolin SRY ChIP DNA sample 3 is compared to Control IgG ChIP DNA sample 3

hyb_protocol: Purified DNA was sent to Nimblegen for ChIP-chip hybridization (Nimblegen, Iceland). The ChIP-Chip hybridization used a Roche Nimblegen’s Rat ChIP-Chip 3x720K RefSeq Promoter Array.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For each hybridization experiment raw data from both the Cy3 can Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), and data checked for quality and converted to MA values (M = Cy5-Cy3; A = (Cy5+Cy3)/2). The R codes that were used for analysis and annotation are available in the following website: http//www.skinner.wsu.edu.   All the tiling array Chip data was deposited in the NCBI GEO site. Within each array, probes were separated into groups by GC content and each group was separately normalized using the LOESS normalization procedure. This allowed for groups with optimal GC content, which exhibited a reduced quality issue, to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized across arrays using the A-quantile normalization procedure.   Following normalization the probe's normalized M values (and then A) were replaced with the median value of all probe M values (and then A) within a sliding window of 1000 bp, due to the size of DNA fragments used.   Following normalization each probe's M value represents the median intensity difference between Cy5 and Cy3 of a 1000 bp window. Significance was assigned to probe differences between experimental (SRY) and IgG control by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of M. Regions of interest were then determined by combining consecutive probes with significance p-values less than 10-3. Significance was assigned to probe differences between experimental and control by calculating the median value of the increasing differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the mean. A Z-score and P-value were computed from that distribution with the use of R code analysis.  The statistical package was similar to the edgeR bioconductor package and used empirical Bayes methods.  The statistically significant peaks of hybridization were identified and P-value associated with each peak presented. Each peak of interest was then annotated for the gene. Every promoter exceeding the intensity threshold was considered positive for SRY binding. The ﬁnal list of SRY targets includes the promoter-proximal regions that made the threshold in an average of the three replicates.  Hybridization signals for all the candidate promoters that were within the cutoff line (p≤ 1x10-4) were plotted (average of the three replicates).
Value definitions for processed data files: #ClusterID= ID and chrolosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control),  #Chromosome= Chromosome number, #cSTART= Cluster start site,  #cSTOP= Cluster stop site,  #meanM= mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group,  #meanA= mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group,  #minP= p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files. P-value must be p<1.0E-5 or less for inclusion,  #nProbes= number of consecutive probes with p<1.0E-5 included in cluster,  #CG= CG content of cluster,  #CpG= CpG content of cluster, and #CpGdensity= number of CpGs per hundred base pairs.
Submitter states "lacks a matrix of the complete normalized data" and "because we do not have files such as this because of how data is processed."

molecule: genomic DNA

source_name: Vinclozolin SRY ChIP DNA from F3, embryonic day 13 (E13) gonads

label_protocol: Samples for SRY ChIP DNA were labeled with Cy3 and control DNA from IgG control were labeled with Cy5.

growth_protocol: Harlan Sprague-Dawley rats were used for the study. All the rats were kept in a temperature controlled environment.  Estrous cycles of female rats were monitored by cellular morphology from vaginal smears.  Rats in early estrus were paired with males overnight and mating confirmed by sperm positive smears, denoting day 0 of pregnancy.  Sister littermates were divided into control and vinclozolin treatment groups and mated to similar males to minimize the genetic variation between the control and vinclozolin lineages.   Sufficient females were used so no inbreeding (sibling or cousin) occurred in any generation.  The F1 generation was bred within the lineage to generate the F2 generation and these F2 generation bred to generate the F3 generation.  The only exposure was the F0 generation females. They were exposed to vinclozolin or DMSO through IP injection daily from E8-E14. The F2 generation pregnant rats were euthanized at gestational embryonic day 13 (E13) of pregnancy, and F3 generation embryonic gonads were collected for chromatin immunoprecipitation.

extract_protocol: Embryo tails were collected to make genomic DNA by standard procedures. Briefly, the tissue was homogenized through a 25-gauge needle in digestion buffer (100 mM NaCl, 10 mM Tris, pH 8, 25 mM EDTA, 0.5% SDS) and digested with proteinase K (0.15 mg/ml) for at least 4 h at 60°C. The samples were then extracted twice with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) and once with chloroform:isoamyl alcohol. The DNA was precipitated by adding 1/10 volume 7.5 M NH4Ac and 3 volumes cold ethanol and incubating at −80°C for 1 h before centrifugation at 4°C for 30 min. Pellets were dried and resuspended in 10 μl H2O.

treatment_protocol: Vinclozolin

tag: generation

value: F3, Embryonic day 13 (E13)

source_name: Control IgG ChIP DNA  from F3, embryonic day 13 (E13) gonads

treatment_protocol: vehicle control (DMSO)


title: Mature zone Severe drought stress replicate 3

description: Biological replicate 3 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: ET3X2_rat_high_salt_diet_39802_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39802 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39802 left kidney


title: Mature zone Mild drought stress replicate 4

description: Biological replicate 4 of 4. Segment 10 (10th centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: E13-F3V1 / E13-F3C1

description: Vinclozolin SRY ChIP DNA sample 1 is compared to Control IgG ChIP DNA sample 1


title: E13-F3V2 / E13-F3C2

description: Vinclozolin SRY ChIP DNA sample 2 is compared to Control IgG ChIP DNA sample 2


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (7101)

description:
Bos taurus x Bos indicus F2
Biological replicate 4 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7123)

description:
Bos taurus x Bos indicus F2
Biological replicate 7 of 47: high v low residual shear force


title: ET3X1_rat_low_salt_diet_39850_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39850 left kidney, low salt diet

source_name: ET3x1 rat 39850 left kidney

value: S.R(ET3x1), diet:low salt (Harlan Teklad TD7034, 0.4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: ET3X2_rat_high_salt_diet_39799_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39799 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39799 left kidney


title: Meristem Severe drought stress replicate 1

description: Biological replicate 1 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress

source_name: Proliferating tissue Severe drought stress

value: proliferation


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7005)

description:
Bos taurus x Bos indicus F2
Biological replicate 1 of 47: high v low residual shear force


title: Meristem Severe drought stress replicate 2

description: Biological replicate 2 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: Longissimus cervicisMuscle_<1hrPostMortem_rep4 (7112)

description:
Bos taurus x Bos indicus F2
Biological replicate 5 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7021)

description:
Bos taurus x Bos indicus F2
Biological replicate 3 of 47: high v low residual shear force


title: Longissimus cervicisMuscle_<1hrPostMortem_rep2 (7115)

description:
Bos taurus x Bos indicus F2
Biological replicate 6 of 47: high v low residual shear force


title: ET3X1_rat_low_salt_diet_39854_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39854 left kidney, low salt diet

source_name: ET3x1 rat 39854 left kidney


title: Meristem Mild drought stress replicate 3

description: Biological replicate 3 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress

source_name: Proliferating tissue Mild drought stress


title: ET3X2_rat_high_salt_diet_39797_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39797 left kidney after 24 hours on high salt diet

source_name: ET3x2 rat 39797 left kidney


title: Longissimus cervicisMuscle_<1hrPostMortem_rep1 (7009)

description:
Bos taurus x Bos indicus F2
Biological replicate 2 of 47: high v low residual shear force

source_name: Muscle tissue collected < 1hr post-mortem before electrical-stimulation


title: Meristem Severe drought stress replicate 3

description: Biological replicate 3 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress


title: Meristem Mild drought stress replicate 1

description: Biological replicate 1 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: Meristem Control replicate 4

description: Biological replicate 4 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants

source_name: Proliferating tissue Control


title: activated osteoclast

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

country: China

institute: Third Military Medical University

description: RAW264.7 cells were induced with RANKL (100 ng/ml) and M-CSF (50 ng/ml)for 96 h.

hyb_protocol: Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube. Mix well but gently on a vortex mixer. Incubate at 60°C for exactly 30 minutes to fragment RNA. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. Hybridize at 65°C for 17 hours.

scan_protocol: 1.Assemble the slides into an slide holder.  2.Place assembled slide holders into scanner carousel. 3.Verify scan settings for one-color scans. Parameters, Scan region: Scan Area (61 x 21.6 mm), Scan resolution (μm): 5, 5μm scanning mode: Single Pass, eXtended Dynamic range: (selected), Dye channel: Green, Green PMT: XDR Hi 100%, XDR Lo 10%.

data_processing: Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.  1.Open the Agilent Feature Extraction (FE) software. 2.Add the images (.tif) to be extracted to the FE Project. 3.Set FE Project Properties. 4.Check the Extraction Set Configuration. 5.Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

organism: Mus musculus

source_name: RAW264.7 cells

label_protocol: Add 1ug of total RNA to a 1.5-mL microcentrifuge tube. Add 1.2 μL of T7 Promoter Primer. Use nuclease-free water to bring the total reaction volume to 11.5 μL. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. Incubate samples at 40°C in a circulating water bath for 2 hours. Move samples to a 65°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.

value: RAW264.7 cells


title: Meristem Mild drought stress replicate 2

description: Biological replicate 2 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to mild drought stress


title: ET3X1_rat_high_salt_diet_39849_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39849 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39849 left kidney

value: S.R(ET3x1), diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: Meristem Control replicate 3

description: Biological replicate 3 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants

value: leaf


title: ET3X1_rat_low_salt_diet_39851_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39851 left kidney, low salt diet

source_name: ET3x1 rat 39851 left kidney


title: pre-osteoclast

description: RAW264.7 cells were induced with RANKL (100 ng/ml) and M-CSF (50 ng/ml)for 24 h.


title: ET3X1_rat_high_salt_diet_39848_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39848 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39848 left kidney


title: mature osteoclast

description: RAW264.7 cells were induced with RANKL (100 ng/ml) and M-CSF (50 ng/ml)for 72 h.


title: monocyte

description: RAW264.7 cells were induced with RANKL (100 ng/ml) and M-CSF (50 ng/ml)for 0 h.


title: ET3X1_rat_low_salt_diet_39855_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39855 left kidney, low salt diet

source_name: ET3x1 rat 39855 left kidney


title: S_rat_low_salt_diet_S7426_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7426 left kidney, low salt diet

source_name: S rat S7426 left kidney

value: SS/jr, diet:low salt (Harlan Teklad TD7034, 0.4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: Meristem Control replicate 2

description: Biological replicate 2 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants

value: control


title: Meristem Control replicate 1

description: Biological replicate 1 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of well-watered maize plants


title: Meristem Severe drought stress replicate 4

description: Biological replicate 4 of 4. Segment 1 (1st centimeter from leaf basis) of leaf 5, three days after its emergence, of maize plants, subjected to severe drought stress

value: severe drought stress


title: S_rat_low_salt_diet_S7427_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7427 left kidney, low salt diet

source_name: S rat S7427 left kidney


title: S_rat_high_salt_diet_S7418_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7418 left kidney after 24 hours on high salt diet

source_name: S rat S7418 left kidney

value: SS/jr, diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: ET3X1_rat_high_salt_diet_39847_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39847 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39847 left kidney


title: ET3X1_rat_high_salt_diet_39845_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x1) rat 39845 left kidney after 24 hours on high salt diet

source_name: ET3x1 rat 39845 left kidney


title: S_rat_low_salt_diet_S7428_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7428 left kidney, low salt diet

source_name: S rat S7428 left kidney


title: ET3X2_rat_low_salt_diet_39807_kidney_RNA_RAE230B

description: Gene expression data from S.R(ET3x2) rat 39807 left kidney, low salt diet

source_name: ET3x2 rat 39807 left kidney


title: Longissimus cervicisMuscle_<1hrPostMortem_rep3 (7303)

description:
Bos taurus x Bos indicus F2
Biological replicate 15 of 47: high v low residual shear force

value: HIGH

value: Longissimus cervicis

value: Steer


title: S_rat_high_salt_diet_S7435_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7435 left kidney after 24 hours on high salt diet

source_name: S rat S7435 left kidney


title: S_rat_low_salt_diet_S7429_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7429 left kidney, low salt diet

source_name: S rat S7429 left kidney


title: S_rat_high_salt_diet_S7419_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7419 left kidney after 24 hours on high salt diet

source_name: S rat S7419 left kidney


title: S_rat_low_salt_diet_S7436_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7436 left kidney, low salt diet

source_name: S rat S7436 left kidney


title: SCCOHT1

city: Phoenix

first: Pilar

last: Ramos

state: Arizona

address: 445 N. 5th Street

institute: Translational Genomics Research Institute (TGen)

description: Normal ovary unaffected by endometriosis

hyb_protocol: 825 ng of labeled tumor RNA and 825 ng of labeled reference RNA were prepared and hybridized to Agilent 4x44K (V1) gene expression microarrays following manufacturer protocols (Agilent Technologies; Palo Alto, CA).

scan_protocol: Slides were washed with Agilent's Gene Expression Wash Buffers (Part Number 5188-5327) following Agilent's protocol and scanned at 5 μm using an Agilent Microarray Scanner (model G2505B) in an ozone-controlled environment.

data_processing: Agilent Feature Extraction software (v10.5) was used for background subtraction and normalization. Array control features and control targets were removed. Data transformed from Log10 Ratio to Log2 Ratio.

source_name: SCCOHT1 cell line (Otte et al. Int J. Oncol. 41, 2012)

label_protocol: 200 ng of RNA from each tumor and cell line sample were labeled with Cy3 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. For the reference, 100 ng of RNA from each of the 2 commercial normal ovary samples were combined and labeled with Cy5 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. Labeling efficiency was measured with a Nanodrop ND-1000 Spectrophotometer.

extract_protocol: Homogenization of frozen PDX tumors was conducted with a Covaris S-2 tissue disrupter followed by addition of TRIzol reagent (Life Technologies). BIN67 and SCCOHT1 cells were washed with PBS and lysed using TRIzol reagent. Total RNA was purified using the RNeasy micro kit (Qiagen) following the manufacturer's instructions. The RNA integrity and purity of all samples was measured using a 2100 Bioanalyzer (Agilent) and a Nanodrop ND-1000 Spectrophotometer. RIN# for RNAs from PDX tumors were >7, while RIN# for RNAs from cell lines were 9.9.

tag: diagnosis

value: Small cell carcinoma of the ovary, hypercalcemic type

tag: age at diagnosis

tag: ethnicity

value: Unknown

tag: figo stage

value: Ia

tag: hypercalcemia

value: Yes

tag: excision to snap freeze (min)

source_name: Pool of 2 commercial normal ovary RNA samples

tag: case diagnosis

value: Endometriosis, endometriosis

tag: supplier

value: OriGene Technologies

tag: catalog numbers


title: 75 hpf RA sample 3B

city: Moscow

first: Deborah

middle: Lynn

last: Stenkamp

state: Idaho

address: 875 Perimeter Drive, MS 3051

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Algorithm: ExpressionStat 5.0

organism: Danio rerio

source_name: 75 hpf eyes RA

label_protocol: Standard Affymetrix protocol

growth_protocol: 28.5 deg C

extract_protocol: total RNA qiagen from dissected eye tissues

tag: FISH

tag: developmental stage

value: 75 hpf

value: embryonic eye

tag: agent

value: RA


title: 75 hpf control/dmso sample 3A

source_name: 75 hpf eyes

tag: tissue


title: SCCOHT PDX_065

source_name: Fresh-frozen PDX SCCOHT xenograft tumor (P0 mouse)


title: 75 hpf RA sample 4B


title: 75 hpf control/dmso sample 1A


title: Empty vector 3

status: Public on Aug 27 2015

city: Worcester

first: Amy

last: Walker

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: UMASS Medical School

hyb_protocol: 3 ug of fragmented and labeled cDNA were hybridized for 16 hrs at 45C on GeneChip C elegans ST 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: Data was processed using RMA

organism: Caenorhabditis elegans

source_name: young adult

label_protocol: Biotinylated cDNA was prepared using the Affymetrix WT PLUS Reagent Kit from 500ng total RN

growth_protocol: C. elegans were hatched oton Normal growth media, plus ampicillin, tetracycline and IPTG and harvested with 80% of the animals had reached young adulthood

extract_protocol: RNA was extracted using Tri-regent and cleaned with a Qiaquick RNA column.

treatment_protocol: IPTG concentration was 6mM

value: young adult

tag: RNAi

value: empty vector


title: sams-1(RNAi) 3


title: Empty vector 1


title: sams-1(RNAi) CH C

growth_protocol: C. elegans were hatched on to Normal growth media, plus ampicillin, tetracycline and IPTG and harvested with 80% of the animals had reached young adulthood

treatment_protocol: IPTG concentration was 6mM, choline treated animals were grown on NGM with 30mM choline

tag: choline treatment

value: yes


title: sbp-1(RNAi) 1


title: sams-1(RNAi) 1


title: Empty vector 2


title: 75 hpf control/dmso sample 4A

value: control


title: sams-1(RNAi) 2


title: sams-1(RNAi) CH A


title: 75 hpf RA sample 1B


title: sams-1(RNAi) B

value: no


title: sbp-1(RNAi) 3


title: sbp-1(RNAi) 2


title: sams-1(RNAi) CH B


title: Empty vector CH C


title: sams-1(RNAi) C


title: sams-1(RNAi) A


title: Empty vector CH B


title: Meristem Mild drought stress replicate 4

source_name: Proliferating tissue Mild drought stress

treatment_protocol: For control plants the pots were re-watered daily to a Relative Soil Water Content (RSWC) of 54%. For drought treatments water contents were allowed to drop after sowing to43% RSWC (mild stress, no wilting), and 34% RSWC (severe stress, leaves are wilting during the day), respectively, where they were maintained. Three days after emergence of the fifth leaf, the plants were harvested and the growth zone (the first 10 cm from the leaf basis) of leaf 5 of each plant was cut in 10 segments of 1 cm and the samples were stored at -80°C. Total RNA was extracted from segment 1 (meristem) for the three conditions, segment 3 (elongation zone/severe stress), segment 4 (elongation zone/mild stress), segment 5 (elongation/control), segment 7 (mature zone/severe stress), segment 8 (mature zone/mild stress), and segment 10 (mature zone/control). For each sample, segments of 4 plants were pooled.

value: proliferation

tag: treatment

value: mild drought stress

value: leaf


title: SCCOHT PDX_040

value: Small cell carcinoma of the ovary, hypercalcemic type

tag: age


title: Empty vector A


title: Empty vector C


title: Empty vector CH A


title: Empty vector B


title: BIN67

source_name: BIN67 cell line (Gamwell et al. Orphanet J. Rare Dis. 8, 2013)

tag: diagnosis

value: Unknown


title: IL-22-1 [miRNA]

city: Jinan

first: Meng

last: Jiang

state: Shandong

address: lixia street

institute: Qilu hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G

data_processing: GeneChip  Command Console Software (AGCC).

source_name: IL-22-1 [miRNA]

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15ug total RNA

growth_protocol: HaCaT cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS),100 U/ml penicillin and 100µg/ml streptomycin at 37℃ in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: To prepare them for recombinant human IL-22 (Sangon Biological Engineering Technology Company, Shanghai, China) treatment, HaCaT cells were starved in serum-free DMEM for 24 h and then treated with IL-22 (100 ng/ml) in serum-free DMEM for another 24 h or not treated.

tag: cell line

value: HaCaT

value: IL-22 stimulation


title: HO1

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in untreated LNCaP cell culture

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two cell dishes were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.5.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: not treated HL-60 cells_Replicate 1

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: HL-60 cell line

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: untreated or treated with 5nM Capridine

tag: cell type

value: acute promyelocytic leukemia cell line


title: HA3

description: Gene expression in 5nM Capridine treated LNCaP cell culture

source_name: Capridine-treated HL-60 cells_ Replicate 3


title: HA1

source_name: Capridine-treated HL-60 cells_ Replicate 1


title: IL-22-2 [miRNA]

source_name: IL-22-2 [miRNA]


title: HA4

source_name: Capridine-treated HL-60 cells_ Replicate 4


title: HO3

source_name: not treated HL-60 cells_Replicate 3


title: FL_LSK

city: Chiba

first: Motohiko

last: Oshima

state: State...

address: 1-8-1 Inohana

institute: Chiba University

description: Gene expression in LSK cells from mice Fetal liver at E14.5

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner (Agilent Technologies)

data_processing: Standard Agilent protocol

source_name: Fetal liver LSK cells, replicate 1

label_protocol: 20 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly isolated Fetal liver or bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: genotype

value: wild type

tag: transplantation

value: Fetal liver LSK cells


title: LA3

source_name: Capridine-treated LNCaP cells_ Replicate 3

growth_protocol: LNCaP cell culture

value: metastatic lesion of human prostatic adenocarcinoma


title: BM_LSK

description: Gene expression in LSK cells from mice Bone marrow at 8 weeks old

source_name: Bone marrow LSK cells, replicate 1

tag: strain

value: Bone marrow LSK cells


title: HA2

source_name: Capridine-treated HL-60 cells_ Replicate 2


title: HaCaT-1 [miRNA]

source_name: HaCaT-1 [miRNA]


title: LA1

source_name: Capridine-treated LNCaP cells_ Replicate 1


title: LA4

source_name: Capridine-treated LNCaP cells_ Replicate 4


title: LO3

source_name: not treated LNCaP cells_Replicate 3


title: HO4

source_name: not treated HL-60 cells_Replicate 4


title: HO2

source_name: not treated HL-60 cells_Replicate 2


title: LO4

source_name: not treated LNCaP cells_Replicate 4


title: LA2

source_name: Capridine-treated LNCaP cells_ Replicate 2


title: LO2

source_name: not treated LNCaP cells_Replicate 2


title: HaCaT-2 [miRNA]

source_name: HaCaT-2 [miRNA]


title: LO1

source_name: not treated LNCaP cells_Replicate 1


title: 12_M4455_0_Low

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

description:
R M4455 N=4
chip ID: 451215
_12_Cy3
PM

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 6.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Saccharomyces cerevisiae

growth_protocol: Yeast Peptone Dextrose medium were used for general yeast growth, which was at a temperature between 30 °C and 35 °C. To establish a consistent growth rate, chemostats were utilized.

extract_protocol: RNA was extracted using a previously described method that involved resuspending previously frozen cells in TRIzol reagent (Invitrogen, CA) and lysis via a bead beating method [23]. Briefly, frozen cell pellets were resuspended into 3 mL TRIzol reagent. Cells were lysed by adding ~1.5 mL of cell pellet/TRIzol mixture to 2 mL screw top tubes containing 0.25 g glass beads (MoBio Laboratories, CA) and bead beating at three 20 second cycles at 6500 rpm for several aliquots. Bead beating was conducted in a Precellys-24 (Bertin Technologies, Montigny-le-Bretonneux, France) bead beater. RNA was treated with DNAse I (Ambion, TX), purified using an RNeasy mini kit (Qiagen, CA), and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE). The quality of extracted RNA was determined with an Agilent BioAnalyzer. Purified RNA of high quality was used as the template to generate ds-cDNA using Invitrogen Superscript double-stranded synthesis kit according to the manufacturers protocols (Invitrogen, CA). ds-cDNA was labeled, hybridized and washed according to the NimbleGen protocols essentially as described previously  ( Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD: Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 2012, 13:336.)

treatment_protocol: Three 2L chemostat reactors with a base media of Yeast Nitrogen Base supplemented with synthetic complete amino acids (Sigma) were inoculated with either the 2-copy (M3201), 6- copy (M4294) or control strain (M4455). The reactor was controlled at 35 °C with continuous flushing of nitrogen/carbon dioxide (95:5).  After 3 exchanges of base media, a consistent growth rate of either 0.03 h-1 (low rate) or 0.3 h-1 (high rate) was achieved and a sample was taken for further analysis.  After sampling, 3 exchanges of base media were allowed for the strains to re-establish a steady state.  The chemostats were sampled again and this procedure was repeated for a total of 4 samples for the low growth reactor or 3 samples for the high growth reactor.

tag: pull

tag: growth rate

value: Low


title: IL-22-2 [RNA]


title: 11_M4455_0_Low

description:
R M4455 N=3
chip ID: 451215
_11_Cy3
PM

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: 9_M4455_0_Low

description:
M4455 N=4
chip ID: 451215
_9_Cy3
PM

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: IL-22-1 [RNA]


title: 10_M4455_0_Low

description:
R M4455 N=1
chip ID: 451215
_10_Cy3
PM


title: 140103-131449A_xhCRhigh_(HG-U133_Plus_2)

city: Wuhan

first: Chang

last: Yan

state: Hubei

address: Jiefang Road

department: Gastrointestinal Surgery

institute: Tongji Hospital

description: Gene expression data from xhCRC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method. The RMA-normalized values are q-value < 5% and fold change >2 or <0.5.

source_name: CEA high cells from xenograft tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: LoVo cells were cultured DMEM-10% FBS in a 37°C  humidified  incubator  with  an atmosphere of 5% CO2 and 95% air. xhCRC cells were implanted and cultured in female NOD/SCID mice

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

value: xenogrft tumor derived from colorectal cancer

tag: xenograft host

value: female NOD/SCID mouse


title: HaCaT-1 [RNA]

source_name: HaCaT-1 [RNA]


title: control

city: Shanghai

first: Jin

last: Hou

address: 800 Xiangyin Road

institute: Second Military Medical University

description: control SMMC-7721 cells

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: HCC.CELl line SMMC-7721 were obtained from ATCC and cultured under standard conditions

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: HCC.CELl line SMMC-7721 were treated with control medium or artemin for 12 hours


title: HaCaT-2 [RNA]

source_name: HaCaT-2 [RNA]


title: S_rat_high_salt_diet_S7416_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7416 left kidney, high salt diet

hyb_protocol: Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual with quality assessed by hybridization of a 5 g aliquot to a test chip (TestChip3, Affymetrix). Fragmented cRNA probe (5 g) was then hybridized to each of a set of 2 rat GeneChips (RAE230A and RAE230B; Affymetrix).

source_name: S rat S7416 left kidney

value: SS/jr, diet:high salt (Harlan Teklad TD83033, 4% NaCl), age:40-42 days, gender:male, tissue:left kidney


title: 140103-131449A_xhCRlow_(HG-U133_Plus_2)

description: Gene expression data from xhCRC

source_name: CEA low cells from xenograft tumor


title: 8_M4455_0_Low

description:
M4455 N=3
chip ID: 451215
_8_Cy3
PM


title: artemin treatment

description: SMMC-7721 cell treatment with artemin for 12 hours

value: artemin for 12 hours


title: 140103-131449A_LoVohigh_(HG-U133_Plus_2)

description: Gene expression data from LoVo

source_name: CEA high LoVo cells

value: colorectal cancer cell line

value: LoVo


title: S_rat_high_salt_diet_S7417_kidney_RNA_RAE230B

description: Gene expression data from SS/jr rat S7417 left kidney after 24 hours on high salt diet

source_name: S rat S7417 left kidney


title: 140103-131449A_LoVolow_(HG-U133_Plus_2)

description: Gene expression data from LoVo

source_name: CEA low LoVo cells


title: 5_M4294_6_Low

description:
M4294 N=3
chip ID: 451215
_5_Cy3
PM


title: 6_M4294_6_Low

description:
M4294 N=4
chip ID: 451215
_6_Cy3
PM


title: 7_M4455_0_Low

description:
M4455 N=1
chip ID: 451215
_7_Cy3
PM


title: Spontaneous_2

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description: unique sample, no replicate

hyb_protocol: Hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays, according to Affymetrix protocol

scan_protocol: Used an HR3000 scanner. Data extraction was performed with the Affymetrix Gene-Chip Operating System V1.1, according to Affymetrix protocol

data_processing: Probe sets were mapped to unique Entrez Gene IDs using a custom Chip Description File (CDF HGU133plus2_Hs_ENTREZG in R package “hgu133plus2hsentrezg.db” version 14.1, March 2011). Expression data were normalized and background corrected with the Robust Multichip Average method using R/Bioconductor. Genes with low variability between different time points were discarded. Differentially expressed genes were found by using the limma package in R/Bioconductor. P-values were corrected for multiple-hypothesis testing with the Benjamini-Hochberg algorithm

organism: Papio anubis

source_name: Spontaneous endometriosis

label_protocol: According to Affymetrix protocol

growth_protocol: Endometriosis was experimentally induced in four female baboons (Papio anubis) by intraperitoneal inoculation with menstrual endometrium on two consecutive menstrual cycles. Under laparoscopic guidance, approximately 1 g of menstrual tissue and fluid was deposited from the Pipelle at four sites: the pouch of Douglas, the uterine fundus, the cul de sac, and the ovaries. At the subsequent mense, the animals underwent a second laparoscopy and endometrial reseeding at the same ectopic sites.

extract_protocol: Eutopic endometria were homogenized in TRI-ZOL reagent (Invitrogen, Carlsbad, CA), and RNA was extracted. Total RNA was then subjected to DNase digestion to remove genomic DNA and was purified using the RNeasy Kit (Qiagen, Valencia, CA). RNA purity was confirmed by 260/280-nm absorbance ratios and analysis on an Agilent Bioanalyzer, following which cDNA was prepared according to the Affymetrix microarray preparation protocol (Affymetrix, Santa Clara, CA)

treatment_protocol: Eutopic endometrial tissues were harvested between days 9-11 postovulation and were snap frozen in liquid nitrogen for RNA extraction. Eutopic endometrium from the functionalis layer was consecutively harvested by endometriectomy from the same animals following experimental induction of endometriosis.

tag: Sex

value: female

value: eutopic endometrium


title: 3_M3201_2_Low

description:
M3201 N=4
chip ID: 451215
_3_Cy3
PM


title: UT_SCC115

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: Gene expression data from cutaneous SCC cell lines

hyb_protocol: Each sample was hybridized to Human Genome Array U133 Plus 2.0 according to Affymetrix GeneChip Analysis Technical Manual.

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

data_processing: Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control hybridization process and in summarizing probe cell intensity data. After hybridization, quality was checked with AGCC and Expression ConsoleTM 1.1. The data were normalized to remove variation between samples caused by non-biological reasons. Normalization of the array was performed using GCRMA. Data were subjected to statistical analysis with Chipster (CSC-IT Center for Science, Ltd, Espoo, Finland). R package Limma was used for performing the statistical analysis between the groups.

source_name: Cutaneous squamous cell carcinoma 115

label_protocol: Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol for GeneChip® expression analysis technical manual with specific protocols for using the GeneChip hybridization, wash and stain kit.

growth_protocol: NHEKs and cSCC cell lines were cultured and incubated at 37C.

extract_protocol: Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water ( Qiagen Rneasy kit, Qiagen GmbH, Hilden, Germany)

treatment_protocol: NHEK and cSCC cell lines were serum starved for 24 hours and the cell lysates were harvested.

value: Cutaneous SCC


title: 23_M4455_0_High

description:
R M4455 N=2 High
chip ID: 451215
_23_Cy3
PM

source_name: R M4455 N=2 High

value: High