title: RPEChoroid_146

description: RC_IA124-00 Mac_AMD

value: pool


title: RPEChoroid_151

status: Public on Feb 14 2012

type: RNA

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

state: CA

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

country: USA

institute: University of California, Santa Barbara

description: RC_IA213-99 Mid_AMD

hyb_protocol: Probe fragmentation and hybridization was carried out using the Agilent Gene Expression Hybridization Kit (Part #: 5188-5242) according to the methods of the manufacturer (Quick Amp Labeling Protocol, Version 5.7). Arrays were hybridized for 17 hr at 65°C. Arrays were washed for 1 min using Agilent Gene Expression Wash Buffer 1 (Part #: 5188-5325) + 0.005% Triton X-102 at room temperature and for 1 min at 37°C with Agilent Gene Expression Wash Buffer 2 (Part #: 5188-5326) + 0.005% Triton X-102. The washed arrays were then rinsed with acetonitrile for 10 sec and coated with Agilent Stabilization and Drying solution for 30 sec.

scan_protocol: Scanner: Bio-Rad VersArray™ ChipReader 3mm System.  Raw Data Quantification: VersArray™ Analyzer 4.5 [Median raw spot intensity within thresholds (5-65,535), Global Median Background Subtraction (Global background from negative control cells, zero order polynomial approximation), Local Regression Cross-channel Normalization (span = 10%, sub-sampling = 5, single pass)].

data_processing:
The data were processed and normalized using a universal reference design. The Lowess normalized raw data were further background corrected by subtraction of the minimum value of the Agilent negative controls (3xSLv1) to obtain the net intensity. Any values less than one standard deviation of the negative control probes were set to a value equal to the standard deviation of the negative controls for that sample. The individual probe net intensity values for both the experimental and reference samples were then divided by the sum of all array probes for that sample and experimental:reference probe ratios were calculated. Each experimental:reference probe ratio was then multiplied by the geometric mean of the corresponding reference probe expressed as percent total of all reference array probes. Values less than the equivalent of the standard deviation of all experimental array negative control spots were set to that equivalent and all values were then multiplied by an arbitrary constant (100,000) so that all expression values were greater than 1. For the two samples with replicates, the average expression values were calculated.

The supplementary files include the raw data (GSMxxx_*_raw.txt) and the data after Lowess normalization and background correction (GSMxxx_*.txt).

molecule: total RNA

organism: Homo sapiens

source_name: Extramacular RPE-choroid, AMD

label_protocol: All probe labeling was carried out using the Agilent Low Input Quick Amp Labeling Kit (Part #: 5190-2306, Version 5.7) according to the methods of the manufacturer using 250 ng of total RNA with the exception that spike-in controls were not used.

growth_protocol: RPE-choroid and retinal samples were isolated from human eye cups obtained from direct sources at the University of Iowa (G.S.H.), the Lion's Eye Bank of Oregon, or direct sources at the University of California, Santa Barbara. The Iowa eyes were selected from a well-characterized repository of 3,903 donors. Medical and ophthalmic histories, a family questionnaire, blood, and sera, were obtained from the majority of donors. All Iowa eyes were read and classified by retinal specialists using gross pathologic features, and when available, the corresponding fundus photographs and angiograms. Iowa eyes were subsequently graded for AMD subtypes using a modified scheme based on the Rotterdam Grading Scale (Normal: no signs of ocular abnormalities; MD1: hard  macular drusen only; MD2: soft distinct drusen only; Dry AMD: soft indistinct or reticular drusen only, soft distinct drusen with pigmentary abnormalities, or soft indistinct or reticular drusen with pigmentary abnormalities; CNV: sub-retinal choroidal neovascularization; GA: sharply demarcated area of apparent absence of the RPE (>175 mm)  involving central macular region; GA/CNV: geographic atrophy with choroidal neovascularization). Eight mm macular trephine punches and 6 mm temporally adjacent extramacular trephine punches of the RPE-choroid and retina were collected from Iowa eyes within 4 hr postmortem, flash frozen in liquid N2, and stored at -80 oC. The Oregon and Santa Barbara eyes only received a general classification of AMD based on patient histories supported by ophthalmological records. Detailed sample preparation for these eyes is published in Radeke et al. Exp. Eye Res. 85, 366-380 (2007).

extract_protocol: Total RNA was purified from the RPE-choroid and retina samples obtained from the University of Iowa ocular tissue repository using a Qiagen RNeasy Miniprep kit and on-column DNAse 1 digestion according to the methods of the manufacturer. Total RNA was purified from samples obtained from the Lion's Eye Bank of Oregon and the University of California, Santa Barbara using a Qiagen RNeasy Miniprep kit according to the methods of the manufacturer. Contaminating DNA was digested off-column with DNase I and the DNA-depleted RNA was repurified using the Qiagen RNeasy Miniprep.

tag: tissue

value: extramacular RPE-choroid

tag: gender

value: female

tag: age (years)

tag: ocular disease

value: AMD

tag: amd classification

value: dry AMD

tag: patient identifier

tag: rna integrity number (rin)

source_name: Reference RNA

value: RPE-choroid and retina

tag: disease state

value: normal and AMD

tag: sample type


title: RPEChoroid_158

description: RC_IA113-00 Mid_AMD

value: male

value: CNV


title: RPEChoroid_165

description: RC_IA068-00 Mac_AMD

source_name: Macular RPE-choroid, AMD

value: macular RPE-choroid


title: RPEChoroid_156

description: RC_OR012-99 Mid_AMD

value: clinical AMD diagnosis


title: RPEChoroid_155

description: RC_OR012-99 Mac_AMD


title: RPEChoroid_164

description: RC_IA100-98 Mid_AMD

value: not determined


title: RPEChoroid_157

description: RC_IA113-00 Mac_AMD


title: RPEChoroid_150

description: RC_IA213-99 Mac_AMD


title: RPEChoroid_143

description: RC_OR004-00 Mid_AMD


title: RPEChoroid_144

description: RC_OR009-99 Mac_AMD


title: RPEChoroid_145

description: RC_OR009-99 Mid_AMD


title: RPEChoroid_154

description: RC_IA256-00 Mac_AMD


title: RPEChoroid_149

description: RC_IA173-00 Mid_AMD

value: GA/CNV


title: RPEChoroid_137

description: RC_IA316-99 Mac_AMD


title: RPEChoroid_136

description: RC_IA285-99 Mid_AMD


title: RPEChoroid_141

description: RC_IA294-00 Mid_AMD


title: RPEChoroid_134

description: RC_IA239-00 Mid_AMD


title: RPEChoroid_127

description: RC_IA117-00 Mac_AMD


title: RPEChoroid_132

description: RC_IA405-99 Mid_AMD


title: RPEChoroid_130

description: RC_IA163-00 Mid_AMD


title: RPEChoroid_140

description: RC_IA294-00 Mac_AMD


title: RPEChoroid_142

description: RC_OR004-00 Mac_AMD


title: RPEChoroid_135

description: RC_IA285-99 Mac_AMD


title: RPEChoroid_125

description: RC_OR011-99 Mac_AMD


title: RPEChoroid_133

description: RC_IA239-00 Mac_AMD


title: RPEChoroid_128

description: RC_IA117-00 Mid_AMD


title: RPEChoroid_123

description: RC_IA363-99 Mac_AMD


title: RPEChoroid_126

description: RC_OR011-99 Mid_AMD


title: RPEChoroid_138_139

description:
RC_IA316-99 Mid_AMD
RC_IA316-99b Mid_AMD
This Sample represents two replicates.


title: RPEChoroid_131

description: RC_IA405-99 Mac_AMD


title: RPEChoroid_129

description: RC_IA163-00 Mac_AMD


title: RPEChoroid_124

description: RC_IA363-99 Mid_AMD


title: RPEChoroid_122

description: RC_IA356-99 Mac_AMD


title: RPEChoroid_118_119

description:
RC_IA306-99 Mid_AMD
RC_IA306-99b Mid_AMD
This Sample represents two replicates.


title: RPEChoroid_121

description: RC_IA186-98 Mid_AMD


title: RPEChoroid_120

description: RC_IA186-98 Mac_AMD


title: RPEChoroid_111

description: RC_IA035-98 Mac_AMD


title: RPEChoroid_112

description: RC_IA035-98 Mid_AMD


title: RPEChoroid_116

description: RC_IA199-00 Mid_AMD


title: RPEChoroid_113

description: RC_IA090-98 Mac_AMD


title: RPEChoroid_115

description: RC_IA199-00 Mac_AMD


title: RPEChoroid_114

description: RC_IA090-98 Mid_AMD


title: RPEChoroid_106

description: RC_IA357-99 Mid_AMD


title: RPEChoroid_117

description: RC_IA306-99 Mac_AMD


title: RPEChoroid_105

description: RC_IA357-99 Mac_AMD


title: RPEChoroid_107

description: RC_IA139-98 Mac_AMD


title: RPEChoroid_104

description: RC_IA191-97 Mid_AMD


title: RPEChoroid_100

description: RC_IA005-98 Mid_AMD


title: RPEChoroid_110

description: RC_IA407-99 Mid_AMD

value: GA


title: RPEChoroid_109

description: RC_IA407-99 Mac_AMD


title: RPEChoroid_108

description: RC_IA139-98 Mid_AMD


title: RPEChoroid_102

description: RC_IA262-00 Mid_AMD


title: RPEChoroid_101

description: RC_IA262-00 Mac_AMD


title: RPEChoroid_94

description: RC_IA448-99 Mid

source_name: Extramacular RPE-choroid, normal

value: normal


title: RPEChoroid_103

description: RC_IA191-97 Mac_AMD


title: RPEChoroid_98

description: RC_IA202-99 Mid_AMD


title: RPEChoroid_93

description: RC_IA448-99 Mac

source_name: Macular RPE-choroid, normal


title: RPEChoroid_95

description: RC_IA177-00 Mac


title: RPEChoroid_91

description: RC_IA205-98 Mac


title: RPEChoroid_87

description: RC_IA195-00 Mid


title: RPEChoroid_96

description: RC_IA177-00 Mid


title: RPEChoroid_89

description: RC_IA436-99 Mac


title: RPEChoroid_92

description: RC_IA205-98 Mid


title: RPEChoroid_88

description: RC_OR013-99 Mac


title: RPEChoroid_90

description: RC_IA436-99 Mid


title: RPEChoroid_97

description: RC_IA202-99 Mac_AMD


title: RPEChoroid_86

description: RC_IA195-00 Mac


title: RPEChoroid_85

description: RC_IA059-00 Mid


title: RPEChoroid_83

description: RC_OR001-02 Mac


title: RPEChoroid_76

description: RC_OR003-02 Mac


title: RPEChoroid_84

description: RC_IA059-00 Mac


title: RPEChoroid_82

description: RC_OR019-99 Mac


title: RPEChoroid_79

description: RC_SB005-98 Mac


title: RPEChoroid_81

description: RC_IA200-00 Mid


title: RPEChoroid_72

description: RC_IA031-98 Mid


title: RPEChoroid_80

description: RC_IA200-00 Mac


title: RPEChoroid_69

description: RC_OR002-01 Mid


title: RPEChoroid_78

description: RC_OR018-99 Mac


title: RPEChoroid_71

description: RC_IA031-98 Mac


title: RPEChoroid_64

description: RC_OR002-02 Mid


title: RPEChoroid_63

description: RC_OR002-02 Mac


title: RPEChoroid_75

description: RC_OR008-01 Mid


title: RPEChoroid_73

description: RC_SB006-98 Mac


title: RPEChoroid_68

description: RC_OR002-01 Mac


title: RPEChoroid_74

description: RC_OR008-01 Mac


title: RPEChoroid_77

description: RC_OR003-02 Mid


title: RPEChoroid_66

description: RC_IA420-99 Mac


title: RPEChoroid_67

description: RC_IA420-99 Mid


title: RPEChoroid_70

description: RC_OR005-99 Mid


title: RPEChoroid_62

description: RC_IA020-98 Mac


title: RPEChoroid_59

description: RC_OR011-01 Mac


title: RPEChoroid_58

description: RC_OR010-01 Mid


title: RPEChoroid_56

description: RC_IA266-99 Mac


title: RPEChoroid_65

description: RC_IA172-97 Mac


title: RPEChoroid_54

description: RC_IA377-99 Mac


title: RPEChoroid_61

description: RC_OR020-99 Mid


title: RPEChoroid_55

description: RC_IA377-99 Mid


title: RPEChoroid_51

description: RC_OR005-01 Mac


title: RPEChoroid_60

description: RC_OR011-01 Mid


title: RPEChoroid_52

description: RC_IA106-00 Mac


title: RPEChoroid_57

description: RC_IA266-99 Mid


title: RPEChoroid_45

description: RC_IA039-98 Mid


title: RPEChoroid_53

description: RC_IA106-00 Mid


title: RPEChoroid_47

description: RC_IA092-00 Mid


title: RPEChoroid_46

description: RC_IA092-00 Mac


title: RPEChoroid_42

description: RC_IA041-99 Mac


title: RPEChoroid_49

description: RC_OR015-99 Mid


title: RPEChoroid_44

description: RC_IA039-98 Mac


title: RPEChoroid_48

description: RC_OR015-99 Mac


title: RPEChoroid_37

description: RC_IA070-99 Mac


title: RPEChoroid_39

description: RC_OR006-99 Mac


title: RPEChoroid_41

description: RC_OR010-99 Mid


title: RPEChoroid_50

description: RC_OR004-99 Mid


title: RPEChoroid_40

description: RC_OR010-99 Mac


title: RPEChoroid_34

description: RC_IA073-98 Mac


title: RPEChoroid_38

description: RC_IA070-99 Mid


title: RPEChoroid_35

description: RC_IA073-98 Mid


title: RPEChoroid_43

description: RC_IA041-99 Mid


title: RPEChoroid_36

description: RC_OR007-99 Mid


title: RPEChoroid_29

description: RC_OR003-01 Mac


title: RPEChoroid_28

description: RC_IA359-99 Mid


title: RPEChoroid_22

description: RC_OR014-99 Mid


title: RPEChoroid_30

description: RC_OR003-01 Mid


title: RPEChoroid_23

description: RC_OR021-99 Mac


title: RPEChoroid_24

description: RC_OR021-99 Mid


title: RPEChoroid_26

description: RC_IA156-98 Mid


title: RPEChoroid_31

description: RC_OR016-99 Mid


title: RPEChoroid_19

description: RC_OR003-99 Mid


title: RPEChoroid_25

description: RC_IA156-98 Mac


title: RPEChoroid_32

description: RC_IA358-99 Mac


title: RPEChoroid_18

description: RC_OR003-99 Mac


title: RPEChoroid_33

description: RC_IA358-99 Mid


title: RPEChoroid_20

description: RC_OR004-02 Mac


title: RPEChoroid_16

description: RC_IA194-00 Mid


title: RPEChoroid_9

description: RC_IA387-99 Mac


title: RPEChoroid_11

description: RC_IA100-99 Mac


title: RPEChoroid_27

description: RC_IA359-99 Mac


title: RPEChoroid_99

description: RC_IA005-98 Mac_AMD


title: RPEChoroid_12

description: RC_IA100-99 Mid


title: RPEChoroid_13

description: RC_IA341-99 Mac


title: RPEChoroid_5

description: RC_IA343-99 Mac


title: RPEChoroid_15

description: RC_IA194-00 Mac


title: RPEChoroid_6

description: RC_IA343-99 Mid


title: RPEChoroid_8

description: RC_IA132-98 Mid


title: RPEChoroid_4

description: RC_IA151-98 Mid


title: RPEChoroid_14

description: RC_IA341-99 Mid


title: RPEChoroid_21

description: RC_OR014-99 Mac


title: RPEChoroid_17

description: RC_IA115-98 Mid


title: RPEChoroid_10

description: RC_IA387-99 Mid


title: RPEChoroid_3

description: RC_IA151-98 Mac


title: RPEChoroid_7

description: RC_IA132-98 Mac


title: RPEChoroid_2

description: RC_IA177-96 Mid


title: Conceptus 3961 D35 Chorion [GPL15190]

city: Ithaca

first: Donald

last: Miller

state: NY

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health

institute: Cornell University

description:
pure chorion from a day 35 horse conceptus
3961 Chr

hyb_protocol: 825ng per sample of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 11ul 25x Agilent fragmentation buffer and 2.2 ul 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized 100ul to Agilent-021322 Horse Gene Expression Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and both the Red and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using parameters (protocol GE1-105_DEC8 and Grid: 021322_D_F_20080905) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Samples were analyzed with GeneSpring GX 11.0.  In short, samples were quantile normalized then filtered where at least 100% of the values representing one condition were acceptable.  Where replicates were available, paired T-Tests were performed to identify genes with p-values of p ≤0.05 [Series Supplementary files: *t-tests.txt].

organism: Equus caballus

source_name: Conceptus 3961 D35 Chorion

label_protocol: 1ug of total RNA from each sample was linearly amplified and Cy3 labeled using the Ambion Amino Allyl MessageAmp™ II  kit (Applied Biosystems, Foster City, CA).

extract_protocol: Total RNA was extracted from samples using the Qiagen RNeasy (lymphocytes) or RNeasy Plus (conceptus and fetal tissue) kits following the manufacturer’s protocol.  RNA quality and concentration was initially quantified using a Nano-Drop spectrophotometer, and then assayed on an Agilent BioAnalyer. All samples had a RIN score above 9.0, and most had a score of 10.0.

treatment_protocol: Conceptuses were recovered between days 33-35 by non-surgical uterine lavage and then immediately returned to the laboratory where they were microdissected into unique pure tissues including chorionic girdle and chorion.  The samples were snap frozen in liquid nitrogen and stored at -80oC.  Lymphocytes were obtained from venous blood samples via Ficoll separation.  Cells were split into two groups.  The first group was immediately snap frozen in liquid nitrogen and stored at -80oC before RNA isolation.  The remaining cells were stimulated with Pokeweed Mitogen, and harvested on day one through five post stimulation.  Equal molar volumes of RNA from cells representing each day of stimulation were pooled and used for microarray experiments.

tag: tissue source

value: pure chorion from a day35 conceptus

value: Non-invasive trophoblast


title: Leukemia stem cells (LSC), biological rep1

city: Augusta

first: Mingqiang

last: Ren

state: GA

address: 1120 15th Street

department: Cancer Center

institute: Georgia Regents University

description:
LSC_1
Gene expression data from  normal sorted LSC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Raw .cel files were processed for background correction and quantile normalization (median scaling) using the robust multiarray averaging (RMA) method using GenePattern software (http://genepattern.broadinstitute.org).

label: biotin

organism: Mus musculus

source_name: ZMYM2-FGFR1 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was amplified using a GeneChip Two-Cycle Target Labeling and Control Reagents kit (Affymetrix)

value: Bone marrow and spleen

tag: cell sorting status

value: Sorted

tag: cell type

value: LSC (LSK, GFP+ Lin-Sca-1+c-kit+ cells)


title: Leukemia stem cells (LSC), biological rep2

description:
LSC_3
Gene expression data from  normal sorted LSC


title: Conceptus 3961 D35 Chorionic Girdle [GPL15190]

description:
pure chorionic girdle from a day 35 horse conceptus
3961 CG

source_name: Conceptus 3961 D35 Chorionic Girdle

value: pure chorionic girdle from a day35 conceptus

value: Invasive trophoblast


title: Normal HSC, biological rep1

description:
HSC_1
Gene expression data from  normal sorted HSC

source_name: Normal Balb/c

tag: strain

value: Balb/c

value: Normal

value: Bone marrow

value: HSC (Lin-Sca-1+c-kit+)


title: ZNF112 cells

description:
ZNF112
Gene expression data from ZNF112 cells

source_name: ZNF112 cell line

tag: cell line

value: Unsorted


title: Resting Peripheral Blood Lymphocytes [GPL15190]

description:
Peripheral blood lymphocytes from an adult mare
3729_Resting Lo

source_name: Mare 3729 Resting Peripheral Blood Lymphocytes

value: adult mare

value: Peripheral Blood Lymphocytes


title: Conceptus 3879 D34 Chorion [GPL15190]

description:
pure chorion from a day 34 horse conceptus
3879 Chr

source_name: Conceptus 3879 D34 Chorion

value: pure chorion from a day34 conceptus


title: Pokeweed Mitogen Stimulated Peripheral Blood Lymphocytes [GPL15190]

description:
PWM stimulated peripheral blood lymphocytes from an adult mare
3729_Stim_Lo

source_name: Mare 3729 Pokeweed Mitogen Stimulated Peripheral Blood Lymphocytes


title: RPEChoroid_1

description: RC_IA177-96 Mac

value: macular RPE-choroid

value: male

value: not determined

value: RPE-choroid and retina

value: normal and AMD

value: pool


title: T-cell lymphoma, biological rep3

description:
T-lym_3
Gene expression data from T-cell lymphoma

value: T-cell Lymphoma

value: >90% of cells were GFP+Thy1+DP+


title: Conceptus 3637 D33 Chorionic Girdle [GPL15190]

description:
pure chorionic girdle from a day 33 horse conceptus
3637 CG

source_name: Conceptus 3637 D33 Chorionic Girdle

value: pure chorionic girdle from a day33 conceptus

value: Invasive trophoblast


title: Conceptus 3637 D33 Chorion [GPL15190]

description:
pure chorion from a day 33 horse conceptus
3637 Chr

source_name: Conceptus 3637 D33 Chorion

value: pure chorion from a day33 conceptus

value: Non-invasive trophoblast


title: HDF-breast_donor12_60yrs_P3

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz-Institute for Biomedical Engineering

country: Germany

institute: Aachen University Medical School

description: Human dermal fibroblasts-breast_60yrs

hyb_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was hybridized with 200ng DNA.

scan_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.

data_processing: Initial data analysis was performed with the BeadStudio Methylation software from Illumina (ie, BeadStudio Methylation Analysis Module 3.2.0). Raw data were background normalized.

label: Biotin

molecule: genomic DNA

source_name: Human dermal fibroblast from breast of donor12 (60 years old) - passage 3

label_protocol: Genomic DNA (600 ng) from each sample was bisulfite converted using the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany). This step leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine. After bisulfate conversion each sample was whole genome amplified and enzymatically fragmented.

growth_protocol:
Human fibroblasts were isolated from different dermal regions of healthy donors. All samples were taken after written consent, using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen.
Skin samples were treated with dispase (Roche Diagnostics, Mannheim, Germany) for 12 hours to separate the dermis from the epidermis. The dermis was digested with 0,2% collagenase and 1,5% BSA in collagenase buffer (100mM HEPES, 120mM NaCl, 50mM KCl, 1mM CaCl2, 5mM Glucose) for 45 minutes. Dermal remnants were removed by filtering the digest through a 100µm nylon strainer (Falcon, Becton Dickinson [BD], San Jose, USA). The cells were subsequently washed and expanded in standard medium consisting of DMEM (PAA; 1g/L glucose) supplemented with glutamine (PAA), penicillin/sptrepamycin (PAA) and 10% fetal calf serum (Biochrom, Berlin, Germany) in a humidified atmosphere at 5% CO2. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (80%) cells were always replated at a density of 5x10(3) cells/cm(2).

extract_protocol: Genomic DNA of approximately 10(6) dermal fibroblasts was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.

treatment_protocol: Cells were harvested by trypsination after passage 3.

value: human dermal fibroblasts from breast

tag: age

value: 60 year old human donor

tag: cell passage


title: Normal HSC, biological rep2

description:
HSC_3
Gene expression data from  normal sorted HSC

value: Balb/c

value: Normal

value: Bone marrow

value: Sorted

value: HSC (Lin-Sca-1+c-kit+)


title: HDF-arm_donor7_63yrs_P3

description: Human dermal fibroblasts-arm_63yrs

scan_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was hybridized with 200ng DNA. The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.

source_name: Human dermal fibroblast from arm of donor7 (63 years old) - passage 3

value: human dermal fibroblasts from arm

value: 63 year old human donor


title: T-cell lymphoma sorted, biological rep4

description:
T-lym sorted
Gene expression data from sorted T-cell lymphoma

value: GFP+Thy1+DP+ cells


title: Conceptus 3879 D34 Chorionic Girdle [GPL15190]

description:
pure chorionic girdle from a day 34 horse conceptus
3879 CG

source_name: Conceptus 3879 D34 Chorionic Girdle

value: pure chorionic girdle from a day34 conceptus


title: HDF-blepharoblast_donor11_64yrs_P3

description: Human dermal fibroblasts-blepharoblast_64yrs

source_name: Human dermal fibroblast from blepharoblast of donor11 (64 years old) - passage 3

value: human dermal fibroblasts from blepharoblast

value: 64 year old human donor


title: T-cell lymphoma, biological rep2

description:
T-lym_2
Gene expression data from T-cell lymphoma

value: T-cell Lymphoma

value: Unsorted

value: >90% of cells were GFP+Thy1+DP+


title: T-cell lymphoma, biological rep1

description:
T-lym_1
Gene expression data from T-cell lymphoma


title: HDF-leg_donor10_61yrs_P3

description: Human dermal fibroblasts-leg_61yrs

source_name: Human dermal fibroblast from leg of donor10 (61 years old) - passage 3

value: human dermal fibroblasts from leg

value: 61 year old human donor


title: Normal Thy1+DP_08N6, biological rep1

description:
DP+ #1
Gene expression data from sorted normal thymus cells

value: Thymus

value: Thy1+DP+ (CD4+CD8+) cells


title: HDF-abdomen_donor8_73yrs_P3

description: Human dermal fibroblasts-abdomen_73yrs

source_name: Human dermal fibroblast from abdomen of donor8 (73 years old) - passage 3

value: human dermal fibroblasts from abdomen

value: 73 year old human donor


title: HDF-abdomen_donor14_23yrs_P3

description: Human dermal fibroblasts-abdomen_23yrs

source_name: Human dermal fibroblast from abdomen of donor14 (23 years old) - passage 3

value: 23 year old human donor


title: Normal Thy1+DP_08N7, biological rep2

description:
DP+ #2
Gene expression data from sorted normal thymus cells

value: Balb/c

value: Normal

value: Sorted


title: HDF-breast_donor6_18yrs_P3

description: Human dermal fibroblasts-breast_18yrs

source_name: Human dermal fibroblast from breast of donor6 (18 years old) - passage 3

value: human dermal fibroblasts from breast

value: 18 year old human donor


title: HDF-leg_donor4_8yrs_P3

description: Human dermal fibroblasts-leg_8yrs

source_name: Human dermal fibroblast from leg of donor4 (8 years old) - passage 3

value: 8 year old human donor


title: HDF-otoplastic_donor15_6yrs_P3

description: Human dermal fibroblasts-otoplastic_6yrs

source_name: Human dermal fibroblast from otoplastic of donor15 (6 years old) - passage 3

value: human dermal fibroblasts from otoplastic

value: 6 year old human donor


title: HDF-abdomen_donor9_63yrs_P3

description: Human dermal fibroblasts-abdomen_63yrs

source_name: Human dermal fibroblast from abdomen of donor9 (63 years old) - passage 3

value: 63 year old human donor


title: Normal Thy1+DP_08N8, biological rep3

description:
DP+ #3
Gene expression data from sorted normal thymus cells

source_name: Normal Balb/c


title: HDF-otoplastic_donor5_6yrs_P3

source_name: Human dermal fibroblast from otoplastic of donor5 (6 years old) - passage 3


title: MDS erythroid sample 5 Day 10

city: Paris

first: olivier

last: kosmider

address: 27 Rue du faubourg St Jacques

country: France

institute: Hopital Cochin

description: Gene expression data from erythroid cell

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: Image data were quantified with Microarray Software Suite Version 5.0 (Affymetrix). Data from 10820_at labeled probes were normalized to median of 3 replicates by GC-Robust MultiChip Analysis and significance analysis of microarrays used for marker selection was performed in the software R. Neighborhood analysis was performed using the published methods. Genes differentially expressed (ANOVA test; P<.01) were identified by hierarchic clustering using the GeneSpring Version 6.0 software (Silicon Genetics).

source_name: MDS erythroid Day 10

label_protocol: standard Affymetrix protocols

growth_protocol: CD34+ cells were in erythroid conditions in IMDM-BIT medium added with Epo, SCF, DXM and IGF1 during 10 days then into Epo and Insuline only during 4 days

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

treatment_protocol: Erythroids cells at the appropriate day were collected, whashed twice in PBS and placed on ice in the Trizol solution.

value: MDS erythroid


title: HDF-otoplastic_donor15_6yrs_P21

source_name: Human dermal fibroblast from otoplastic of donor15 (6 years old) - passage 21


title: EMLe2 10_CD34- CD103- Epo

city: London

first: Shamit

last: Soneji

address: 72 Huntley Street

country: United Kingdom

institute: UCL

description: EMLe2 10

hyb_protocol: Each Cy3-labeled cRNA sample (1.6mg as per NanoDrop reading) was hybridised to an individual 44K subarray of 4x44K high-density microarray slide (Whole Mouse Gene Expression Microarrays, Agilent), washed, scanned and feature-extracted as per Agilent protocols.

scan_protocol: Scanning and feature extraction was performed as per Agilent protocols

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: EML subfraction_CD34- CD103- Epo

label_protocol: Total RNA (150ng) and Agilent One-Color RNA Spike-In were reverse-transcribed and linearly amplified in the presence of Cy3-labeled CTP using Low RNA Input One-Color Kit (Agilent) following Agilent protocols, to generate Cy3-labeled cRNA for hybridisation to high-density microarrays. Quality and yield/specific activity of cRNA were determined using RNA 6000 Nano kit and spectrophotometer (NanoDrop ND- 1000). All samples generated comparable quality cRNA profiles, with specific activities in the range of 10.3 to 12.2 pmol Cy3/mg cRNA.

growth_protocol: EML cells were grown as described in IMDM with 5% horse serum and 10% SCF-conditioned medium. Epo-driven differentiation was performed as described.

extract_protocol: Total RNA was isolated from triplicate or quadruplicate samples of EML cell fractions using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).

treatment_protocol: Epo-driven erythroid differentiation was performed on the CD34- CD103- fraction as described.

tag: cell line origin

value: erythroid myeloid lymphoid (EML)

tag: subfration

value: CD34- CD103- Epo


title: MDS erythroid sample 4 Day 10


title: EMLe2 11_CD34- CD103- Epo

description: EMLe2 11


title: EMLe2 9_CD34- CD103- Epo

description: EMLe2 9


title: MDS erythroid sample 5 Day 14

source_name: MDS erythroid Day 14


title: HDF-abdomen_donor3_17yrs_P3

description: Human dermal fibroblasts-abdomen_17yrs

source_name: Human dermal fibroblast from abdomen of donor3 (17 years old) - passage 3

value: 17 year old human donor


title: HDF-abdomen_donor2_17yrs_P3

description: Human dermal fibroblasts-abdomen_17yrs

source_name: Human dermal fibroblast from abdomen of donor2 (17 years old) - passage 3


title: MDS erythroid sample 5 Day 7

source_name: MDS erythroid Day 7


title: MDS erythroid sample 4 Day 7


title: EMLe2 8_CD34+ CD103-

description: EMLe2 8

source_name: EML subfraction_CD34+ CD103-


title: EMLe2 6_CD34+ CD103-

description: EMLe2 6


title: MDS erythroid sample 4 Day 14


title: MDS erythroid sample 3 Day 14


title: EMLe2 7_CD34+ CD103-

description: EMLe2 7


title: MDS erythroid sample 3 Day 10


title: EMLe2 5_CD34+ CD103-

description: EMLe2 5


title: HOXA10_Day 3_R2

city: Mumbai

first: Geeta

middle: Bhalchandra

last: Godbole

state: Maharashtra

address: Jehangir Merwanji Street, Parel

department: Molecular and Cellular Biology

country: India

institute: National Institute for Research in Reproductive Health

description:
Case control experimental design - dual channel-equimolar hybridization
HOXA10_Day 3_rep2.txt

hyb_protocol: The microarray slides were processed for pre-hybridization using the Pronto hybridization kit as described by the manufacturer. The slides were loaded onto the GeneTac automated hybridization station and primed with the labeled cDNA as per the manufacturer's instructions. A step down hybridization was performed for 18 hours with the following protocol – 6 hrs at 42 degree centigrade, 6 hours at 35 degree centigrade and 6 hours at 30 degree centigrade. At the end of the hybridization cycle, the slides were removed from the hybridization station, washed and processed for scanning as described by the manufacturer (Corning Pronto, USA). The slides were spun dry by centrifugation at 1600 rpm for 10 minutes and loaded onto a laser scanner for scanning the Cy3 and Cy5 intensities.

scan_protocol: The microarray slides were scanned with the “autogain” function of the scanner (GeneTAC UC4) so as to optimize the laser power for amplifying the low intensity spots versus avoiding the over-saturation of the high intensity spots on the slide. The resultant scanned tiff image files were gridded using the GAL file generated from the spotting run with use of the GeneTac Integrator software.

data_processing: Foreground and background intensity values were recorded for every gene in the array using a fixed threshold boundary by GeneTAC Integrator software. Background intensity values were subtracted from the foreground and normalized using global normalization algorithm used by GeneTAC Integrator software. The resultant comma separated file with the background subtracted, globally normalized intensity ratio between the HOXA10 siRNA transfected versus scrambled siRNA transfected (Treated/Control) values were used for statistical analysis.

source_name: Primary Human endometrial stromal cells

label_protocol: The total RNA from control Scrambled siRNA transfected cells were labeled with fluorescent dyes (Cy3), whereas total RNA from HOXA10 siRNA transfected cells were labelled with Cy5 using the indirect labeling method. Briefly, twenty micrograms of total RNA from decidual cells were converted to cDNA using modified amino-allyl dUTP. The resultant cDNA was purified using the silica columns provided by the kit and subsequently used for dye conjugation. The purified cDNA was eluted in binding buffer and incubated with the DMSO dissolved Cy3 dye suspension for 3 hours in a thermo mixer at room temperature. Excess dye was quenched using 20mM hydroxylamine and the resultant labeled cDNA was again purified using the silica columns as provided by the kit. The purified and labeled cDNA was eluted using 65μL elution buffer. The exultant was dried under vacuum and resuspended in 65μl of hybridization buffer. The resuspended cDNA was heated at 95 degree centigrade for 5 minutes, flash chilled on ice and microfuged on ice before use in hybridization.

growth_protocol: Primary culture of endometrial stromal cells (endometrial tissue taken from early follicular phase of 5 women of age 30-46yrs)were passaged 3 times. The cells were administered with estradiol (10-8M) and progesterone (10-6M) (Sigma) for 18 days to induce decidualization in vitro. The decidualization was confirmed by checking high secreted levels of Insulin like growth factor binding protein-1 and Prolactin and high level of mRNA expression of HOXA10 as compared to control (vehicle control). These cells were transfected with HOXA10 siRNA (Qiagen Hiperfect transfection kit) and scrambled siRNA (that served as control). The cells were harvested after 24, 48 and 72 hrs and microarray was performed from total RNA.

extract_protocol: The siRNA transfected cells (HOXA10 siRNA and Scrambled siRNA) were harvested with chilled Trizol reagent (Invitrogen Corp, Carlsbad, USA). The volume of Trizol was maintained at 1 ml for every 1 x 106 cells. The cells with Trizol were stored at -80 degree centigrade until used for RNA extraction. The lysates were thawed at room temperature and passed through a 21-gauge needle for 10 times. This ensured that the lysates was uniformly homogenized. Post homogenization, the lysates were allowed to settle for 5 minutes at room temperature. The lysates were then spun at 12000 rpm for 15 minutes in a fixed angle rotor centrifuge at 4 degree centigrade. The upper aqueous phase was then transferred to a new microfuge tube and equal volumes of chilled 70% ethanol were added to the tubes. The ethanol-aqueous phase was mixed gently with a pipette and total RNA was purified using the RNeasy Mini kit (Qiagen, Valencia, USA). The lysates were then transferred to a purification column and spun at 10,000 rpm for 10 seconds. The flow-through is discarded and the column is filled with 500μl of RW1 buffer provided by the kit. The columns are spun at 10,000 rpm for 10 seconds and the flow-through is discarded. The columns are then filled with 500μl of RPE buffer and spun at 10,000 rpm for 10 seconds. The RPE buffer spin is repeated once more and a dry spin is performed by centrifugation of the empty column at 13,000 rpm for 2 minutes. The final elution step was performed by adding 32μl of nuclease free water and spinning the column for 5 minutes at 13,000 rpm. The concentration of the RNA is determined using 1μl of RNA with a Nanodrop spectro-photometer (ND-1000,).  Amount of RNA per sample observed was 32-36µgs.

treatment_protocol: Decidualized cells were transfected with a siRNA againts HOXA10 (5nM concentration, 4.5ul HiPerfect Transfection reagent, Qiagen). Parallel scrambled siRNA (5nM, 4.5 ul transfection reagent) transfected cells were maintained as controls.

tag: sirna transfection

value: Control (scrambled siRNA)

tag: time

value: 72 hrs

value: Treated (HOXA10)


title: EMLe2 4_CD34- CD103-

description: EMLe2 4

source_name: EML subfraction_CD34- CD103-


title: MDS erythroid sample 3 Day 7


title: HOXA10_Day 3_R3

description:
Case control experimental design - dual channel - dye swap
HOXA10_Day 3_dye swap.txt

value: Primary culture of endometrial stromal cells


title: HOXA10_Day 3_R1

description:
Case control experimental design - dual channel-equimolar hybridization
HOXA10_Day 3_rep1.txt


title: HDF-arm_donor1_21yrs_P3

description: Human dermal fibroblasts-arm_21yrs

source_name: Human dermal fibroblast from arm of donor1 (21 years old) - passage 3

value: human dermal fibroblasts from arm

value: 21 year old human donor


title: MDS erythroid sample 2 Day 10


title: EMLe2 3_CD34- CD103-

description: EMLe2 3


title: MDS erythroid sample 1 Day 14


title: MDS erythroid sample 2 Day 14


title: HOXA10_Day 2_R2

description:
Case control experimental design - dual channel - dye swap
HOXA10_Day 2_dye swap.txt

value: 48 hrs


title: EMLe2 2_CD34- CD103-

description: EMLe2 2


title: EML14_EryCP_repeat

description: EML 14

source_name: EML subfraction_EryCP

growth_protocol: EML cells were grown as described in IMDM with 5% horse serum and 10% SCF-conditioned medium. Epo-driven differentiation was performed as described (Ediff).

treatment_protocol: Ediff samples were prepared from CD34-negative cKit-negative cells, derived from Epo-driven differentiation of the EryCP fraction as described.

tag: subfraction

value: EryCP


title: MDS erythroid sample 2 Day 7


title: HOXA10_Day 2_R1

description:
Case control experimental design - dual channel-equimolar hybridization
HOXA10_Day 2_rep1.txt


title: HOXA10_Day 1_R3

description:
Case control experimental design - dual channel - dye swap
HOXA10_Day 1_dye swap.txt

value: 24 hrs


title: MDS erythroid sample 1 Day 10


title: EML15_EryCP_repeat

description: EML 15


title: HOXA10_Day 1_R1

description:
Case control experimental design - dual channel-equimolar hybridization
HOXA10_Day 1_rep1.txt


title: HOXA10_Day 1_R2

description:
Case control experimental design - dual channel-equimolar hybridization
HOXA10_Day 1_rep2.txt


title: EMLe2 1_CD34- CD103-

description: EMLe2 1


title: MDS erythroid sample 1 Day 7


title: EML13_EryCP_repeat

description: EML 13


title: Resting Peripheral Blood Lymphocytes

description: SAMPLE 11

hyb_protocol: 300ng per sample of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 5ul 25x Agilent fragmentation buffer and 1 ul 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized 40ul to Agilent Whole Human Genome Oligo Microarrays (#018932) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and both the Red and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using parameters (protocol GE1-105_DEC8 and Grid: 018932_D_F_20081216) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  Samples were analyzed with GeneSpring GX 11.0.  In short, samples were quantile normalized then filtered where at least 100% of the values representing one condition were acceptable.
The two samples [3959 D34 Chorionic Girdle & 3961 D35 Chorionic Girdle] were used in two separate GeneSpring analyses, one comparing four Chorionic Girdle samples to four matched Chorion samples [CG vs Ch], and the other comparing two Chorionic Girdle samples to two matched fetal samples [CG vs Fetus].  When the quantile normalization step is performed in GeneSpring, it is carried out across all samples in the sample set simultaneously.
Where replicates were available, paired T-Tests were performed with Benjamini-Hochberg FDR corrections to identify genes with a corrected p-value of p ≤0.05 [*t-tests.txt available as Series Supplementary files].

source_name: Mare 3729 Resting Peripheral Blood Lymphocytes

label_protocol: 1ug of total RNA from each sample was linearly amplified and Cy3 labeled using the Ambion Amino Allyl MessageAmp™ II kit (Applied Biosystems, Foster City, CA).

treatment_protocol: Conceptuses were recovered between days 33-35 by non-surgical uterine lavage and then immediately returned to the laboratory where they were microdissected into unique pure tissues which included chorionic girdle, chorion, and fetal tissue.  The samples were snap frozen in liquid nitrogen and stored at -80oC.  Lymphocytes were obtained from venous blood samples via Ficoll separation.  Cells were split into two groups.  The first group was immediately snap frozen in liquid nitrogen and stored at -80C before RNA isolation.  The remaining cells were stimulated with Pokeweed Mitogen (PWM), and harvested on day one through five post stimulation.  Equal molar volumes of RNA from cells representing each day of stimulation were pooled and used for microarray experiments.

value: adult mare

tag: tissue

value: Peripheral Blood Lymphocytes


title: normal erythroid sample 5 Day 10

source_name: normal erythroid Day 10

value: normal erythroid


title: Conceptus 3959 D34 Fetus

description: SAMPLE 7

source_name: Conceptus 3959 D34 Fetus

value: fetus from a day34 conceptus

value: Fetus


title: Conceptus 3961 D35 Chorionic Girdle [reanalysis]

description: SAMPLE 8

source_name: Conceptus 3961 D35 Chorionic Girdle

value: pure chorionic girdle from a day35 conceptus

value: Invasive trophoblast


title: EML11_Ediff

source_name: EML subfraction_Ediff

value: erythroid myeloid lymphoid (EML)

value: Ediff


title: Conceptus 3961 D35 Fetus

description: SAMPLE 10

source_name: Conceptus 3961 D35 Fetus

value: fetus from a day35 conceptus


title: normal erythroid sample 5 Day 14

source_name: normal erythroid Day 14


title: normal erythroid sample 3 Day 14


description: SAMPLE 12

source_name: Mare 3729 Pokeweed Mitogen Stimulated Peripheral Blood Lymphocytes

value: PWM stimulated peripheral blood lymphocytes


title: normal erythroid sample 4 Day 10


title: normal erythroid sample 3 Day 10


title: EML8_EryCP


title: normal erythroid sample 2 Day 7

source_name: normal erythroid Day 7


title: Conceptus 3959 D34 Chorionic Girdle [reanalysis]

description: SAMPLE 5

source_name: Conceptus 3959 D34 Chorionic Girdle

value: pure chorionic girdle from a day34 conceptus


title: Conceptus 3961 D35 Chorionic Girdle

description: SAMPLE 8


title: normal erythroid sample 3 Day 7


title: Conceptus 3959 D34 Chorion

description: SAMPLE 6

source_name: Conceptus 3959 D34 Chorion

value: pure chorion from a day34 conceptus

value: Non-invasive trophoblast


title: EML9_EryCP


title: EML7_EryCP


title: Conceptus 3961 D35 Chorion

description: SAMPLE 9

source_name: Conceptus 3961 D35 Chorion

value: pure chorion from a day35 conceptus


title: Conceptus 3959 D34 Chorionic Girdle

description: SAMPLE 5


title: EML12_Ediff


title: normal erythroid sample 4 Day 14


title: EML6_CR Sca1lo

source_name: EML subfraction_CR Sca1lo

value: CR Sca1lo


title: EML5_CR Sca1lo


title: EML4_CR Sca1lo


title: normal erythroid sample 1 Day 14


title: normal erythroid sample 1 Day 10


title: Emerin intensity averaged duplicates

city: Chicago

first: Joseph

middle: M

last: Zullo

state: IL

address: 929 E 57th Street

department: MGCB

institute: University of Chicago

description: As opposed to prior arrays which used 2 color hybs, these were done in a single color on separate chips

hyb_protocol: Standard Affymetrix (10ug of DNA)  for more details contact the University of Chicago Functional Genomics facility

scan_protocol: Standard Affymetrix

data_processing:
Quantile normalized using Affymetrix tiling array software
REMEMBER TO USE THE 2006 GENOME BUILDS.  THESE HAVE NOT BEEN LIFTED OVER (unless an updated probe library becomes available from Affy).  We performed Dam-ID with LMNA, included in this file are probe positions and intensities (can be displayed in IGB using the 2006 genome build) and are in the process of recovering the .Cel files from a failed hard drive, when available they will be added to the submission.  If you would like the .bar files (more useful anyway, contact Joseph Zullo.  GADAcallsMerged is the annotation of the LADs as called by the GADA algorithm.
Both Samples in this Series use the same 2 control CEL files available on the Series record (Dam 0519.CEL and Dam 0612.CEL)

source_name: 2 EMD-DAM and 2 Dam transduced 3T3 lines

label_protocol: Standard Affymetrix

growth_protocol: Standard 3T3 fibroblast.  10% FCS, DMEM

extract_protocol: As per Vogel et al 2008 (PMID:17545983)

treatment_protocol: Transduced with self-inactivating retroviruses bearing either a fusion-DAM (test) or Dam-alone (control)

tag: inm protein

value: EMD

source_name: Dam alone Chips are control

tag: control

value: Control Dam Only construct


title: LMNB intensity averaged duplicates

source_name: 2 LMNB-DAM and 2 Dam transduced 3T3 lines

value: LMNB


title: Conceptus 3879 D34 Chorionic Girdle

description: SAMPLE 3

source_name: Conceptus 3879 D34 Chorionic Girdle


title: normal erythroid sample 1 Day 7

value: normal erythroid


title: Conceptus 3637 D33 Chorionic Girdle

description: SAMPLE 1

source_name: Conceptus 3637 D33 Chorionic Girdle

value: pure chorionic girdle from a day33 conceptus


title: EML1_Sca1hi

source_name: EML subfraction_Sca1hi


title: EML3_Sca1hi


title: Conceptus 3637 D33 Chorion

description: SAMPLE 2

source_name: Conceptus 3637 D33 Chorion

value: pure chorion from a day33 conceptus


title: EML2_Sca1hi


title: Sw_H1N1_2009_Mock_Day5_E5_10

status: Public on Feb 13 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: US93503719_252010910524_S01_GE1-v5_95_Feb07_1_1.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C).

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
Agilent Feature extractor software: 9.5.3.1
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method="normexp", offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

organism: Sus scrofa

source_name: Lung

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol  with Low Input Quick Amp Labeling was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

growth_protocol: In each experiment, 10 pigs were inoculated with noninfectious cell culture supernatant as controls. For the classical H1N1 SIV experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 50% tissue culture infective doses (TCID50)/pig of egg-derived IA30 virus. For the pH1N1 virus experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 TCID50/pig of either egg-derived CA/09 or Alb/09 virus. Five animals per group were euthanized at 3 and 5 days postinfection (dpi), respectively.

extract_protocol: Global gene expression was measured by microarray in samples of lung lobes of animals that were euthanized and necropsied  on days 3 and 5 post infection with A/California/04/2009 (n=5 per time point),  A/swine/Alberta/25/2009 (n=5 per time point), or A/swine/Iowa/15/1930 (n=5 per time point), or mock infected (n=5 per time point) . All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Tissue samples were prepared as TRIZol homogenates for subsequent RNA extraction (QIAGEN, RNeasy kit).

tag: viral strain

value: none - mock

tag: dose

tag: animal id

tag: date of viral origin

tag: day of sample collection post-innoculation

value: lung


title: Sw_H1N1_2009_Mock_Day5_E5_9

description: US93503719_252010910509_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_2009_Sw_ALB25_Day5_E5_34

description: US93503719_252010910527_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_2009_Sw_ALB25_Day3_E5_29

description: US93503719_252010910512_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_Sw_ALB25_Day3_E5_32

description: US93503719_252010910521_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_Mock_Day5_E5_7

description: US93503719_252010910509_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_2009_Sw_ALB25_Day3_E5_33

description: US93503719_252010910521_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_Mock_Day3_E5_3

description: US93503719_252010910523_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_Sw_ALB25_Day5_E5_35

description: US93503719_252010910519_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_Sw_ALB25_Day3_E5_31

description: US93503719_252010910517_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_2009_Mock_Day5_E5_6

description: US93503719_252010910516_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_Sw_ALB25_Day5_E5_36

description: US93503719_252010910524_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_2009_Sw_ALB25_Day5_E5_37

description: US93503719_252010910517_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_2009_Sw_ALB25_Day3_E5_30

description: US93503719_252010910515_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_CA04_Day5_E5_22

description: US93503719_252010910527_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_Sw_ALB25_Day5_E5_38

description: US93503719_252010910511_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_2009_Mock_Day3_E5_4

description: US93503719_252010910523_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_2009_Mock_Day3_E5_2

description: US93503719_252010910518_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_Mock_Day3_E5_5

description: US93503719_252010910509_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_Mock_Day3_E5_1

description: US93503719_252010910525_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_CA04_Day5_E5_23

description: US93503719_252010910517_S01_GE1-v5_95_Feb07_1_1.txt


title: EML10_Ediff

source_name: EML subfraction_Ediff

value: erythroid myeloid lymphoid (EML)


title: Sw_H1N1_2009_CA04_Day5_E5_20

description: US93503719_252010910526_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Sw_IA15_Day5_E3_50

description: US93503719_252010910519_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Sw_IA15_Day5_E3_48

description: US93503719_252010910511_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_CA04_Day5_E5_21

description: US93503719_252010910520_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_2009_CA04_Day3_E5_15

description: US93503719_252010910510_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_2009_CA04_Day3_E5_18

description: US93503719_252010910509_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_CA04_Day3_E5_17

description: US93503719_252010910517_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_CA04_Day3_E5_16

description: US93503719_252010910514_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_1930_Sw_IA15_Day3_E3_45

description: US93503719_252010910526_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_2009_CA04_Day3_E5_14

description: US93503719_252010910526_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_1930_Sw_IA15_Day5_E3_49

description: US93503719_252010910522_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Mock_Day5_E3_38

description: US93503719_252010910526_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_2009_CA04_Day5_E5_19

description: US93503719_252010910518_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Sw_IA15_Day5_E3_47

description: US93503719_252010910525_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_1930_Mock_Day5_E3_36

description: US93503719_252010910516_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_1930_Sw_IA15_Day3_E3_43

description: US93503719_252010910515_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Mock_Day3_E3_33

description: US93503719_252010910519_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_1930_Mock_Day3_E3_34

description: US93503719_252010910521_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Sw_IA15_Day3_E3_41

description: US93503719_252010910512_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_1930_Mock_Day5_E3_39

description: US93503719_252010910510_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_1930_Sw_IA15_Day5_E3_46

description: US93503719_252010910524_S01_GE1-v5_95_Feb07_1_3.txt


title: Sw_H1N1_1930_Sw_IA15_Day3_E3_44

description: US93503719_252010910518_S01_GE1-v5_95_Feb07_1_1.txt


title: Sw_H1N1_1930_Sw_IA15_Day3_E3_42

description: US93503719_252010910522_S01_GE1-v5_95_Feb07_1_4.txt


title: Sw_H1N1_1930_Mock_Day3_E3_59

description: US93503719_252010910525_S01_GE1-v5_95_Feb07_1_2.txt


title: Sw_H1N1_1930_Mock_Day5_E3_37

description: US93503719_252010910510_S01_GE1-v5_95_Feb07_1_2.txt


title: J2D-3

city: Taian

first: Yubo

last: Liu

state: Shandong

address: Daizong Street 61#

department: Life Science

country: China

institute: Shandong Agricultural University

hyb_protocol: standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K/A (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

organism: Arabidopsis thaliana

source_name: the secondary somatic embryos protuberances in SEIM for 2 days

label_protocol: 4μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

extract_protocol: Total RNA from embryonic calli was isolated using trizol reagent (Invitrogen, USA) according to manufacturer's directions.

value: callus

tag: developmental stage


title: J2D-1

value: the secondary somatic embryos protuberances in SEIM for 2 days


title: 14D-3

source_name: the edge of embryonic calli in ECIM for 14 days


title: J2D-2


title: Primary sample of CMML [39221 (CMML-23)]

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

description: CMML sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Bone Marrow sample of CMML patient

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAmp DNA Mini Kit following the manufacturer's instructions (Qiagen, Hilden, Germany).

value: Bone Marrow

tag: gender

value: Male

tag: karyotype

tag: genotype/variation


title: Primary sample of CMML [38896 (CMML-22)]

description: CMML sample


title: Primary sample of CMML [39259 (CMML-24)]

description: CMML sample


title: Primary sample of CMML [37403 (CMML-20)]

description: CMML sample


title: 14D-2

value: the edge of embryonic calli in ECIM for 14 days


title: Primary sample of CMML [34775 (CMML-14)]

description: CMML sample


title: Primary sample of CMML [34778 (CMML-15)]

description: CMML sample


title: Primary sample of CMML [34932 (CMML-16)]

description: CMML sample

value: Female


title: Primary sample of CMML [36255 (CMML-19)]

description: CMML sample

value: TET2-mut, JAK2V617F


title: Primary sample of CMML [37775 (CMML-21)]

description: CMML sample


title: Primary sample of CMML [35615 (CMML-18)]

description: CMML sample


title: Primary sample of CMML [34629 (CMML-13)]

description: CMML sample

source_name: Peripheral Blood sample of CMML patient

value: Peripheral Blood


title: Primary sample of CMML [35277 (CMML-17)]

description: CMML sample

value: TET2-wt, JAK2V617F


title: Primary sample of CMML [34563 (CMML-12)]

description: CMML sample


title: Primary sample of CMML [33668 (CMML-10)]

description: CMML sample


title: Primary sample of CMML [33483 (CMML-9)]

description: CMML sample


title: Primary sample of CMML [33118 (CMML-8)]

description: CMML sample


title: 14D-1


title: Primary sample of CMML [32113 (CMML-6)]

description: CMML sample


title: Primary sample of CMML [32033 (CMML-5)]

description: CMML sample


title: Conceptus 3879 D34 Chorion

description: SAMPLE 4

source_name: Conceptus 3879 D34 Chorion

tag: tissue source

value: pure chorion from a day34 conceptus

value: Non-invasive trophoblast


title: Primary sample of CMML [32424 (CMML-7)]

description: CMML sample

value: TET2-mut, EZH2-mut


title: KO

city: Nanjing

first: Xiu-Xing

last: Wang

state: Jiangsu

address: #22 Hankou Road

department: MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center and the School of Medicine

institute: Nanjing University

description: Gene expression data from primary sertoli cells of 3 days old mice

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

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

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

source_name: primary sertoli cells from 3 days old mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual  Affymetrix).

growth_protocol: 3 days old mice were anesthetized with CO2 and then killed by cervical dislocation. Decapsulated testes were incubated with 2 mg/ml collagena (Gibco, Invitrogen, Carlsbad, CA, USA) at room temperature for 10 min with gentle oscillation and then filtered through 80 um copper meshes to remove interstitial cells. The seminiferous tubules were resuspended in the collagenase at room temperature for an additional 15 min to remove myoid cells. The tubules were then incubated with 0.5 mg/ml hyaluronidase (Sigma, St. Louis, MO, USA) at room temperature for 15 min with gentle oscillation and pipetting. After washing twice with PBS, the cells were cultured in DMEM /F12 (Sigma, St. Louis, MO, USA) supplemented with sodium bicarbonate (1.2 mg/ml), penicillin (100 U/ml), streptomycin (100 mg/ml), and 10% fetal bovine serum (Life Technologies, Gaithersburg, MD, USA). The cells were maintained in a humidified atmosphere containing5% CO2 at 37 ℃ for 24 h. After the incubation, cells were treated with a hypotonic solution (20 mM Tris, pH 7.4) for 1 min to remove the spermatogenic cells adhering to the Sertoli cells.

extract_protocol: After cultured sertoli cell twenty-four hours, cell were washed  with PBS and placed on ice in the Trizol solution (invitrogen,Carlsbad, CA, USA).

tag: strain

value: GGPP knockout

tag: age

value: 3 days old

tag: cell type

value: primary sertoli cells


title: Primary sample of CMML [34556 (CMML-11)]

description: CMML sample


title: Primary sample of CMML [29285 (CMML-2)]

description: CMML sample


title: Primary sample of CMML [30790 (CMML-4)]

description: CMML sample


title: Healthy donor sample [MO5]

description: Control sample

source_name: Bone Marrow of Healthy donor


title: SP4, biological rep3

city: Beijing

first: Qing

last: Ge

address: 38 Xueyuan Road

department: Immunology

institute: Peking University Health Science Center

description:
Gene expression data from SP4 thymocytes with phenotype of Qa-2+6C10-CD69-
Mouse_SP4-3

hyb_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

growth_protocol: Thymi from mice with 6-8 wks of age were pooled.  Cells were purified according to the sample description via FACS Arial I.  Trizol was added directly to the purified cells without any further culture.

value: thymus

value: 6-8 wks

tag: cd4 single positive (sp) thymocyte subset

tag: phenotype


title: Control (hetzerozygous littermates)

value: control


title: Healthy donor sample [MO1]

description: Control sample

tag: tissue


title: Primary sample of CMML [29549 (CMML-3)]

description: CMML sample


title: SP3, biological rep2

description:
Gene expression data from SP3 thymocytes with phenotype of Qa-2-6C10-CD69-
Mouse_SP3-2


title: Primary sample of CMML [28610 (CMML-1)]

description: CMML sample


title: SP3, biological rep3

description:
Gene expression data from SP3 thymocytes with phenotype of Qa-2-6C10-CD69-
Mouse_SP3-3


title: SP2, biological rep3

description:
Gene expression data from SP2 thymocytes with phenotype of Qa-2-6C10-CD69+
Mouse_SP2-3


title: Healthy donor sample [F4-SP]

description: Control sample

source_name: Peripheral Blood of healthy donor


title: SP1, biological rep3

description:
Gene expression data from SP1 thymocytes with phenotype of Qa-2-6C10+CD69+
Mouse_SP1-3


title: SP2, biological rep2

description:
Gene expression data from SP2 thymocytes with phenotype of Qa-2-6C10-CD69+
Mouse_SP2-2


title: Healthy donor sample [MO2]

description: Control sample


title: Healthy donor sample [MO6]

description: Control sample


title: SP3, biological rep1

description:
Gene expression data from SP3 thymocytes with phenotype of Qa-2-6C10-CD69-
Mouse_SP3-1


title: SP4, biological rep1

description:
Gene expression data from SP4 thymocytes with phenotype of Qa-2+6C10-CD69-
Mouse_SP4-1


title: Healthy donor sample [F3-SP]

description: Control sample


title: MDA-468.shp53 cells_3D culture, 8 days, -DOX_rep3

city: New York

first: William

last: Freed-Pastor

department: Biological Sciences

institute: Columbia University

hyb_protocol: Samples were hybridized using the Affymetrix Hybridization, Wash and Scan kit (P/N 900720) according to Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2), using fluidics protocol FS450_0007 in a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Software on a 3000 7G Affymetrix GeneChip Scanner (P/N GCS 3000).

data_processing: .cel files were processed with R-2.11.1 RMA algorithm to give expression signals.  Paired t-test was applied for each probes.

source_name: MDA-468.shp53 cells grown in 3D culture for 8 days in the absence of doxycycline (-DOX)

label_protocol: Samples were Amplified by a Modified T7 IVT, with Ambion's Message WT Expression kit, and then Fragemented and Terminally labeled with Affymetrix Terminal Labeling kit,  according to Manufacturer's instruction.

extract_protocol: RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: cell line

value: Human breast cancer cell


title: Healthy donor sample [F2-SP]

description: Control sample


title: MDA-468.shp53 cells_3D culture, 8 days, +DOX_rep3

source_name: MDA-468.shp53 cells grown in 3D culture for 8 days in the presence of doxycycline (+DOX)


title: SP4, biological rep2

description:
Gene expression data from SP4 thymocytes with phenotype of Qa-2+6C10-CD69-
Mouse_SP4-2


title: MDA-468.shp53 cells_3D culture, 8 days, -DOX_rep2


title: MDA-468.shp53 cells_3D culture, 8 days, +DOX_rep2


title: MDA-468.shp53 cells_3D culture, 8 days, +DOX_rep1


title: Healthy donor sample [F1-SP]

description: Control sample


title: SP1, biological rep2

description:
Gene expression data from SP1 thymocytes with phenotype of Qa-2-6C10+CD69+
Mouse_SP1-2


title: SP1, biological rep1

description:
Gene expression data from SP1 thymocytes with phenotype of Qa-2-6C10+CD69+
Mouse_SP1-1


title: SP2, biological rep1

description:
Gene expression data from SP2 thymocytes with phenotype of Qa-2-6C10-CD69+
Mouse_SP2-1


title: Sw_H1N1_1930_Mock_Day5_E3_40

description: US93503719_252010910518_S01_GE1-v5_95_Feb07_1_3.txt

tag: viral strain

value: none - mock

value: lung


title: Aoryzae_Glucose_CF1.1_rep3

status: Public on Feb 12 2012

city: Gothenburg

first: wanwipa

last: vongsangnak

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus oryzae

source_name: Aspergillus oryzae grown on glucose medium

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.

tag: growth medium

value: Minimal glucose-based medium

tag: growth conditions

value: Controlled fermenter kept at pH 6.0

tag: sampling time

value: mid-late exponential phase

tag: replicate no.


title: Aoryzae_Glucose_CF1.1_rep2


title: Aoryzae_Maltose_CF1.1_rep3

source_name: Aspergillus oryzae grown on maltose medium

value: Minimal maltose-based medium


title: b cell_d0 islets 5361180013_A

city: Montreal

first: Steven

last: Paraskevas

state: Quebec

address: 687 Pine Avenue West

department: Department of Surgery

country: Canada

institute: McGill University

description: beta cells captured by LCM, bological replicate 2

hyb_protocol: Standard Illumina hybridization protocol performed at 48 deg.

scan_protocol: Arrays were scanned using iScan system

data_processing: Raw gene expression levels were normalized with Illumina specific lumi package of the FlexArray software

source_name: beta-cells from fresh isolated islets

label_protocol: amplified RNA was biotinylated using UNG enzyme (to create abasic site; Epicentre Biotech.) and labeling with ARP solution (Molecular Probes), followed by elution with TE (Tris 1mM, EDTA 0.1mM; pH 8.0) using Zymo kit.

growth_protocol: A wedge biopsy from donor pancreas was frozen in tissue-TEK OCT. Pancreas was processed for islet isolation according to standard protocol. Approximately, 2500 IE of isolated islets were frozen and embedded in Tissue-TEK OCT and 5000 IE cultured in CMRL-1066 (Invitrogen) supplemented with 10% FBS, Penicillin/Streptomycin (100 µg/mL)(Wisent), and Fungizone (Invitrogen) at 37°C in a 5% CO2 incubator. Culture medium was changed every other day. On the third day, the cultured islets embedded in Tissue-TEK OCT, snap frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Total RNA was purified from extracted cells using the Qiagen RNeasy Micro-plus kit. Total RNA was isolated following the manufacturer’s protocol. RNA quantity and purity were evaluated using the NanoDop 2000 (NanoDrop Technologies) and the Agilent Bioanalyzer, respectively. RNA was amplified using the Ovation Pico WTA System (Nugen) based on Ribo-SPIA Technology using manufacturer's instruction (except 6ul RNA was taken as starting material and for SPIA amplification 200ul of mastermix was used at 4°C – 1 min, 47°C – 70 min, 95°C – 5 min, hold at 4°C).

treatment_protocol: Frozen sections of pancreas,  freshly isolated islets and cultured islets were dehydrated in 70% ethanol for 30 seconds, 100% ethanol twice for 1 minute, and xylene for 4 minutes. The sections were air dried for 5 minutes, and LCM was performed using the PixCell II Laser Capture Microdissection System (Arcturus Engineering) using 25mW pulse power. LCM was performed by melting thermoplastic films mounted on LCM caps (Arcturus) on beta-cells within islets identified by their intrinsic autofluorescence.

value: b cell

tag: day

value: islets

tag: sample origin

value: Brain dead donors


title: Aoryzae_Maltose_CF1.1_rep2


title: Aoryzae_Maltose_CF1.1_rep1


title: 21P_Glucose_Enzyme_rep1

hyb_protocol: GeneChip® Hybridization Oven, Fluidics Station FS-450.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 was used to generate CEL files from the scanned microarrays. Data analysis was performed by using the statistical open source language R. Data preprocessing was carried out by using the Robust Multichip Average (RMA) method. The function rma is contained in the R/affy package and it implements RMA by correcting the Perfect Match (PM) probes, performing normalization and calculating the expression measure by using median polish method. In order to select genes whose expression levels were related to the experimental factors, Two-Way Analysis Of Variance (ANOVA) was performed. The P-value was corrected for multiple testing by applying the False Discovery Rate (FDR) methodology and genes were selected by imposing a cut-off value of 0.05.

organism: Saccharomyces pastorianus Weihenstephan 34/70

source_name: 21 Plato with enzyme grown on glucose

label_protocol: The cDNA and cRNA syntheses, labeling and cRNA hybridization on the oligonucleotide Yeast Genome 2.0 Array (Affymetrix, CA) were performed as described in the Affymetrix GeneChip® expression analysis manual.

growth_protocol: Fermentation was performed in 2.2 L bioreactor. Dissolved oxygen was monitored with an autoclavable polarographic oxygen electrode. The pH was recorded on-line, but not controlled.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the protocol for total RNA isolation from yeast.

value: Weihenstephan 34/70

tag: medium

value: glucose-based medium with enzyme supplementation

value: stationary phase


title: 21P_Glucose_Enzyme_rep2


title: 21P_Maltose_Enzyme_rep1

source_name: 21 Plato with enzyme grown on maltose

value: maltose-based medium with enzyme supplementation


title: MDA-468.shp53 cells_3D culture, 8 days, -DOX_rep1


title: b cell_pancreas 5361180013_B

description: beta cells captured by LCM, bological replicate 1

source_name: beta-cells from pancreas

value: pancreas


title: b cell_d0 islets 5361180013_D


title: Aoryzae_Glucose_CF1.1_rep1


title: b cell_pancreas 5167820084_C


title: Aoryzae_Maltose_A1560_rep3


title: b cell_d0 islets 5167820084_A


title: b cell_d3 islets 5167820084_D

description: beta cells captured by LCM, bological replicate 3

source_name: beta-cells from fresh 3-days cultured islets


title: Aoryzae_Maltose_A1560_rep2


title: b cell_d3 islets 4810781043_E


title: b cell_pancreas 5361180013_C


title: b cell_d0 islets 4810781003_D


title: b cell_d3 islets 4810781043_D


title: b cell_pancreas 4810781043_B


title: b cell_d3 islets 4810781043_F


title: 21P_Maltose_Control_rep2

source_name: 21 Plato wth contol grown on maltose

value: maltose-based medium


title: Aoryzae_Maltose_A1560_rep1


title: b cell_pancreas 5167820084_B


title: b cell_d0 islets 4810781003_E


title: b cell_pancreas 4810781003_F


title: 21P_Maltose_Control_rep1


title: b cell_d3 islets 4810781043_C


title: Aoryzae_Glucose_A1560_rep2


title: 21P_Glucose_Control_rep1

source_name: 21 Plato with control grown on glucose

value: glucose-based medium


title: 21P_Glucose_Control_rep2


title: Aoryzae_Glucose_A1560_rep1


title: Aoryzae_Glucose_A1560_rep3


title: b cell_d0 islets 4810781003_B


title: b cell_d0 islets 4810781003_A


title: b cell_pancreas 4810781042_C


title: b cell_d0 islets 4810781003_C


title: LRK1 060615 transgenic rice

city: shanghai

first: Mengfei

last: Yang

address: Handan Road 220

institute: Fudan university

description:
LRK1
Gene expression data from leaf tissues of 6-week-old seedlings (10 plants each).

hyb_protocol: Array hybridization and washing were performed using the GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following 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 the MAS 5.0 algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: 6-week-old LRK1 060615 transgenic leaves

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

growth_protocol: LRK1 060615 transgenic rice and control 9311 were grown in a greenhouse under a 14/10 h (light/dark) photoperiod at 28°C.

extract_protocol: Total RNA was extracted and purified using the RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: No treatment.

tag: genotype

value: LRK1 transgenic 9311

value: leaf

value: 6 weeks


title: b cell_pancreas 4810781042_E


title: Control 9311 rice

description:
9311
Gene expression data from leaf tissues of 6-week-old seedlings (10 plants each).

source_name: 6-week-old control 9311 leaves


title: Ewing sarcoma sample EW662

status: Public on Feb 11 2012

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

hyb_protocol: As according to the manufacturer's instructions.

scan_protocol: GCOS 1.4

data_processing: All data were normalized using the gcrma package version 2.18.1 in R 2.10.1 environment (R Development Core Team, 2005) with quantile normalisation

source_name: Ewing sarcoma sample EW662

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

treatment_protocol: FrozenTumor biopsy

tag: gender

value: Male

tag: tumor type

value: Primary Tumor


title: Ewing sarcoma sample EW669

source_name: Ewing sarcoma sample EW669

value: Female

tag: age


title: Ewing sarcoma sample EW585

source_name: Ewing sarcoma sample EW585


title: Ewing sarcoma sample EW665

source_name: Ewing sarcoma sample EW665


title: Ewing sarcoma sample EW587

source_name: Ewing sarcoma sample EW587


title: Ewing sarcoma sample EW616

source_name: Ewing sarcoma sample EW616


title: Ewing sarcoma sample EW604

source_name: Ewing sarcoma sample EW604


title: Ewing sarcoma sample EW579

source_name: Ewing sarcoma sample EW579


title: Ewing sarcoma sample EW577

source_name: Ewing sarcoma sample EW577


title: Ewing sarcoma sample EW613

source_name: Ewing sarcoma sample EW613


title: Ewing sarcoma sample EW582

source_name: Ewing sarcoma sample EW582


title: Ewing sarcoma sample EW612

source_name: Ewing sarcoma sample EW612


title: Ewing sarcoma sample EW666

source_name: Ewing sarcoma sample EW666


title: Ewing sarcoma sample EW661

source_name: Ewing sarcoma sample EW661


title: Ewing sarcoma sample EW608

source_name: Ewing sarcoma sample EW608


title: Ewing sarcoma sample EW667

source_name: Ewing sarcoma sample EW667


title: Ewing sarcoma sample EW652

source_name: Ewing sarcoma sample EW652


title: Ewing sarcoma sample EW563

source_name: Ewing sarcoma sample EW563


title: Ewing sarcoma sample EW658

source_name: Ewing sarcoma sample EW658


title: Ewing sarcoma sample EW668

source_name: Ewing sarcoma sample EW668


title: Ewing sarcoma sample EW556

source_name: Ewing sarcoma sample EW556


title: Ewing sarcoma sample EW531

source_name: Ewing sarcoma sample EW531


title: Ewing sarcoma sample EW554

source_name: Ewing sarcoma sample EW554


title: Ewing sarcoma sample EW576

source_name: Ewing sarcoma sample EW576


title: Ewing sarcoma sample EW381

source_name: Ewing sarcoma sample EW381


title: Ewing sarcoma sample EW517

source_name: Ewing sarcoma sample EW517


title: Ewing sarcoma sample EW379

source_name: Ewing sarcoma sample EW379


title: Ewing sarcoma sample EW525b

source_name: Ewing sarcoma sample EW525b


title: Ewing sarcoma sample EW378

source_name: Ewing sarcoma sample EW378


title: Ewing sarcoma sample EW557

source_name: Ewing sarcoma sample EW557


title: Ewing sarcoma sample EW532

source_name: Ewing sarcoma sample EW532


title: Ewing sarcoma sample EW340

source_name: Ewing sarcoma sample EW340


title: Ewing sarcoma sample EW299

source_name: Ewing sarcoma sample EW299


title: Ewing sarcoma sample EW309

source_name: Ewing sarcoma sample EW309


title: Ewing sarcoma sample EW308

source_name: Ewing sarcoma sample EW308


title: Ewing sarcoma sample EW298

source_name: Ewing sarcoma sample EW298


title: Ewing sarcoma sample EW369

source_name: Ewing sarcoma sample EW369


title: Ewing sarcoma sample EW343

source_name: Ewing sarcoma sample EW343


title: Ewing sarcoma sample EW306

source_name: Ewing sarcoma sample EW306


title: Ewing sarcoma sample EW303

source_name: Ewing sarcoma sample EW303


title: Ewing sarcoma sample EW296

source_name: Ewing sarcoma sample EW296


title: Ewing sarcoma sample EW341

source_name: Ewing sarcoma sample EW341


title: Ewing sarcoma sample EW284

source_name: Ewing sarcoma sample EW284


title: Ewing sarcoma sample EW338

source_name: Ewing sarcoma sample EW338


title: Ewing sarcoma sample EW288

source_name: Ewing sarcoma sample EW288


title: Ewing sarcoma sample EW294

source_name: Ewing sarcoma sample EW294


title: Ewing sarcoma sample EW377

source_name: Ewing sarcoma sample EW377


title: Ewing sarcoma sample EW278

source_name: Ewing sarcoma sample EW278


title: Ewing sarcoma sample EW279

source_name: Ewing sarcoma sample EW279


title: Ewing sarcoma sample EW297

source_name: Ewing sarcoma sample EW297


title: Ewing sarcoma sample EW258

source_name: Ewing sarcoma sample EW258


title: Ewing sarcoma sample EW257b

source_name: Ewing sarcoma sample EW257b


title: Ewing sarcoma sample EW252b

source_name: Ewing sarcoma sample EW252b


title: Ewing sarcoma sample EW250

source_name: Ewing sarcoma sample EW250


title: Ewing sarcoma sample EW248

source_name: Ewing sarcoma sample EW248


title: Ewing sarcoma sample EW247

source_name: Ewing sarcoma sample EW247


title: Ewing sarcoma sample EW251

source_name: Ewing sarcoma sample EW251


title: Ewing sarcoma sample EW237

source_name: Ewing sarcoma sample EW237


title: Ewing sarcoma sample EW241

source_name: Ewing sarcoma sample EW241


title: Ewing sarcoma sample EW242

source_name: Ewing sarcoma sample EW242


title: Ewing sarcoma sample EW236

source_name: Ewing sarcoma sample EW236


title: Ewing sarcoma sample EW227b

source_name: Ewing sarcoma sample EW227b


title: Ewing sarcoma sample EW220

source_name: Ewing sarcoma sample EW220


title: Ewing sarcoma sample EW215

source_name: Ewing sarcoma sample EW215


title: Ewing sarcoma sample EW197

source_name: Ewing sarcoma sample EW197


title: Ewing sarcoma sample EW218

source_name: Ewing sarcoma sample EW218


title: Ewing sarcoma sample EW231

source_name: Ewing sarcoma sample EW231


title: Ewing sarcoma sample EW224b

source_name: Ewing sarcoma sample EW224b


title: Ewing sarcoma sample EW200

source_name: Ewing sarcoma sample EW200


title: Ewing sarcoma sample EW195

source_name: Ewing sarcoma sample EW195


title: Ewing sarcoma sample EW167

source_name: Ewing sarcoma sample EW167


title: Ewing sarcoma sample EW168

source_name: Ewing sarcoma sample EW168


title: Ewing sarcoma sample EW158

source_name: Ewing sarcoma sample EW158


title: Ewing sarcoma sample EW162

source_name: Ewing sarcoma sample EW162


title: Ewing sarcoma sample EW155

source_name: Ewing sarcoma sample EW155


title: Ewing sarcoma sample EW127

source_name: Ewing sarcoma sample EW127


title: Ewing sarcoma sample EW128

source_name: Ewing sarcoma sample EW128


title: Ewing sarcoma sample EW149

source_name: Ewing sarcoma sample EW149


title: Ewing sarcoma sample EW196

source_name: Ewing sarcoma sample EW196


title: Ewing sarcoma sample EW141

source_name: Ewing sarcoma sample EW141


title: Ewing sarcoma sample EW159

source_name: Ewing sarcoma sample EW159


title: Ewing sarcoma sample EW165

source_name: Ewing sarcoma sample EW165


title: Ewing sarcoma sample EW139

source_name: Ewing sarcoma sample EW139


title: Ewing sarcoma sample EW207

source_name: Ewing sarcoma sample EW207


title: Ewing sarcoma sample EW153b

source_name: Ewing sarcoma sample EW153b


title: Ewing sarcoma sample EW174

source_name: Ewing sarcoma sample EW174


title: Ewing sarcoma sample EW143

source_name: Ewing sarcoma sample EW143


title: Ewing sarcoma sample EW198

source_name: Ewing sarcoma sample EW198


title: Ewing sarcoma sample EW135

source_name: Ewing sarcoma sample EW135


title: Ewing sarcoma sample EW132

source_name: Ewing sarcoma sample EW132


title: Ewing sarcoma sample EW121

source_name: Ewing sarcoma sample EW121


title: Ewing sarcoma sample EW112

source_name: Ewing sarcoma sample EW112


title: Ewing sarcoma sample EW116

source_name: Ewing sarcoma sample EW116


title: Ewing sarcoma sample EW105

source_name: Ewing sarcoma sample EW105


title: Ewing sarcoma sample EW108

source_name: Ewing sarcoma sample EW108


title: RBP10 overexpression 1-1

city: Heidelberg

first: Martin

last: Wurst

address: INF 282

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

hyb_protocol: Slides were pre-hybridized in 5xSSC, 0.1 % SDS and 1% BSA at 42 °C for 45 min. Meanwhile, the Cy3- and Cy5- labelled cDNAs were mixed and vacuum dried to about 10 µl. The cDNAs were then added to 40 µl of hybridisation buffer (5xSSC, 0.1 % SDS, 40 % Formamide, 0.6 mg/ml salmon sperm DNA), denatured at 95 °C for 5 min, placed on ice for 2 min and applied ot the pre-hybridised slides. A lifterslip (Implen) was mounted and the slides were incubated at 42 °C overnight in the Slidebooster SB800 hybridisation station (Advalytix). Slides were washed for 10 min each at 50 °C in low stringency buffer (2 x SSC, 0.5 % SDS), at room temperature in medium stringency buffer (0.2xSSC, 0.5 %SDS) and in high stringency buffer (0.1xSSC), then airdried.

scan_protocol: Slides were scanned with SanArray 5000 (Packard BioScience, Dreieich, Germany) and analysis of resulting images was performed using GenePix Pro 6 software

data_processing: Data analysis was performed using the ExpressConverter and MIDAS software which are freely available at http://www.tm4.org. Files obtained from the scan were transformed into .mev – files and background substracted using the ExpressConverter. Using MIDAS the signal intensities were normalized by locally weighted linear regression (LOWESS), duplicate spots on each slide were merged and dye-swap reversed. Intensities of Cy3 and Cy5 were used to calculate log2 ratios. Log2 transformed data were exported to SAM. Only RNAs with a p-value of 0.05 or lower were considered as significantly regulated.

organism: Trypanosoma brucei

source_name: PC WT

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using M-MuLV Reverse Transcriptase (FERMENTAS) as manufacturers instructions, labelling reaction for 2 hours. Samples purified using QIAGEN oligo nucleotide removal kit before hybridization.

extract_protocol: PC trypanosomes were grown to 2x105 and induced with 100ng/ml tetracyclin. Cells were harvested after 24h with a densitiy of about 1.5x106 and RNA was isolated using RNAeasy mini kit (QIAGEN).

tag: strain

value: Lister 427 Procyclic form

source_name: PC overexpressing RBP10

value: Lister 427 Procyclic form overexpressing RBP10


title: RBP10 overexpression 3-1


title: Ewing sarcoma sample EW095

source_name: Ewing sarcoma sample EW095


title: RBP10 overexpression 1-2


title: Ewing sarcoma sample EW093

source_name: Ewing sarcoma sample EW093


title: RBP10 overexpression 2-2


title: RBP10 overexpression 2-1


title: Ewing sarcoma sample EW117b

source_name: Ewing sarcoma sample EW117b


title: Ewing sarcoma sample EW106

source_name: Ewing sarcoma sample EW106


title: Ewing sarcoma sample EW088

source_name: Ewing sarcoma sample EW088


title: Ewing sarcoma sample EW096

source_name: Ewing sarcoma sample EW096


title: BS RBP10 RNAi5

data_processing: Data analysis was performed using the ExpressConverter and MIDAS software which are freely available at http://www.tm4.org. Files obtained from the scan were transformed into .mev files and background substracted using the ExpressConverter. Using MIDAS the signal intensities were normalized by locally weighted linear regression (LOWESS), duplicate spots on each slide were merged and dye-swap reversed. Intensities of Cy3 and Cy5 were used to calculate log2 ratios. Log2 transformed data were exported to SAM. Only RNAs with a p-value of 0.05 or lower were considered as significantly regulated.

source_name: BS WT

extract_protocol: BS trypanosomes were grown to 2x105. RBP10 RNAi was induced with 100ng/ml tetracyclin. Cells were harvested after 24h with a densitiy of about 1.2x106 and RNA was isolated using RNAeasy mini kit (QIAGEN).

value: Lister 427 Bloodstream form

source_name: BS RBP10 RNAi

value: Lister 427 Bloodstream form with inducible RBP10 RNAi


title: Ewing sarcoma sample EW089

source_name: Ewing sarcoma sample EW089


title: Ewing sarcoma sample EW086

source_name: Ewing sarcoma sample EW086


title: Ewing sarcoma sample EW082

source_name: Ewing sarcoma sample EW082


title: Ewing sarcoma sample EW123

source_name: Ewing sarcoma sample EW123


title: Ewing sarcoma sample EW090

source_name: Ewing sarcoma sample EW090


title: BS RBP10 RNAi6

source_name: BS RRBP10 RNAi

source_name: WT


title: Ewing sarcoma sample EW092

source_name: Ewing sarcoma sample EW092


title: Ewing sarcoma sample EW076

source_name: Ewing sarcoma sample EW076


title: Ewing sarcoma sample EW098

source_name: Ewing sarcoma sample EW098


title: Ewing sarcoma sample EW111

source_name: Ewing sarcoma sample EW111


title: Ewing sarcoma sample EW071

source_name: Ewing sarcoma sample EW071


title: Ewing sarcoma sample EW080

source_name: Ewing sarcoma sample EW080


title: BS RBP10 RNAi4


title: BS RBP10 RNAi1

description: Slide 1.mev


title: BS RBP10 RNAi2

description: Slide 2.mev


title: BS RBP10 RNAi3


title: bas1delta grown without adenine vs. bas1delta grown with adenine

status: Public on Feb 10 2012

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

institute: Ecole Normale Supérieure

description: Technical replicate 1 of 2.

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scanning

scan_protocol: Scanned on a GenePix 4000B scanner (Axon). Scanning software: GenePix Pro 6.1

data_processing:
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
GenePix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalization method.

organism: Saccharomyces cerevisiae

source_name: bas1delta grown without adenine

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

growth_protocol: Strains were grown in SD medium containing glucose (2%), adenine (300 mM), arginine (115 mM), histidine (130 mM), isoleucine (230 mM), leucine (1,2 mM), lysine (660 mM), tryptophan (150 mM), uracil (300 mM) and valine (1,3 mM) at 30°C and diluted 1:200 in 10 ml of the same medium containing adenine (300 mM) or no adenine, to reach a concentration of 107 cells/ml the day after (A600=1). The cultures were then diluted again in the same media to grow for 3-4 generations and harvested at a concentration of 107 cells/ml

extract_protocol: Hot phenol extract procedure followed by RNeasy Mini Kit purification step (Qiagen).

value: Mat alpha his3delta1 leu2delta0 bas1delta::KanMX

tag: growth condition

value: growth medium lacking adenine

source_name: bas1delta grown with adenine

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

value: growth medium containing adenine


title: Ewing sarcoma sample EW070

source_name: Ewing sarcoma sample EW070


title: Ewing sarcoma sample EW054

source_name: Ewing sarcoma sample EW054


title: Ewing sarcoma sample EW059

source_name: Ewing sarcoma sample EW059


title: Ewing sarcoma sample EW069

source_name: Ewing sarcoma sample EW069


title: bas1delta grown with adenine vs. bas1delta grown without adenine

description: Technical replicate 2 of 2.


title: WT grown with adenine vs. WT grown without adenine

description: Technical replicate 2 of 2.

source_name: WT grown with adenine

value: Mat alpha his3delta1 leu2delta0 lys2delta0 ura3delta0

source_name: WT grown without adenine


title: st0minrep3

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

country: Japan

institute: Japan Aerospace Exploration agency

description: Gene profile during rearrangement of actin stress fiber in HUVEC

hyb_protocol: Performed as described in One-Color Processing Protocol (Agilent, Version 5.0.1, September 2006).

data_processing:
Data were analyzed with GeneSpring GX 7.3.1. The parameters for normalization are as follows:
Data transformation: Set measurement less than 0.01 to 0.01
Per chip: Normalize to 50th percentile

source_name: HUVEC Cyclic stretch

growth_protocol:
Cells were passaged and meintained in EGM-2 medium (Lonza)
4th passaged cells were used.

extract_protocol: Total RNA was isolated with RNeasy

treatment_protocol: 20% Cyclic stretch exposed to HUVEC on silicon membrane

tag: cyclic stretch

value: 0 min

tag: cell type

value: Pooled HUVECs

tag: replicate


title: st30minrep3

scan_protocol: Performed as described in One-Color Processing Protocol (Agilent, Version 5.0.1, September 2006).

value: 30 min


title: st30minrep2

label_protocol: Performed as described in One-Color Processing Protocol (Agilent, Version 5.0.1, September 2006).


title: st10minrep3

value: 10 min


title: Ewing sarcoma sample EW066

source_name: Ewing sarcoma sample EW066

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


title: st60minrep2

value: 60 min


title: st90minrep2

value: 90 min


title: WT 6m pooled6

city: Los Angeles

first: Yofre

last: Cabeza-Arvelaiz

state: California

address: 650 Charles E. Young Drive South

department: Pathology and Environmental Health Sciences

institute: University of California, Los Angeles

hyb_protocol: cRNA probes were hybridized to mouse MOE-430A GeneChip arrays (Affymetrix) following the manufacturer’s protocol at the UCLA microarray core facility.

scan_protocol: GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.

data_processing: Significant differential gene expression between pooled tg and wt samples was ascertained by estimation of signal log2 ratios (or fold changes in expression values), after quality control checks, data normalization and estimating expression values using the Affymetrix Microarray Suite 5.0 Software (MAS 5.0) by using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mouse striatum from 6 six-month old wild-type animals

label_protocol: After synthesis, using Superscript (Invitrogen), labeling was p\erformed by using the ENZO labeling kit (Affymetrix Inc., Santa Clara, CA)

growth_protocol: Animal care was conducted in accordance with the U. S. Public Health Service Guide for the Care and Use of Laboratory Animals and procedures were approved by the University of California, Los Angeles (UCLA), I.A.C.U. Committee.  Only male mice were used in the study.  Animals were maintained on a 12 hr light/dark cycle with free access to water and food. Six-month old male Thy1-aSyn and wt littermates were sacrificed by decapitation.

extract_protocol: whole striata from each hemisphere were immediately dissected and pooled for each brain. Tissue was permeated in RNAlater (Qiagen, Valencia, CA), frozen in liquid nitrogen, and stored at - 80 C until used for RNA preparation. Total RNA was extracted from striata of Thy1-aSyn and wt littermates (all males) with Trizol (Invitrogen, Carlsbad, CA), followed by a clean-up step with RNeasy columns (Qiagen) and RNA integrity check using a Bioanalyzer  (Agilent Tech., Foster city, CA). RNA samples were pooled, one pool representing the six control wt mice and the other representing the six SNCA overexpressing animals.

treatment_protocol: Transgenic (tg) mice overexpressing human wt SNCA under the Thy-1 promoter (Thy1-aSyn) created in a mixed C57BL/6-DBA background were kept in this background by breeding mutant females with wt males.

tag: tissue

value: Striatum

value: Wild type mice in  C57BL/6-DBA background

value: 6 month

value: Male

tag: genetic background


title: st60minrep3