title: Peripheral blood from child I010_NAA_328

description:
S1313_010_NAA_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)

value: anti-CD3/CD28 (CD328)


title: Peripheral blood from child I010_NAA_M

status: Public on Oct 01 2014

type: RNA

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description:
S1312_010_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Normalized data by RMA and imputated data corrected for labelling batch effect.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood_NAA_M

label_protocol: Total RNA (200 ng) was amplified and labeled with biotin using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) cells were isolated within 24 hours after blood withdrawal by density-gradient centrifugation with Ficoll-Hypaque (Amersham Bioscience, Uppsala, Sweden) after dilution in phosphate buffer saline (PBS, Gibco, Invitrogen, Karlsruhe, Germany). Cells were washed with RPMI 1640 and diluted to a concentration of 5x106 cells/ml in X-Vivo (Lonza, Cologne, Germany).

extract_protocol: RNA from isolated PBMCs and CD4+ cells was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The RNA quality and quantity was determined with Agilent Bioanalyzer chips (Bio-Rad Laboratories).

treatment_protocol: For RNA isolation, 2x10^6 cells were cultured (24-well plate; BD) in X-Vivo for 48 hours without stimulation, stimulated with plate-bound anti-CD3 (3µg/ml) plus soluble anti-CD28 (1µg/ml), lipid A (LpA, 0.1µg/ml) or peptidoglycan (Ppg, 1mg/ml) at 37°C. Cell pellets were used for RNA isolation.

tag: tissue

value: Peripheral blood

tag: cell type

tag: stimulation

value: M (no stimulation)

tag: group

value: non-allergic asthmatic (NAA)

tag: labelling batch

tag: batch year


title: Medium 4634633043_F_1

city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

description: Medium

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: This is a sister series to GSE40566. This GEO entry includes all samples including technical replicates. Background-corrected bead-level summarization was conducted using Illumina's Bead studio. Normalized version of the data was quantile normalized using R's preprocessCore package (normalize.quantilies function) and batch corrected using ComBat from the SVA package with Batch variable as batch and batchcovar as covariate

organism: Mus musculus

source_name: Spleen Cell Cultures

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

growth_protocol: Preparation of Mouse Spleen Cell Cultures: All experimental procedures conformed to accepted ethical standards for use of animals in research and were in accordance with Committee for the Care and Use of Experimental Animals guidelines and approved by the Teva Institutional Animal Care and Use Committee (Protocols #506 and #512). To stimulate induction of GA-reactive T cells, eight female 8- to 12-week-old F1 hybrid (SJL X BALB/C) mice (purchased from Harlan Biotech Israel, Rehovot, Israel) were inoculated with 100 µL of a 2.5 mg/mL solution of GA reference standard (GA-RS) in PBS to achieve an immunization dose of 250 µg GA-RS per mouse. Mice were housed in individually ventilated cages for 3 days after immunization, and on the third day, were sacrificed by cervical dislocation. Mouse spleens (SPL) were excised via side incision using sterile procedures, placed in sterile 50-mL CellStar polypropylene tubes (2 spleens/tube) containing RPMI 1640 without glutamine (Biological Industries, Beit Haemek, Israel), and placed on ice to prevent tissue degradation. Primary cultures of pooled SPL cells were collected as follows: SPL tissue in RPMI was filtered (70 µm nylon) and centrifuged at 300xg for 10 minutes at room temperature (RT). The precipitate was resuspended in Ack lysing buffer (Invitrogen, Carlsbad, CA) incubated for 3 minutes at RT, diluted 1:10 with RPMI, and centrifuged again at 200xg for 10 minutes at RT. The pellet was re-washed (10 mL RPMI), re-centrifuged (200xg, 10 minutes at RT), and then resuspended in enriched defined cell culture media (DCCM1). DCMM1 (Biological Industries, Beit Haemek, Israel) (96.7% v/v) was enriched with L-glutamine 2mM (1% v/v), MEM 2mM (1% v/v), sodium pyruvate 1 mM (1% v/v), antibiotic/antimycotic solution (0.2% v/v), and 2-mercaptoethanol (0.1% v/v). All SPL samples were pooled. Cell density and viability were assessed using the Trypan Blue Exclusion method (22) (hemacytometer, Sigma Z35,962-9). Viable cells were diluted with enriched DCCM1 to a concentration of 10 x 106 cells/mL.

extract_protocol: PerfectPure RNA Cultures CEKK kit 50 (5Prime GmbH, Hamburg, Germany) according to manufacturer’s instructions. RNA quality was assessed by the absorbance ratio at 260/280 nm and gel electrophoresis (Experionä, Bio-Rad, Hercules, CA).

treatment_protocol: Aqueous activator samples (125 µL per well of 80 µg/mL solutions of Verified GA, DM-GA, Unverified Glatiramoid [TV-5010 concentration was 40 µg/mL since 80 µg/mL was cytotoxic], Unverified Generic GA, MBP, and mannitol [the non-active excipient in Copaxone]) and medium samples were added to 96-well tissue culture plates (3 wells per sample).Viable SPL cells (125 µL 10x106 SPL cell/mL suspension) were added to the activator solutions and incubated for 24 hours at 37°C in a humidified incubator with a 5% CO2 atmosphere. Incubated samples were then centrifuged at 3000g x 5 minutes at RT, washed, diluted RNA stabilization solution (RNAlaterÒ solution, Applied Biosystems), and stored at 4°C.

tag: batch

tag: experiment

tag: batchcovar

value: Medium

tag: genetic background

value: SJL X BALB/C

value: spleen cell

tag: treatment


title: 68

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

country: USA

institute: University of California, San Francisco

description: SAMPLE 106

hyb_protocol: Fragmented biotinylated cRNAs were hybridized overnight to a high density Affimetrix Human Genome (HG) U133 Plus 2.0 oligonucleotide microarray genechip containing 54600 probe sets (42203 annotated genes and 12397 expressed sequence tags [EST]) at the Gladstone Genomics Core Facility

scan_protocol: Fluorescent labeling and laser confocal scanning with a GeneChip Scanner 3000. Generated data were extracted for analysis using the Affymetrix Gene-Chip Operating Software and Microsoft Corp. (Redmond, WA) Excel/Mac2001 software.

data_processing: We imported all of the microarray data files into R and normalized them simultaneously. The normalization procedure consists of two steps executed with programs in the Bioconductor package GCRMA. First, we compute the probe affinities using the annotation file hgu133plus2cdf. Second, we normalize the data by setting two options and leaving the rest at default values. The affinity.info option is set to use the probe affinities computed in the first step. The type option is set to fullmodel which uses both the sequence information and mismatch probe model.

label: Biotin

label_protocol: Biotinylated-cRNA was then prepared using the Ambion MessageAmp II-Biotin Enhanced Kit according to manufacturer instructions.

extract_protocol: Total RNA was isolated from endometrial tissue using Trizol (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, followed by DNase treatment and purification with Qiagen RNeasy Plus Kit. The purity and quality of the RNA were assessed with Agilent 2100 Bioanalyzer. First and second strand cDNAs were prepared according to the Affymetrix microarray preparation protocol (Affymetrix).

value: Mid-Secretory Endometrial tissue

tag: endometriosis/no endometriosis

value: Non-Endometriosis

tag: presence or absence of uterine/pelvic pathology

value: Uterine Pelvic Pathology


title: GA FD (Acid) 4634633043_D_2

description: GA FD

value: GA FD (Acid)


title: 934701438_T

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

description: FFPE

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the manufacturer's protocol

scan_protocol: Scanned using the Illumina Bead Array Reader

data_processing: The microarray data was processed and normalized through BeadStudio software, version 3.0. (Illumina Inc.) using the quantile normalization method.

source_name: Lung carcinoid

label_protocol: Biotinylated cDNA were prepared from 100-200ng total RNA using the DASL Assay (cDNA-mediated annealing, selection, extension and ligation)

extract_protocol: RNA was extracted using the miRNeasy FFPE kit (Qiagen Inc, Valencia, California, USA) using the manufacturer’s protocols. Quality control was performed with Agilent Bioanalyser

value: Tumor


title: 934701441_N

description: FFPE

source_name: Lung normal

value: Normal


title: 67

description: SAMPLE 105


title: Peripheral blood from child I001_NAA_328

description:
S1307_001_NAA_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_NAA_328

value: Peripheral blood mononuclear cells (PBMCs)


title: 43

description: SAMPLE 104

value: Proliferative Endometrial tissue


title: Peripheral blood from child I002_NAA_M

description:
S1309_002_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 66

description: SAMPLE 103


title: GA FD (Acid) 4634633043_D_1

description: GA FD


title: Peripheral blood from child I001_NAA_LpA

description:
S1308_001_NAA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_NAA_LpA

value: LpA


title: 930301358_N

description: FFPE


title: 930301352_N

description: FFPE


title: Generic B2 4634633043_C_1

description: GA Q

value: Generic B2


title: Generic B2 4634633043_C_2

description: GA Q


title: Peripheral blood from child I001_NAA_M

description:
S1306_001_NAA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: Peripheral blood from child I027_GK_328

description:
S1304_027_GK_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_control_328

value: anti-CD3/CD28 (CD328)

value: healthy control (GK)


title: 42

description: SAMPLE 102


title: 934701307_T

description: FFPE


title: 920203660b_N

description: FFPE


title: 930301346_N

description: FFPE


title: 930301339_N

description: FFPE


title: 930301334_N

description: FFPE


title: 41

description: SAMPLE 101


title: Generic B1 4634633043_B_2

description: GA Q

value: Generic B1


title: Generic B1 4634633043_B_1

description: GA Q


title: 50

description: SAMPLE 99

value: Early Secretory Endometrial tissue


title: 51

description: SAMPLE 100


title: Peripheral blood from child I027_GK_M

description:
S1303_027_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_control_M

value: Peripheral blood

value: M (no stimulation)


title: Peripheral blood from child I022_AA_LpA

description:
S1302_022_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_LpA

value: allergic asthmatic (AA)


title: GA DP 4637105025_F_1

description: GA DP

value: SJL X BALB/C

value: spleen cell

value: GA DP


title: 930301331_T

description: FFPE


title: GA RS 4634633043_A_2

description: GA RS

value: GA RS


title: GA RS 4634633043_A_1

description: GA RS


title: 930301328_T

description: FFPE

value: Tumor


title: Peripheral blood from child I018_AA_LpA

description:
S1299_018_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 65

description: SAMPLE 98

value: Mid-Secretory Endometrial tissue

value: Non-Endometriosis

value: Uterine Pelvic Pathology


title: GA DP 4637105025_E_2

description: GA DP


title: 64

description: SAMPLE 97


title: Peripheral blood from child I018_AA_328

description:
S1298_018_AA_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_328

value: Peripheral blood mononuclear cells (PBMCs)


title: 930301325_T

description: FFPE


title: 63

description: SAMPLE 95


title: 62

description: SAMPLE 94


title: Peripheral blood from child I022_AA_328

description:
S1301_022_AA_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)


title: Peripheral blood from child I018_AA_M

description:
S1297_018_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_AA_M


title: 930301319_T

description: FFPE


title: 39

description: SAMPLE 93

value: Proliferative Endometrial tissue


title: GA DP 4637105025_D_2

description: GA DP


title: Peripheral blood from child I022_AA_M

description:
S1300_022_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: Peripheral blood from child I027_GK_LpA

description:
S1305_027_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

source_name: Peripheral blood_control_LpA

value: LpA


title: 930301310_T

description: FFPE


title: 930301313_T

description: FFPE


title: 40

description: SAMPLE 96


title: GA DP 4637105025_D_1

description: GA DP


title: GA DP 4637105025_E_1

description: GA DP


title: Peripheral blood from child I008_AA_328

description:
S1295_008_AA_CD3_CD28
Gene expression data from peripheral blood of children (average age 8.4 years)

value: anti-CD3/CD28 (CD328)


title: 930301304_T

description: FFPE


title: GA DP 4637105025_F_2

description: GA DP


title: 920203795_N

description: FFPE

value: Normal


title: Peripheral blood from child I008_AA_M

description:
S1294_008_AA_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 37

description: SAMPLE 90


title: Peripheral blood from child I021_GK_LpA

description:
S1292_021_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: healthy control (GK)


title: GA DP 4637105025_C_1

description: GA DP


title: GA DP 4637105025_C_2

description: GA DP


title: 61

description: SAMPLE 91


title: 38

description: SAMPLE 92


title: 920203780_N

description: FFPE


title: 920203777_N

description: FFPE


title: 36

description: SAMPLE 89


title: Peripheral blood from child I008_AA_LpA

description:
S1296_008_AA_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)

value: Peripheral blood


title: GA DP 4637105025_B_2

description: GA DP


title: Peripheral blood from child I006_GK_LpA

description:
S1289_006_GK_LpA
Gene expression data from peripheral blood of children (average age 8.4 years)


title: Peripheral blood from child I021_GK_M

description:
S1290_021_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)

value: M (no stimulation)


title: Peripheral blood from child I021_GK_328

description:
S1291_021_GK_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)


title: GA DP 4637105025_B_1

description: GA DP


title: 920203771_N

description: FFPE


title: Peripheral blood from child I006_GK_328

description:
S1288_006_GK_CD3_28
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 60

description: SAMPLE 88


title: Manitol 4637105025_A_2

description: Manitol

value: Manitol


title: 920203743_N

description: FFPE


title: Manitol 4637105025_A_1

description: Manitol

value: SJL X BALB/C


title: 920203774_N

description: FFPE


title: 58

description: SAMPLE 85


title: 920203737_T

description: FFPE


title: Medium 4634633053_F_2

description: Medium

value: Medium

value: spleen cell


title: 35

description: SAMPLE 87


title: 59

description: SAMPLE 86


title: 57

description: SAMPLE 84


title: 56

description: SAMPLE 83


title: 920203725_T

description: FFPE


title: GA DM (SFC-962) 4634633053_E_1

description: GA DM

value: GA DM (SFC-962)


title: Medium 4634633053_F_1

description: Medium


title: 8

description: SAMPLE 82

source_name: Non-Endometriosis_No Uterine Pelvic Pathology

value: No Uterine Pelvic Pathology


title: Peripheral blood from child I006_GK_M

description:
S1287_006_GK_M
Gene expression data from peripheral blood of children (average age 8.4 years)


title: 920203722_T

description: FFPE

value: Tumor


title: 7

description: SAMPLE 81

value: Non-Endometriosis


title: GA DM (SFC-958) 4634633043_E_1

description: GA DM

value: GA DM (SFC-958)


title: 920203716_T

description: FFPE


title: GA DM (SFC-962) 4634633053_E_2

description: GA DM


title: 28

description: SAMPLE 80

value: Mid-Secretory Endometrial tissue


title: 920203713_T

description: FFPE


title: shERK2, biological rep1

city: Montréal

first: Xavier

last: Deschênes-Simard

state: Québec

address: 3655 Sir William Osler

department: Medicine

country: Canada

institute: McGill University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C with rotation (60 rpm) on Human Gene 1.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed with FlexArray 1.6.1.1 using Affymetrix default analysis settings and RMA as normalization method. Transcripts with a fold change higher or equal to 2 (log2) and a p-value˂ 0.05 according to the two-sample student's t-test were selected for final determination.

source_name: IMR90 cells stably expressing H-RasV12 and shRNA against ERK2

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Wisent, Montréal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent) and 1% penicillin G/streptomycin sulfate (Wisent).

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

treatment_protocol: Cells were co-infected with H-RasV12 and shCTR or shERK2 retroviruses and selected during three days with 2,5 µg/ml puromycin, then 5 days with hygromycin. Cells were kept 10 days in culture after selection, before RNA extraction.

value: IMR90 (Normal human diploid lung fibroblast)

tag: gender

value: Female

tag: overexpression

tag: shRNA


title: shERK2, biological rep2


title: shCTR, biological rep3

source_name: IMR90 cells stably expressing H-RasV12 and a non-targeting shRNA

value: shCTR


title: 920203683_T

description: FFPE


title: shCTR, biological rep2


title: GA DM (SFC-958) 4634633043_E_2

description: GA DM


title: shERK2, biological rep3


title: 920203719_T

description: FFPE


title: Generic B3 4634633053_C_2

description: GA Q

value: Generic B3


title: Generic B3 4634633053_C_1

description: GA Q


title: 920203631_N

description: FFPE

value: Normal


title: Pdx-1CreAPCL/+p53L/L, PDAC cells, biological rep2

city: Kaohsiung

first: Tzu-Lei

last: Kuo

state: Taiwan

address: 70 Lien-Hai Rd

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Sun Yat-Sen University

description: primary PDAC cells

hyb_protocol: Samples were hybridized to Mouse Gene ST 1.0 arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data generated were analyzed using Affymetrix Transcriptome Analysis Console software with Gene Level Differential Expression Analysis.
MoGene-1_0-st-v1.na34.mm10.probeset.csv
MoGene-1_0-st-v1.na34.mm10.transcript.csv
Affymetrix Transcriptome Analysis Console 1.0.0.234

source_name: primary PDAC cells

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: primary PDAC cells were grown in RPMI+10% FBS for less than 6 passages

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

tag: genotype

value: primary PDAC cells


title: 25

description: SAMPLE 78

tag: tissue

value: Early Secretory Endometrial tissue


title: 920203674_N

description: FFPE


title: 6

description: SAMPLE 79

value: Proliferative Endometrial tissue


title: GA RS 4634633053_A_2

description: GA RS

value: SJL X BALB/C

tag: cell type

value: GA RS


title: 920203592_N

description: FFPE


title: 920203598_N

description: FFPE


title: normalized log2 ratio (miR26a Podo/Cont Podo)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Cont Podo

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

value: Control

value: podocyte

source_name: miR26a Podo


title: shCTR, biological rep1


title: Pdx-1CreAPCL/+p53L/L, PDAC cells, mutant cell, biological rep3

description: primary PDAC cells


title: 5

description: SAMPLE 77

value: No Uterine Pelvic Pathology


title: GA RS 4634633053_A_1

description: GA RS

source_name: Spleen Cell Cultures

value: spleen cell


title: 920203568_T

description: FFPE

source_name: Lung carcinoid

value: Tumor


title: GA DP 4634633053_B_2

description: GA DP

value: GA DP


title: Pdx-1 p53L/L, normal pancreatic cells, biological rep2

description: normal pancreatic ductal cells

source_name: normal pancreatic ductal cells

value: normal pancreatic ductal cells


title: Pdx-1CreAPCL/+p53L/L, PDAC cells, biological rep1

description: primary PDAC cells


title: GA DP 4634633053_B_1

description: GA DP


title: 4

description: SAMPLE 73

value: Non-Endometriosis


title: 23

description: SAMPLE 74


title: 27

description: SAMPLE 76

value: Mid-Secretory Endometrial tissue


title: MBP 4634633002_F_2

description: MBP

value: MBP


title: 24

description: SAMPLE 75


title: 920203550_T

description: FFPE


title: Pdx-1Cre p53L/L, normal pancreatic ductal cells, biological rep1

description: normal pancreatic ductal cells


title: GA DP 4634633002_E_2

description: GA DP


title: 920203516_T

description: FFPE


title: Alveolar macrophage of WT, biological rep2

city: Cincinnati

first: Takuji

last: Suzuki

state: OH

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from Alveolar macrophages in untreated WT mice

hyb_protocol: For each sample a hybridization cocktail was created that includes a total of 2.5 micrograms of fragmented cDNA. Probe arrays were filled with hybridization cocktail and placed in a GeneChip® Hybridization Oven 640 (Affymetrix) for 18 hours. Arrays were then washed and stained using the Fluidics Station 450 (Affymetrix).

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

data_processing: All files including .dat, .cel, and .chp files were created by the scanning and analysis software, the Genechip Operating Software (Affymetrix).

source_name: Alveolar macrophages from untreated WT

label_protocol: Assays from NuGEN were used to create biotin-labeled cDNA target. Specifically the Ovation Pico WTA System Version 2 (Nugen) was used to create cDNA targets. The FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragmented and labeled the sense-strand cDNA targets.

growth_protocol: Bone marrow derived macrophages were administered by endotracheal instillation into 2 month-old Csf2rb–/– mice (PMT). Alveolar macrophages were analyzed one year after PMT in PMT-KO and age-adjusted untreated Csf2rb–/– mice (KO) and wild-type C57Bl/6 mice (WT).

extract_protocol: Total RNA was isolated from alveolar macrophages using TRIzol Reagent (Life Technologies, Carlsbad, CA) and then used to purify mRNA using RNeasy (Qiagen, Valencia, CA), both as directed by the manufacturers.

treatment_protocol: Alveolar macrophages were isolated by bronchoalveolar lavage and purified by brief adherence of BAL cells to plastic.

value: C57Bl/6 (WT) mice

value: Untreated WT

value: alveolar macrophage


title: 920203465_T

description: FFPE


title: Alveolar macrophage of WT, biological rep3


title: Alveolar macrophage of WT, biological rep1


title: 22

description: SAMPLE 72

value: Early Secretory Endometrial tissue


title: 3

description: SAMPLE 71

value: Proliferative Endometrial tissue


title: MBP 4634633002_F_1

description: MBP

value: SJL X BALB/C


title: GA DP 4634633002_D_2

description: GA DP


title: Alveolar macrophage of KO, biological rep1

description: Gene expression data from Alveolar macrophages in untreated Csf2rb-/- mice

source_name: Alveolar macrophages from untreated Csf2rb-/-

value: Csf2rb-/- (KO) mice

value: Untreated KO


title: GA DP 4634633002_E_1

description: GA DP


title: 21

description: SAMPLE 69


title: Alveolar macrophage of KO, biological rep3


title: Alveolar macrophage of KO, biological rep2


title: GA DP 4634633002_C_2

description: GA DP


title: 115

description: SAMPLE 67

value: Endometriosis

tag: endometriosis severity

value: Moderate/Severe


title: 2

description: SAMPLE 70

value: No Uterine Pelvic Pathology


title: 920203453_T

description: FFPE

value: Tumor


title: 77

description: SAMPLE 66

value: Minimal/Mild


title: GA DP 4634633002_D_1

description: GA DP

value: spleen cell

value: GA DP


title: GA DP 4634633002_B_1

description: GA DP


title: 1

description: SAMPLE 68

value: Non-Endometriosis


title: C57Bl/6J Bmal1fxfx pituitary 90hours post conception (ZT12)_fx12-3

city: Madison

first: Brian

middle: P

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

description: genotype Bmal1: Bmal1fxfx

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 3um 16bit

data_processing: Agilent Feature extraction version 10.7.3.1 for background subtraction - Background and Multiplicitive detrending. Data analyzed in Genespring 12.0   Threshold: 1.0   Logbase: 2   Technology: Agilent.SingleColor.28005  Normalization: Shift to 75 percentile   Baseline Transformation: median of all samples   FlagSettings:  Feature is not Uniform:A  Feature is a population outlier:A  Feature is Saturated:A  Feature is not above background:M  Feature is not positive and significant:M

source_name: Pregnant female mouse pituitary, sacked at given ZT time 3.5 days post conception

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent One Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking. 12hours light:12hours dark. ZT0=time lights turn on the room ~6:00 AM.

extract_protocol: Polytron 10 seconds and processed with an Qiagen Rneasy Mini kit

treatment_protocol: Time mated females were sacrificed and ovaries were harvested at given time and placed in RNAlater. Conception was assumed to occur at midnight(12 AM (ZT18)) before the plug was found in the morning.

tag: strain

tag: genotype/variation

tag: developmental stage

value: 90hours post conception (ZT12)

value: pituitary


title: GA DP 4634633002_C_1

description: GA DP

tag: batch


title: Alveolar macrophage of PMT, biological rep1

description: Gene expression data from Alveolar macrophages in Csf2rb-/- mice one year after pulmonary macrophage transplantation

source_name: Alveolar macrophages from Csf2rb-/- one year after pulmonary macrophage transplantation

value: One year after PMT


title: GA DP 4634633002_B_2

description: GA DP

tag: experiment


title: 128

description: SAMPLE 64


title: C57Bl/6J Bmal1fxfx pituitary 78hours post conception (ZT0)_fx0-2

description: genotype Bmal1: Bmal1fxfx

value: 78hours post conception (ZT0)


title: Alveolar macrophage of PMT, biological rep3

value: alveolar macrophage


title: Smutans_42C_60min_rep03

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

description: Smutans were cultured in 42C with 60 minutes heat stress, in total of 3 biological repeats, and this is the third one.

hyb_protocol: Hybridization  was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

scan_protocol: Scanning  was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

data_processing: The Raw data (txt files) were preprocessed by R/Bioconductor package limma, in which we chose quantile method for normalizaion. For the sibiling probes (multiple probes to one gene), we used the median indensity for representation.

organism: Streptococcus mutans UA159

source_name: Smutans, 42C, 60min

label_protocol: Labeling was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

growth_protocol: S. mutans strain was routinely grown without shaking in brain heart infusion broth supplemented with 1% sucrose if necessary at 37℃ anaerobically.

extract_protocol: Immediately after heat stress, all the cell cultures were collected and treated with RNAprotect reagent (Qiagen, Valencia, CA, USA). RNA was extracted and purified using RNeasy Mini kits (Qiagen) and digested with DNase. Purified RNA samples were analyzed by Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA)

treatment_protocol: For the heat stress groups, mid-logarithmic phase cell cultures of S. mutans (OD600nm = 0.5) were incubated at 42℃ for 5 min, 10 min, 15 min, 30 min, 45 min and 60 min, respectively.

tag: culture temperature

tag: heat stress time

value: 60  minutes


title: C57Bl/6J Bmal1fxfx pituitary 90hours post conception (ZT12)_fx12-2

description: genotype Bmal1: Bmal1fxfx


title: 93

description: SAMPLE 63

value: Mid-Secretory Endometrial tissue


title: C57Bl/6J Bmal1fxfx Sf1Cre pituitary 90hours post conception (ZT12)_cre12-3

description:
genotype Bmal1: Bmal1fxfx
genotype Cre: Sf1Cre

value: Bmal1fx/fx x CreSf1


title: Recovery from imiquimod treatment of the epidermis injured area, biol rep2, Grhl3 cKO (Krt14cre)

city: Irvine

first: William

last: Gordon

address: Sprague Hall

department: Biological Chemistry

institute: University of California Irvine

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Mouse ST1.0 Arrays

scan_protocol: standard Affymetrix protocol

data_processing: The data was analyzed with Affymetrix Gene Expression Console software using PLIER normalization, differential expression was performed with CyberT algorithm

source_name: Dorsal epidermis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Gene ST arrays from 5ug total RNA

extract_protocol: RNA was extracted using Precellys hard tissue tubes and Invitrogen's Trizol reagent with RNA purification columns and DNASE treatment

treatment_protocol: Dorsal skin was shaved, injured with wax tape or treated with imiquimod cream, removed 4 days later or 8 days later for recovery.  The epidermis was removed via dispase and placed into cold Trizol for immediate processing

tag: Sex

value: Male

tag: treatment

value: recovery from imiquimod treatment of the epidermiss injured area

value: Grhl3 cKO


title: GA RS 4634633002_A_1

description: GA RS

tag: batchcovar

tag: genetic background

value: SJL X BALB/C

value: GA RS


title: Smutans_42C_60min_rep01

description: Smutans were cultured in 42C with 60 minutes heat stress, in total of 3 biological repeats, and this is the first one.


title: 145

description: SAMPLE 62

tag: endometriosis/no endometriosis

value: Endometriosis

value: Moderate/Severe


title: Smutans_42C_45min_rep03

description: Smutans were cultured in 42C with 45 minutes heat stress, in total of 3 biological repeats, and this is the third one.

source_name: Smutans, 42C, 45min

value: 45  minutes


title: Recovery from imiquimod treatment of the epidermis injured area, biol rep2, Grhl3 WT (Krt14cre)

value: Grhl3 WT


title: C57Bl/6J Bmal1fxfx Sf1Cre pituitary 90hours post conception (ZT12)_cre12-2

value: 90hours post conception (ZT12)


title: 83

description: SAMPLE 61

value: Early Secretory Endometrial tissue

value: Minimal/Mild


title: Recovery from imiquimod treatment of the epidermis injured area, biol rep1, Grhl3 cKO (Krt14cre)


title: Recovery from imiquimod treatment of the epidermis (unaffected), biol rep2, Grhl3 cKO (Krt14cre)

value: recovery from imiquimod treatment of the epidermis (unaffected)


title: Smutans_42C_60min_rep02

description: Smutans were cultured in 42C with 60 minutes heat stress, in total of 3 biological repeats, and this is the second one.


title: C57Bl/6J Bmal1fxfx Sf1Cre pituitary 78hours post conception (ZT0)_cre0-3

value: 78hours post conception (ZT0)

value: pituitary


title: 127

description: SAMPLE 60


title: C57Bl/6J Bmal1fxfx pituitary 90hours post conception (ZT12)_fx12-1

description: genotype Bmal1: Bmal1fxfx


title: Recovery from imiquimod treatment of the epidermis (unaffected), biol rep1, Grhl3 cKO (Krt14cre)


title: 144

description: SAMPLE 59

value: Mid-Secretory Endometrial tissue


title: GA RS 4634633002_A_2

description: GA RS

value: spleen cell


title: Recovery from imiquimod treatment of the epidermis (unaffected), biol rep2, Grhl3 WT (Krt14cre)

value: Male


title: 131

description: SAMPLE 58


title: C57Bl/6J Bmal1fxfx pituitary 78hours post conception (ZT0)_fx0-1

description: genotype Bmal1: Bmal1fxfx


title: Recovery from imiquimod treatment of the epidermis injured area, biol rep1, Grhl3 WT (Krt14cre)

value: recovery from imiquimod treatment of the epidermiss injured area


title: C57Bl/6J Bmal1fxfx pituitary 90hours post conception (ZT12)_fx12

description: genotype Bmal1: Bmal1fxfx


title: Smutans_42C_45min_rep02

description: Smutans were cultured in 42C with 45 minutes heat stress, in total of 3 biological repeats, and this is the second one.


title: Smutans_42C_45min_rep01

description: Smutans were cultured in 42C with 45 minutes heat stress, in total of 3 biological repeats, and this is the first one.


title: Smutans_42C_30min_rep03

description: Smutans were cultured in 42C with 30 minutes heat stress, in total of 3 biological repeats, and this is the third one.

source_name: Smutans, 42C, 30min

value: 30  minutes


title: Smutans_42C_30min_rep01

description: Smutans were cultured in 42C with 30 minutes heat stress, in total of 3 biological repeats, and this is the first one.

value: 30 minutes


title: Smutans_42C_30min_rep02

description: Smutans were cultured in 42C with 30 minutes heat stress, in total of 3 biological repeats, and this is the second one.


title: Recovery from imiquimod treatment of the epidermis (unaffected), biol rep1, Grhl3 WT (Krt14cre)


title: C57Bl/6J Bmal1fxfx pituitary 78hours post conception (ZT0)_fx0

description: genotype Bmal1: Bmal1fxfx


title: 112

description: SAMPLE 57

value: Proliferative Endometrial tissue


title: Smutans_42C_15min_rep03

description: Smutans were cultured in 42C with 15 minutes heat stress, in total of 3 biological repeats, and this is the third one.

source_name: Smutans, 42C, 15min

value: 15 minutes


title: 88

description: SAMPLE 56

value: Endometriosis


title: 114

description: SAMPLE 55

value: Moderate/Severe


title: Smutans_42C_15min_rep02

description: Smutans were cultured in 42C with 15 minutes heat stress, in total of 3 biological repeats, and this is the second one.


title: C57Bl/6J Bmal1fxfx Sf1Cre pituitary 90hours post conception (ZT12)_cre12

value: Bmal1fx/fx x CreSf1


title: C57Bl/6J Bmal1fxfx Sf1Cre pituitary 78hours post conception (ZT0)_cre0


title: C57Bl/6J Bmal1fxfx Sf1Cre pituitary 78hours post conception (ZT0)_cre0-1


title: Imiquimod treatment of the epidermis injured area after 4 days, biol rep2, Grhl3 cKO (Krt14cre)

value: Female

value: imiquimod of the epidermis injured area after 4 days

value: Grhl3 cKO


title: Imiquimod treatment of the epidermis injured area after 4 days, biol rep1, Grhl3 WT (Krt14cre)

value: Grhl3 WT


title: Imiquimod treatment of the epidermis injured area after 4 days, biol rep2, Grhl3 WT (Krt14cre)


title: 85

description: SAMPLE 53

value: Early Secretory Endometrial tissue

value: Minimal/Mild


title: Imiquimod treatment of the epidermis (unaffected), biol rep2, Grhl3 cKO (Krt14cre)

value: imiquimod of the epidermis (unaffected)


title: 113

description: SAMPLE 51


title: 143

description: SAMPLE 52

value: Mid-Secretory Endometrial tissue


title: Imiquimod treatment of the epidermis injured area after 4 days, biol rep1, Grhl3 cKO (Krt14cre)


title: Smutans_42C_15min_rep01

description: Smutans were cultured in 42C with 15 minutes heat stress, in total of 3 biological repeats, and this is the first one.


title: Smutans_42C_10min_rep03

description: Smutans were cultured in 42C with 10 minutes heat stress, in total of 3 biological repeats, and this is the third one.

source_name: Smutans, 42C, 10min

value: 10 minutes


title: Bmal1 null Ovary 90hours post conception (ZT12)_mop3nullovary3.5zt12b549-3

description: Bmal1 null Ovary 90hours post conception (ZT12)mop3nullovary3.5zt12b549-3.txt:gProcessedSignal

data_processing:
Agilent Feature extraction version 10.7.3.1 for background subtraction - Background and Multiplicitive detrending. Data analyzed in Genespring 12.0
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.28005
Normalization: Shift to 75 percentile
Baseline Transformation: median of all samples
FlagSettings:
Feature is not Uniform:A
Feature is a population outlier:A
Feature is Saturated:A
Feature is not above background:M
Feature is not positive and significant:M

source_name: Pregnant female mouse ovary, sacked at given ZT time  2.5 to 3.5 days post conception

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark. ZT0=time lights turn on the room ~6:00 AM.

extract_protocol: Polytron 10 seconds  and processed with an Qiagen Rneasy Mini kit

treatment_protocol: Time mated females were sacrificed and ovaries were harvested at given time and placed in RNAlater.  Conception was assumed to occur at midnight(12 AM (ZT18)) before the plug was found in the morning.

value: congenic on a C57Bl/6J background

value: Bmal1 null

value: 90 hours post conception (ZT12)

value: Ovary


title: 75

description: SAMPLE 50

source_name: Endometriosis_Severity Not Available

value: Proliferative Endometrial tissue


title: Imiquimod treatment of the epidermis (unaffected), biol rep1, Grhl3 cKO (Krt14cre)


title: Smutans_42C_10min_rep02

description: Smutans were cultured in 42C with 10 minutes heat stress, in total of 3 biological repeats, and this is the second one.


title: Bmal1 null Ovary 90hours post conception (ZT12)_mop3nullovary3.5zt12b547-3

description: Bmal1 null Ovary 90hours post conception (ZT12)mop3nullovary3.5zt12b547-3.txt:gProcessedSignal


title: Bmal1 null Ovary 90hours post conception (ZT12)_mop3nullovary3.5zt12b436-2

description: Bmal1 null Ovary 90hours post conception (ZT12)mop3nullovary3.5zt12b436-2.txt:gProcessedSignal


title: Smutans_42C_10min_rep01

description: Smutans were cultured in 42C with 10 minutes heat stress, in total of 3 biological repeats, and this is the first one.


title: Smutans_42C_5min_rep03

description: Smutans were cultured in 42C with 5 minutes heat stress, in total of 3 biological repeats, and this is the third one.

source_name: Smutans, 42C, 5min

value: 5 minutes


title: 76

description: SAMPLE 54

value: Endometriosis


title: Smutans_42C_5min_rep02

description: Smutans were cultured in 42C with 5 minutes heat stress, in total of 3 biological repeats, and this is the second one.


title: Imiquimod treatment of the epidermis (unaffected), biol rep2, Grhl3 WT (Krt14cre)


title: Wax Stripping of the epidermis day 4 after injury, biol rep2, Grhl3 cKO (Krt14cre)

value: Male

value: wax stripping of the epidermis day 4 after injury


title: 126

description: SAMPLE 49

value: Moderate/Severe


title: Imiquimod treatment of the epidermis (unaffected), biol rep1, Grhl3 WT (Krt14cre)

value: Female


title: Smutans_42C_5min_rep01

description: Smutans were cultured in 42C with 5 minutes heat stress, in total of 3 biological repeats, and this is the first one.


title: 98

description: SAMPLE 48


title: Bmal1 null Ovary 78hours post conception (ZT0)_b562-4nullzt0

description: Bmal1 null Ovary 78hours post conception (ZT0)b562-4nullzt0.txt:gProcessedSignal

value: 78 hours post conception (ZT0)


title: 111

description: SAMPLE 47


title: Bmal1 null Ovary 78hours post conception (ZT0)_b561-8nullzt0

description: Bmal1 null Ovary 78hours post conception (ZT0)b561-8nullzt0.txt:gProcessedSignal


title: Smutans_37C_rep03

description: Smutans were cultured in 37C without heat stress, in total of 3 biological repeats, and this is the third one.

source_name: Smutans, 37C

value: 0 minute


title: Bmal1fx/fx x CreSf1 Ovary 90hours post conception (ZT12)_sf1cre3.5dpczt12-4

description: Bmal1fx/fx x CreSf8 Ovary 90hours post conception (ZT12)sf1cre3.5dpczt12-4.txt:gProcessedSignal

value: Bmal1fx/fx x CreSf1


title: Bmal1 null Ovary 78hours post conception (ZT0)_b567-6nullzt0

description: Bmal1 null Ovary 78hours post conception (ZT0)b567-6nullzt0.txt:gProcessedSignal


title: 81

description: SAMPLE 46

value: Minimal/Mild


title: Wax Stripping of the epidermis day 4 after injury, biol rep1, Grhl3 WT (Krt14cre)

value: Grhl3 WT


title: 142

description: SAMPLE 45

value: Mid-Secretory Endometrial tissue


title: Bmal1fx/fx x CreSf1 Ovary 90hours post conception (ZT12)_sf1cre3.5dpczt12-3

description: Bmal1fx/fx x CreSf7 Ovary 90hours post conception (ZT12)sf1cre3.5dpczt12-3.txt:gProcessedSignal

value: congenic on a C57Bl/6J background


title: Smutans_37C_rep02

description: Smutans were cultured in 37C without heat stress, in total of 3 biological repeats, and this is the second one.


title: Wax Stripping of the epidermis day 4 after injury, biol rep2, Grhl3 WT (Krt14cre)


title: 130

description: SAMPLE 44


title: Wax Stripping of the epidermis day 4 after injury, biol rep1, Grhl3 cKO (Krt14cre)

value: Grhl3 cKO


title: Smutans_37C_rep01

description: Smutans were cultured in 37C without heat stress, in total of 3 biological repeats, and this is the first one.


title: Bmal1fx/fx x CreSf1 Ovary 90hours post conception (ZT12)_sf1cre3.5dpczt12-2

description: Bmal1fx/fx x CreSf6 Ovary 90hours post conception (ZT12)sf1cre3.5dpczt12-2.txt:gProcessedSignal

value: 90 hours post conception (ZT12)


title: 125

description: SAMPLE 43

value: Early Secretory Endometrial tissue


title: Run-rep5

city: Orlando

first: Ling

last: Lai

state: FL

address: 6400 Sanger Rd

institute: Sanford-Burnham Medical Research Institute

hyb_protocol: Following the labeling of sscDNA, 2.5 microgram of sscDNA was used to prepare hybridization cocktail. The cocktail was immediately added to the Affymetrix WT GENE 1.0 ST chip and hybridized using GeneChip Hybridization oven 645 for 17hrs at 45C.

scan_protocol: After Hybridization, the arrays were washed and stained using Fluidics protocol FS450_0007 on GeneChip Fluidics Station 450. Following wash and stain the GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed using RMA algorithm using the Expression Console software Version 1.1 default settings.

source_name: Bi-ventricle

label_protocol: sscDNA were prepared from 450ng of total RNA using the Ambion’s WT expression kit protocol, followed by fragmentation and labeling using the WT Terminal label kit according to the protocol provided by affymetrix. The Affymetrix proprietary DNA labeling reagent covalently linked to biotin was used to label the sscDNA.

extract_protocol: RNA zol extract of total RNA

tag: age

value: 2 month-old

value: bi-ventricle

tag: condition

value: voluntary wheel training for 2 months


title: Bmal1fx/fx x CreSf1 Ovary 90hours post conception (ZT12)_sf1cre3.5dpczt12

description: Bmal1fx/fx x CreSf5 Ovary 90hours post conception (ZT12)sf1cre3.5dpczt12.txt:gProcessedSignal

tag: tissue

value: Ovary


title: 97

description: SAMPLE 42

value: Endometriosis


title: Bmal1fx/fx x CreSf1 Ovary 78hours post conception (ZT0)_sf1cre3.5dpczt0-4

description: Bmal1fx/fx x CreSf4 Ovary 78hours post conception (ZT0)sf1cre3.5dpczt0-4.txt:gProcessedSignal


title: Alveolar macrophage of PMT, biological rep2

description: Gene expression data from Alveolar macrophages in Csf2rb-/- mice one year after pulmonary macrophage transplantation

tag: genotype

value: Csf2rb-/- (KO) mice

value: One year after PMT

tag: cell type

value: alveolar macrophage


title: Run-rep4

value: Female

tag: strain


title: Bmal1fx/fx x CreSf1 Ovary 78hours post conception (ZT0)_sf1cre3.5dpczt0-3

description: Bmal1fx/fx x CreSf3 Ovary 78hours post conception (ZT0)sf1cre3.5dpczt0-3.txt:gProcessedSignal

tag: genotype/variation

value: Bmal1fx/fx x CreSf1

value: 78 hours post conception (ZT0)


title: Run-rep2


title: Bmal1fx/fx x CreSf1 Ovary 78hours post conception (ZT0)_sf1cre3.5dpczt0-2

description: Bmal1fx/fx x CreSf2 Ovary 78hours post conception (ZT0)sf1cre3.5dpczt0-2.txt:gProcessedSignal

tag: developmental stage


title: 92

description: SAMPLE 40

tag: endometriosis severity

value: Minimal/Mild


title: 74

description: SAMPLE 41

value: Proliferative Endometrial tissue


title: Bmal1fx/fx x CreSf1 Ovary 78hours post conception (ZT0)_g344-1crezt0

description: Bmal1fx/fx x CreSf1 Ovary 78hours post conception (ZT0)g344-1crezt0.txt:gProcessedSignal

value: congenic on a C57Bl/6J background


title: 73

description: SAMPLE 39


title: 129

description: SAMPLE 65

value: Moderate/Severe


title: Run-rep3


title: Bmal1fx/fx Ovary 90hours post conception (ZT12)_fx3.5dpczt12-3

description: Bmal1fx/fx Ovary 90hours post conception (ZT12)fx3.5dpczt12-3.txt:gProcessedSignal

value: 90 hours post conception (ZT12)


title: 80

description: SAMPLE 37


title: Sedentary-rep4

value: sedentary (control)


title: Sedentary-rep5

value: 2 month-old


title: Sedentary-rep3

value: bi-ventricle


title: Bmal1fx/fx Ovary 90hours post conception (ZT12)_fx3.5dpczt12-2

description: Bmal1fx/fx Ovary 90hours post conception (ZT12)fx3.5dpczt12-2.txt:gProcessedSignal


title: Ch-rep5

value: 3 month-old

value: transverse aortic constriction


title: 96

description: SAMPLE 38

value: Mid-Secretory Endometrial tissue

value: Endometriosis


title: Run-rep1

value: voluntary wheel training for 2 months


title: Sedentary-rep1


title: Bmal1fx/fx Ovary 78hours post conception (ZT0)_fx3.5dpczt0-4

description: Bmal1fx/fx Ovary 78hours post conception (ZT0)fx3.5dpczt0-4.txt:gProcessedSignal

value: Ovary


title: Sedentary-rep2

value: Female


title: Bmal1fx/fx Ovary 90hours post conception (ZT12)_fx3.5dpczt12-4

description: Bmal1fx/fx Ovary 90hours post conception (ZT12)fx3.5dpczt12-4.txt:gProcessedSignal


title: Bmal1fx/fx Ovary 78hours post conception (ZT0)_fx3.5dpczt0-3

description: Bmal1fx/fx Ovary 78hours post conception (ZT0)fx3.5dpczt0-3.txt:gProcessedSignal


title: Ch-rep4


title: 91

description: SAMPLE 36


title: 79

description: SAMPLE 32


title: Bmal1fx/fx Ovary 78hours post conception (ZT0)_fx3.5dpczt0-2

description: Bmal1fx/fx Ovary 78hours post conception (ZT0)fx3.5dpczt0-2.txt:gProcessedSignal


title: Bmal1fx/fx Ovary 90hours post conception (ZT12)_fx3.5dpczt12

description: Bmal1fx/fx Ovary 90hours post conception (ZT12)fx3.5dpczt12.txt:gProcessedSignal


title: 72

description: SAMPLE 33


title: 82

description: SAMPLE 34


title: 124

description: SAMPLE 35

value: Early Secretory Endometrial tissue


title: Bmal1fx/fx Ovary 78hours post conception (ZT0)_fx3.5dpczt0

description: Bmal1fx/fx Ovary 78hours post conception (ZT0)fx3.5dpczt0.txt:gProcessedSignal

value: 78 hours post conception (ZT0)


title: C57Bl/6J Ovary 90hours post conception (ZT12)_21 3-5 dpc zt12 wt ovary

description: C57Bl/6J Ovary 90hours post conception (ZT12)21 3-5 dpc zt12 wt ovary.txt:gProcessedSignal

value: WT


title: Ch-rep3


title: 107

description: SAMPLE 28

value: Proliferative Endometrial tissue


title: C57Bl/6J Ovary 86hours post conception (ZT8)_20 3-5 dpc zt8 wt ovary

description: C57Bl/6J Ovary 86hours post conception (ZT8)20 3-5 dpc zt8 wt ovary.txt:gProcessedSignal

value: congenic on a C57Bl/6J background

value: 86 hours post conception (ZT8)


title: CH-sham-rep5

value: sham-operated control


title: Ch-rep2


title: 100

description: SAMPLE 31

value: Minimal/Mild


title: Ch-rep1


title: C57Bl/6J Ovary 82hours post conception (ZT4)_19 3-5dpc zt4 wt ovary

description: C57Bl/6J Ovary 82hours post conception (ZT4)19 3-5dpc zt4 wt ovary.txt:gProcessedSignal

value: 82 hours post conception (ZT4)


title: 78

description: SAMPLE 30


title: 120

description: SAMPLE 29

value: Moderate/Severe


title: 22085_INV

type: genomic

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 8395
AlternateIDRawData: 22085_INV
dual-color florescent staining

hyb_protocol: Infinium HD Assay was performed using the BeadArray system according to the manufacturer's instructions (Illumina)

data_processing: Data was extracted using Illumina’s GenomeStudio v2010.3 with Genotyping module 1.8.4 software, with the default Illumina settings and Illumina HumanOmniExpress‐12v1_H manifest cluster file

molecule: genomic DNA

source_name: microdissected ovarian tumor

label_protocol: Infinium HD Assay was performed according to the manufacturer's instructions (Illumina)

extract_protocol: Total genomic DNA was extracted using a DNeasy Kit (Qiagen, Valencia, CA)

tag: disease state

value: LGSC

tag: component

value: Invasive


title: CH-sham-rep4

value: 3 month-old

value: bi-ventricle


title: 106

description: SAMPLE 27

value: Endometriosis


title: 70117_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 6244
AlternateIDRawData: 70117_INV
dual-color florescent staining

scan_protocol: Infinium HD Assay was performed using the BeadArray system according to the manufacturer's instructions (Illumina)


title: C57Bl/6J Ovary 78hours post conception (ZT0)_18 3-5dpc zt0 wt ovary

description: C57Bl/6J Ovary 78hours post conception (ZT0)18 3-5dpc zt0 wt ovary.txt:gProcessedSignal

value: Ovary


title: 847_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 65672
AlternateIDRawData: 847_INV
dual-color florescent staining

value: Borderline


title: CH-sham-rep3

value: Female


title: C57Bl/6J Ovary 74hours post conception (ZT20)_17 2-5 dpc zt20 wt ovary

description: C57Bl/6J Ovary 74hours post conception (ZT20)17 2-5 dpc zt20 wt ovary.txt:gProcessedSignal

value: 74 hours post conception (ZT20)


title: 1221_LMP

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 65663_SBT
AlternateIDRawData: 1221_LMP
dual-color florescent staining


title: 105

description: SAMPLE 26


title: 60269_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 7200
AlternateIDRawData: 60269_INV
dual-color florescent staining


title: C57Bl/6J Ovary 70hours post conception (ZT16)_16 2-5 dpc zt16 wt ovary

description: C57Bl/6J Ovary 70hours post conception (ZT16)16 2-5 dpc zt16 wt ovary.txt:gProcessedSignal

value: WT

value: 70 hours post conception (ZT16)


title: 141

description: SAMPLE 24

value: Mid-Secretory Endometrial tissue


title: C57Bl/6J Ovary 66hours post conception (ZT12)_15 2-5dpc zt12 wt ovary

description: C57Bl/6J Ovary 66hours post conception (ZT12)15 2-5dpc zt12 wt ovary.txt:gProcessedSignal

value: congenic on a C57Bl/6J background

value: 66 hours post conception (ZT12)


title: 1221_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 65663_INV
AlternateIDRawData: 1221_INV
dual-color florescent staining


title: CH-sham-rep2

value: sham-operated control


title: CH-sham-rep1


title: 89

description: SAMPLE 25

value: Minimal/Mild


title: HF-rep5

value: heart failure


title: C57Bl/6J Ovary 90hours post conception (ZT12)_14 3-5 dpc ZT12 ovary

description: C57Bl/6J Ovary 90hours post conception (ZT12)14 3-5 dpc ZT12 ovary.txt:gProcessedSignal

value: 90 hours post conception (ZT12)


title: 856_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 65673
AlternateIDRawData: 856_INV
dual-color florescent staining

value: LGSC

value: Invasive


title: 805_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 65671
AlternateIDRawData: 805_INV
dual-color florescent staining


title: HF-rep4

value: 3 month-old

value: bi-ventricle


title: C57Bl/6J Ovary 86hours post conception (ZT8)_13 3-5 dpc ZT8 wt ovary

description: C57Bl/6J Ovary 86hours post conception (ZT8)13 3-5 dpc ZT8 wt ovary.txt:gProcessedSignal

value: 86 hours post conception (ZT8)

value: Ovary


title: 95

description: SAMPLE 22

value: Endometriosis


title: 22077_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 7957
AlternateIDRawData: 652_INV
dual-color florescent staining


title: 60318_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 8633
AlternateIDRawData: 60318_INV
dual-color florescent staining


title: C57Bl/6J Ovary 82hours post conception (ZT4)_3.5zt4ovary1rerun111

description: C57Bl/6J Ovary 82hours post conception (ZT4)3.5zt4ovary1rerun111.txt:gProcessedSignal

value: 82 hours post conception (ZT4)


title: C57Bl/6J Ovary 78hours post conception (ZT0)_11 3-5dpc ZT0 wt ovary

description: C57Bl/6J Ovary 78hours post conception (ZT0)11 3-5dpc ZT0 wt ovary.txt:gProcessedSignal

value: WT

value: 78 hours post conception (ZT0)


title: HF-rep3

value: Female


title: 94

description: SAMPLE 20

value: Mid-Secretory Endometrial tissue


title: HF-rep1


title: 140

description: SAMPLE 19

value: Moderate/Severe


title: 1248A_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 65679
AlternateIDRawData: 1248A_INV
dual-color florescent staining


title: HF-rep2


title: 131B_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 65664
AlternateIDRawData: 131B_INV
dual-color florescent staining


title: C57Bl/6J Ovary 74hours post conception (ZT20)_10 2-5dpc ZT20 wt ovary

description: C57Bl/6J Ovary 74hours post conception (ZT20)10 2-5dpc ZT20 wt ovary.txt:gProcessedSignal

value: congenic on a C57Bl/6J background

value: 74 hours post conception (ZT20)


title: 139

description: SAMPLE 18


title: HF-sham-rep5

value: sham-operated control


title: C57Bl/6J Ovary 70hours post conception (ZT16)_2.5dpczt16rererun1108

description: C57Bl/6J Ovary 70hours post conception (ZT16)2.5dpczt16rererun1108.txt:gProcessedSignal

value: 70 hours post conception (ZT16)


title: 110

description: SAMPLE 21

value: Proliferative Endometrial tissue


title: HF-sham-rep4


title: 1024A_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 65670
AlternateIDRawData: 1024A_INV
dual-color florescent staining

value: LGSC

value: Invasive


title: 60111_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 2189
AlternateIDRawData: 60111_INV
dual-color florescent staining


title: 450_INV

description:
Raw data file: ILOE-6486_FullDataTable.txt
Sample name: 15046
AlternateIDRawData: 450_INV
dual-color florescent staining


title: C57Bl/6J Ovary 66hours post conception (ZT12)_2.5dpczt12rererun1108

description: C57Bl/6J Ovary 66hours post conception (ZT12)2.5dpczt12rererun1108.txt:gProcessedSignal

value: 66 hours post conception (ZT12)


title: C57Bl/6J Ovary 90hours post conception (ZT12)_3.5zt12ovaryrerun111

description: C57Bl/6J Ovary 90hours post conception (ZT12)3.5zt12ovaryrerun111.txt:gProcessedSignal

value: 90 hours post conception (ZT12)


title: 138

description: SAMPLE 17


title: HF-sham-rep3

value: 3 month-old

value: bi-ventricle


title: HF-sham-rep1


title: 137

description: SAMPLE 16

value: Endometriosis


title: C57Bl/6J Ovary 82hours post conception (ZT4)_5 3-5dpc ZT4 WT ovary

description: C57Bl/6J Ovary 82hours post conception (ZT4)5 3-5dpc ZT4 WT ovary.txt:gProcessedSignal

value: WT

value: 82 hours post conception (ZT4)

value: Ovary


title: C57Bl/6J Ovary 86hours post conception (ZT8)_6 3-5dpc ZT8 WT ovary

description: C57Bl/6J Ovary 86hours post conception (ZT8)6 3-5dpc ZT8 WT ovary.txt:gProcessedSignal

value: 86 hours post conception (ZT8)


title: 49826_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 11368
AlternateIDRawData: 49826_INV
dual-color florescent staining


title: HF-sham-rep2

value: Female


title: 102

description: SAMPLE 14

value: Moderate/Severe


title: 122

description: SAMPLE 15

value: Early Secretory Endometrial tissue


title: 1101A_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 65677
AlternateIDRawData: 1101A_INV
dual-color florescent staining


title: Gene expression profile of 24 days mouse testis_Rep2

city: Trivandrum

first: Pradeep

middle: G

last: Kumar

state: Kerala

address: Thycaud, Poojappura

department: Molecular Reproduction

country: India

institute: Rajiv Gandhi Centre for Biotechnology

hyb_protocol: Following fragmentation, cDNAs were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

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

data_processing: The raw data .cel file were normalized by ExonRMA16 summarization with All Confidence level: ALL followed by Quantile normalization and Baseline Transformation to median of all samples

source_name: 24 days mouse testis

label_protocol: Biotinylated cDNAs were prepared according to the GeneChip Whole Transcript Sense Target Labeling protocol (Affymetrix).

growth_protocol: Male Swiss albino mice were obtained from an inbred line maintained in  animal house facility.

extract_protocol: Total RNA extraction was performed using Guanidine Thiocyanate (GTC) based QIAzol lysis reagent, miRNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: None. Animals were reared in normal temperature, 26 ±1˚C and humidity controlled environment under 14h light: 10h dark conditions.

value: testis

value: Swiss albino


title: 136

description: SAMPLE 13

value: Mid-Secretory Endometrial tissue


title: 974A_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 65674
AlternateIDRawData: 974A_INV
dual-color florescent staining

value: LGSC


title: C57Bl/6J Ovary 78hours post conception (ZT0)_4 3-5dpc ZT0 WT ovary

description: C57Bl/6J Ovary 78hours post conception (ZT0)4 3-5dpc ZT0 WT ovary.txt:gProcessedSignal

value: congenic on a C57Bl/6J background

value: 78 hours post conception (ZT0)


title: 1263A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65680
AlternateIDRawData: 1263A_INV
dual-color florescent staining

value: Invasive


title: 152C_INV

description:
Raw data file: ILOE-5745_FullDataTable.txt
Sample name: 15018
AlternateIDRawData: 152C_INV
dual-color florescent staining


title: C57Bl/6J Ovary 74hours post conception (ZT20)_3 2-5dpc ZT20 WT ovary

description: C57Bl/6J Ovary 74hours post conception (ZT20)3 2-5dpc ZT20 WT ovary.txt:gProcessedSignal

value: 74 hours post conception (ZT20)


title: 109

description: SAMPLE 12

value: Proliferative Endometrial tissue


title: 90

description: SAMPLE 23

value: Endometriosis


title: Gene expression profile of 24 days mouse testis


title: Gene expression profile of 24 days mouse testis_Rep1


title: 1073A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65676
AlternateIDRawData: 1073A_INV
dual-color florescent staining


title: Gene expression profile of 16 days mouse testis_Rep1

source_name: 16 days mouse testis


title: Gene expression profile of 16 days mouse testis_Rep2


title: C57Bl/6J Ovary 66hours post conception (ZT12)_1 2-5dpc ZT12 WT ovary

description: C57Bl/6J Ovary 66hours post conception (ZT12)1 2-5dpc ZT12 WT ovary.txt:gProcessedSignal

value: WT

value: 66 hours post conception (ZT12)


title: Gene expression profile of 16 days mouse testis


title: 1005A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65675
AlternateIDRawData: 1005A_INV
dual-color florescent staining


title: 22048_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 5349
AlternateIDRawData: 627A_INV
dual-color florescent staining


title: 108

description: SAMPLE 11


title: 121

description: SAMPLE 9


title: 135

description: SAMPLE 10


title: 104

description: SAMPLE 8


title: 134

description: SAMPLE 7


title: Gene expression profile of 8 days mouse testis_Rep2

source_name: 8 days mouse testis


title: 133

description: SAMPLE 6


title: C57bl6 macrophages infected with killed parasite (KP) at T24, rep3

city: Tunis

first: lamia

last: Guizani-Tabbane

address: 13, Place Pasteur BP74. Tunis-Belvedere

department: Immunopathology

country: Tunisia

institute: Insitut Pasteur de Tunis

description: Gene expression data from C57bl6 macrophages infected with KP at T24

hyb_protocol: 100 ng of Total RNA were proceeded according to the GeneChip whole transcript sense target labeling assay manual using the GeneChip WT cDNA Synthesis, amplification Kit and WT terminal labeling Kit. The fragmented and labeled ssDNA was hybridized to a GeneChip Mouse Gene 1.0 ST array, washed with the Fluidics station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: The data preprocessing step included intrachip and interchip normalisation and summarisation. The intrachip normalisation step corrects for the GC content of the probes, the interchip normalisation step reduces non-biological differences between chips and the summarisation step combines the probe intensities into single gene expression values. For the intrachip normalisation the 'Model-based Analysis of Tiling-arrays' (MAT) was implemented as described by Kapur, Ket al., 2007. Genome Biol 8:R82, since this method  provides the most advanced GC correction for whole-transcript prepared samples. As a last step in the preprocessing of the data we applied a summarisation of probe intensities to a probe set expression [Processed/nomalized data and additional data processing details were provided as Series supplementary files].

source_name: macrophages at 24 hrs post infection with heat killed Leishmania major parasite

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

growth_protocol: Bone Marrow cells were grown for 7 days, with re-feeding on day 3, to induce macrophage differentiation. Generated macrophages were assessed by flow cytometry for expression of F4/80 (around 90% were positive).

treatment_protocol: BMdM were incubated at a parasite to cell ratio of 10:1 with Ficoll purified metacyclic promastigotes of Leishmania major at 37°C in 5% CO2 during respectively T1,T3,T6,T12 and T24 hours post infection.

value: wild type C57bl6 (Elevage Janvier)

value: Bone Marrow-derived macrophage (BMdM)


title: C57bl6 macrophages infected with killed parasite (KP) at T24, rep1


title: 507A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 15060
AlternateIDRawData: 507A_INV
dual-color florescent staining


title: Gene expression profile of 8 days mouse testis


title: C57bl6 macrophages infected with killed parasite (KP) at T24, rep2


title: C57bl6 macrophages infected with killed parasite (KP) at T12, rep2

description: Gene expression data from C57bl6 macrophages infected with KP at T12

source_name: macrophages at 12 hrs post infection with heat killed Leishmania major parasite


title: 533A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 15014
AlternateIDRawData: 533A_INV
dual-color florescent staining


title: Gene expression profile of 8 days mouse testis_Rep1


title: 749A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65666
AlternateIDRawData: 749A_INV
dual-color florescent staining


title: C57bl6 macrophages infected with killed parasite (KP) at T12, rep1


title: 119

description: SAMPLE 5


title: C57bl6 macrophages infected with killed parasite (KP) at T12, rep3


title: C57Bl/6J Ovary 70hours post conception (ZT16)_2 2-5dpc ZT16 WT ovary

description: C57Bl/6J Ovary 70hours post conception (ZT16)2 2-5dpc ZT16 WT ovary.txt:gProcessedSignal

value: 70 hours post conception (ZT16)

value: Ovary


title: 1235A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65678
AlternateIDRawData: 1235A_INV
dual-color florescent staining


title: 561A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 15071
AlternateIDRawData: 561A_INV
dual-color florescent staining


title: 118

description: SAMPLE 2

value: Early Secretory Endometrial tissue

value: Moderate/Severe


title: 103

description: SAMPLE 3


title: C57bl6 macrophages infected with killed parasite (KP) at T6, rep3

description: Gene expression data from C57bl6 macrophages infected with KP at T6

source_name: macrophages at 6 hrs post infection with heat killed Leishmania major parasite


title: C57bl6 macrophages infected with killed parasite (KP) at T6, rep2


title: C57bl6 macrophages infected with killed parasite (KP) at T6, rep1


title: C57bl6 macrophages infected with killed parasite (KP) at T3, rep3

description: Gene expression data from C57bl6 macrophages infected with KP at T3

source_name: macrophages at 3 hrs post infection with heat killed Leishmania major parasite


title: 123

description: SAMPLE 1


title: C57bl6 macrophages infected with killed parasite (KP) at T3, rep2


title: C57bl6 macrophages infected with killed parasite (KP) at T3, rep1


title: C57bl6 macrophages infected with killed parasite (KP) at T1, rep3

description: Gene expression data from C57bl6 macrophages infected with KP at T1

source_name: macrophages at 1 hr post infection with heat killed Leishmania major parasite


title: BM1.replicate4

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

description: Affymetrix Human Genome U133 Plus 2.0 Array

hyb_protocol: 3.75 mg cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a  Fluidics 450 Station (Affymetrix, Santa Clara, CA). Each sample was hybridized with an Affymetrix Human Genome U133APlus2.0 microarray.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Data was quantile normalized and RMA summarized using Bioconductor.

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: MCF7 media (Control media): DMEM (Life Technologies), 1X Glutamax (Gibco 35050) and 10% FBS (Biological Industires) when passaging.  See  growth conditions in Tarragona et al., Journal of Biological Chemistry, 2012), for more details.

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies) and quantified using a Nanodrop spectrophotometer. Quality was assessed using a Bioanalyzer (Agilent) and only high quality samples (RIN ≥9) were used for hybridization.

treatment_protocol: Cells were grown for 2 days following the growth protocol outlined above and RNA extracted

tag: group

tag: date

tag: progenitor (father)

value: A

tag: progenitor (mother)

value: F


title: BM2.replicate1

value: B

value: D


title: BM1.replicate3


title: 901A_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65668
AlternateIDRawData: 901A_INV
dual-color florescent staining

value: LGSC


title: Parental.replicate3

value: P


title: BM1.replicate2


title: BM0.replicate2


title: BM1.replicate1

value: C


title: C57bl6 macrophages infected with killed parasite (KP) at T1, rep2


title: LSK HOXB4+ 20 weeks rep_3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six (6) micrograms of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT_MG-430_PM array. Following hybridization, arrays were washed and stained using the GeneTitan system

scan_protocol: HT_MG-430_PM arrays were scanned using the Affymetrix GeneTitan system

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

source_name: HOXB4+ LSKs 20 weeks post BMT

label_protocol: Twenty (20) nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were not subject to culture prior to RNA extraction

extract_protocol: Total RNA was extracted from sorted, transduced LSK cells using the RNAqueous-Micro kit (Invitrogen) according to the manufacturer's recommended protocol

treatment_protocol: No treatment was applied to cells prior to RNA extraction

tag: background strain

tag: gender

value: female

value: bone marrow


title: 51104_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 51104_LMP
AlternateIDRawData: 51104_LMP
dual-color florescent staining

data_processing: Data was extracted using Illumina’s GenomeStudio with the default Illumina settings

tag: patient

value: Borderline


title: C57bl6 macrophages infected with live parasite (P) at T24, rep3

description: Gene expression data from C57bl6 macrophages infected with P at T24

source_name: macrophages at 24 hrs post infection with Leishmania major parasite


title: BM0.replicate1

value: E


title: 32054_INV

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 32054_INV
AlternateIDRawData: 32054_INV
dual-color florescent staining

value: Invasive


title: LSK HOXB4+ 20 weeks rep_2


title: 32023_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 32023_LMP
AlternateIDRawData: 32023_LMP
dual-color florescent staining


title: 711B_INV

description:
Raw data file: ILOE-5627_Reanalyzed_FullDataTable.txt
Sample name: 65665
AlternateIDRawData: 711B_INV
dual-color florescent staining


title: LSK GFP+ 20 weeks rep_3

source_name: GFP+ LSKs 20 weeks post BMT


title: 34208_INV

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 34208_INV
AlternateIDRawData: 34208_INV
dual-color florescent staining


title: MAFshort

hyb_protocol: 3.75 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

data_processing: Data were quantile normalized and RMA summarized using Bioconductor.

source_name: MAFshort

tag: cell line


title: 34208_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 34208_LMP
AlternateIDRawData: 34208_LMP
dual-color florescent staining


title: LSK HOXB4+ 20 weeks rep_1

tag: tissue


title: 51104_INV

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 51104_INV
AlternateIDRawData: 51104_INV
dual-color florescent staining


title: C57bl6 macrophages infected with live parasite (P) at T24, rep1

value: wild type C57bl6 (Elevage Janvier)

value: Bone Marrow-derived macrophage (BMdM)


title: MAFlong

source_name: MAFlong


title: 132

description: SAMPLE 4

data_processing: We imported all of the microarray data files into R and normalized them simultaneously. The normalization procedure consists of two steps executed with programs in the Bioconductor package GCRMA. First, we compute the probe affinities using the annotation file hgu133plus2cdf. Second, we normalize the data by setting two options and leaving the rest at default values. The affinity.info option is set to use the probe affinities computed in the first step. The type option is set to fullmodel which uses both the sequence information and mismatch probe model.

value: Mid-Secretory Endometrial tissue

tag: endometriosis/no endometriosis

value: Endometriosis


title: C57bl6 macrophages infected with killed parasite (KP) at T1, rep1


title: Parental.replicate2


title: C57bl6 macrophages infected with live parasite (P) at T12, rep2

description: Gene expression data from C57bl6 macrophages infected with P at T12

source_name: macrophages at 12 hrs post infection with Leishmania major parasite


title: C57bl6 macrophages infected with live parasite (P) at T6, rep3

description: Gene expression data from C57bl6 macrophages infected with P at T6

source_name: macrophages at 6 hrs post infection with Leishmania major parasite


title: C57bl6 macrophages infected with live parasite (P) at T12, rep1


title: 32054_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 32054_LMP
AlternateIDRawData: 32054_LMP
dual-color florescent staining


title: LSK GFP+ 20 weeks rep_1


title: C57bl6 macrophages infected with live parasite (P) at T12, rep3


title: Parental

source_name: Parental


title: LSK HOXB4+ 12 weeks rep_3

source_name: HOXB4+ LSKs 12 weeks post BMT


title: LSK HOXB4+ 12 weeks rep_1


title: 801B_Inv

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 801B_Inv
AlternateIDRawData: 801B_Inv
dual-color florescent staining

source_name: microdissected ovarian tumor


title: 460A_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 460A_LMP
AlternateIDRawData: 460A_LMP
dual-color florescent staining


title: LSK GFP+ 12 weeks rep_2

source_name: GFP+ LSKs 12 weeks post BMT


title: 801B_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 801B_LMP
AlternateIDRawData: 801B_LMP
dual-color florescent staining


title: LSK GFP+ 12 weeks rep_3


title: LSK HOXB4+ 12 weeks rep_2


title: 460A_Inv

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 460A_Inv
AlternateIDRawData: 460A_Inv
dual-color florescent staining


title: C57bl6 macrophages infected with live parasite (P) at T6, rep1


title: 428A_LMP

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 428A_LMP
AlternateIDRawData: 428A_LMP
dual-color florescent staining


title: OVCA432-MFAP5-rep3

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from MFAP5 treated OVCA432 cell line

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

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

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.

source_name: Ovarian cancer cell line OVCA432 treated with exogenous MFAP5

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: OVCA432 ovarian cancer cell line was cultured in humidified incubator at 37C and 5% carbon dioxide. Culture medium RPMI1640 supplemented with 10% Fetal bovine serum was used as growth medium.

extract_protocol: Total RNA extraction was performed using the Purelink RNA mini kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Prior to treatment, cells were trypsinized, counted and seeded in 6-well cell culture plate. After cell seeding overnight, cells were fasted in serum free RPMI medium for 24hrs. After that, cells were treated with fresh serum free RPMI medium supplemented with either 200ng/mL of recombinant human MFAP5 protein or equal amount of solvent control in the MFAP5 treatment group and the control group respectively. At 48 hours post treatment, OVCA432 cells from both groups were harvested and total RNA was extracted.

value: High grade serous ovarian cancer cell line OVCA432

tag: agent

value: recombinant human MFAP5 protein


title: OVCA432-MFAP5-rep1


title: C57bl6 macrophages infected with live parasite (P) at T24, rep2

tag: strain


title: C57bl6 macrophages infected with live parasite (P) at T3, rep2

description: Gene expression data from C57bl6 macrophages infected with P at T3

source_name: macrophages at 3 hrs post infection with Leishmania major parasite


title: OVCA432-control-rep2

description: Gene expression data from control OVCA432 cell line

source_name: Ovarian cancer cell line OVCA432-Control sample

value: control


title: OVCA432-MFAP5-rep2


title: OVCA432-control-rep3


title: C57bl6 macrophages infected with live parasite (P) at T3, rep1


title: C57bl6 macrophages infected with live parasite (P) at T1, rep3

description: Gene expression data from C57bl6 macrophages infected with P at T1

source_name: macrophages at 1 hr post infection with Leishmania major parasite


title: C57bl6 macrophages infected with live parasite (P) at T1, rep2


title: Non Infected C57bl6 macrophages at T24, rep3

description: Gene expression data from non infected (NI) C57bl6 macrophages at T24

source_name: Non infected (NI) macrophages at 24 hrs


title: C57bl6 macrophages infected with live parasite (P) at T1, rep1


title: Non Infected C57bl6 macrophages at T24, rep2


title: LSK GFP+ 12 weeks rep_1


title: OVCA432-control-rep1


title: LSK HOXB4+ 6 weeks rep_3

source_name: HOXB4+ LSKs 6 weeks post BMT


title: Non Infected C57bl6 macrophages at T24, rep1


title: LSK HOXB4+ 6 weeks rep_2


title: Non Infected C57bl6 macrophages at T12, rep3

description: Gene expression data from non infected (NI) C57bl6 macrophages at T12

source_name: Non infected (NI) macrophages at 12 hrs


title: 6219

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: shoot apex _in vitro/LD/stage 1.02_rep c

hyb_protocol: A mixture of 10 pmol Cy5 incorporated dye and 14 pmol Cy3 incorporated dye was fragmented and resuspended in hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 10.1.1.1 (Agilent Technologies).

data_processing: We use the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal) from Agilent Feature Extraction software v10.1.1.1 and compute log2-(Cy5/Cy3)-ratios. We remove Agilent control probes, as well as probes with signals below background on all arrays (absent spots). To decide whether a signal is significantly above background, we use the features gIsPosAndSignif and rIsPosAndSignif, also provided by the Agilent software. In case of multiple probes for the same Agilent ID, log2-(Cy5/Cy3)-ratios are averaged.

organism: Arabidopsis thaliana

source_name: ron3 mutant

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

extract_protocol: RNeasyPlant mini kit

value: shoot apex

tag: genotype

value: ron3 mutant

source_name: Ler control

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

value: Ler control


title: 6220

description: shoot apex _in vitro/LD/stage 1.02_rep d


title: LSK HOXB4+ 6 weeks rep_1


title: mouse 2-3-3

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: 750 ng of the obtained biotinylated cDNA samples was hybridized onto the Illumina MouseRef8 v2 BeadChips according to the protocol from Illumina  ”Whole-Genome Gene Expression Direct Hybridization Assay”

scan_protocol: Illumina’s Genomestudio v. 2011.1 software with default settings.

data_processing: Data was normalized using the Bioconducter library limma by control background correction, quantile normalization and log2 transformation (R version 3.0.2 neqc function).

source_name: spleen, unsorted

label_protocol: NuGEN Ovation PicoSL WTA System kit (# 3310-48) followed by Encore BiotinIL Module (#4210-48) was used to generate Biotin labeled ss cDNA

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN)

treatment_protocol: single cell suspensions were made from spleen. 100.000 cells were stored as pellets in -80F.

tag: leukemia type

value: erythroid

value: spleen

tag: mouse model


title: Non Infected C57bl6 macrophages at T12, rep2


title: 32023_INV

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 32023_INV
AlternateIDRawData: 32023 INV Repeat
dual-color florescent staining

tag: disease state

value: LGSC


title: mouse 2-3-2


title: mouse 5-1, repl2

value: T-cell


title: 6217

description: shoot apex _in vitro/LD/stage 1.02_rep a


title: 6218

description: shoot apex _in vitro/LD/stage 1.02_rep b


title: mouse 5-5, repl2


title: Parental.replicate1

description: Affymetrix Human Genome U133 Plus 2.0 Array

value: P

value: A

value: D


title: mouse 4-3

value: undifferentiated


title: B6.MRLc1.Glo_14m_rep2

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: isolated glomeruli by beads perfusion

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Female B6.MRL and C57BL/6 mice (9–14-months of age) were maintained under specific pathogen-free conditions.

treatment_protocol: No treatment was perfomed to mice.

tag: age

value: glomeruli

value: late glomerulonephritis


title: Non Infected C57bl6 macrophages at T6, rep2

description: Gene expression data from non infected (NI) C57bl6 macrophages at T6

source_name: Non infected (NI) macrophages at 6 hrs

value: wild type C57bl6 (Elevage Janvier)

value: Bone Marrow-derived macrophage (BMdM)


title: B6.MRLc1.Glo_14m_rep1


title: Non Infected C57bl6 macrophages at T6, rep1


title: Non Infected C57bl6 macrophages at T3, rep3

description: Gene expression data from non infected (NI) C57bl6 macrophages at T3

source_name: Non infected (NI) macrophages at 3 hrs


title: Non Infected C57bl6 macrophages at T12, rep1


title: B6.MRLc1.Glo_9m_rep3

value: early glomerulonephritis


title: mouse 5-3


title: B6.MRLc1.Glo_9m_rep2


title: B6.MRLc1.Glo_14m_rep3


title: B6.MRLc1.Glo_9m_rep1


title: Non Infected C57bl6 macrophages at T6, rep3


title: B6.Glo_9m_rep3

value: healthy


title: Non Infected C57bl6 macrophages at T3, rep2


title: Non Infected C57bl6 macrophages at T3, rep1


title: B6.Glo_9m_rep2


title: 428B_Inv

description:
Raw data file: IL610Q-4377_FullDataTable.txt
Sample name: 428B_Inv
AlternateIDRawData: 428B_Inv
dual-color florescent staining

tag: component

value: Invasive


title: mouse 4-2


title: LSK GFP+ 20 weeks rep_2

source_name: GFP+ LSKs 20 weeks post BMT

value: female

value: bone marrow


title: Non Infected C57bl6 macrophages at T1, rep3

description: Gene expression data from non infected (NI) C57bl6 macrophages at T1

source_name: Non infected (NI) macrophages at 1 hr


title: B6.Glo_9m_rep1


title: mouse 5-5, repl1

value: erythroid


title: mouse 2-2

value: spleen


title: mouse 5-1, repl1


title: Non Infected C57bl6 macrophages at T1, rep2


title: WRO-2

city: brussels

first: aline

last: hébrant

address: 808 route de Lennik

department: iribhm

institute: ulb

description:
raw data file 1: WRO2-WROhy5-Nhy3.gpr
raw data file 2 (dye-swap): WRO2-Nhy5-WROhy3.gpr

hyb_protocol: samples were hybridized using Corning Pronto! Microarray Hybridization Kit, and were dye swapped. So for each sample, we have two microarray slide (raw data file 1 and raw data file 2 as indicated as description field). The raw data file 1 is labelled as 'tumor-Hy5+normal tissue-Hy3' and the raw data file 2 is labelled as tumor-Hy3+normal tissue-Hy5 as dye-swap experiments.

scan_protocol: the slides were scanned using a GenePix 4000B scanner (Axon, Sunnyvale, CA)

data_processing:
Please note that sample data table contains data combined across arrays. All hybridizations were performed in duplicates with dye swap and each probes are present in duplicate on the same array. For each probes, a mean was performed on their four replicates. We have kept the data for the probe for which we have at least 2 values.
A Normex + offset background correction and LOESS normalization were carried out by using functions of the LIMMA 3.4.5 package for the R 2.8.1 language. Data points were removed when intensity values for both dyes were below 200% of the background and absent calls were removed before subsequent statistical analyses.

label: Hy5, Hy3

source_name: Cell Line

label_protocol: total RNA was labelled using the miRCURY LNA microRNA Power Labelling Kit (Hy3/Hy5) (Exiqon, Copenhagen, Denmark), according to the manufacturer’s protocol. Labeled RNA was purified on a miRNeasy column (Qiagen)

extract_protocol: total RNA was extracted using a TRIzol Reagent kit (Invitrogen) followed by purification on miRNeasy columns (Qiagen, Hilden, Germany

treatment_protocol: Cells cultures were stoped using Trizol. Tissues were immediately dissected, placed on ice, snap-frozen in liquid nitrogen, and stored at -80°C until processing

tag: tissue/cell type

value: thyroid cancer cell line

label: Hy3. Hy5

source_name: Control Cells

value: Non treated primary culture


title: mouse 5

value: T-cell


title: Non Infected C57bl6 macrophages at T0, rep3

description: Gene expression data from non infected (NI) C57bl6 macrophages at T0

source_name: Non infected (NI) macrophages at 0 hr

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


title: WRO-1

description:
raw data file 1: WRO1-WROhy5-Nhy3.gpr
raw data file 2 (dye-swap): WRO1-Nhy5-WROhy3.gpr


title: Non Infected C57bl6 macrophages at T0, rep2


title: mouse 2


title: BCPAP-1

description:
raw data file 1: BCPAP1-BCPAPhy5-Nhy3.gpr
raw data file 2 (dye-swap): BCPAP1-Nhy5-BCPAPhy3.gpr


title: mouse 2-3


title: Non Infected C57bl6 macrophages at T0, rep1


title: 2.TAU/LysM

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using quantile normalisation in R

source_name: TAU/LysM

label_protocol: Biotinylated cRNA were prepared with Illumina  kit for Illumina arrays

extract_protocol: RNA was extracted  with standard methods

treatment_protocol: Adult microglia were isolated from SIRT1F/F or LysM-Cre/SIRT1F/F mice as described with some modifications. Brains were placed in a culture dish with enzyme solution and the digested brains were triturated with a 20-ml pipette and passed through 70-μm filter. After centrifugation, cells were incubated with anti-myelin microbeads, centrifuged, resuspendend and washed. Myelin-negative fractions were collected and further processed by incubating with anti-CD11b microbeads at 4°C for 15 min. After washing, the resuspended myelin negative fraction was passed through an autoMACS Pro Separator, and then the CD11b-positive population was separated from CD11b-negative population. Cells were centrifuged, and the pellets were lysed with RNA lysis buffer (QIAGEN) for microarray or quantitative RT-PCR.

value: TAU/LysM

tag: cell type

value: microglia

tag: genetic background

value: BL6 and 129/Sv


title: Non Infected C57bl6 macrophages at T1, rep1


title: TPC1-2

description:
raw data file 1: TPC12-Nhy5-TPC1hy3.gpr
raw data file 2 (dye-swap): TPC12-TPC1hy5-Nhy3.gpr


title: mouse 4-1


title: 1.TAU/LysM


title: TPC1-1

description:
raw data file 1: TPC11-Nhy5-TPC1hy3.gpr
raw data file 2 (dye-swap): TPC11-TPC1hy5-Nhy3.gpr


title: 1.TAU

source_name: TAU

value: TAU


title: Day 15 EEM from Female Control Replicate 3

city: Gainesville

first: Kyle

last: Dobbs

state: Florida

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

description:
raw data file: 252829810235_area2_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

hyb_protocol: 825 ng of one Cy3 labeled aRNA sample and 825 ng of one Cy5 aRNA sample were combined and hybridized to one area of a 4x44,000 Agilent EmbryoGene microarray slide

scan_protocol: Slides were scanned using a Agilent High-resolution C Scanner (Agilent Technologies, CA, USA) while features were extracted using Agilent's feature extraction software (Agilent)

data_processing: Data were sent to BioDiscovery Inc. (Hawthorne, CA ,USA) which generated separate datasets for each color (Cy3 and Cy5).  Spots were aligned to the corresponding Genepix aray list follwoed by examination for spots on the array that were larger than the spot or contaiend a bliemish.  Raw data was log transformed,normalized by both Loess and quantile normalization by JMP Genomic (SAS, Cary, NC, USA).

organism: Bos taurus

source_name: Female Control 3

label_protocol: aRNA was labeled using the Universal Linkage System (ULS) by Kreatech for gene expression analysis.  Microarray slides were made by Agilent and designed by EmbryoGene.  ULS directly labels the aRNA through a non-enzymatic protocol which labels through the formation of a coordinate bond on the N7 position of guanine.  The Cy3 and Cy5 are linked by a spacer to the ULS molecule.

growth_protocol: Fertilized embryos were grown in culture to Day 7 after fertilization and transferred into Holstein recipients.  At Day 15, they were flushed from the recipient using DPBS/PVP

extract_protocol: RNA was extracted according to manufacturer's instructions using the Qiagen Allprep DNA/RNA mini kit

treatment_protocol: 10 ng/ml of CSF2 or Control (DPBS/BSA)  from Day 5-7 post-insemination during in vitro culture of bovine embryos.

value: Filamentous Day 15 extra-embryonic membrane


title: 3.LysM old

source_name: LysM old

value: old


title: BCPAP-2

description:
raw data file 1: BCPAP2-BCPAPhy5-Nhy3.gpr
raw data file 2 (dye-swap): BCPAP2-Nhy5-BCPAPhy3.gpr


title: C57bl6 macrophages infected with live parasite (P) at T6, rep2

description: Gene expression data from C57bl6 macrophages infected with P at T6

source_name: macrophages at 6 hrs post infection with Leishmania major parasite

value: wild type C57bl6 (Elevage Janvier)

value: Bone Marrow-derived macrophage (BMdM)


title: K1-2

description:
raw data file 1: K12-K1hy5-Nhy3.gpr
raw data file 2 (dye-swap): K12-Nhy5-K1hy3.gpr


title: 2.TAU


title: Day 15 EEM from Female CSF2 Replicate 3

source_name: Female CSF2 3


title: Day 15 EEM from Female CSF2 Replicate 2

description:
raw data file: 252829810235_area1_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

source_name: Female CSF2 2


title: C57bl6 macrophages infected with live parasite (P) at T3, rep3

description: Gene expression data from C57bl6 macrophages infected with P at T3

source_name: macrophages at 3 hrs post infection with Leishmania major parasite


title: 2.LysM old


title: 24 hour biofilm vs Mixed Reference 5

city: San Francisco

first: Emily

middle: Patricia

last: Fox

address: 600 16th Street, GH - N374

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: 252016610038-block 4

hyb_protocol: 0.4 mg Cy3-labelled cDNA and 0.4 mg Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)

scan_protocol: Scanned on a 4000B Axon Instrument Scanner

data_processing: Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R, Probes were collapsed to a median value using a custom java script

organism: Candida albicans

source_name: 24 hour Biofilm (experiment 5)

label_protocol: cDNA was synthesized from 8 mg total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)

growth_protocol: C. albicans was grown in biofilms or in planktonic cultures at 30 deg or 37 deg in Spider media

extract_protocol: Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)

tag: source strain background

source_name: Mixed reference pool#5: cDNA from 252016610036 - blocks 1 - 5


title: 48 hour biofilm vs Mixed Reference 5

description: 252016610038-block 5

source_name: 48 hour Biofilm (experiment 5)


title: 1.LysM old


title: K1-1

description:
raw data file 1: K11-K1hy5-Nhy3.gpr
raw data file 2 (dye-swap): K11-Nhy5-K1hy3.gpr


title: FTC-133-2

description:
raw data file 1: FTC1332-FTC133hy5-Nhy3.gpr
raw data file 2 (dye-swap): FTC1332-Nhy5-FTC133hy3.gpr


title: Day 15 EEM from Female Control Replicate 1

description:
raw data file: 252829810234_area4_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

source_name: Female Control 1

tag: gender


title: 8 hour biofilm vs Mixed Reference 5

description: 252016610038-block 3

source_name: 8 hour Biofilm (experiment 5)


title: Adhered biofilm cells vs Mixed Reference 5

description: 252016610038-block 2

source_name: Adhered Biofilm (experiment 5)


title: 3.SIRT1 old

source_name: SIRT1 old


title: FTC-133-1

description:
raw data file 1: FTC1331-FTC133hy5-Nhy3.gpr
raw data file 2 (dye-swap): FTC1331-Nhy5-FTC133hy3.gpr

source_name: Cell Line

source_name: Control Cells


title: Day 15 EEM from Female CSF2 Replicate 1

source_name: Female CSF2 1


title: Day 15 EEM from Female Control Replicate 2

source_name: Female Control 2


title: 8505C-2

description:
raw data file 1: 8505c2-8505chy5-Nhy3.gpr
raw data file 2 (dye-swap): 8505c2-Nhy5-8505chy3.gpr


title: Day 15 EEM from Male Control Replicate 2

description:
raw data file: 252829810234_area3_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

source_name: Male Control 2

value: male


title: Log phase 37 degrees vs Mixed Reference 5

description: 252016610038-block 1

source_name: Planktonic Log Phase 37 degrees (experiment 5)


title: 2.SIRT1 old


title: 3.LysM young

source_name: LysM young

value: young


title: Day 15 EEM from Male CSF2 Replicate 4

source_name: Male CSF2 4


title: 48 hour biofilm vs Mixed Reference 4

description: 252016610066-block 10

source_name: 48 hour Biofilm (experiment 4)

source_name: Mixed reference pool#4: cDNA from 252016610066 - blocks 5 - 10


title: 8505C-1

description:
raw data file 1: 8505C1-8505chy5-Nhy3.gpr
raw data file 2 (dye-swap): 8505c1-Nhy5-8505chy3.gpr


title: Day 15 EEM from Male CSF2 Replicate 3

description:
raw data file: 252829810234_area2_2013_05_24_results.txt
Within the raw files, channel 1= Cy3 and channel 2= Cy5

source_name: Male CSF2 3


title: 1.LysM young


title: 2.LysM young


title: 1.SIRT1 old