title: MSK0366 SP

value: Primary Malignant Fibrous Histiocytoma

value: pleomorphic undifferentiated sarcoma

value: SP


title: breast cancer pre-treatment biopsy subject 6 FL2105_364_0509

status: Public on Jan 17 2012

type: RNA

city: Houston

first: TAKAYUKI

last: IWAMOTO

state: TX

address: 1515 Holcombe Blvd

department: Breast medical Oncology

country: USA

institute: UT MD Anderson

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.

data_processing: The data were normalized using dChip version 1.3 followed by logrithm-base-10 transformation. The dChip version 1.3 was used to calculate Model Based Expression Index (MBEI) values of the arrays using the digital standard microarray MDA-BCNorm.CEL and the probe sensitivity index file UTMDACC-BreastCancerNormalizer.psi as described in Hess, et. al, Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and 5-Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer, Journal of Clinical Oncology, 24 (26), 2006.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer FNA biopsy, pre-treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).

extract_protocol: total RNA was extracted from the FNA and surgical specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).

tag: array qc

value: Pass

tag: treatment

value: pre-neoadjuvant systemic therapy

tag: prepost-pair

tag: molecular subtype

value: LumA

tag: er status

value: ERpos

tag: her2 status

tag: disease state

value: breast cancer

tag: tissue

value: breast cancer tumor


title: Non-side population, biological rep 2

city: Toronto

first: Qingxia

last: Wei

state: ON

address: 101 College Street

department: Development Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Following fragmentation, GeneChips were washed and stained using EukGE-WS2v4

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

data_processing: The .cel files where imported into Genespring GX11 program and summarized using RMA normalization. The expression value of each gene from the SP and NSP fraction of each distinct tumour is normalized to the expression value of that particular gene from the NSP fraction. The NSP normalized matrix is provided as a supplementary file on the Series record.

source_name: NSP 199

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The tumours were freshly harvested from human.

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

treatment_protocol: The tumours were stained with Hoeschst Dye, and sorted via flow-cytomentry

value: soft-tissue sarcoma

tag: cell type

value: Non-side population cells


title: breast cancer pre-treatment biopsy subject 4 U133A_FL48_312_07_12_05

value: Basal

value: ERneg


title: Side population, biological rep 1

value: Side population cells


title: Non-side population, biological rep 1

source_name: NSP 732


title: WT-elf-1

city: Birmingham

first: Karolina

last: Pajerowska-Mukhtar

state: Alabama

address: 1300 University Blvd

department: Department of Biology

institute: University of Alabama at Birmingham

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm.

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

data_processing: The data were normalized with RMA algorithm using Gene-Spring GX default analysis settings

organism: Arabidopsis thaliana

source_name: WT-elf

label_protocol: RNA probes were labelled using MessageAmp Premier RNA Amplification Kit (Ambion)

growth_protocol: Arabidopsis plants (Columbia-0 and tbf1 mutant) were grown on soil (Metro Mix 360) at 22˚C under a 16/8 hr light/dark cycle for 3 weeks

extract_protocol: The RNA was extracted with TRIzol (Ambion)

treatment_protocol: Treated with 1 mM SA for 6 hrs (spray) or 10 µM elf18 for 2 hrs (infiltration into leaves). Mock treatments with water were included for both spray and infiltration.

value: mature leaf

tag: genotype

value: wild type

tag: biological replicate


title: poly mutant vs. wt rep 3

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Hybridisation to FL002 arrays: Hybridisation to amino-modified long oligonucleotide arrays using Genomics Solutions hybridisation station with Biosolutions hybridisation buffer (see http://www.flychip.org.uk/protocols/gene_expression/hyb_oligoMWG.php).

scan_protocol: Scanning was with Genepix 4000B dual laser scanner (see http://www.flychip.org.uk/protocols/gene_expression/scanning2.php).

data_processing: Spot quantification via the Dapple package. Data normalised with the vsn (variance stabilisation normalisation) Bioconductor package.

organism: Drosophila melanogaster

label_protocol: Klenow Labelling: Between 3 to 5µg total RNA are reverse transcribed to cDNA [anchored oligo (dT)23 (Sigma), Superscript III (Invitrogen)] and second strand synthesis is then performed [Second strand buffer (Invitrogen), DNA Polymerase I (Invitrogen), RNaseH (New England Biolabs), E. coli DNA ligase (GE Healthcare)] to obtain double stranded DNA. Random primers are annealed to this denatured DNA template and extended by Klenow fragment using the Bioprime DNA Labeling System (Invitrogen) while fluorescent dyes Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated. (http://www.flychip.org.uk/protocols/gene_expression/klenow_v2.php) - used 5 ug total RNA starting material and labelled 500ng cDNA with the Klenow kit.

growth_protocol: Fly stocks were maintained at 25 degrees Celcius

extract_protocol: RNA extraction using Trizol (see http://www.flychip.org.uk/protocols/gene_expression/standard_extraction.php)

treatment_protocol: No treatment: genotype comparison.

tag: genetic background

value: Canton S

value: whole organism

value: Poly mutant (poly05137/TM6B)

tag: developmental stage

value: larva

value: Wild-type (Canton S)


title: poly mutant vs. wt rep 2

source_name: controlE 6 wt


title: Side population, biological rep 3


title: poly mutant vs. wt rep 1

source_name: controlE 5 wt


title: breast cancer pre-treatment biopsy subject 3 FL2732_269

value: Pass

value: pre-neoadjuvant systemic therapy


title: Side population, biological rep 2


title: breast cancer pre-treatment biopsy subject 9 FL2734_467

value: LumA

value: ERpos


title: poly mutant vs. wt rep 4


title: breast cancer pre-treatment biopsy subject 1 FL956-151

value: breast cancer

value: breast cancer tumor


title: breast cancer pre-treatment biopsy subject 2 U133A_FL44-208_07_08_05


title: Side population, biological rep 4

value: soft-tissue sarcoma


title: Colon cancer sample 5 using 250ng input DNA

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
Sample5
Colon cancer sample 5
US22502676_252252210025_S01_CGH_105_Dec08_1_4.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Median normalization in R/Bioconductor

molecule: genomic DNA

source_name: colon cancer

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

tag: sample id

value: Colon cancer, FFPE

tag: input dna

source_name: Normal colon mucosa

value: Normal colon mucosa (Patient own normal, FFPE)


title: Primary TNBC (BT8) xenograft_SHP2 miR2_3

status: Public on Jan 16 2012

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Human Gene 1.0 st v1 GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: CEL files were read into R (v2.10) using the R/Bioconductor (v2.4) package oligo (v1.8) and normalized probeset level expression values were calculated with the command rma and the R/Bioconductor annotation package pd.hugene.1.0.st.v1

label: Biotin

source_name: Primary TNBC (BT8) xenograft_SHP2 miR2

label_protocol: 100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: Primary TNBC cells were injected orthotopically into the fat pad of mammary gland 2/3 of imuunodeficient mice. After tumor development, we depleted SHP2 for 30 days in vivo.

extract_protocol: Tumors were dissected and total RNA was isolated with a standard TRIZOL extraction method.

treatment_protocol: Doxycycline in drinking water (2 g per liter). The treatment started after tumor development and continued until the end of the experiment (day 30). The drinking water containing doxycycline was refreshed every two days.

tag: xenografted cells

value: Primary triple-negative breast cancer (BT8)

tag: transduced with

value: doxycycline-inducible lentiviral vector expressing a SHP2 miR2

tag: tissue isolated

value: tumor developed in recipient mice


title: Primary TNBC (BT8) xenograft_SHP2 miR2_4


title: Primary TNBC (BT8) xenograft_SHP2 miR2_2


title: Primary TNBC (BT8) xenograft_SHP2 miR2_1


title: Whole_Cell_Lysate_IP

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

description: Reference RNA  precipitated with anti-FLAG M2 affinity gel from whole cell extract of HeLa S3 cells transfected with pFLAG-EWS

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

data_processing: CEL files were quantified with Factor for Robust Microarray Summarization (FARMS), using the statistical language R and Bioconductor.

source_name: Whole cell lysate of HeLa S3 cells transfected with pFLAG-EWS

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Human cervical cancer cell line HeLa S3 was grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% calf serum in a humidified atmosphere containing 5% CO2 at 37° C.

extract_protocol: Total RNA was isolated using TRI reagent (Sigma).

treatment_protocol: The cells were transfected with pFLAG-EWS and incubated for 48 h.

tag: cell line

value: Human cervical cancer cell line HeLa S3

tag: rip antibody

value: anti-FLAG M2

tag: rip antibody vendor

value: Sigma

tag: rip antibody lot#

tag: rip antibody catalog#

tag: fraction


title: WT rep1

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: WT, replicate 1

hyb_protocol: 1.65 micrograms of Cy3-labeled aRNA were hybridized for 17 hours at 65ºC in an Agilent hybridization oven (G2545A, Agilent Technologies) set to 10 rpm in a final concentration of 1x GEx Hybridization Buffer HI-RPM (Agilent Technologies)

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays

data_processing: Images provided by the scanner were analyzed using Feature Extraction software v10.1.1.1 (Agilent Technologies).

organism: Mus musculus

source_name: WT, replicate 1

label_protocol: cDNA was then converted to anti-sense RNA (aRNA) by using T7 RNA polymerase that amplifies target material and incorporates cyanine 3 (Cy3)-labeled CTP simultaneously

growth_protocol: Chow diet, 4 weeks of age

extract_protocol: RNeasy® Mini kit (Qiagen Ltd, Crawley, UK)

treatment_protocol: Islets isolation, RNA extraction and purification

tag: class

value: WT

value: wild type

tag: tissue

value: pancreatic islet


title: WT rep2

description: WT, replicate 2

source_name: WT, replicate 2

tag: genotype


title: WT rep3

description: WT, replicate 3

source_name: WT, replicate 3


title: Primary TNBC (BT8) xenograft_SHP2 miR1_4

source_name: Primary TNBC (BT8) xenograft_SHP2 miR1

value: doxycycline-inducible lentiviral vector expressing a SHP2 miR1


title: Whole_Cell_Lysate

description: Reference RNA from whole cell extract of HeLa S3 cells transfected with pFLAG-EWS


title: PPARg2KO rep3

description: PPARg2KO, replicate 3

source_name: PPARg2KO, replicate 3

value: PPARg2 KO


title: IP_3

description: RNA precipitated with anti-FLAG M2 affinity gel from the cytosol extract of HeLa S3 cells transfected with pFLAG-EWS, biological rep3

source_name: Cytosol extract of HeLa S3 cells transfected with pFLAG-EWS

value: IP


title: Primary TNBC (BT8) xenograft_SHP2 miR1_3


title: IP_2

description: RNA precipitated with anti-FLAG M2 affinity gel from the cytosol extract of HeLa S3 cells transfected with pFLAG-EWS, biological rep2


title: PPARg2KO rep2

description: PPARg2KO, replicate 2

source_name: PPARg2KO, replicate 2


title: IP_1

description: RNA precipitated with anti-FLAG M2 affinity gel from the cytosol extract of HeLa S3 cells transfected with pFLAG-EWS, biological rep1


title: PPARg2KO rep1

description: PPARg2KO, replicate 1

source_name: PPARg2KO, replicate 1


title: Primary TNBC (BT8) xenograft_SHP2 miR1_2


title: Primary TNBC (BT8) xenograft_SHP2 miR1_1


title: Cytosol_Extract_2

description: Input RNA from cytosol extract of HeLa S3 cells transfected with pFLAG-EWS, biological rep2


title: Cytosol_Extract_1

description: Input RNA from cytosol extract of HeLa S3 cells transfected with pFLAG-EWS, biological rep1


title: Cytosol_Extract_3

description: Input RNA from cytosol extract of HeLa S3 cells transfected with pFLAG-EWS, biological rep3


title: Plant_vs_Insect-rep6

city: Bunkyo

first: Kenro

last: Oshima

state: Tokyo

institute: The University of Tokyo

description:
Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers; Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris.
Phytoplasma grown in plant vs  Phytoplasma grown in insect Replicate 6

hyb_protocol: Hybridization was performed 14 hours at 65°C (6 x SSC, 0.2% SDS, 5 x Denhardt’s solution). The hybridized slides were washed three times with 2 x SSC/0.2% SDS (55°C), and washed one time with 0.05 x SSC (at room temperature).

scan_protocol: The slides were scanned with a Affymetrix 428 Array Scanner (Affymetrix INC.).

data_processing: Background subtracted data obtained from log2 of processed signal (Cy5/cy3) were global normalized by BioDiscovery ImaGene ver. 4.2 and the open source R software package.

organism: Candidatus Phytoplasma asteris

source_name: Phytoplasma grown in garland chrysanthemum

label_protocol: 10 µg of total RNA were used for cDNA synthesis, and labeled with RNA Fluorescence Labeling Core Kit （M-MLV Version） Ver.2.0 (TaKaRa) following manufacturer's instructions

growth_protocol: Phytoplasma asteris OY strain (OY-M) was maintained in garland chrysanthemum (Chrysanthemum coronarium), using the leafhopper vector Macrosteles striifrons.

extract_protocol: Total RNA was extracted using Isogen following manufacturer's instructions

tag: phytoplasma growth

source_name: Phytoplasma grown in leafhopper

value: Phytoplasma grown in leafhopper


title: Plant_vs_Insect-rep5

description:
Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers; Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris.
Phytoplasma grown in plant vs  Phytoplasma grown in insect Replicate 5

value: Phytoplasma grown in garland chrysanthemum


title: Plant_vs_Insect-rep3

description:
Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers; Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris.
Phytoplasma grown in plant vs  Phytoplasma grown in insect Replicate 3


title: Primary TNBC (BT8) xenograft_CTRL miR_4

source_name: Primary TNBC (BT8) xenograft_CTRL miR

value: doxycycline-inducible lentiviral vector expressing a CTRL miR


title: Plant_vs_Insect-rep4

description:
Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers; Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris.
Phytoplasma grown in plant vs  Phytoplasma grown in insect Replicate 4


title: OB rep2

description: OB, replicate 2

source_name: OB, replicate 2

value: OB

value: OB KO

tag: genetic background


title: OB rep1

description: OB, replicate 1

source_name: OB, replicate 1


title: Plant_vs_Insect-rep2

description:
Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers; Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris.
Phytoplasma grown in plant vs  Phytoplasma grown in insect Replicate 2


title: DKO rep3

description: DKO, replicate 3

source_name: DKO, replicate 3

value: DKO

value: OB PPARg2 double KO


title: A3 II.2

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Hybridized to Affymetrix SNP 6.0

hyb_protocol: According to standard manufacturer protocol (Affymetrix).

scan_protocol: The arrays were  washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Affymetrix GeneChip Command Console software was used for image processing and CEL files were processed by Affymetrix GTC using the BRLMM-P-Plus algorithm and regional GC correction configuration for Copy Number/LOH analysis. The HapMap270 file supplied by Affymetrix was used as the reference.

source_name: Whole blood

extract_protocol: Genomic DNA was extracted from whole blood using the QIAgen DNA Blood Midi Kit. DNA quality and quantity were assessed using a Nanodrop Spectophotometer and Agilent BioAnalyzer.

tag: sibling phenotype

value: affected


title: A3 II.10

description: Hybridized to Affymetrix SNP 6.0

label_protocol: According to standard manufacturer protocol (Affymetrix).

value: unaffected (healthy)


title: A2 II.1

description: Hybridized to Affymetrix SNP 6.0


title: A2 II.2

description: Hybridized to Affymetrix SNP 6.0


title: A2 I.2

description: Hybridized to Affymetrix SNP 6.0


title: OB rep3

description: OB, replicate 3

source_name: OB, replicate 3


title: Primary TNBC (BT8) xenograft_CTRL miR_2

value: Primary triple-negative breast cancer (BT8)

value: tumor developed in recipient mice


title: A3 I.1

description: Hybridized to Affymetrix SNP 6.0


title: A1 I.1

description: Hybridized to Affymetrix SNP 6.0


title: CE3

description: Hybridized to Affymetrix SNP 6.0


title: Primary TNBC (BT8) xenograft_CTRL miR_3


title: A2 II.4

description: Hybridized to Affymetrix SNP 6.0


title: Phytoplasma grown in insect Replicate 3

description: Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris

hyb_protocol: Labeled cDNA was hybridized with the microarrays by IntelliGene chip system (TaKaRa BIO INC.) according to manufacturer's instructions. Hibridization temparature was 65°C.

scan_protocol: The slides were scanned with a Microarray Scanner (Agilent Technologies) at a resolution of 5 µm, and extraction and image analysis software (Feature Extraction, ver. 9.5.3.1; Agilent Technologies) was used to integrate the intensity of each spot.

data_processing: Background subtracted data were re-scaled by global normalisation method with subtraction of the 10% highest and lowest signal intensities.

source_name: Phytoplasma grown in insect

tag: infection

value: Phytoplasma asteris OY strain

tag: host

value: insect (Macrosteles striifrons)


title: P1 II.1

description: Hybridized to Affymetrix SNP 6.0


title: P1 I.2

description: Hybridized to Affymetrix SNP 6.0


title: A1 I.2

description: Hybridized to Affymetrix SNP 6.0


title: DKO rep2

description: DKO, replicate 2

source_name: DKO, replicate 2

value: pancreatic islet


title: CE4 II.1

description: Hybridized to Affymetrix SNP 6.0


title: A1 II.1

description: Hybridized to Affymetrix SNP 6.0


title: Phytoplasma grown in insect Replicate 1


title: Phytoplasma grown in plant Replicate 4

description: Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers.

source_name: Phytoplasma grown in plant

value: Phytoplasma asteris OY strain (inoculation with phytoplasma-infected leafhoppers)

value: plant (Chrysanthemum coronarium)


title: Primary TNBC (BT8) xenograft_Parental_2

source_name: Primary TNBC (BT8) xenograft_Parental

tag: xenografted cells


title: Phytoplasma grown in plant Replicate 2


title: Plant_vs_Insect-rep1

description:
Total RNA from 1 month-old plant after inoculation with phytoplasma-infected leafhoppers; Total RNA from thirty-day-old leafhoppers carrying Phytoplasma asteris.
Phytoplasma grown in plant vs  Phytoplasma grown in insect Replicate 1


title: Phytoplasma grown in insect Replicate 2


title: Phytoplasma grown in plant Replicate 3


title: Phytoplasma grown in plant Replicate 1


title: A3 I.2

description: Hybridized to Affymetrix SNP 6.0


title: Primary TNBC (BT8) xenograft_CTRL miR_1

tag: transduced with


title: Primary TNBC (BT8) xenograft_Parental_1

tag: tissue isolated


title: P1 I.1

description: Hybridized to Affymetrix SNP 6.0


title: A1 II.2

description: Hybridized to Affymetrix SNP 6.0


title: DKO rep1

description: DKO, replicate 1

source_name: DKO, replicate 1


title: A2 II.3

description: Hybridized to Affymetrix SNP 6.0


title: P12(delta)modC5 replicate 2

city: St Lucia

first: Jason

last: Steen

address: Carmody Road

department: IMB

country: Australia

institute: University of Queensland

description: US22502591_252959710001_S01_GE1-v5_95_Feb07_2_1.txt

hyb_protocol: Arrays were hybridised in accordance with the Agilent single colour gene expression handbook

scan_protocol: Arrays were scanned on an Agilent G2565BA scanner with setting in accordance with the manufacurers directions

data_processing: Features were extracted using Agilent Feature Extraction V9.5. Analysis was preformed using LIMMA as follows. Background correction was applied, spots from duplicate probes were averaged and log transformed. Between-array quantile normalization was then applied to the log transformed spot intensities. A moderated t-test on the normalized log intensities was performed to identify differentially expressed genes and the False Discovery Rate (FDR) used to control for multiple testing.

organism: Helicobacter pylori P12

source_name: Liquid Culture

label_protocol: Reverse transcription reactions were performed in 40 ul volumes, containing 10 µg total RNA, 300 ng random hexamers, 0.5mM dNTPs and 300 U SuperScript III Reverse Transcriptase (Invitrogen) at 42ºC for 2.5 h. RNA contamination was removed from the cDNA by the addition of NaOH followed by column purification (Qiagen minElute, Qiagen). A total of 1 µg of purified cDNA was labeled using KREAtech Cy3-ULS (KREAtech, The Netherlands).

growth_protocol: H. pylori strains were routinely grown from glycerol stocks for 2 days on GC agar (Oxoid, Basingstoke, UK) plates supplemented with 10% (v/v) horse serum (Invitrogen Corp, Carlsbad, CA), vitamin mix and antibiotics (nystatin, 20 ug/ml; trimethoprim, 2.5 ug/ml; vancomycin, 10 ug/ml) in a microaerobic atmosphere

extract_protocol: Triplicate cultures of H.pylori strain wild-type P12modC5 ON and P12(delta)modC5 mutant, were grown to exponential phase (optical density at 550 nm = 0.9) in BHI broth (Oxoid) supplemented with 10% (v/v) foetal bovine serum (Invitrogen), vitamin mix and vancomycin. Bacterial cells were stabilised using RNAprotect Bacteria Reagent (Qiagen) prior to RNA extraction and approximately 50 µg of total RNA was prepared from each sample using the RNeasy Maxi Kit according to the manufacturer's instructions (Qiagen). The integrity and concentration of RNA was determined via micro-fluidic analysis on a bio-analyser (Agilent Technologies).

tag: genotype/variation

value: modC5 Knockout


title: CE2

description: Hybridized to Affymetrix SNP 6.0


title: Phytoplasma grown in insect Replicate 4


title: A2 II.5

description: Hybridized to Affymetrix SNP 6.0


title: A2 I.1

description: Hybridized to Affymetrix SNP 6.0


title: P12(delta)modC5 replicate 1

description: US22502591_252959710001_S01_GE1-v5_95_Feb07_1_4.txt


title: CE1

description: Hybridized to Affymetrix SNP 6.0


title: Wild Type P12 Replicate 2

description: US22502591_252959710001_S01_GE1-v5_95_Feb07_1_2.txt

value: modC5 ON


title: Wild Type P12 Replicate 3

description: US22502591_252959710001_S01_GE1-v5_95_Feb07_1_3.txt


title: Whole worm_control vs Dox-treated_rep1_lowpmt

city: St. Louis

first: Michael

last: Heinz

state: MO

address: 4320 Forest Park Blvd.

department: Genetics

institute: Washington University School of Medicine

hyb_protocol: Each sample pair (~18ul) is resuspended in Formamide-based  hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and Rnase/Dnase-free water (6ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 900MPX kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere)  (26ul), and Rnase/Dnase-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 4 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degradation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence.  Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low pmt setting scan is also performed to recover signal from saturated elements.  Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of Red median signal/Green median signal. ScanArray v3.0 (Perkin Elmer) software was used.

organism: Brugia malayi

label_protocol: First strand cDNA is generated by random primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900MPX  kit (Genisphere).  For cDNA synthesis, 2x mass of random primer (4ul) is added to 2ug of total RNA, and the solution is incubated at 80C for 10 minutes, then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul).  The cDNA is cleaned using MinElute PCR Purification columns (Qiagen).  Water is added (6.5ul) to the eluted cDNA (10ul), heated to 80C for 10 minutes, then cooled on ice for 2 minutes.  The cDNA is poly-T tailed by adding 10x Tailing buffer (2.5ul), 10mM dTTP (4ul), and Terminal Deoxynucleotidyl Transferase (2ul).  The reaction is incubated at 37C for 30 minutes.  The reaction is terminated by heating to 95C for 10minutes, then cooled on ice for 2 minutes.  Fluorophore/dendrimer specific oligos are then ligated to the appropriate cDNAs by adding 6X Ligation Mix (cy3 or cy5 specific) (5ul) and T4 DNA Ligase (2ul).  The reactions are incubated at room temperature for 30 minutes.  The ligation reaction is terminated by adding 0.5M EDTA and then vortexing for 10 seconds.  The cDNA is again cleaned using MinElute PCR Purification columns (Qiagen).  The cDNAs are quantitated via spectrophotometry to confirm recovery.  Samples are paired and balanced by mass.

growth_protocol: Mongolian gerbils were infected subcutaneously with Brugia malayi L3 larvae and adult worms were recovered after 180 days post infection.

extract_protocol: Total RNA was isolated from two groups of 15 female B. malayi worms using the Trizol (Invitrogen Corporation, Carlsbad, CA) extraction method, following the manufacturer’s protocol with some modifications. RNA was treated with RNAse-free DNAse I (Ambion/Applied Biosystems). Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. The quality of total RNA was determined by an Agilent 2100 bioanalyzer (Agilent Technologies)

treatment_protocol: Subcutaneously infected Mongolian gerbils were untreated.

tag: gender

value: female

tag: developmental stage

value: mature adult

source_name: whole worm (somatic,reproductive,embryonic tissue) treated with Doxy

treatment_protocol: Subcutaneously infected Mongolian gerbils were  treated  orally for 6 wks. with  doxycycline (100 mg/kg).


title: Whole worm_control vs Dox-treated_rep2_lowpmt

source_name: whole worm (somatic,reproductive,embryonic tissue)


title: Whole worm_control vs Dox-treated_rep2_dye-flip

treatment_protocol: Subcutaneously infected Mongolian gerbils were  treated  orally for 6 wks. at approximately 140 days post infection with  doxycycline (100 mg/kg).


title: Wild Type P12 Replicate 1

description: US22502591_252959710001_S01_GE1-v5_95_Feb07_1_1.txt


title: Onion_Bulb_Wellington_Pre_sprouting_Curing_temp_20_rep_3

status: Public on Jan 15 2012

city: Crawley

first: John

last: Hammond

state: WA

address: 35 Stirling Highway

department: School of Plant Biology

institute: University of Western Australia

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a custom Agilent 8 x 15k Onion array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and eXtended Dynamic range mode active, with Green PMT set to 100% for XDR Hi and 10% for XDR Lo).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 023780_D_F_20090803) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
gProcessedSignal values within arrays were subjected to quantile normalisation Normalized signal values for individual probes were standardized to the median signal value for the probe across all arrays. Values are the log2 normalized signal values.

organism: Allium cepa

source_name: Onion bulb from cultivar Wellington, cold storage, pre sprouting, cured at 20°C, rep 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick AMp Labelling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Onion seeds for cultivars ‘Wellington’ (brown, long-storing) and ‘Sherpa’ (brown, average-storing) were drilled on sandy clay loam (Alistair Findlay’s, Cardington, Beds., UK; 1.2 x 0.3 ha) on 5 March 2008 at a rate of 57 seeds m-2 with pesticides applied as per commercial practice, although remained MH-free. Plants were machine-harvested at 100% fall-down on 17 September 2008. Onion bulbs were stored in 72 large net bags (approx. 60 bulbs) and 24 half net bags (approx. 30 bulbs) buried amongst loose bulbs in one tonne wooden crates for batch curing at the Sutton Bridge Crop Storage Research (Lincs., UK).

extract_protocol: For each treatment and timepoint, four bulbs were selected and two longitudinal wedges for each bulb were cut and snap-frozen in liquid nitrogen and stored at -80°C for RNA extraction. Total RNA was isolated according to Chang et al. (1993) with modifications. Total RNA was extracted from frozen, ground onion tissue (100 mg) homogenised in 1 mL extraction buffer (2% (w/v) CTAB (cetyl trimethylammonium bromide), 0.8 M NaCl, 20 mM Na2EDTA, 0.2 M boric acid, adjusted to pH 7.6 with TRIZMA base, β-mercaptoethanol added to 1% (v/v) just prior to use) using a pestle and mortar. The mixture was transferred to a 2 mL microtube and incubated at 65ºC for 10 min, then allowed to return to room temperature. Chloroform (1 mL) was added and mixed before being centrifuged at 16.2 g for 5 min at room temperature. The aqueous phase was removed to a clean tube and an equal volume of precipitation buffer (0.5% (w/v) CTAB, 50 mM Na2EDTA, 50 mM MES (2-(N-morpholino) ethanesulfonic acid), adjusted to pH 5.8 with NaOH, and filtered through a 0.2 μM sterile filter), mixed and incubated on ice for 30 min. Samples were centrifuged at 13 000 rpm for 20 min at 4ºC and the supernatant removed. The pellet was resuspended in SSTE (1.0 M NaCl, 0.5% SDS, 10 mM TrisHCl (pH 8.0), 1 mM Na2EDTA (pH 8.0)) and briefly incubated at 37ºC, before being allowed to return to room temperature. Chloroform (1 mL) was added and mixed, before being centrifuged at 13 000 rpm for 5 min at room temperature. The aqueous phase was removed to a clean tube and an equal volume of isopropanol added and incubated on ice for 20 min. Samples were centrifuged at 13 000 rpm for 20 min at 4ºC and the supernatant removed. The pellet containing total nucleic acid was washed with 1 mL 70% (v/v) ethanol, then left to air dry and finally resuspended in 50 μL DEPC-treated water. Then, 30 μL 8 M lithium chloride solution was added and the samples incubated on ice overnight to selectively precipitate RNA. Samples were centrifuged for at 16.2 g for 30 min at 4ºC, the supernatant was removed, the pellet washed with 0.5 mL 70% ethanol and resuspended in 15 µL RNase-free water. Sample purity and integrity were verified using the RNA 6000 Nano Assay on the Agilent 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA) and then treated with Baseline Zero DNase (Epicentre, Madison, WI, USA) according to the supplier’s instructions.

treatment_protocol: Bulbs were artificially cured at either 20 or 28°C for 6 weeks as per normal commercial practice in the UK with relative humidity controlled at 65 – 75%. After curing samples were stored at 1°C in cold storage. Samples were taken at harvest, post curing, and pre and post-sprouting whilst in cold storage.

tag: subspecies

value: Allium cepa L.

tag: curing temperature (°c)

tag: time

value: cold storage, pre sprouting


title: Whole worm_control vs Dox-treated_rep1_dye-flip_lowpmt


title: Whole worm_control vs Dox-treated_rep2

description: Whole worm_control vs Dox-treated_rep2


title: Onion_Bulb_Wellington_Pre_sprouting_Curing_temp_20_rep_2

source_name: Onion bulb from cultivar Wellington, cold storage, pre sprouting, cured at 20°C, rep 2


title: Onion_Bulb_Wellington_Pre_sprouting_Curing_temp_28_rep_2

source_name: Onion bulb from cultivar Wellington, cold storage, pre sprouting, cured at 28°C, rep 2


title: Whole worm_control vs Dox-treated_rep1_dye-flip


title: Onion_Bulb_Wellington_Pre_sprouting_Curing_temp_28_rep_3

source_name: Onion bulb from cultivar Wellington, cold storage, pre sprouting, cured at 28°C, rep 3


title: Onion_Bulb_Wellington_Pre_sprouting_Curing_temp_28_rep_1

source_name: Onion bulb from cultivar Wellington, cold storage, pre sprouting, cured at 28°C, rep 1


title: Whole worm_control vs Dox-treated_rep2_dye-flip_lowpmt


title: Onion_Bulb_Sherpa_Pre_sprouting_Curing_temp_28_rep_2

source_name: Onion bulb from cultivar Sherpa, cold storage, pre sprouting, cured at 28°C, rep 2


title: Onion_Bulb_Wellington_Pre_sprouting_Curing_temp_20_rep_1

source_name: Onion bulb from cultivar Wellington, cold storage, pre sprouting, cured at 20°C, rep 1


title: P12(delta)modC5 replicate 3

description: US22502591_252959710001_S01_GE1-v5_95_Feb07_2_2.txt


title: Whole worm_control vs Dox-treated_rep1

description: Whole worm_control vs Dox-treated_rep1


title: Onion_Bulb_Sherpa_Pre_sprouting_Curing_temp_20_rep_3

source_name: Onion bulb from cultivar Sherpa, cold storage, pre sprouting, cured at 20°C, rep 3


title: Onion_Bulb_Sherpa_Pre_sprouting_Curing_temp_20_rep_2

source_name: Onion bulb from cultivar Sherpa, cold storage, pre sprouting, cured at 20°C, rep 2


title: Onion_Bulb_Wellington_sprouting_Curing_temp_28_rep_2

source_name: Onion bulb from cultivar Wellington, cold storage, sprouting, cured at 28°C, rep 2

value: cold storage, sprouting


title: Onion_Bulb_Sherpa_Pre_sprouting_Curing_temp_28_rep_1

source_name: Onion bulb from cultivar Sherpa, cold storage, pre sprouting, cured at 28°C, rep 1


title: Onion_Bulb_Sherpa_Pre_sprouting_Curing_temp_20_rep_1

source_name: Onion bulb from cultivar Sherpa, cold storage, pre sprouting, cured at 20°C, rep 1


title: Onion_Bulb_Sherpa_Pre_sprouting_Curing_temp_28_rep_3

source_name: Onion bulb from cultivar Sherpa, cold storage, pre sprouting, cured at 28°C, rep 3


title: Onion_Bulb_Wellington_sprouting_Curing_temp_28_rep_3

source_name: Onion bulb from cultivar Wellington, cold storage, sprouting, cured at 28°C, rep 3


title: Onion_Bulb_Wellington_sprouting_Curing_temp_20_rep_3

source_name: Onion bulb from cultivar Wellington, cold storage, sprouting, cured at 20°C, rep 3


title: Onion_Bulb_Sherpa_sprouting_Curing_temp_28_rep_1

source_name: Onion bulb from cultivar Sherpa, cold storage, sprouting, cured at 28°C, rep 1


title: Onion_Bulb_Wellington_sprouting_Curing_temp_20_rep_2

source_name: Onion bulb from cultivar Wellington, cold storage, sprouting, cured at 20°C, rep 2


title: Onion_Bulb_Sherpa_sprouting_Curing_temp_20_rep_3

source_name: Onion bulb from cultivar Sherpa, cold storage, sprouting, cured at 20°C, rep 3


title: Onion_Bulb_Wellington_sprouting_Curing_temp_20_rep_1

source_name: Onion bulb from cultivar Wellington, cold storage, sprouting, cured at 20°C, rep 1


title: Onion_Bulb_Wellington_Post_curing_Curing_temp_28_rep_3

source_name: Onion bulb from cultivar Wellington, post curing at 28°C, rep 3

value: post curing


title: Onion_Bulb_Sherpa_sprouting_Curing_temp_28_rep_3

source_name: Onion bulb from cultivar Sherpa, cold storage, sprouting, cured at 28°C, rep 3


title: Onion_Bulb_Sherpa_sprouting_Curing_temp_28_rep_2

source_name: Onion bulb from cultivar Sherpa, cold storage, sprouting, cured at 28°C, rep 2


title: Onion_Bulb_Wellington_Post_curing_Curing_temp_20_rep_3

source_name: Onion bulb from cultivar Wellington, post curing at 20°C, rep 3


title: Onion_Bulb_Sherpa_sprouting_Curing_temp_20_rep_2

source_name: Onion bulb from cultivar Sherpa, cold storage, sprouting, cured at 20°C, rep 2


title: Onion_Bulb_Sherpa_sprouting_Curing_temp_20_rep_1

source_name: Onion bulb from cultivar Sherpa, cold storage, sprouting, cured at 20°C, rep 1


title: Onion_Bulb_Wellington_Post_curing_Curing_temp_28_rep_2

source_name: Onion bulb from cultivar Wellington, post curing at 28°C, rep 2


title: Onion_Bulb_Sherpa_Post_curing_Curing_temp_28_rep_2

source_name: Onion bulb from cultivar Sherpa, post curing at 28°C, rep 2


title: Onion_Bulb_Sherpa_Post_curing_Curing_temp_28_rep_1

source_name: Onion bulb from cultivar Sherpa, post curing at 28°C, rep 1


title: Onion_Bulb_Wellington_Post_curing_Curing_temp_28_rep_1

source_name: Onion bulb from cultivar Wellington, post curing at 28°C, rep 1


title: Onion_Bulb_Sherpa_Post_curing_Curing_temp_28_rep_3

source_name: Onion bulb from cultivar Sherpa, post curing at 28°C, rep 3


title: Onion_Bulb_Sherpa_Post_curing_Curing_temp_20_rep_3

source_name: Onion bulb from cultivar Sherpa, post curing at 20°C, rep 3


title: Onion_Bulb_Sherpa_Post_curing_Curing_temp_20_rep_2

source_name: Onion bulb from cultivar Sherpa, post curing at 20°C, rep 2


title: Onion_Bulb_Wellington_Post_curing_Curing_temp_20_rep_1

source_name: Onion bulb from cultivar Wellington, post curing at 20°C, rep 1


title: L.monocytogenes (mono culture) in broth after 24 hrs of incubation

city: Agra

first: Prem Saran

last: Tirumalai

state: Uttar Pradesh

address: Dayalbagh

department: Faculty of Science

country: India

institute: Dayalbagh Educational Institute

description: Sample 6A

hyb_protocol: 600 ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent Technologies G2505C scanner and Images were quantified using Agilent Feature Extraction Software 10.5.1.1

data_processing: The normalization was done using GeneSpring GX 11 Software.

organism: Listeria monocytogenes J0161

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then  the samples  were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Overnight cultures were used for inoculation. For broth 1ml (each) of the overnight cultures were inoculated to freshly prepared Tryptone Soy Broth in a tube and incubated at 37 C for the required period of time intervals. For biofilm 1ml (each ) of the overnight cultures were inoculated into freshly prepared Tryptone Soy Broth in a Petridish. Glass slide was immeresed in the broth in the petridish and incubated at 37 C for the required period of time.

extract_protocol: Extraction was done using standard protocol of RiboPure Bacterial RNA extraction method (Ambion - AM 1925)

treatment_protocol: Cells from the broth were pelleted directly. For cells from biofilm the slides immeresed in the petridish were removed of excess media, cells from the slide (biofilm) were scrapped using scalpe to microfuge tubes and pelleted there after. Cells pelleted were stored in RNA later (Ambion) till extraction.

tag: growth state

value: Broth, Mono-culture

tag: incubation hours

value: 24 hrs


title: Onion_Bulb_Sherpa_Harvest_rep_2

source_name: Onion bulb from cultivar Sherpa, freshly harvested, rep 2

value: Pre-curing

value: freshly harvested


title: Onion_Bulb_Sherpa_Harvest_rep_1

source_name: Onion bulb from cultivar Sherpa, freshly harvested, rep 1


title: Onion_Bulb_Sherpa_Harvest_rep_3

source_name: Onion bulb from cultivar Sherpa, freshly harvested, rep 3


title: Onion_Bulb_Wellington_Harvest_rep_1

source_name: Onion bulb from cultivar Wellington, freshly harvested, rep 1


title: L.monocytogenes (mono culture) in biofilm after 24 hrs of incubation

description: Sample 3A

value: Biofilm, Mono-culture


title: Onion_Bulb_Wellington_Harvest_rep_2

source_name: Onion bulb from cultivar Wellington, freshly harvested, rep 2


title: Onion_Bulb_Wellington_Harvest_rep_3

source_name: Onion bulb from cultivar Wellington, freshly harvested, rep 3


title: L.monocytogenes (mono culture) in biofilm after 12 hrs of incubation

description: Sample 2A

value: 12 hrs


title: Onion_Bulb_Sherpa_Post_curing_Curing_temp_20_rep_1

source_name: Onion bulb from cultivar Sherpa, post curing at 20°C, rep 1


title: Onion_Bulb_Wellington_sprouting_Curing_temp_28_rep_1

source_name: Onion bulb from cultivar Wellington, cold storage, sprouting, cured at 28°C, rep 1


title: L.monocytogenes (mono culture) in biofilm after 4 hrs of incubation

description: Sample 1A

value: 4 hrs


title: L.monocytogenes in broth with B.subtilis after 4 hrs of incubation

description: Sample 1

value: Broth, co-culture


title: L.monocytogenes in broth with B.subtilis after 24 hrs of incubation

description: Sample 7


title: R_solanacearum_GMI1000_28C_Inplanta_rep4

city: Madison

first: Lavanya

last: Babujee

address: Department of Plant Pathology

institute: UW-Madison

hyb_protocol: Hybridization was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA) following Nimblegen's standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249),  without background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Ralstonia pseudosolanacearum GMI1000

source_name: Ralstonia solanacearum GMI1000, Inplanta, 28 C

label_protocol: Labeling was performed following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Ralstonia solanacearum strain GMI1000 was grown to mid-log phase (~6x108 cfu ml-1) at 28 °C or in 20 °C  in rich CPG medium or harvested from plants showing early symptoms of wilt with stems colonization of 1x108 cfu g-1 to1x109 cfu g-1.

extract_protocol: Total RNA was extracted using the hot-phenol method (Jahn et al 2008) followed by 4 DNA digestion steps. RNA  concentration and quality was assessed using Nanodrop and Agilent 2100 bioanalyzer (Bioanalyzer is not accurate for measuring concentration) at the Gene expression Center (University of Wisconsin-Madison, Madison, WI USA).

tag: genotype

value: Wild Type


title: R_solanacearum_GMI1000_28C_Inplanta_rep3


title: R_solanacearum_GMI1000_28C_Inplanta_rep1


title: L.monocytogenes in biofilm with B.subtilis after 24 hrs of incubation

description: Sample 4A

value: Biofilm, co-culture


title: L.monocytogenes in broth with B.subtilis after 12 hrs of incubation

description: Sample 4


title: R_solanacearum_GMI1000_20C_Inplanta_rep4

source_name: Ralstonia solanacearum GMI1000, Inplanta, 20 C


title: miR-371-372-373-HepG2 vs. mock-HepG2 biological repeat 1

city: Beijing

first: Hongyan

last: Guo

address: Chengfu

department: School of Medcine

country: China

institute: Tsinghua University

description: This entry represents two dye-swap slides.

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

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were maintained in minimal essential medium, supplemented with 1mM sodium pyruvate, nonessential amino acids, 2mM glutamine, 25μg/ml gentamicin, 100U/ml penicillin, 100U/ml streptomycin and 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. RQ1 RNase-Free DNase (Promega) was then used to digest the contaminat genomic DNA and Nucleospin RNA Clean-up kit (Machery-Nagel, Germany) was used to purify the digested RNA.

treatment_protocol: To generate stable cell populations, 2x106 HepG2 cells were transfected with 10μg of pcDNA3.1/miR-371-372-373 or pcDNA3.1 empty vector by the calcium phosphate method. After 48h, the transfected cells were passaged at 1:5 and maintained in 1mg/ml G418 selective medium for at least two weeks. The overexpression of mature miRNAs were verified by the quantative RT-PCR.

tag: cell line

value: HepG2 cells that stably integrate pcDNA3.1 empty vector

value: HepG2 Cells that stably integrate pcDNA3.1/miR-371-372-373 vector


title: R_solanacearum_GMI1000_20C_Inplanta_rep3


title: miR-371-372-373-HepG2 vs. mock-HepG2 biological repeat 2


title: R_solanacearum_GMI1000_20C_Inplanta_rep1


title: Gonadipose_t5_Adlib_a8

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

description: Ad libitum fed dog gene expression data from gonadal adipose tissure at 24 weeks

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine 2.0  Genome Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages.

organism: Canis lupus familiaris

source_name: Gonadal adipose tissue at 24 weeks

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

growth_protocol: Dogs were fed ad libitum (n=5) or to maintain baseline body weight (control; n=4).

extract_protocol: Total RNA was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were randomized to either ad libitum (n=5) or body weight maintenance (n=4) feeding.  All dogs were fed Purina® Pro Plan® Performance Formula.  All subcutaneous and visceral adipose samples were collected after an overnight fasting period.

tag: breed

value: Beagle

tag: age

value: 4 yr-old

tag: animal id

tag: tissue

value: Gonadal adipose

tag: time point

value: 24 weeks

tag: treatment

value: Ad libitum


title: R_solanacearum_GMI1000_28C_CPG_rep4

source_name: Ralstonia solanacearum GMI1000, CPG, 28 C


title: Gonadipose_t5_Con_a9

description: Control dog gene expression data from gonadal adipose tissure at 24 weeks

value: Control


title: R_solanacearum_GMI1000_28C_Inplanta_rep2


title: R_solanacearum_GMI1000_28C_CPG_rep3


title: Onion_Bulb_Wellington_Post_curing_Curing_temp_20_rep_2

source_name: Onion bulb from cultivar Wellington, post curing at 20°C, rep 2

value: Allium cepa L.

value: post curing


title: R_solanacearum_GMI1000_20C_Inplanta_rep2


title: R_solanacearum_GMI1000_28C_CPG_rep1


title: R_solanacearum_GMI1000_28C_CPG_rep2


title: R_solanacearum_GMI1000_20C_CPG_rep4

source_name: Ralstonia solanacearum GMI1000, CPG, 20 C


title: Gonadipose_t5_Adlib_a7


title: R_solanacearum_GMI1000_20C_CPG_rep3


title: R_solanacearum_GMI1000_20C_CPG_rep2


title: R_solanacearum_GMI1000_20C_CPG_rep1


title: Gonadipose_t5_Adlib_a6


title: Gonadipose_t5_Con_a3


title: Gonadipose_t5_Adlib_a5


title: Gonadipose_t5_Adlib_a2


title: Gonadipose_t5_Con_a4


title: R_solanacearum_UW551_28C_Inplanta_rep4

organism: Ralstonia solanacearum UW551

source_name: Ralstonia solanacearum UW551, Inplanta, 28 C

growth_protocol: Ralstonia solanacearum strain UW551 was grown to mid-log phase (~6x108 cfu ml-1) at 28 °C or in 20 °C  in rich CPG medium or harvested from plants showing early symptoms of wilt with stems colonization of 1x108 cfu g-1 to1x109 cfu g-1.


title: Gonadipose_t5_Con_a1


title: R_solanacearum_UW551_28C_Inplanta_rep3


title: R_solanacearum_UW551_28C_Inplanta_rep2


title: Sqadipose_t5_Adlib_a8-1

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593171 (RMA data differs))

source_name: Subcutaneous adipose tissue at 24 weeks

value: subcutaneous adipose


title: Sqadipose_t5_Con_a9-1

description: Control dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593168 (RMA data differs))


title: R_solanacearum_UW551_28C_Inplanta_rep1


title: Sqadipose_t5_Adlib_a7-1

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593172 (RMA data differs))


title: Sqadipose_t5_Adlib_a6-1

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593173 (RMA data differs))


title: R_solanacearum_UW551_20C_Inplanta_rep4

source_name: Ralstonia solanacearum UW551, Inplanta, 20 C


title: ATCC 31479 curdlan vs. no curdlan rep4

city: Albuquerque

first: Anne

middle: M

last: Ruffing

state: NM

department: Bioenergy and Defense Technologies

institute: Sandia National Laboratories

scan_protocol: A microarray scanner model G2505B from Agilent Technologies was employed for microarray imaging, and Agilent's Feature Extraction 10.5 Image Analysis Software was used to measure the signal intensities.

data_processing: Using the Agilent feature extraction software, the mean local background signal intensity was subtracted from the mean signal intensity for each individual spot on the microarray. The background-subtracted signals were then normalized using a lowess normalization to account for any dye-labeling bias. The lowess-normalized data was uploaded into GeneSpring GX 10 for additional processing, and a 75th percentile normalization was applied. The normalized data was then analyzed for statistically significant changes in gene expression using a paired T-test with a p-value cutoff of 0.05.

organism: Agrobacterium sp. 31749

source_name: ATCC 31749, curdlan, stationary phase, 100h

label_protocol: The RNA was converted to cDNA and labeled with either Cy-3 or Cy-5 using the Fairplay III Microarray Labeling kit from Agilent. This step was performed by Gene Logic, Inc.

growth_protocol: ATCC 31749 colonies were inoculated into test tubes containing 4 mL of LB media and grown overnight at 30°C with 250 rpm. The culture was used to inoculate a flask of 150 mL LB media (1500x dilution). After 17 hours of growth, the cells were concentrated by centrifugation (3000 x g, 10 min, 4°C), reducing the liquid volume from to 30 mL. The concentrated culture was added to 450 mL of the minimal fermentation media. The minimal fermentation media was described previously with 1.4 g/L of KH2PO4 (Kim MK, et al. (2000) Residual phosphate concentration under nitrogen-limiting conditions regulates curdlan production in Agrobacterium species. Journal of Industrial Microbiology & Biotechnology 25:180-183). NaOH and HCl (1 M) solutions were used for pH control. A Multifors fermenter system from Infors was employed for fermentation with four parallel 500 mL fermentation vessels. Agitation was set at 600 rpm with 1 vvm for the air flowrate, and the pH was controlled at pH 7 for growth.

extract_protocol: The RNA was immediately stabilized using Qiagen’s RNAprotect Bacteria Reagent and stored at -80°C for no longer than 2 weeks prior to RNA isolation. RNA was isolated using Qiagen’s RNeasy mini kit with on-column DNase digestion using the RNase-free DNase set (15 mg/mL lysozyme, 15 min for lysis). For samples containing high levels of curdlan, the volumes of lysozyme solution, RLT buffer, and ethanol were doubled, and a centrifugation step (5,000 x g for 5 min at 10°C) was added after the addition of RLT buffer. Contaminating genomic DNA was removed using Ambion’s DNA-free kit.

tag: growth phase

value: stationary phase, 100h

tag: state

value: curdlan

source_name: ATCC 31479, no curdlan, exponential growth, 22h

value: no curdlan


title: R_solanacearum_UW551_20C_Inplanta_rep3


title: Sqadipose_t5_Adlib_a5-1

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593170 (RMA data differs))


title: Sqadipose_t5_Con_a4-1

description: Control dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593167 (RMA data differs))


title: ATCC 31479 curdlan vs. no curdlan rep3

hyb_protocol: This step was performed by Gene Logic, Inc.


title: ATCC 31479 curdlan vs. no curdlan rep2

value: exponential growth, 22h


title: ATCC 31479 curdlan vs. no curdlan rep1


title: PeripheralBlood_DBA_Proband_1687 [NG]

city: Little Rock

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

description:
Selected samples for which a deletion was identified by SNP genotyping array were confirmed by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505303A03_DBslide3

hyb_protocol: DNA mixture was hybridized for 72 hours at 42 °C and washed according to standard Nimblegen protocols

scan_protocol: Data were scanned on an Agilent 2micron scanner

data_processing: Featue extraction and normalization was performed with DEVA software (Nimblegen) according to the standard CGH workflow

source_name: gDNA from proband 1687

label_protocol: 500 ng of experimental DNA was labeled with Cy3 and 500 ng of reference DNA male/female (Promega) was labeled with Cy5 using the Nimblegen labeling kit according to manufacturer's instructions

extract_protocol: DNA is extracted from WBC pelleted from peripheral blood  after RBC lysis in 0.15M NH4Cl.  WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen).  DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.

tag: gender

value: Female

value: Peripheral Blood

tag: relationship to proband

value: Proband

source_name: Commercial Reference DNA

value: Male and Female


title: R_solanacearum_UW551_20C_Inplanta_rep2

value: Wild Type


title: PeripheralBlood_DBA_Proband_1382 [NG]

description:
Selected samples for which a deletion was identified by SNP genotyping array were confirmed by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505303A02_DBslide3

source_name: gDNA from proband 1382


title: PeripheralBlood_DBA_Proband_1314 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3H1-1314

hyb_protocol: Standard Illumina Infinium HD protocol

scan_protocol: Standard Illumina scanning protocol on S101 BeadArray reader

data_processing:
Intensity data were extracted in Genome Studio (v2010.3); SNPs with GenTrain score <0.15 were not called.
Gtype:  genotype of this SNP for the sample; Score: GenTrain score indicating how well sample clustered for this locus;  Theta: the allelic intensity ratio; B Allele Freq: B allele frequency calculated as theta value for a SNP corrected for cluster position; Log R ratio: normalized intesity ratio for sample marker relative to values of the surrounding clusters

label: C-Bio; A-DNP

label_protocol: Standard Illumina Infinium HD protocol

tag: dba phenotype

value: DBA


title: PeripheralBlood_DBA_Mother_910 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3H4-0910_Mother

value: Mother

value: Unaffected


title: PeripheralBlood_DBA_Proband_1HOU [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3H6-1HOU


title: PeripheralBlood_DBA_Father_924 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3H3-0924_Father

value: Male

value: Father


title: PeripheralBlood_DBA_Proband_20QL [NG]

description:
Selected samples for which a deletion was identified by SNP genotyping array were confirmed by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505157A03_DBCGH061711

source_name: gDNA from proband 20QL


title: pax_3pdg

city: Munich

first: Divya

last: Mehta

country: Germany

institute: MPI

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Microarray expression analysis was performed in R, using beadarray (providing routines to handle Illumina BeadStudio data) , limma (for statistical routines) and vsn (for normalization) packages. Raw microarray scan files were exported using the Illumina Beadstudio program and loaded into R for downstream analysis. The data were transformed and normalized using the variance stabilizing normalization method. Of the 48804 probes present on the Human HT-12v3, probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01 in the individuals leaving 8203 transcripts after normalization and filtering for analysis. Raw qPCR data from the Roche LightCycler 480 System was extracted and the crossing thresholds (CT) from the technical replicates were averaged across all samples. Transcripts were normalized to housekeeping gene TBP.

source_name: pax

label_protocol: biotin

extract_protocol: PAXgeneTM Blood RNA Kit, TempusTM Spin RNA Isolation Kit

treatment_protocol: orally administration of 1.5 mg dexamethasone (dexamethasone-induced sample)

value: male

value: whole blood

value: dexamethasone induced

tag: blood colletion tube type

value: PAXgene™

tag: globin mrna status

value: globin-mRNA-reduced


title: PeripheralBlood_DBA_Proband_16HQ [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3H5-16HQ


title: PeripheralBlood_DBA_Proband_1504 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3H2-1504


title: PeripheralBlood_DBA_Proband_1FCV [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3G6-1FCV


title: PeripheralBlood_DBA_Proband_1178 [NG]

description:
Selected samples for which a deletion was identified by SNP genotyping array were confirmed by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505157A01_DBCGH061711

source_name: gDNA from proband 1178


title: PeripheralBlood_DBA_Proband_1579 [NG]

description:
Selected samples without a deletion identified by SNP genotyping array were re-tested by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505303A01_DBslide3

source_name: gDNA from proband 1579


title: Sqadipose_t5_Adlib_a2-1

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593169 (RMA data differs))

value: Beagle

value: 4 yr-old

value: subcutaneous adipose

value: 24 weeks

value: Ad libitum


title: PeripheralBlood_DBA_Proband_886 [NG]

description:
Selected samples for which a deletion was identified by SNP genotyping array were confirmed by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505157A02_DBCGH061711

source_name: gDNA from proband 886

value: Female

value: Peripheral Blood

value: Proband

value: Male and Female


title: R_solanacearum_UW551_28C_CPG_rep4

source_name: Ralstonia solanacearum UW551, CPG, 28 C

value: Wild Type


title: R_solanacearum_UW551_28C_CPG_rep3


title: Skmu_24wk_Con_A9

description: Control dog gene expression data from muscle tissue at 24wk

source_name: Skeletal muscle tissue 24 wk control

treatment_protocol: Dogs were randomized to either ad libitum (n=5) or body weight maintenance (n=4) feeding.  All dogs were fed Purina® Pro Plan® Performance Formula.  All muscle samples were collected after an overnight fasting period.

value: Skeletal muscle

value: Control

value: 24 wk


title: R_solanacearum_UW551_20C_Inplanta_rep1


title: pax_3pdn

value: male

value: whole blood

value: non globin-mRNA-reduced


title: PeripheralBlood_DBA_Proband_987 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3G1-987

value: DBA


title: R_solanacearum_UW551_28C_CPG_rep2


title: Skmu_24wk_Adlib_A8

description: Ad libitum fed dog gene expression data from muscle tissue at 24wk

source_name: Skeletal muscle tissue 24 wk adlib

value: Beagle


title: Sqadipose_t5_Con_a3-1

description: Control dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593166 (RMA data differs))

value: 4 yr-old


title: PeripheralBlood_DBA_Mother_396 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3G4-0396_Mother

value: Mother

value: Unaffected


title: PeripheralBlood_DBA_Father_910 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3G5-0910_Father

value: Male

value: Father


title: pax_3pnn

value: baseline

value: PAXgene™


title: tempus_3tdg

source_name: tempus

value: dexamethasone induced

value: Tempus Tube™

value: globin-mRNA-reduced


title: pax_3png


title: R_solanacearum_UW551_28C_CPG_rep1

value: Wild Type


title: R_solanacearum_UW551_20C_CPG_rep4

source_name: Ralstonia solanacearum UW551, CPG, 20 C


title: PeripheralBlood_DBA_Proband_1066 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3G2-1066

value: Peripheral Blood

value: Proband


title: Skmu_24wk_Adlib_A7

value: Skeletal muscle

value: Ad libitum

value: 24 wk


title: Skmu_24wk_Adlib_A5

value: Beagle


title: R_solanacearum_UW551_20C_CPG_rep3


title: PeripheralBlood_DBA_Proband_440 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3F3-0440

value: Female

value: DBA


title: PeripheralBlood_DBA_Proband_910 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3F2-910


title: tempus_3tng

value: male

value: whole blood


title: PeripheralBlood_DBA_Father_418 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3F6-0418_Father

value: Male

value: Father

value: Unaffected


title: tempus_3tdn

value: dexamethasone induced

value: non globin-mRNA-reduced


title: Skmu_24wk_Con_A4

value: 4 yr-old

value: Control


title: R_solanacearum_UW551_20C_CPG_rep2

value: Wild Type


title: Skmu_24wk_Adlib_A6


title: Sqadipose_t5_Con_a1-1

description: Control dog gene expression data from subcutaneous adipose tissure at 24 weeks (this sample previously accessioned in GEO as GSM593165 (RMA data differs))

source_name: Subcutaneous adipose tissue at 24 weeks

value: subcutaneous adipose

value: 24 weeks


title: R_solanacearum_UW551_20C_CPG_rep1


title: Skmu_24wk_Adlib_A2

value: Skeletal muscle

value: Ad libitum


title: pax_2png

value: baseline

value: PAXgene™

value: globin-mRNA-reduced


title: Skmu_24wk_Con_A1

value: Beagle

value: 24 wk


title: pax_2pdn

value: male

value: whole blood


title: PeripheralBlood_DBA_Father_1382 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3E5-1382_Father

value: Male

value: Peripheral Blood

value: Father

value: Unaffected


title: pax_2pnn

value: non globin-mRNA-reduced


title: tempus_2tdg

value: dexamethasone induced

value: Tempus Tube™


title: Skmu_24wk_Con_A3

value: 4 yr-old

value: Control


title: tempus_2tng


title: PeripheralBlood_DBA_Proband_1076 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3F1-1076

value: Proband

value: DBA


title: PeripheralBlood_DBA_Proband_18JN [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3E4-18JN


title: tempus_2tdn


title: tempus_3tnn

value: baseline


title: PeripheralBlood_DBA_Mother_418 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3E6-0418_Mother

value: Female

value: Mother


title: PeripheralBlood_DBA_Proband_1MJK [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3F5-1MJK


title: pax_2pdg

value: PAXgene™

value: globin-mRNA-reduced


title: PeripheralBlood_DBA_Father_396 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3F4-0396_Father


title: tempus_2tnn

value: male

value: whole blood


title: pax_1png


title: PeripheralBlood_DBA_Proband_703 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3E3-0703

value: Male

value: Peripheral Blood


title: pax_1pdn


title: PeripheralBlood_DBA_Mother_1480 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3D5-1480_Mother

value: Unaffected


title: PeripheralBlood_DBA_Proband_20QL [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3D6-20QL


title: PeripheralBlood_DBA_Proband_1514 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3E2-1514


title: PeripheralBlood_DBA_Proband_2012 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3E1-2012


title: pax_1pnn

value: non globin-mRNA-reduced


title: tempus_1tdg

value: dexamethasone induced


title: pax_1pdg


title: PeripheralBlood_DBA_Mother_2302 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2H01-2302_MO


title: PeripheralBlood_DBA_Proband_1480 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3D2-1480


title: tempus_1tng

value: Tempus Tube™


title: PeripheralBlood_DBA_Proband_396 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3D3-0396


title: PeripheralBlood_DBA_Sibling_802 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2G02-802_SIB

value: Sibling


title: PeripheralBlood_DBA_Proband_38 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3C3-0038


title: tempus_1tdn


title: PeripheralBlood_DBA_Father_2302 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2D02-2302_FA

value: Father


title: PeripheralBlood_DBA_Proband_1M9G [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3C4-1M9G

value: Proband


title: PeripheralBlood_DBA_Mother_866 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3C5-866_Mother


title: PeripheralBlood_DBA_Proband_2552 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3D1-2552

value: DBA


title: PeripheralBlood_DBA_Proband_203Y [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3B6-203Y


title: PeripheralBlood_DBA_Proband_886 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2F01-886


title: PeripheralBlood_DBA_Father_1480 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3B5-1480_Father


title: PeripheralBlood_DBA_Proband_1EAC [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3C6-1EAC


title: PeripheralBlood_DBA_Mother_802 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2E02-802_MO


title: tempus_1tnn

value: baseline


title: yolk sac_Baf250_E9.5_replicate 3

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description: Biological replicate 3 of 3

hyb_protocol: Cy-5 labeled cRNA was co-hybridized to Agilent 014868 Whole Mouse Genome Microarrays with equimolar amounts of Cy-3 labeled WMRR-derived cRNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.5.5.1.

data_processing: Data files uploaded into Genespring 11.5.1 using a median value baseline transformation.  Probes found in at least 70 percent of samples in any 1 out of 4 conditions have flags in Present or Marginal were retained for analysis.

source_name: Whole Mouse Reference RNA (WMRR)

label_protocol: 500 ng of WMRR or yolk sac RNA labeled with Cy-3 or Cy-5, respectively (Perkin Elmer) and amplified using the Low Input RNA Amplification Kit (Agilent) as described by the manufacturer.

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen), followed by an RNA cleanup step and on-column DNA digestion using the Rneasy miniprep kit according manufacturers' instructions

treatment_protocol: Tissues were isolated by dissection from E8.5 and 9.5, wild-type and Baf250a/Arid1aV1068G/V1068G yolk sacs

tag: developmental stage

value: neonatal

tag: tissue type

value: whole animal

tag: background strain

value: mixed 129Sv and C57BL/6

tag: genotype/variation

value: wild type

source_name: RNA purified from whole yolk sac, embryonic day 9.5, Baf250HM mouse

value: yolk sac

tag: strain


title: yolk sac_Baf250_E9.5_replicate 2

description: Biological replicate 2 of 3


title: PeripheralBlood_DBA_Proband_1967 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2E01-1967


title: Umblical Cord Blood from LBW newborn [E8]

city: Bangalore

first: Bionivid

last: Technology

address: Bangalore

institute: Bionivid Technology

description: Gene Expression Data from Low Birth Weight Newborn

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 450C on Gene chip H-GU133Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Operating Software (GCOS) including the GeneChip Scanner 3000 High-Resolution Scanning Patch

data_processing: The ratios represent the normalized values obtained from Genespring after the following processing of raw data (cel files): Summarization Algorithm: GCRMA; Normalization: Quantile; Baseline Transformation: median of Control Samples (samples mentioned with C).

source_name: Newborn infant with less than 2500 gm of their body weight

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The RNA was extracted using Tri-reagent (Sigma) as per manufacture's instructions.

value: Umblical Cord Blood


title: Umblical Cord Blood from LBW newborn [E6]


title: Umblical Cord Blood from LBW newborn [E7]


title: PeripheralBlood_DBA_Proband_1382 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2D01-1382

value: Female


title: PeripheralBlood_DBA_Sibling_2302 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2A02-2302_SIB

value: Male

value: Peripheral Blood


title: Umblical Cord Blood from LBW newborn [E5]


title: PeripheralBlood_DBA_Proband_418 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3B3-0418


title: Umblical Cord Blood from LBW newborn [E4]


title: PeripheralBlood_DBA_Proband_20C1 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3A6-20C1


title: PeripheralBlood_DBA_Proband_842 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 2A01-842


title: PeripheralBlood_DBA_Proband_1687 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3C2-1687


title: PeripheralBlood_DBA_Proband_1786 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3B1-1786


title: PeripheralBlood_DBA_Proband_164 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1H02-164


title: yolk sac_wild-type_E9.5_replicate 2

description: Biological replicate 2 of 3

source_name: RNA purified from whole yolk sac, embryonic day 9.5, wild-type mouse


title: Umblical Cord Blood from LBW newborn [E3]


title: Umblical Cord Blood from LBW newborn [E2]


title: yolk sac_Baf250_E9.5_replicate 1

description: Biological replicate 1 of 3


title: PeripheralBlood_DBA_Proband_2681 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3B4-2681


title: PeripheralBlood_DBA_Father_866 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3A5-866_Father

value: Unaffected


title: PeripheralBlood_DBA_Proband_561 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1H01-561


title: Umblical Cord Blood from LBW newborn [E1]


title: PeripheralBlood_DBA_Proband_30 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3A3-0030


title: yolk sac_Baf250_E8.5_replicate 2

description: Biological replicate 2 of 3

source_name: RNA purified from whole yolk sac, embryonic day 8.5, Baf250HM mouse


title: Umblical Cord Blood from NBW newborn [C4]

description: Gene Expression Data from Normal Birth Weight Newborn

source_name: Newborn infant with more than 2500 gm of their body weight


title: Collecting lymphatic duct from Apex-VEGFD xenograft, biological rep2

city: Melbourne

first: tara

last: karnezis

address: St.Andrews place

institute: Peter macallum cancer center

description:
af1c909-35-clec5-290107.CHP
af1c909-35-clec5-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex-VEGFD xenograft
Collecting_Lymphatic_Endothelial_Cell_VEGFD_2

hyb_protocol: Samples were prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300 ul was prepared for each sample and 200 ul loaded into a Mouse 430 version 2.0 GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which was then used for generating subsequent CEL and CHP files for analysis.

data_processing: Raw intensity data was analysed using GeneChip Operating Software (Affymetrix Inc) and profiles compared using AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9).

label_protocol: Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the Nanochip protocol. A total of 3 ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millennium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: 293EBNA tumor cells were injected into the flank of mice. The tumors were grown until they reached a volume of 2000 mm3.

extract_protocol: RNA was extracted from lymph node endothelial cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Patent Blue V was injected into the tumor to visualize the draining collecting lymphatics which were subsequently microdissected. Single cell suspensions were prepared and endothelial cell populations isolated by MAC sorting.

tag: xenograft

value: 293EBNA cells transfected with vector containing VEGFD

tag: cell type

value: collecting lymphatic endothelial cells


title: yolk sac_Baf250_E8.5_replicate 3

description: Biological replicate 3 of 3


title: yolk sac_Baf250_E8.5_replicate 1

description: Biological replicate 1 of 3


title: yolk sac_wild-type_E8.5_replicate 3

description: Biological replicate 3 of 3

source_name: RNA purified from whole yolk sac, embryonic day 8.5, wild-type mouse


title: Umblical Cord Blood from NBW newborn [C2]

tag: tissue


title: PeripheralBlood_DBA_Proband_802 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1G02-802


title: Collecting lymphatic duct from Apex xenograft, biological rep2

description:
af1c909-32-clec2-290107.CHP
af1c909-32-clec2-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex xenograft
Collecting_Lymphatic_Endothelial_Cell_Apex_2

value: 293EBNA cells transfected with empty APEX vector


title: yolk sac_wild-type_E9.5_replicate 1

description: Biological replicate 1 of 3


title: yolk sac_wild-type_E8.5_replicate 2

description: Biological replicate 2 of 3


title: yolk sac_wild-type_E8.5_replicate 1

description: Biological replicate 1 of 3


title: Umblical Cord Blood from NBW newborn [C1]


title: Collecting lymphatic duct from Apex-VEGFD xenograft, biological rep1

description:
af1c909-34-clec4-290107.CHP
af1c909-34-clec4-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex-VEGFD xenograft
Collecting_Lymphatic_Endothelial_Cell_VEGFD_1


title: Collecting lymphatic duct from Apex xenograft, biological rep1

description:
af1c909-31-clec1-290107.CHP
af1c909-31-clec1-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex xenograft
Collecting_Lymphatic_Endothelial_Cell_Apex_1


title: PeripheralBlood_DBA_Proband_763 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1F02-763


title: HEK293-Vc-rep2

status: Public on Jan 14 2012

city: New Haven

first: Dan

last: Wu

address: 10 Amistad Street

institute: Yale University

description: Gene expression data from HEK293 cells

hyb_protocol: After labeling the samples are prepared for hybridization and then rotate in oven at 45 degrees for 16 hours. GeneChips were washed and stained on GeneChip 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.

label_protocol: Fragment and label the single-stranded cDNA were prepared according to  the standard Affymetrix protocol (GeneChip WT Terminal Lableing and Hybridization User Manual).

growth_protocol: HEK293 cells were incubated in DMEM with 10% FBS

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

treatment_protocol: The cells were incubated with serum-free medium for overnight and then stimulated with LPA (1uM) for 2 hours.

tag: cell line


title: HEK293-LPA-rep1

description: Gene expression data from HEK293 cells treatment with LPA

tag: treatment

value: LPA


title: Day-28 triple 1

city: Augusta

first: Biaoru

last: Li

state: GA

department: Pediatrics

institute: MCG

description:
Sample 10_1872863106_D
triple 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Model Base Background Correction (MBCB)

label: biotin-UTP

source_name: PNMN_28 days after adding growth factors

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPre RNA amplification kit with T-7 RNA polymerase IVT for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by quality check using the BioRad Experion system

tag: donor

value: adult, normal

tag: time point

value: Peripheral blood mononuclear cells

tag: growth factors added on day 0

value: stem cell factor (50 ng/mL), interleukin-3 (10 ng/mL) and erythropoietin (4 U/mL)


title: PeripheralBlood_DBA_Proband_2027 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3A2-2027

tag: gender

tag: relationship to proband

value: Proband

value: DBA


title: Day-28 triple 3

description:
Sample 12_1872863106_F
triple 3


title: Day-28 triple 2

description:
Sample 11_1872863106_E
triple 2


title: HEK293-Vc-rep1

description: Gene expression data from HEK293 cells


title: HEK293-LPA-rep2


title: MII-stage oocytes, biological rep 2

city: San Francisco

first: Jing

last: Chen

state: CA

address: 513 Parnassus Ave. HSW 1456

institute: UCSF

description:
pMII 2
Polysome-bound mRNA.

hyb_protocol: Hybridization was performed following the GeneChip Expression Analysis Technical Manual 702232 Rev. 2.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 microarray system.

data_processing: The data were analyzed with dChip using default analysis settings and global scaling as normalization method.

source_name: polysome-bound transcripts from mouse MII-stage oocytes

label_protocol: cDNA was fragmented and labeled using the NuGEN WT-Ovation FFPE System & Encore Biotin Module.

extract_protocol: Polysome-bound mRNAs were purified using the RNeasy Plus Micro kit (Qiagen), and then reverse-transcribed and linearly amplified with the WT-Ovation FFPE RNA Amplification System V2 (NuGEN).

treatment_protocol: Forty-eight hours (h) after pregnant mare's serum gonadotropin (PMSG) injection, mice were stimulated with human chorionic gonadotrophin (hCG) for 0, 4, or 14 h, and GV-, MI- and MII-stage oocytes were collected.

value: oocyte

tag: oocyte stage

value: metaphase II (MII)


title: PeripheralBlood_DBA_Proband_1178 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1F01-1178

tag: dba phenotype


title: MII-stage oocytes, biological rep 3

description:
pMII 3
Polysome-bound mRNA.


title: PeripheralBlood_DBA_Proband_710 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1D02-710


title: Day-21 triple 1

description:
Sample 7_1872863106_A
triple 1

source_name: PNMN_21 days after adding growth factors


title: PeripheralBlood_DBA_Proband_072 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1E02-072


title: MII-stage oocytes, biological rep 1

description:
pMII 1
Polysome-bound mRNA.


title: yolk sac_wild-type_E9.5_replicate 3

description: Biological replicate 3 of 3

tag: developmental stage

value: neonatal

value: whole animal

value: mixed 129Sv and C57BL/6

value: wild type

value: yolk sac


title: PeripheralBlood_DBA_Proband_1579 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1D01-1579

value: Male

value: Peripheral Blood


title: MI-stage oocyte, biological rep 2

description:
pGVB 2
Polysome-bound mRNA.

source_name: polysome-bound transcripts from mouse MI-stage oocytes

value: metaphase I (MI)


title: MI-stage oocyte, biological rep 3

description:
pGVB 3
Polysome-bound mRNA.


title: Day-14 triple 2

description:
Sample 5_1872863008_E
triple 2

source_name: PNMN_14 days after adding growth factors


title: MI-stage oocyte, biological rep 1

description:
pGVB 1
Polysome-bound mRNA.


title: GV-stage oocyte, biological rep 3

description:
pGV 3
Polysome-bound mRNA.

source_name: polysome-bound transcripts from mouse GV-stage oocytes

value: germinal vesicle (GV)


title: NOD.Pan.CD45 #5

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Gender: female; Age: 10 weeks; Isolation: FACS of CD45+ cells from pancreas; Strain: NOD

hyb_protocol: BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

scan_protocol: Standard Affymetrix protocol

data_processing: Standard RMA normalization (RMA-bg adjustment, quantile normalization, median polish probeset summarization) using Affymetrix Power Tools. Output on 2^ scale.

source_name: pancreatic CD45+ cells

extract_protocol: TriZol

value: WT NOD

value: female

tag: age

value: 10 week

value: FACS of CD45+ cells from pancreas

tag: mri t2 value


title: Day-14 triple 3

description:
Sample 6_1872863008_F
triple 3

value: adult, normal

value: Peripheral blood mononuclear cells

value: stem cell factor (50 ng/mL), interleukin-3 (10 ng/mL) and erythropoietin (4 U/mL)


title: Day-7 triple 2

description:
Sample 2_1872863008_B
triple 2

source_name: PNMN_7 days after adding growth factors


title: Day-14 triple 1

description:
Sample 4_1872863008_D
triple 1


title: PeripheralBlood_DBA_Proband_1008 [OmniExpress]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmniExpress Genotyping BeadChips (Illumina).
Sample name: R3A1-1008

value: Female

value: Proband

value: DBA


title: Day-21 triple 2

description:
Sample 8_1872863106_B
triple 2


title: Day-7 triple 3

description:
Sample 3_1872863008_C
triple 3


title: NOD.Pan.CD45 #3


title: NOD.Pan.CD45 #2


title: NOD.Pan.CD45 #4


title: Day-21 triple 3

description:
Sample 9_1872863106_C
triple 3


title: GV-stage oocyte, biological rep 2

description:
pGV 2
Polysome-bound mRNA.

value: oocyte


title: Day-7 triple 1

description:
Sample 1_1872863008_A
triple 1


title: Umblical Cord Blood from NBW newborn [C3]

value: Umblical Cord Blood


title: GV-stage oocyte, biological rep 1

description:
pGV 1
Polysome-bound mRNA.


title: PeripheralBlood_DBA_Proband_1020 [Omni1-Quad]

description:
Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanOmni1_Quad Genotyping BeadChips (Illumina).
Sample name: 1B01-1020