title: mad389

description: primary tumor


title: digestive_gland-offshore-OF4

status: Public on Jun 07 2011

type: RNA

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

country: USA

institute: Brown University

description: mature adult conch, normal female, technical replicate of NF3

hyb_protocol: 600 ng of each labeled cRNA sample was fragmented and hybridized for 17h according to the Agilent Protocol One-color Microarray-based Gene Expression Analysis (Publication no. G4140-90040). Prior to scanning, slides were washed with the Agilent wash buffers and Stabilization and Drying Solution, to prevent ozone damage.

scan_protocol: Slides were scanned at the UF Interdisciplinary Center for Biotechnology Research (ICBR) on the Agilent G2505B microarray scanner.

data_processing:
Feature Extraction was performed at ICBR using the Agilent Feature Extraction software. The two technical replicates for NF3 were averaged prior to normalization. The data were Loess-normalized (smoothing factor = 0.2, 1 iteration) in JMP-Genomics, and ANOVA was performed on all probes, primarily to check controls and expression of probes for multiple contigs annotated to the same Gene Title. Afterward, raw data for multiple probes with the same gene title were averaged, these data were again Loess-normalized (smoothing parameter = 0.2, 1 iteration), and differentially regulated genes were determined using one-way ANOVA (p<0.01, FDR = 0.05).
Gene Title-averaged matrix is provided as a supplementary file on the Series record

molecule: total RNA

organism: Aliger gigas

source_name: digestive gland

label_protocol: 1 ug total RNA from each sample was labeled with Cy3 according to the Agilent protocol titled One-color Microarray-based Gene Expression Analysis (Publication no. G4140-90040). Labeled samples were quantified using the NanoDrop ND-1000 spectrophotometer.

growth_protocol: These were wild queen conchs, sampled from the field on February 15, 2007, by the Florida Fish and Wildlife Conservation Commission

extract_protocol: Total RNA was extracted using Method B described in Spade et al. (2011) J Exper Mar Biol Ecol 402:43-48. Briefly, RNA was twice extracted using RNA STAT-60 reagent and chloroform. The aqueous extract was purified over a 1.4 mL cushion of 5.7M CsCl in an ultracentrifuge (228,000g for 3h), precipitated in ethanol twice at -80C, and reconstituted in ultrapure water.

treatment_protocol: No experimental treatment; the factor in the experiment was field location: offshore (normal reproduction) versus nearshore (impaired reproduction)

tag: location

value: offshore

tag: Sex

value: F

tag: apparent sex

value: normal female


title: Breast_IDC_62A

city: New York

first: Thalia

last: Farazi

state: NY

address: 1230 York Ave, BOX 186

department: Lab of RNA Molecular Biology

institute: Rockefeller University

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11430.str.r.txt, 11430.str.n.txt
control vs. experiment raw data files: 11431.swp.r.txt, 11431.swp.n.txt
raw data matrix file: 18907.c.txt

hyb_protocol: Preheated hybridization buffer (25% formamide, 5X SSC, 0.1% SDS) was added and arrays were hybridised overnight 42C to human 35K oligo microarrays

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing:
Images were quantified using Genepix 5.1 Software. The Limma (linear models for microarray data) package of Bioconductor (http://www.bioconductor.org) was used for importing the data, normalizing the arrays and identifying differentially expressed genes. Control spots and spots with more than 10% saturation, a diameter smaller than 60 um or signal intensity less than 20 counts above background were excluded from the analysis. Data were corrected for local background (method normexp) and normalized within arrays by print-tip loess normalization and between arrays by quantile normalization
Supplementary data files are labeled as follows: str.r.txt represent raw and str.n.txt normalized data for comparison of experiment (Cy3) vs. reference (Cy5); swp.r.txt represent raw and swp.n.txt normalized data for comparison of reference (Cy3) vs. experiment (Cy5); c.txt contain processed data for the dye-swap merged comparison of experimental vs. reference.

organism: Homo sapiens

source_name: Breast tissue

label_protocol: Two ug of total RNA was amplified and labeled using Ambion's Amino Allyl MessageAmp‚® aRNA kit and protocol (Ambion Inc., Austin, TX). For each microarray experiment, 2.0 ug aliquots of aRNA were labeled with Cy5 (Amersham Biosciences, Buckinghamshire, UK). The labeled aRNAs were mixed with equal amounts of Cy3-labeled reference aRNA. To the mixture of labeled reference and sample RNA, 20 ug human COT-1 DNA (Invitrogen, Carlsbad, CA), 8 ug yeast tRNA (Invitrogen) and 20 ug polyadenylic acid (Sigma-Aldrich, St. Louis, MO) were added.

growth_protocol: Tissues Collected from patients.

extract_protocol: Fresh-frozen (frozen immediately after surgery and stored at -80°C) normal and tumor tissue was collected. RNA was isolated from approximately thirty 30-µm cryosections corresponding to approximately 20 mg of tissue, using the first and last section to assess tumor content; only samples containing more than 50% tumor were further characterized. The tissues were homogenized in Trizol using a Polytron instrument (polytron®, PT, MR2100, Kinematica AG, Luzern) for 1 min and total RNA was isolated according to manufacturer's instructions.

treatment_protocol: No treatment.

tag: esr/er ihc (1=positive, 0=negative)

tag: pgr/pr ihc (1=positive, 0=negative)

tag: erbb2 ihc (1=positive, 0=negative)

tag: tag

value: Reference pool of 100 breast carcinomas


title: Breast_IDC_61A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11559.str.r.txt, 11559.str.n.txt
control vs. experiment raw data files: 11560.swp.r.txt, 11560.swp.n.txt
raw data matrix file: 19060.c.txt


title: digestive_gland-offshore-OF1

description: mature adult conch, normal female


title: digestive_gland-nearshore-NF2

description: mature adult conch, normal female

value: nearshore


title: Breast_Atypical Medullary_64

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7064.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7063.txt
experiment vs. control raw data files: 7063.str.r.txt, 7063.str.n.txt
control vs. experiment raw data files: 7064.swp.r.txt, 7064.swp.n.txt
raw data matrix file: 12022.c.txt


title: digestive_gland-offshore-OF3

description: mature adult conch, normal female


title: mad442

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using the RMA algorithmn

label: Biotin

organism: Mus musculus

source_name: mouse model primary retinoblastoma tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: details and references in manuscript

treatment_protocol: all samples are untreated tissues

tag: genotype/variation


title: mad388

description: primary tumor

source_name: retinoblastoma

tag: cell type

value: primary tumor


title: mad444


title: Breast_IDC_63A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11426.str.r.txt, 11426.str.n.txt
control vs. experiment raw data files: 11427.swp.r.txt, 11427.swp.n.txt
raw data matrix file: 18901.c.txt


title: digestive_gland-nearshore-NM3

description: mature adult conch, apparent imposex female

value: apparent imposex female


title: mad441


title: digestive_gland-nearshore-NF3_2-replicates

description: mature adult conch, normal female


title: digestive_gland-offshore-OF2

description: mature adult conch, normal female


title: mad387

description: primary tumor


title: Breast_IDC_60

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11422.str.r.txt, 11422.str.n.txt
control vs. experiment raw data files: 11423.swp.r.txt, 11423.swp.n.txt
raw data matrix file: 18895.c.txt


title: Human MCF7 cells, E2F6 Replicate 1

type: genomic

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human MCF7 cells

hyb_protocol: Cy-labedled ChIP Samples

scan_protocol: NimbleScan

data_processing: Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel

molecule: genomic DNA

source_name: MCF7 cells

label_protocol: standard NimbleGen protocol

extract_protocol: ChIP-chip

tag: antibody

tag: cell line

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot #

tag: sample type

value: control total input


title: ovary-offshore-OF3

description: mature adult conch, normal female

data_processing:
Feature Extraction was performed at ICBR using the Agilent Feature Extraction software. The data were Loess-normalized (smoothing factor = 0.2, 1 iteration) in JMP-Genomics, and ANOVA was performed on all probes, primarily to check controls and expression of probes for multiple contigs annotated to the same Gene Title. Afterward, raw data for multiple probes with the same gene title were averaged, these data were again Loess-normalized (smoothing parameter = 0.2, 1 iteration), and differentially regulated genes were determined using one-way ANOVA (p<0.01, FDR = 0.05).
Gene Title-averaged matrix is provided as a supplementary file on the Series record

source_name: ovary

value: Offshore (Pelican Shoal)


title: ovary-offshore-OF1

description: mature adult conch, normal female


title: mad440


title: ovary-nearshore-NF3

description: mature adult conch, normal female

value: Nearshore (Tingler Island)


title: mad386

description: primary tumor


title: Breast_IDC_59

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11492.str.r.txt, 11492.str.n.txt
control vs. experiment raw data files: 11493.swp.r.txt, 11493.swp.n.txt
raw data matrix file: 19003.c.txt


title: Breast_IDC_58

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11563.str.r.txt, 11563.str.n.txt
control vs. experiment raw data files: 11564.swp.r.txt, 11564.swp.n.txt
raw data matrix file: 19062.c.txt


title: Human MCF7 cells, L3MBTL1 Replicate 1

description: Human MCF7 cells

value: produced in Danny Reinber's lab


title: ovary-offshore-OF2

description: mature adult conch, normal female


title: mad439


title: mad437


title: mad385

description: primary tumor


title: mad383

description: primary tumor


title: mad438


title: mad384

description: primary tumor


title: ovary-nearshore-NF1

description: mature adult conch, normal female


title: ovary-offshore-OF4

description: mature adult conch, normal female


title: mad435

description: TKO

value: TKO


title: mad436


title: Breast_IDC_56

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11553.str.r.txt, 11553.str.n.txt
control vs. experiment raw data files: 11554.swp.r.txt, 11554.swp.n.txt
raw data matrix file: 19057.c.txt


title: Breast_IDC_55A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12519.str.r.txt, 12519.str.n.txt
control vs. experiment raw data files: 12520.swp.r.txt, 12520.swp.n.txt
raw data matrix file: 20844.c.txt


title: Breast_IDC_57A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11557.str.r.txt, 11557.str.n.txt
control vs. experiment raw data files: 11558.swp.r.txt, 11558.swp.n.txt
raw data matrix file: 19059.c.txt


title: mad382

description: primary tumor


title: Breast_IDC_53

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11424.str.r.txt, 11424.str.n.txt
control vs. experiment raw data files: 11425.swp.r.txt, 11425.swp.n.txt
raw data matrix file: 18898.c.txt


title: mad375

description: primary tumor


title: mad374

description: cell line RB355

value: cell line RB355


title: mad433

description: TKO


title: Breast_IDC_54

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11738.str.r.txt, 11738.str.n.txt
control vs. experiment raw data files: 11739.swp.r.txt, 11739.swp.n.txt
raw data matrix file: 19406.c.txt


title: mad432

description: TKO


title: Human MCF7 cells, L3MBTL2 Replicate 1

description: Human MCF7 cells


title: Breast_IDC_51

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11963.str.r.txt, 11963.str.n.txt
control vs. experiment raw data files: 11964.swp.r.txt, 11964.swp.n.txt
raw data matrix file: 20473.c.txt


title: mad373

description: cell line RB1 13

value: cell line RB1 13


title: mad431

description: TKO


title: Breast_IDC_52A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12579.str.r.txt, 12579.str.n.txt
control vs. experiment raw data files: 12580.swp.r.txt, 12580.swp.n.txt
raw data matrix file: 21004.c.txt


title: mad428

description: TKO


title: mad429

description: TKO


title: mad370

description: primary tumor


title: mad427

description: TKO


title: mad372

description: primary tumor


title: Breast_IDC_48

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11967.str.r.txt, 11967.str.n.txt
control vs. experiment raw data files: 11968.swp.r.txt, 11968.swp.n.txt
raw data matrix file: 20475.c.txt


title: mad369

description: primary tumor


title: mad425

description: TKO


title: mad424

description: TKO


title: Breast_IDC_45A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11969.str.r.txt, 11969.str.n.txt
control vs. experiment raw data files: 11970.swp.r.txt, 11970.swp.n.txt
raw data matrix file: 20476.c.txt


title: Breast_IDC_49

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12183.str.r.txt, 12183.str.n.txt
control vs. experiment raw data files: 12184.swp.r.txt, 12184.swp.n.txt
raw data matrix file: 20489.c.txt


title: Adult Chondrocyte ha-Chon

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: Gene expression of human adult re-differentiation chondrocytes

hyb_protocol: 1,650 ng of the labeled cRNA was used for each hybridization. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent Technologies) and a Gene Expression Wash Pack (Agilent Technologies) respectively.

scan_protocol: Hybridization signals were detected using the DNA microarray scanner G2505B (Agilent Technologies) at a resolution of 5 µm.

data_processing: Intensity values of each feature of the scanned image were quantified using Feature Extraction software (version 10.7.3.1, Agilent).

source_name: Human Adult Re-Differentiation Chondrocytes

label_protocol: 250 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent Technologies), amplified and labeled with Cyanine 3 using a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, which generated single-color labeled cRNA.

growth_protocol: DMEM (Sigma) supplemented with 10% fetal bovine serum (FBS) (Hyclone), penicillin, and streptomycin, and were maintained in a 5% CO2 atmosphere at 37℃.

extract_protocol: Total RNA was extracted using an Isogen extraction kit according to the manufacturer's protocol. RNA quantity and quality were determined using a Nanodrop ND-1000 spectrophometer (Thermo Fisher Scientific Inc., Waltham, MA) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), as recommended.

treatment_protocol: The amnion of the fetal part and the decidua of the maternal part were separated and discarded. The smooth chorion from the fetal part was cut into pieces approximately 2 mm3 in size. The pieces were washed in DMEM (high glucose; Sigma) supplemented with 100 U/ml penicillin-streptomycin (Gibco), 1 µg/ml Amphotericin B (Gibco) and 4 U/ml Novo-Heparin Injection 1000 (Mochidaseiyaku Co., Ltd), until the supernatant was free of erythrocytes. Some pieces of smooth chorion were attached to the substratum in a 10 cm diameter dish (Falcon, Becton, Dickinson and Company (BD), San Jose, CA, USA). Culture medium consisting of DMEM (high glucose; Sigma) supplemented with 10% FBS (CCT, Cansera, Canada) was added.

value: Chondrocyte


title: Amnion cells hSC

description: Gene expression of human amnion

source_name: Human amnion

value: Amnion cells


title: Breast_IDC_50A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12321.str.r.txt, 12321.str.n.txt
control vs. experiment raw data files: 12322.swp.r.txt, 12322.swp.n.txt
raw data matrix file: 20446.c.txt


title: mad368

description: primary tumor


title: Chondrocyte (Chondrosarcoma) iCS06

description: Gene expression of human amnion infected 5 genes

source_name: Human amnion 5F-010

value: Chondrosarcoma Chondrocyte

tag: expression

value: BCL6, T (also called BRACHYURY), c-MYC, MITF and BAF60C (also called SMARCD3)


title: Breast_IDC_47A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12545.str.r.txt, 12545.str.n.txt
control vs. experiment raw data files: 12546.swp.r.txt, 12546.swp.n.txt
raw data matrix file: 20987.c.txt


title: mad367

description: primary tumor


title: mad423

description: TKO


title: Fetal Chondrocyte hf-Chon

description: Gene expression of human fetal re-differentiation chondrocytes

source_name: Human Fetal Re-Differentiation Chondrocytes


title: Breast_IDC_44

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11622.str.r.txt, 11622.str.n.txt
control vs. experiment raw data files: 11623.swp.r.txt, 11623.swp.n.txt
raw data matrix file: 19262.c.txt


title: mad421

description: TKO


title: Breast_IDC_46

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12007.str.r.txt, 12007.str.n.txt
control vs. experiment raw data files: 12008.swp.r.txt, 12008.swp.n.txt
raw data matrix file: 20486.c.txt


title: Breast_IDC_36A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11626.str.r.txt, 11626.str.n.txt
control vs. experiment raw data files: 11627.swp.r.txt, 11627.swp.n.txt
raw data matrix file: 19261.c.txt


title: mad420

description: TKO


title: mad366

description: primary tumor


title: Breast_IDC_42

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11682.str.r.txt, 11682.str.n.txt
control vs. experiment raw data files: 11683.swp.r.txt, 11683.swp.n.txt
raw data matrix file: 19287.c.txt


title: Chondrocyte (Chondrosarcoma) iCS05

source_name: Human amnion 5F-004


title: Chondrocyte (Chondrosarcoma) iCS04

source_name: Human amnion 5F-003


title: mad364

description: primary tumor


title: mad419

description: TKO


title: Chondrocyte (Chondrosarcoma) iCS03

source_name: Human amnion 5F-015


title: ovary-nearshore-NM3

description: mature adult conch, apparent imposex female

value: F


title: Breast_IDC_35A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11628.str.r.txt, 11628.str.n.txt
control vs. experiment raw data files: 11629.swp.r.txt, 11629.swp.n.txt
raw data matrix file: 19260.c.txt

value: Reference pool of 100 breast carcinomas


title: Chondrocyte (Chondrosarcoma) iCS01

source_name: Human amnion 5F-013


title: Chondrocyte (Chondrosarcoma) iCS02

source_name: Human amnion 5F-014


title: Breast_IDC_33A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11635.str.r.txt, 11635.str.n.txt
control vs. experiment raw data files: 11636.swp.r.txt, 11636.swp.n.txt
raw data matrix file: 19258.c.txt


title: mad362

description: primary tumor


title: Breast_IDC_32A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11639.str.r.txt, 11639.str.n.txt
control vs. experiment raw data files: 11640.swp.r.txt, 11640.swp.n.txt
raw data matrix file: 19257.c.txt


title: Liver_HCC_5

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: spontaneous tumor

hyb_protocol: 15 μg of amplified biotin-cRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

label: biotin

label_protocol: One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.

growth_protocol: NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.

extract_protocol: RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples.   RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.

treatment_protocol: NA; no treatment was performed.

tag: strain

tag: tissue

value: Liver


title: mad361

description: primary tumor

value: primary tumor


title: Proliferating cells, Donor 2, hsa-miR-Neg overexpression

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Gene expression data

hyb_protocol: Affymetrix protocol for huGene chips.

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: The data were processed using the RMA (Robust Multi-Chip Average) algorithm, which performs a background correction, a normalization step, and a probe-level summary (Irizarry et al., 2003). Data were normalized following a linear model and an empirical Bayes method  in R (Bioconductor) using LIMMA package.

label: Biotin-Affy

source_name: Human nasal epithelial cells

label_protocol: Total RNAs were labelled and hybridized using the whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software, as indicated by the manufacturer’s instructions. Slides were quantified using Feature Extraction software (Agilent Technologies).

growth_protocol: Dissociated cells from nasal polyps were seed in 12 well plastic plate in proliferating medium.

extract_protocol: Trizol extraction of total RNAs was performed according to the manufacturer's instructions and purified on a Qiagen RNeasy kit column (Qiagen, France) according to the manufacturer’s instructions. Purity and concentration of total RNA samples were first evaluated using Nanodrop spectrophotometer (Nanodrop, Labtech, Palaiseau, France). Ratio 260/280 and 260/230 were checked to be near a value of 2. Then, RNA samples were ran in a RNA nano-chip into a 2100 Bioanalyzer System (Agilent Tecnologies, France) to verify the integrity or degradation of the RNA samples.

treatment_protocol: Proliferating cells were transfected with indicated pre-miR (10nM) for 48h with LipofectamineTM RNAiMAX (Invitrogen) and lysed.

value: human nasal mucosa

tag: experimantal conditions

value: hsa-pre-miR-Neg transfection

tag: rin number

tag: amount in (µg)


title: mad360

description: primary tumor


title: Breast_IDC_31A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11618.str.r.txt, 11618.str.n.txt
control vs. experiment raw data files: 11619.swp.r.txt, 11619.swp.n.txt
raw data matrix file: 19255.c.txt

tag: esr/er ihc (1=positive, 0=negative)

tag: pgr/pr ihc (1=positive, 0=negative)


title: Liver_HCC_6

description: spontaneous tumor


title: Liver_HCC_4

description: spontaneous tumor


title: Proliferating cells, Donor 3, hsa-miR-34a overexpression

description: Gene expression data

value: hsa-pre-miR-34a transfection


title: Proliferating cells, Donor 3, hsa-miR-Neg overexpression

description: Gene expression data


title: mad358

description: primary tumor


title: Liver_HCC_2

description: spontaneous tumor


title: Breast_IDC_29

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11687.str.r.txt, 11687.str.n.txt
control vs. experiment raw data files: 11688.swp.r.txt, 11688.swp.n.txt
raw data matrix file: 19295.c.txt

tag: erbb2 ihc (1=positive, 0=negative)

tag: tag


title: mad371

description: primary tumor

tag: cell type


title: mad355

description: cell line Y79

value: cell line Y79


title: Proliferating cells, Donor 2, hsa-miR-449a overexpression

description: Gene expression data

value: hsa-pre-miR-449a transfection


title: Proliferating cells, Donor 4, hsa-miR-449a overexpression

description: Gene expression data


title: mad359

description: primary tumor


title: mad357

description: primary tumor


title: Proliferating cells, Donor 3, hsa-miR-34b-5p overexpression

description: Gene expression data

value: hsa-pre-miR-34b-5p transfection


title: Liver_HCC_1

description: spontaneous tumor


title: Proliferating cells, Donor 4, hsa-miR-Neg overexpression

description: Gene expression data


title: Breast_IDC_23

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11641.str.r.txt, 11641.str.n.txt
control vs. experiment raw data files: 11642.swp.r.txt, 11642.swp.n.txt
raw data matrix file: 19251.c.txt


title: Breast_IDC_28A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11630.str.r.txt, 11630.str.n.txt
control vs. experiment raw data files: 11631.swp.r.txt, 11631.swp.n.txt
raw data matrix file: 19253.c.txt


title: Breast_Mucinous A_26

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: E-NCMF-3
ArrayExpress data file: BioDataCube_For_MeasuredData_7261.txt
ArrayExpress data file: BioDataCube_For_MeasuredData_7262.txt
experiment vs. control raw data files: 7262.str.r.txt, 7262.str.n.txt
control vs. experiment raw data files: 7261.swp.r.txt, 7261.swp.n.txt
raw data matrix file: 12439.c.txt


title: Breast_IDC_34

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11637.str.r.txt, 11637.str.n.txt
control vs. experiment raw data files: 11638.swp.r.txt, 11638.swp.n.txt
raw data matrix file: 19259.c.txt


title: mad365

description: primary tumor


title: Breast_IDC_22

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11684.str.r.txt, 11684.str.n.txt
control vs. experiment raw data files: 11686.swp.r.txt, 11686.swp.n.txt
raw data matrix file: 19285.c.txt


title: Liver_normal_4

description: control


title: mad353

description: cell line Weril

value: cell line Weril


title: Liver_normal_6

description: control


title: Tendon_lesional_rep22

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

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

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

tag: gender

value: Female

value: Tendon;Suspraspinatus

tag: age

tag: donor

tag: disease state

value: Lesional


title: Proliferating cells, Donor 4, hsa-miR-449b overexpression

description: Gene expression data

value: hsa-pre-miR-449b transfection


title: Tendon_lesional_rep21

value: Male


title: Proliferating cells, Donor 4, hsa-miR-34a overexpression

description: Gene expression data


title: Proliferating cells, Donor 4, hsa-miR-34b-5p overexpression

description: Gene expression data


title: Liver_normal_5

description: control


title: Breast_DCIS_18A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12501.str.r.txt, 12501.str.n.txt
control vs. experiment raw data files: 12502.swp.r.txt, 12502.swp.n.txt
raw data matrix file: 20835.c.txt


title: Proliferating cells, Donor 3, hsa-miR-34c-5p overexpression

description: Gene expression data

value: hsa-pre-miR-34c-5p transfection


title: Breast_DCIS_17

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12201.str.r.txt, 12201.str.n.txt
control vs. experiment raw data files: 12202.swp.r.txt, 12202.swp.n.txt
raw data matrix file: 20498.c.txt


title: Breast_IDC_30A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11632.str.r.txt, 11632.str.n.txt
control vs. experiment raw data files: 11633.swp.r.txt, 11633.swp.n.txt
raw data matrix file: 19254.c.txt


title: Proliferating cells, Donor 4, hsa-miR-34c-5p overexpression

description: Gene expression data


title: Tendon_lesional_rep19


title: Liver_normal_3

description: control


title: Liver_normal_1

description: control


title: Tendon_lesional_rep20


title: Breast_DCIS_16A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 12509.str.r.txt, 12509.str.n.txt
control vs. experiment raw data files: 12510.swp.r.txt, 12510.swp.n.txt
raw data matrix file: 20839.c.txt


title: Tendon_lesional_rep23


title: Liver_normal_2

description: control


title: Proliferating cells, Donor 3, hsa-miR-449a overexpression

description: Gene expression data


title: Breast_DCIS_14

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13174.str.r.txt, 13174.str.n.txt
control vs. experiment raw data files: 13175.swp.r.txt, 13175.swp.n.txt
raw data matrix file: 21895.c.txt


title: Tendon_lesional_rep18

value: Tendon;ECRB


title: Tendon_lesional_rep16


title: Proliferating cells, Donor 2, hsa-miR-449b overexpression

description: Gene expression data


title: Proliferating cells, Donor 1, hsa-miR-449b overexpression

description: Gene expression data


title: Breast_DCIS_9A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13154.str.r.txt, 13154.str.n.txt
control vs. experiment raw data files: 13155.swp.r.txt, 13155.swp.n.txt
raw data matrix file: 21885.c.txt

value: Reference pool of 100 breast carcinomas


title: Proliferating cells, Donor 1, hsa-miR-Neg overexpression

description: Gene expression data


title: Breast_DCIS_11

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13164.str.r.txt, 13164.str.n.txt
control vs. experiment raw data files: 13165.swp.r.txt, 13165.swp.n.txt
raw data matrix file: 21890.c.txt


title: Tendon_lesional_rep15


title: Tendon_lesional_rep17


title: Breast_DCIS_15

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13178.str.r.txt, 13178.str.n.txt
control vs. experiment raw data files: 13179.swp.r.txt, 13179.swp.n.txt
raw data matrix file: 21897.c.txt


title: Breast_DCIS_12

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13172.str.r.txt, 13172.str.n.txt
control vs. experiment raw data files: 13173.swp.r.txt, 13173.swp.n.txt
raw data matrix file: 21894.c.txt


title: Breast_DCIS_10

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13152.str.r.txt, 13152.str.n.txt
control vs. experiment raw data files: 13153.swp.r.txt, 13153.swp.n.txt
raw data matrix file: 21884.c.txt


title: Tendon_lesional_rep11


title: Breast_DCIS_8

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13160.str.r.txt, 13160.str.n.txt
control vs. experiment raw data files: 13161.swp.r.txt, 13161.swp.n.txt
raw data matrix file: 21888.c.txt


title: Donor 3, Culture Cells at ALI-D7

description: Gene expression data

growth_protocol: Dissociated cells from nasal polyps were either seed on collagen-type IV coated permeable supports for differentiation.

treatment_protocol: At confluency (day 7 after seeding), cultures cells were switched in air-liquid interface (ALI) in the differentiating medium.

tag: differentiation step

value: Polarization


title: Tendon_lesional_rep12


title: Donor 3, Culture Cells at ALI-D0

description: Gene expression data

value: End of proliferation


title: Tendon_lesional_rep10


title: Tendon_lesional_rep13


title: Proliferating cells, Donor 3, hsa-miR-449b overexpression

description: Gene expression data

value: human nasal mucosa


title: Proliferating cells, Donor 1, hsa-miR-449a overexpression

description: Gene expression data


title: Tendon_lesional_rep14


title: Donor 3, Culture Cells at ALI-D14

description: Gene expression data

value: Onset of mucociliary differentiation


title: Tendon_lesional_rep9

value: Tendon;Flexor-Pronator


title: Ad-Null

city: New Haven

first: Masahiro

last: Murakami

state: CT

address: 300 George St. Rm 759

department: Internal Medicine

institute: Yale University School of Medicine

scan_protocol: SABiosciences standard protocol

data_processing: Using web-based software analysis (RT² Profiler™ PCR Array Data Analysis) from SABiosciences

label: Sybr Green/ROX

source_name: Primary lung endothelial cells

label_protocol: RNA was reverse-transcribed into cDNA using RT2first strand kit (SA Biosciences)

growth_protocol: high glucose DMEM (Bio-Whitaker cat # 12-709F) + 20% FBS + 1X non essential amino acids + 1X glutamate + 1X pen/strep (all three from Invitrogen).

extract_protocol: Total RNA was isolated with an Rneasy plus mini kit (Qiagen)

value: primary lung endothelial cells transduced with adeno-Null

tag: transduction

value: Adeno-null empty vector

tag: genetic background


title: ALI-D7, donor 3

description: MicroRNA expression data

hyb_protocol: Cy3-labeled RNA were hybridized following manufacturer's instructions (MiRNA complete labeling and hybridization kit, Agilent Technologies) 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA Scanner.

data_processing: GeneView files were generated using Agilent's Feature Extraction software version 9.5.3.1

label_protocol: The microRNAs were labled using the miRNA Complete Labeling and Hyb Kit. Details were that 100 ng total RNA was treated with phosphatase at 37 ℃for 30min. The dephosphorylated RNA was ligated and labeled using the ligation master mix  following the kit instructions

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


title: Donor 3, Culture Cells at ALI-D21

description: Gene expression data

value: Terminal mucociliary differentiation


title: mad363

description: primary tumor

value: primary tumor


title: Breast_DCIS_7

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13166.str.r.txt, 13166.str.n.txt
control vs. experiment raw data files: 13167.swp.r.txt, 13167.swp.n.txt
raw data matrix file: 21891.c.txt


title: Ad-FGFR1DN

value: primary lung endothelial cells transduced with adeno-dominant negative FGFR1

value: Adeno-dominant negative FGF receptor 1


title: ALI-D0, donor 3

description: MicroRNA expression data


title: ALI-D21, donor 3

description: MicroRNA expression data


title: Donor 1, Culture Cells at ALI-D7

description: Gene expression data


title: ALI-D14, donor 3

description: MicroRNA expression data


title: Breast_DCIS_4

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13168.str.r.txt, 13168.str.n.txt
control vs. experiment raw data files: 13169.swp.r.txt, 13169.swp.n.txt
raw data matrix file: 21892.c.txt


title: ALI-D7, donor 1

description: MicroRNA expression data


title: Donor 1, Culture Cells at ALI-D0

description: Gene expression data


title: Tendon_lesional_rep8

value: Tendon;Suspraspinatus

value: Lesional


title: Breast_DCIS_3

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13156.str.r.txt, 13156.str.n.txt
control vs. experiment raw data files: 13157.swp.r.txt, 13157.swp.n.txt
raw data matrix file: 21886.c.txt


title: Tendon_lesional_rep7

value: Female


title: Breast_DCIS_5A

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13162.str.r.txt, 13162.str.n.txt
control vs. experiment raw data files: 13163.swp.r.txt, 13163.swp.n.txt
raw data matrix file: 21889.c.txt


title: Tendon_lesional_rep6

value: Male

value: Tendon;Patellar


title: Liver_HCC_3

description: spontaneous tumor

tag: strain

value: Liver


title: Breast_DCIS_6

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 13158.str.r.txt, 13158.str.n.txt
control vs. experiment raw data files: 13159.swp.r.txt, 13159.swp.n.txt
raw data matrix file: 21887.c.txt

value: Reference pool of 100 breast carcinomas


title: Donor 1, Culture Cells at ALI-D21

description: Gene expression data

tag: tissue


title: Donor 1, Culture Cells at ALI-D14

description: Gene expression data


title: ALI-D21, donor 1

description: MicroRNA expression data


title: Tendon_lesional_rep5


title: Donor 2, Culture Cells at ALI-D0

description: Gene expression data

value: End of proliferation


title: Tendon_lesional_rep4


title: ALI-D21, donor 2

description: MicroRNA expression data

value: human nasal mucosa


title: ALI-D0, donor 1

description: MicroRNA expression data


title: Donor 2, Culture Cells at ALI-D7

description: Gene expression data

value: Polarization


title: Breast_DCIS_1

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11732.str.r.txt, 11732.str.n.txt
control vs. experiment raw data files: 11733.swp.r.txt, 11733.swp.n.txt
raw data matrix file: 19403.c.txt


title: Donor 2, Culture Cells at ALI-D14

description: Gene expression data

value: Onset of mucociliary differentiation


title: Tendon_lesional_rep3


title: Breast_DCIS_2

description:
See Supplementary Table S1 and S2 for further experimental sample information
Reference Sample description: Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007;9(5):R65.
ArrayExpress accession: NA
ArrayExpress data file: NA
ArrayExpress data file: NA
experiment vs. control raw data files: 11722.str.r.txt, 11722.str.n.txt
control vs. experiment raw data files: 11723.swp.r.txt, 11723.swp.n.txt
raw data matrix file: 19399.c.txt


title: ALI-D7, donor 2

description: MicroRNA expression data


title: Tendon_lesional_rep2

value: Tendon;ECRB


title: Donor 2, Culture Cells at ALI-D21

description: Gene expression data


title: ALI-D0, donor 2

description: MicroRNA expression data


title: ALI-D14, donor 1

description: MicroRNA expression data


title: ALI-D14, donor 2

description: MicroRNA expression data


title: Tendon_non-lesional_rep23

value: Tendon;Subscapularis

value: Non-lesional


title: Tendon_lesional_rep1

value: Tendon;Biceps


title: Control ileum, replicate 1

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

description: transcript profile of mouse ileum  28d after tamoxifin induction of transgene deletion, 10 wks at harvest

hyb_protocol: Standard Affymetrix hybridization protocols for the mouse Gene 1.0 ST array

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data was analyzed using the Affymetrix Expression Console

source_name: control mouse ileum, whole

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for mouse Gene 1.0 ST array

growth_protocol: mice grown under standard conditions, chow diet and water fed ad libitum

extract_protocol: Rneasy kit (Qiagen) with DNAse treatment

treatment_protocol: 6-8 wk old mice were treated for 5 consecutive days with 100 mg/ml tamoxifen then killed 28 days later (10-12 wks final age)

value: whole ileum

tag: treatment

value: control


title: GATA6 KO ileum,  replicate 1

source_name: induced, intestine-specific GATA6 knockout mouse ileum, whole

value: tamoxifen induced intestine-specific GATA6 knockout


title: Tendon_non-lesional_rep17


title: Tendon_non-lesional_rep21


title: Control ileum, replicate 3


title: Tendon_non-lesional_rep13


title: Tendon_non-lesional_rep19


title: Tendon_non-lesional_rep22


title: GATA6 KO ileum,  replicate 3


title: GATA6 KO ileum,  replicate 2


title: Tendon_non-lesional_rep12


title: Tendon_non-lesional_rep20

source_name: Tendon;Teres minor_Non-lesional

value: Tendon;Teres minor


title: Control ileum, replicate 2


title: Tendon_non-lesional_rep18

value: Tendon;ECRL


title: Tendon_non-lesional_rep15

value: Male


title: Tendon_non-lesional_rep16


title: 37-2651

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

description:
CoQ_2B
Replicate 2

hyb_protocol: Arrays were hybridized and washed according to standard Illumina protocols with Cy3-conjugated streptavidin used for secondary labeling of the hybridized target.

scan_protocol: Arrays were scanned at 532 nM using standard Illumina settings and protocols.

data_processing: Average signals on probes were log-2 transformed and then normalized between samples by the Loess method.

source_name: Mouse liver, missense mutant, CoQ10

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays.  Two hundred nanograms of total RNA was used as the starting material for cDNA synthesis.

growth_protocol: B6.Pdss2(kd/kd) mice were derived by backcrossing a recombinant chromosome derived by positional cloning onto the B6 background (Dell, Li et al. 2000).  B6.Pdss2(kd/kd) mice in this report were in the 13th backcross generation.

extract_protocol: Total RNA from each mouse liver was isolated by Trizol extraction (Invitrogen, CA), purified, and combined into a single aliquot from 100 mg flash-frozen liver specimens collected at the time of sacrifice, as previously described (Peng, Falk et al. PLoS Genetics, 2008 [PMID 18437205]).

treatment_protocol: Untreated mice were fed a standard LabDiet rodent chow obtained from PMI Nutrition International (Brentwood, MO).  Probucol-treated mice were given the same diet to which 1% (w/w) probucol was added (Animal Specialties and Provisions, Quakertown, PA), which we estimate resulted in a final daily dosage of approximately 95 mg per kg body weight.  The amount of CoQ10 added was 1 mg/ml, which we estimate resulted in a final daily dosage of approximately 400 mg CoQ10 per kg body weight.

tag: genotype

value: Pdss2(kd/kd) missense mutation

value: female

value: liver

tag: age (days)

tag: urine albumin (mg/24 hrs)

value: not done

tag: glomerular nephritis score


title: 37-2646

description:
Prob_4B
Replicate 5

source_name: Mouse liver, missense mutant, untreated


title: 37-2653

description:
CoQ_4C
Replicate 4


title: Tendon_non-lesional_rep9

value: Tendon;Flexor-Pronator


title: Tendon_non-lesional_rep10

value: Female


title: 37-2648

description:
CoQ_1E
Replicate 1


title: 37-2645

description:
Prob_3E
Replicate 4


title: Tendon_non-lesional_rep11


title: 37-2652

description:
CoQ_3F
Replicate 3


title: 37-2614

description:
Prob_2C
Replicate 2


title: 37-2615

description:
Prob_2F
Replicate 3


title: Tendon_non-lesional_rep7


title: 37-2654

description:
CoQ_4D
Replicate 5


title: LZS011

description: HIF1a-deficient TH17 cells

scan_protocol: GeneChips were scanned using the GeneTitan system

source_name: Naïve T cells

label_protocol: Affymetrix standard methods were applied using the high throughput protocal for PM arrays

growth_protocol: Naïve T cells were activated under TH17 conditions for 2.5 days.

extract_protocol: RNA was extracted using RNeasy kit (Qiagen).

treatment_protocol: Two types of cells (wild-type and HIF1a-deficient) were treated under the identifical conditions.

value: Naïve CD4 T cells

tag: genotype/variation


title: 37-2613

description:
Prob_1D
Replicate 1


title: LZS012

description: HIF1a-deficient TH17 cells


title: LZS010

description: HIF1a-deficient TH17 cells


title: Tendon_non-lesional_rep5


title: Tendon_non-lesional_rep6

value: Tendon;Patellar


title: 37-2612

description:
Untr_4F
Replicate 5

source_name: Mouse liver, missense mutant, probucol

value: probucol


title: Tendon_non-lesional_rep4

value: Non-lesional


title: 37-2611

description:
Untr_3D
Replicate 4


title: LZS002

description: wild-type TH17 cells

value: wild-type


title: 37-2609

description:
Untr_2E
Replicate 2


title: Tendon_non-lesional_rep8

value: Tendon;Subscapularis


title: Tendon_non-lesional_rep3

value: Tendon;Quadriceps


title: LZS001

description: wild-type TH17 cells


title: Tendon_non-lesional_rep2

value: Tendon;EDC


title: Tendon_non-lesional_rep1

value: Tendon;Brachialis


title: 37-2608

description:
Untr_1C
Replicate 1


title: B6-1299

description:
Ctrl_4E
Replicate 5

source_name: Mouse liver, control


title: dental follicle cells DLX3 1

city: Regensburg

first: Christian

last: Morsczeck

address: Franz-Josef Strauss Allee 11

country: Germany

institute: University of Regensburg

description: Gene expression of dental follicle cells after 48 hours of transfection with a DLX3 plasmid

hyb_protocol: Hybridization to Affymetrix oligonucleotide microarray Human Gene 1.0 ST array was carried out overnight with 1biotin-labeled cRNA in a hybridization oven 640

scan_protocol: GeneChip Scanner 3000 (Affymetrix)

data_processing:
Affymetrix GeneChip Operating Software (GCOS) 1.4 and the Expression Console 1.1. Software
For the creation of the summarized log-signal the robust multi-chip analysis (RMA) algorithm was used

source_name: dental follicle cells in standard  medium

label_protocol: Double-stranded cDNA was prepared from 5 μg of total cellular RNA (cDNA synthesis kit, Affymetrix Santa Clara, CA, USA), in vitro transcribed using an IVT labeling kit, and the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix). All procedures according to the Affymetrix protocol.

growth_protocol: Cell were grown in DMEM medium (PAA, Pasching, Austria) at 37°C in 5% CO2

extract_protocol: Total RNAs were extracted using the kit NucleoSpin® RNA II kit (Macherey Nagel, Düren, Germany) and quality-controlled using the RNA 6000 Nano LabChip (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Transfection was performed using FUGEN®HD (Roche) kit and the expression plasmid pCMV-V5DLX3 (pDLX3), which expresses DLX3 under the control of the constitutive CMV promoter and as control an empty vector without an insert.

value: primary dental progenitor stem cells

tag: overexpression


title: WT, FGF15, 2

city: Dallas

first: Matthew

middle: Joseph

last: Potthoff

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

description: gene expression data

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430A 2.0 Array

scan_protocol: Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000

data_processing: For the minimization of discrepancies due to variables, the raw expression data were scaled with Affymetrix MICROARRAY SUITE 5.0 software, and pairwise comparisons were performed. The trimmed mean signal of all probe sets was adjusted to a user-specified target signal value (200) for each array for global scaling. No specific exclusion criteria were applied.

source_name: liver from mouse administered FGF15

label_protocol: biotin

growth_protocol: Wild-type C57Bl/6 male mice were ordered from Jackson Laboratories.

extract_protocol: Stat-60 extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Wild-type mice were administered vehicle, purified FGF15 or recombinant FGF19 for 6 hr via a jugular vein injection

value: Liver

value: male


title: WT, FGF19, 1

description: gene expression data

source_name: liver from mouse administered FGF19


title: dental follicle cells DLX3 2

tag: cell type


title: dental follicle cells control 1

description: Gene expression of dental follicle cells after 48 hours of transfection with an empty vector

value: control


title: dental follicle cells control 2


title: WT, FGF15, 1

description: gene expression data

tag: gender


title: WT, Vehicle, 2

description: gene expression data

source_name: liver from mouse administered vehicle


title: B6-1297

description:
Ctrl_2D
Replicate 3

value: female

value: liver


title: B6-1298

description:
Ctrl_3C
Replicate 4


title: WT, FGF19, 2

description: gene expression data


title: Negative Control ASO Treatment rep3

status: Public on Jun 06 2011

city: Carlsbad

first: Mahyar

last: Sabripour

state: CA

address: 1896 Rutherford Ave.

institute: Isis Pharmaceuticals

description:
D3
Negative Control ASO replicate3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: mouse brain

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

extract_protocol: RNeasy mini kit (cat # 74106, Qiagen) was used to purify total RNA from animal tissues. Tissue was lysed and homogenized, precipitated with ethanol, washed, and then eluted in double distilled RNase free water.

value: BACHD

tag: age

value: brain

value: Negative Control antisense oligonucleotide (ASO)


title: B6-1295

description:
Ctrl_1B
Replicate 1


title: Wig-1 ASO Treatment rep3

description:
B3
Wig1 ASO replicate3

value: Wig-1 antisense oligonucleotide (ASO)


title: Wig-1 ASO Treatment rep1

description:
B1
Wig1 ASO replicate1


title: Negative Control ASO Treatment rep4

description:
D4
Negative Control ASO replicate4


title: Wig-1 ASO Treatment rep2

description:
B2
Wig1 ASO replicate2


title: B6-1296

description:
Ctrl_1F
Replicate 2


title: Wig-1 ASO Treatment rep4

description:
B4
Wig1 ASO replicate4


title: WT, Vehicle, 1

description: gene expression data


title: PBS (no treatment) rep3

description:
A3
PBS replicate3

value: PBS


title: PBS (no treatment) rep1

description:
A1
PBS replicate1


title: Timepoint19_Hive07_APM_P02-1041

city: San Francisco

first: Charles

last: Runckel

department: Biochemistry

institute: UCSF

description: Total nucleic acid was randomly amplified by random priming and single primer PCR, and labeled with a Cy3-labelled primer prior to hybridization

hyb_protocol: Samples were hybridized overnight at 65C in an SSC/SDS/HEPES buffer

scan_protocol: Samples were scanned at 5 um resolution in the 532 and 635 channels by an Axon 4000A scanner

data_processing:
The software analysis used is E-predict ("E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns" and http://derisilab.ucsf.edu/software/epredict/index.html). The data was analyzed using e-predict V1.0 and V2.02 (they use identical algorithms, but different user interfaces). The default "sum normalization" parameter was used.
Samples were analyzed manually and scored as positive for a pathogen if at least three unique oligonucleotides hybridized with at least five times background intensity. Arrays were further analyzed by a second unbiased method using the E-Predict algorithm [52,53] (version 2.02), wherein all virus genomes were computationally hybridized to the array oligos and array results are compared to expected binding profiles. The top 5 unique oligos were removed and the algorithm reiterated twice in order to improve detection of low titer target(s) during a co-infection. Known honey bee pathogens were called positive if they exceeded a similarity score of 0.001 and were the highest ranked call in any iteration. In the event of a disagreement between the two analysis methods, a specific PCR reaction was performed, using material from the first PCR step, to resolve the call.

organism: Apis mellifera

source_name: Whole Bee Homogenate

label_protocol: Randomly amplifed material was further amplified with a Cy3-labelled oligo

growth_protocol: Samples were collected as adults

extract_protocol: Samples were extracted by Trizol and isopropanol precipitation

treatment_protocol: Samples were stored on dry ice prior to extraction

tag: number of bees

tag: timepoint

tag: hive


title: Timepoint19_Hive06_APM_P02-1032


title: Timepoint19_Hive04_APM_P02-1022


title: Timepoint19_Hive05_APM_P02-1031


title: PBS (no treatment) rep2

description:
A2
PBS replicate2


title: Timepoint19_Hive02_APM_P02-1012


title: Timepoint19_Hive03_APM_P02-1021


title: Timepoint18_Hive20_APM_P01-1302


title: Timepoint19_Hive01_APM_P02-1011


title: Timepoint18_Hive18_APM_P01-1292


title: Timepoint18_Hive19_APM_P01-1301


title: PBS (no treatment) rep4

description:
A4
PBS replicate4


title: Negative Control ASO Treatment rep2

description:
D2
Negative Control ASO replicate2


title: Timepoint18_Hive16_APM_P01-1282


title: Timepoint18_Hive15_APM_P01-1281


title: Timepoint18_Hive14_APM_P01-1272


title: Timepoint18_Hive13_APM_P01-1271


title: Timepoint18_Hive17_APM_P01-1291


title: Timepoint18_Hive11_APM_P01-1261


title: Timepoint18_Hive08_APM_P01-1242


title: Timepoint18_Hive10_APM_P01-1252


title: Timepoint18_Hive09_APM_P01-1251


title: Timepoint18_Hive12_APM_P01-1262


title: Timepoint18_Hive05_APM_P01-1231


title: Timepoint18_Hive06_APM_P01-1232


title: Negative Control ASO Treatment rep1

description:
D1
Negative Control ASO replicate1


title: Tendon_non-lesional_rep14

value: Male

value: Tendon;ECRB

tag: donor

tag: disease state

value: Non-lesional


title: 37-2610

description:
Untr_3B
Replicate 3

tag: strain

value: Pdss2(kd/kd) missense mutation

value: probucol


title: Timepoint18_Hive07_APM_P01-1241


title: Timepoint18_Hive03_APM_P01-1221


title: Timepoint18_Hive02_APM_P01-1212


title: Timepoint18_Hive01_APM_P01-1211


title: Timepoint17_Hive20_APM_P02-0402


title: Timepoint18_Hive04_APM_P01-1222


title: Timepoint17_Hive19_APM_P02-0401


title: Timepoint17_Hive13_APM_P02-0371


title: Timepoint17_Hive15_APM_P02-0381


title: Timepoint17_Hive14_APM_P02-0372


title: Timepoint17_Hive09_APM_P02-0351


title: Timepoint17_Hive17_APM_P02-0391


title: Timepoint17_Hive16_APM_P02-0382


title: Timepoint17_Hive12_APM_P02-0362


title: Timepoint17_Hive08_APM_P02-0342


title: Timepoint17_Hive18_APM_P02-0392


title: Timepoint17_Hive07_APM_P02-0341


title: Timepoint17_Hive06_APM_P02-0332


title: LZS003

description: wild-type TH17 cells

value: Naïve CD4 T cells

value: wild-type


title: Timepoint16_Hive18_APM_P02-0302


title: Timepoint17_Hive03_APM_P02-0321


title: Timepoint17_Hive02_APM_P02-0312


title: Timepoint17_Hive10_APM_P02-0352


title: Timepoint17_Hive01_APM_P02-0311


title: Timepoint17_Hive05_APM_P02-0331


title: Timepoint17_Hive04_APM_P02-0322


title: Timepoint16_Hive12_APM_P02-0271


title: Timepoint16_Hive11_APM_P02-0262


title: Timepoint16_Hive09_APM_P02-0252


title: Timepoint16_Hive16_APM_P02-0291


title: Timepoint16_Hive17_APM_P02-0301


title: Timepoint16_Hive15_APM_P02-0282


title: Timepoint16_Hive06_APM_P02-0232


title: Timepoint16_Hive14_APM_P02-0281


title: Timepoint16_Hive13_APM_P02-0272


title: Timepoint16_Hive05_APM_P02-0231


title: Timepoint16_Hive07_APM_P02-0242


title: Timepoint16_Hive03_APM_P02-0221


title: Timepoint16_Hive04_APM_P02-0222


title: Timepoint16_Hive02_APM_P02-0212


title: Timepoint14_Hive20_APM_P02-0672


title: Timepoint16_Hive08_APM_P02-0251


title: Timepoint14_Hive19_APM_P02-0671


title: Timepoint16_Hive01_APM_P02-0211


title: Timepoint16_Hive10_APM_P02-0261


title: Timepoint14_Hive18_APM_P02-0662


title: Timepoint14_Hive17_APM_P02-0661


title: Timepoint14_Hive16_APM_P02-0652


title: Timepoint14_Hive15_APM_P02-0651


title: Timepoint14_Hive14_APM_P02-0642


title: Timepoint14_Hive12_APM_P02-0632


title: Timepoint14_Hive13_APM_P02-0641


title: Timepoint14_Hive11_APM_P02-0631


title: Timepoint14_Hive10_APM_P02-0622


title: Timepoint14_Hive08_APM_P02-0612


title: Timepoint14_Hive06_APM_P02-0602


title: Timepoint14_Hive07_APM_P02-0611


title: Timepoint14_Hive04_APM_P02-0592


title: Timepoint14_Hive01_APM_P02-0581


title: Timepoint14_Hive05_APM_P02-0601


title: Timepoint10_Hive15_APM_P02-1581


title: Timepoint10_Hive14_APM_P02-1572


title: Timepoint10_Hive17_APM_P02-1591


title: Timepoint10_Hive16_APM_P02-1582


title: Timepoint10_Hive20_APM_P02-1602


title: Timepoint10_Hive18_APM_P02-1592


title: Timepoint10_Hive19_APM_P02-1601


title: Timepoint10_Hive13_APM_P02-1571


title: Timepoint10_Hive06_APM_P02-1532


title: Timepoint10_Hive11_APM_P02-1561


title: Timepoint10_Hive12_APM_P02-1562


title: Timepoint10_Hive10_APM_P02-1552


title: Timepoint10_Hive09_APM_P02-1551


title: Timepoint10_Hive08_APM_P02-1542


title: Timepoint10_Hive04_APM_P02-1522


title: Timepoint14_Hive03_APM_P02-0591


title: Timepoint10_Hive07_APM_P02-1541


title: Timepoint14_Hive02_APM_P02-0582


title: Timepoint10_Hive03_APM_P02-1521


title: Timepoint10_Hive01_APM_P02-1511


title: Timepoint07_Hive20_APM_P01-1102


title: Timepoint07_Hive19_APM_P01-1101


title: Timepoint07_Hive18_APM_P01-1092


title: Timepoint10_Hive05_APM_P02-1531


title: Timepoint07_Hive17_APM_P01-1091


title: Timepoint10_Hive02_APM_P02-1512


title: Timepoint07_Hive15_APM_P01-1081


title: Timepoint07_Hive14_APM_P01-1072


title: Timepoint07_Hive16_APM_P01-1082


title: Timepoint07_Hive11_APM_P01-1061


title: Timepoint07_Hive13_APM_P01-1071


title: Timepoint07_Hive10_APM_P01-1052


title: Timepoint07_Hive12_APM_P01-1062


title: Timepoint07_Hive09_APM_P01-1051


title: Timepoint07_Hive02_APM_P01-1012


title: Timepoint01_Hive19_APM_P01-1401


title: Timepoint01_Hive18_APM_P01-1392


title: Timepoint07_Hive06_APM_P01-1032


title: Timepoint07_Hive04_APM_P01-1022


title: Timepoint07_Hive05_APM_P01-1031


title: Timepoint07_Hive08_APM_P01-1042


title: Timepoint07_Hive07_APM_P01-1041


title: Timepoint01_Hive20_APM_P01-1402


title: Timepoint07_Hive03_APM_P01-1021


title: Timepoint07_Hive01_APM_P01-1011


title: Timepoint01_Hive16_APM_P01-1382


title: Timepoint01_Hive17_APM_P01-1391


title: Timepoint01_Hive15_APM_P01-1381


title: Timepoint01_Hive11_APM_P01-1361


title: Timepoint01_Hive12_APM_P01-1362


title: Timepoint01_Hive07_APM_P01-1341


title: Timepoint01_Hive09_APM_P01-1351


title: Timepoint01_Hive06_APM_P01-1332


title: Timepoint01_Hive05_APM_P01-1331


title: Timepoint01_Hive08_APM_P01-1342


title: Timepoint01_Hive14_APM_P01-1372


title: Timepoint01_Hive03_APM_P01-1321


title: Timepoint01_Hive01_APM_P01-1311


title: Timepoint01_Hive13_APM_P01-1371


title: Timepoint14_Hive09_APM_P02-0621


title: Timepoint38_Hive13_APM_P03-1012


title: Timepoint38_Hive20_APM_P03-1051


title: Timepoint38_Hive11_APM_P03-1002


title: Timepoint38_Hive12_APM_P03-1011


title: Timepoint38_Hive16_APM_P03-1022


title: Timepoint38_Hive05_APM_P03-0981


title: Timepoint38_Hive18_APM_P03-1032


title: Timepoint38_Hive09_APM_P03-1001


title: Timepoint38_Hive02_APM_P03-0962


title: Timepoint01_Hive04_APM_P01-1322


title: Timepoint01_Hive10_APM_P01-1352


title: Timepoint38_Hive04_APM_P03-0972


title: Timepoint38_Hive08_APM_P03-0992


title: Timepoint38_Hive15_APM_P03-1021


title: Timepoint38_Hive07_APM_P03-0991


title: Timepoint01_Hive02_APM_P01-1312


title: Timepoint36_Hive17_APM_P03-0181


title: Timepoint36_Hive20_APM_P03-0192


title: Timepoint17_Hive11_APM_P02-0361


title: Timepoint36_Hive12_APM_P03-0161


title: Timepoint36_Hive13_APM_P03-0162


title: Timepoint36_Hive15_APM_P03-0171


title: Timepoint38_Hive03_APM_P03-0971


title: Timepoint36_Hive11_APM_P03-0152


title: Timepoint38_Hive17_APM_P03-1031


title: Timepoint38_Hive01_APM_P03-0961


title: Timepoint36_Hive09_APM_P03-0151


title: Timepoint36_Hive07_APM_P03-0141


title: Timepoint36_Hive08_APM_P03-0142


title: Timepoint36_Hive06_APM_P03-0132


title: Timepoint36_Hive02_APM_P03-0112


title: Timepoint35_Hive13_APM_P03-0062


title: Timepoint36_Hive01_APM_P03-0111


title: Timepoint35_Hive20_APM_P03-0092


title: Timepoint35_Hive16_APM_P03-0072


title: Timepoint36_Hive03_APM_P03-0121


title: Timepoint36_Hive16_APM_P03-0172


title: Timepoint35_Hive15_APM_P03-0071


title: Timepoint35_Hive18_APM_P03-0082


title: Timepoint35_Hive09_APM_P03-0051


title: Timepoint35_Hive19_APM_P03-0091


title: Timepoint35_Hive12_APM_P03-0061


title: Timepoint35_Hive06_APM_P03-0032


title: Timepoint35_Hive08_APM_P03-0042


title: Timepoint35_Hive05_APM_P03-0031


title: Timepoint35_Hive04_APM_P03-0022


title: Timepoint35_Hive03_APM_P03-0021


title: Timepoint36_Hive04_APM_P03-0122


title: Timepoint36_Hive05_APM_P03-0131


title: Timepoint35_Hive17_APM_P03-0081


title: Timepoint35_Hive02_APM_P03-0012


title: Timepoint34_Hive19_APM_P03-0402


title: Timepoint34_Hive18_APM_P03-0401


title: Timepoint35_Hive11_APM_P03-0052


title: Timepoint35_Hive01_APM_P03-0011


title: Timepoint34_Hive17_APM_P03-0392


title: Timepoint35_Hive07_APM_P03-0041


title: Timepoint34_Hive16_APM_P03-0391


title: Timepoint34_Hive15_APM_P03-0381


title: Timepoint34_Hive12_APM_P03-0362


title: Timepoint34_Hive14_APM_P03-0372


title: Timepoint34_Hive10_APM_P03-0352


title: Timepoint34_Hive11_APM_P03-0361


title: Timepoint34_Hive08_APM_P03-0342


title: Timepoint34_Hive09_APM_P03-0351


title: Timepoint34_Hive07_APM_P03-0341


title: Timepoint34_Hive06_APM_P03-0332


title: Timepoint34_Hive05_APM_P03-0331


title: Timepoint34_Hive13_APM_P03-0371


title: Timepoint34_Hive04_APM_P03-0322


title: Timepoint34_Hive01_APM_P03-0311


title: Timepoint34_Hive02_APM_P03-0312


title: Timepoint33_Hive19_APM_P03-0301


title: Timepoint33_Hive20_APM_P03-0302


title: Timepoint33_Hive18_APM_P03-0292


title: Timepoint33_Hive15_APM_P03-0281


title: Timepoint33_Hive16_APM_P03-0282


title: Timepoint33_Hive17_APM_P03-0291


title: Timepoint33_Hive14_APM_P03-0272


title: Timepoint33_Hive11_APM_P03-0261


title: Timepoint33_Hive13_APM_P03-0271


title: Timepoint33_Hive12_APM_P03-0262


title: Timepoint34_Hive03_APM_P03-0321


title: Timepoint33_Hive09_APM_P03-0251


title: Timepoint33_Hive07_APM_P03-0241


title: Timepoint33_Hive03_APM_P03-0221


title: Timepoint33_Hive08_APM_P03-0242


title: Timepoint33_Hive01_APM_P03-0211


title: Timepoint31_Hive18_APM_P03-0911


title: Timepoint33_Hive05_APM_P03-0231


title: Timepoint33_Hive02_APM_P03-0212


title: Timepoint31_Hive17_APM_P03-0901


title: Timepoint31_Hive16_APM_P03-0892


title: Timepoint31_Hive19_APM_P03-0912


title: Timepoint33_Hive04_APM_P03-0222


title: Timepoint38_Hive06_APM_P03-0982


title: Timepoint31_Hive15_APM_P03-0891


title: Timepoint33_Hive10_APM_P03-0252


title: Timepoint31_Hive12_APM_P03-0562


title: Timepoint31_Hive13_APM_P03-0571


title: Timepoint33_Hive06_APM_P03-0232


title: Timepoint31_Hive11_APM_P03-0561


title: Timepoint31_Hive10_APM_P03-0552


title: Digestive gland_Stage4_rep2

city: Alessandria

first: Francesco

last: Dondero

address: Via Michel 11

department: Department of Environmental and Life Sciences

country: Italy

institute: University of Piemonte Orientale "Amedeo Avogadro"

description:
Stage 4
Test/reference design (female/male)

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Bio-rad Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, loess normalized. Data obtained from log2 of processed Ch1 signal / processed Ch2 signal. LIMMA software was used

organism: Mytilus galloprovincialis

source_name: Digestive gland tissue, individual sampled on March 2008, Bizerta Lagoon, Tunisia, stage 4 of female gonad development

label_protocol: 15 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

tag: tissue

value: digestive gland

tag: date

tag: geographical location

value: Bizerta Lagoon, Tunisia

tag: developmental stage

value: stage 4 of female gonad development

source_name: Digestive gland tissue, individual sampled on March 2008, Bizerta Lagoon, Tunisia, stage 4 of male gonad development

value: stage 4 of male gonad development


title: Timepoint31_Hive14_APM_P03-0572


title: Digestive gland_Stage4_rep3

value: female

value: male


title: Timepoint31_Hive09_APM_P03-0551


title: Digestive gland_Stage4_rep1


title: Digestive gland_Stage4_rep4


title: Timepoint31_Hive07_APM_P03-0541


title: Digestive gland_Stage3_rep2

description:
Stage 3
Test/reference design (female/male)

source_name: Digestive gland tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia, stage 3 of female gonad development

value: stage 3 of female gonad development

source_name: Digestive gland tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia, stage 3 of male gonad development

value: stage 3 of male gonad development


title: Digestive gland_Stage3_rep3


title: Digestive gland_Stage3_rep1


title: Digestive gland_Stage3_rep4


title: Timepoint31_Hive05_APM_P03-0531


title: Timepoint31_Hive08_APM_P03-0542


title: Timepoint31_Hive04_APM_P03-0522


title: Timepoint31_Hive03_APM_P03-0521


title: Digestive gland_Stage2_rep4

description:
Stage 2
Test/reference design (female/male)

source_name: Digestive gland tissue, individual sampled on January 2007, Bizerta Lagoon, Tunisia, stage 2 of female gonad development

value: stage 2 of female gonad development

source_name: Digestive gland tissue, individual sampled on January 2007, Bizerta Lagoon, Tunisia, stage 2 of male gonad development

value: stage 2 of male gonad development


title: Digestive gland_Stage2_rep3


title: Timepoint31_Hive06_APM_P03-0532


title: Digestive gland_Stage2_rep2


title: Digestive gland_Stage1_rep4

description:
Stage 1
Test/reference design (female/male)

source_name: Digestive gland tissue, individual sampled on November 2007, Bizerta Lagoon, Tunisia, stage 1 of female gonad development

value: stage 1 of female gonad development

source_name: Digestive gland tissue, individual sampled on November 2007, Bizerta Lagoon, Tunisia, stage 1 of male gonad development

value: stage 1 of male gonad development


title: Timepoint31_Hive02_APM_P03-0512


title: Timepoint31_Hive01_APM_P03-0511


title: Digestive gland_Stage1_rep2


title: Digestive gland_Stage2_rep1


title: Timepoint27_Hive16_APM_P03-0502


title: Timepoint27_Hive14_APM_P03-0491


title: Timepoint27_Hive15_APM_P03-0501


title: Timepoint27_Hive13_APM_P03-0482


title: Digestive gland_Stage1_rep1


title: Digestive gland_Stage1_rep3


title: Mantle_Stage2/Stage1_rep2 [male]

description: loop design

source_name: Mantle tissue, individual sampled on January 2008, Bizerta Lagoon, Tunisia, stage 2 of male gonad development

extract_protocol: Total RNA extracted from the mantle of a single individual mussel using Trizol following manufacturer's instructions

value: Mantle

source_name: Mantle tissue, individual sampled on November 2007, Bizerta Lagoon, Tunisia, stage 1 of male gonad development


title: Timepoint27_Hive09_APM_P03-0451


title: Timepoint27_Hive11_APM_P03-0462


title: Mantle_Stage2/Stage1_rep4 [male]

description: loop design


title: Mantle_Stage2/Stage1_rep3 [male]

description: loop design


title: Timepoint27_Hive10_APM_P03-0461


title: Mantle_Stage3/Stage2_rep2 [male]

description: loop design

source_name: Mantle tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia, stage 3 of male gonad development


title: Timepoint27_Hive08_APM_P03-0442


title: Mantle_Stage3/Stage2_rep3 [male]

description: loop design


title: Mantle_Stage3/Stage2_rep4 [male]

description: loop design


title: Mantle_Stage4/Stage3_rep4 [male]

description: loop design

source_name: Mantle tissue, individual sampled on March 2008, Bizerta Lagoon, Tunisia, stage 4 of male gonad development


title: Mantle_Stage3/Stage2_rep1 [male]

description: loop design

source_name: Mantle tissue, individual sampled on February  2008, Bizerta Lagoon, Tunisia, stage 3 of male gonad development


title: Timepoint27_Hive07_APM_P03-0441


title: Timepoint27_Hive06_APM_P03-0432


title: Timepoint27_Hive05_APM_P03-0431


title: Mantle_Stage2/Stage1_rep1 [male]

description: loop design


title: Timepoint27_Hive12_APM_P03-0481


title: Timepoint27_Hive03_APM_P03-0421


title: Mantle_Stage4/Stage3_rep3 [male]

description: loop design


title: Timepoint27_Hive01_APM_P03-0411


title: Timepoint27_Hive02_APM_P03-0412


title: Mantle_Stage4/Stage3_rep2 [male]

description: loop design


title: Timepoint27_Hive04_APM_P03-0422


title: Timepoint23_Hive19_APM_P01-1501


title: Mantle_Stage4/Stage3_rep1 [male]

description: loop design


title: Timepoint36_Hive18_APM_P03-0182


title: Timepoint23_Hive18_APM_P01-1492


title: Mantle_Stage4/Stage1_rep4 [male]

description: loop design


title: Mantle_Stage4/Stage1_rep3 [male]

description: loop design


title: Timepoint23_Hive14_APM_P01-1472


title: Timepoint23_Hive16_APM_P01-1482


title: Mantle_Stage4/Stage1_rep2 [male]

description: loop design


title: Timepoint23_Hive15_APM_P01-1481


title: Timepoint23_Hive12_APM_P01-1462


title: Timepoint23_Hive13_APM_P01-1471


title: Mantle_Stage3/Stage2_rep4 [female]

description: loop design

source_name: Mantle tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia, stage 4 of female gonad development

source_name: Mantle tissue, individual sampled on January 2008, Bizerta Lagoon, Tunisia, stage 2 of female gonad development


title: Timepoint23_Hive20_APM_P01-1502


title: Timepoint23_Hive09_APM_P01-1451


title: Timepoint23_Hive11_APM_P01-1461


title: Timepoint23_Hive10_APM_P01-1452


title: Mantle_Stage4/Stage1_rep1 [male]

description: loop design


title: Timepoint23_Hive08_APM_P01-1442


title: Mantle_Stage4/Stage1_rep3 [female]

description: loop design

source_name: Mantle tissue, individual sampled on March 2008, Bizerta Lagoon, Tunisia, stage 4 of female gonad development

source_name: Mantle tissue, individual sampled on November 2007, Bizerta Lagoon, Tunisia, stage 1 of female gonad development


title: Timepoint23_Hive17_APM_P01-1491

source_name: Whole Bee Homogenate


title: Timepoint23_Hive07_APM_P01-1441


title: Mantle_Stage4/Stage1_rep2 [female]

description: loop design


title: Mantle_Stage4/Stage1_rep4 [female]

description: loop design


title: Timepoint23_Hive04_APM_P01-1422


title: Timepoint23_Hive05_APM_P01-1431


title: Timepoint23_Hive02_APM_P01-1412


title: Timepoint23_Hive03_APM_P01-1421


title: Timepoint23_Hive01_APM_P01-1411


title: Timepoint22_Hive20_APM_P02-1802


title: Timepoint22_Hive19_APM_P02-1801


title: Timepoint22_Hive18_APM_P02-1792


title: Timepoint22_Hive11_APM_P02-1761


title: Timepoint22_Hive16_APM_P02-1782


title: Timepoint22_Hive17_APM_P02-1791


title: Timepoint22_Hive12_APM_P02-1762


title: Timepoint22_Hive13_APM_P02-1771


title: Timepoint22_Hive14_APM_P02-1772


title: Timepoint22_Hive15_APM_P02-1781


title: Timepoint22_Hive02_APM_P02-1712


title: Timepoint22_Hive03_APM_P02-1721


title: Timepoint22_Hive05_APM_P02-1731


title: Mantle_Stage4/Stage1_rep1 [female]

description: loop design


title: Timepoint23_Hive06_APM_P01-1432


title: Timepoint22_Hive04_APM_P02-1722


title: Timepoint21_Hive20_APM_P02-1402


title: Mantle_Stage3/Stage2_rep1 [female]

description: loop design

source_name: Mantle tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia, stage 3 of female gonad development


title: Timepoint21_Hive17_APM_P02-1391


title: Mantle_Stage4/Stage3_rep4 [female]

description: loop design


title: Mantle_Stage4/Stage3_rep3 [female]

description: loop design


title: Timepoint22_Hive01_APM_P02-1711


title: Timepoint22_Hive10_APM_P02-1752


title: Timepoint22_Hive09_APM_P02-1751


title: Timepoint21_Hive19_APM_P02-1401


title: Timepoint21_Hive16_APM_P02-1382


title: Mantle_Stage2/Stage1_rep2 [female]

description: loop design


title: Mantle_Stage2/Stage1_rep3 [female]

description: loop design


title: Timepoint21_Hive18_APM_P02-1392


title: Mantle_Stage3/Stage2_rep3 [female]

description: loop design

source_name: Mantle tissue, individual sampled on January 2007, Bizerta Lagoon, Tunisia, stage 2 of female gonad development


title: Timepoint22_Hive07_APM_P02-1741


title: Timepoint22_Hive08_APM_P02-1742


title: Timepoint22_Hive06_APM_P02-1732


title: Timepoint21_Hive15_APM_P02-1381


title: Digestive_gland_Mar/Feb_rep4

description: loop design representing month n+1 / month n (example, Feb/Jan, Mar/Feb, April/March, etc.)

source_name: digestive gland tissue, individual sampled on March 2008, Bizerta Lagoon, Tunisia

extract_protocol: Total RNA extracted a the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

source_name: digestive gland tissue, individual sampled on February 2008, Bizerta Lagoon, Tunisia


title: Mantle_Stage3/Stage2_rep2 [female]

description: loop design


title: Mantle_Stage2/Stage1_rep1 [female]

description: loop design


title: Timepoint21_Hive14_APM_P02-1372


title: Timepoint21_Hive13_APM_P02-1371


title: Mantle_Stage4/Stage3_rep1 [female]

description: loop design


title: Mantle_Stage4/Stage3_rep2 [female]

description: loop design


title: Timepoint21_Hive11_APM_P02-1361


title: Timepoint21_Hive10_APM_P02-1352


title: Timepoint21_Hive12_APM_P02-1362


title: Timepoint21_Hive08_APM_P02-1342


title: Timepoint21_Hive06_APM_P02-1332


title: Timepoint21_Hive09_APM_P02-1351


title: Timepoint21_Hive05_APM_P02-1331


title: Digestive_gland_Apr/Mar_rep3

source_name: digestive gland tissue, individual sampled on April 2008, Bizerta Lagoon, Tunisia


title: Digestive_gland_Mar/Feb_rep2


title: Digestive_gland_Mar/Feb_rep1


title: Digestive_gland_Mar/Feb_rep3


title: Digestive_gland_Apr/Mar_rep2


title: Digestive_gland_Apr/Mar_rep4


title: Digestive_gland_Apr/Mar_rep1


title: Digestive_gland_May/Apr_rep4

source_name: digestive gland tissue, individual sampled on May 2007, Bizerta Lagoon, Tunisia


title: Timepoint20_Hive20_APM_P02-1202


title: Timepoint21_Hive07_APM_P02-1341


title: Timepoint21_Hive01_APM_P02-1311


title: Timepoint20_Hive19_APM_P02-1201


title: Timepoint20_Hive18_APM_P02-1192


title: Digestive_gland_May/Apr_rep3


title: Timepoint20_Hive17_APM_P02-1191


title: Timepoint21_Hive03_APM_P02-1321


title: Digestive_gland_May/Apr_rep2


title: Timepoint20_Hive14_APM_P02-1172


title: Digestive_gland_May/Apr_rep1


title: Timepoint20_Hive15_APM_P02-1181


title: Timepoint21_Hive02_APM_P02-1312


title: Timepoint20_Hive11_APM_P02-1161


title: Digestive_gland_Jun/May_rep3

source_name: digestive gland tissue, individual sampled on June 2007, Bizerta Lagoon, Tunisia


title: Digestive_gland_Jun/May_rep2


title: Timepoint20_Hive12_APM_P02-1162


title: Timepoint20_Hive09_APM_P02-1151


title: Timepoint20_Hive10_APM_P02-1152


title: Mantle_Stage2/Stage1_rep4 [female]

description: loop design


title: Timepoint20_Hive07_APM_P02-1141


title: Timepoint20_Hive08_APM_P02-1142


title: Timepoint20_Hive05_APM_P02-1131


title: Timepoint20_Hive16_APM_P02-1182


title: Timepoint20_Hive04_APM_P02-1122


title: Timepoint20_Hive13_APM_P02-1171


title: Timepoint20_Hive06_APM_P02-1132


title: Timepoint20_Hive03_APM_P02-1121


title: Digestive_gland_Jun/May_rep1


title: Digestive_gland_Jul/Jun_rep3

source_name: digestive gland tissue, individual sampled on July 2007, Bizerta Lagoon, Tunisia


title: Digestive_gland_Jul/Jun_rep2


title: Timepoint20_Hive01_APM_P02-1111


title: Timepoint19_Hive20_APM_P02-1102


title: Timepoint19_Hive19_APM_P02-1101


title: Digestive_gland_Aug/Jul_rep3

source_name: digestive gland tissue, individual sampled on August 2007, Bizerta Lagoon, Tunisia


title: Timepoint20_Hive02_APM_P02-1112


title: Digestive_gland_Jul/Jun_rep1


title: Digestive_gland_Aug/Jul_rep2


title: Digestive_gland_Aug/Jul_rep1


title: Digestive_gland_Sep/Aug_rep3

source_name: digestive gland tissue, individual sampled on September 2007, Bizerta Lagoon, Tunisia


title: Timepoint19_Hive18_APM_P02-1092


title: Timepoint19_Hive16_APM_P02-1082


title: Timepoint19_Hive12_APM_P02-1062


title: Digestive_gland_Sep/Aug_rep2


title: Timepoint19_Hive10_APM_P02-1052


title: Timepoint19_Hive11_APM_P02-1061


title: Digestive_gland_Sep/Aug_rep1


title: Timepoint19_Hive13_APM_P02-1071


title: Timepoint19_Hive14_APM_P02-1072


title: Timepoint19_Hive08_APM_P02-1042


title: Digestive_gland_Oct/Sep_rep2

source_name: digestive gland tissue, individual sampled on October 2007, Bizerta Lagoon, Tunisia


title: Timepoint19_Hive09_APM_P02-1051


title: Timepoint19_Hive15_APM_P02-1081


title: Digestive_gland_Nov/Oct_rep3

source_name: digestive gland tissue, individual sampled on November 2007, Bizerta Lagoon, Tunisia


title: Digestive_gland_Oct/Sep_rep1


title: Digestive_gland_Nov/Oct_rep1


title: Timepoint19_Hive17_APM_P02-1091


title: Digestive_gland_Nov/Oct_rep2


title: Digestive_gland_Oct/Sep_rep3


title: A36 vs a36-2_Sample 14

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

institute: Yale University

description: dye-swap

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Neurospora crassa

source_name: myceilia

label_protocol: 2 µg of mRNA were primed with .5 µl of 10 µM MTP or Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 40 U SuperScript II RTase (Invitrogen), and .8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: Bird media, room temperature

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

treatment_protocol: constant light

value: mat A FGSC 2489

tag: developmental stage (culture time)

value: mat-a FGSC 4200


title: Digestive_gland_Jan/Dec_rep2

source_name: digestive gland tissue, individual sampled on January 2008, Bizerta Lagoon, Tunisia

source_name: digestive gland tissue, individual sampled on December 2007, Bizerta Lagoon, Tunisia


title: a60 vs a96_Sample 26

description: dye-swap


title: A60 vs A36-2_Sample 21

description: dye-swap


title: A96 vs a96_Sample 19


title: a60 vs a96_Sample 20


title: A36 vs A60-2_Sample 22

description: dye-swap


title: A96 vs A60_Sample 23

description: dye-swap


title: Digestive_gland_Dec/Nov_rep2


title: Digestive_gland_Jan/Dec_rep3


title: Digestive_gland_Dec/Nov_rep1


title: a96 vs a60_Sample 25

description: dye-swap


title: A60 vs A96_Sample 24

description: dye-swap


title: a36 vs a60-2_Sample 12

description: dye-swap


title: a36 vs A36-2_Sample 13

description: dye-swap


title: a96 vs A96_Sample 15

description: dye-swap


title: a36 vs a60_Sample 10

description: dye-swap


title: a60 vs A60_Sample 17

description: dye-swap


title: A60 vs a60_Sample 18

description: dye-swap


title: Digestive_gland_Jan/Dec_rep1