title: A673 control

description:
S1315_A673_nsiRNA
knock-down control A673 cells treated with control siRNA


title: triple negative breast cancer cells T155

status: Public on Dec 21 2012

type: RNA

city: Tokushima

first: Masato

last: Komatsu

address: Kuramoto-cho 3-18-15

country: Japan

institute: Genome Medicine

hyb_protocol: 2 μg of Cy3-labeled cRNA was fragmented and hybridized onto the Agilent Whole Human Genome Microarray 4 × 44K slide (Agilent-014850, G4110F), with rotating incubation at 65˚C for 18 h.

scan_protocol: Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation, and scanned by the Agilent Microarray scanner system (G2505B) in an ozone protection fume hood.

data_processing: Features of scanned image files containing the Cy3-fluorescence signals of the hybridized Agilent Microarrays were extracted using the Agilent Feature Extraction (ver. 9.5).  The data files were subjected to the GeneSpring (ver. 11.5) for analysis.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: triple negative breast cancer cells

label_protocol: For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit according to the manufacture’s guidance.  100 ng of total RNA of each sample and normal organs including heart, lung, liver, and kidney (Takara) was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

extract_protocol: We purified 30 TNBC, 13 normal ductal cells using lasermicrobeam microdissection system (PALM MicroBeam, Carl Zeiss MicroImaging Co., Ltd) in accordance with the manufacturer’s guidance.  Dissected cancer and normal ductal cells were dissolved in RLT lysis buffer (QIAGEN, Maryland, CA) containing 1% β-mercaptoethanol.  The extracted total RNAs were purified with RNeasy Mini Kit (QIAGEN, Velanica, CA) according to the manufacture’s protocol.  For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit according to the manufacture’s guidance.  Briefly, 100 ng of total RNA of each sample was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

tag: disease state

value: triple negative breast cancer

tag: cell type

value: triple negative breast cancer cells

tag: gender

value: female

tag: age (y)


title: Mouse#33

city: Koeln

first: Bernhard

last: Schermer

address: Kerpener Str. 62

department: Dept. II for Internal Medicine

country: Germany

institute: Universitaet zu Koeln

description: SAMPLE 14

hyb_protocol: Manufacturer's protocol (Affymetrix GeneChip)

scan_protocol: Affymetrix GeneChip 3000 6G scanner

data_processing: Robust Multiarray Average (RMA), Affymetrix Power Tools, v1.12.0

label: biotin

organism: Mus musculus

source_name: Ercc1 mouse at 4 wks

label_protocol: Encore Biotin Module, NuGen Technologies, San Carlos, CA, USA

extract_protocol: Frozen glomeruli were thawn and total RNA was extracted and purified using commercial homogenization (Bio 101 FastPrep FP120-120V, Savant, Midland, MI, USA) and the RNeasy kit (Qiagen, Hilden, Germany).

tag: strain background

value: genetically uniform hybrid C57BL/6-FVB [PMID 22953029]

tag: genotype/variation

tag: age

value: 4 weeks


title: MII siAPC, biological replicate C

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from  MII cells depleted of APC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.

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

treatment_protocol: Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions

tag: cell line

value: MCF10-T1k (MII)

tag: treatment

value: transfected with APC siRNA


title: triple negative breast cancer cells T56


title: MII siGFP, biological replicate B

description: Gene expression data from control MII cells

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with Control siRNA

value: transfected with Control siRNA


title: Mouse#35

description: SAMPLE 16


title: triple negative breast cancer cells T1


title: triple negative breast cancer cells T60


title: Mouse#44

description: SAMPLE 21

source_name: Ercc1 mouse at 14 wks

value: 14 weeks


title: Mouse#27

description: SAMPLE 12

source_name: wild type mouse at 96 wks

value: wild type

value: 96 weeks


title: Mouse#28

description: SAMPLE 13


title: triple negative breast cancer cells T363


title: MII siGFP, biological replicate C


title: triple negative breast cancer cells T528


title: C3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: LNCaP-abl cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: LNCaP-abl cells were grown on 10 cm dished to 70% confluence in charcoal stripped RPMI media

extract_protocol: RNA was extracted with Qiagen kit according to the manufacturers instructions

treatment_protocol: cells were treated with compounds to a final concentration of 1 micromolar (20 micromolar for C3)

value: LNCaP-abl cells

tag: agent


title: Mouse#26

description: SAMPLE 11


title: cyc

value: cyc


title: Mouse#25

description: SAMPLE 10


title: Mouse#24

description: SAMPLE 9


title: Mouse#16

description: SAMPLE 7

source_name: wild type mouse at 14 wks


title: n=8


title: Mouse#15

description: SAMPLE 6


title: Mouse#23

description: SAMPLE 8


title: Mouse#8

description: SAMPLE 3

source_name: wild type mouse at 4 wks


title: Mouse#5

description: SAMPLE 1


title: triple negative breast cancer cells T481


title: triple negative breast cancer cells T265


title: triple negative breast cancer cells T415


title: Mouse#6

description: SAMPLE 2


title: triple negative breast cancer cells T420


title: vehicle

value: vehicle


title: S2N monolayer, biol. Replicate 3

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

institute: Roche Pharma

description: Gene expression data from tumorigenic (S2N), normal-like to basal-like breast cancer cell lines derived from primary tumors (monolayer).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: breast cancer tumor initiating cells

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

growth_protocol: Freshly purified breast tumor cells were depleted of erythrocytes and leukocytes by ammonium chloride lysis and Microbeads, respectively (Miltenyi Biotec, Bergisch-Gladbach, Germany). Mammospheres were grown as described previously in mammary epithelial basal medium (Lonza, Cologne, Germany) in T75 low adhesion cell culture flasks (Corning Life Sciences, Wiesbaden, Germany) and passaged every 3 to 4 days after sphere formation (32). Monolayer cultures were derived from mammosphere cells and  cultivated in collagen coated T75 cell culture flasks (BD Bioscience) in mammary epithelial basal medium supplemented with 10 %  FBS (Invitrogen). Monolayer cells were allowed to differentiate for at least 10 days prior analysis.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Hilden, Germany) followed by cDNA synthesis using a cDNA synthesis kit (Roche).

treatment_protocol: Cells from spheres or monolayers were used without further pretreatment

tag: sample type

value: monolayer


title: Mouse#14

description: SAMPLE 5


title: S2N spheres, biol. Replicate 3

description: Gene expression data from tumorigenic (S2N), normal-like to basal-like breast cancer cell lines derived from primary tumors (sphere culture).

value: spheres


title: S2N monolayer, biol. Replicate 1


title: S2N spheres, biol. Replicate 2


title: Mouse#13

description: SAMPLE 4


title: triple negative breast cancer cells T116


title: S2N monolayer, biol. Replicate 2


title: triple negative breast cancer cells T252


title: T7 neg control IP Rep3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Swiss Webster mouse (Taconic) E13-14 cortex T7 immunoprecipitated RNA negative control

hyb_protocol: biotinylated sense strand cDNA was hybridized using standard Affymetrix protocol for 16hrs

scan_protocol: Affymetrix Standard protocol on GCS3000 7G scanner

data_processing: The data were normalized using PLIER in Expression Console

source_name: T7 immunoprecipitated RNA

label_protocol: Biotin labeling was done using standard NuGEN pico protocol starting with approximately 10ng RNA

growth_protocol: Cortex Tissue was dissected from E13-14 brains of timed-pregnant Swiss Webster mice (Taconic)

extract_protocol: RNA immunoprecipitation with Stau2 antibody (Abcam ab60724) and T7 antibody (Novagen 69522). RNA isolation and purification with acid phenol/choloform extraction (also as described in Baroni, T.E., Chittur, S.V., George, A.D., and Tenenbaum, S.A. (2008). Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods in molecular biology.) and RNA resuspended in Rnase-free water.

treatment_protocol: Lysis buffer and protocol reference: Baroni, T.E., Chittur, S.V., George, A.D., and Tenenbaum, S.A. (2008). Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods in molecular biology.

tag: strain

value: Swiss Webster

tag: tissue

value: embryonic cortex

tag: antibody

value: T7 (Novagen 69522)


title: Stau2 IP Rep3

description: Swiss Webster mouse (Taconic) E13-14 cortex Stau2 immunoprecipitated RNA

source_name: Stau2 immunoprecipitated RNA

value: Stau2 (Abcam ab60724)


title: triple negative breast cancer cells T313

value: triple negative breast cancer

value: triple negative breast cancer cells

value: female


title: Stau2 Input Rep3

description: Swiss Webster mouse (Taconic) E13-14 cortex total RNA

source_name: total RNA

value: none (input)


title: T7 neg control IP Rep2


title: triple negative breast cancer cells T558


title: triple negative breast cancer cells T366


title: triple negative breast cancer cells T384


title: Stau2 IP Rep2


title: S2 monolayer, biol. Replicate 3

description: Gene expression data from non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines derived from primary tumors (monolayer).


title: S2N spheres, biol. Replicate 1


title: triple negative breast cancer cells T362


title: Blood_LPS treatment_C

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: miRNA

hyb_protocol: Cy5-labelled enrichment miRNA was denatrued at 95°C for 5 minutes in a reaction volume of 90 μl containing 1x miRNA hybridization buffer. On completion of the denature reaction, the mixture are hybridized to Phalanx Mouse & Rat miRNA OneArray  for 16 hours at 37 °C in a rotating hybridization oven.  After hybridization, microarrays were washed 5 minute at 37 °C with Wash Buffer 1 (Phalanx), 5 minute at 37 °C with Wash Buffer 2 (Phalanx) and 5 minute at room temperature with Wash Buffer 2 (Phalanx) and then rinsed with Wash Buffer 3 (Phalanx). Finally, the arrays were dried by centrifuge.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B Microarray Scanner (Molecular Devices) using two color scan (Scan resolution 10um, Laser power setting is 100%).

data_processing: The scanned images were analyzed with GenePix 4.0 (Molecular Devices)

source_name: Blood_LPS treatment

label_protocol: Cyanine-5 (Cy5) labeled total RNA was prepared from 2.5 ug RNA using the ULSTM microRNA Labeling kit (Kreatech, Netherlands) according to the manufacturer's instructions, followed by Nanosep 100K miRNA enrichment (Pall Corporation).  Dye incorporation andRNA amount were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA extraction

treatment_protocol: 100 ug LPS v.s. PBS intraperitoneal injection & harvest of the sample tissue 6 h later

tag: background strain

tag: tissue type

value: blood


title: Ministat vs sixfor sulfate limitation RNA replicate 3

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: B26_2-18-11-Cy5 vs F3_3-2-4-Cy3

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf

scan_protocol: Pixel Size : 909.090909090909 Scan Date : 2011-03-25 Scan Time : 14:05:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

growth_protocol:
limiting nutrient : sulfate
dilution rate : 0.17 volumes/hour
Culture Methods : chemostat (sixfors)

extract_protocol:
Extracted molecule : RNA
Extraction method : acid phenol extraction with Qiagen RNeasy cleanup

tag: strain name

tag: genotype

value: diploid prototroph

tag: culture method

value: chemostat (sixfors)

growth_protocol:
limiting nutrient : sulfate
dilution rate : 0.17 volumes/hour
Culture Methods : chemostat (ministat)

value: chemostat (ministat)


title: Stau2 Input Rep2


title: T7 neg control IP Rep1


title: Ministat vs sixfor sulfate limitation RNA replicate 1

description: B29_2-18-11-Cy5 vs F3_3-2-4-Cy3

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf


title: Stau2 Input Rep1


title: Stau2 IP Rep1


title: Blood_LPS treatment_B

description: miRNA


title: S2 monolayer, biol. Replicate 1


title: S2 monolayer, biol. Replicate 2


title: Blood_LPS treatment_A

description: miRNA


title: triple negative breast cancer cells T359

tag: disease state

tag: cell type

tag: gender


title: Ministat vs sixfor sulfate limitation RNA replicate 2

description: B25_2-18-11-Cy5 vs F3_3-2-4-Cy3


title: S2 spheres, biol. Replicate 2

description: Gene expression data from non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines derived from primary tumors (sphere culture).


title: Blood_Control_B

description: miRNA


title: Noggin1

description: K14 promoter-driven noggin overexpressing

hyb_protocol: Standard Affymetrix WT protocol for Gene 1.0 ST arrays

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA

label: Biotin

source_name: Laser capture microdissected epidermis, Noggin-overexpressing

label_protocol: Total RNA was biotin labeled using the NuGEN pico amplification protocol

extract_protocol: Glabrous hindpaw skin samples from euthanized transgenic animals were quickly dissesected free, placed on a small sponge to maintain a flattened orientation, and snap frozen in liquid N2 cooled isopentane. Samples were cryostat sectioned at 14mm thickness and placed onto a series of RNAse-free glass slides with suffiecient separation between adjacent section to allow for LCM. Slides were then quickly stained with Hematoxilin and Eosin, dehydrated through ethanols and xylene, and placed onto the AutoPixII LCM, where the epidermis of each sample was outlined. Once dry, the epidermis strips from each section were laser etched and captured for RNA extraction.  Total RNA was extracted using the Arcturus Picopure isolation kit using manufacturer recommended protocols.

value: glabrous hindpaw skin


title: triple negative breast cancer cells T253

tag: age (y)


title: S2 spheres, biol. Replicate 1


title: Spleen_LPS treatment_A

description: miRNA

source_name: Spleen_LPS treatment

value: spleen


title: Spleen_LPS treatment_B

description: miRNA


title: Spleen_Control_C

description: miRNA


title: Spleen_LPS treatment_C

description: miRNA


title: BMP4_1

description: K14 promoter-driven BMP4 overexpressing

scan_protocol: Standard Affymetrix WT protocol for Gene 1.0 ST arrays

source_name: Laser capture microdissected epidermis, BMP4-overexpressing


title: Blood_Control_C

description: miRNA


title: Noggin2


title: BMP4_2

description: K14 promoter-driven BMP4 overexpressing


title: p100(-/-)_rep5

city: Jena

first: Daniela

last: Albrecht

address: Wildenbruchstr. 15

institute: BioControl Jena GmbH

hyb_protocol: according to manufacturers instructions (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: GenePix 4000B Array Scanner and GenePix Pro 4.0 software according to the settings suggested by GE Healthcare (supplier of CodeLink microarrays at experiment time, http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

data_processing: Raw data were analysed using Codelink Expression Analysis v.4.1 software to extract MDFCs (minimal detectable fold changes). Subsequent analysis was done using R and Bioconductor. Only probes with probe type DISCOVERY were considered (34967 transcripts). Intensity values <0.01 were set to 0.01. Raw intensities were scaled to array median. After logarithmizing, quantile normalization was applied across all arrays.

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from E14.5 wild-type and p100-/- mouse embryos. Five independent wild-type and five independent p100-/- fibroblast cell lines were cultured at 37C in Dulbecco’s modified Eagle's medium (GIBCO/Invitrogen, Karlsruhe, Germany) supplemented with 10% heat-inactivated fetal bovine serum (PAA Laboratories, Cölbe, Germany), penicillin (100 U/ml), streptomycin (100 mg/ml) and L-glutamine (2 mM) (GIBCO/Invitrogen).

extract_protocol: total cellular RNA was isolated using RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions, possible contamination by genomic DNA was removed by DNAseI treatment using the RNAse-Free DNAse Set (Qiagen), quality was checked by spectrophotometry and agarose gel electrophoresis, 2ug RNA per sample was used for cDNA preparation when A260:A280 ratio was 1.8-2.1 and RNA was intact

treatment_protocol: At age passage 3, MEFs were left untreated and total RNA was isolated for microarray experiments. To paralelly monitor signaling events, cytoplasmic and nuclear proteins were extracted, as well.

tag: development stage

tag: genotype/variation

value: NF-kB2/p100-deficient (p100-/-)

tag: tissue origin

value: embryo

value: mouse embryonic fibroblasts (MEF)


title: Blood_Control_A

description: miRNA


title: Liver_LPS treatment_C

description: miRNA

source_name: Liver_LPS treatment

value: liver


title: wt_rep5

source_name: wt

label_protocol: according to manufacturers instructions (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

value: wild type


title: Liver_LPS treatment_A

description: miRNA


title: Spleen_Control_A

description: miRNA


title: MCF7 + AMD3100 + estrogen

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: MCF7 + AMD3100 + estrogen

hyb_protocol: Standard Affymetrix protocols

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA; software was R using Bioconductor packages.

source_name: MCF7 + AMD3100 + estrogen

label_protocol: GeneChip 3? IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA)

treatment_protocol: Estrogen pellets, 1.7 mg/90 days release;AMD3100: 25 mg/ml, 0.25 ul/h release

tag: cell line

tag: agent

value: AMD3100 + estrogen


title: MCF7 + estrogen

description: MCF7 + estrogen

source_name: MCF7 + estrogen

treatment_protocol: Estrogen pellets, 1.7 mg/90 days release

value: estrogen


title: p100(-/-)_rep4


title: Liver_Control_C

description: miRNA


title: MCF7(TAM-R) + estrogen

description: MCF7(TAM-R) + estrogen

source_name: MCF7(TAM-R) + estrogen


title: p100(-/-)_rep3


title: Spleen_Control_B

description: miRNA


title: MCF7(TAM-R) + AMD3100 + estrogen

description: MCF7(TAM-R) + AMD3100 + estrogen

source_name: MCF7(TAM-R) + AMD3100 + estrogen


title: MCF7(TAM-R) + AMD3100 + tamoxifen

description: MCF7(TAM-R) + AMD3100 + tamoxifen

source_name: MCF7(TAM-R) + AMD3100 + tamoxifen

treatment_protocol: athymic nude mice with implanted xenografts were treated with 500 ug tamoxifen 5 days per week, and AMD3100: 25 mg/ml, 0.25 ul/h release

value: AMD3100 + tamoxifen


title: Brain_LPS treatment_B

description: miRNA

source_name: Brain_LPS treatment

value: brain


title: Liver_Control_B

description: miRNA


title: wt_rep3


title: wt_rep4


title: Liver_Control_A

description: miRNA


title: Brain_LPS treatment_C

description: miRNA


title: Brain_Control_C

description: miRNA


title: MCF7(TAM-R) + tamoxifen

description: MCF7(TAM-R) + tamoxifen

source_name: MCF7(TAM-R) + tamoxifen

treatment_protocol: athymic nude mice with implanted xenografts were treated with 500 ug tamoxifen 5 days per week

value: tamoxifen


title: p100(-/-)_rep2


title: Brain_LPS treatment_A

description: miRNA


title: wt_rep2


title: p100(-/-)_rep1


title: wt_rep1


title: MCF7 + AMD3100 + tamoxifen

description: MCF7 + AMD3100 + tamoxifen

source_name: MCF7 + AMD3100 + tamoxifen


title: Lung_LPS treatment_C

description: miRNA

source_name: Lung_LPS treatment

value: lung


title: Brain_Control_B

description: miRNA


title: Brain_Control_A

description: miRNA


title: MCF7 + tamoxifen

description: MCF7 + tamoxifen

source_name: MCF7 + tamoxifen


title: Lung_LPS treatment_B

description: miRNA


title: Lung_LPS treatment_A

description: miRNA


title: Lung_Control_B

description: miRNA


title: Lung_Control_C

description: miRNA


title: Lung_Control_A

description: miRNA


title: Liver_LPS treatment_B

description: miRNA


title: 8_d42

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: A total of 15 µg of fragmented cRNA was hybridized on an Affymetrix GeneChip (human U133A) at 45ºC for 16 hours at 60 rpm followed by washing/staining procedures.

scan_protocol: All probe arrays were scanned using the GeneChip scanner 3000, and operating software (MAS 5.0) was used to scan the images and for data acquisition.

data_processing: Affymetrix Microarray Suite version 5.0.

source_name: peripheral white blood cells, D42

label_protocol: A total of 5 µg of purified RNA was reverse-transcribed into cDNA using T7-oligo (dT) primer (Affymetrix, Santa Clara, CA) and SuperScript II RT (Invitrogen). The biotin-labeled cRNA was synthesized from cDNA using the BioArray RNA transcript labeling kit (Enzo, Farmingdale, NY) and was followed by fragmentation.

growth_protocol: Peripheral blood was collected using PAXgene tubes, and then stored immediately to -80 degree freezer until ready for RNA extraction. Cells were not grown or cultured.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified using an RNeasy mini kit (Qiagen, Valencia, CA).

treatment_protocol: No treatment for the cells for this natural history study.

value: male

value: non-metastatic prostate cancer

tag: treatment

value: external beam radiation therapy (EBRT)

value: peripheral blood

value: white blood cells

tag: time of wbc and fatigue score collection

tag: individual


title: 8_d72

source_name: peripheral white blood cells, D72

tag: tissue

value: D72 (30 days post-EBRT)


title: 8_d14

source_name: peripheral white blood cells, D14


title: 8_c

source_name: peripheral white blood cells, matched control

value: healthy

tag: sample type

value: matched control


title: 8_b

source_name: peripheral white blood cells, baseline

value: baseline


title: Cdx2 induced leukemia_primary rep2

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description:
SAMPLE 10
Gene expression data from murine Cdx2-induced myeloid leukemia

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: spleen cells from Cdx2-initiated leukemic animals

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).

treatment_protocol:
Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.

tag: strain background

tag: recipient strain

value: lethally irradiated syngeneic mice

tag: cell source

tag: injected with

value: 8x10e5 GFP-positive bone marrow cells (pMSCV-Cdx2-IRES-GFP)


title: murine Cdx2 rep1

description:
SAMPLE 4
Gene expression data from murine hematopoietic stem and progenitor cells

source_name: sorted GFP-positive cells

treatment_protocol:
Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.

Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.

value: bone marrow cells

tag: cell population

value: Lineage-depleted c-Kit+ Lin– cells

tag: transduction


title: Cdx2 induced leukemia_secondary_rep1

description:
SAMPLE 7
Gene expression data from murine Cdx2-induced myeloid leukemia

value: spleen cells from secondary leukemic animals

value: 1x10e6 spleen cells from primary leukemic animal


title: 8_d21

source_name: peripheral white blood cells, D21

tag: gender

tag: disease state

tag: cell type


title: 8_d1

source_name: peripheral white blood cells, D1


title: Cdx2 induced leukemia_secondary_rep2

description:
SAMPLE 8
Gene expression data from murine Cdx2-induced myeloid leukemia


title: murine Cdx2 rep2

description:
SAMPLE 5
Gene expression data from murine hematopoietic stem and progenitor cells


title: Cdx2 induced leukemia_primary rep1

description:
SAMPLE 9
Gene expression data from murine Cdx2-induced myeloid leukemia

value: spleen cells from primary leukemic animal


title: control rep2

description:
SAMPLE 2
Gene expression data from murine hematopoietic stem and progenitor cells

value: MSCV-IRES-GFP-empty


title: murine Cdx2 rep3

description:
SAMPLE 6
Gene expression data from murine hematopoietic stem and progenitor cells


title: 6_d21

value: male


title: 6_d42

value: non-metastatic prostate cancer


title: 6_d14

value: external beam radiation therapy (EBRT)


title: 6_d72

value: peripheral blood


title: 6_d7

source_name: peripheral white blood cells, D7

value: white blood cells


title: 8_d7


title: Rb_p107_carcinoma_rep9

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

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

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

data_processing: The data were analyzed with RMA using RMAExpress

source_name: skin carcinoma, tamoxifen tretaed

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: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

treatment_protocol: Tamoxifen treatment was topically administered in the shaved backskin of animals (2x2 cm) at 20 mg/per day dissolved in DMSO/acetone for 5 consecutive days

tag: strain

value: FVB/N genetic background

value: skin carcinoma


title: control rep3

description:
SAMPLE 3
Gene expression data from murine hematopoietic stem and progenitor cells


title: Ampelisca Mdl.Tric rep6

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

hyb_protocol: Sample placement on the slides was randomized.  Due to the large number of samples, hybridizations were carried out over two consecutive days.  Hybridizations were done according to the manufacturer’s protocol (v 6.5: part number G4140-90040, Agilent).  Following hybridizations and washing, the arrays were immersed in drying and stabilization solution (Agilent), and covered with ozone barrier slide covers.

scan_protocol: Two single pass scans were conducted (10% and 100% PMT) at 5 mm resolution, using an Agilent G2565BA scanner, and combined using the scanner's dual-scan software. Dual-scanning merges two 16-bit images to form a 20 bit image, and serves to increase the potential dynamic range of the scan.

data_processing: Raw data files were imported into R. Data from arrays displaying substantial technical issues apparent in MA-plots, spatial plots, or an analysis of the agreement between replicated probes were removed. Median (across pixels) non-background corrected probe intensities were quantile normalized (BM Bolstad et al., 2003). Technical replicates for a given biological sample were replaced with a single virtual array in which probe intensity was the median of the intensity of the corresponding probe in those technical replicate arrays. Intensities for probes replicated within each array (ESTs are represented by either 2 or 22 identical probes per array) were summarized as the median intensity of the replicate probes. Data from control probesets was removed.

organism: Ampelisca abdita

source_name: Model chemical exposure: Triclosan

label_protocol: Ninety ng of total RNA was labeled with cyanine 3-labeled CTP using the One-color Low Input Quick Amp Labeling kit (Agilent, Santa Clara, CA) according to the manufacturer’s protocol (v 6.5: part number G4140-90040).  Labeled RNAs were purified using RNeasy mini spin columns (Qiagen) and the yield and specific activity were determined using a Nanodrop-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).  If cRNA yield was below 0.825 mg or the specific activity was below 6 pmol per mg cRNA, another tube from the same exposure vessel was extracted and labeled.  If none existed, a new labeling reaction with the original extract was conducted.

growth_protocol: A. abdita were field collected from the Narrow River, Narragansett, RI (N 41 26.921’, W 71 27.515’; May 2011) and juvenile organisms that passed through a 1.0  mm screen, but were retained on a 0.7 mm screen were selected for the experiments.  During holding and acclimation, amphipods were fed cultured algae (Tetraselmis suecica), and held in LIS reference sediment at 20 + 2 oC for at least 24 h prior to testing.

extract_protocol: Total RNA from each tube of organisms was separately isolated using TriReagent (MRC Research, Cincinnati, OH) according to the manufacturer’s protocol and genomic contamination was removed (DNA-free, Life Technologies, Grand Island, NY).  RNA purity and quality were assessed using 260:280 ratios and glyoxal gel electrophoresis.

treatment_protocol: Each exposure replicate consisted of 20 g  of sediment and 60 ml of overlying reconstituted seawater (Ho, 2000; U.S.EPA, 2007). Ten amphipods were added to each replicate. All tests were seven-day, static, aerated exposures using 30 ppt reconstituted seawater. Two initial toxicity tests were performed to determine the concentration of ER that caused 30-40% mortality in organisms, one covering a high (100%, 75%, 50% and 25% ER) and another the low range (50%, 25%, 12.5%, 6.25%, 3.13% and 1.56% ER). The initial TIE was performed on a mixture of 10:90 ER to LIS sediment to ensure that the manipulations would not be overwhelmed by the toxicants in ER. TIE manipulations included additions of: (1) coconut charcoal to assess organic toxicity, (2) cation resin to assess metal toxicity, and (3) zeolite to assess ammonia toxicity (U.S.EPA, 2007). Operational controls were performed for each manipulation using LIS sediment. No significant mortality was observed using the 10% ER sediment sample, therefore a second TIE was performed as described above except a 40:60 ER to LIS sediment mixture was used. Upon test termination, the amphipods were sieved through a 0.5 mm screen and enumerated. Missing organisms were considered dead. For all exposures except the model toxicant exposures, but including the high and low toxicity tests, as well as the 10% ER TIE and 40% ER TIE:  live organisms from each replicate were divided into groups of no more than three organisms, placed in a microcentrifuge tube, immediately frozen in liquid nitrogen and stored at -80 deg C until analyzed. For the model toxicant exposures all surviving organisms from an exposure replicate (jar) were placed in a single tube and snap-frozen in liquid nitrogen. Only a single tube from each exposure replicate (exposure replicates started with 10 amphipods) was used for microarray analysis. The remaining tubes were saved and were used if technical issues arose.  Each sample name in the samples section of the metadata matrix and in the processed data matrix represents the organisms from one tube.

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: FALSE


title: 6_d1

tag: gender

tag: treatment

tag: tissue

tag: time of wbc and fatigue score collection

tag: individual


title: Rb_p107_carcinoma_rep10

tag: strain


title: 6_c

tag: disease state

value: healthy

tag: cell type

tag: sample type

value: matched control


title: rpfF mutant vs. wild type strain

city: Lake Alfred

first: Nian

last: Wang

state: Florida

address: 700 Experiment Station Road

department: Citrus Research and Education Center/Department of Microbiology and Cell Science

institute: University of Florida

description: 2 biological merged replicates

hyb_protocol: A total of 825 ng of labeled cDNA per sample was used in hybridizations on each microarray. A dye swap was performed to reduce any bias from the labeling dyes. Two biological replicates were used for this study.  Hybridization was performed in an oven for 17.5 hr at 65°C using a Gene Expression Hybridization Kit (Agilent Technologies) according to the user’s manual.

scan_protocol: The arrays were washed using the manufacturer’s recommended protocols and scanned using a dual-laser DNA microarray scanner (Model G2505C Agilent Technologies). Fluorescence intensities of each element were extracted from the scanned image using Feature Extraction 10.1.1.1 software (Agilent Technologies).

data_processing: Data pre-processing and differential expression analyses of mean signals provided by the Agilent Feature Extraction were done using the Bioconductor Limma package (Smyth et. al.  2004).  Data were first normalized within the array by Lowess algorithm (Yang et al. 2002), and then normalized between arrays using a quantile approach. Probe-level expression values were summarized into gene-level signal data. A model-based cluster analysis approach was applied to normalized data to assign detection calls based on negative control probe information.  Probesets lacking detection calls were removed in all the samples before further analysis.  For differential expression analysis, the expression value for each gene was fit to a linear model to assess the significance of the difference between mutant and wild-type strain.  Limma applies empirical Bayes methods to construct moderated statistic and incorporates statistical tools to adjust for the multiplicity of the tests (Smyth et. al.  2004). The Benjamini and Hochberg approach was used to compute the false discovery rate (FDR).

label: Cy5, Cy3

organism: Xylella fastidiosa

source_name: total RNA from wild type strains growing in PW broth medium

label_protocol: Labeled cDNA was generated using the Agilent Two-Color Microarray-Based Prokaryote Analysis kit (Fairplay III labeling, Agilent Technologies).  cDNA synthesized from 5 µg of total RNA using AffinityScript HC and random primers was then labeled with either cy3 or cy5 and purified following manufacturer's instructions.

growth_protocol: Wild-type strain X. fastidiosa Temecula (ATCC 700964) and an isogenic rpfF mutant (Newman et al. 2004) were grown at 28°C in PW liquid media (Hill and Purcell 1995; Newman et al. 2004) with shaking at 160 rpm.  The rpfF mutant was confirmed to grow in media containing kanamycin (50 μg per m) (Sigma-Aldrich, St. Louis, U.S.A.) but was grown without antibiotics for transcriptome analysis.

extract_protocol: RNA was isolated using an RNeasy Mini Kit (Qiagen Inc., Valencia, CA, U.S.A.). Cells were pelleted directly into RNAprotect Bacteria Reagent (Qiagen) 6 days after inoculation.  Contaminating DNA was digested with a TURBO DNA-free™ Kit (Ambion, Austin, TX, U.S.A.).  RNA concentration was determined with a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc) and sample quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

tag: genotype/variation

value: wild type Temecula (ATCC 700964)

tag: sampling time

value: 6 days after inoculation

value: isogenic rpfF mutant

source_name: total RNA from rpfF mutant growing in PW broth medium


title: S2 spheres, biol. Replicate 3

source_name: breast cancer tumor initiating cells

tag: cell line

value: spheres


title: Ampelisca Mdl.Tric rep5

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch


title: Ampelisca Mdl.Tric rep2

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: 6_b

tag: gender

tag: disease state

tag: tissue

tag: cell type

tag: time of wbc and fatigue score collection

value: baseline

tag: individual


title: Ampelisca Mdl.Tric rep4

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)


title: Rb_p107_carcinoma_rep8

tag: strain


title: 5_d21

tag: treatment


title: Rb_p107_carcinoma_rep5


title: Rb_p107_carcinoma_rep4


title: Rb_p107_carcinoma_rep6


title: Rb_p107_carcinoma_rep7


title: 5_d72

value: D72 (30 days post-EBRT)


title: Ampelisca Mdl.Tric rep3

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch


title: Rb_p107_carcinoma_rep3


title: Ampelisca Mdl.Phen rep6

source_name: Model chemical exposure: Phenanthrene

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: Ampelisca Mdl.Phen.and.Ben rep1

source_name: Model chemical exposure: Phenanthrene and Benzo[a]pyrene


title: Ampelisca Mdl.Phen.and.Ben rep3


title: Ampelisca Mdl.Phen.and.Ben rep2


title: Ampelisca Mdl.Phen rep4


title: 5_d7

tag: gender

value: male

tag: disease state

tag: tissue

tag: cell type

tag: time of wbc and fatigue score collection


title: Ampelisca Mdl.Phen rep5

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)


title: Ampelisca Mdl.Tric rep1

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch


title: 5_d42

source_name: peripheral white blood cells, D42

value: non-metastatic prostate cancer

tag: treatment

tag: individual


title: Ampelisca Mdl.Phen rep3

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch


title: Skin_Normal_4

source_name: skin tissue, tamoxifen tretaed

tag: strain

value: normal skin tissue


title: Ampelisca Mdl.Phen rep1

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: 5_d1

tag: gender

tag: disease state

value: external beam radiation therapy (EBRT)

tag: tissue

value: peripheral blood

tag: cell type

tag: time of wbc and fatigue score collection


title: Ampelisca Mdl.Phen rep2

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch


title: Skin_Normal_2

value: FVB/N genetic background


title: 5_d14

source_name: peripheral white blood cells, D14

tag: treatment

value: white blood cells

tag: individual


title: Rb_p107_carcinoma_rep2

tag: strain

value: skin carcinoma


title: Ampelisca Mdl.MetalMix rep5

source_name: Model chemical exposure: Metal Mixture

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

value: FALSE


title: 5_c

source_name: peripheral white blood cells, matched control

tag: gender

tag: disease state

value: healthy

tag: sample type

value: matched control


title: Ampelisca Mdl.MetalMix rep4

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: 5_b

source_name: peripheral white blood cells, baseline

tag: tissue

tag: cell type

tag: time of wbc and fatigue score collection


title: Skin_Normal_1


title: Ampelisca Mdl.MetalMix rep3

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch


title: 4_d72

source_name: peripheral white blood cells, D72

tag: treatment

tag: individual


title: Ampelisca Mdl.MetalMix rep2

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number


title: Ampelisca Mdl.GrandMix rep4

source_name: Model chemical exposure: Grand Mixture

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: Skin_Normal_3

tag: strain

tag: tissue


title: Ampelisca Mdl.GrandMix rep5

value: b

tag: used in classifier training


title: 4_d42

tag: gender

tag: disease state

tag: cell type

tag: time of wbc and fatigue score collection


title: Ampelisca Mdl.MetalMix rep1

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch


title: Ampelisca Mdl.GrandMix rep2

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch


title: Ampelisca Mdl.GrandMix rep3

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)


title: 4_d14

tag: treatment

tag: tissue

tag: individual


title: 4_d21

source_name: peripheral white blood cells, D21

tag: gender

tag: disease state


title: FABP4-cre-HighFatDiet-rep4

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: Gene expression data from mouse white adipose tissue without Sirt1 fed a high fat diet

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.1, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.1, Biobase_2.8.0

source_name: White adipose tissue dissected from mice that with adipocyte-specific deletion of Sirt1 on a high fat diet for 8 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: 12 week old mice with indicated genotypes fed high or low fat diets for 8 weeks-feeding started at 4 weeks of age

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was DNAseI treated and further purified using the QIAgen Rneasy mini columns

treatment_protocol: White adipose tissue dissected from mice andimmediately processed immediately to isolate RNA

tag: background strain

tag: cre transgene

value: Fatty acid binding protein 4 promoter-Cre (FABP4-Cre)

tag: diet

value: High Fat


title: FABP4-cre-HighFatDiet-rep2


title: FABP4-cre-HighFatDiet-rep3


title: Ampelisca Mdl.Diel rep4

source_name: Model chemical exposure: Dieldrin

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: FABP4-cre-HighFatDiet-rep1


title: Ampelisca Mdl.Diel rep6

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch


title: Ampelisca Mdl.Diel rep3

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)


title: 4_c

tag: gender

tag: disease state

tag: tissue

tag: cell type

tag: sample type


title: 4_d7

source_name: peripheral white blood cells, D7

tag: treatment

tag: time of wbc and fatigue score collection

tag: individual


title: Ampelisca Mdl.Diel rep2

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: WT-HighFatDiet-rep4

description: Gene expression data from mouse white adipose tissue with Sirt1 fed a high fat diet

source_name: White adipose tissue dissected from wild type mice on a high fat diet for 8 weeks

tag: background strain

tag: cre transgene

tag: diet


title: 4_d1

source_name: peripheral white blood cells, D1


title: Ampelisca Mdl.Deg rep5

source_name: Model chemical exposure: Degradate

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)


title: Ampelisca Mdl.Deg rep6


title: Ampelisca Mdl.Diel rep1


title: Ampelisca Mdl.Diel rep5


title: Ampelisca Mdl.Deg rep3


title: 4_b

tag: gender

tag: disease state

tag: tissue

tag: cell type

tag: time of wbc and fatigue score collection

value: baseline

tag: individual


title: WT-HighFatDiet-rep3

tag: background strain


title: Ampelisca Mdl.Deg rep2

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: FABP4-cre-LowFatDiet-rep4

description: Gene expression data from mouse white adipose tissue without Sirt1 fed a low fat diet

source_name: White adipose tissue dissected from mice that with adipocyte-specific deletion of Sirt1 on a low fat diet for 8 weeks

tag: cre transgene

tag: diet

value: Low Fat


title: Ampelisca Mdl.Deg rep1

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch


title: WT-HighFatDiet-rep2


title: Ampelisca Mdl.GrandMix rep1

tag: microarray slide number

tag: microarray slide half number (unique within slide)


title: 2a_d42

tag: gender

value: male

tag: disease state

tag: treatment

tag: tissue

tag: cell type

tag: time of wbc and fatigue score collection

tag: individual


title: WT-HighFatDiet-rep1

tag: background strain

tag: cre transgene


title: FABP4-cre-LowFatDiet-rep3

tag: diet


title: Ampelisca Mdl.Deg rep4

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: 2a_d72

tag: gender

value: non-metastatic prostate cancer

value: D72 (30 days post-EBRT)


title: 2a_d21

tag: disease state

value: external beam radiation therapy (EBRT)


title: Ampelisca Mdl.DDT rep6

source_name: Model chemical exposure: DDT

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)


title: Ampelisca Mdl.DDT rep5


title: Ampelisca Mdl.DDT rep4


title: Ampelisca Mdl.Benz rep5

source_name: Model chemical exposure: Benzo[a]pyrene


title: FABP4-cre-LowFatDiet-rep1

tag: background strain

tag: cre transgene


title: 2a_d14

tag: treatment

tag: tissue

value: peripheral blood

tag: cell type

tag: time of wbc and fatigue score collection

tag: individual


title: Ampelisca Mdl.Benz rep4

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: microarray slide array number (unique within slide half)


title: WT-LowFatDiet-rep4

description: Gene expression data from mouse white adipose tissue with Sirt1 fed a low fat diet

source_name: White adipose tissue dissected from wild type mice on a low fat diet for 8 weeks

tag: diet


title: FABP4-cre-LowFatDiet-rep2


title: 2a_d7

tag: gender

tag: disease state


title: Ampelisca Mdl.DDT rep1

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: used in classifier training


title: Ampelisca Mdl.DDT rep3


title: Ampelisca Mdl.DDT rep2


title: 2a_c

tag: tissue

tag: cell type

tag: sample type


title: 2a_b

tag: time of wbc and fatigue score collection

tag: individual


title: Ampelisca Mdl.Benz rep2

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch


title: WT-LowFatDiet-rep1

tag: background strain

tag: cre transgene

tag: diet


title: Ampelisca Mdl.Benz rep3

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide array number (unique within slide half)


title: Ampelisca Mdl.Benz rep1

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: used in classifier training


title: WT-LowFatDiet-rep3


title: WT-LowFatDiet-rep2


title: control rep1

description:
SAMPLE 1
Gene expression data from murine hematopoietic stem and progenitor cells

source_name: sorted GFP-positive cells

tag: strain background

tag: cell source

value: bone marrow cells

tag: cell population

value: Lineage-depleted c-Kit+ Lin– cells

tag: transduction

value: MSCV-IRES-GFP-empty


title: Ampelisca LIS.Zeol 40% rep6

source_name: Zeolite extract of Long Island Sound sediment (non-toxic), as a control to Zeolite extract of 40% Elizabeth River sediment (toxic) diluted in LIS sediment

tag: treatment (short label)

value: LIS.Zeol 40%

tag: control group for this treatment/batch

value: LIS 40%

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

value: a


title: Ampelisca Mdl.Benz rep6

tag: treatment batch

value: FALSE


title: 2a_d1

tag: gender

tag: disease state

tag: treatment

tag: tissue

tag: cell type

value: white blood cells

tag: time of wbc and fatigue score collection

tag: individual


title: 2_d72


title: 2_d42

source_name: peripheral white blood cells, D42


title: Ampelisca LIS.Zeol 40% rep1

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: Ampelisca LIS.Zeol 10% rep5

source_name: Zeolite extract of Long Island Sound sediment (non-toxic), as a control to Zeolite extract of 10% Elizabeth River sediment (toxic) diluted in LIS sediment

tag: treatment (short label)

value: LIS.Zeol 10%

tag: control group for this treatment/batch

value: LIS 10%

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)


title: Ampelisca LIS.Zeol 40% rep2

tag: treatment batch


title: Rb_p107_carcinoma_rep1

source_name: skin carcinoma, tamoxifen tretaed

tag: strain

value: FVB/N genetic background

tag: tissue

value: skin carcinoma


title: Ampelisca LIS.Zeol 40% rep5


title: Ampelisca LIS.Zeol 10% rep4


title: Ampelisca LIS.Zeol 10% rep3


title: Ampelisca LIS.Zeol 40% rep4


title: Ampelisca LIS.Zeol 40% rep3


title: 2_d21

tag: gender

value: male

tag: disease state

tag: treatment

tag: cell type

tag: time of wbc and fatigue score collection


title: 2_d14

source_name: peripheral white blood cells, D14

value: non-metastatic prostate cancer

tag: individual


title: Ampelisca LIS.Zeol 10% rep2

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number


title: Ampelisca LIS.M rep2

source_name: Long Island Sound sediment (non-toxic), control for model chemical exposures

tag: treatment (short label)

tag: control group for this treatment/batch

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: TRUE


title: Ampelisca LIS.M rep1

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch


title: Ampelisca LIS.Zeol 10% rep1


title: Ampelisca LIS.M rep5


title: 2_c

source_name: peripheral white blood cells, matched control

tag: gender

tag: disease state

value: healthy

tag: tissue

tag: sample type

value: matched control


title: Ampelisca LIS.M rep3

tag: replicate (jar; unique within treatment/batch)


title: Ampelisca LIS.M rep4

tag: critter collection tube (unique within treatment/batch/replicate)


title: Ampelisca LIS.Dil rep8

source_name: Long Island Sound sediment (non-toxic), control for 1.56%, 3.13%, 6.25%, 12.5%, and 25% dilutions of Elizabeth River sediment (toxic) into LIS sediment

tag: labeling batch


title: Ampelisca LIS.Dil rep9

tag: hybridization batch


title: 2_b

source_name: peripheral white blood cells, baseline

value: peripheral blood

tag: cell type

tag: time of wbc and fatigue score collection

value: baseline

tag: individual


title: 2_d7

source_name: peripheral white blood cells, D7

tag: treatment

value: external beam radiation therapy (EBRT)


title: 2_d1

source_name: peripheral white blood cells, D1


title: 1a_d72

source_name: peripheral white blood cells, D72

value: D72 (30 days post-EBRT)


title: Ampelisca LIS.Dil rep6

tag: treatment (short label)

tag: control group for this treatment/batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: 1a_d42

tag: gender


title: 1a_d14

tag: disease state


title: Tick-infested mouse, 12 hour after tick attachment, biological rep3

city: Galveston

first: Dar

last: Heinze

state: Texas

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

description: Gene expression from mice infested for 12 hrs

hyb_protocol: Total fragmented cRNA (10micrograms) was hybridized to the Affymetrix Mouse GeneChip 430A 2.0 array according to the manufacturer’s (Affymetrix, CA) conditions.

scan_protocol: Fluorescence was detected with an Affymetrix-7G Gene Array scanner using the Affymetrix GeneChip Command Console software (AGCC1.1).

data_processing: Gene expression changes were identified using Partek Genomics Suite (Partek, MO) following the default gene expression workflow.

source_name: BALB/cJ mouse ear, 4mm biopsy punch

label_protocol: Biotinylated cRNA was prepared using the Ambion MessageAmp™ Premier RNA Amplification Kit from 500nanograms total RNA.

growth_protocol: Mice were housed at the University of Texas Medical Branch ABSL-2 animal facility, and fed with food and water ad libitum.  All experiments were approved by the UTMB IACUC.

extract_protocol: RNA was extracted using a combination of Trizol and Rneasy microkit protocols.

treatment_protocol: Mice were anesthetized and infested with 8 Ixodes scpularis nymphs.  Attachment was monitored visually.  At the proper times after attachment, mice were euthanized and 4mm biopsy punches from tick attachment sites were collected in RNALater (Ambion).

tag: strain

value: BALB/cJ

tag: stress

value: tick infestation

tag: time

value: 12 hr

tag: tissue

value: Skin


title: 1a_d21

description: JJB110112_XRT P1E

source_name: peripheral white blood cells, D21

value: white blood cells


title: Ampelisca LIS.Dil rep7

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: labeling batch

tag: used in classifier training


title: Tick-infested mouse, 12 hour after tick attachment, biological rep2


title: Ampelisca LIS.Dil rep4

tag: treatment (short label)

tag: control group for this treatment/batch

tag: hybridization batch


title: Ampelisca LIS.Dil rep2

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: Ampelisca LIS.Dil rep3


title: Ampelisca LIS.Dil rep14


title: Ampelisca LIS.Dil rep5

value: b


title: Ampelisca LIS.Dil rep13


title: Ampelisca LIS.Dil rep11


title: Tick-infested mouse, 6 hour after tick attachment, biological rep2

description: Gene expression from mice infested for 6 hrs

tag: strain

value: 6 hr


title: Tick-infested mouse, 6 hour after tick attachment, biological rep3

tag: stress


title: 1a_d7

tag: gender

value: male

tag: disease state

tag: treatment

tag: cell type

tag: time of wbc and fatigue score collection

tag: individual


title: 1a_b

value: non-metastatic prostate cancer

tag: tissue


title: Ampelisca LIS.Dil rep12

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

value: TRUE


title: Ampelisca LIS.Dil rep10

tag: treatment (short label)

tag: control group for this treatment/batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: used in classifier training


title: Tick-infested mouse, 3 hour after tick attachment, biological rep3

description: Gene expression from mice infested for 3 hrs

tag: strain

tag: stress

tag: time

value: 3 hr


title: Tick-infested mouse, 12 hour after tick attachment, biological rep1


title: 1a_d1

tag: gender

tag: disease state

tag: treatment

tag: cell type

tag: time of wbc and fatigue score collection

tag: individual


title: Tick-infested mouse, 3 hour after tick attachment, biological rep2

tag: tissue


title: 1a_c

value: healthy

tag: sample type

value: matched control


title: Tick-infested mouse, 6 hour after tick attachment, biological rep1


title: 13a_d42

value: peripheral blood


title: Tick-infested mouse, 1 hour after tick attachment, biological rep3

description: Gene expression from mice infested for 1hr

value: 1 hr


title: Tick-infested mouse, 3 hour after tick attachment, biological rep1


title: Ampelisca LIS.Dil rep1

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: microarray slide array number (unique within slide half)


title: Ampelisca LIS.Char 40% rep6

source_name: Long Island Sound sediment (non-toxic), control for charcoal extract of 40% Elizabeth River sediment (toxic) diluted into LIS sediment

value: LIS.Char 40%

tag: control group for this treatment/batch

value: LIS 40%

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: used in classifier training

value: FALSE


title: Tick-infested mouse, 1 hour after tick attachment, biological rep2

tag: strain

value: BALB/cJ

tag: stress

value: tick infestation

tag: time


title: 13a_d1

tag: gender

tag: disease state

tag: treatment

value: external beam radiation therapy (EBRT)

tag: tissue

tag: cell type

value: white blood cells

tag: time of wbc and fatigue score collection

tag: individual


title: 13a_d14


title: 13a_d21


title: Ampelisca LIS.Char 40% rep5

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: labeling batch


title: Ampelisca LIS.Char 40% rep1

tag: control group for this treatment/batch

tag: hybridization batch

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: 13a_d7

tag: gender

tag: disease state

tag: treatment

tag: tissue


title: Ampelisca LIS.Char 40% rep4

tag: treatment (short label)


title: Ampelisca LIS.Char 40% rep2

tag: total number survived treatment (sum across treatment replicates)


title: Ampelisca LIS.Char 40% rep3

tag: total number died from treatment (sum across treatment replicates)


title: Tick-free mouse, biological rep2

description: Gene expression from tick-free mice

tag: strain

tag: stress

value: tick-free

tag: time

value: control

value: Skin


title: Tick-free mouse, biological rep3

description: Gene expression from tick-free mice


title: 13a_b

value: male

value: non-metastatic prostate cancer

tag: cell type

tag: time of wbc and fatigue score collection

value: baseline

tag: individual


title: Tick-free mouse, biological rep1

description: Gene expression from tick-free mice


title: 11a_d72

value: D72 (30 days post-EBRT)


title: Tick-infested mouse, 1 hour after tick attachment, biological rep1


title: Ampelisca LIS.Char 10% rep5

source_name: Long Island Sound sediment (non-toxic), control for charcoal extract of 10% Elizabeth River sediment (toxic) diluted into LIS sediment

value: LIS.Char 10%

tag: control group for this treatment/batch

value: LIS 10%

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number


title: Dystrophic Single fibers from quadriceps replicate 1

type: mixed

city: Milano

first: Yvan

last: Torrente

address: Francesco Sforza 35

department: Neuroscience

institute: University of the Studies of Milan

hyb_protocol: Miltenyi manifacture

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: single fibers isolated from quadriceps

label_protocol: Miltenyi manifacture's instructions

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

tag: muscle type

value: single fibers isolated from quadriceps

value: mdx mouse

molecule: other

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

extract_protocol: not applicable

tag: reference

value: synthetic miRNA pool of 950 miRNA sequences from human, mouse, rat, and virus


title: Dystrophic Single fibers from diaphragm replicate 1

source_name: single fibers isolated from diaphragm

value: single fibers isolated from diaphragm


title: Dystrophic Single fibers from diaphragm replicate 3


title: Dystrophic Single fibers from quadriceps replicate 2


title: Dystrophic Single fibers from quadriceps replicate 3


title: Ampelisca LIS.Char 10% rep3

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: FALSE


title: Ampelisca LIS.Char 10% rep4

tag: total number died from treatment (sum across treatment replicates)


title: 11a_d7

tag: gender

tag: disease state

tag: treatment

value: external beam radiation therapy (EBRT)

tag: tissue

value: peripheral blood

tag: cell type

tag: time of wbc and fatigue score collection


title: 11a_d1

value: white blood cells

tag: individual


title: 11a_d21


title: 11a_c

value: healthy

tag: sample type

value: matched control


title: 11a_b


title: Ampelisca LIS.Char 10% rep2

tag: control group for this treatment/batch

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: labeling batch

tag: hybridization batch

tag: microarray slide number


title: 11a_d42

source_name: peripheral white blood cells, D42

value: male


title: 13a_d72

value: non-metastatic prostate cancer


title: 11a_d14


title: Dystrophic Single fibers from diaphragm replicate 2

tag: muscle type

tag: strain

tag: reference


title: Dystrophic Single fibers from tibialis replicate 3

source_name: single fibers isolated from tibialis

value: single fibers isolated from tibialis


title: Dystrophic Single fibers from tibialis replicate 1


title: Dystrophic Single fibers from tibialis replicate 2


title: Control Single fibers from quadriceps replicate 3

value: c57bl mouse


title: Ampelisca LIS.CatEx 40% rep5

source_name: Long Island Sound sediment (non-toxic), control for cation exchange extract of 40% Elizabeth River sediment (toxic) diluted into LIS sediment

tag: treatment (short label)

value: LIS.CatEx 40%

value: LIS 40%

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

value: b

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: Control Single fibers from quadriceps replicate 2

value: single fibers isolated from quadriceps


title: Ampelisca LIS.Char 10% rep1

value: LIS.Char 10%

value: LIS 10%


title: Ampelisca LIS.CatEx 40% rep2

value: FALSE


title: Ampelisca LIS.CatEx 40% rep3


title: Ampelisca LIS.CatEx 40% rep4


title: 13a_c

tag: gender

tag: disease state

tag: tissue

tag: cell type

tag: sample type


title: Ampelisca LIS.CatEx 10% rep6

source_name: Long Island Sound sediment (non-toxic), control for cation exchange extract of 10% Elizabeth River sediment (toxic) diluted into LIS sediment

value: LIS.CatEx 10%

tag: control group for this treatment/batch

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch


title: Control Single fibers from diaphragm replicate 2

tag: muscle type

value: single fibers isolated from diaphragm

tag: strain

tag: reference

value: synthetic miRNA pool of 950 miRNA sequences from human, mouse, rat, and virus


title: Ampelisca LIS.CatEx 40% rep1

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: hybridization batch

tag: microarray slide number


title: 10_d21

tag: gender

tag: disease state

tag: treatment

value: external beam radiation therapy (EBRT)

value: peripheral blood

value: white blood cells

tag: time of wbc and fatigue score collection

tag: individual


title: Control Single fibers from diaphragm replicate 1


title: 10_d72

value: male

tag: tissue

tag: cell type

value: D72 (30 days post-EBRT)


title: Control Single fibers from tibialis replicate 3

value: single fibers isolated from tibialis


title: Ampelisca LIS.CatEx 10% rep5

tag: control group for this treatment/batch

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training


title: Control Single fibers from diaphragm replicate 3

tag: muscle type

tag: strain

value: c57bl mouse

tag: reference


title: 10_d14

source_name: peripheral white blood cells, D14

tag: gender

value: non-metastatic prostate cancer


title: 10_d7

tag: disease state


title: Ampelisca LIS.CatEx 10% rep4

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number


title: 10_c

source_name: peripheral white blood cells, matched control

value: healthy

tag: tissue

tag: cell type

tag: sample type

value: matched control


title: 10_d1

tag: treatment

tag: time of wbc and fatigue score collection

tag: individual


title: 10_b

source_name: peripheral white blood cells, baseline

value: baseline


title: Control Single fibers from quadriceps replicate 1

tag: muscle type

value: single fibers isolated from quadriceps


title: Ampelisca LIS.CatEx 10% rep3

tag: control group for this treatment/batch

value: LIS 10%

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: FALSE


title: Control Single fibers from tibialis replicate 2

tag: strain

tag: reference


title: ID_Array-6

city: Greenwood

first: Chin-Fu

last: Chen

state: South Carolina

address: 113 Gregor Mendel Circle

department: Center for Molecuar Studies

institute: Greenwood Genetic Center

description: Contrast pair 22

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1 & version A.9.1.1 ).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Normalized log10 (Cy5/Cy3) ratios are available in the supplementary files.

source_name: Lymphoblastoid cell line, ID12

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

growth_protocol: Lymphoblastoid cells were grown with a complete medium in standard tissue culture conditions.

extract_protocol: Total RNA was extracted using the Qiagen RNA kit following manufacturer's instructions.

value: lymphoblastoid cells

tag: condition

value: intellectual disability

source_name: Lymphoblastoid cell line, ID8


title: Control Single fibers from tibialis replicate 1

value: synthetic miRNA pool of 950 miRNA sequences from human, mouse, rat, and virus


title: ID_Array-5

description: Contrast pair 21

source_name: Lymphoblastoid cell line, control11

value: control


title: ID_Array-4

description: Contrast pair 20

source_name: Lymphoblastoid cell line, ID4


title: ID_Array-3

description: Contrast pair 19

source_name: Lymphoblastoid cell line, ID3


title: 10_d42

tag: gender

tag: disease state

value: external beam radiation therapy (EBRT)

tag: tissue

value: peripheral blood

value: white blood cells


title: ID_Array-2

description: Contrast pair 18

source_name: Lymphoblastoid cell line, control9

tag: cell type


title: ID_Array-1

description: Contrast pair 17


title: Ampelisca LIS.CatEx 10% rep2

tag: treatment (short label)

value: LIS.CatEx 10%

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: labeling batch

tag: hybridization batch

tag: microarray slide number


title: Ampelisca LIS.CatEx 10% rep1

tag: control group for this treatment/batch

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: a


title: Ampelisca LIS 40% rep5

source_name: Long Island Sound sediment (non-toxic), control for exposures to 10% Elizabeth River (toxic) sediment diluted in LIS sediment

value: LIS 40%

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

tag: used in classifier training

value: TRUE


title: Ampelisca LIS 40% rep4


title: Ampelisca LIS 40% rep3


title: Ampelisca LIS 40% rep6


title: Ampelisca LIS 40% rep1


title: Ampelisca LIS 10% rep6


title: Ampelisca LIS 10% rep5


title: SCL60_Control_0_h_Replicate 1

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: Sample name: 3

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadArray

source_name: SCL60 (responsive GnRH receptor-transfected HEK293 cells)

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: HEK293 and SCL60 cells were grown in DMEM 10% FCS + P/S. SCL60 cells were supplemented with G418 (0.5mg/ml). Tissue culture plates were coated with a diluted Matrigel solution (200ul Matrigel per 6ml media, 37C for 1-2h, remove excess before gently adding cells) to assist cell adherence.

extract_protocol: Absolutely RNA miniprep kit (Stratagene).

treatment_protocol: 100nM Triptorelin (Sigma)

tag: cell line

tag: gnrhr

value: High

tag: agent

value: Control

tag: time point (h)

tag: labelling batch

tag: chip#

tag: hybridisation batch


title: Ampelisca LIS 40% rep2

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: labeling batch


title: Ampelisca LIS 10% rep4

tag: control group for this treatment/batch

tag: treatment batch

tag: hybridization batch

tag: microarray slide number


title: HEK293_Control_1_h_Replicate 1

description: Sample name: 10

source_name: HEK293 (unresponsive parental cells)

value: Undetectable


title: SCL60_Treated_8_h_Replicate 1

description: Sample name: 17

value: Triptorelin


title: SCL60_Treated_1_h_Replicate 1

description: Sample name: 15


title: HEK293_Control_0_h_Replicate 1

description: Sample name: 2


title: HEK293_Treated_24_h_Replicate 2

description: Sample name: 21


title: SCL60_Treated_0.5_h_Replicate 1

description: Sample name: 12


title: SCL60_Treated_2_h_Replicate 1

description: Sample name: 7


title: Ampelisca LIS 10% rep3

value: LIS 10%

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: HEK293_Control_24_h_Replicate 1

description: Sample name: 16

tag: cell line

tag: gnrhr

tag: agent


title: HEK293_Treated_1_h_Replicate 1

description: Sample name: 13

tag: time point (h)

tag: labelling batch

tag: chip#


title: HEK293_Treated_24_h_Replicate 1

description: Sample name: 1

tag: hybridisation batch


title: Ampelisca LIS 10% rep2

tag: treatment (short label)

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: used in classifier training


title: SCL60_Control_8_h_Replicate 1

description: Sample name: 9


title: SCL60_Treated_24_h_Replicate 1

description: Sample name: 8


title: Ampelisca ER.Zeol 40% rep3

source_name: Zeolite extract of 40% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

value: ER.Zeol 40%

tag: control group for this treatment/batch

tag: treatment batch

tag: labeling batch

tag: hybridization batch

value: FALSE


title: TO1 cadmium vs. TO2 cadmium

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: TO1 cadmium biol. rep 2 vs. TO2 cadmium biol. rep 4

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 × 15 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm) 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), washed in acetonitril for 10 seconds, then dried immediately by air.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, Normexp for background correction was used (offset = 50), Loess correction, and quantile normalizion was done between all arrays.

organism: Folsomia candida

source_name: TO1 cadmium

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from ~300 ng total RNA using the Low input Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer’s guidelines, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield was checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil as follows, 10-20 adult animals were incubated per plastic rings; containing plaster of Paris mixed with charcoal, to lay eggs and were removed after 2 days. The incubation conditions were 20°C with a 12 hour light/dark regime. It took approximately 10 days before the eggs hatched.

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 d old, were exposed for two days in glass jars containing ~30 g of: soil spiked with cadmium (41.2 mg/kg soil), or non-spiked soil. Exposure was done at 20°C, a 12 h light/dark regime, and 75% humidity. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: clone

tag: treatment

value: cadmium

tag: tissue

value: whole organism

source_name: TO2 cadmium


title: Ampelisca ER.Zeol 40% rep2

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: TO2 control vs. TO1 control

description: TO2 control biol. rep 2 vs. TO1 control biol. rep 4

source_name: TO2 control

value: control

source_name: TO1 control


title: TO2 cadmium vs. TO1 cadmium

description: TO2 cadmium biol. rep 2 vs. TO1 cadmium biol. rep 4


title: TO1 control vs. TO2 control

description: TO1 control biol. rep 2 vs TO2 control biol. rep 4


title: Ampelisca LIS 10% rep1


title: SCL60_Control_8_h_Replicate 4

description: Sample name: 74

tag: cell line

tag: gnrhr

tag: agent

tag: time point (h)

tag: labelling batch

tag: chip#

tag: hybridisation batch


title: SCL60_Control_24_h_Replicate 1

description: Sample name: 20


title: SCL60_Treated_0.5_h_Replicate 4

description: Sample name: 64


title: TO2 cadmium vs. TO1 control

description: TO2 cadmium biol. rep 1 vs. TO1 control biol. rep 3


title: HEK293_Control_1_h_Replicate 4

description: Sample name: 65


title: SCL60_Control_1_h_Replicate 3

description: Sample name: 43


title: Ampelisca ER.Zeol 40% rep1

tag: treatment (short label)

tag: control group for this treatment/batch

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: labeling batch

tag: used in classifier training


title: Ampelisca ER.Char 40% rep6

source_name: Charcoal extract of 40% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

value: ER.Char 40%

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

value: b

tag: hybridization batch

tag: microarray slide number


title: amyloid-beta + C1q treated neurons, replicate 2

city: Irvine

first: Marie

middle: Emeline

last: Benoit

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UC Irvine

description:
0908F-02_CIQ + AB 2
gene expression data form neurons treated for 3h with fibrillar amyloid beta and C1q

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Gene 1.0 ST Array. GeneChips were washed and stained in the GeneChip Fluidics Stations 450

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

data_processing:
The data were analyzed with JMP genomics (v5.0) using the basic expression workflow and median signal intensity as normalization method.
Processed data (probe-level) is available on Series record.

organism: Rattus norvegicus

source_name: immature primary cortical neurons

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (performed by the personnel of the microarray facility at University of California Irvine)

growth_protocol: primary cortical neurons are isolated form E16 rat embryos and maintained for 3 days in Neurobasal media supplement with N2 before stimulation

extract_protocol: Total RNA was extracted using QIAGEN Rneasy extraction kit according to manufacturer's instructions

treatment_protocol: Neurons are treated with 5 μM amyloid beta and/or 10 nM human purified C1q

tag: cell type

value: immature primary cortical neurons

tag: treatment

value: fibrillar amyloid beta and C1q


title: Ampelisca ER.Char 40% rep3

value: a

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: Ampelisca ER.Char 40% rep4

value: LIS 40%


title: TO1 cadmium vs. TO2 control

description: TO1 cadmium biol. rep 1 vs. TO2 control biol. rep 3

tag: clone

tag: tissue


title: TO2 control vs. TO2 cadmium

description: TO2 control biol. rep 1 vs. TO2 cadmium biol. rep 3


title: Ampelisca ER.Char 40% rep5

tag: treatment (short label)


title: amyloid-beta + C1q treated neurons, replicate 1

description:
0908F-02_CIQ + AB 1
gene expression data form neurons treated for 3h with fibrillar amyloid beta and C1q


title: Ampelisca ER.Char 40% rep2

tag: control group for this treatment/batch


title: amyloid-beta treated neurons, replicate 3

description:
0908F-02_AB3
gene expression data form neurons treated for 3h with fibrillar amyloid beta

value: fibrillar amyloid beta


title: amyloid-beta + C1q treated neurons, replicate 3

description:
0908F-02_CIQ + AB 3
gene expression data form neurons treated for 3h with fibrillar amyloid beta and C1q


title: SCL60_Treated_2_h_Replicate 2

description: Sample name: 40

tag: cell line

tag: gnrhr

value: High

tag: agent

tag: time point (h)

tag: labelling batch

tag: chip#

tag: hybridisation batch


title: amyloid-beta treated neurons, replicate 2

description:
0908F-02_AB2
gene expression data form neurons treated for 3h with fibrillar amyloid beta


title: HEK293_Control_24_h_Replicate 2

description: Sample name: 22

value: Control


title: TO1 control vs. TO1 cadmium

description: TO1 control biol. rep 1 vs. TO1 cadmium biol. rep 3


title: amyloid-beta treated neurons, replicate 1

description:
0908F-02_AB1
gene expression data form neurons treated for 3h with fibrillar amyloid beta


title: Ampelisca ER.Char 40% rep1

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: used in classifier training


title: SCL60_Treated_1_h_Replicate 3

description: Sample name: 56


title: HEK293_Control_0_h_Replicate 3

description: Sample name: 50

value: Undetectable


title: SCL60_Treated_1_h_Replicate 2

description: Sample name: 30

value: Triptorelin


title: SCL60_Control_0_h_Replicate 2

description: Sample name: 35


title: SCL60_Treated_24_h_Replicate 4

description: Sample name: 77


title: Ampelisca ER.CatEx 40% rep3

source_name: Cation-exchange resin extract of 40% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: treatment (short label)

value: ER.CatEx 40%

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)


title: SCL60_Control_8_h_Replicate 3

description: Sample name: 47

tag: cell line

tag: gnrhr

tag: agent


title: Ampelisca ER.CatEx 40% rep1

tag: control group for this treatment/batch


title: HEK293_Treated_24_h_Replicate 4

description: Sample name: 78

tag: time point (h)

tag: labelling batch

tag: chip#

tag: hybridisation batch


title: Ampelisca ER.CatEx 40% rep4

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)


title: Ampelisca ER.CatEx 40% rep2

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch

tag: used in classifier training


title: Ampelisca ER 6.25% rep3

source_name: 6.25% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: treatment (short label)

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: microarray slide array number (unique within slide half)

value: TRUE


title: Ampelisca ER 6.25% rep4

tag: control group for this treatment/batch


title: Ampelisca ER 6.25% rep2


title: Ampelisca ER 6.25% rep1


title: HEK293_Control_0_h_Replicate 4

description: Sample name: 62

tag: cell line

tag: gnrhr

tag: agent

tag: time point (h)


title: Ampelisca ER 40% rep2

source_name: 40% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: total number survived treatment (sum across treatment replicates)


title: Ampelisca ER 40% rep3

tag: total number died from treatment (sum across treatment replicates)


title: Ampelisca ER 40% rep1

tag: treatment batch


title: HEK293_Control_1_h_Replicate 2

description: Sample name: 28

tag: labelling batch

tag: chip#

tag: hybridisation batch


title: SCL60_Treated_0.5_h_Replicate 3

description: Sample name: 57


title: SCL60_Control_1_h_Replicate 4

description: Sample name: 66


title: SCL60_Treated_0.5_h_Replicate 2

description: Sample name: 25


title: SCL60_Control_0_h_Replicate 3

description: Sample name: 60


title: HEK293_Treated_1_h_Replicate 2

description: Sample name: 26


title: SCL60_Control_24_h_Replicate 2

description: Sample name: 37


title: HEK293_Treated_1_h_Replicate 4

description: Sample name: 67


title: Ampelisca ER 40% rep4

tag: replicate (jar; unique within treatment/batch)

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch

tag: hybridization batch


title: Ampelisca ER 3.13% rep3

source_name: 3.13% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: treatment (short label)

tag: microarray slide number

tag: microarray slide half number (unique within slide)

tag: used in classifier training

value: FALSE


title: HEK293_Control_0_h_Replicate 2

description: Sample name: 27

tag: cell line

tag: gnrhr


title: Ampelisca ER 3.13% rep1

tag: control group for this treatment/batch

tag: microarray slide array number (unique within slide half)


title: Ampelisca ER 3.13% rep2

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)


title: SCL60_Control_1_h_Replicate 2

description: Sample name: 29

tag: agent

tag: time point (h)

tag: labelling batch


title: Ampelisca ER 25% rep2

source_name: 25% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: treatment batch

tag: replicate (jar; unique within treatment/batch)


title: Ampelisca ER 25% rep3

tag: critter collection tube (unique within treatment/batch/replicate)

tag: labeling batch


title: Ampelisca ER 25% rep1

tag: treatment (short label)

tag: hybridization batch


title: Ampelisca ER 12.5% rep1

source_name: 12.5% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: microarray slide number

tag: microarray slide half number (unique within slide)


title: Ampelisca ER 12.5% rep2

tag: used in classifier training


title: SCL60_Treated_8_h_Replicate 2

description: Sample name: 38

tag: cell line

tag: gnrhr

tag: chip#

tag: hybridisation batch


title: Ampelisca ER 10% rep6

source_name: 10% Elizabeth River sediment (toxic) diluted into Long Island Sound sediment (non-toxic)

tag: control group for this treatment/batch

value: LIS 10%

tag: total number survived treatment (sum across treatment replicates)

tag: total number died from treatment (sum across treatment replicates)

tag: microarray slide array number (unique within slide half)