title: CL2 of C. kokaiensis in ATH1

source_name: Cleistogamous flower

tag: Cardamine kokaiensis Yahara (Brassicaceae) is an annual cleistogamous herb that grows only near the Kokai River, Ibaraki Prefecture, Japan (36°1' N, 140°0' E). This plant was discovered by T. Yahara (Kyushu University, Japan) and has not been described yet. However, this plant will be described this species name in the near future (Yahara in preparation). After the plants were self-pollinated and cultivated for four generations, the single descendant seeds were used in experiments. The chilling treatments were performed at 4°C in darkness before germination for 28 days. The first flowers of plants produced CL flowers.


title: bleo/Neo_polysomal_Rep9

status: Public on May 25 2008

type: other

city: Rochester

first: Hartmut

last: Land

state: NY

address: 601 Elmwood Avenue, Box 633

department: Biomedical Genetics

country: USA

institute: University of Rochester Medical Center

description: Refer to submitted paper, McMurray et al.

hyb_protocol: The cRNA yield was fragmented and hybridization cocktails were prepared using Affymetrix standard protocol for eukaryotic target hybridization.  Targets were hybridized to Affymetrix Mouse Genome 430 2.0 Expression Arrays at 45°C for 16 hours, washed and stained using Affymetrix Fluidics protocol EukGE-WS2v4_450 in the Fluidics Station 450.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Expression values from the 50 microarrays processed were obtained using the RMA procedure with background correction in Bioconductor (http://www.bioconductor.org).

label: biotin

molecule: other

organism: Mus musculus

source_name: bleo/Neo vector cells, polysomal RNA

label_protocol: Five micrograms of RNA was reverse transcribed and labeled using the mAMP kit (Ambion), with the 1x amplification protocol.

growth_protocol: Four polyclonal cell populations, control (Bleo/Neo), mp53 (p53175H/Neo), Ras (Bleo/RasV12) and mp53/Ras (p53175H/RasV12) were derived by retroviral infection of low-passage polyclonal young adult mouse colon (YAMC) cells.  YAMC cells (a gift from R. Whitehead and A.W. Burgess) derived from the Immorto-mouse (aka H-2Kb/tsA58 transgenic mouse) expressing temperaturesensitive simian virus 40 large T (tsA58) under the control of an interferon γ-inducible promoter were maintained at the permissive temperature (33°C) for large T in the presence of interferon γ to support conditional immortalization in vitro. This permits expansion of the cells in tissue culture. In contrast, exposure of YAMC cells to the non-permissive temperature for large T (39°C) in the absence of interferon γ leads to growth arrest followed by cell death, indicating the absence of spontaneous immortalizing mutations in the cell population. The cells were cultured on Collagen IV-coated dishes (1μg/cm2 for 1.5 hr at room temp; Sigma) in RPMI 1640 medium (Invitrogen) containing 10% (v/v) fetal bovine serum (FBS) (Hyclone), 1×ITS-A (Invitrogen), 2.5 μg/ml gentamycin (Invitrogen), and 5 U/ml interferon γ (R&D Systems). All experiments testing the effects of RasV12 and p53175H were carried out at the non-permissive temperature for large T function (39°C) and in the absence of interferon γ.

extract_protocol: Polysomal RNA was harvested from YAMC, bleo/neo, mp53/neo, bleo/Ras and mp53/Ras cells to obtain gene expression profiles reflective of protein synthesis rates.  Cells were lysed in Extraction Buffer (50 mM MOPS, 15 mM MgCl, 150 mM NaCl, 0.5% Triton X-100 with 100 ug/mL cycloheximide, 1 mg/mL heparin, 200U RNAsin (2 uL/mL of buffer), 2mM PMSF).  Supernatants were applied to 10-50% sucrose gradients, centrifuged at 36,000 rpm for 2 hr at 4°C and fractions were collected using an ISCO gradient fractionator reading absorbance at 254 nm.  Polysome containing fractions were pooled and RNA was purified using the RNeasy Mini Kit (Qiagen) following the standard protocol for animal cells, except that sucrose fractions were mixed with 3.5 volumes Buffer RLT before binding to the RNeasy column.  RNA was on-column DNase digested as part of the RNeasy RNA extraction protocol.

treatment_protocol: RNA was harvested from ten replicates for each cell population grown in non-permissive conditions for 48 hr, followed by 24 hr in media with 0% FBS to maximize the contribution of oncogenic signaling to gene expression.  RNA was collected while cells were sub-confluent and all cell populations were actively cycling.

tag: Refer to Whitehead, R. H., VanEeden, P. E., Noble, M. D., Ataliotis, P. & Jat, P. S. Establishment of conditionally immortalized epithelial cell lines from both colon and small intestine of adult H-2Kb-tsA58 transgenic mice. Proc Natl Acad Sci U S A 90, 587-91 (1993) and Xia, M. & Land, H. Tumor suppressor p53 restricts Ras stimulation of RhoA and cancer cell motility. Nat Struct Mol Biol 14, 215-23 (2007).


title: bleo/Neo_polysomal_Rep1


title: bleo/Neo_polysomal_Rep7


title: bleo/Neo_polysomal_Rep3


title: bleo/Neo_polysomal_Rep2


title: bleo/Neo_polysomal_Rep4


title: CL1 of C. kokaiensis in ATH1

status: Public on May 27 2008

type: RNA

city: Fukuoka

first: Shin-Ichi

last: Morinaga

state: Fukuoka

address: 6-10-1, Hakozaki

department: Department of Biology

country: Japan

institute: Kyushu University

description: This data was calibrated by gDNA hybridization of Accession no. GSM246369 in GEO.

hyb_protocol: According to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

data_processing: Data analysis was conducted according to Hammond et al. (2005).

molecule: total RNA

organism: Cardamine sp. SIM-2007

extract_protocol: A primordium of a first inflorescence with primordia of the first to eighth flowers was collected from each plant when the first flower primordium was visible. We collected 160 inflorescence primordia and placed them in the same microtube. The total RNA of sample was extracted using Isogen (Nippon Gene, Japan). The quality and quantity of total RNA were checked using an RNA Nano Labchip and 2100 Bioanalyzer (Agilent Technologies, USA).


title: bleo/Neo_polysomal_Rep6


title: mp53_polysomal_Rep10

source_name: mp53-expressing cells, polysomal RNA


title: mp53_polysomal_Rep1


title: Ras_polysomal_Rep10

source_name: Ras-expressing cells, polysomal RNA


title: bleo/Neo_polysomal_Rep8


title: bleo/Neo_polysomal_Rep10


title: mp53_polysomal_Rep4


title: mp53_polysomal_Rep3


title: Ras_polysomal_Rep6


title: mp53_polysomal_Rep5


title: mp53_polysomal_Rep6


title: mp53_polysomal_Rep9


title: Ras_polysomal_Rep8


title: mp53_polysomal_Rep7


title: Ras_polysomal_Rep7


title: Ras_polysomal_Rep5


title: Ras_polysomal_Rep2


title: Ras_polysomal_Rep4


title: Ras_polysomal_Rep1


title: Ras_polysomal_Rep9


title: mp53/Ras_polysomal_Rep1

source_name: mp53/Ras cells, polysomal RNA


title: Ras_polysomal_Rep3


title: mp53_polysomal_Rep2


title: mp53/Ras_polysomal_Rep8


title: mp53/Ras_polysomal_Rep9

source_name: mp53/Ras cells, polysomal


title: mp53/Ras_polysomal_Rep5


title: YAMC_polysomal_Rep10

source_name: YAMC cells, polysomal RNA


title: mp53/Ras_polysomal_Rep10


title: mp53/Ras_polysomal_Rep4


title: mp53/Ras_polysomal_Rep2


title: YAMC_polysomal_Rep9


title: YAMC_polysomal_Rep2


title: YAMC_polysomal_Rep5


title: YAMC_polysomal_Rep1


title: YAMC_polysomal_Rep8


title: YAMC_polysomal_Rep6


title: mp53/Ras_polysomal_Rep7


title: mp53/Ras_polysomal_Rep3


title: YAMC_polysomal_Rep3


title: YAMC_polysomal_Rep7


title: mp53/Ras_polysomal_Rep6


title: YAMC_polysomal_Rep4


title: intestine_WT_WY_6hr_rep3

status: Public on May 22 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: Pure bred wild-type (129S1/SvImJ) and PPAR-null (129S4/SvJae) mice were treated for 6 hours with the synthetic triacylglycerols triolein [oleic acid (OA, C18:1)], trieicosapentaenoin [eicosapentaenoic acid (EPA, C20:5)] or tridocosahexaenoin [ocosahexaenoic acid (DHA, C22:6)], or the potent PPAR agonist WY14,643

hyb_protocol: Arrays were hybridized according to the standard protocols of Affymetrix

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 7G, according to the standard protocols of Affymetrix

data_processing: Expression estimates were calculated using GCRMA, applying the emperical Bayes estimate

source_name: small intestine complete, wild type, WY14643 treatment, 6hr

label_protocol: The RNA (5µg) was labled using the ENZO labeling kit, according to the manufacteror's instructions

extract_protocol: Small intestines were excised, homogenized in TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns

tag: 129S1/SvImJ, Male


title: intestine_PPARaKO_WY_6hr_rep1

source_name: small intestine complete, PPARalpha knockout, WY14643 treatment, 6hr

tag: 129S4/SvJae, Male


title: intestine_PPARaKO_tridocosahexaenoin_6hr_rep3

source_name: small intestine complete, PPARalpha knockout, tridocosahexaenoin treatment, 6hr


title: intestine_PPARaKO_tridocosahexaenoin_6hr_rep2


title: intestine_WT_WY_6hr_rep2


title: Mouse Air pouch treated with Monosodium Urate crystal (Pessler)

status: Public on May 23 2008

city: Rahway

first: Joseph

middle: P

last: Menetski

state: NJ

address: PO Box; RY80M-162

department: Molecular Profiling

institute: Merck & Co

description:
Identification of novel monosodium urate crystal-induced mRNAs
by transcript profiling of the dissected murine air pouch membrane
Pessler, F., Mayer, C.T., Jung, S.M., Behrens, E., Dai, L., Menetski, J.P.,
and Schumacher, H.R.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label: biotin-phycoerythrin

source_name: Mouse Air pouch

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted over RNeasy columns (Qiagen, Valencia, CA) and tested for integrity and quantity on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Mouse strain

value: female Balb/C,  6-8 weeks old

tag: Number of mice= 3

tag: Air pouches raised on back for 7 days by injecting 2ml of sterile air.

tag: On day 7, injection of 1ml PBS or 2mg MSU crystals in 1ml PBS (n=3 each)

tag: 9 h after injection, dissection of the air pouch membranes from the adjacent soft tissues, RNA extraction with RNeasy columns. Pooling of RNA from the 3 control pouches or the 3 MSU crystal pouches.  Processing and labeling of 5g aliquots in the U Penn microarray core according to standard Affy protocols. Hybridization to Affy Mo430_2 oligonucleotide microarrays.


title: intestine_PPARaKO_WY_6hr_rep2


title: Mouse air pouch control (Pessler)

source_name: mouse air pouch membrane


title: intestine_PPARaKO_tridocosahexaenoin_6hr_rep1


title: intestine_PPARaKO_trieicosapentaenoin_6hr_rep3

source_name: small intestine complete, PPARalpha knockout, trieicosapentaenoin treatment, 6hr


title: intestine_PPARaKO_trieicosapentaenoin_6hr_rep4


title: intestine_PPARaKO_trieicosapentaenoin_6hr_rep1


title: intestine_PPARaKO_WY_6hr_rep3


title: intestine_PPARaKO_tridocosahexaenoin_6hr_rep4


title: intestine_WT_WY_6hr_rep1


title: intestine_WT_tridocosahexaenoin_6hr_rep3

source_name: small intestine complete, wild type, tridocosahexaenoin treatment, 6hr


title: intestine_WT_tridocosahexaenoin_6hr_rep4


title: intestine_WT_WY_6hr_rep4


title: intestine_WT_trieicosapentaenoin_6hr_rep3

source_name: small intestine complete, wild type, trieicosapentaenoin treatment, 6hr


title: intestine_WT_tridocosahexaenoin_6hr_rep5


title: intestine_PPARaKO_WY_6hr_rep4


title: intestine_WT_tridocosahexaenoin_6hr_rep2


title: intestine_WT_trieicosapentaenoin_6hr_rep5


title: intestine_PPARaKO_trieicosapentaenoin_6hr_rep2


title: intestine_WT_tridocosahexaenoin_6hr_rep1


title: intestine_WT_trieicosapentaenoin_6hr_rep1


title: intestine_WT_trieicosapentaenoin_6hr_rep2


title: intestine_PPARaKO_trieicosapentaenoin_6hr_rep5


title: intestine_PPARaKO_triolein_6hr_rep2

source_name: small intestine complete, PPARalpha knockout, triolein treatment, 6hr


title: intestine_PPARaKO_triolein_6hr_rep4


title: intestine_WT_triolein_6hr_rep3

source_name: small intestine complete, wild type, triolein treatment, 6hr


title: intestine_WT_triolein_6hr_rep4


title: intestine_PPARaKO_triolein_6hr_rep3


title: intestine_PPARaKO_triolein_6hr_rep1


title: intestine_WT_triolein_6hr_rep1


title: intestine_WT_triolein_6hr_rep2


title: intestine_WT_trieicosapentaenoin_6hr_rep4


title: platelet_Ctrl_9

city: Bethesda

first: Xiuli

last: Xu

state: MD

address: Building 10-CRC, Room 5-5140

department: VMB,

institute: NHLBI, NIH

description: two-round amplification

hyb_protocol: Twenty μg of biotin-labeled RNA was fragmented to ~200 bp size by incubating in fragmentation buffer containing 200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 500 mM magnesium acetate for 35 minutes at 94ºC prior to hybridization. Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 plus 2.0 chips for 16 hours, washed, stained on an Affymetrix fluidics station.

scan_protocol: Hybridized chips were scanned using Affymetrix genechip scanner 3000

data_processing: Affymetrix GCOS version 1.4 was used to calculate the signal intensity and the percent present calls on the hybridized Affymetrix chip. To select genes differentially expressed between patients and normals, the signal intensity values obtained for probe sets in the microarrays were transformed using an adaptive variance-stabilizing, quantile-normalizing transformation (Munson, P.J., GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html.) The transform, termed S10 is scaled to match the logarithm transform, base 10.

organism: Homo sapiens

source_name: platelet from control

label_protocol: T7 based RNA amplification was carried out on 10 ng of the isolated platelet total RNA (corresponding to ~ 4-5 ml of collected blood) using Riboamp OA two-round amplification kit as suggested by the manufacturer (Arcturus, Mountain View, CA). Briefly, total RNA was incubated with oligo dT/T7 primers and reverse transcribed into double stranded cDNA. In vitro transcription of the purified cDNA was performed using T7 RNA polymerase at 42ºC for 6 hours. The amplified RNA was purified and subjected to a second round of amplification and biotin labeling using Affymetrix’s IVT labeling kit following the manufacturer’s directions. The yield and integrity of the biotin labeled cRNA were determined using the Nanodrop ND-1000 spectrophotometer and the Agilent 2100 bioanalyzer.

extract_protocol: Total Platelet RNA was extracted using RNAqueous micro RNA isolation kit (Ambion, Austin, TX) following the manufacturer’s directions. Platelets were lysed in lysis buffer containing guanidinium thiocyanate and the cell lysate was mixed with ethanol and applied to a silica based filter that selectively binds RNA. Genomic DNA was removed by DNase treatment. The concentration of the isolated RNA was determined using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).Total Platelet RNA was extracted using RNAqueous micro RNA isolation kit (Ambion, Austin, TX) following the manufacturer’s directions. Platelets were lysed in lysis buffer containing guanidinium thiocyanate and the cell lysate was mixed with ethanol and applied to a silica based filter that selectively binds RNA. Genomic DNA was removed by DNase treatment. The concentration of the isolated RNA was determined using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Twenty ml of peripheral blood from patients and normal volunteers was collected in EDTA tubes and centrifuged at 150 x g for 10 minutes and platelet rich plasma (PRP) was carefully aspirated and re centrifuged at 150 x g for 5 minutes to remove remaining red and white cells. PRP was centrifuged again at 1500 x g for 10 min to pellet the platelets. The cell pellet was lysed twice with erythrocyte lysis buffer to remove traces of contaminating red blood cells. The pellet was than washed with phosphate buffered saline and checked for purity in a Cell-Dyn coulter counter (Abbott Diagnostics, Abbott Park, IL).

tag: Tissue

value: peripheral blood, Subject:Healthy Control


title: platelet_Ctrl_6

description: two-round amplification


title: platelet_sickle_14

description: two-round amplification

source_name: platelet from sickle cell patient

value: peripheral blood, Subject:Sickle cell patient


title: platelet_sickle_16

description: two-round amplification


title: platelet_Ctrl_11

description: two-round amplification


title: platelet_Ctrl_1

description: two-round amplification


title: platelet_Ctrl_4

description: two-round amplification


title: platelet_Ctrl_2

description: two-round amplification


title: platelet_Ctrl_10

description: two-round amplification


title: platelet_Ctrl_8

description: two-round amplification


title: platelet_sickle_15

description: two-round amplification


title: platelet_Ctrl_5

description: two-round amplification


title: platelet_Ctrl_3

description: two-round amplification


title: platelet_sickle_17

description: two-round amplification


title: platelet_sickle_13

description: two-round amplification


title: platelet_Ctrl_7

description: two-round amplification


title: platelet_sickle_12

description: two-round amplification


title: platelet_sickle_11

description: two-round amplification


title: platelet_sickle_18

description: two-round amplification


title: platelet_Ctrl_12

description: two-round amplification


title: platelet_sickle_6

description: two-round amplification


title: platelet_sickle_5

description: two-round amplification


title: platelet_sickle_10

description: two-round amplification


title: platelet_sickle_9

description: two-round amplification


title: platelet_sickle_7

description: two-round amplification


title: platelet_sickle_2

description: two-round amplification


title: platelet_sickle_1

description: two-round amplification


title: platelet_sickle_8

description: two-round amplification


title: platelet_sickle_3

description: two-round amplification


title: EPC214

status: Public on May 20 2008

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description: Gene expression data from endometrial cells with E6, E7, hTERT.

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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: total RNA

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences), according to the manufacturer's protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy Mini Kit (Qiagen), according to manufacture's instructions.). Genomic DNA was eliminated by DNase I (TAKARA BIO INC.) treatments.

tag: E6, E7, hTERT, Human endometrial cell (2611-Re_1301EPC214)


title: UCB302

description: Gene expression data from cord blood cells (primary).

tag: Cord blood, primary (2612-Re_1302UCB302)


title: UCB408

tag: Cord blood, primary (2617-Re_1759UCB408)


title: E4

description: Gene expression data from menstruation blood cells (primary).

tag: Menstruation blood, primary (2614-Re_1687#E4)


title: PLD-1

description: Gene expression data from decidua basalis cells (primary).

tag: Decidua basalis, primary (2647-PLD-1)


title: UCB302TERT

description: Gene expression data cord blood cells with hTERT.

tag: hTERT, cord blood (2613-Re_1501UCB302TERT)


title: UCB408E7-32

description: Gene expression data from cord blood cells with E7, hTERT.


title: platelet_sickle_4

description: two-round amplification


title: E5

tag: Menstruation blood, primary (2615-Re_1689#E5)


title: E6

tag: Menstruation blood, primary (2616-Re_1691#E6)


title: EPC100

tag: E6, E7, hTERT, Human endometrial cell (2610-Re_1300EPC100)


title: UCB408E6E7-31

description: Gene expression data from cord blood cells with E6, E7, hTERT.


title: PLCV539

description: Gene expression data from villous chorion cells (primary).

tag: Villous chorion, primary (2646-PLCV539)


title: Bulun 3-6h+

city: Chicago

first: Zhihong

last: Lin

state: IL

address: 303 East Superior Street

department: Obstetrics and Gynecology

institute: Northwestern University

description: biological replicate: Bulun 1-6h+,Bulun 2-6h+,Bulun 3-6h+

hyb_protocol: Following fragmentation, cRNA were hybridized to Human Genome U133Plus2.0 GeneChips. GeneChips were washed and stained in an Affymetrix Fluidics Station.

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

data_processing: Probe level data was converted to probe set expression values using RMA (Irizarry RA et al., Biostatistics 2003 Apr;4(2):249-64).

source_name: MCF-7 cells treated with E2 for 6h.

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

growth_protocol: MCF-7 cells (American Type Culture Collection) were maintained in MEM (Invitrogen) containing 25 units/mL penicillin, 25 units/mL streptomycin, and 10% fetal bovine serum (FBS) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted from the MCF-7 breast cancer cell line using Tri-Reagent (Sigma) according to the manufacturer's instruction. Total RNA samples were treated with DNase I (Ambion) for 20 min at 37°C according to the product manual.

treatment_protocol: After MCF-7 cells were grown to 75% to 80% confluence in MEM supplemented with 10% FBS, the cells were serum starved in DMEM/F-12 without phenol red (Invitrogen) and FBS for 24 h.  MCF-7 cells were then treated with vehicle or E2 at a concentration of 10–9 mol/L for 3 and 6 h.  All experiments were performed in triplicate.

tag: breast adenocarcinoma from 69yr old female caucasian


title: Bulun 2-6h+


title: AM920

description: Gene expression data from amniotic mesoderm cells (primary).

tag: Amniotic mesoderm, primary (2644-AM920.)


title: UC719

description: Gene expression data from umbilical cord cells (primary).

tag: Umbilical cord, primary (2640-UC719)


title: UC723

tag: Umbilical cord, primary (2645-UC723)


title: PLCP535

description: Gene expression data from chorionic plate cells (primary).

tag: Chorionic plate, primary (2641-PLCP535)


title: AE919

description: Gene expression data from amniotic epithelium cells (primary).

tag: Amniotic epithelium, primary (2642-AE919)


title: Bulun 1-6h+


title: New 3 hr 1

description: biological replicate: New 3 hr 1,New 3 hr 2,New 3 hr 3

source_name: MCF-7 cells treated with E2 for 3h.


title: New 3 hr 2


title: Bulun 3-3h-

description: biological replicate: Bulun 1-3h-,Bulun 2-3h-,Bulun 3-3h-

source_name: MCF-7 cells treated with vehicle for 3h.


title: Mutant epidermis, sample 2

city: New York

first: Sarah

middle: E

last: Millar

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from activated beta-catenin mutant E15.5 embryo epidermis

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol using GeneCHIP hybridization and wash buffer FS450 according to the manufacturer's instructions.

scan_protocol: Data were scanned using an Affymetrix scanner

data_processing: Scanned microarray images were imported into Gene Chip Operating Software (GCOS, Affymetrix, Santa Clara, CA) to generate signal values and prenet/absent calls for each probe set using the MAS 5.0 statistical expression algorithm.

source_name: Mouse activated beta-catenin E15.5 epidermis

label_protocol: Total RNA was subjected to 1 cycle of amplification/biotin labeling using the GeneCHIP IVT Affymetrix labeling kit, according to the manufacturer's instructions.

extract_protocol: Dissected E15.5 dorsal embryonic skin was dispase treated to separate epidermis and dermis. RNA was isolated from epidermis using RNAeasy minikit (Qiagen) following the manufacturer's instructions.

tag: E15.5 epidermis


title: Bulun 1-3h-


title: New 3 hr 3


title: Control epidermis, sample 2

description: Gene expression data from control E15.5 embryo epidermis

source_name: Mouse control E15.5 epidermis


title: hES_VUB01_2

city: EVRY

first: Christelle

last: ROCHON-BEAUCOURT

address: 5 rue H. Desbruères

country: France

institute: INSERM/UEVE UMR 861/ISTEM,AFM

description: gene expression data from undifferentiated hES cells line VUB01

hyb_protocol: Hybridization, washing and staining procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

scan_protocol: Scanning procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

data_processing: The statistical treatment of the expression data was achieved using the Array Assist 4.1 software (Stratagene). Normalization was performed using the GC-RMA algorithm.

label: Biotin

source_name: human embryonic stem (hES) cells line VUB01, biological replicate 2

label_protocol: 100 ng of total RNA was used to generate biotinylated cRNA using the GeneChip® Two-Cycle Target Labeling and Control Reagents from Affymetrix according to the manufactures protocol

growth_protocol:
The hES cell lines were maintained on a feeder layer of mitomycin C-inactivated murine embryonic fibroblast (MEF) cells. The culture media (DMEM/F12 supllemented with 20% KRS and 4ng/ml bFGF) was changed daily and routine passages were performed by mechanical cutting of hES cells on a fresh feeder layer every 4-5 days.
Mesenchymal Stem Cells (MSC) were derived from hES by plating cells on 0,1% Gelatin coated dishes in KO-DMEM medium supplemented with 20% FBS.

extract_protocol: Total RNA was extracted from the cells using the RNeasy Mini kit (Qiagen) according to the manufacturer protocol

tag: human ES cells line from AZ-VUB laboratory, Belgium  derived from normal embryos

tag: Karyotype

value: X,Y


title: Control dermis, sample 2

description: Gene expression data from control E15.5 embryo dermis

source_name: Mouse control E15.5 dermis

extract_protocol: Dissected E15.5 dorsal embryonic skin was dispase treated to separate epidermis and dermis. RNA was isolated from dermis using RNAeasy minikit (Qiagen) following the manufacturer's instructions.

tag: E15.5 dermis


title: Control epidermis, sample 1


title: Mutant skin, sample 2

description: Gene expression data from activated beta-catenin mutant E14.5 embryo skin

source_name: Mouse activated beta-catenin E14.5 skin

extract_protocol: Total RNA was isolated from dissected E14.5 embryonic skin, including epidermis and dermis, using RNAeasy minikit (Qiagen) and following the manufacturer's instructions.

tag: E14.5 skin


title: Bulun 2-3h-


title: Control dermis, sample 1


title: hES_SA01_1

description: gene expression data from undifferentiated hES cells line SA01

source_name: human embryonic stem (hES) cells line SA01, biological replicate 1

tag: human ES cells line from Cellartis, Sweden  commercial line derived from normal embryos


title: Mutant epidermis, sample 1


title: hES_SA01_3

source_name: human embryonic stem (hES) cells line SA01, biological replicate 3


title: Mutant dermis, sample 2

description: Gene expression data from activated beta-catenin mutant E15.5 embryo dermis

source_name: Mouse activated beta-catenin E15.5 dermis


title: Control skin, sample 2

description: Gene expression data from control E14.5 embryo skin

source_name: Mouse control E14.5 skin


title: hES_VUB01_1

source_name: human embryonic stem (hES) cells line VUB01, biological replicate 1


title: Mutant dermis, sample 1


title: Control skin, sample 1


title: hES_VUB01_3

source_name: human embryonic stem (hES) cells line VUB01, biological replicate 3


title: Choroid plexus epithelium, Whole brain: RAG_011907_le1

status: Public on May 17 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: B10.PL RAG -/- Samples

source_name: choroid plexus epithelium, Whole brain


title: Choroid plexus epithelium, Whole brain: RAG_122205_le1

description: B10.PL RAG -/- Samples


title: Choroid plexus epithelium, Whole brain: B10_011907_le1

description: B10.PL WT Samples


title: Choroid plexus epithelium, Whole brain: RAG_102406_le1

description: B10.PL WT (samples were reversed)


title: Mutant skin, sample 1


title: hES_SA01_2

source_name: human embryonic stem (hES) cells line SA01, biological replicate 2


title: Choroid plexus epithelium, Whole brain: B10_122205_le1

description: B10.PL WT Sample


title: SThdh111/111 sample 2

city: Charlestown

first: Ghazaleh

last: Sadri-Vakili

state: MA

department: Neurology

institute: Massachusetts General Hospital

description: Affymetrix protocol

hyb_protocol: MOE40.3K oligonucleotide microarrays using Affymetrix Fluidics Station 400

scan_protocol: scanned and normalized using global scaling. All quality control parameters calculated by Affymetrix GCOS Software were monitored. The images of the chips were analyzed to find spotted or damaged array regions and to ensure data quality. The Presence/Absence calls from Affymetrix MAS5 were monitored and compared throughout the different samples.

data_processing: All data were normalized using the GeneChip Robust Multi-Chips Analysis (GCRMA) algorithm, performed with R in BioConductor.

source_name: SThdh111/111 sample 2

label_protocol: Affymetrix protocol

extract_protocol: Tri-reagent and RNeasy column for purification

tag: Huntington's disease knock-in mouse striatal immortalized cell lines


title: Choroid plexus epithelium, Whole brain: B10_102406_le1

description: B10.PL RAG (samples were reversed)


title: CD8 T cells_IL-2 complex treatment_1 h

city: Seattle

first: Michael

middle: J

last: Bevan

state: WA

address: I604H HSC, 1959 NE Pacific Street

department: Immunology

institute: Univerisity of Washington, HHMI

description: Labeling, hybridization, and scanning were performed at the Center for Array Technologies at the University of Washington.

hyb_protocol: Labeled cRNA was processed further as recommended by Affymetrix, where 15 ug of cRNA was fragmented, a hybridization cocktail was assembled with addition of spike-in controls, and chips were hybridized for 16 hours. The chips were then washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip System.

scan_protocol: The genechips were placed in the GeneChip Scanner 3000, which scans the chips at a resolution of less than 2 microns.

data_processing: Image processing and expression analysis were performed using Affymetrix GCOS software.

source_name: CD8 T cells_IL-2 complex treatment_1 h

label_protocol: Total RNA (~4.65ug) was used to create the first strand cDNA using a T7-linked oligo(dT) primer. Once second strand synthesis was complete, an in vitro transcription reaction was performed using biotinylated UTP and CTP in the Affymetrix IVT Kit.

extract_protocol: Total RNA was extracted from purified CD8 T cells using RNeasy Mini Kit (QIAGEN), then concentrated by EtOH precipitation.

treatment_protocol: IL-2 complex was prepared by mixing 50 ug anti-IL-2 mAb (S4B6) and 1.5 ug recombinant mouse IL-2, which was then injected i.p. into C57BL/6J mice. Total CD8 T cells from the spleen at 1 h post treatment were purified by magnetic cell sorting using the CD8a T cell isolation kit, supplemented with biotinylated anti-CD11c, anti-CD19, anti-Gr-1, anti-TCRγδ, anti-I-Ab, and anti-NK1.1 mAbs. The purity was > 95%. Total RNA from the purified CD8 T cells was subject to DNA microarray analysis using GeneChip Mouse genome 430 2.0 array. Target labeling, hybridization and scanning were performed at the Center for Array Technologies at the University of Washington.

tag: strain

tag: gender

value: male

tag: tissue

value: spleen


title: SThdh7/7 sample 3

description: Affymetrix protocol

source_name: SThdh7/7 sample 3


title: SThdh7/7 sample 4

description: Affymetrix protocol

source_name: SThdh7/7 sample 4


title: SeV PI day 49 rep 2

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: mouse whole lung gene expression, 49 days post-Sendai virus infection, C57BL/6J, male

hyb_protocol: standard Affymetrix procedures

scan_protocol: Chips were scanned, and hybridization data were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software.

data_processing: Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004, ver 2.0), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).

source_name: whole lung, SeV PI day 49 rep 2

label_protocol: Second-strand cDNA synthesis, was performed using a T7-promoter coupled oligo(d)T primer (GeneChip T7-Oligo(d)T Promoter Primer Kit, Affymetrix, Santa Clara, CA), after which an in vitro transcription (IVT) reaction was performed using an Enzo BioArray High Yield RNA transcript labeling kit (Affymetrix).

growth_protocol: Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.

extract_protocol: Mice were sacrificed 49 days post-infection with Sendai virus. Lungs were flash frozen liquid nitrogen, and subsequently, total RNA was isolated by the acid guanidinium thiocyanate-phenol-chloroform extraction method (Trizol, Invitrogen, Carlsbad, CA).

treatment_protocol: Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Mice were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) intranasally. 3-5 week old male C57BL/6J mice were obtained from Jackson Laboratory. Airway hyperreactivity was assessed 49 days post infection as previously described (Patel et al, 2005), after which mice were sacrificed and lungs were harvested, right for RNA, left for histology and analysis of goblet cell metaplasia.

tag: Strain

tag: Time

value: 49 days post-infection

tag: Infection

value: active Sendai virus

tag: Gender

value: Male


title: SThdh7/7 sample 2

description: Affymetrix protocol

source_name: SThdh7/7 sample 2


title: UV-SeV PI day 49 rep 3

description: mouse whole lung gene expression, 49 days post-UV-inactivated Sendai virus infection, C57BL/6J, male

source_name: whole lung, UV-SeV PI day 49 rep 3

value: UV-inactivated Sendai virus


title: CD8 T cells_IL-2 complex treatment_3 h

source_name: CD8 T cells_IL-2 complex treatment_3 h

treatment_protocol: IL-2 complex was prepared by mixing 50 ug anti-IL-2 mAb (S4B6) and 1.5 ug recombinant mouse IL-2, which was then injected i.p. into C57BL/6J mice. Total CD8 T cells from the spleen at 3 h post treatment were purified by magnetic cell sorting using the CD8a T cell isolation kit, supplemented with biotinylated anti-CD11c, anti-CD19, anti-Gr-1, anti-TCRγδ, anti-I-Ab, and anti-NK1.1 mAbs. The purity was > 95%. Total RNA from the purified CD8 T cells was subject to DNA microarray analysis using GeneChip Mouse genome 430 2.0 array. Target labeling, hybridization and scanning were performed at the Center for Array Technologies at the University of Washington.


title: SThdh111/111 sample 3

description: Affymetrix protocol

source_name: SThdh111/111 sample 3


title: SeV PI day 49 rep 1

source_name: whole lung, SeV PI day 49 rep 1


title: CD8 T cells_IL-2 complex treatment_0 h

source_name: CD8 T cells_IL-2 complex treatment_0 h (untreated)

treatment_protocol: Total CD8 T cells from the spleen of C57BL/6J mice were purified by magnetic cell sorting using the CD8a T cell isolation kit (Miltenyi Biotec), supplemented with biotinylated anti-CD11c, anti-CD19, anti-Gr-1, anti-TCRγδ, anti-I-Ab, and anti-NK1.1 mAbs. The purity was > 95%. Total RNA from the purified CD8 T cells was subject to DNA microarray analysis using GeneChip Mouse genome 430 2.0 array. Target labeling, hybridization and scanning were performed at the Center for Array Technologies at the University of Washington.


title: SeV PI day 49 rep 3

source_name: whole lung, SeV PI day 49 rep 3


title: UV-SeV PI day 49 rep 2

source_name: whole lung, UV-SeV PI day 49 rep 2


title: UV-SeV PI day 49 rep 1

source_name: whole lung, UV-SeV PI day 49 rep 1


title: HVT5

status: Public on May 15 2008

city: San Francisco

first: James

middle: A

last: Frank

state: CA

address: 4150 Clement St

institute: UCSF

hyb_protocol: Standard Affymetrix Procedures

scan_protocol: Standard Affymetrix Procedures

source_name: Lung tissue after mechanical ventilation for 3h

label_protocol: Single round aRNA sythesis followed by in vitro transcription (Ambion MessageAmp II-Biotin Enhanced)

extract_protocol: RNeasy (Qiagen) from whole lung tissue (30 mg) stabilized in RNALater

treatment_protocol: Mice were anesthetized with isoflurane followed by ketamine/xylaxine. Saline (0.25 ml) was given every hour ip. A tracheotomy tube was placed and the mice were ventilated with an initial peak airway pressure of 20 cmH2O approximating a tidal volume of 20 ml/kg and without end-expiratory pressure. Ventilation was continued for 3h. Tidal volume was not adjusted. Body temperature was monitored with a digital rectal thermometer and maintained at 37C with a heating table and external heating lamp. Control mice were treated identically, but were not mechanically ventilated (i.e. breathed spontaneously).

tag: C57BL\6 male mice, 22-25g lung tissue (30 mg) after 3h high tidal volume ventilation


title: NV3

source_name: Lung tissue, no mechanical ventilation

tag: C57BL\6 male mice, 22-25g lung tissue (30 mg) No mechanical ventilation


title: HVT3


title: SThdh7/7 sample 1

description: Affymetrix protocol

source_name: SThdh7/7 sample 1


title: SThdh111/111 sample 1

description: Affymetrix protocol

source_name: SThdh111/111 sample 1


title: HVT4


title: HVT2


title: NV4


title: NV1

tag: C57BL\6 male mice, 22-25g lung tissue (30 mg) no mechanical ventilation


title: HVT1

source_name: Lung tissue following 3h high tidal volume mechanical ventilation

tag: C57BL\6 male mice, 22-25g, lung tissue (30mg).


title: Total_RNA_EB, Biological Rep-3

status: Public on May 14 2008

first: Charles

last: Murry

address: 815 Mercer st., Rm # 454

department: Pathology

institute: University of Washington

description: Transcript abundance analysis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix 430_2 mouse expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed from .CEL files with Microarray Suite version  5.0 (MAS 5) algorithm using the affy package of the Bioconductor project with scaling between arrays disabled. In subsequent steps of the analysis data was normalized with the affymetrix spike-in controls.

source_name: R-1, Differentiated day-5 Embryoid bodies from mouse ESCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug of RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Embryonic stem cells (ESC) maintained in the presence of LIF in an undifferentiated state and its differentiated progeny, grown in the absence of LIF, the day-5 Embryoid bodies (EB) were selected for the experiment.

extract_protocol: Cytoplasmic lysate was subjected to sucrose-gradient centrifugation followed by fractionation. Fractions were further pooled and RNA was precipitated from each pool and purified using Qiagen RNeasy midi-columns. The quality of RNA was determined using an Agilent Bioanalyzer and quantitated by absorbance at 260 nm.

treatment_protocol: Cells were incubated with 150 ug/ml of cycloheximide for 15 min to arrest ribosome movement on mRNAs before harvesting the cells.

tag: Differentiated day-5 Embryoid Bodies


title: Total_RNA_ESC, Undifferentiated, Biological Rep-2

description: Transcript abundance analysis

source_name: R-1, Undifferentiated Mouse Embryonic stem cells

tag: Undifferentiated Embryonic stem cells


title: NV5


title: NV2


title: Total_RNA_EB, Biological Rep-1

description: Transcript abundance analysis


title: Total_RNA_EB, Biological Rep-2

description: Transcript abundance analysis


title: Total_RNA_ESC, Undifferentiated, Biological Rep-3

description: Transcript abundance analysis


title: Total_RNA_ESC, Undifferentiated, Biological Rep-1

description: Transcript abundance analysis


title: EB, Pool-4, Biological Rep-1

description: Translation state array analysis

source_name: R-1, Differentiated day-5 Embryoid bodies from mouse ESCs; Fractionated Polysomal RNA


title: EB, Pool-4, Biological Rep-2

description: Translation state array analysis


title: EB, Pool-3, Biological Rep-1

description: Translation state array analysis


title: EB, Pool-3, Biological Rep-3

description: Translation state array analysis


title: EB, Pool-1, Biological Rep-3

description: Translation state array analysis


title: EB, Pool-4, Biological Rep-3

description: Translation state array analysis


title: EB, Pool-1, Biological Rep-2

description: Translation state array analysis


title: EB, Pool-2, Biological Rep-2

description: Translation state array analysis


title: SThdh111/111 sample 4

description: Affymetrix protocol

source_name: SThdh111/111 sample 4


title: ESC, Undifferentiated, Pool-4, Biological Rep-1

description: Translation state array analysis

source_name: R-1, Undifferentiated Mouse Embryonic stem cells; Fractionated Polysomal RNA


title: EB, Pool-3, Biological Rep-2

description: Translation state array analysis


title: EB, Pool-1, Biological Rep-1

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-4, Biological Rep-2

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-3, Biological Rep-3

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-3, Biological Rep-1

description: Translation state array analysis


title: EB, Pool-2, Biological Rep-1

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-2, Biological Rep-3

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-2, Biological Rep-2

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-4, Biological Rep-3

description: Translation state array analysis


title: GFP dsRNA-treated S2 Cells (2)

first: Nicolas

last: Robine

address: 430, East 67th Street, RRL 517

department: Developmental Biology

institute: Sloan-Kettering Institute

hyb_protocol: 10 ug of labeled and fragmented cRNA was then hybridized onto the Drosophila Genome 2.0 array  (Affymetrix) for 16 hours at 45 degres celsius.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software 1.4

organism: Drosophila melanogaster

source_name: Drosophila melanogaster Schneider2 (S2) cells , S2 cells treated with double-stranded RNA (dsRNA)

label_protocol: 2 ug of good quality total RNA were then labeled according to protocols recommended by manufacturers. Briefly, after reverse-transcription with an oligo-dT-T7 (Affymetrix), double stranded cDNA was generated with the supercript double stranded cDNA synthesis custom kit (Invitrogen Life Technologies, Carlsbad, CA). In an in vitro Transcription step (IVT) with T7 RNA polymerase (MessageAmp aRNA kit from Ambion, Austin, TX) the cDNA was linearly amplified and labeled with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: S2 cells were grown at 25°C in Schneider's insect medium supplemented with 10% fetal bovine serum, 100U/ml penicillin and 100ug/ml streptomycin.

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol:
S2 cells were soaked with dsRNA against GFP for 4 days.
After 4 days of initial soaking, cells were treated with a second round of dsRNA. Cells were harvested another 4 days later.

tag: GFP dsRNA-treated S2 Cells


title: ESC, Undifferentiated, Pool-3, Biological Rep-2

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-2, Biological Rep-1

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-1, Biological Rep-3

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-1, Biological Rep-2

description: Translation state array analysis


title: ESC, Undifferentiated, Pool-1, Biological Rep-1

description: Translation state array analysis


title: GFP dsRNA-treated S2 cells (1)

tag: GFP dsRNA-treated S2 cells


title: C2C12 myotube differentiation Day 5 replicate 3

status: Public on May 13 2008

city: Cambridge

first: Qicheng

last: Ma

address: 250 Mass Ave

institute: Novartis

description: C2C12 Differentiation timecourse to observe changes between myoblasts and myotubes

hyb_protocol: RNA were hybridized on Affymetrix mouse whole-genome microarray, MOE430 Plus 2.0 chips, Each time point was performed in triplicate, from independent experiments.

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

data_processing: The data were analyzed with Bioconductor GCRMA normalization method. The log-scaled data were unlogged to be comparable to MAS 5 raw value. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: C2C12 myotube differentiation Day 5

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol

growth_protocol: C2C12 mouse skeletal myoblasts were cultured in DMEM high glucose with 10% FBS and 1% penicillin/streptomycin (Gibco) and maintained at 37°C and 5% CO2.

extract_protocol: C2C12 cell RNA was harvested using the RNeasy Midiprep kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Differentiation of C2C12 myoblasts into myotubes was achieved by culturing cells in medium containing reduced serum concentration (2% v/v) for up to 5 days with medium changes every 2 days.

tag: Age

value: C2C12 myotube differentiation Day 5


title: C2C12 myotube differentiation Day 4 replicate 3

source_name: C2C12 myotube differentiation Day 4

value: C2C12 myotube differentiation Day 4


title: C2C12 myotube differentiation Day 5 replicate 2


title: NHDF at passage 13, from adult donor, biological rep 3

city: Indianapolis

first: Tao

last: Wei

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: Gene expression data from NHDF in culture

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C and 60 rpm on human whole genome U133 plus 2 GeneChip . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Chip processing, image capturing, and raw data analysis were performed using the Affymetrix Microarray Suite MAS adopting default parameters. The chip signals were normalized using the default method in Affymetrix MAS5, but setting the target at 2%-trimmed mean to 1500.

source_name: NHDF in culture

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

growth_protocol: Normal human dermal fibroblasts (NHDFs) were maintained in FGM with 10% FBS, 5% CO2 and at 37 oC

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by RNA clean up using RNeasy spin columns.

treatment_protocol: No treatment. Cells were cultured to various passage and harvested for RNA isolation.

tag: Fibroblast cells


title: C2C12 myotube differentiation Day 5 replicate 1


title: NHDF at passage 13, from adult donor, biological rep 1


title: C2C12 myotube differentiation Day 3 replicate 3

source_name: C2C12 myotube differentiation Day 3

value: C2C12 myotube differentiation Day 3


title: NHDF at passage 13, from adult donor, biological rep 2


title: C2C12 myotube differentiation Day3 replicate 1

source_name: C2C12 myotube differentiation Day3

value: C2C12 myotube differentiation Day3


title: NHDF at passage 4, from adult donor, biological rep 2


title: C2C12 myotube differentiation Day 3 replicate 2


title: C2C12 myotube differentiation Day 4 replicate1


title: NHDF at passage 6, from neonatal donor, biological rep 1


title: NHDF at passage 4, from adult donor, biological rep 1


title: C2C12 myotube differentiation Day 4 replicate 2


title: NHDF at passage 6, from neonatal donor, biological rep 3


title: NHDF at passage 6, from neonatal donor, biological rep 2


title: C2C12 myotube differentiation Day2 replicate 3

source_name: C2C12 myotube differentiation Day2

value: C2C12 myotube differentiation Day2


title: C2C12 myotube differentiation Day 2 replicate 1

source_name: C2C12 myotube differentiation Day 2

value: C2C12 myotube differentiation Day 2


title: C2C12 myotube differentiation Day 1 replicate 3

source_name: C2C12 myotube differentiation Day 1

value: C2C12 myotube differentiation Day 1


title: C2C12 myotube differentiation Day 2 replicate 2


title: C2C12 myotube differentiation 6 hours replicate 2

source_name: C2C12 myotube differentiation 6 hours

value: C2C12 myotube differentiation 6 hours


title: C2C12 myotube differentiation Day1 replicate 2

source_name: C2C12 myotube differentiation Day1

value: C2C12 myotube differentiation Day1


title: C2C12 myoblasts 90% confluency replicate 1

source_name: C2C12 myoblasts

value: C2C12 myoblasts  differentiation 0


title: C2C12 myoblasts 90% confluency replicate 3


title: C2C12 myoblasts 90% confluency replicate 2


title: C2C12 myotube differentiation 6 hours replicate 1


title: C2C12 myoblasts at 50% confluency replicate 1

value: C2C12 myoblasts  differentiation -1


title: C2C12 myotube differentiation 6 hours replicate 3


title: C2C12 myotube differentiation Day 1 replicate 1


title: SI2_wk4_LF

description: pooled total RNA sample of 6 mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000

data_processing: Data analysis was performed using Microarray Analysis Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 500.

source_name: SI2 after 4 wks on a LF diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix)

growth_protocol: Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group and per time point (n=6).

treatment_protocol: After a run-in period of 3 weeks on a low-fat diet, 9 weeks old mice were fed a high- (HF) or a low-fat (LF) purified diet for 2, 4, and 8 weeks

tag: C57Bl/6J male mice, 9wks old at start of diet intervention


title: SI3_wk2_HF (high fat diet, high calcium)

description: Pooled total RNA sample of 6 mice.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000.

source_name: SI3 after 2 wks on a HFD, HCa diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).

treatment_protocol: After a run-in period of 3 weeks on a low-fat diet, 9-week-old mice were fed a high-fat (HF) purified diet with a high calcium concentration of 150mmol/kg (HCa diet) for 8 weeks.

tag: strain

tag: gender

value: male

value: small intestine, SI 3

tag: dietary fat

value: high

tag: dietary calcium

tag: age

value: 9wks old at start of diet intervention

tag: diet intervention time


title: SI3_wk8_HF

description: pooled total RNA sample of 6 mice

source_name: SI3 after 8 wks on a HF diet


title: SI3_wk8_LF

description: pooled total RNA sample of 6 mice

source_name: SI3 after 8 wks on a LF diet


title: SI2_wk4_HF

description: pooled total RNA sample of 6 mice

source_name: SI2 after 4 wks on a HF diet


title: SI2_wk8_HF

description: pooled total RNA sample of 6 mice

source_name: SI2 after 8 wks on a HF diet


title: SI1_wk8_LF

description: pooled total RNA sample of 6 mice

source_name: SI1 after 8 wks on a LF diet


title: SI3_wk2_LF

description: pooled total RNA sample of 6 mice

source_name: SI3 after 2 wks on a LF diet


title: SI2_wk8_LF

description: pooled total RNA sample of 6 mice

source_name: SI2 after 8 wks on a LF diet


title: SI2_wk2_HF (high fat diet, high calcium)

description: Pooled total RNA sample of 6 mice.

source_name: SI2 after 2 wks on a HFD, HCa diet

tag: tissue

value: small intestine, SI 2


title: C2C12 myoblasts 50% confluency replicate 3


title: SI2_wk2_LF

description: pooled total RNA sample of 6 mice

source_name: SI2 after 2 wks on a LF diet


title: SI3_wk4_HF

description: pooled total RNA sample of 6 mice

source_name: SI3 after 4 wks on a HF diet


title: SI1_wk8_HF

description: pooled total RNA sample of 6 mice

source_name: SI1 after 8 wks on a HF diet


title: C2C12 myoblasts 50% confluency replicate 2


title: EB, Pool-2, Biological Rep-3

description: Translation state array analysis

source_name: R-1, Differentiated day-5 Embryoid bodies from mouse ESCs; Fractionated Polysomal RNA


title: SI3_wk4_LF

description: pooled total RNA sample of 6 mice

source_name: SI3 after 4 wks on a LF diet


title: SI1_wk4_HF

description: pooled total RNA sample of 6 mice

source_name: SI1 after 4 wks on a HF diet


title: SI1_wk4_LF

description: pooled total RNA sample of 6 mice

source_name: SI1 after 4 wks on a LF diet


title: Nerve_Control_Rosi_715

status: Public on May 10 2008

city: Ann Arbor

first: Timothy

middle: David

last: Wiggin

state: MI

address: 109 Zina Pitcher Pl., Rm 5368

institute: University of Michigan

description: Normalization performed May 02, 2008

data_processing: RMA normalized with GenePattern module ExpressionFileCreator, non-log transformed.  Affy probeset annotation used in processed data.

source_name: Mouse Sciatic Nerve, Control Rosi

label_protocol: Ovation Biotin—RNA Amplification and Labeling System (NuGen Inc., San Carlos, CA)

extract_protocol: RNeasy Mini Kit, Qiagen, Valencia, CA

tag: Strain

tag: Tissue

value: Peripheral Nerve (sciatic)

tag: Treatment

value: Rosiglitazone


title: Nerve_Diabetic_Rosi_718

description: Normalization performed May 02, 2008

source_name: Mouse Sciatic Nerve, Diabetic Rosi

value: STZ and Rosiglitazone


title: Nerve_Diabetic_Vehicle_710

description: Normalization performed May 02, 2008

source_name: Mouse Sciatic Nerve, Diabetic Vehicle

value: STZ


title: Nerve_Control_Rosi_713

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Rosi_716

description: Normalization performed May 02, 2008


title: SI1_wk2_HF (high fat diet, high calcium)

first: Guido

last: Hooiveld

institute: Wageningen University

description: Pooled total RNA sample of 6 mice.

source_name: SI1 after 2 wks on a HFD, HCa diet

value: small intestine, SI 1


title: Nerve_Control_Rosi_714

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Rosi_720

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Rosi_719

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Rosi_717

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Vehicle_706

description: Normalization performed May 02, 2008


title: Nerve_Control_Rosi_712

description: Normalization performed May 02, 2008


title: SI1_wk2_LF

description: pooled total RNA sample of 6 mice

source_name: SI1 after 2 wks on a LF diet


title: Nerve_Diabetic_Vehicle_708

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Vehicle_707

description: Normalization performed May 02, 2008


title: Nerve_Control_Vehicle_702

description: Normalization performed May 02, 2008

source_name: Mouse Sciatic Nerve, Non-diabetic Vehicle


title: Nerve_Control_Vehicle_703

description: Normalization performed May 02, 2008


title: Nerve_Control_Vehicle_704

description: Normalization performed May 02, 2008


title: Nerve_Diabetic_Vehicle_709

description: Normalization performed May 02, 2008


title: Nerve_Control_Vehicle_705

description: Normalization performed May 02, 2008


title: AFB1+H. hepaticus cecum, biological rep 1

status: Public on May 09 2008

city: Chapel Hill

first: Arlin

middle: B

last: Rogers

state: NC

address: Campus Box 7431

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

description: Gene expression data from AFB1+H. hepaticus-treated 40 wk old female mouse cecum

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

data_processing: The data were analyzed with GeneChip Operating Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Female mouse cecum, 40 wk, AFB1 & H. hepaticus inoculated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ng total RNA

growth_protocol: C3H/HeN mice were inoculated with AFB1 and/or H. hepaticus or vehicle only as described above, and collected at 40 weeks

extract_protocol: Total RNA was isolated from freshly thawed tissues using Trizol according to manufacturer's protocol

treatment_protocol: Liver and cecum samples were removed and flash frozen in liquid N2 at necropsy

tag: C3H/HeN, female


title: Generation of pluripotent stem cells from adult human testis_haGSC1

city: Tuebingen

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

description: haGSC cells from testis, cultivated with KO Medium+GDNF

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol with the GeneChip scanner 3000

data_processing: GC-RMA normalisation with ArrayAssist 5.1 software

label: Affymetrix standard protocol

label_protocol: Affymetrix standard protocol

growth_protocol: human adult germ stem cells (haGSCs) were derived from hGS cells from 3 different normal patients after the enrichment and further cultivation in LIF supplemented medium. haGSC from patient 52, 54 and 35 (from lower and higher passages) were cultured for 10 days in basic medium (DMEM high glucose, 15% FCS (Biochrom), 1% non-essential amino acids (NEAA), 1% L-glutamine and 0.05 mM ß-mercaptoethanol (Gibco) with 103 units/ml leukemia inhibitory factor (LIF, human, Chemicon) on 0,1% gelatine coated dishes. After  the clusters were manually cut, the isolated clusters were  washed with phosphate buffered saline (PBS) and pelleted at 1000rpm/10min./4°C and lysed with RLT buffer + ß-Mercaptoethanol and stored at -80°C.

extract_protocol: standard Qiagen Mini protocol


title: Nerve_Control_Rosi_711

description: Normalization performed May 02, 2008

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol


title: AFB1+H. hepaticus liver, biological rep 2

description: Gene expression data from AFB1+H. hepaticus-treated 40 wk old female mouse liver

source_name: Female mouse liver, 40 wk, AFB1 & H. hepaticus inoculated


title: Control cecum, biological rep 1

description: Gene expression data from control 40 wk old female mouse cecum

source_name: Female mouse cecum, 40 wk, control


title: Generation of pluripotent stem cells from adult human testis_haGSC2

source_name: haGSC cells from testis, cultivated with KO Medium+GDNF


title: Generation of pluripotent stem cells from adult human testis_haGSC3

tag: haGSC cells from testis, cultivated with KO Medium+GDNF


title: AFB1+H. hepaticus cecum, biological rep 2


title: AFB1+H. hepaticus liver, biological rep 1


title: PSF8, Fascin-knockdown, biological rep1

status: Public on May 08 2008

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

country: China

institute: Shantou university, medical college

description: expression genes data from PSF8 (Fascin-knockdown cells)

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.

source_name: Fascin-knockdown

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

growth_protocol: cell lines were maintained in 199 medium(Invitrogen) containing 10% fetal calf serum (FCS)at 5% CO2 at 37℃

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

tag: esophageal squamous cell carcinoma

tag: Fascin-knockdown


title: Control liver, biological rep 1

description: Gene expression data from control 40 wk old female mouse liver

source_name: Female mouse liver, 40 wk, control


title: Control cecum, biological rep 2


title: AFB1 liver, biological rep 2

description: Gene expression data from AFB1-treated 40 wk old female mouse liver

source_name: Female mouse liver, 40 wk, AFB1 inoculated


title: Control liver, biological rep 2


title: AFB1 liver, biological rep 1


title: 12hr timepoint - E2 treated - biological rep3

status: Public on May 07 2008

city: Singapore

first: Lance

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

country: Singapore

institute: Genome Institute of Singapore

description: E2 treated or untreated (control) cells.

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: 5 micrograms MCF7 total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was purified using the Qiagen RNAeasy kit according to the manufacturers instructions

treatment_protocol: MCF7 cells were grown to 30-50% confluency and exposed to 10 nM E2 (or vehicle only) at 12, 24, and 48 hours. Each timepoint was performed in triplicate  (ie, biological replicates).

tag: E2 treated


title: Generation of pluripotent stem cells from adult human testis_hGS1

description: hGS cells from testis, cultivated with KO Medium+GDNF

growth_protocol: Spermatogonial cells (hGS) from 3 different normal patients (patient 59, 73 and 81, passage 0) were cultured for 4 days in Knockout medium, 20% Knockout-FBS, 1% L-glutamine and 4ng/ml GDNF. After enrichment with CD49f and matrix selection with collagen and laminin the cells were washed with phosphate buffered saline (PBS) and pelleted at 1000rpm/10min./4°C, lysed with RLT buffer + ß-Mercaptoethanol and stored at -80°C.


title: 24hr timepoint - Untreated control - biological rep2

tag: untreated control


title: Generation of pluripotent stem cells from adult human testis_ES1

description: H1 cells from testis, cultivated in ES Medium+FGF2

growth_protocol: hES(H1) cells (hES) were cultured for 10 days (passage 48, 57 and 67) in Knockout medium, 20% Knockout-Serum-Replacer, 1% L-glutamine, 1% NEAA, 1% penicillin/streptomycin and 4ng/ml FGF-2, on CF1 inactivated feeder on 0,1% gelatine coated dishes. After the clusters were manually cut, the isolated clusters were washed with phosphate buffered saline (PBS) and pelleted at 1000rpm/10min./4°C and lysed with RLT buffer + ß-Mercaptoethanol and stored at -80°C.

tag: H1 cells from testis, cultivated with ES Medium+FGF2


title: 48hr timepoint - E2 treated - biological rep3


title: 24hr timepoint - E2 treated - biological rep2


title: 24hr timepoint - Untreated control - biological rep1


title: 48hr timepoint - E2 treated - biological rep2


title: 24hr timepoint - E2 treated - biological rep3


title: 24hr timepoint - E2 treated - biological rep1


title: 48hr timepoint - Untreated control - biological rep3


title: 48hr timepoint - Untreated control - biological rep2


title: 12hr timepoint - E2 treated - biological rep1


title: 12hr timepoint - E2 treated - biological rep2


title: 48hr timepoint - E2 treated - biological rep1


title: 48hr timepoint - Untreated control - biological rep1


title: 24hr timepoint - Untreated control - biological rep3


title: 12hr timepoint - Untreated control - biological rep3


title: 12hr timepoint - Untreated control - biological rep1


title: GUYT2_50402

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description: Tumor samples from Tamoxifen-only treated primary breast cancer patients

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: RMA Bioconductor

source_name: breast

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc)olation of RNA was performed using the Trizol method (Invitrogen) according to the manufacturers instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the bioanalyzer (Agilent Inc).


title: GUYT2_50403


title: T84 IL17

city: Davis

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: phycoerythrin-strepavidin used as fluorophore

hyb_protocol: Standard manual-based protocol for hybridization of samples onto Affymetrix GeneChips

scan_protocol: Affymetrix protocol and scanner 3000

data_processing: data was processed by Affymetrix GeneChip Operating System using default parameters

source_name: T84 human colonic epithelial cell line

label_protocol: Standard manual-based protocol for biotin labeling of samples for Affymetrix GeneChip analysis

extract_protocol: Trizol extraction protocol

tag: Grown to confluence in transwell plate and treated with IL17


title: T84 control

tag: Grown to confluence in transwell plates


title: GUYT2_50404


title: 12hr timepoint - Untreated control - biological rep2


title: T84 IL22

tag: Grown to confluence in transwell plate treated with IL22


title: GUYT2_50398


title: GUYT2_50401


title: GUYT2_50400


title: GUYT2_50389


title: GUYT2_50385


title: GUYT2_50405


title: GUYT2_50395


title: GUYT2_50391


title: GUYT2_50383


title: GUYT2_50384


title: GUYT2_50382


title: GUYT2_50378


title: GUYT2_50374


title: GUYT2_50377


title: GUYT2_50380


title: GUYT2_50361


title: GUYT2_50368


title: GUYT2_50366


title: GUYT2_50369


title: GUYT2_50357


title: GUYT2_50373


title: GUYT2_50362


title: GUYT2_50353


title: GUYT2_50356


title: GUYT2_50341


title: GUYT2_50345


title: GUYT2_50349


title: GUYT2_50337


title: GUYT2_50338


title: GUYT2_50354


title: GUYT2_50344


title: GUYT2_50326


title: GUYT2_50339


title: GUYT2_50333


title: GUYT2_50330


title: GUYT2_50335


title: GUYT2_50327


title: GUYT2_50318


title: GUYT2_50321


title: GUYT2_50328


title: GUYT2_50320


title: GUYT2_50336


title: GUYT2_50319


title: GUYT2_50317


title: GUYT2_50313


title: GUYT2_50307


title: GUYT2_50305


title: GUYT2_50308


title: GUYT2_50302


title: GUYT2_50296


title: GUYT2_50316


title: GUYT2_50301


title: GUYT2_50294


title: GUYT2_50299


title: GUYT2_50298


title: GUYT2_50300


title: GUYT2_50287


title: GUYT2_50291


title: GUYT2_50293


title: GUYT2_50290


title: GUYT2_50282


title: GUYT2_50284


title: GUYT2_50269


title: GUYT2_50270


title: GUYT2_50266


title: GUYT2_50271


title: GUYT2_50267


title: ST-HSC_Control_Rep4

city: Rozzano

first: Francesca

last: Ficara

address: via Manzoni 56

country: Italy

institute: CNR/Istituto Clinico Humanitas

description: See GeneChip Two-Cycle Target labeling assay protocol (Affymetrix)

hyb_protocol: GeneChip Hybridization Kit (Affymetrix)

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.

data_processing: Scanned data were exported to dChip software for normalization, statistical analysis and heat mapping. A perfect-match/mismatch (PM/MM) model was used for the calculation of expression values.

molecule: polyA RNA

source_name: Short-term hematopoietic stem cells, control

label_protocol: GeneChip IVT Labeling Kit (Affymetrix)

extract_protocol: RNA from sorted cells was purified using Trizol and subjected to two rounds of amplification.

treatment_protocol: 7 poly (I:C) injections every other day, last injection 4 wks before sacrifice

tag: Mouse model

value: MxCre+.Pbx1+/f on a C57BL/6 background

tag: Age

value: 7.5 wks old

value: Bone marrow ST-HSC (Lin-cKit+Sca1+CD34+CD135-)


title: GUYT2_50263


title: GUYT2_50273


title: ST-HSC_Control_Rep2

description: See GeneChip® Two-Cycle Target Labeling Assay protol (Affymetrix)

hyb_protocol: GeneChip® Hybridization Control Kit (Affymetrix)

label_protocol: GeneChip® IVT Labeling Kit (Affymetrix)

treatment_protocol: 7 poly(I:C) injections every other day, last injection 4wks before sacrifice

value: MxCre-.Pbx1f/f on a C57B/6 background

value: Bone marrow LT-HSC (Lin-cKit+Sca1+CD34+CD135-)


title: GUYT2_50264


title: GUYT2_50265


title: LT-HSC_Mutant_Rep3

source_name: Long-term hematopoietic stem cells, mutant

value: MxCre+.Pbx1f/f on a C57B/6 background

value: Bone marrow LT-HSC (Lin-cKit+Sca1+CD34-CD135-)


title: ST-HSC_Control_Rep3

treatment_protocol: 7 poly(I:C) injections every other day, last injection 3wks before sacrifice

value: 8.5 wks old


title: LT-HSC_Mutant_Rep1


title: LT-HSC_Mutant_Rep2


title: GUYT2_50262


title: LT-HSC_Control_Rep2

source_name: Long-term hematopoietic stem cells, control


title: GUYT2_50261


title: LT-HSC_Control_Rep1

value: MxCre-.Pbx1f/f on a C57BL/6 background

value: Bone marrow LT-HCS (Lin-cKit+Sca1+CD34-CD135-)


title: Subject #8046-Preinfection

status: Public on May 06 2008

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description: Clinical Study - Sham Infected

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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 1500.

source_name: Nasal Epithelium

label_protocol: Purified RNA was converted to biotinylated cDNA target using NuGEN Ovation Biotin kit and protocol provided by supplier.

extract_protocol: Total RNA was extracted from nasal scrapings using Trizol Reagent and protocol provided by supplier.  Extracted RNA was further purified using Qiagen RNEasy Micro columns and protocol provided by supplier.

treatment_protocol: Subjects infected with HPV-16 rhinovirus or sham-infected prior to nasal epithelial scraping.  Only subjects exhibiting rhinovirus infection were used for collection.

tag: CONTROL

tag: Age = 20

tag: Sex = F


title: Subject #8046-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8042-2d Postinfection

description: Clinical Study - Sham Infected

tag: Age = 22

tag: Sex = M


title: Subject #8045-Preinfection

description: Clinical Study - Sham Infected

tag: Age = 19


title: Subject #8045-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8046-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8041-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8039-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8042-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8041-Preinfection

description: Clinical Study - RV Infected


title: Subject #8039-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8042-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8040-Preinfection

description: Clinical Study - RV Infected


title: Subject #8038-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8040-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8038-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8040-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8045-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8041-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8039-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8037-Preinfection

description: Clinical Study - RV Infected


title: Subject #8037-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8037-8hr Postinfection

description: Clinical Study - RV Infected


title: GUYT2_50322


title: Subject #8035-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8035-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8034-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8034-Preinfection

description: Clinical Study - RV Infected


title: Subject #8034-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8038-Preinfection

description: Clinical Study - RV Infected


title: Subject #8032-Preinfection

description: Clinical Study - RV Infected

tag: Age = 18


title: Subject #8032-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8032-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8030-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8031-8hr Postinfection

description: Clinical Study - Sham Infected

tag: Age = 21


title: Subject #8031-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8031-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8030-Preinfection

description: Clinical Study - RV Infected


title: Subject #8028-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8028-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8024-Preinfection

description: Clinical Study - RV Infected


title: Subject #8027-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8024-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8027-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8023-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8023-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8027-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8019-Preinfection

description: Clinical Study - RV Infected


title: Subject #8028-Preinfection

description: Clinical Study - RV Infected


title: Subject #8022-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8024-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8030-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8022-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8023-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8019-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8019-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8018-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8017-2d Postinfection

description: Clinical Study - Sham Infected

tag: Age = 24


title: Subject #8018-Preinfection

description: Clinical Study - RV Infected


title: Subject #8018-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8017-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8015-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8015-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8015-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8017-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8013-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8012-Preinfection

description: Clinical Study - RV Infected


title: Subject #8022-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8013-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8010-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8010-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8012-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8011-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8008-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8011-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8010-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8011-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8008-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8009-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8009-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8013-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8008-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8012-8hr Postinfection

description: Clinical Study - RV Infected


title: Subject #8007-Preinfection

description: Clinical Study - RV Infected


title: Subject #8007-2d Postinfection

description: Clinical Study - RV Infected


title: NCCs at P90, biological rep1

city: genoa

first: Domenico

last: Albino

address: L.go R. Benzi, 10

institute: National Institute for Cancer Research (IST)

description: Gene expression data from adult mouse at P90.

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

scan_protocol: GeneChips were scanned using the GeneChip® laser confocal fluorescence scanner.

data_processing:
The data were analyzed with Affymetrix Microarray Suite Software.
CEL files obtained by GeneChip Operating Software (GCOS, Affymetrix) were analyzed with the program dChip: a statistical method for model-based expression analysis (Li and Wong, 2001: "Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection." Proc Natl Acad Sci USA. 98, 31–36). After normalization, measures of the expression levels of each gene in each experiment were calculated using the perfect match/mismatch model described in Li and Wong, 2001: "Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application." Genome Biol. 2, 0032.1–0032.11
In parallel, CEL files obtained by GeneChip Operating Software (GCOS, Affymetrix)  were analyzed with the program SAM. Data were normalized according to the GeneChip robust multiarray average (GCRMA) algorithm  of the R/Bioconductor 1.4 package (http://www.bioconductor.org). Statistically significant expression changes were determined using permutation tests SAM  (http://www-stat.stanford.edu/~tibs/SAM/). Genes regulated at least two fold between conditions were considered. The âˆ† value was set to return a median false significant number = 0. The q values were 0 for the different gene lists created. Annotations were obtained through the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.niaid.nih.gov/david/beta/index.htm).

source_name: NCCs at P90 in adult adrenal medulla gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Arcturus PicoPure RNA extraction kit was used for total RNA extraction according to the manufacturer's instructions.

tag: CD1 adult mouse


title: Subject #8002-Preinfection

description: Clinical Study - Sham Infected


title: Subject #8007-8hr Postinfection

description: Clinical Study - RV Infected


title: NCCs at P90, biological rep2


title: NCCs at P90, biological rep3


title: Subject #8009-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8002-2d Postinfection

description: Clinical Study - Sham Infected


title: Subject #8035-Preinfection

description: Clinical Study - RV Infected


title: Subject #8002-8hr Postinfection

description: Clinical Study - Sham Infected


title: Subject #8001-2d Postinfection

description: Clinical Study - RV Infected


title: Subject #8001-Preinfection

description: Clinical Study - RV Infected


title: hippocampus: Control IP #2_e1_le1

city: Phoenix

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

description:
RNA bound to protein-G beads that contain non-immune IgGs
Treatment, type=purify, description=IP of RNAs bound to transgenic HuD

source_name: hippocampus


title: hippocampus: HuDpulldown #1_e1_le1

description:
RNA bounf to protein-G beads that was immunuprecipitated with anti-myc antibodies to transgenic HuD
Treatment, type=purify, description=IP of RNAs bound to transgenic HuD


title: NCCs at E8.5, biological rep1

description: Gene expression data from embryos at E8.5.

source_name: NCCs at E8.5 during neural tube closure

tag: CD1 embryo of litter


title: NCCs at E13.5, biological rep2

description: Gene expression data from embryos at E13.5.

source_name: NCCs at E13.5 in dorsal root ganglion


title: head/neck: UM_Control_e1_le1

source_name: head/neck


title: NCCs at E13.5, biological rep1


title: hippocampus: IgG RNA 1_le1


title: hippocampus: HuD RNA1_le1


title: hippocampus: HuDpulldown #2_e1_le1


title: head/neck: UM_Mutant_e1_le1


title: head/neck: LM_Mutant_e1_le1


title: hippocampus: _le1

description: total RNA input


title: NCCs at E13.5, biological rep3


title: Subject #8001-8hr Postinfection

description: Clinical Study - RV Infected


title: NCCs at E8.5, biological rep3


title: 12hr 1_redo2

status: Public on May 02 2008

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: biological replicate: 12hr 1_redo2, 12hr 2, 12hr 3

hyb_protocol: Following fragmentation, cRNA were hybridized to Human Genome U133Plus2.0 GeneChips. GeneChips were washed and stained in an Affymetrix Fluidics Station.

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

data_processing: Probe level data was converted to probe set expression values using RMA (Irizarry RA et al., Biostatistics 2003 Apr;4(2):249-64).

source_name: MCF-7 cells treated with estrogen for 12h.

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

growth_protocol: MCF-7 cells were maintained and deprived of hormones as previously described in Carroll, J.S. et al.  Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33–43 (2005).

extract_protocol: Total RNA was collected using Trizol (Invitrogen).

treatment_protocol: MCF-7 cells were stimulated with 100 nM estrogen for 0, 3, 6 or 12 h.

tag: breast adenocarcinoma from 69yr old female caucasian


title: 6hr 3

description: biological replicate: 6hr 1, 6hr 2, 6hr 3

source_name: MCF-7 cells treated with estrogen for 6h.


title: head/neck: OFT_Control_e1_le1


title: 6hr 2


title: 6hr 1


title: head/neck: LM_Control_e1_le1


title: 3hr 3

description: biological replicate: 3hr 1, 3hr 2, 3hr 3

source_name: MCF-7 cells treated with estrogen for 3h.


title: 12hr 3


title: head/neck: OFT _Mutant_e1_le1

description: OFT _Mutant


title: NCCs at E8.5, biological rep2


title: 3hr 1


title: head/neck: E11.5FAKMut_le1

description:
p75 sorted cranial neural crest cells from disected e11.5 head and torax (3 pooled mutant embryos)
Treatment, type=nucleic_acid_extraction, description=We will use this method as it was recommended by TGEN for small amounts of sample


title: 3hr 2


title: head/neck: E11.5FAKCtls_le1

description:
p75 sorted cranial neural crest cells from disected e11.5 head and torax (3 pooled control embryos)
Treatment, type=nucleic_acid_extraction


title: 12hr 2


title: 0hr 3

description: biological replicate: 0hr 1, 0hr 2, 0hr 3

source_name: MCF-7 cells treated with estrogen for 0h.


title: CKO Wild Type V1

status: Public on May 01 2008

city: Baltimore

first: William

middle: O

last: Osburn

address: 615 N. Wolfe St

department: Environmental Health

institute: Johns Hopkins Bloomberg School of Public Health

description: Basal gene expression in genetic control strain

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets CKO V x 3 sets CKOWT V comparison (1.5 fold cutoff (FC), Signal strength values were log-transformed to generate a normal distribution followed by independent two sample t-test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: liver, genetic control Alb-Cre:Keap1(flox/+)

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

extract_protocol: Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS)

tag: genetic control Alb-Cre:Keap1(flox/+), gender- male, age- 9 weeks, n = 1, # of tissue = 1 tissue

value: Liver


title: CKO Wild Type V2


title: 0hr 1


title: CKO Wild Type V3


title: CKO V4

description: Basal conditional Keap1 knockout gene expression

source_name: liver, conditional Keap1 knockout, Alb-Cre::Keap1(flox/-)

tag: conditional Keap1 knockout Alb-Cre:Keap1(flox/-), gender- male, age- 9 weeks, n = 1, # of tissue = 1 tissue


title: 0hr 2


title: CKO V3


title: CKO V5


title: woodchuck 6337 HCC, mouse array

city: Cleveland

first: Fangjing

last: Wang

address: Bishop building, Room s731, UH

department: Biomedical Engineering

institute: case Western Reserve University

description: cross-specieis hybridization using Affymetrix mouse 430-2   GeneChips® on woodchucks

hyb_protocol: After purification and fragmentation, 15 ug of biotin-labeled cRNA was used in a 300 ul hybridization cocktail containing spiked transcript controls. 200 ul of cocktail was loaded onto Affymetrix mouse microarrays (Santa Clara, CA) and hybridized for 16 hr at 45 C with agitation.

scan_protocol: Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 450. Arrays were scanned using the high resolution Gene Array scanner 3000.

data_processing: the hybridization results for each transduced/untransduced sample pair were first analyzed using GCOS 1.2 from Affymetrix (Santa Clara, CA). The genes that were differentially expressed in all the sample pairs were considered, and were further analyzed by SAM (developed by the Stanford University). A fold change of 1.5 and delta value above 1.0 was used as the criteria for SAM analysis.

organism: Marmota monax

source_name: woodchuck liver HCC tumor confirmed with ultrasound, mouse array

label_protocol: 3 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA. After second strand synthesis, double stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA.

growth_protocol: In a saparate room at ARC facilty, with dialy water and food change, monitor dialy.

extract_protocol: Qiagen RNeasy Midi Kit according to the protocols provided by the supplier with respect to tissues

treatment_protocol: woodchuck were infected with WHC virus at birth, 1-2 years old, 2.3-5kg, were euthanized using FatalPlus (Vortech Pharmaceuticals, Ltd., Dearborn, MI). All experiments were approved in accordance with the guidelines and recommendations of the Institutional Animal Care and Use Committees of Case Western Reserve University (Cleveland, OH) and Cornell University (Ithaca, NY). HCCs and surrounding liver tissuesLiver tissues were immediately removed from the animals. A pathaologist separated non-cancerous liver and HCC. Tissues were , snap- frozen in liquid nitrogen and stored at -80 C.


title: CD4+ cells IL1RN knockout 4 month rep2

city: Memphis

first: Jian

last: Yan

state: TN

address: 956 Court Ave

department: Orthopedics Surgery

institute: University of Tennessee Health Science Center

description: Gene expression data

hyb_protocol: Standard Affymetrix protocol with Fluidics Station 450

scan_protocol: Standard Affymetrix protocol with GeneChip Scanner 3000

data_processing: The data were analyzed with Expressiojn Console 1.1 using default MAS5 method. The target intensity was 500.

source_name: Mouse spleen at 4 month

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol

tag: Male wild-type BALB/c


title: Spleen_wt_4m_rep2

description: Gene expression data


title: woodchuck 5904 normal tissue surrounding the liver HCC, mouse array

source_name: woodchuck liver tissue with no HCC, but surrouding the HCCs, mouse array


title: woodchuck 6337 normal tissue surrounding the liver HCC, mouse array

tag: woodchuck liver tissue with no HCC, but surrouding the HCCs


title: woodchuck 6361 normal tissue surrounding the liver HCC, mouse array


title: Spleen_wt_1m_rep3

description: Gene expression data

source_name: Mouse spleen at 1 month


title: CD4+ cells IL1RN wild type 1 month rep2

description: Gene expression data


title: CD4+ cells IL1RN wild type 1 month rep3

description: Gene expression data


title: CD4+ cells IL1RN knockout 1 month rep2

description: Gene expression data


title: CD4+ cells IL1RN wild type 4 month rep3

description: Gene expression data


title: Spleen_wt_4m_rep3

description: Gene expression data


title: Spleen_wt_4m_rep1

description: Gene expression data


title: Spleen_wt_1m_rep2

description: Gene expression data


title: CD4+ cells IL1RN knockout 1 month rep1

description: Gene expression data


title: CD4+ cells IL1RN wild type 4 month rep1

description: Gene expression data


title: woodchuck 6361 HCC, mouse array

tag: woodchuck liver HCC tumor confirmed with ultrasound


title: woodchuck 5904 HCC, mouse array


title: CD4+ cells IL1RN wild type 1 month rep1

description: Gene expression data


title: CD4+ cells IL1RN wild type 4 month rep2

description: Gene expression data


title: CD4+ cells IL1RN knockout 4 month rep1

description: Gene expression data


title: Spleen_wt_1m_rep1

description: Gene expression data


title: woodchuck 6337 HCC

description: cross-specieis hybridization using Affymetrix Human U133 plus 2.0 GeneChips® on woodchucks

hyb_protocol: After purification and fragmentation, 15 ug of biotin-labeled cRNA was used in a 300 ul hybridization cocktail containing spiked transcript controls. 200 ul of cocktail was loaded onto Affymetrix human microarrays (Santa Clara, CA) and hybridized for 16 hr at 45 C with agitation.

source_name: woodchuck liver HCC tumor confirmed with ultrasound, human array


title: woodchuck 5904 HCC tissue

source_name: woodchuck liver HCC as confirmed with ultrasound, human array


title: woodchuck 6337 normal tissue surrounding the liver HCC

source_name: woodchuck liver tissue with no HCC, but surrouding the HCCs, human array


title: Uterine plexiform leiomyoma (aka sample 1030i)

city: Boston

first: Bradley

last: Quade

address: 75 Francis Street

institute: Brigham and Women's Hospital

description: Gene expression data from human uterine leiomyoma, plexiform histological subtype

hyb_protocol: Following fragmentation, cRNA was hybridized to the U133 Plus 2.0 microarrays, washed and stained according to the standard Affymetrix protocol at the Harvard Med School - Partners Healthcare Center for Genetics and Genomics.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol at the Harvard Med School - Partners Healthcare Center for Genetics and Genomics.

data_processing: standardy Affymetrix protocol

source_name: uterus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the Harvard Med School - Partners Healthcare Center for Genetics and Genomics.

extract_protocol: Total RNA was isolated using the RNeasy Fibrous Tissue kit (QIAGEN, Valencia, CA) following the manufacturer's instructions.

treatment_protocol: Discarded tumor and normal myometrial tissues were obtained by myomectomy or hysterectomy in the Division of Women's and Perinatal Pathology at Brigham and Women's Hospital.

tag: Gender

value: female

tag: Age

value: 53 years

tag: Karyotype

tag: Race

value: Asian

tag: Menstraual Cycle

value: perimenopausal

tag: Tumor Size


title: Spleen_ko_4m_rep2

description: Gene expression data

tag: Male BALB/c deficient in Il1rn


title: Spleen_ko_1m_rep3

description: Gene expression data


title: woodchuck 6361 liver HCC

source_name: woodchuck liver HCC as indicated by ultrasound, human array


title: Spleen_ko_1m_rep1

description: Gene expression data


title: Uterine plexiform leiomyoma (aka sample 1030s)

value: 46 years

value: White

value: menstruation


title: woodchuck 5904 normal tissue surrounding the liver HCC


title: Uterine plexiform leiomyoma (aka sample 1030e)

value: 44 years

value: 4 cm