title: Mortality_replicate 20

status: Public on Jun 12 2011

city: Nanaimo

first: Tyler

middle: G

last: Evans

state: British Columbia

address: 3190 Hammond Bay Road

department: Pacific Biological Station

country: Canada

institute: Fisheries and Oceans Canada

hyb_protocol: The array hybridization was performed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). Two µl of poly dA was added to the targets, which were then denatured for 10min at 80°C, followed by the addition of 125 µl of pre-warmed SlideHybe3 buffer (Ambion, TX, USA) before loading into the hybridization chamber. Hybridizations were performed in batches of 12-24 samples and conducted over a two-week period to minimize technical variance. Slide processing steps within the Tecan HS were conducted as follows: two 30 s slide wash steps (0.1% SDS followed by water) at 23°C, 3 min slide denaturation at 85°C with agitation, 1 min wash (5x SSC, 0.01% SDS, 1% BSA) at 43°C with a 30 s soak time, 1 h prehybridization at 43°C with medium agitation, two 1 min washes (water followed by 8x SSC, 0.1% SDS, 4X Denhardt’s) at 43°C, sample injection at 43°C with agitation, hybridization for 16 h at 43°C with low frequency agitation, two 30 s wash steps, one at 43°C (2x SSC, 0.01% SDS) followed by one at 23°C (0.25x SSC), slide drying at 23°C for 2.5 min.

scan_protocol: All arrays were scanned using a Perkin Elmer ScanArray Express (Perkin Elmer, Boston, MA), adjusting the PMT gain for optimized visualization of each image.

data_processing: The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com) and processed to GeneSight (version 4.1, BioDiscovery, Inc. El Segundo, CA, www.biodiscovery.com). Data was prepared in GeneSight according to the following steps: correct for background intensity using local background correction; omit multiple spots with flags; raise all values below a specified value to the minimum threshold (20.0); replace missing values by the experimental means for each gene; LOWESS normalization is done locally with smoothing parameter of 0.2 and linear degree of fitness; finally, calculate the log base 2 and the difference of the log2 of 2 channels. This pairMean log difference was used for all subsequent data analysis.

label: Alexa 555

organism: Oncorhynchus nerka

source_name: River gill biopsy

label_protocol: Five µg of aRNA were reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer’s instructions. Briefly, the cDNA was purified using Zymo-25 clean-up columns (Zymo Research, Orange, CA) and eluted using the 2X coupling buffer, supplied by Invitrogen. During dye labelling, samples were processed individually by first adding DMSO, then cDNA to the Alexa dye tube and incubating for 1h at room temperature. Then labeled sample were cleaned up by adding 50 µl of DNA binding buffer (Zymo) to each Alexa tube and then combining the sample and references for each slide into Zymo-25 clean-up columns. The unbound portion of the labelled cDNA was removed by centrifugation at 13,000 rpm/min. The labelled cDNA was washed three times with DNA wash buffer (Zymo) and eluted in 9 µl of 1X TE buffer.

extract_protocol: Samples stored at -80°C were removed and processed immediately by adding 0.75 ml of Trizol (Invitrogen) and one stainless steel 3 mm ball. The tubes were placed in a Retsch mixer mix for two cycles of 3 min/20Hz. Chloroform (0.3 ml) was added to the resulting homogenate and vortexed for 30 sec. The phases were separated by centrifugation at 13000 rpm at 5°C for 15 min. The aqueous phase was transferred to a tube containing 0.2 ml isopropanol and mixed. The RNA was precipitated for 5 min and then centrifuged as before. The total RNA pellet was washed with 80% cold ethanol, centrifuged, and incubated with 1 U of DNase for 15 min followed by gel electrophoresis and spectrophotometric analysis for quality and quantity. Equal quantities of aRNA from each sample were mixed for the pooled reference sample.

treatment_protocol: Fish captured in the wild were sampled as is at the sites descibed previously

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be an unsuccessful migrant (mortality)

label: Alexa 647

source_name: Pooled reference sample from all individuals lethally sampled

tag: reference


title: Mortality_replicate 19

type: RNA

molecule: total RNA

tag: cell type

value: Pooled reference sample from all individuals lethally sampled


title: Taichung 65_shoot_biological rep 3

status: Public on Jun 13 2011

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

country: Japan

institute: RIKEN

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

label: biotin

organism: Oryza sativa

source_name: Oryza sativa Taichung 65_shoot

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Grown in green house under natural condition

extract_protocol: Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).

tag: cultivar

value: Taichung 65

tag: genotype/variation

value: control (parental cultivar)

tag: tissue

value: shoot

tag: age

value: five weeks after germination


title: gid1-3_ shoot_biological rep 1

source_name: Oryza sativa gid1-3 mutant (Taichung 65 background)_shoot

value: gid1-3 mutant


title: D1C20AL

city: Los Angeles

first: Juyong

middle: Brian

last: Kim

state: CA

address: 675 Charles Young Dr.

department: Department of Medicine

country: USA

institute: UCLA School of Medicine

description:
Gene expression data from HAEC
29370
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using median invariant normalization with Microarray Suite 5.0 software.

organism: Homo sapiens

source_name: HAEC treated with 20ug/ml OxPAPC

label_protocol: Double stranded cDNA were prepared with the Invitrogen reverse transcription kit. Biotin-labeled cRNA was generated and used to probe Affymetrix arrays

growth_protocol: Human aortic endothelial cells were isolated from aortic samples retrieved at the time of organ harvest for cardiac transplantation and used at passages 4–7

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with PAPC or oxPAPC (10–50 μg/ml), in medium containing 1% FBS.

tag: individual identifier

tag: cell line

value: human aortic endothelial cell (HAEC) cell line

tag: agent

value: OxPAPC

tag: dose


title: Taichung 65_shoot_biological rep 2


title: Human dermal microvascular endothelial cell si-GATA2 #2

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

institute: The University of Tokyo

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: HMVEC, si-control 48h #2

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using Trizol (Invitrogen). 2 micrograms of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

tag: cell

value: HMVEC

tag: stimulation

value: si-control 48h #2


title: RE:SN12C [251485031062_1_4]

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

hyb_protocol: Samples were hybridized to the Agilent Whole Human Genome Oligo Microarray (G4112F, design ID 014850, Agilent Technologies).

scan_protocol: Agilent Technologies Scanner G2505B US22502705

data_processing: Data was extracted from scanned images using Feature Extraction (version 9.5, Agilent Technologies). Data quality was confirmed using the Agilent quality control metrics.

source_name: Renal cell carcinoma

label_protocol: The mRNA samples were labeled and processed following the Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol version 5.5 with a total RNA input of 200 ng.

growth_protocol: NCI60Adherent; RNA harvesting protocol for adherent cells           Media used:         RPMI 1640 500 ml          FBS 25 ml -use the DTP serum if possible, from Bio Whittaker, not heat         inactivated          200 mM Glutamine 5 ml           1 flask = ~15 x 106 cells yields ~ 100 ugr RNA. Grow 10 flasks.                    Cells: start from growing cells from Frederick (not frozen). Started before at         passage #8-12. Do not use past passage 20.                    Growth schedule prior to harvest: Grow cells to         ~80 confluencey. Trypsinize cells with 5 ml try-EDTA per T162, 15 min., 370C. Pipet up and         down several times w 10 ml pipet to get good dispersment of cells. Count cells. Pass cells         to as many flasks as there are cells for. When passing cells, combine flasks into a single         pool. Pass 1x106 cells into each T162 w 30 ml media.  Repeat growth cycle until 10 flasks         are available.   Refeed Refeed cells the day prior to harvest without harvesting).  Draw off         media (wo cells). Add back media, 30 ml per T162. Add back to T-162Ã¢s. 37 deg C, ON  Harvest         Target confluency 80%  # of flasks = 10   Draw off media from 1st flask. Lyse cells in 15         ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162Ã¢s. Pipet into         50 ml tube.  Repeat w next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a         20 guage needle 12xÃ¢s. Freeze at Ã¶800C.  Purify using Quiagen Midi Kit.  Use a maximun of         100 x 106 cells per column. More will not bind to the column.                           Company Info         ------------           Quiagen Midi Kit Cat # 75144  RLT Buffer (lysis buffer) Cat. # 79216 $60-list, $51- discounted 1-800-362-7737                    Fetal Bovine Serum 500 ml, list $261- Cat #14-502F Lot # 9S083F Cambrex (old Bio Whittaker) 1-800-638-8174                   1x PBS pH 7.3-7.5 Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11)                    250 ml conical tubes Corning cat #25350-250                    RPMI-1640 wo L-glutamine cat # 12-167F  $13.25 per 500 ml bottle (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025 1-800-638-8174                  Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and magnesium. cat # 118-087-061 $4.20 per 100 ml bottle Quality Biological, Inc. 301-840-9331                    L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-149 20 ml 1-800-828-6686                    162 cm2 flask cat # 3150                    Costar Tissue Culture Cell Scrapper, 25 cm Sarstedt Cat. # 83.1830                    Cells are received from Nick Scudiero,  E-mail: SCUDIERO@dtpax2.ncifcrf.gov          Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow;

extract_protocol: NCI60 Extraction Protocol; Harvest         Target confluency  80%            # of flasks = 10                  Draw off media from 1st flask.         Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml).         Scrape cells.         Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2.         Repeat lysis with up to 4 T162â€™s.         Pipet into 50 ml tube.                  Repeat w next set of 4 flasks.                  When done, vortex 10 sec..         Draw lysate thru a 20 guage needle 12xâ€™s.         Freeze at â€“800C.                  Purify using Quiagen Midi Kit.          Use a maximun of 100 x 106 cells per column. More will not bind to the column.         ; Protocol Type = nucleic_acid_extraction;

treatment_protocol: No treatment

tag: tissue of origin

value: Renal

tag: Sex

tag: prior treatment

tag: epithelial

value: yes

tag: source

tag: ploidy

value: 3n, Triploid (69)

tag: p53 mutation

value: MT

tag: doubling time

tag: contributing institute

value: MD Anderson Hospital and Tumor Institute

tag: contributing person

tag: description

value: Renal cell carcinoma-poor differentiation


title: RE:UO_31 [251485031057_1_1]

tag: age

value: WT

value: National Cancer Institute, NIH

tag: reference

value: Renal cell carcinoma-very poorly differentiated


title: Human dermal microvascular endothelial cell control #2


title: RE:CAKI_1 [251485031064_1_4]

source_name: Clear cell carcinoma

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975

value: Clear cell carcinoma


title: RE:TK_10 [251485031059_1_3]

source_name: Renal Spindle cell carcinoma

value: 4n, Tetraploid (92)

value: R.V.Clayman, Washington Univ.School of Medicine

value: Renal Spindle cell carcinoma


title: Taichung 65_shoot_biological rep 1

tag: cultivar

value: Taichung 65

tag: genotype/variation

value: control (parental cultivar)

tag: tissue

value: shoot

value: five weeks after germination


title: RE:TK_10 [251485031058_1_3]

value: Renal

value: yes

value: MT


title: RE:RXF_393 [251485031058_1_1]

source_name: hypernephroma

value: MD Anderson Hospital and Tumor Institute

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992

value: hypernephroma-poor differentiation


title: RE:UO_31 [251485031058_1_4]

value: WT

value: National Cancer Institute, NIH

value: Renal cell carcinoma-very poorly differentiated


title: RE:CAKI_1 [251485031061_1_4]

value: Metastasis

value: 3n, Triploid (69)

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975

value: Clear cell carcinoma


title: RE:ACHN [251485031064_1_2]

value: Rad/VB/CCNU/Mto/Pred

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)

value: Renal cell carcinoma-poor to moderate differentiation


title: K562 cell control

source_name: K562, control #1

tag: cell

tag: stimulation


title: Human dermal microvascular endothelial cell control #3

source_name: HMVEC, si-control 48h #3

value: HMVEC

value: si-control 48h #3


title: Human dermal microvascular endothelial cell control #1

source_name: HMVEC, si-control 48h #1

value: si-control 48h #1


title: RE:CAKI_1 [251485031065_1_3]

tag: tissue of origin

value: Renal

tag: Sex

value: yes


title: RE:RXF_393 [251485031062_1_3]

tag: prior treatment

tag: epithelial

value: MT

value: MD Anderson Hospital and Tumor Institute

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992

value: hypernephroma-poor differentiation


title: RE:ACHN [251485031061_1_2]

tag: source

tag: ploidy

value: WT


title: Mortality_replicate 18

tag: cell type

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be an unsuccessful migrant (mortality)

value: Pooled reference sample from all individuals lethally sampled


title: Human dermal microvascular endothelial cell si-GATA2 #1

source_name: HMVEC, si-GATA2 48h #1

value: si-GATA2 48h #1


title: gid1-3_ shoot_biological rep 2

value: Taichung 65

value: gid1-3 mutant

value: shoot

value: five weeks after germination


title: RE:A498 [251485031060_1_4]

source_name: Adenocarcinoma

value: 3n, Triploid (69)

tag: p53 mutation

tag: doubling time

tag: contributing institute

value: National Cancer Institute, NIH

value: Adenocarcinoma


title: RE:SN12C [251485031060_1_3]

value: Renal

tag: age

value: yes

tag: contributing person

tag: description

value: Renal cell carcinoma-poor differentiation


title: Mortality_replicate 16

tag: reference


title: Mortality_replicate 17


title: PR:DU_145 [251485031065_1_1]

source_name: prostate; metastatic site: brain; carcinoma

value: Prostate

value: Androgen independent and unresposive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone

value: prostate; metastatic site:brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)


title: Mortality_replicate 10

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be an unsuccessful migrant (mortality)

value: Pooled reference sample from all individuals lethally sampled


title: Mortality_replicate 14


title: Mortality_replicate 12


title: RE:A498 [251485031063_1_4]

value: WT


title: RE:786_0 [251485031062_1_1]

value: MT

value: R.D.Williams, Univ. of Iowa


title: Mortality_replicate 13


title: PR:PC_3 [251485031062_1_2]

source_name: Adenocarcinoma-prostate; metastatic site: bone;

value: 4n, Tetraploid (92)

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: RE:CAKI_1 [251485031060_1_2]

value: Renal

value: 3n, Triploid (69)

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975

value: Clear cell carcinoma


title: PR:PC_3 [251485031064_1_3]

value: Prostate

value: yes


title: RE:786_0 [251485031059_1_2]

value: Adenocarcinoma


title: Mortality_replicate 15

source_name: River gill biopsy

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be an unsuccessful migrant (mortality)


title: Mortality_replicate 3

source_name: Pooled reference sample from all individuals lethally sampled


title: Mortality_replicate 7

value: Pooled reference sample from all individuals lethally sampled


title: OV:SK_OV_3 [251485031035_1_4]

value: Ovarian

value: Thiotepa

value: Ascites

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: Mortality_replicate 9


title: Mortality_replicate 5


title: Mortality_replicate 11


title: OV:SK_OV_3 [251485031035_1_2]


title: PR:DU_145 [251485031063_1_2]

value: Androgen independent and unresposive to hormone therapy

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone

value: prostate; metastatic site:brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)


title: OV:OVCAR_8 [251485031063_1_3]

source_name: Carcinoma

value: Ctx/Adr/CsPt/CyPh

value: 2n+, Hyperdiploid (47-57)

value: MT

value: National Cancer Institute, NIH

value: T.C. Hamilton

value: Carcinoma-undifferentiated


title: OV:OVCAR_5 [251485031035_1_3]

value: yes

value: R. Ozols

value: Adenocarcinoma-well differentiated


title: Mortality_replicate 4

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be an unsuccessful migrant (mortality)

value: Pooled reference sample from all individuals lethally sampled


title: Mortality_replicate 6


title: Mortality_replicate 8


title: OV:OVCAR_5 [251485031035_1_1]

value: Ovarian


title: OV:OVCAR_8 [251485031059_1_1]


title: Survivor_replicate 23

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be a successful migrant


title: Survivor_replicate 21


title: Mortality_replicate 2


title: OV:IGROV1 [251485031064_1_1]

source_name: Cystoadenocarcinoma

value: Rad

value: Institute Gustave Roussy, France


title: OV:OVCAR_4 [251485031057_1_2]

value: CyPh/CsPt/Adr

value: WT

value: Adenocarcinoma-moderate differentiation


title: OV:OVCAR_3 [251485031057_1_3]

value: Ascites


title: Mortality_replicate 1


title: Survivor_replicate 20


title: Survivor_replicate 25


title: OV:OVCAR_3 [251485031057_1_4]

value: MT


title: Survivor_replicate 18


title: Survivor_replicate 19


title: Survivor_replicate 22


title: Survivor_replicate 24


title: Survivor_replicate 15


title: ME:UACC_257 [251485031054_1_2]

source_name: Melanotic melanoma

value: Melanoma

value: no

value: 3n+, Hypertriploid (70-80)

value: University of Arizona

value: A. Leibovitz, UACC

value: Melanotic melanoma


title: OV:NCI_ADR_RES [251485031061_1_3]

value: yes

value: National Cancer Institute, NIH

value: K.Cowan, NCI

value: Adenocarcinoma


title: ME:UACC_62 [251485031053_1_1]


title: OV:IGROV1 [251485031059_1_4]

value: Ovarian

value: Rad


title: Survivor_replicate 14

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be a successful migrant

value: Pooled reference sample from all individuals lethally sampled


title: Survivor_replicate 13


title: Survivor_replicate 17


title: ME:SK_MEL_5 [251485031049_1_4]

source_name: Malignant melanotic melanoma

value: Metastasis

value: 4n+, Hypertetraploid (93-103)

value: WT

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi

value: Malignant melanotic melanoma


title: ME:SK_MEL_5 [251485031054_1_1]

value: Melanoma

value: no


title: OV:NCI_ADR_RES [251485031065_1_2]

value: MT


title: Survivor_replicate 16


title: ME:UACC_62 [251485031055_1_1]

value: University of Arizona

value: A. Leibovitz, UACC

value: Melanotic melanoma


title: OV:OVCAR_4 [251485031065_1_4]

value: CyPh/CsPt/Adr

value: yes

value: National Cancer Institute, NIH

value: T.C. Hamilton

value: Adenocarcinoma-moderate differentiation


title: ME:UACC_257 [251485031053_1_3]

value: 3n+, Hypertriploid (70-80)


title: ME:SK_MEL_28 [251485031049_1_2]

value: 4n-, Hypotetraploid (81-91)


title: Survivor_replicate 12

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be a successful migrant

value: Pooled reference sample from all individuals lethally sampled


title: Survivor_replicate 11


title: Survivor_replicate 8


title: ME:MDA_MB_435 [251485031056_1_1]

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)

value: R. Cailleau

value: Ductal carcinoma-mammary gland; breast; duct; metastatic site:pleural effusion;


title: ME:SK_MEL_28 [251485031056_1_4]

value: Melanoma

value: no

value: MT

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi

value: Malignant melanotic melanoma


title: Survivor_replicate 9


title: Survivor_replicate 5


title: ME:SK_MEL_2 [251485031049_1_1]

value: Metastasis

value: WT

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: Survivor_replicate 4


title: Survivor_replicate 3


title: ME:MDA_N [251485031050_1_3]


title: ME:SK_MEL_2 [251485031051_1_4]

value: 4n-, Hypotetraploid (81-91)


title: ME:MDA_N [251485031050_1_1]


title: ME:SK_MEL_2 [251485031055_1_2]


title: ME:SK_MEL_2 [251485031051_1_2]


title: Survivor_replicate 7

value: Non-lethal biopsy of gill tissue from fish subsequently shown to be a successful migrant


title: Survivor_replicate 10

value: Pooled reference sample from all individuals lethally sampled


title: Survivor_replicate 6


title: Liver_W_replicate 10

source_name: River (W) sampled liver

value: Lethally sampled liver tissue from river site W


title: Survivor_replicate 1


title: Liver_W_replicate 9


title: Liver_W_replicate 7


title: Survivor_replicate 2


title: Liver_W_replicate 8


title: ME:MDA_MB_435 [251485031052_1_2]

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)


title: Liver_W_replicate 6


title: ME:MALME_3M [251485031055_1_3]

value: J. Fogh


title: ME:M14 [251485031052_1_4]

value: Melanoma

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine

value: Melanotic melanoma


title: ME:LOXIMVI [251485031053_1_4]

source_name: Malignant amelanotic melanoma

value: no

value: Norsk Hydro's Institut, Norway

value: Malignant amelanotic melanoma


title: ME:M14 [251485031052_1_1]

value: MT

value: John Wayne Cancer Clinic, UCLA School of Medicine


title: Liver_W_replicate 1


title: Liver_JDFS_replicate 13

source_name: Ocean (JDFS) sampled liver

value: Lethally sampled liver tissue from ocean site JDFS


title: Liver_W_replicate 4


title: ME:MALME_3M [251485031051_1_1]

value: Metastasis

value: WT

value: Memorial Sloan Kettering Cancer Center

value: Malignant melanotic melanoma


title: LE:SR [251485031050_1_4]

source_name: Lymphoma

value: Leukemia

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.

value: Lymphoma


title: LE:RPMI_8226 [251485031056_1_3]

source_name: Myeloma

value: PB

value: 3n-, Hypotriploid (58-68)

value: G.E. Moore

value: Myeloma


title: Liver_JDFS_replicate 12

value: Pooled reference sample from all individuals lethally sampled


title: Liver_W_replicate 5

value: Lethally sampled liver tissue from river site W


title: LE:SR [251485031054_1_3]

value: no


title: Liver_W_replicate 3


title: LE:MOLT_4 [251485031056_1_2]

source_name: ALL

value: 4n, Tetraploid (92)

value: Roswell Park Memorial Institute

value: J. Minowada

value: ALL (cells were taken when patient was in relapse)


title: LE:MOLT_4 [251485031054_1_4]

value: WT


title: Liver_JDFS_replicate 11

value: Lethally sampled liver tissue from ocean site JDFS


title: LE:RPMI_8226 [251485031052_1_3]

value: Leukemia


title: Liver_JDFS_replicate 10


title: LE:K_562 [251485031051_1_3]

source_name: CML

value: Bisulfan/PiBr

value: Pleural effusion

value: MT

value: University of Tennesse

value: H.T. Holden

value: CML


title: LE:K_562 [251485031055_1_4]

value: 3n-, Hypotriploid (58-68)


title: LE:K_562 [251485031050_1_2]


title: LE:K_562 [251485031053_1_2]


title: Liver_W_replicate 2

value: Pooled reference sample from all individuals lethally sampled


title: ME:LOXIMVI [251485031049_1_3]

value: Melanoma

value: Norsk Hydro's Institut, Norway

value: Malignant amelanotic melanoma


title: LE:HL_60 [251485031046_1_1]

source_name: Pro myelocytic leukemia

value: no

value: PBL

value: National Cancer Institute, NIH

value: R.C. Gallo

value: Pro myelocytic leukemia


title: LE:HL_60 [251485031045_1_4]

value: Leukemia


title: Liver_JDFS_replicate 8

value: Lethally sampled liver tissue from ocean site JDFS


title: LE:CCRF_CEM [251485031046_1_4]

value: Rad/Mtx/Cyx

value: Children's Cancer research Foudation

value: G.E. Foley

value: ALL


title: Liver_JDFS_replicate 9


title: Liver_JDFS_replicate 1


title: Liver_JDFS_replicate 7


title: Liver_JS_replicate 15

source_name: Ocean (JS) sampled liver

value: Lethally sampled liver tissue from ocean site JS


title: Liver_JS_replicate 14


title: Liver_JDFS_replicate 4


title: LC:NCI_H522 [251485031075_1_3]

source_name: Adenocarcinoma

value: Non-Small Cell Lung

value: yes

value: MT


title: Liver_JDFS_replicate 3

value: Pooled reference sample from all individuals lethally sampled


title: LC:NCI_H522 [251485031074_1_3]


title: LE:CCRF_CEM [251485031044_1_2]


title: LC:NCI_H322M [251485031045_1_1]

source_name: Small cell Bronchioalveolar Carcinoma

value: Small cell Bronchioalveolar Carcinoma


title: Liver_JS_replicate 8

source_name: Pooled reference sample from all individuals lethally sampled


title: LC:NCI_H23 [251485031047_1_4]

value: 2n+, Hyperdiploid (47-57)

value: J.D. Minna; A.F. Gazdar

value: Adenocarcinoma-undifferentiated


title: LC:NCI_H322M [251485031074_1_1]

value: National Cancer Institute, NIH


title: Liver_JDFS_replicate 5


title: Liver_JS_replicate 13


title: Liver_JS_replicate 9


title: LC:NCI_H460 [251485031044_1_1]

source_name: Large Cell Carcinoma

value: Pleural effusion

value: WT

value: Large Cell Carcinoma-undifferentiated


title: Liver_JS_replicate 12


title: LC:NCI_H460 [251485031044_1_3]


title: Liver_JS_replicate 10


title: LC:HOP_92 [251485031045_1_3]

source_name: Large cell

value: Johns Hopkins University

value: Large cell-undifferentiated


title: Liver_JS_replicate 11


title: Liver_JS_replicate 7


title: LC:HOP_92 [251485031076_1_2]


title: LC:NCI_H226 [251485031034_1_1]

source_name: Squamous cell carcinoma

value: None (non smoker)

value: 3n, Triploid (69)

value: Squamous cell carcinoma-very poorly differentiated


title: Liver_JS_replicate 6

value: Lethally sampled liver tissue from ocean site JS


title: Liver_JS_replicate 5


title: LC:NCI_H23 [251485031074_1_4]

value: Non-Small Cell Lung

value: yes


title: LC:NCI_H226 [251485031034_1_3]

value: MT


title: LC:HOP_62 [251485031033_1_4]

source_name: adenocarcinoma

value: 4n+, Hypertetraploid (93-103)

value: adenocarcinoma-undifferentiated


title: LC:HOP_62 [251485031033_1_2]


title: LC:EKVX [251485031047_1_3]

value: Norsk Hydro's Institut, Norway

value: Adenocarcinoma-moderate differentiation


title: Liver_JS_replicate 1

value: Pooled reference sample from all individuals lethally sampled


title: Liver_JS_replicate 3


title: LC:EKVX [251485031047_1_2]


title: CO:SW_620 [251485031075_1_4]

source_name: Carcinoma

value: Colon

value: Scott White Clinic

value: A. Leibovitz

value: Carcinoma-undifferentiated


title: LC:A549 [251485031048_1_2]

value: WT

value: National Cancer Institute, NIH

value: Giard DJ

value: Adenocarcinoma-poor to moderate differentiation


title: Liver_JS_replicate 2

value: Lethally sampled liver tissue from ocean site JS


title: Liver_JS_replicate 4


title: Gill_W_replicate 10

source_name: River (W) sampled gill

value: Lethally sampled gill tissue from river site W


title: LC:A549 [251485031044_1_4]

value: Non-Small Cell Lung

value: yes


title: Gill_W_replicate 11


title: CO:KM12 [251485031075_1_1]

source_name: Adenocarcinome

value: MT

value: MD Anderson Hospital and Tumor Institute

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute

value: Adenocarcinome-poor differentiation


title: CO:SW_620 [251485031075_1_2]


title: CO:KM12 [251485031076_1_1]


title: Gill_W_replicate 8

value: Pooled reference sample from all individuals lethally sampled


title: Gill_W_replicate 9


title: CO:HT29 [251485031076_1_3]

value: Colon

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975

value: Adenocarcinoma-moderate differentiation


title: CO:HT29 [251485031046_1_2]


title: CO:HT29 [251485031047_1_1]


title: CO:HT29 [251485031045_1_2]


title: Gill_W_replicate 6


title: Gill_W_replicate 1


title: Gill_JDFS_replicate 15

source_name: Ocean (JDFS) sampled gill

value: Lethally sampled gill tissue from ocean site JDFS


title: CO:HCT_15 [251485031048_1_1]

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)

value: Adenocarcinoma-poor to moderate differentiation


title: Gill_JDFS_replicate 14


title: Gill_W_replicate 3

value: Lethally sampled gill tissue from river site W


title: Gill_W_replicate 2


title: CO:HCC_2998 [251485031071_1_3]

source_name: carcinoma

value: yes

value: carcinoma


title: CO:HCT_15 [251485031046_1_3]


title: Gill_W_replicate 4


title: Gill_W_replicate 7


title: Gill_JDFS_replicate 12


title: CO:HCC_2998 [251485031073_1_1]

value: MT

value: MD Anderson Hospital and Tumor Institute


title: CNS:U251 [251485031072_1_2]

source_name: Glioblastoma

value: CNS

value: no

value: 2n+, Hyperdiploid (47-57)

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981

value: Glioblastoma-undifferentiated


title: Gill_W_replicate 5

value: Pooled reference sample from all individuals lethally sampled


title: Gill_JDFS_replicate 11


title: CO:HCT_116 [251485031073_1_3]

value: Colon

value: 2n-, Hypodiploid (35-45)

value: Baylor College

value: carcinoma-very poorly differentiated


title: CO:COLO205 [251485031033_1_3]

value: Ascites

value: 3n, Triploid (69)

value: Denver Medical Hospital

value: G.E. Moore

value: Adenocarcinoma


title: Gill_JDFS_replicate 8

value: Lethally sampled gill tissue from ocean site JDFS


title: Gill_JDFS_replicate 10


title: Gill_JDFS_replicate 13


title: Gill_JDFS_replicate 6


title: Gill_JDFS_replicate 9


title: CO:HCT_116 [251485031068_1_3]

value: yes


title: CO:COLO205 [251485031033_1_1]

value: MT


title: Gill_JDFS_replicate 7


title: CNS:SNB_19 [251485031070_1_3]

value: CNS

value: no

value: NINCDS

value: P.L. Kornblith


title: CO:HCT_116 [251485031072_1_1]


title: CNS:SNB_75 [251485031073_1_4]

source_name: Astrocytoma

value: 2n+, Hyperdiploid (47-57)

value: Astrocytoma


title: CNS:U251 [251485031068_1_4]

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981

value: Glioblastoma-undifferentiated


title: CO:HCT_116 [251485031069_1_1]

value: Colon

value: 2n-, Hypodiploid (35-45)

value: Baylor College

value: carcinoma-very poorly differentiated


title: Gill_JDFS_replicate 5

value: Pooled reference sample from all individuals lethally sampled


title: CNS:SNB_19 [251485031070_1_2]


title: Gill_JDFS_replicate 4

value: Lethally sampled gill tissue from ocean site JDFS


title: CNS:SF_539 [251485031070_1_1]

source_name: Glial cell neoplasm

value: WT

value: University of California

value: M.L. Rosenblum

value: J Neuropathol Exp Neurol 40:201-229, 1981

value: Glial cell neoplasm


title: CNS:SNB_75 [251485031066_1_1]

value: CNS

value: no

value: MT

value: NINCDS

value: P.L. Kornblith


title: Gill_JDFS_replicate 2


title: Gill_JS_replicate 14

source_name: Ocean (JS) sampled gill

value: Lethally sampled gill tissue from ocean site JS


title: Gill_JS_replicate 11


title: Gill_JS_replicate 12


title: CNS:SF_268 [251485031069_1_2]

value: Rad

value: 2n+, Hyperdiploid (47-57)

value: Acta Neuropathol 75:92-103, 1987

value: Glioblastoma-undifferentiated


title: Gill_JS_replicate 13

value: Pooled reference sample from all individuals lethally sampled


title: CNS:SF_295 [251485031071_1_2]

value: Acta Neuropathol 75:92-103, 1988


title: BR:T47D [251485031072_1_3]

source_name: infiltrating ductal carcinoma

value: Breast

value: yes

value: I. Keydar

value: infiltrating ductal carcinoma


title: CNS:SF_268 [251485031066_1_3]


title: Gill_JDFS_replicate 1

value: Lethally sampled gill tissue from ocean site JDFS


title: CNS:SF_539 [251485031071_1_4]

value: CNS

value: WT

value: University of California

value: M.L. Rosenblum

value: J Neuropathol Exp Neurol 40:201-229, 1981

value: Glial cell neoplasm


title: Gill_JDFS_replicate 3


title: Gill_JS_replicate 6

value: Lethally sampled gill tissue from ocean site JS


title: BR:MDA_MB_231 [251485031073_1_2]

source_name: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)

value: MT

value: MD Anderson Hospital and Tumor Institute

value: R. Cailleau

value: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site:pleural effusion;


title: CNS:SF_295 [251485031069_1_4]

value: Rad

value: no

value: Acta Neuropathol 75:92-103, 1988

value: Glioblastoma-undifferentiated


title: Gill_JS_replicate 7

value: Pooled reference sample from all individuals lethally sampled


title: Gill_JS_replicate 2


title: Gill_JS_replicate 3


title: Gill_JS_replicate 4


title: Gill_JS_replicate 5


title: Gill_JS_replicate 8


title: BR:MCF7 [251485031068_1_2]

source_name: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: Breast

value: yes

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath

value: Adenocarcinoma-mammary gland; breast; metastatic site:pleural effusion;


title: BR:MDA_MB_231 [251485031067_1_3]

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)


title: BR:MCF7 [251485031068_1_1]


title: BR:BT_549 [251485031072_1_4]

source_name: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues

value: no pub


title: BR:HS578T [251485031070_1_4]

source_name: Carcinosarcoma-mammary gland; breast

value: Primary

value: MT

value: Naval Bioscience Laboratory

value: A.J. Hackett

value: Carcinosarcoma-mammary gland; breast


title: BR:HS578T [251485031067_1_4]

value: Breast


title: Gill_JS_replicate 1

value: Lethally sampled gill tissue from ocean site JS

source_name: Pooled reference sample from all individuals lethally sampled


title: Gill_JS_replicate 9

value: Pooled reference sample from all individuals lethally sampled


title: BR:T47D [251485031066_1_2]

value: yes

value: I. Keydar

value: infiltrating ductal carcinoma


title: BR:BT_549 [251485031071_1_1]

value: Papillary infiltrating ductal carcinoma-mammary gland; breast


title: R1.10 uninfected study2 sample2

status: Public on Jun 11 2011

city: Manchester

first: David

last: Robertson

address: Michael Smith Building

department: Faculty of Life Sciences

country: United Kingdom

institute: University of Manchester

hyb_protocol: 100ng of RNA from each sample was used to prepare cDNA with the Affymetrix GeneChip 3’ IVT Express Kit and hybridised to Affymetrix U133 Plus 2 microarrays following the manufacturer's instructions. The washing and staining procedure was performed in the Affymetrix Fluidics Station 450. The probe array was exposed to 10 washes in 6xSSPE-T at 250C followed by 4 washes in 0.5xSSPE-T at 500C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 mg/ml (Molecular Probes, Eugene, OR) in 6xSSPE-T for 30 min at 250C followed by 10 washes in 6xSSPE-T at 250C An antibody amplification step followed using normal goat IgG as blocking reagent, final concentration 0.1 mg/ml (Sigma) and biotinylated anti-streptavidin antibody (goat), final concentration 3 mg/ml (Vector Laboratories). This was followed by a staining step with a streptavidin-phycoerythrin conjugate, final concentration 2 mg/ml (Molecular Probes, Eugene, OR) in 6xSSPE-T for 30 min at 250C and 10 washes in 6xSSPE-T at 250C.

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope  (Affymetrix Scanner 3000 7G). CEL files were generated and used for further analysis. All microarray procedures were done at AROS, Denmark.

data_processing: All analysis of microarray intensity data was carried out using R statistical software including Bioconductor packages. GeneChip  probe sets definitions were assigned using Entrez gene version 12.1 of a custom chip description file (CDF) from Psychiatry/MBNI Microarray Lab. This CDF included 17726 probe sets that correspond to an NCBI gene. Initial quality checks of each chip were carried out using Bioconductor core tools and package affyQCReport. Quality checks and visual inspection of array intensities showed that the quality of the array data was good. Robust Multichip Average (RMA) expression values were computed using the Bioconductor affy package. Genes that were called not present on all 39 GeneChip array data sets using Microarray Suite version 5.0 (MAS5) presence calls were removed from the analysis, leaving a total of 13760 genes. Probability, false discovery rate (FDR) and fold-change values for differential expression of genes between cells, using three biological replicates from each, were calculated in a pairwise manner using the limma method in the R limma package. Genes were defined to be significantly differentially expressed if they achieved an FDR of <0.01 and a minimum fold-change of >1.5.

source_name: R1.10 hepatoma cells, study 2

extract_protocol: Cell cultures were centrifuged at 1000rpm for 5 minutes and the cell pellet was resuspent in 350 microlitre lysis buffer (Qiagen).  Each lysate was homogenised with a Qiashedder column (Qiagen) and the RNA was extracted using the RNeasy Mini Kit following the manufactures instructions. On-column DNA digestion was carried out by means of the RNase-Free DNase Set (Qiagen) and the integrity of the RNA was confirmed via Agilent (RIN of 9.7-10).

tag: hcv infection susceptibility

value: very resistant to HCV infection

tag: hcv infected

value: no


title: R1.10 uninfected study2 sample3

label_protocol: 100ng of RNA from each sample was used to prepare cDNA with the Affymetrix GeneChip 3’ IVT Express Kit and hybridised to Affymetrix U133 Plus 2 microarrays following the manufacturer's instructions


title: Huh-7.5.1 uninfected study2 sample1

source_name: Huh-7.5.1 hepatoma cells, study 2

value: very susceptible to HCV infection


title: R2.1 uninfected study2 sample3

source_name: R2.1 hepatoma cells, study 2

value: resistant to HCV infection


title: R1.10 uninfected study2 sample1


title: Gill_JS_replicate 10


title: R2.1 uninfected study2 sample1


title: Huh-7.5.1 uninfected study2 sample2


title: Huh-7.5.1 uninfected study2 sample3


title: R1.09 uninfected study2 sample3

source_name: R1.09 hepatoma cells, study 2

value: extremely resistant to HCV infection


title: R1.09 uninfected study2 sample2


title: R1.09 uninfected study2 sample1


title: Huh-7 uninfected 20hr study1 sample3

source_name: Huh-7 hepatoma cells,  20 hours in culture, not HCV infected, study 1

value: susceptible to HCV infection


title: BR:MCF7 [251485031069_1_3]

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath

value: Adenocarcinoma-mammary gland; breast; metastatic site:pleural effusion;


title: R2.1 uninfected study2 sample2


title: Huh-7.5.1c2 uninfected 20hr study1 sample3

source_name: Huh-7.5.1c2 hepatoma cells,  20 hours in culture, not HCV infected, study 1

value: extremely susceptible to HCV infection


title: BR:MCF7 [251485031067_1_2]

value: Breast

value: yes


title: Huh-7.5.1 uninfected 20hr study1 sample2

source_name: Huh-7.5.1 hepatoma cells,  20 hours in culture, not HCV infected, study 1


title: Huh-7.5.1 uninfected 20hr study1 sample3


title: Huh-7 infected 168hr study1 sample2

description: Cells were infected with wild type JFH-1 virus at an moi=0.05. Infected cells were harvested for microarray analysis when virtually 100% of the cells were infected as determined by staining of cells for viral E2 protein.

source_name: Huh-7 hepatoma cells, 168 hours in culture, HCV infected, study 1


title: Huh-7 uninfected 20hr study1 sample1


title: Huh-7.5.1 uninfected 20hr study1 sample1


title: Huh-7 uninfected 20hr study1 sample2


title: Huh-7.5.1 infected 120hr study1 sample3

source_name: Huh-7.5.1 hepatoma cells, 120 hours in culture, HCV infected, study 1


title: Huh-7 infected 168hr study1 sample3


title: Huh-7.5.1c2 uninfected 20hr study1 sample1

source_name: Huh-7.5.1c2 hepatoma cells, 20 hours in culture, not HCV infected, study 1


title: Huh-7 infected 168hr study1 sample1


title: Huh-7.5.1c2 uninfected 20hr study1 sample2


title: Huh-7.5.1c2 infected 96hr study1 sample2

source_name: Huh-7.5.1c2 hepatoma cells, 96 hours in culture, HCV infected, study 1


title: Huh-7.5.1 infected 120hr study1 sample1


title: Huh-7.5.1 infected 120hr study1 sample2


title: Huh-7.5.1c2 infected 96hr study1 sample1


title: Huh-7 uninfected 168hr study1 sample3

source_name: Huh-7 hepatoma cells, 168 hours in culture, not HCV infected, study 1


title: Huh-7 uninfected 168hr study1 sample1


title: Huh-7 uninfected 168hr study1 sample2


title: Huh-7.5.1 uninfected 120hr study1 sample1

source_name: Huh-7.5.1 hepatoma cells, 120 hours in culture, not HCV infected, study 1


title: Huh-7.5.1 uninfected 120hr study1 sample3


title: Huh-7.5.1c2 infected 96hr study1 sample3


title: Huh-7.5.1c2 uninfected 96hr study1 sample3

source_name: Huh-7.5.1c2 hepatoma cells, 96 hours in culture, not HCV infected, study 1


title: Huh-7.5.1c2 uninfected 96hr study1 sample2


title: Huh-7.5.1 uninfected 120hr study1 sample2


title: Huh-7.5.1c2 uninfected 96hr study1 sample1


title: M184S5

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

institute: Université Laval

hyb_protocol: The labeled and purified cDNA from L. amazonensis was mixed with 200 µg/ml sonicated salmon sperm DNA (Stratagene); 200 µg/ml yeast tRNA (Sigma); 1 x blocking agent buffer (Agilent Technologies, Santa Clara, CA USA) and 1 x hybridization buffer (Agilent Technologies, Santa Clara, CA USA), then mixed, denaturated 3 min at 95 °C and incubated 30 min at 37 °C. Mixed labeled cDNA were applied on the hybridization chamber (Agilent Technologies, Santa Clara, CA USA) and the hybridization was performed for 24 h at 65 °C into a hybridization oven (GeneChip®, Stovall Life Sciences, Greensboro, NC, USA). Slides were washed 5 min at room temperature in 0,5X SSC, 5% Triton-X102 with gentle agitation and subsequently washed 5 min in pre-warmed 0,1X SSC, 0,005% Triton-X102 at room temperature with occasional stirring.

scan_protocol: Detection of Alexa Fluor 555 and Alexa Fluor 647 signals were performed on a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA USA) at 5 µm resolution as previously described.

data_processing:
The signal intensity data were extracted from the primary scanned images using GenePix Pro 6.0 software (Axon Instruments, Union City, CA, USA). Normalization and statistical analyses were performed in R 2.2.1 software using the LIMMA (Linear Models for Microarray Data) 2.7.3 package. Background correction was performed using the “edwards” method; within-array normalization was done by loess and between array normalization by the Aquantile method. Multiple testing corrections were done using the false discovery rate method with a threshold p value of 0.05. Only genes statistically significant with an absolute ratio greater than 1.5 were considered.
Results of the statistical analysis of replicates are provided in the full_Matrix.txt file on the Series record. Please see readme.txt file for data column definitions.

label: Alexa Fluor 555

organism: Leishmania amazonensis

label_protocol: For each probe, 7 µg of RNA were converted to aminoallyl-dUTP incorporated cDNA using random hexamers (Roche, Basel, Switzerland) in presence of Superscript III RNase H reverse transcriptase (Invitrogen, Carlsbad, CA, USA). Aminoallyl-dUTP incorporated cDNA were thereafter coupled to Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen, Carlsbad, CA, USA) according to manufacturer recommendations. Fluorescent cDNA were then purified using the probe purification kit ArrayIt (TeleChem International, Sunnyvale, CA, USA) and quantified spectrophotometrically.

growth_protocol: Leishmania amazonensis (MHOM/BR/1989/Ba199) promastigotes were maintained in minimum essential culture medium (alpha-MEM) (Gibco, Invitrogen, NY, USA), supplemented with 10% (v/v) heat-inactivated fetal calf serum (Multicell, Wisent Inc. Québec, CA), 100 µg/ml kanamycin, 50 µg/ml ampicillin, 2mM L-glutamine, 5 µg/ml hemin, 5 µM biopterin, (Sigma-Aldrich, St Louis, USA), pH 7.0 and incubated at 25 °C in B.O.D incubator (Johns Scientific-VWR, Toronto, CA).

extract_protocol: Total RNA was extracted from 1e8 promastigotes during the mid-log growth phase using RNeasy Plus mini kit (Qiagen Sciences, Maryland, USA) as described by the manufacturer. The quality and quantity of RNA were assessed using RNA 6000 Nano Assay chips on Bioanalyzer 2100 (Agilent Technologies Santa Clara, CA, USA).

treatment_protocol: The four independent mutants of L. amazonensis Ba199SbIII2700.1 to Ba199SbIII2700.4 were individually selected in 25 cm2 flasks containing 5 ml of alpha-MEM medium in the presence of SbIII concentrations up to 2700 uM.

tag: genotype/variation

label: Alexa Fluor 647

source_name: Wt

value: Wt


title: M184S3


title: M184S4


title: M184S2


title: M184S1


title: Glucose WT alpha factor block-release timepoint 55

city: Stanford

first: Umut

last: Eser

address: 337 Campus Drive

department: Biology

institute: Stanford University

description: W303 alpha factor arrested cells 55 minutes after release

hyb_protocol: 1 Equilibrate water bath to 60°C.2.For 8x15K microarray format, add  cyanine 3-labeled, linearly amplified cRNA 300 ng cyanine 3-labeled, linearly amplified cRNA  300ng, 10X GEx Blocking Solution 5ul, Nulease free H2O bring Vol to 24ul, 25X Fragmentation Buffer 1ul, Total Vol 25ul, 3. Incubate at 60°C for exactly 30 minutes to fragment RNA. 4. Add 25ul 2x GEx Hybridization Buffer HI-RPM to the 8X15K. 5. Place sample on ice and load 40ul onto the array. 6. Assemble Hybridization Chamber 7 Hybridize at 65°C for 17 hours.

scan_protocol: Scan region is set to Scan Area (61 × 21.6 mm).Scan resolution (μm) is set to 5um. Dye channel is set to Red & Green. Green PMT is set to 100% (high); 10% (low) Red PMT is set to 100 % ( high); 10 % ( low). Check eXtended Dynamic Range check box for both High and low PMT scanning 3. Scan.

data_processing: Use the Feature Extraction (FE) software v9.5.

organism: Saccharomyces cerevisiae

source_name: alpha factor synchronized cells 0 minute

label_protocol: RNAs were labeled by Aglient “Quick Amp Labeling Kit Two-color”

growth_protocol: Yeast cells were grown to log phase in SCD complete media, in 300C.

extract_protocol: RNAs were isolated by using Ambion Yeast RiboPure Kit,

treatment_protocol: Then, cells were arrested by adding 240nM alpha factor into the media and let them wait for 120 minutes to arrest. Cells are released by transfering to fresh SCD. Then samples are drawn every 5 minutes for 60 minutes. RNAs are hybridized on the first time point, i.e. 0 minute

tag: strain

tag: time

value: 0 min

tag: media

value: glucose

tag: genotype

value: wild type

source_name: alpha factor synchronized cells

value: 55 min


title: Glucose WT alpha factor block-release timepoint 15

description: W303 alpha factor arrested cells 15 minutes after release

value: 15 min


title: Galactose WT alpha factor block-release timepoint 30

description: W303 alpha factor arrested cells 30 minutes after release

growth_protocol: Yeast cells were grown to log phase in SCG complete media, in 300C.

treatment_protocol: Then, cells were arrested by adding 240nM alpha factor into the media and let them wait for 120 minutes to arrest. Cells are released by transfering to fresh SCG. Then samples are drawn every 5 minutes for 60 minutes. RNAs are hybridized on the first time point, i.e. 0 minute

value: galactose

value: 30 min


title: Glucose WT alpha factor block-release timepoint 30


title: Galactose WT alpha factor block-release timepoint 40

description: W303 alpha factor arrested cells 40 minutes after release

value: 40 min


title: Glucose WT alpha factor block-release timepoint 20

description: W303 alpha factor arrested cells 20 minutes after release

value: 20 min


title: Galactose WT alpha factor block-release timepoint 25

description: W303 alpha factor arrested cells 25 minutes after release

value: 25 min


title: Glucose WT alpha factor block-release timepoint 45

description: W303 alpha factor arrested cells 45 minutes after release

value: 45 min


title: Glucose WT alpha factor block-release timepoint 35

description: W303 alpha factor arrested cells 35 minutes after release

value: 35 min


title: Glucose WT alpha factor block-release timepoint 10

description: W303 alpha factor arrested cells 10 minutes after release

value: 10 min


title: Glucose WT alpha factor block-release timepoint 40


title: Glucose WT alpha factor block-release timepoint 50

description: W303 alpha factor arrested cells 50 minutes after release

value: 50 min


title: Glucose WT alpha factor block-release timepoint 5

description: W303 alpha factor arrested cells 5 minutes after release

value: 5 min


title: Glucose WT alpha factor block-release timepoint 60

description: W303 alpha factor arrested cells 60 minutes after release

value: 60 min


title: Galactose WT alpha factor block-release timepoint 10


title: Galactose WT alpha factor block-release timepoint 15


title: Galactose WT alpha factor block-release timepoint 5


title: Galactose WT alpha factor block-release timepoint 20


title: Glucose WT alpha factor block-release timepoint 25


title: Galactose WT alpha factor block-release timepoint 35


title: RR2_CRHydplushydrogen01_Cy3_ch1_CRHyd01_Cy5_ch2_7DE13915827

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Thu Mar 18 11:55:09 2010

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 1, dye swapped

label_protocol: Standard labeling using Cy3-dUTP with reverse transcriptase and random hexamers

extract_protocol: After immediate treatment with 0.15 volumes of ethanol: phenol (95 %: 5 % vol/vol) cells were pelleted, resuspended in lysis buffer (10 mM Tris, 1 mM EDTA, 0.5 mg/ml lysozyme) and treated with 1 ml of 10 % SDS for 2 min at 64°C. The suspensions were treated with sodium acetate, pH 5.2, then nucleic acids were phenol/chloroform extracted and subsequently precipitated with 0.1 vol 3M sodium acetate and 1.0 vol of cold isopropanol. Finally, DNAse treatment at 37°C for 30min degraded present DNA, leaving clean ribonucleic acid after a second round of phenol/chloroform extraction and precipitation.

tag: growth

value: anaerobically to log phase after presence of 20% hydrogen for 15 min

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 1, dye swapped

label_protocol: Standard labeling using Cy5-dUTP with reverse transcriptase and random hexamers

value: anaerobically to log phase without hydrogen


title: RR2_CRHydplushydrogen01_Cy5_ch1_CRHyd01_Cy3_ch2_7DE13915828

description: biological replicate, Date of Scan Thu Mar 18 12:04:49 2010

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 1

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 1


title: RR2_CRHydplushydrogen03_Cy3_ch1_CRHyd03_Cy5_ch2_7DE13915856

description: biological replicate, Date of Scan Thu Jun 24 15:55:43 2010

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 3, dye swapped

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 3, dye swapped


title: RR2_CRHydplushydrogen03_Cy5_ch1_CRHyd03_Cy3_ch2_7DE13915825

description: biological replicate, Date of Scan Thu Jun 24 15:47:38 2010

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 3

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 3


title: RR2_CRHydplushydrogen02_Cy5_ch1_CRHyd02_Cy3_ch2_7DE13915128

description: biological replicate, Date of Scan Thu Jun 24 15:26:59 2010

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 2

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 2


title: RR2_CRHydplushydrogen02_Cy3_ch1_CRHyd02_Cy5_ch2_7DE13915826

description: biological replicate, Date of Scan Thu Jun 24 15:37:35 2010

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd in presence of 20% hydrogen, replicate 2, dye swapped

source_name: Transcription profile from 14028s grown anaerobically to log phase in CRHyd without hydrogen, replicate 2, dye swapped


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 50

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 50 minutes after methionine addition

source_name: lack of G1 cyclin synchronized cells 0 minute

growth_protocol: Yeast cells were grown over night in SCD complete media, in 300C.

treatment_protocol: Then, cells were transferred to SCD-methionine (lacking methionine) and let them wait for 120 minutes to arrest. Cells are released by adding .25Xmethionine which leads to express CLN2 at physiological level under MET3 promoter. Then samples are drawn every 5 minutes for 60 minutes. RNAs are hybridized on the first time point, i.e. 0 minute

value: cln1,2,3∆ MET3pr-CLN2

value: 0 min

value: glucose

source_name: lack of G1 cyclin synchronized cells


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 25

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 25 minutes after methionine addition


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 20

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 20 minutes after methionine addition


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 35

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 35 minutes after methionine addition


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 60

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 60 minutes after methionine addition


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 55

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 55 minutes after methionine addition

value: 55 min


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 40

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 40 minutes after methionine addition


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 45

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 45 minutes after methionine addition


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 15

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 15 minutes after methionine addition

value: 15 min


title: Ramified microglia from 4-week rat brain biological rep2

city: Singapore

first: S Thameem

last: Dheen

address: Medical Drive 10

country: Singapore

institute: National University of Singapore

description: Gene expression data from ramified microglia isolated from corpus callosum of 4-week rat brain

hyb_protocol: The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).

scan_protocol: The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).

data_processing: CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also  analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]

organism: Rattus norvegicus

label_protocol: Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.

extract_protocol: Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.

value: Postnatal day 28

tag: tissue origin

value: brain

tag: tissue type

value: corpus callosum

value: Microglia

tag: cell morphology

value: Ramified (RMC)


title: Ramified microglia from 4-week rat brain biological rep3

tag: cell type


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 30

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 30 minutes after methionine addition

value: 30 min


title: Amoeboid microglia from 5-day rat brain biological rep3

description: Gene expression data from amoedboid microglia isolated from corpus callosum of 5-day rat brain

source_name: Amoeboid microglia from 5-day rat brain

value: Postnatal day 5

value: Amoeboid (AMC)


title: t(8;21) [CBF#16]

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

description:
CBF#16
SH_02102008_06KM7333.CEL

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

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

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

label: Biotin

source_name: mononuclear cells from bone marrow

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

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: age (years)

tag: gender

value: m

value: WT

tag: nras

value: MUT

tag: kit


title: Ramified microglia from 4-week rat brain biological rep1

tag: age


title: t(8;21) [CBF#11]

description:
CBF#11
UB_110806_05KM4148.CEL


title: inv(16) [CBF#13]

description:
CBF#13
UB_110806_05KM4272.CEL


title: inv(16) [CBF#19]

description:
CBF#19
UB_13012009_08KM3870.CEL

value: f


title: Amoeboid microglia from 5-day rat brain biological rep2


title: t(8;21) [CBF#15]

description:
CBF#15
SH_02102008_06KM7146.CEL


title: inv(16) [CBF#14]

description:
CBF#14
UB_06KM4240_10062008.CEL


title: inv(16) [CBF#17]

description:
CBF#17
SH_02102008_07KM2609.CEL


title: inv(16) [CBF#18]

description:
CBF#18
UB_14082008_07KM3381.CEL


title: inv(16) [CBF#10]

description:
CBF#10
UB_270706_05PB2554.CEL

source_name: mononuclear cells from peripheral blood


title: inv(16) [CBF#12]

description:
CBF#12
UB_210806_05KM4251.CEL


title: Amoeboid microglia from 5-day rat brain biological rep1

data_processing: CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also  analyzed with Microarray Suite version 5.0 (MAS5.0)using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 5

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 5 minutes after methionine addition

value: cln1,2,3∆ MET3pr-CLN2

value: 5 min


title: Streptococcus pneumoniae ParB-GFP_ChIP-on-chip

type: genomic

city: Groningen

first: Jan-Willem

last: Veening

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

description: Amplified ChIP DNA was fluorescently labelled using the BioPrime Total Genomic Labeling kit from Invitrogen. Eluate DNA was labelled with AlexA Fluor 3 and input DNA with Alexa Fluor 5. Labelled DNA was hybridized to a DNA-microarray containing amplicons of all open reading frames of S. pneumoniae (Kloosterman et al., 2006).

hyb_protocol: Labelled DNA was hybridized to a DNA-microarray containing amplicons of all open reading frames of S. pneumoniae (Kloosterman et al., 2006).The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519).

scan_protocol: Images were acquired with a GeneTac LS IV confocal laser scanner (Genomics Solutions).

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Expression ratios of eluate over input DNA were calculated. Ratio's smaller than 1 were set to 1. The VALUEs were not scaled or normalized.

label: Alexa Fluor 3

molecule: genomic DNA

organism: Streptococcus pneumoniae

source_name: Strain MT2 ChIP eluate

label_protocol: ChIP DNA from strain MT2 (ParB-GFP) was randomly amplified using the WGA2 kit from Sigma according to the manufacturer’s instructions. Next, amplified DNA was fluorescently labelled using the BioPrime Total Genomic Labeling kit from Invitrogen. Eluate DNA was labelled with AlexA Fluor 3 and input DNA was labeled with Alexa Fluor 5.

growth_protocol: Cells were grown to mid-exponential phase (OD600nm ~0.2) in GM17 medium at 37°C (with 0.15 mM ZnSO4 where relevant).

extract_protocol: One aliquot of each strain was resuspended in 2 ml ice cold lysis buffer (50 mM Hepes-KOH, pH 7.55, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate and RNase A (100 µg/ml)) and transferred to a 5 ml plastic tube. Cells were sonicated on ice using a Sonics vibra cell vcx 130. Pulse was on for 30 sec, then off for 30 sec and this was repeated for a total time of 3 min with amplitude of 75%. The lysates were transferred to 2 ml tubes and centrifuged for 10 min at 4°C at 13200 rpm. The supernatant was transferred to a clean 2 ml tube and centrifuged for 10 min 4°C 13200 rpm. The supernatant was pre-cleared with 100 µl proteinG-coupled Dyna Beads (Invitrogen) and subsequently incubated on a turning wheel with powersetting 18 for 1 hour at 4°C (cold room). Beads were pelleted using a magnet and the precleared supernatant was transferred to a new 2 ml eppendorf tube. 200 µl of the supernatant was kept at -20°C as the Whole Cell Extract (WCE) control. To 1500 µl of the precleared supernatant, 10 µl of anti-GFP antibodies (rabbit serum, polyclonal, Invitrogen A-6455, lot:622086) was added and incubated on a turning wheel for 2 hrs at 4°C. 100 µl of proteinG-coupled Dyna Beads (invitrogen) were added to the samples and incubated for 12 hours or more (overnight) on the turning wheel at 4°C. A magnet pelleted the beads and the supernatant was discarded. The beads were washed once for 5 min (vortex approximately 800 rpm) at room temperature with 1 ml lysis buffer containing 500 mM NaCl. The beads were pelleted with a magnet and subsequently washed with 1 ml wash buffer. Beads were pelleted and resuspended in 520 µl TES buffer. The WCE samples were thawed and combined with 300 µl TES and 20 µl 10% SDS. The samples were kept shaking at 65°C (little oven) for 6 hours (to overnight). This eluted the DNA from the beads and reversed cross links. Beads were collected using a magnet and 500 µl of the supernatants was transferred to a fresh 2 ml eppendorf cup. 12.5 µl Proteinase K (20 mg/ml in TE) was added to the samples and shaken for 2 hours at 37°C. 520 µl phenol was added and the solution was mixed by inverting and centrifuged for 2 min at max. speed. 450 µl of the top layer was pipetted off and transferred to a clean 1.5 ml eppendorfcup. 450 µl chloroform was added and the solution was mixed by inverting, spinned for 2 min at max. speed, 400 µl of the top layer was collected and transferred to a clean 1.5 ml eppendorfcup. 1 µl glycogen (20 mg/ml from Roche) was added, mixed by inverting and 40 µl NaOAc (sodium Acetate, pH 5.3) was added and mixed by inverting. 1 ml of pure ethanol was added, mixed by inverting and incubated for 20 min at 20°C. The mixture was centrifuged for 15 min at 4°C max speed, the supernatant was carefully removed. 200 µl of 70% ethanol was added and the cup was inverted several times, subsequently centrifuged for 15 min at 4°C and the supernatant was removed. The pellet was air dried at 45°C and resuspended in 50 µl TE, pH 8 for 15 min at 45°C. The ChIP samples were stored at -20°C, and 5 µl of the WCE was diluted ten-fold and also stored at -20°C.

treatment_protocol: 84 ml of culture was mixed by inverting with 8.4 ml of fixing solution (50 mM Tris 8.0, 100 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 30% (v/v) formaldehyde) and incubated at room temperature for 30 min. Cells were centrifuged for 3 min at 4°C at 6000 rpm and resuspended in 30 ml ice cold PBS. Cells were washed again with PBS and the pellet was resuspended in 1.5ml of TSEMS (50 mM Tris/HCl 7.4, 50 mM NaCl, 10 mM EDTA, 0.5 M Sucrose and 1 mM PMSF). Cells were washed twice more with TSEMS, and the pellets were aliquoted in three portions. The cells were snap freezed in liquid nitrogen and subsequently stored at -80°C.

value: MT2 (a D39 derivative)

tag: sample type

value: eluate

tag: chip antibody

value: rabbit anti-GFP polyclonal

tag: antibody vendor

value: Invitrogen

tag: antibody catalog number

tag: antibody lot number

label: Alexa Fluor 5

source_name: Strain MT2 ChIP input

value: input


title: inv(16) [CBF#6]

description:
CBF#6
UB_SL_01072010_10KM2260.CEL


title: inv(16) [CBF#4]

description:
CBF#4
UB_SL_01072010_09PB7178.CEL


title: Animal 1 vermis cerebelli BSE infected

status: Public on Jun 10 2011

city: Neuherberg

first: Michelle

last: Vincendeau

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

hyb_protocol: All handling steps involving fluorochromes are performed under dimmed light conditions, incubations are carried out in the dark.For hybridization, a 22x22 mm glass lifter slip (Erie Scientific Co., Portsmouth, NH, USA) is taped to the microarray. Subsequently, 25 μl of the denatured (5 min at 95 °C) Cy3-labeled probe (containing 3x SSC, 0.1x SDS, 50% formamide) is applied to the small space between cover slip and microarray and sealed with Fixogum rubber cement (Marabu GmbH, Tamm, Germany). Sealed slides are incubated in a humid chamber for at least 16 h at 42 °C.

scan_protocol: Hybridized microarrays were scanned using an Affymetrix GMS 418 scanner (laser power setting, 100%; gain setting, 50%), and the resulting images (16-bit TIFF files) were subjected to densitometric analysis using ImaGene 4.0 software (BioDiscovery Inc.).

data_processing: Data analysis using ImaGene 4.0 software (BioDiscovery Inc.). Normalization: Signal-Background

organism: Macaca fascicularis

source_name: Brain material

label_protocol: Subsequently, 25 ng of each cDNA was labbeled by PCR with retroviral mixed oligo primers (MOP) labbeled with CY3.

extract_protocol:
Total RNA (RNA >200 bases) was isolated from each sample using a mirVANA kit
(Ambion). To remove genomic DNA, all RNA samples were treated with 1 U/μg RQ1
RNase-free DNase I (Promega).

treatment_protocol: Cynomolgus macaque was intracerebrally inoculated with 50 mg bovine BSE-positive brain stem material derived from an EU-standard inoculum. Inoculation was performed by slow injection of 250 μl of a 20% BSE brain homogenate (w/v) diluted in sucrose into the right hemisphere through the dura mater into the caudo-putamen. The preclinical incubation time was on average 1,100 days. Animal was sacrificed, and the brain was dorso-ventrally sliced and snap-frozen on dry-ice plates.Three different brain regions (vermis cerebelli, basis pontis) were macroscopically identified on the frozen brain slices, isolated via a bore device and ground to powder under liquid nitrogen (for extraction of RNA).

tag: tissue

value: vermis cerebelli

tag: agent

value: BSE infected


title: Animal 1 basis pontis non infected

value: basis pontis


title: Animal 4 vermis cerebelli non infected


title: Animal 3 vermis cerebelli BSE infected


title: Animal 2 basis pontis non infected


title: Animal 5 basis pontis BSE infected


title: Animal 5 vermis cerebelli BSE infected


title: Animal 2 basis pontis BSE infected


title: Animal 4 basis pontis BSE infected


title: Animal 1 basis pontis BSE infected


title: Animal 3 basis pontis BSE infected


title: Animal 6 basis pontis BSE infected


title: Animal 6 vermis cerebelli BSE infected


title: Animal 2 vermis cerebelli non infected


title: Animal 2 vermis cerebelli BSE infected


title: Animal 3 basis pontis non infected


title: Animal 4 basis pontis non infected


title: Animal 1 vermis cerebelli non infected


title: Animal 3 vermis cerebelli non infected


title: LF endometrium day 7, biological rep5, animal 7524

city: Grange

first: aideen

middle: patricia

last: killeen

state: Co. Meath

address: Dunsany

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

description: Gene expression data from early luteal endometrium of low fertility heifers

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GCOS v 1.x

data_processing: All microarray analyses including preprocessing, normalization and statistical analysis were carried out using R (R, 2007) version 2.6 and Bioconductor version 2.1. Data were quality assessed before and after normalization using a number of in-built quality control methods implemented in the Bioconductor affycoretools and associated packages. Microarray data were preprocessed using the mmgMOS normalization method using the default settings and differential expression (DE) was calculated using the puma DE method both implemented in the Bioconductor package “puma”.

organism: Bos taurus

source_name: Bovine endometrium in early luteal phase; low fertility

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (Genechip Expression Analysis Technical Manual, 2005-2008, Affymetrix). cRNA was subjected to two rounds of linear amplification using the GeneChip® Expression 3’-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix Inc., Santa Clara, CA) according to the manufacturer’s instructions. cDNA was synthesized during the first cycle and biotin-labeled nucleotides were incorporated during the second in vitro transcription reaction.

extract_protocol: Total RNA was prepared from 100-200 mg of fragmented frozen endometrial tissue using the TRIzol extraction method. Samples were subsequently purified and treated for contaminating genomic DNA using RNeasy clean-up kits in accordance with manufacturer’s guidelines supplied (QIAGEN, Crawley, West Sussex, UK).

value: uterine endometrium

tag: genotype

value: Charolais X


title: LF endometrium day 7, biological rep1, animal 7720


title: Animal 4 vermis cerebelli BSE infected


title: LF endometrium day 7, biological rep3, animal 7500


title: LF endometrium day 7, biological rep2, animal 7619


title: HF endometrium day 7, biological rep5, animal 7525

description: Gene expression data from early luteal endometrium of high fertility heifers

source_name: Bovine endometrium in early luteal phase; high fertility


title: LF endometrium day 7, biological rep4, animal 7755

value: Simmental X


title: Glucose cln1,2,3∆ MET3pr-CLN2 timepoint min 10

description: W303 cln1,2,3∆ MET3pr-CLN2 cells 10 minutes after methionine addition

tag: strain

tag: time

value: 0 min

tag: media

value: glucose

value: 10 min


title: HF endometrium day 7, biological rep6, animal 7465


title: LF endometrium day 7, biological rep6, animal 7507

value: Limousin X


title: HF endometrium day 7, biological rep3, animal 7656


title: HF endometrium day 7, biological rep2, animal 7751


title: oxLDL, HUAEC, rep 3

city: Valencia

first: Carlos

last: Hermenegildo

address: Avda. Blasco Ibanez 15

country: Spain

institute: University of Valencia

description: Gene expression data from oxLDL-treated HUAECs.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station EukGene_ws_2v5.

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

data_processing: Files obtained from GCOS (.cel) were used to analyze significant changes in expression profiles of different experimental groups using the dCHIP Analysis Software and the SpotFire Decision Site software. Data were normalized using the Invariant Set Method and modeled using the PM/MM model.

source_name: HUAEC treated with 100 µg/ml oxLDL for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

growth_protocol: Primary HUAECs were isolated and grown in human endothelial cell-specific medium EBM-2 supplemented with EGM-2 (Lonza) in an incubator at 37 ºC with 5% CO2.

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

treatment_protocol: Cells were exposed to 1 nmol/L 17β-estradiol, 100 µg/ml oxLDL, estradiol + oxLDL, or its vehicle (0.1% ethanol) for 24 hours. Medium was discarded, cells washed with PBS and then collected in Trizol.

tag: cell type

value: endothelial cell

tag: treatment

value: oxLDL

tag: treatment duration

value: 24 hrs


title: Estradiol + oxLDL, HUAEC, rep 1

description: Gene expression data from estradiol- and oxLDL-treated HUAECs.

source_name: HUAEC treated with 1 nM estradiol and 100 µg/ml oxLDL for 24 h

value: 17β-estradiol and oxLDL


title: Estradiol, HUAEC, rep 4

description: Gene expression data from estradiol-treated HUAECs.

source_name: HUAEC treated with 1 nM estradiol for 24 h


title: Estradiol + oxLDL, HUAEC, rep 4


title: oxLDL, HUAEC, rep 1


title: Estradiol, HUAEC, rep 1


title: Estradiol + oxLDL, HUAEC, rep 2


title: Estradiol + oxLDL, HUAEC, rep 5


title: Estradiol, HUAEC, rep 5


title: HF endometrium day 7, biological rep4, animal 7718


title: Estradiol, HUAEC, rep 2


title: oxLDL, HUAEC, rep 4


title: Estradiol, HUAEC, rep 3


title: Estradiol + oxLDL, HUAEC, rep 3


title: Control, HUAEC, rep 4

description: Gene expression data from control HUAECs.

source_name: HUAEC, control

value: ethanol control


title: HF endometrium day 7, biological rep1, animal 7476


title: Control, HUAEC, rep 5


title: oxLDL, HUAEC, rep 5


title: Control, HUAEC, rep 1


title: oxLDL, HUAEC, rep 2


title: large airway, basal cells [DGM-01683]

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
DGM-01683_lg_BC.CHP
DGM-01683_lg_BC.CEL

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: large airway, basal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: department of genetic medicine id

tag: airway region

value: large airway

value: basal cell


title: large airway, basal cells [DGM-01270]

description:
DGM-01270_lg_BC.CHP
DGM-01270_lg_BC.CEL


title: large airway, basal cells [DGM-02012]

description:
DGM-02012_lg_BC.CHP
DGM-02012_lg_BC.CEL


title: large airway, basal cells [DGM-00564]

description:
DGM-00564_lg_BC.CHP
DGM-00564_lg_BC.CEL


title: Control, HUAEC, rep 2


title: large airway, basal cells [DGM-01610]

description:
DGM-01610_lg_BC.CHP
DGM-01610_lg_BC.CEL


title: Exp-7-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

description: Comparison of gene expression in the S.pyogenes M1SF370 internalized in Detroit 562 human pharyngeal cells vs S.pyogenes M1SF370 cultured in MEM without Detroit 562 cells.

hyb_protocol: cDNA probes labeled with Alexafluor 555 (green test)and 647(red- control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS.

scan_protocol: Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix-4100) at 10um/pixel resolution. The resulting images were processed using GenePix Pro 4100 software (version 4.0, Axon instruments). The raw data were obtained in the form of GenPix .gpr output files.

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signal was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were given a weight of zero. The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. CARMAweb allows to set Log2 cut-off values for both the M (regulation) and the A (average expression) values. Differentially expressed genes (Log2 values of Invasion647-red vs. Non-Detroit 555-green or Log2 values  Invasion -555(green) vs  Non Detroit 647-red) were defined based on cut-off value >1 Log2< -1. i.e. all genes that show a two or more-fold up- or down-regulation. Bioconductors Multtest package provided suitable method to adjust P values according to multiple hypothesis testing problems.

label: Alexafluor 555

organism: Streptococcus pyogenes

source_name: Detroit 562 pharyngeal cells-internalized Streptococcus pyogenes

label_protocol: For synthesis and labeling of cDNA, 5 ug of total RNA, 1.5 ug of random hexamer, 0.5mM dNTPs (except that 0.2mM of dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) were used in each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino-allyl modified cDNA was then purified  using QIAQuick PCR Spin column and labeled with Alexafluor 555 in 0.3M sodium carbonate (pH9.0) for 1 h in dark according to the manufacturer's instructions.

growth_protocol:
M1-SF370 Wild-type strain was grown in Todd-Hewitt broth to their late log phase. Bacteria were harvested by centrifugation and washed twice with sterile PBS and adjusted to O.D. 1.0 (2 x108 cfu/ml). The latter was then centrifuged and brought back to the same volume in MEM. 4 75mm2 Tissue culture flasks with confluent culture of Detroit 562 cells were infected with M1SF370 bacterial suspension in MEM at MOI 100: 1 (Bacteria:Detroit cells) and incubated for 3 hr. at 37 C. In parallel, 4 tissue culture flasks without Detroit cells were seeded with the same volume of M1-SF370-MEM suspension  and incubated for 3 hr at 37C. The latter was treated as control.
At the end of the incubation, non-adherent bacteria were removed by repeated washing. Following this, Detroit cells with adherent bacteria were detached using trypsin EDTA treatment. Adherent bacteria from the Detroit cell were then removed by slow speed centrifugation (400 g) for 10 min. By repeated washing at low speed by the buffer containing trypsin, the adherent bacteria associated with Detroit cell were removed. These cells were then treated with a buffer containing trypsin, triton (0.05%) RNASe free DNAse to lyse the cells and free up the internalized bacteria. DNase was used to reduce the viscosity of the lysed suspension. The latter suspension was then subjected to low centrifugation to obtain internalized bacteria in the supernatant. The supernatant was then subjected to high centrifugation to pellet the internalized bacteria. Subsequently, this bacterial pellet was washed thoroughly with sterile PBS and suspended in small volume to extract Total RNA. M1SF370 grown in tissue culture flask without Detroit cells were also washed and total RNA was extracted. The latter was treated as control RNA from M1SF370 that never faced intracellular host cell environment.

extract_protocol:
Isolated internalized bacteria were lysed with recombinant PlyC and
total RNA was isolated from the DEtroit 562 cells-internalized bacteria using Qia RNAeasy kit (cat#74104). RNA was digested with RNAse-free DNAse and the RNA quality  was analyzed using nucleic acid bioanalyzed (Agilent technologies).

treatment_protocol: After infection of Detroit 562 cells with S.pyogenes M1SF370 (MOI100:1) or 3 hr at 37 c in humidified CO2 incubator, the internalized S. pyogenes  were isolated by lysis of the cells followed differential centrifugation.

value: wild-type

value: Detroit 562 cell-internalized

label: Alexafluor 647

source_name: Control Streptococcus pyogenes grown in MEM without Detroit 562 cells

label_protocol: For synthesis and labeling of cDNA, 5 ug of total RNA, 1.5 ug of random hexamer, 0.5mM dNTPs (except that 0.2mM of dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) were used in each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino-allyl modified cDNA was then purified  using QIAQuick PCR Spin column and labeled with Alexafluor 647 in 0.3M sodium carbonate (pH9.0) for 1 h in dark according to the manufacturer's instructions.

extract_protocol: Total RNA from S. pyogenes was isolated by Qiagen RNAeasy kit.RNA was digested with RNAse-free DNAse and the RNA quality  was analyzed using nucleic acid bioanalyzed (Agilent technologies).

treatment_protocol: Streptococcus pyogenes Type M1 SF370 bacterial suspension in MEM without Detroit 562 cells.

value: Cultured only in MEM without Detroit 562


title: Control, HUAEC, rep 3


title: large airway [DGM-00757]

description:
DGM-00757_lg.CHP
DGM-00757_lg.CEL

source_name: large airway

value: mixture of epithelium, basal, ciliated, secretory, undifferentiated and inflammatory cells


title: large airway [DGM-00778]

description:
DGM-00778_lg.CHP
DGM-00778_lg.CEL


title: Exp-1-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

hyb_protocol: cDNA probes labeled with Alexafluor555(green- test)and 647 (red control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS

extract_protocol:
Isolated internalized bacteria were lysed with recombinant PlyC and
total RNA was isolated from the DEtroit 562 cells-internalized bacteria using Qia RNAeasy kit (cat#74104). RNA was digested with RNAse-free DNAse and the RNA quality  was analyzed using nucleic acid bioanalyzed ( Agilent technologies).

treatment_protocol: After infection of Detroit 562 cells with S. pyogenes M1SF370 (MOI100:1) or 3 hr at 37 c in humidified CO2 incubator, the internalized S. pyogenes  were isolated by lysis of the cells followed differential centrifugation.

extract_protocol: Total RNA from S. pyogenes was isolated by qiagen RNAeasy kit.


title: large airway [DGM-00529]

description:
DGM-00529_lg.CHP
DGM-00529_lg.CEL


title: Exp-8-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

hyb_protocol: cDNA probes labeled with Alexafluor 647(Red- test)and 555(green- control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS.


title: large airway [DGM-00342]

description:
DGM-00342_lg.CHP
DGM-00342_lg.CEL


title: Exp-6-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

hyb_protocol: cDNA probes labeled with Alexafluor 647 (red test)and 555(green- control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS.


title: Exp-4-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

hyb_protocol: cDNA probes labeled with Alexafluor 647(red test)and 555 (green control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS.


title: large airway [DGM-00052]

description:
DGM-00052_lg.CHP
DGM-00052_lg.CEL


title: Exp-5-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

hyb_protocol: cDNA probes labeled with Alexafluor 555 (green test)and 647 (red- control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS.


title: large airway [DGM-00465]

description:
DGM-00465_lg.CHP
DGM-00465_lg.CEL


title: [Control9]-[Healthy]-[CD4+T-cells]

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Healthy

scan_protocol: Illumina iScan

data_processing:
The relative level of methylation for each CG site was calculated as the ratio of methylated-probe signal to total locus signal intensity, and defined within 0 to 1 range, exported from the Illumina BeadStudio software package.
The data were normalized as described previously, (Dozmorov I, Knowlton N, Tang Y, Shields A, Pathipvanich P, Jarvis JN, et al. Hypervariable genes--experimental error or hidden dynamics. Nucleic Acids Res 2004; Dozmorov I, Lefkovits I. Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 2009) using the variability of areas with low methylation level as a reference point. In order to find genes with methylation level above the level of technical noise, a frequency histogram of raw methylation signal was determined for each array. The histogram yielded a right-skewed unimodal distribution curve with a mode of approximately 0.013.  A normal distribution curve representing the variability of the data around zero was then fitted around the mode, mirroring the Gaussian profile of the left part of the histogram. Its parameters were then defined (mean, SD) and the data were normalized to the standard deviation of the noise after subtraction of the mean. The data were then Log10-transformed and adjusted to each other by robust linear regression under the assumption that the methylation of most genes does not change. The data were then filtered to remove genes with a methylation level value less than 3.0, equivalent to setting a threshold at three standard deviations above the noise level. Genes with methylation differential below the noise level under all experimental conditions (about 1,600) were excluded from consideration, as their methylation cannot be reliably assessed.

source_name: CD4+T-cells, whole genomic DNA

label_protocol: Bisulfite-converted patient and control DNA samples were prepared and quantified using a NanoDrop scanning spectrophotometer (Thermo, Wilmington, DE).  For each sample, 500ng of whole-genome bisulfite-converted DNA was denatured, fragmented, and amplified using Illumina-supplied reagents according to manufacturer instructions.  Following precipitation, DNA was hybridized to Illumina Infinium HumanMethylation27 arrays, containing 50-mer oligonucleotides designed to hybridize either methylated (N-CG-N following bisulfite conversion) or unmethylated (N-TG-N following bisulfite conversion) cytosine on each CG pair interrogated, coupled to beads mounted on glass slides.  Microarrays were washed under high stringency, labeled with biotin (C and G nucleotides) or dinitrophenyl (A and T nucleotides), and scanned with an Illumina iScan.

growth_protocol: Twelve female lupus patients and 12 female controls were studied. The mean age was 42.83±3.61 in patients and 43.75±3.40 in controls (mean±SEM).

extract_protocol: CD4+ T lymphocytes were obtained via Ficoll/Paque PBMC enrichment (GE Healthcare Life Sciences, Piscataway, NJ) followed by CD4+ isolation using a MACS magnetic bead CD4+ T-cell isolation kit (Miltenyi Biosystems, Auburn, CA).  Whole genomic DNA was then prepared using a Qiagen DNEasy kit (Qiagen, Germantown, MD) and bisulfite-treated using a Zymo EZ DNA Methylation Kit (Zymo, Orange, CA).

treatment_protocol: Peripheral blood was collected from patient samples and controls.

tag: disease status

value: healthy control


title: Exp-3-Streptococcus pyogenes internalized in Detroit 562 human pharyngeal cells

hyb_protocol: cDNA probes labeled with Alexafluor 647(red test)and 555 (green control)were mixed and PCR purified. The labeled cDNA was hybridized with the array slide in the hybridization buffer ( 3x SSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C for 16h using HybChamber-Tm frm GeneMachine-Tm. The hybridized array slides were washed consecutively with 1xSSC, 0.2x SSC, and 0.05% SSC each with 0.3% SDS     The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory and were further analyzedUsing appropriate navigation tree, background correction from the foreground signal was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were given a weight of zero. The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. CARMAweb allows to set Log2 cut-off values for both the M (regulation) and the A (average expression) values. Differentially expressed genes (Log2 values of Invasion555-green vs. Non-Detroit 645-red) was measured by subtracting red chanel background values from the test Green Channel values

label_protocol: For synthesis and labeling of cDNA, 5 ug of total RNA, 1.5 ug of random hexamer, 0.5mM dNTPs (except that 0.2mM of dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) were used in each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino-allyl modified cDNA was then purified using QIAQuick PCR Spin column and labeled with Alexafluor 555 in 0.3M sodium carbonate (pH9.0) for 1 h in dark according to the manufacturer's instructions.

extract_protocol:
Isolated internalized bacteria were lysed with recombinant PlyC and
total RNA was isolated from the DEtroit 562 cells-internalized bacteria using Qia RNAeasy kit (cat#74104). RNA was digested with RNAse-free DNAse and the RNA quality was analyzed using nucleic acid bioanalyzed ( Agilent technologies).

treatment_protocol: After infection of Detroit 562 cells with S.pyogenes M1SF370 (MOI100:1) or 3 hr at 37 c in humidified CO2 incubator, the internalized S. pyogenes were isolated by lysis of the cells followed differential centrifugation.

label_protocol: For synthesis and labeling of cDNA, 5 ug of total RNA, 1.5 ug of random hexamer, 0.5mM dNTPs (except that 0.2mM of dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) were used in each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino-allyl modified cDNA was then purified using QIAQuick PCR Spin column and labeled with Alexafluor 647 in 0.3M sodium carbonate (pH9.0) for 1 h in dark according to the manufacturer's instructions.

extract_protocol: Total RNA from S. pyogenes was isolated by Qiagen RNAeasy kit.RNA was digested with RNAse-free DNAse and the RNA quality was analyzed using nucleic acid bioanalyzed ( Agilent technologies).


title: [Control8]-[Healthy]-[CD4+T-cells]

description: Healthy

hyb_protocol: DNA was hybridized to Illumina Infinium HumanMethylation27 arrays, containing 50-mer oligonucleotides designed to hybridize either methylated (N-CG-N following bisulfite conversion) or unmethylated (N-TG-N following bisulfite conversion) cytosine on each CG pair interrogated, coupled to beads mounted on glass slides.

label: biotin (C and G nucleotides) or dinitrophenyl (A and T nucleotides)


title: [Control12]-[Healthy]-[CD4+T-cells]

description: Healthy


title: [Control10]-[Healthy]-[CD4+T-cells]

description: Healthy


title: large airway [DGM-00044]

description:
DGM-00044_lg.CHP
DGM-00044_lg.CEL


title: large airway [DGM-00661]

description:
DGM-00661_lg.CHP
DGM-00661_lg.CEL


title: large airway [DGM-00192]

description:
DGM-00192_lg.CHP
DGM-00192_lg.CEL


title: [Control11]-[Healthy]-[CD4+T-cells]

description: Healthy


title: [Control7]-[Healthy]-[CD4+T-cells]

description: Healthy


title: large airway [DGM-00073]

description:
DGM-00073_lg.CHP
DGM-00073_lg.CEL


title: large airway [DGM-00041]

description:
DGM-00041_lg.CHP
DGM-00041_lg.CEL