title: SATB1-siRNA 48h Th1 (set 3)

status: Public on Jan 07 2010

city: Turku

first: Helena

last: Ahlfors

address: Tykistökatu 6A

country: Finland

institute: Turku Centre for Biotechnology

description: biological replicate 1

hyb_protocol: 1.5 microg each sample was hybridized to Illumina's Sentrix Human-6 Expression BeadChip Arrays (cat no BD-25-112) at 55 C overnight (18 h) according to Illumina Whole-Genome Gene Expression with IntelliHyb protocol, revision A. Hybridization was detected with 1microg/ml Cyanine3-streptavidine (Amersham Bioscience, cat no 146065)

scan_protocol: Chips were scanned with Illumina BeadArray Reader and the numerical results were extracted with Bead Studio v2.3.41 without any normalization or background subtraction.

data_processing: The data were quantile normalized (Bolstad et al., 2003) and log-transformed using R package limma (Wettenhall and Smyth, 2004), a part of the Bioconductor project http://www.bioconductor.org.

source_name: umbilical cord blood

label_protocol: RNA amplification was started from 100 ng total RNA with Ambion's Illumina RNA TotalPrep Amplification kit (cat no IL1791). In vitro translation reaction was performed overnight (14h) and during it cRNA was biotinylated.

growth_protocol: Cell culture was started 24 h post-nucleofection. Cell culturing was performed in Yssel’s medium (Yssel et al. 1984) supplemented with 1% human AB-serum (Finnish Red Cross) in the density of 1.5–4x106 cells/ml. Cells were activated with plate-bound anti-CD3 (2.5 μg/ml for coating) and 0.5 μg/ml soluble anti-CD28 (Immunotech, Marseille, France). Th1 polarization was induced with IL-12 (2.5 ng/ml) and Th2 differentiation with IL-4 (10 ng/ml; both from R&D Systems, Minneapolis, MN). Part of the cells was cultured without any polarizing cytokines, in “Th0” conditions.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. DNase I (Qiagen) treatment was included in the RNA isolation procedure to eliminate genomic DNA from the samples. Both before and after the amplifications the RNA/cRNA concentrations where checked with Nanodrop ND-1000 and RNA/cRNA quality was controlled by BioRad’s Experion electrophoresis station.

treatment_protocol: CD4+ T cells were purified from umbilical cord blood of healthy neonates (Turku University Central Hospital, Turku, Finland) using Ficoll-Paque gradient centrifugation (Amersham Pharmacia Biotech, Uppsala, Sweden) and anti-CD4 conjugated magnetic beads (Dynal, Oslo, Norway). Four million human cord blood primary CD4+ T cells were nucleofected with 1.5 μg of SATB1-siRNA or scramble control siRNA oligonucleotides. Nucleofections were carried out in 100 µl Opti-MEM I (Invitrogen) using Nucleofector™ device (program U-14) (Amaxa, Cologne, Germany). Several parallel nucleofections were performed. After the pulse before starting the culture, the cells were kept in RPMI-1640 medium containing 10 % FBS, L-glutamine and antibiotics (pen/strep) in the density of 2-2.5x106 cells/ml at 37 °C, in 5 % CO2.

tag: differentiation

tag: cell origin

value: CD4+ T cells


title: Normal PBMC

status: Public on Jan 08 2010

type: RNA

city: New Delhi

first: Alok

last: Bhattacharya

state: New Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

description: PBMCs were isolated by ficoll gradient from the blood of normal volunteer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneST 1.0 Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) using Affymetrix default analysis settings in Expression Console software.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip® WholeTranscript (WT) Sense Target Labeling Assay Manual Version 4.0, Affymetrix).

growth_protocol: Cells were grown in RPMI medium with 10% fetal bovine serum in 5% CO2 and passaged after every 2 days.

extract_protocol: Trizol Extraction of total RNA was performed according to manufacturer's protocol.

tag: cell type

value: PBMC


title: SATB1-siRNA 24h Th1 (set 3)

description: biological replicate 1

label: biotin


title: SATB1-siRNA 24h Th2 (set 3)

description: biological replicate 1


title: HL60

description: HL60 cell line is derived from acute promyelocytic leukemia patient

source_name: Acute Promyelocytic Leukemia cell lines

tag: cell line


title: SATB1-siRNA 12h Th2 (set 3)

description: biological replicate 1


title: Scramble-siRNA 48h Th2 (set 3)

description: biological replicate 1


title: CpG ODN-5 days-repeat 3 - mAdbID:88965

city: Frederick

first: Dennis

middle: M

last: Klinman

state: MD

department: CIP

country: USA

institute: NCI Frederick

description: mAdb experiment ID: 88965

hyb_protocol: Murine oligonucleotide microarrays were produced by the NCI microarray facility (Gaithersburg, MD). Cy-labeled reference and sample cDNAs (10 microliter each) were combined, de-naturated by heating for 2' at 98 C and mixed with 36 microliter of hybridization solution at 42 C (Ambion, Austin, TX). A low volume active mixing chamber was applied to the microarray via an adhesive gasket (MAUI mixer FL, BioMicro Systems, Salt Lake City, Utah), the hybridization solution containing the sample was added to the array, and was placed for 18 h at 42 C in the base unit of the actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah). Post hybridization, the arrays were washed in 1X SSC/0.05X SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100; 100 LaserPower: 3.14798; 3.69701 Temperature: 27.7917

data_processing: BRB Data Processing Protocol: Data were up-loaded to the mAdb database (Microarray Database, a collaboration of CIT/BIMAS and NCI/CCR at the NIH; http://nciarray.nci.nih.gov/) and formatted via the export function for use with BRB ArrayTools. Data from 4 independent experiments/time point and 6 untreated controls were used for all statistical analyses. Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes (21). Analysis was restricted to genes present on >70% of the arrays after filtering.

organism: Mus musculus

source_name: Universal Mouse Reference RNA

label_protocol: Cy3 Labeling Protocol: 20 microgram of total RNA (universal reference mouse RNA, Stratagene, La Jolla, CA) was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy3 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol: Strategene UHR RNA Extraction

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: CpG ODN - 5 days

label_protocol: Cy5 Labeling Protocol: 20 microgram of total RNA was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy5 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol: TRIzol Extraction Protocol: Total RNA was extracted from spleens using TRIzol reagent (Invitrogen) as specified by the manufacturer.

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 5 days
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0 hr, 3 hr, 9 hr, 24 hr, 3 days, 5 days, 7 days, 9 days, and 14 days.

tag: strain

value: BALB/c

tag: gender

value: female

tag: tissue

value: spleen


title: SATB1-siRNA 48h Th2 (set 3)

description: biological replicate 1


title: K562

description: K562 cell line is derived from a CML patient in terminal blast crisis and used as model for CML studies

source_name: Chronic Myelogenous Leukemia cell line


title: SATB1-siRNA 48h Th0 (set 3)

description: biological replicate 1


title: Scramble-siRNA 48h Th1 (set 3)

description: biological replicate 1


title: SATB1-siRNA 12h Th1 (set 3)

description: biological replicate 1


title: SATB1-siRNA 12h Th0 (set 3)

description: biological replicate 1


title: SATB1-siRNA 0h Thp (set 3)

description: biological replicate 1

value: Thp


title: Scramble-siRNA 24h Th0 (set 3)

description: biological replicate 1


title: SATB1-siRNA 24h Th0 (set 3)

description: biological replicate 1


title: Scramble-siRNA 48h Th0 (set 3)

description: biological replicate 1


title: Scramble-siRNA 12h Th2 (set 3)

description: biological replicate 1


title: Scramble-siRNA 24h Th2 (set 3)

description: biological replicate 1


title: Scramble-siRNA 24h Th1 (set 3)

description: biological replicate 1


title: Scramble-siRNA 12h Th0 (set 3)

description: biological replicate 1


title: Scramble-siRNA 0h Thp (set 3)

description: biological replicate 1


title: Scramble-siRNA 12h Th1 (set 3)

description: biological replicate 1


title: 07054

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description:
A4by44_251485034101B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07054, TEST SET

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty

extract_protocol: Qiagen Rneasy Kit

tag: age

value: 29 years


title: 07053

description:
A4by44_251485034101A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07053, TEST SET

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: 49 years


title: 07097

description:
251485034106A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07097, TEST SET

value: 22 years


title: 07096_rep1

description:
251485036092D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07096, replicate, TEST SET

value: 33 years


title: 07096

description:
251485034105D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07096, TEST SET


title: 07084_rep1

description:
251485036092B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07084, replicate, TEST SET

value: 17 years


title: 07079_rep1

description:
251485036092A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07079, replicate, TEST SET

value: 23 years


title: 07098

description:
251485034106B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07098, TEST SET

value: 14 years


title: 07093_rep1

description:
251485036092C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07093, replicate, TEST SET

value: 27 years


title: 07050

description:
A4by44K_4881B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07050

value: 39 years


title: 07047

description:
A4by44K_4878C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07047


title: 07084

description:
251485034105B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07084, TEST SET


title: 07048

description:
A4by44K_4878D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07048

value: 55 years


title: 07049

description:
A4by44k_5405D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07049


title: 07099

description:
251485034106C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07099, TEST SET

value: 36 years


title: 07042

description:
A4by44K_4878
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07042


title: 07041

description:
A4by44K_1063D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07041

value: 51 years


title: 07093

description:
251485034105C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07093, TEST SET


title: 07078

description:
251485034103D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07078, TEST SET

value: 34 years


title: 07043

description:
A4by44k_5405B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07043


title: 07046

description:
A4by44k_5405C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07046


title: 07052

description:
A4by44K_4881D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07052

value: 30 years


title: 07045

description:
A4by44K_4878B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07045

value: 43 years


title: 07044

description:
A4by44K_4881
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07044

value: 20 years


title: 07039

description:
A4by44K_1063C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07039

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 56 years


title: 07038

description:
A4by44K_1063B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07038

value: 40 years


title: 07036

description:
A4by44k_5405A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07036

value: 50 years


title: 07079

description:
251485034105A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07079, TEST SET


title: 07051

description:
A4by44K_4881C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07051

value: 33 years


title: 07034

description:
A4by44K_1062C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07034


title: 07037

description:
A4by44K_1063
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07037

value: 17 years


title: 07032

description:
A4by44K_1062B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07032


title: 07030

description:
A4by44K_1061D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07030

value: 49 years


title: 07031

description:
A4by44K_1062A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07031

value: 45 years


title: 07029

description:
A4by44k_1059D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07029

value: 42 years


title: 07028

description:
A4by44k_1059C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07028

value: 39 years


title: 07028_rep2

description:
A4by44k_5404D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07028, replicate


title: 07027

description:
A4by44k_1058D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07027

value: 54 years


title: 07023

description:
A4by44K_1061A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07023

value: 31 years


title: 07020

description:
A4by44k_1058A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07020

value: 59 years


title: 07026

description:
A4by44K_1061B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07026


title: 07018

description:
A4by44k_1057C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07018

value: 29 years


title: 07019

description:
A4by44k_1057D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07019

value: 36 years


title: 07017

description:
A4by44K_1060D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07017

value: 32 years


title: 07021

description:
A4by44k_1059B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07021


title: 07015

description:
A4by44k_5404CR
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07015

value: 19 years


title: 07016

description:
A4by44k_1057B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07016

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: 15 years


title: 07025

description:
A4by44k_1058C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07025


title: 07022

description:
A4by44k_1058B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07022


title: 07010

description:
A4by44k_5404B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07010

value: 53 years


title: 07011

description:
A4by44k_1056B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07011


title: 07008

description:
A4by44K_1060C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07008

value: 51 years


title: 07012_rep1

description:
A4by44k_1059A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07012, replicate 1


title: 07013

description:
A4by44k_1056D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07013

value: 43 years


title: 07029_rep1

description:
A4by44K_1061C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07029, replicate


title: 07014

description:
A4by44k_1057A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07014


title: 07009

description:
A4by44k_1056A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07009


title: 07035

description:
A4by44K_1062D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07035

value: 55 years


title: 07004

description:
A4by44K_1060A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07004

value: 50 years


title: 07003

description:
A4by44k_1055B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07003

value: 46 years


title: 07005

description:
A4by44k_1055C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07005


title: 07006

description:
A4by44k_1055D
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07006

value: 44 years


title: Scramble-siRNA 24h Th1 (set 5)

description: biological replicate 3

hyb_protocol: 1.5 microg each sample was hybridized to Illumina's Sentrix Human-6 Expression BeadChip, version 2 (cat no BD-25-113) Arrays at 58 C overnight (18 h) according to Illumina Whole-Genome Gene Expression with IntelliHyb protocol, revision A. Hybridization was detected with 1microg/ml Cyanine3-streptavidine (Amersham Bioscience, cat no 146065)

scan_protocol: Chips were scanned with Illumina BeadArray Reader and the numerical results were extracted with Bead Studio v3.2.3 without any normalization or background subtraction.

tag: origin

value: CD4+ T cells


title: SATB1-siRNA 24h Th2 (set 5)

description: biological replicate 3


title: Scramble-siRNA 24h Th2 (set 5)

description: biological replicate 3


title: SATB1-siRNA 24h Th1 (set 5)

description: biological replicate 3


title: Replicate 5

city: East Lansing

first: Laura

last: Schaefer

state: MI

address: 6144 Biomedical Physical Sciences

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: no additional information

hyb_protocol: Microarray slides that were cross-linked by exposure to 350 mJ UV were prehybridized at 42°C for 1 hour in 5X SSC, 0.1% SDS, and 0.01% (w/v) BSA. The slides were submersed in water, then submersed in 100% isopropanol, then allowed to dry. The Cy3- and Cy5-labeled probes were combined then denatured at 95C for 5 minutes in the presence of 0.1µg/ml yeast tRNA and 0.1µg/ml salmon testes DNA. Slides were hybridized in a total volume of 200 µl with denatured probe, 50% formamide, 10XSSC, 0.1% SDS in an Agilent G2534A microarray hybridization chamber (Agilent Technologies) at 42°C overnight. Slides were washed for 4 minutes at 42°C in 1× SSC and 0.2% SDS, 4 minutes at 25°C in 0.1× SSC and 0.2% SDS, then 4 minutes at 25°C in 1× SSC.

scan_protocol: Slides were scanned on a GenePix 4000B scanner (Axon Instruments, Inc.).

data_processing: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices). To be considered a valid signal, 40% of the pixels in a spot had to be at least 1 standard deviation above the local background in at least one of the channels. Spots not making this cutoff were excluded from further analysis. Because many of the genes in the analysis are expressed under only one condition, we had to assign a value to the spots that did not contain a significant signal in one channel. This value was the lowest signal in a channel that met our criterion of being at least 1 standard deviation above background. Background signal was not subtracted from the signal intensity of the spots. Once spots with significant signals were identified, the two channels were normalized by making the total signal in each of the channels equal. Microarray data were analyzed using iterative outlier analysis with three iterations. Briefly, iterative outlier analysis calculates the geometric mean and standard deviation of the entire data set. Differentially expressed genes (outliers) were selected as being more than 2.5 standard deviations away from the mean of the population. To identify additional differentially expressed genes in the data set, the outliers were removed, the geometric mean and standard deviations were recalculated, and any genes that were more than 2.5 standard deviations from the mean were identified as differentially expressed.

organism: Escherichia coli DH5[alpha]

source_name: DH5alpha treated with reuterin

label_protocol: 10 µg of total RNA was incubated with 2.5 µg of random hexamers in a final volume of 17.8 µl at 70°C for 10 min and then placed on ice for 4 min. 12.2 µl of a labeling mix containing Superscript III reverse transcriptase buffer (Invitrogen), 10 mM dithiothreitol, deoxynucleoside triphosphates (0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.3 mM dTTP, and 0.2 mM 5-(3-Aminoallyl)-dUTP), 20 units RNase Out (Invitrogen) and 300 units Superscript III reverse transcriptase (Invitrogen) was added to the RNA-primer mixture and incubated at 25°C for 5 min and then at 50°C for 60 min. The reaction was stopped by heating the reaction mixture to 70°C for 15 minutes. RNA was hydrolyzed by adding 15 µl 0.1M sodium hydroxide and incubating the mixture at 70°C for 10 minutes, then adding 15 µl 0.1M hydrochloric acid and 40 µl water. Unincorporated nucleotides were removed by using Qiagen MinElute spin columns (Qiagen) and samples were eluted from the columns using 10 µl water. For the coupling reaction, 0.5 µl 1M sodium carbonate (pH 9) was added to the eluent and the mixture was used to resuspend either Cy5 or Cy3 dye aliquots (CyDye Post-labeling Reactive Dye Pack, GE Healthcare), incubated at 25°C for 1 hour, and purified using Qiagen MinElute spin columns (Qiagen).

extract_protocol: Samples of cells taken for RNA isolation were immediately mixed with an equal volume of prechilled methanol (-20°C) and kept at room temperature for 1 to 2 min. Cells were centrifuged for 5 min, and cell pellets were stored at -80°C. Total RNA extracted using Qiagen RNeasy RNA Isolation Kit following manufacturer's instructions.

treatment_protocol: Overnight cultures of E. coli were diluted 1:100 in 25 ml LB broth and grown to mid-log phase (OD600 = 0.25) under hypoxic conditions (2% O2) shaking at 250 rpm. Reuterin-containing cell-free supernatant that had been determined to have a MIC assay value of 32 units reuterin/ml was added to the culture at 1/5 of the total culture volume. 2X LB broth was added at the same time to maintain the same nutrient concentration. The cells were allowed to double before samples were removed for RNA extraction.

tag: genome/variation

value: F- endA1 glnV44 thi-1 relA1 gyrA96 deoR nupG lacZdeltaM15 hsdR17

source_name: DH5alpha not treated with reuterin

treatment_protocol: Overnight cultures of E. coli were diluted 1:100 in 25 ml LB broth and grown to mid-log phase (OD600 = 0.25) under hypoxic conditions (2% O2) shaking at 250 rpm. 250mM glycerol was added to the culture at 1/5 of the total culture volume as a control. 2X LB broth was added at the same time to maintain the same nutrient concentration. The cells were allowed to double before samples were removed for RNA extraction.


title: Scramble-siRNA 24h Th0 (set 5)

description: biological replicate 3


title: SATB1-siRNA 48h Th0 (set 4)

description: biological replicate 2

hyb_protocol: 1.5 microg each sample was hybridized to Illumina's Sentrix Human-6 Expression BeadChip, version 2 (cat no BD-25-113) Arrays at 58 C overnight (19 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridization was detected with 1microg/ml Cyanine3-streptavidine (GE Healthcare Biosciences, cat no PA43001)

label_protocol: RNA amplification was started from 200 ng total RNA with Ambion's Illumina RNA TotalPrep Amplification kit (cat no IL1791). In vitro translation reaction was performed overnight (14h) and during it cRNA was biotinylated.


title: Scramble-siRNA 48h Th2 (set 4)

description: biological replicate 2


title: SATB1-siRNA 48h Th1 (set 4)

description: biological replicate 2


title: SATB1-shRNA 48h Th2 (set 2)

description: biological replicate 1

hyb_protocol: 1.5 microg each sample was hybridized to Illumina's Sentrix WG-6 BeadChip Arrays at 55 C overnight (19 h). Hybridization was detected with 1microg/ml Cyanine3-streptavidine (Amersham Bioscience, cat no 146065)

scan_protocol: Chips were scanned with Illumina BeadArray Reader and the numerical results were extracted with Bead Studio v1.5.1.3 without any normalization or background subtraction.

source_name: peripheral blood

label_protocol: RNA amplification was started from 50 ng total RNA with Ambion's Illumina RNA TotalPrep Amplification kit (cat no IL1791). In vitro translation reaction was performed overnight (14h) and during it cRNA was biotinylated.

growth_protocol: Cell culture was started 48 h post-nucleofection. Cell culturing was performed in Yssel’s medium (Yssel et al. 1984) supplemented with 1% human AB-serum (Finnish Red Cross) in the density of 1.5–4x106 cells/ml. Cells were activated with plate-bound anti-CD3 (2.5 μg/ml for coating) and 0.5 μg/ml soluble anti-CD28 (Immunotech, Marseille, France). Th1 polarization was induced with IL-12 (2.5 ng/ml) and Th2 differentiation with IL-4 (10 ng/ml; both from R&D Systems, Minneapolis, MN).

treatment_protocol: CD4+ T cells were purified from peripheral blood (buffy coats) from healthy blood donors (Finnish Red Cross) using Ficoll-Paque gradient centrifugation (Amersham Pharmacia Biotech, Uppsala, Sweden) and anti-CD4 conjugated magnetic beads (Dynal, Oslo, Norway). Five million human buffy coat primary CD4+ T cells were nucleofected with 10 μg of SATB1-shRNA or scramble control plasmid DNA containing H-2Kk marker for selection. Nucleofections were carried out in 100 µl Opti-MEM I (Invitrogen) using Nucleofector™ device (program U-14) (Amaxa, Cologne, Germany). Several parallel nucleofections were performed. After the pulse, the cells were kept in RPMI-1640 medium containing 10 % FBS, L-glutamine and antibiotics (pen/strep) in the density of 2-2.5x106 cells/ml at 37 °C, in 5 % CO2. Sixteen hours after nucleofection cells were enriched for viable transfected cells using Dead Cell Removal Kit and MACSelect Kk MicroBeads coated with the H-2Kk antibody for positive selection (Miltenyi Biotech). After enrichment of cells and before starting the culture, the cells were kept in Yssel’s medium at 37 °C, in 5 % CO2.


title: SATB1-siRNA 24h Th0 (set 5)

description: biological replicate 3


title: 07012

description:
A4by44k_1056C
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07012


title: Scramble-shRNA 48h Th2 (set 2)

description: biological replicate 1


title: Replicate 4

description: no additional information


title: Scramble-siRNA 48h Th0 (set 4)

description: biological replicate 2


title: Replicate 3

description: no additional information


title: Scramble-siRNA 48h Th1 (set 4)

description: biological replicate 2


title: 07039C_rep2

description:
A244K_251780410230
Agilent custom array of reduction mammoplasty patient 07039, replicate

value: 56 years


title: SATB1-siRNA 24h Th2 (set 4)

description: biological replicate 2


title: Replicate 2

description: no additional information


title: 07007

description:
A4by44K_1060B
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07007


title: 07002

description:
A4by44k_1055A
Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient 07002

value: 35 years


title: 07014_rep1

description:
A244K_251780410227
Agilent custom array of reduction mammoplasty patient 07014

value: 29 years


title: SATB1-shRNA 48h Th1 (set 2)

description: biological replicate 1


title: SATB1-shRNA 24h Th2 (set 2)

description: biological replicate 1


title: SATB1-siRNA 24h Th0 (set 4)

description: biological replicate 2


title: 07013_rep1

description:
A244K_251780410226
Agilent custom array of reduction mammoplasty patient 07013


title: Scramble-siRNA 24h Th2 (set 4)

description: biological replicate 2


title: 07036_rep1

description:
244k_251767710109
Agilent custom array of reduction mammoplasty patient 07036


title: Control tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 8

city: Charlottesville

first: Zhen

last: Yan

state: VA

address: 409 Lane Rd

department: Medicine

institute: University of Virginia

description: Gene expression data from the contralateral control tibialis anterior muscle in a muscle-specific p38gamma knockout mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software (AGCC) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Adult (8 weeks of age) male skeletal muscle-specific p38gamma knockout mice (MKO) and the wild type littermates in C57BL/6 background were subject to surgery with electrodes implantation under the left deep peroneal nerve followed by 30 min of recovery, 2 hours of motor nerve stimulation at 10 Hz (0.25 ms duration) between 1-3 V and an additional 1 hour of recovery under the aneasthesia. Both the stimulated and the contralateral control tabialis anterior (TA) muscles were harevested for microarray analysis.

value: Tibialis anterior muscle

tag: genotype

value: 8 weeks old

tag: mouse type

value: p38gamma knockout mouse


title: 07016_rep1

description:
A244K_251780410228
Agilent customarray of reduction mammoplasty patient 07016

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: SATB1-siRNA 48h Th2 (set 4)

description: biological replicate 2


title: SATB1-shRNA 0h Thp (set 2)

description: biological replicate 1

value: Thp


title: Scramble-siRNA 24h Th1 (set 4)

description: biological replicate 2


title: 07039B_rep1

description:
A244K_251780410229
Agilent custom array of reduction mammoplasty patient 07039


title: Replicate 1

description: no additional information


title: Stimulated tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 8

description: Gene expression data from the motor nerve-stimulated tibialis anterior muscle in a muscle-specific p38gamma knockout mouse


title: UNC07-2471A

description:
251976010088-244K
Agilent Catalog 4 by 44k whole genome array UNC07-2471A, TEST SET

source_name: Normal Tissue Adjacent to Breast Tumor

value: 47 years


title: Stimulated tibialis anterior muscle in a wild type mouse 7

description: Gene expression data from the motor nerve-stimulated tibialis anterior muscle in a wild type mouse

value: wild type


title: Scramble-shRNA 0h Thp (set 2)

description: biological replicate 1


title: SATB1-siRNA 12h Th0 (set 4)

description: biological replicate 2


title: UNC06-0747A

description:
H1AUNC244k-v3-0084
Agilent Custom array of UNC06-0747A

value: 53 years


title: SATB1-siRNA 12h Th2 (set 4)

description: biological replicate 2


title: Scramble-shRNA 24h Th2 (set 2)

description: biological replicate 1


title: SATB1-shRNA 48h Th1 (set 1)

description: biological replicate 1


title: SATB1-siRNA 12h Th1 (set 4)

description: biological replicate 2


title: Scramble-shRNA 24h Th1 (set 2)

description: biological replicate 1


title: SATB1-shRNA 48h Th2 (set 1)

description: biological replicate 1


title: SATB1-shRNA 24h Th1 (set 2)

description: biological replicate 1


title: Scramble-siRNA 24h Th0 (set 4)

description: biological replicate 2


title: UNC98-2049A

description:
H1AUNC244k-0325
Agilent Custom array of UNC98-2049A

value: 72 years


title: UNC06-0756A

description:
H1AUNC244k-v3-0085
Agilent Custom array of UNC06-0756A

value: 74 years


title: 07028_rep1

description:
244k_251767710108
Agilent custom array of reduction mammoplasty patient 07028

value: 39 years


title: Scramble-shRNA 48h Th1 (set 1)

description: biological replicate 1


title: Scramble-shRNA 48h Th2 (set 1)

description: biological replicate 1


title: Stimulated tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 5


title: Scramble-siRNA 12h Th1 (set 4)

description: biological replicate 2


title: Control tibialis anterior muscle in a wild type mouse 7

description: Gene expression data from the contralateral control tibialis anterior muscle in a wild type mouse


title: fem-3(q20ts)-1day old adults at 25C-technicalrep1-biolrep2

city: Cambridge

first: Ezequiel

last: Alvarez-Saavedra

state: MA

address: 77 Massachusetts Avenue  Room 68-411

department: Biology

institute: MIT

hyb_protocol: Hybridization was done at 50°C for 10 hrs in 5X SSC, 0.1% SDS, 0.1 mg/ml salmon sperm DNA.

scan_protocol: The hybridized arrays were scanned using an arrayWoRxe biochip reader (Applied Precision) and primary data were analyzed using the Digital Genome System suite (Molecularware).

data_processing: Normalized spot intensities (signal (spot mean intensity) - background (median background intensity of the spot)) were used as "raw" data for subsequent data analysis. For inter-array comparisons, all data were scaled based on total array intensities, and data for each sample and each gene were averaged. Total array intensity was calculated as the sum of the normalized spot intensity for all spots in the microarray.

organism: Caenorhabditis elegans

label_protocol: Short RNAs were isolated using denaturing polyacrylamide gels and RNA was labeled by ligation to pCU Cy3 as described in Wienholds, E., Kloosterman, W.P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., de Bruijn, E., Horvitz, H.R., Kauppinen, S., and Plasterk, R.H. (2005). MicroRNA expression in zebrafish embryonic development. Science 309, 310-311.

growth_protocol: Synchronized animals were grown at 25ºC and harvested 24 h after the late L4 stage.

extract_protocol: Total RNA was isolated from staged one day old adult populations of C. elegans by freeze cracking (Reinke, V., Smith, H.E., Nance, J., Wang, J., Van Doren, C., Begley, R., Jones, S.J., Davis, E.B., Scherer, S., Ward, S., et al. (2000). A global profile of germline gene expression in C. elegans. Mol Cell 6, 605-616.) and extracted using Trizol (Invitrogen) according to the manufacturer’s protocol.

tag: mutant

tag: developmental stage

value: Adult


title: Scramble-siRNA 12h Th0 (set 4)

description: biological replicate 2

value: CD4+ T cells


title: SATB1-shRNA 24h Th2 (set 1)

description: biological replicate 1


title: Control tibialis anterior muscle in a wild type mouse 3


title: Stimulated tibialis anterior muscle in a wild type mouse 3


title: Array_8_reference_control_red_runt_replicate_4_green

city: Salisbury Cove

first: Anthony

middle: James

last: Robertson

state: ME

address: Box 35 Old Bar Harbor Road

department: Functional Genomics

institute: Mount Desert Island Biolabs

description:
The reference control was taken from the same embryo cultures and at the same time (18 hours post fertilization) as the SpRunt-1 morphants.  The control embryos from four different experiments were pooled together to form a common reference for all of the array sectors on the 8x15 k chip
Adult outbred (wild) sea urchins (Strongylocentrotus purpuratus) were induced to spawn by vigorous shaking.  Gamete collection and fertilization were carried out using standard methods, and embryos were developed to hatched blastula stage (18 hours post-fertilization) in filtered seawater at 15°C.

hyb_protocol: Hybridization and washing protocols were according to the standard, optimized protocols of the microarray core facility (Cornell  University Microarray Core Facility, Ithaca, NY).

scan_protocol: Agilent scanner and Feature Extraction Software

data_processing: Green (Cy3) and red (Cy5) median signal intensities for each array were obtained using the Agilent Feature Extraction Software (version 10.7.1.1) with default parameters accepted.  The log(base 2) ratios of (test/reference) median signal intensities following local LOWESS (rlowess) normalization computed using R/maanova.

organism: Strongylocentrotus purpuratus

source_name: RNA from untreated blastula stage embryos

label_protocol: Total RNA extracted from blastula stage embryos was provided to an Agilent-approved Core Facility (Cornell University Microarray Core Facility, Ithaca, NY) where the labeling was performed using an Ambion MessageAmp kit (Applied Biosystems/Ambion, Austin, TX) optimized to produce maximum length, labeled aRNA from an oligo dT directed polymerase start position

growth_protocol: The reference controls were grown in filtered sea water with identical conditions to those used for corresponding SpRunt-1 morphants.  A few control embryos were developed to late gastrula stage to confirm that normal development occurred.

extract_protocol: Total RNA was extracted with the RNeasy Kit (Qiagen, Valencia, CA).

tag: agent

tag: tissue type

value: blastula stage embryos

source_name: RNA from blastula stage embryos developed from zygotes injected with a splice-blocking morpholino antisense oligonucleotide (MASO) targeted to SpRunt-1.

label_protocol: Total RNA extracted from blastula stage embryos was provided to an Agilent-approved Core Facility (Cornell University Microarray Core Facility, Ithaca, NY) where the labeling was performed using an Ambion MessageAmp kit (Applied Biosystems/Ambion, Austin, TX) optimized to produce maximum length labeled aRNA from an oligo dT directed polymerase start position.

growth_protocol: The SpRunt-1 morphants were developed in filtered sea water with conditions identical to those used for corresponding untreated control embryos.  A few SpRunt-1 morphants were developed to gastrula stage to confirm the documented SpRunt-1 morphant phenotype

treatment_protocol: Biological replicate 4 is the fourth of four separate embryo cultures of SpRunt-1 morphants (representing four true biological replicates, each from a different mating pair) and each was developed to hatched blastula stage (18 hrs post-fertilization).


title: Stimulated tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 4


title: Scramble-shRNA 24h Th1 (set 1)

description: biological replicate 1

tag: differentiation


title: Control tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 4


title: SATB1-shRNA 24h Th1 (set 1)

description: biological replicate 1

tag: cell origin


title: Scramble-siRNA 0h Thp (set 4)

description: biological replicate 2


title: SATB1-siRNA 0h Thp (set 4)

description: biological replicate 2


title: Scramble-shRNA 48h Th1 (set 2)

description: biological replicate 1


title: SATB1-shRNA 0h Thp (set 1)

description: biological replicate 1


title: Array_7_reference_control_red_runt_replicate_3_green

treatment_protocol: Biological replicate 3 is the third of four separate embryo cultures of SpRunt-1 morphants (representing four true biological replicates, each from a different mating pair) and each was developed to hatched blastula stage (18 hrs post-fertilization).

value: splice-blocking morpholino antisense oligonucleotide (MASO) targeted to SpRunt-1


title: Scramble-shRNA 0h Thp (set 1)

description: biological replicate 1


title: Stimulated tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 2


title: Scramble-siRNA 12h Th2 (set 4)

description: biological replicate 2


title: Scramble-shRNA 24h Th2 (set 1)

description: biological replicate 1


title: Array_6_reference_control_red_runt_replicate_2_green

treatment_protocol: Biological replicate 2 is the second of four separate embryo cultures of SpRunt-1 morphants (representing four true biological replicates, each from a different mating pair) and each was developed to hatched blastula stage (18 hrs post-fertilization).


title: fem-3(q20ts)-1day old adults at 25C-technicalrep2-biolrep1


title: Control tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 5


title: fem-2(b245ts)-1day old adults at 25C-technicalrep1-biolrep2


title: fem-2(b245ts)-1day old adults at 25C-technicalrep2-biolrep1


title: fem-2(b245ts)-1day old adults at 25C-technicalrep1-biolrep1


title: fem-3(q20ts)-1day old adults at 25C-technicalrep1-biolrep1


title: Array_5_reference_control_red_runt_replicate_1_green

treatment_protocol: Biological replicate 1 is the first of four separate embryo cultures of SpRunt-1 morphants (representing four true biological replicates, each from a different mating pair) and each was developed to hatched blastula stage (18 hrs post-fertilization).


title: Control tibialis anterior muscle in a muscle-specific p38gamma knockout mouse 2


title: Array_3_reference_control_green_runt_replicate_3_red

description:
The reference control was taken from the same embryo cultures and at the same time (18 hours post fertilization) as the SpRunt-1 morphants.  The control embryos from four different experiments were pooled together to form a common reference for all of the array sectors on the 8x15 k chip
Adult outbred (wild) sea urchins (Strongylocentrotus purpuratus) were induced to spawn by vigorous shaking.  Gamete collection and fertilization were carried out using standard methods, and embryos were developed to hatched blastula stage (18 hours post-fertilization) in filtered seawater at 15°C


title: HCMV-infected/LY-pretreated monocyte, 48 hr post-infection, biological rep1

city: Shreveport

first: Andrew

middle: D.

last: Yurochko

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: LSUHSC-S

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human U95Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling with a target intensity value of 2500 as normalization method.

source_name: HCMV-infected/LY-pretreated monocytes at 48 hours post infection

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

growth_protocol: Monocytes were incubated in RPMI supplemented with 10% human AB serum at 37C and 5% CO2.

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

treatment_protocol: Isolated monocytes were pretreated with or without LY294002. Cells wre HCMV infected (MOI 15) or mock infected, and incubated adherently at 37C for 48 hours.

value: peripheral blood

tag: cell type

value: monocytes

tag: hcmv strain

value: Towne/E

tag: pretreatment

tag: infection

value: HCMV

tag: time post-infection

value: 48 hours


title: Array_4_reference_control_green_runt_replicate_4_red


title: HCMV-infected/LY-pretreated monocyte, 48 hr post-infection, biological rep2

tag: tissue


title: Array_2_reference_control_green_runt_replicate_2_red


title: HCMV-infected monocyte, 48 hr post-infection, biological rep2

source_name: HCMV-infected monocytes at 48 hours post infection


title: HCMV-infected monocyte, 48 hr post-infection, biological rep1


title: Stimulated tibialis anterior muscle in a wild type mouse 1

value: Tibialis anterior muscle

tag: age

value: 8 weeks old


title: Mock-infected monocyte, 48 hr post-infection, biological rep2

source_name: Mock-infected monocytes at 48 hours post infection


title: Control tibialis anterior muscle in a wild type mouse 1


title: Array_1_reference_control_green_runt_replicate_1_red

treatment_protocol: Biological replicate one is the first of four separate embryo cultures of SpRunt-1 morphants (representing four true biological replicates, each from a different mating pair) and each was developed to hatched blastula stage (18 hrs post-fertilization).


title: Mock-infected monocyte, 48 hr post-infection, biological rep1


title: Case#5

status: Public on Jan 06 2010

city: Bergen

first: Mads

last: Aarhus

address: Jonas Lies v 65

department: Center for Medical Genetics and Molecular Medicine

country: Norway

institute: Haukeland University Hospital

hyb_protocol: Fifteen ug mRNA was hybridized to the ABI Human Genome Survey Microarray v1.

scan_protocol: DIG-labeled targets hybridize to the probes on the arrays and anti-digoxigenin-alkaline phosphatase is added to bind digoxigenin in cDNA targets. The ABI 1700 Expression Array System (ABI, U.S) was used to scan the arrays for chemiluminescence.

data_processing: Signal intensities generated with the ABI 1700 Expression Array System (Applied Biosystems, U.S) were imported into the the J-Express Pro v2.7 software (MolMine AS, Norway). Interarray quantile normalization was performed, and all control spots and flagged spots were removed. unsupervised cluster analysis and significance analysis of microarrays with  400 and 1000 permutations were then performed.

label: digoxigenin (DIG)

source_name: Arachnoid cyst

label_protocol: Labeling was done with the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit using 2 ug high quality total RNA.

extract_protocol: Total RNA was extracted with the Qiuagen Rneasy minikit (Quiagen, Germany).

tag: gender

value: F

tag: anatomical region

value: right temporal fossa

tag: galassi grade


title: Case#6

value: left temporal fossa


title: Case#7

value: M


title: Th2 24h SATB1

type: genomic

description: biological replicate 1

hyb_protocol: For all hybridizations, 5 micrograms each of Cy3-labeled WCE was mixed with 5 micrograms of Cy5-labeled IP DNA. Hybridization was carried out at 65°C for 40 hrs as per Agilent protocol. Agilent's In situ Hybridization kit 5188-5220.

scan_protocol: Post-hybridization, the slides were washed as per Agilent protocol and scanned at 5 micron resolution using Agilent Microarray Scanner.

data_processing: The text output file generated from the images using Agilent feature extraction software were used for the analysis. The normalization was done using Agilent DNA Analytics software. Normalization method used: Median Blanks substraction, Inter-array median normalization and Dye-bias median normalization.

molecule: genomic DNA

source_name: Th2 24h anti-SATB1 IP

label_protocol: Two hundred nanograms of WCE and IP DNA was blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Mammalian Chip on Chip Protocol Version 10.0 of Agilent Technologies. The blunted DNA was cleaned by phenol:chloroform extraction and the precipitated DNA was resuspended in 25 microlitres of water and the entire DNA was ligated to linkers overnight. The linker-ligated DNA was subjected to two rounds of LMPCR as per protocol and the product was precipitated and resuspended in 20 microliters of water. Two micrograms of each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS and Cy3 or Cy5 dUTP from Agilent. DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

growth_protocol: Cell culturing was performed in Yssel’s medium (Yssel et al. 1984) supplemented with 1% human AB-serum (Finnish Red Cross) in the density of 1.5–4x106 cells/ml. Cells were activated with plate-bound anti-CD3 (2.5 μg/ml for coating) and 0.5 μg/ml soluble anti-CD28 (Immunotech, Marseille, France). Th1 polarization was induced with IL-12 (2.5 ng/ml) and Th2 differentiation with IL-4 (10 ng/ml; both from R&D Systems, Minneapolis, MN).

extract_protocol: Cells were crosslinked for 10 min at room temperature by adding formaldehyde to a final concentration of 1% directly to the culture medium. After cell lysis, chromatin was sonicated such that genomic DNA was sheared into 300–1500 bp fragments. Sheared chromatin was immunoprecipitated with anti-SATB1 antibody (IP), followed by reverse crosslinking with 4 M NaCl for 4 h at 65 °C, proteinase K digestion, phenol-chloroform extraction and ethanol precipitation. Part of the sheared chromatin was saved as Whole Cell Extract (WCE) sample which was treated similarly excluding the immunoprecipitation step. DNA yield and quality were measured using NanoDrop spectrophotometer.

treatment_protocol: CD4+ T cells were purified from umbilical cord blood of healthy neonates (Turku University Central Hospital, Turku, Finland) using Ficoll-Paque gradient centrifugation (Amersham Pharmacia Biotech, Uppsala, Sweden) and anti-CD4 conjugated magnetic beads (Dynal, Oslo, Norway).

value: cord blood

tag: antibody

source_name: Th2 24h whole cell extract


title: Case#2


title: Th1 24h SATB1

description: biological replicate 1

source_name: Th1 24h anti-SATB1 IP

source_name: Th1 24h whole cell extract


title: Case#3


title: Control#2

source_name: Normal arachnoid membrane

value: cisterna magna


title: Case#4


title: sham-3 vs. sham

status: Public on Jan 05 2010

city: peking

first: bing

last: shi

address: NO 39 huayuan north road

department: department of cardiology

country: China

institute: peking university third hospital

description: compare miRNA expression profiles in myocardium in individual  sham-control rat with mixed in  sham-control rat

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

scan_protocol: Luxscan 10K/A (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

source_name: rat, sham-control

label_protocol: 4μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

growth_protocol: male sprague-Dawley rats were kept and bred in facilities of a standard conforming to UK home office requirements.

extract_protocol: Rats were sacrificed with an overdose of pentobarbital 2, 7 or 14 days after myocardial infarction . Myocardium  in border- zone were  immediately  snap frozen in liquid nitrogen for microarray analysis. Total RNA from rat myocardium in the border zone was isolated using trizol reagent (invitrogen, USA) according to manufacturer's directions.

treatment_protocol: The myocardial infarction (MI) models were induced by ligation of anterior descending coronary artery in adult Sprague-Dawley rats(180-200gram) as described by Shyu et al. On the 1st  postoperative day , the survivals were randomly divided into three groups; 2days after MI group, 7 days after AMI group, 14days after AMI groups . These rat were exposed to all surgical procedures except the ligation of LAD artery formed into sham-control group.each group has five individal animals

value: myocardium in left ventricular

tag: state

value: normal  myocardium

tag: strain

value: Sprague Dawley

source_name: sham-control rat

value: myocardium

value: mixed normal myocardium from all sham-control rat


title: sham-2 vs. sham


title: Control sample 26

first: Hem

middle: Chandra

last: Jha

state: Delhi

address: Lab no-204, IOP-ICMR, Safdarjung Hospital Campus,

department: Tissue Culture/Microbiology

institute: Institute of Pathology- Indian Council of Medical Research

description:
Differential gene expression analysis across cHSP60-positive vs. cHSP60-negative samples.
Sample 26

hyb_protocol: 10.0 µg of the labeled aRNA in 100 µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and was used for hybridization with the Human 40 K A chip and printed at Ocimum Biosolutions, Hyderabad. Hybridization was performed at 50°C for two hrs on Tecan HS 4800 automated Hyb station.

scan_protocol: Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains (40, 50, 60). Define scan area: Always set size Y to 0. Use array finder to define the size height (1mm on the array finder » 1mm on the OciChip). Height means the distance from the top of the slide to the end of the spotted array (plus safe distance of 2 mm).Set scan settings: The PMT gain settings of the multiple scanning have to be increased with the same distance (usually a distance of 10 between the settings is used). Set the range of the increasing PMT gain setting to achieve both to avoid saturation of the strongest spots at lowest value and to receive reliable signals from the weak spots at the highest PMT gain setting. Scanning was performed at 40, 50 and 60 PMT gain for the hybridized chips.

data_processing:
Median absolute deviation (MAD) scaling was used for normalization.

Initially, data consisted of 40,320 probes. Empty spots and the control probes were removed from the data. After filtration, 39,400 genes were retained for analyisis. The missing values were imputed by K-nearest neighbor method.

source_name: CAD patient, coronary artery, cHSP60-negative

label_protocol: Five  microgram of total RNA was used for amplification using the Express Art® mRNA amplification Kit Message by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is reverse transcribed followed by second strand synthesis priming with an oligo (dT) primer bearing T7 promoter in a thermal cycler using the conditions described in the manual. The resulting cDNA was purified and then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA was then labelled with Cy3TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3 molecules were removed by a purification process.

extract_protocol: RNA concentration was evaluated by measuring an absorbance at 260 and 280 nm using a NanoDrop (NanoDrop, USA), and RNA quality was evaluated by electrophoretic analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA meeting the quality standards was released for probe generation.

tag: disease

value: coronary artery disease (CAD)

value: coronary artery atheroma

tag: chlamydia pneumoniae

value: negative

tag: sample type

value: control


title: Chlamydia pneumoniae-positive sample 23

description:
Differential gene expression analysis across cHSP60-positive vs. cHSP60-negative samples.
Sample 23

source_name: CAD patient, coronary artery, cHSP60-positive

value: positive


title: Identification of miR-504 target genes in FaDu

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

country: Japan

institute: Chiba University

description: miRNA treated in 72hr in head and neck cancer cell line FaDu

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: control miRNA transfected FaDu

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

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

tag: cell line

value: FaDu

source_name: miR-504 transfected FaDu


title: Case#1


title: Control#1

value: F


title: Identification of miR-133a target genes in T24

description: miRNA treated in 72hr in bladder cancer cell line T24

source_name: control miRNA transfected T24

source_name: miR-133a transfected  T24


title: Gene expression analysis of BOY

description: human bladder cancer cell line: BOY

source_name: human bladder total RNA

value: control RNA purchased from Clontech

source_name: BOY

value: bladder cancer BOY


title: Identification of miR-145 target genes in KK47

description: miRNA treated in 72hr in bladder cancer cell line KK47

source_name: control miRNA transfected KK47

source_name: miR-145 transfected  KK47


title: Gene expression analysis of T24

description: human bladder cancer cell line: T24

value: bladder cancer T24


title: Identification of miR-504 target genes in HSC3

description: miRNA treated in 72hr in head and neck cancer cell line HSC3

source_name: control miRNA transfected HSC3

source_name: miR-504 transfected HSC3


title: day 14-2 vs. sham

description: compare miRNA expression profiles in border-zone  myocardium in rat with acute myocardial infarction  with  myocardium in  sham-control rat

source_name: rat, AMI, 14days

value: myocardium in border zone

value: ischemia myocardium


title: Gene expression analysis of J82

description: human bladder cancer cell line: J82

value: bladder cancer J82


title: day 14-3 vs. sham

description: compare miRNA expression profiles in border-zone  myocardium in rat with acute myocardial infarction  with   myocardium in  sham-control rat


title: Gene expression analysis of UMUC

description: human bladder cancer cell line: UMUC

source_name: UMUC

value: bladder cancer UMUC


title: Identification of miR-133a target genes in KK47

source_name: miR-133a transfected  KK47


title: Gene expression analysis of KK47

description: human bladder cancer cell line: KK47

value: bladder cancer KK47


title: Chlamydia pneumoniae-positive sample 17

description:
Differential gene expression analysis across cHSP60-positive vs. cHSP60-negative samples.
Sample 17


title: sham-1 vs. sham

source_name: rat, sham-control

value: myocardium in left ventricular

value: normal  myocardium

value: Sprague Dawley

value: myocardium


title: Identification of miR-145 target genes in T24

source_name: miR-145 transfected  T24


title: day 14-1 vs. sham

source_name: sham-control rat

value: mixed normal myocardium from all sham-control rat


title: Identification of miR-489 target genes in HSC3

source_name: miR-489 transfected HSC3


title: day 2-1 vs. sham

source_name: rat, AMI , 2days


title: day 2-2 vs. sham

source_name: rat, AMI,  2days


title: Identification of miR-489 target genes in FaDu

source_name: control miRNA transfected FaDu

source_name: miR-489 transfected FaDu


title: SATB1-siRNA 24h Th1 (set 4)

description: biological replicate 2

source_name: umbilical cord blood

tag: differentiation

tag: cell origin

value: CD4+ T cells


title: day 7-2 vs. sham

source_name: rat, AMI , 7days


title: day 7-1 vs. sham


title: Gene expression analysis of LY6K transfectant

description: LY6K target genes in bladder cancer

source_name: control vector transfected T24

value: human bladder T24

source_name: LY6K transfected T24

value: human bladder T24-LY6K


title: day 7-3 vs. sham


title: caf1b 30minW biorep3

city: La Jolla

first: Justin

last: Walley

state: CA

address: 9500 Gilman Ave

department: Biological Sciences

institute: UCSD

hyb_protocol: Labeled cy3 and cy5 cRNA was mixed and hybridized according to Agilent protocol.

scan_protocol: Arrays were scanned on an Agilent G2505B DNA microarray scanner. The raw TIFF images were analyzed and normalized using the Agilent Feature Extraction software using the recommended default settings.

organism: Arabidopsis thaliana

source_name: Pooled reference

label_protocol: Labeled cRNA was produced using the Agilent low RNA input linear amp kit according to the manufactures protocol.  Total RNA was used as a template for cDNA synthesis primed with oligo(dT) followed by production of cRNA labeled with cy5.

extract_protocol: RNA was isolated using TRIzol reagent and further purified using Qiagen RNeasy kit with on column DNase treatment

tag: ecotype

value: 3 week old rosette leaves

source_name: caf1b 30minW

label_protocol: Labeled cRNA was produced using the Agilent low RNA input linear amp kit according to the manufactures protocol.  Total RNA was used as a template for cDNA synthesis primed with oligo(dT) followed by production of cRNA labeled with cy3.

treatment_protocol: 30 min wound


title: caf1b NW biorep1

data_processing: The raw TIFF images were analyzed and normalized using the Agilent Feature Extraction software using the recommended default settings.

source_name: caf1b 0minW

treatment_protocol: 0 min wound


title: caf1b 90minW biorep2

source_name: caf1b 90minW

treatment_protocol: 90 min wound


title: caf1b 30minW biorep2


title: caf1b 90minW biorep3


title: caf1b 30minW biorep1


title: caf1b NW biorep3


title: caf1a 90minW biorep2

source_name: caf1a 90minW


title: caf1a NW biorep3

source_name: caf1a NW


title: caf1b 90minW biorep1


title: caf1a 90minW biorep1


title: caf1a NW biorep2


title: caf1b NW biorep2


title: caf1a 90minW biorep3


title: caf1a 30minW biorep3

source_name: caf1a 30minW


title: caf1a 30minW biorep2


title: caf1a NW biorep1


title: WT_90minW_biorep3

source_name: WT 90minW


title: caf1a 30minW biorep1


title: WT_90minW_biorep1


title: WT_30minW_biorep3

source_name: WT 30minW


title: WT_30minW_biorep1


title: WT_NW_biorep3

source_name: WT NW


title: WT_NW_biorep2


title: WT_30minW_biorep2


title: WT_NW_biorep1


title: OCTT2 Ecad+3

city: Philadelphia

first: Gao

last: Zhang

state: PA

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

description: passage +3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

GEO staff have requested, but not yet received, the normalized data described in this submission.

source_name: OCTT2 Ecad+3

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

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.

tag: cell type

value: head and neck squamous cell carcinoma

tag: ecad status

value: positive

tag: isolate

value: patient 2


title: ProB cells biological rep1

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

description: Gene expression data from Sorted Cells AA4.1+IgM-CD19+CD43+HAS+B220+

hyb_protocol: RNA hybridized to MOE430_2. Chips according to manufacturer manual

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000

data_processing: Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip

source_name: Mouse Bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2000 cell

growth_protocol: 230-238 cells were grown in RPMI supplemented with 10% FCS and 50µg/ml Gentamicin, NIH3T3 and MC3T3 cells were propagated in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% FCS and 50µg/ ml Gentamicin, OP9 Strawberry were maintained in OptiMEM (Gibco) supplemented with 10% FCS, 50µg/ml Gentamicin.

extract_protocol: total RNA extraction was performed with QIAGENE microRNeasy kit according to the manufacturer's instructions.


title: MatureB cells biological rep2

description: Gene expression data from Sorted Cells CD43-CD19+B220+IgM+

source_name: Mouse Spleen

value: Sorted Cells CD43-CD19+B220+IgM+


title: MatureB cells biological rep1


title: OCTT2E1 Ecad+1

description: passage +1

source_name: OCTT2E1 Ecad+1


title: OCTT2E1 Ecad-2

description: passage +2

source_name: OCTT2E1 Ecad-2

value: negative


title: SCC9 Ecad-3

description: passage +3

source_name: SCC9 Ecad-3

value: patient 1


title: Ets2-null_tumor

city: Columbus

first: Michael

last: Ostrowski

state: OH

address: 460 W 12th Ave

institute: Ohio State University

description: Gene expression data from Ets2-deficient tumor-associated mammary macrophages

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the mouse chip 430A.2. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.The data are Log2 values.

source_name: Two copies of Ets2 deleted (tumor)

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from ~10 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Mice used in the experiment endogenously expressed YFP in macrophages. YFP positive macrophages from each genetic group were isolated by digital high-speed fluorescence activated cell sorting (FACS).

extract_protocol: RNA was extracted using the RNeasy Stratagene micro-prep column (Stratagene) as per the manufacturer’s instructions.

treatment_protocol: YFP-positive macrophages isolated by FACS were eluted in DMEM media with 3% FBS. For RNA preparation, the eluant was centrifuged at 1200rpm for 5minutes at 4C to obtain pellet containing the macrophages.

tag: Tissue:mammary gland

tag: Tumor stage

value: early


title: Ets2-wildtype_tumor

description: Gene expression data from Ets2-expressing tumor-associated mammary macrophages

source_name: One copy of Ets2 (tumor)


title: CML Lin+CD34+

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U95Av2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 2μg of total RNA.

hyb_protocol: Affymetrix Human HG-U95Av2 GeneChip arrays hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA).The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U95Av2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=100. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

source_name: Lineage+CD34+ cells purified from peripheral blood (PB) of CML patients at diagnosis and before treatment

label_protocol: One-cycle target labeling assays was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 2 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

extract_protocol: Total cellular RNA was extracted from 0.5x105 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. RNAs originating from 12 CML patients were pooled in order to obtain at least 2μg per sample.

tag: Leukemic cells were obtained from 12 chronic phase Ph+ CML patients at diagnosis and before treatment. The protocol was approved by the ethical committee of the University Hospital and each patient/donor gave written informed consent. Hemopoietic stem/progenitor cell purification and phenotypic analyses were performed as previously described (Lemoli RM et al., Br J Haematol, 2003; Lemoli RM et al., Blood, 1997). Aliquots of sorted Lin-CD34-, Lin-CD34+ and Lin+CD34+ were reanalyzed by FacScan (Becton Dickinson, Franklin Lakes, NJ) to assess their purities which were 99.2±0.6%, 98.8±0.9% and 99±1%, respectively.


title: PreB cells biological rep2

description: Gene expression data from Sorted Cells AA4.1+IgM-CD19+CD43-HAS+B220+


title: Ets2-wildtype_no tumor

description: Gene expression data from Ets2-expressing remodeling mammary macrophages

source_name: wild-type (no tumor)


title: OCTT2E1 Ecad+2

description: passage +2

source_name: OCTT2E1 Ecad+2


title: OCTT2E1 Ecad-1

description: passage +1

source_name: OCTT2E1 Ecad-1


title: SCC9 Ecad-2

description: passage +2

source_name: SCC9 Ecad-2


title: SCC9 Ecad+3

description: passage +3

source_name: SCC9 Ecad+3


title: SCC9 Ecad+2

description: passage +2

source_name: SCC9 Ecad+2


title: ProB cells biological rep2


title: Ets2-null_no tumor

description: Gene expression data from Ets2-deficient remodeling mammary macrophages

source_name: Two copies of Ets2 deleted (no tumor)


title: PreB cells biological rep1


title: OCTT2 Ecad-3

description: passage +3

source_name: OCTT2 Ecad-3


title: Lin-CD34+

source_name: Lineage-CD34+ cells purified from peripheral blood (PB) of normal donors

extract_protocol: Total cellular RNA was extracted from 0.5x105 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. RNAs originating from 12 normal donors were pooled in order to obtain at least 2μg per sample.

tag: To obtain PB Hematopoietic Stem Cells (HSC), 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10 g/kg/d for 5-6 days. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). HSCs purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.

tag: Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).

tag: MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin- cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34 cell population. Aliquots of sorted Lin-CD34-, Lin-CD34+ and Lin+CD34+ were reanalyzed by FacScan (Becton Dickinson, Franklin Lakes, NJ) to assess their purities which were 98.9±1%, 99.2± 0.8% and 98±1%, respectively.


title: SCC9 Ecad-1

description: passage +1

source_name: SCC9 Ecad-1


title: SW480_Input_2

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

institute: The University of Tokyo

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of SW480

hyb_protocol: The mixture containing 2 ug of the labeled DNA was directly used for hybridization.

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

data_processing: raw data

source_name: Colon cancer cell line

label_protocol: The digested cDNA was labeled using 50 U of terminal transferase (Roche, Penzberg, Germany) and 71.4 uM of Biotin-11-ddATP (PerkinElmer, Boston, MA, USA) at 37C for 2 hr

extract_protocol: DNA was extracted using QIAamp DNA Micro Kit (QIAGEN, Hilden, Germany). Genomic DNA was fragmented by sonication, ranging in size from 200 to 700 bp and denatured at 95degrees Celsius for 5 min. 30 ng of input DNA (whole genome) were amplified by in vitro transcription (IVT) randomly. After IVT, amplified cRNA was purified using an RNeasy Mini Kit (QIAGEN). Six hundred nanogram of cRNA were converted into double-strand cDNA with random primers using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). After single-stranded cDNA synthesis, 0.4 uM of T7-A18B primer was added and incubated at 70degrees Celsius for 6 min. Double-stranded cDNA was purified using a QIAquick PCR purification kit (QIAGEN). After 2 cycles of IVT and cDNA synthesis reactions were performed for target amplification, the labeling step was performed. Ten microgram of amplified cDNA was digested into 25-100 bp with 0.008 U of DNase I (Invitrogen), 1 x  One-Phor-All Buffer PLUS (Amersham), and 1.4 mM of CoCl2 by incubation at 37degrees Celsius for 8 min.


title: MC3T3 biological rep2

description: Gene expression data from Sorted Cells

source_name: Mouse osteoblast like cell line

tag: strain

value: Balb/c

value: MC3T3 culture


title: SW480_Input_1


title: SW480_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of SW480

extract_protocol: DNA was extracted using QIAamp DNA Micro Kit (QIAGEN, Hilden, Germany). Genomic DNA was fragmented by sonication, ranging in size from 200 to 700 bp and denatured at 95degrees Celsius for 5 min. A blocking solution containing 25 ul of protein A Sepharose (Amersham, NJ, USA), 2 ug of bacterial tRNA (SIGMA, St. Louis, MO, USA), and 10 ug of bovine serum albumin (BSA) in 400 ul of IP buffer (20 mM Tris-Cl; pH8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl), and an antibody solution containing 10 ug of anti 5-methylcytosine polyclonal antibody (Megabase Research Products, Lincoln NE, USA), 25 ul of protein A Sepharose, 2 ug of bacterial tRNA and 10 ug of BSA, and protease inhibitor cocktail (SIGMA) in 500 ul of IP buffer were preincubated by rotating at 4degrees Celsius overnight. Three microgram of DNA fragments were rotated in the blocking solution at 4degrees Celsius for 30 min. After centrifugation for 2 min at 2,000g, supernatant was added to the antibody solution and incubated at room temperature for 6 h. As a negative control, we prepared DNA fragments incubated with rabbit IgG or protein A Sepharose only, respectively. Antibody conjugated beads were washed with 500 ul of IP buffer for 5 min twice with rotation, followed by successive washes in high salt buffer (20 mM Tris-Cl; pH8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 300 mM NaCl) and in TE buffer twice. The beads were resuspended in 200 ul of elution buffer (25 mM Tris-Cl, 10 mM EDTA, 0.5% SDS, 5 mM DTT), and incubated at room temperature for 30 min by rotating and then incubated at 60degrees Celsius for 15 min. We repeated this elution step once more by rotating at room temperature for 15 min. Immunoprecipitation was repeated six times, and the IP DNA was combined and purified by MiniElute Reaction Cleanup Kit (QIAGEN, Crawley, UK) for amplification. Purified IP DNA and 30 ng of input DNA (whole genome) were amplified by in vitro transcription (IVT) randomly. After IVT, amplified cRNA was purified using an RNeasy Mini Kit (QIAGEN). Six hundred nanogram of cRNA were converted into double-strand cDNA with random primers using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). After single-stranded cDNA synthesis, 0.4 uM of T7-A18B primer was added and incubated at 70degrees Celsius for 6 min. Double-stranded cDNA was purified using a QIAquick PCR purification kit (QIAGEN). After 2 cycles of IVT and cDNA synthesis reactions were performed for target amplification, the labeling step was performed. Ten microgram of amplified cDNA was digested into 25-100 bp with 0.008 U of DNase I (Invitrogen), 1 x  One-Phor-All Buffer PLUS (Amersham), and 1.4 mM of CoCl2 by incubation at 37degrees Celsius for 8 min.


title: CML Lin-CD34+

source_name: Lineage-CD34+ cells purified from peripheral blood (PB) of CML patients at diagnosis and before treatment

tag: Leukemic cells were obtained from 12 chronic phase Ph+ CML patients at diagnosis and before treatment. Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).

tag: MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin- cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34 cell population. Aliquots of sorted Lin-CD34-, Lin-CD34+ and Lin+CD34+ were reanalyzed by FacScan (Becton Dickinson, Franklin Lakes, NJ) to assess their purities which were 99.2±0.6%, 98.8± 0.9% and 99±1%, respectively.


title: HCT116_Input_1

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of HCT116

label_protocol: The digested cDNA was labeled using 50 U of terminal transferase (Roche, Penzberg, Germany) and 71.4 uM of Biotin-11-ddATP (PerkinElmer, Boston, MA, USA) at 37degrees Celsius for 2 h


title: SCC9 Ecad+1

description: passage +1

source_name: SCC9 Ecad+1


title: HCT116_MeDIP_2

description: Methylated DNA immunoprecipitation-on-chip analysis of HCT116


title: MC3T3 biological rep1

description: Gene expression data from MC3T3 culture


title: Lin+CD34+

source_name: Lineage+CD34+ cells purified from peripheral blood of normal donors

tag: Normal samples were leukapheresis products from 12 healthy stem cell donors receiving recombinant human granulocyte colony-stimulating factor (G-CSF; Lenograstim, Sanofi-Aventis, Milan, Italy). The protocol was approved by the ethical committee of the University Hospital and each patient/donor gave written informed consent. Hemopoietic stem/progenitor cell purification and phenotypic analyses were performed as previously described (Lemoli RM et al., Br J Haematol, 2003; Lemoli RM et al., Blood, 1997). Aliquots of sorted Lin-CD34-, Lin-CD34+ and Lin+CD34+  were reanalyzed by FacScan (Becton Dickinson, Franklin Lakes, NJ) to assess their purities which were 98.9±1%, 99.2± 0.8% and 98±1%, respectively.


title: OP9 with 230-238 biological rep2

description: Gene expression data from OP9 cocultured with 230-238

source_name: Mouse bone marrow stroma

value: OP9 cocultured with 230-238


title: OP9 biological rep2

description: Gene expression data from OP9 culture

value: OP9 culture


title: SW480_MeDIP_1

hyb_protocol: The mixture containing 2 ug of the labeled DNA was directly used for hybridization.

label_protocol: The digested cDNA was labeled using 50 U of terminal transferase (Roche, Penzberg, Germany) and 71.4 μM of Biotin-11-ddATP (PerkinElmer, Boston, MA, USA) at 37°C for 2 h

extract_protocol: DNA was extracted using QIAamp DNA Micro Kit (QIAGEN, Hilden, Germany). Genomic DNA was fragmented by sonication, ranging in size from 200 to 700 bp and denatured at 95degrees Celsius for 5 min. A blocking solution containing 25 ul of protein A Sepharose (Amersham, NJ, USA), 2 ug of bacterial tRNA (SIGMA, St. Louis, MO, USA), and 10 ug of bovine serum albumin (BSA) in 400 ul of IP buffer (20 mM Tris–Cl; pH8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl), and an antibody solution containing 10 ug of anti 5-methylcytosine polyclonal antibody (Megabase Research Products, Lincoln NE, USA), 25 ul of protein A Sepharose, 2 ug of bacterial tRNA and 10 ug of BSA, and protease inhibitor cocktail (SIGMA) in 500 ul of IP buffer were preincubated by rotating at 4degrees Celsius overnight. Three microgram of DNA fragments were rotated in the blocking solution at 4degrees Celsius for 30 min. After centrifugation for 2 min at 2,000g, supernatant was added to the antibody solution and incubated at room temperature for 6 h. As a negative control, we prepared DNA fragments incubated with rabbit IgG or protein A Sepharose only, respectively. Antibody conjugated beads were washed with 500 ul of IP buffer for 5 min twice with rotation, followed by successive washes in high salt buffer (20 mM Tris–Cl; pH8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 300 mM NaCl) and in TE buffer twice. The beads were resuspended in 200 ul of elution buffer (25 mM Tris–Cl, 10 mM EDTA, 0.5% SDS, 5 mM DTT), and incubated at room temperature for 30 min by rotating and then incubated at 60degrees Celsius for 15 min. We repeated this elution step once more by rotating at room temperature for 15 min. Immunoprecipitation was repeated six times, and the IP DNA was combined and purified by MiniElute Reaction Cleanup Kit (QIAGEN, Crawley, UK) for amplification. Purified IP DNA and 30 ng of input DNA (whole genome) were amplified by in vitro transcription (IVT) randomly. After IVT, amplified cRNA was purified using an RNeasy Mini Kit (QIAGEN). Six hundred nanogram of cRNA were converted into double-strand cDNA with random primers using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). After single-stranded cDNA synthesis, 0.4 uM of T7-A18B primer was added and incubated at 70degrees Celsius for 6 min. Double-stranded cDNA was purified using a QIAquick PCR purification kit (QIAGEN). After 2 cycles of IVT and cDNA synthesis reactions were performed for target amplification, the labeling step was performed. Ten microgram of amplified cDNA was digested into 25–100 bp with 0.008 U of DNase I (Invitrogen), 1 x  One-Phor-All Buffer PLUS (Amersham), and 1.4 mM of CoCl2 by incubation at 37degrees Celsius for 8 min.

tag: cell line

value: Colon cancer cell line


title: HCT116_MeDIP_1


title: CML Lin-CD34-

source_name: Lineage-CD34- cells purified from peripheral blood (PB) of CML patients at diagnosis and before treatment

tag: Leukemic cells were obtained from 12 chronic phase Ph+ CML  patients at diagnosis and before treatment. Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).

tag: MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin- cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34 cell population. Aliquots of sorted Lin-CD34-, Lin-CD34+ and Lin+CD34+ were reanalyzed by FacScan (Becton Dickinson, Franklin Lakes, NJ) to assess their purities which were 99.2±0.6%, 98.8± 0.9% and 99±1%, respectively. Contamination of CD34+ cells in the CD34- cell population was ruled out by reverse transcription-polymerase chain reaction (RT-PCR) for CD34 mRNA .


title: OP9 with 230-238 biological rep1


title: NIH3T3 cells biological rep2

description: Gene expression data from cultured 3T3

source_name: Mouse embryonic fibroblast cell line

value: cultured 3T3


title: day 2-3 vs. sham

source_name: rat, AMI , 2days

tag: tissue

value: myocardium in border zone

tag: state

value: ischemia myocardium

value: Sprague Dawley

source_name: sham-control rat

value: myocardium

value: mixed normal myocardium from all sham-control rat


title: T24 cell line relative to normal diploid cell

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.

data_processing: Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the gProcessed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Normalized log10 ratio (Cy5/Cy3) was calculated using CGH-v4_95_Feb07 protocol of FE software.

source_name: Normal human diploid genomic DNA

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.

extract_protocol: Chromosomal DNA was isolated from BC cell lines using FlexiGene(QIAGEN) according manufacturer's protocol.

tag: sample type

value: normal human genomic DNA purchased from Promega

source_name: T24 genomic DNA

value: human bladder cancer T24


title: OP9 biological rep1

description: Gene expression data from OP9 culture

tag: cell type


title: NIH3T3 cells biological rep1

description: Gene expression data from cultured 3T3


title: J82 cell line relative to normal diploid cell

source_name: J82 genomic DNA

value: human bladder cancer J82


title: UMUC cell line relative to normal diploid cell

source_name: UMUC genomic DNA

value: human bladder cancer UMUC


title: ST172-T9M

status: Public on Jan 04 2010

city: Stanford

first: Lucinda

last: Thompson

address: Fairchild Bldg., D035, 299 Campus Dr

department: Microbiology and Immunology, School of Medicine

institute: Stanford University

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65057.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.46; Parameter Scan Time = 09:24:34; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45647; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.46; Parameter Scan Time = 09:24:34; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118782; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Strat. aRNA 4ug

label_protocol: not provided

extract_protocol: not provided

tag: Strat. aRNA 4ug

tag: LabeledExtract

source_name: ST172-T9M_4ug aRNA

tag: ST172-T9M_4ug aRNA


title: ST169-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65055.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.36; Parameter Scan Time = 09:12:41; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45634; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.36; Parameter Scan Time = 09:12:41; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118769; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST169-T9M_4ug aRNA

tag: ST169-T9M_4ug aRNA


title: ST179-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64977.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.75; Parameter Scan Time = 09:52:04; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43282; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.75; Parameter Scan Time = 09:52:04; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116416; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST179-T9M_4ug aRNA

tag: ST179-T9M_4ug aRNA