title: Gefitinib-treated_MCF10HER2_18hour

source_name: MCF-10HER-2 cell line, gefitinib, 18 hours


title: Gefitinib-treated_MCF10HER2_36hour

status: Public on Aug 24 2010

type: RNA

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

country: USA

institute: Karmanos Cancer Inst., Wayne State University

description:
The MCF-10HER-2 cell line is derived from the nontransformed breast epithelial cell line MCF-10A and is transduced to stably overexpress the HER-2 oncogene.
Replicate 1 of 1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF-10HER-2 cell line, gefitinib, 36 hours

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit.

growth_protocol: MCF-10HER-2 cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol: RNA was extracted every three hours from parallel cultures with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

treatment_protocol: Cells were treated with the addition of 0.5uM gefitinib to culture media for 45 hours total.

tag: cell line

tag: cell type

value: nontransformed breast epithelial cells stably overexpressing HER-2

tag: treatment

value: gefitinib

tag: treatment time

value: 36 hours


title: Gefitinib-treated_MCF10HER2_27hour

source_name: MCF-10HER-2 cell line, gefitinib, 27 hours

value: 27 hours


title: Gefitinib-treated_MCF10HER2_24hour

source_name: MCF-10HER-2 cell line, gefitinib, 24 hours

value: 24 hours


title: Gefitinib-treated_MCF10HER2_9hour

source_name: MCF-10HER-2 cell line, gefitinib, 9 hours

value: 9 hours


title: Gefitinib-treated_MCF10HER2_42hour

source_name: MCF-10HER-2 cell line, gefitinib, 42 hours

value: 42 hours


title: Gefitinib-treated_MCF10HER2_21hour

source_name: MCF-10HER-2 cell line, gefitinib, 21 hours

value: 21 hours


title: Gefitinib-treated_MCF10HER2_30hour

source_name: MCF-10HER-2 cell line, gefitinib, 30 hours

value: 30 hours


title: Gefitinib-treated_MCF10HER2_39hour

source_name: MCF-10HER-2 cell line, gefitinib, 39 hours

value: 39 hours


title: Gefitinib-treated_MCF10HER2_6hour

source_name: MCF-10HER-2 cell line, gefitinib, 6 hours

value: 6 hours


title: Gefitinib-treated_MCF10A_45hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 45 hours

growth_protocol: MCF-10A cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), insulin (5 µg/mL, and 10 ng/ml epidermal growth factor (EGF).

value: nontransformed breast epithelial cells

value: 45 hours


title: Gefitinib-treated_MCF10HER2_15hour

source_name: MCF-10HER-2 cell line, gefitinib, 15 hours

value: 15 hours


title: Gefitinib-treated_MCF10HER2_12hour

source_name: MCF-10HER-2 cell line, gefitinib, 12 hours

value: 12 hours


title: Gefitinib-treated_MCF10A_36hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 36 hours


title: Gefitinib-treated_MCF10A_39hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 39 hours


title: Gefitinib-treated_MCF10A_24hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 24 hours


title: Gefitinib-treated_MCF10HER2_0hour

source_name: MCF-10HER-2 cell line, untreated

value: 0 hours


title: Gefitinib-treated_MCF10A_30hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 30 hours


title: Gefitinib-treated_MCF10HER2_3hour

source_name: MCF-10HER-2 cell line, gefitinib, 3 hours

value: 3 hours


title: Gefitinib-treated_MCF10A_18hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 18 hours

value: 18 hours


title: Gefitinib-treated_MCF10A_33hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 33 hours

value: gefitinib

value: 33 hours


title: Gefitinib-treated_MCF10A_21hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 21 hours


title: Gefitinib-treated_MCF10A_27hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 27 hours

value: 27 hours


title: Gefitinib-treated_MCF10A_42hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 42 hours


title: Gefitinib-treated_MCF10A_15hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 15 hours


title: Gefitinib-treated_MCF10A_12hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 12 hours


title: Gefitinib-treated_MCF10A_3hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 3 hours


title: Control female 4360118017_R007_C008

city: New Lambton

first: Mathew

last: Cox

state: NSW

address: HMRI, John Hunter Hospital, Lookout Road

country: Australia

institute: University Of Newcastle

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio V3

source_name: whole blood

label_protocol: Standard Illumina miRNA hybridization protocol

extract_protocol: Peripheral blood collected in PAXgene blood RNA tubes. Frozen PAXgene blood RNA samples were thawed overnight at room temperature, centrifuged (4 minutes, 3,000g), and the supernatant discarded. The pellet was resuspended in 1ml TRIzol reagent (Invitrogen), briefly vortexed and homogenised. TRIzol RNA extraction was continued according to manufacturer’s instructions. Briefly, 200µl chloroform was added, mixed thoroughly, incubated for 2 minutes at room temperature and centrifuged (15 minutes, 12,000g, 4°C). The aqueous phase containing the RNA was removed and added to 500µl isoproanol, incubated for 10 minutes at room temperature and centrifuged (10 minutes, 12,000g, 4°C). The supernatant was removed and the RNA pellet washed in 1ml 75% ethanol and centrifuged (5 minutes, 7,500g, 4°C) (repeated once). The supernatant was removed and the RNA resuspended in 20µl water

tag: disease state

value: multiple sclerosis

tag: tissue

value: whole blood

tag: disease subtype

value: Control

tag: gender

value: female

tag: age at collection


title: Secondary progressive female 4360118017_R008_C009

value: Secondary progressive

value: Female

tag: age at disease onset

tag: edss


title: Relapsing remitting female 4360118017_R008_C001

value: Relapsing remitting


title: Primary progressive male 4360118017_R007_C004

value: Primary progressive

value: Male


title: Gefitinib-treated_MCF10A_6hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 6 hours

value: nontransformed breast epithelial cells

value: 6 hours


title: Control male 4360118017_R007_C003


title: Control female 4360118017_R008_C002


title: Primary progressive male 4360118017_R008_C012


title: Secondary progressive female 4360118017_R008_C011


title: Control female 4360118017_R008_C008


title: Gefitinib-treated_MCF10A_0hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, untreated

value: 0 hours


title: Relapsing remitting female 4360118017_R007_C005


title: Relapsing remitting female 4360118017_R007_C009


title: Primary progressive male 4360118017_R008_C006


title: Primary progressive male 4360118017_R008_C010


title: Secondary progressive male 4360118017_R008_C003


title: Control male 4360118017_R008_C004


title: Secondary progressive male 4360118017_R008_C005


title: Control female 4360118017_R007_C012


title: Secondary progressive female 4360118017_R007_C002


title: Relapsing remitting female 4360118017_R007_C011


title: Secondary progressive male 4360118017_R007_C010


title: Relapsing remitting female 4360118017_R008_C007


title: Secondary progressive female 4360118017_R007_C001


title: Gefitinib-treated_MCF10A_9hour

description: Replicate 1 of 1.

source_name: MCF-10A cell line, gefitinib, 9 hours

value: 9 hours


title: Secondary progressive female 4360118017_R006_C009


title: Secondary progressive female 4360118017_R007_C007


title: Secondary progressive female 4360118017_R007_C006


title: Relapsing remitting female 4360118017_R006_C008


title: Control male 4360118017_R006_C007


title: Relapsing remitting female 4360118017_R006_C005


title: Primary progressive male 4360118017_R006_C006


title: Primary progressive male 4360118017_R006_C002


title: Relapsing remitting female 4360118017_R006_C012


title: Secondary progressive male 4360118017_R006_C003


title: Primary progressive female 4360118017_R006_C004


title: Control female 4360118017_R006_C011


title: Control female 4360118017_R006_C010


title: Control male 4360118017_R006_C001


title: Relapsing remitting male 4360118017_R005_C001


title: Primary progressive female 4360118017_R005_C010


title: Control male 4360118017_R005_C004


title: Secondary progressive female 4360118017_R005_C007


title: Secondary progressive female 4360118017_R005_C006


title: Relapsing remitting female 4360118017_R005_C002


title: Control female 4360118017_R005_C011


title: Relapsing remitting male 4360118017_R004_C007


title: Relapsing remitting female 4360118017_R005_C003


title: Control male 4360118017_R004_C009


title: Control female 4360118017_R005_C005


title: Relapsing remitting female 4360118017_R005_C008


title: Relapsing remitting female 4360118017_R004_C006


title: Control female 4360118017_R005_C009


title: Control female 4360118017_R004_C008


title: Primary progressive female 4360118017_R005_C012


title: Relapsing remitting female 4360118017_R004_C005


title: Xpc-/- testis benzo(a)pyrene 5

city: Maastricht

first: Nicole

last: Verhofstad

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description: The 3 pooled reference samples are not among the experimental samples

hyb_protocol: On the basis of incorporation rates, 10 pmol of Cy5 and Cy3 labelled samples were simultaneously hybridized on Agilent 22K Mouse microarrays. Afterwards, slides washed and dried with N2 gas.

scan_protocol: Slides were scanned on a Genepix® 4000B Microarray Scanner.

data_processing: The images obtained were processed with Imagene 8.0.1 software. Microarray spot signal data were normalized in R, using natural log-transformation, quantile normalization, correction of the sample spot signal for the corresponding reference spot signal and averaging data from replicate spots. Normalized values are presented as 'normalized Cy5 ln signal' (the Cy5 signal has been corrected for the Cy3 signal, which has been corrected for the signal under each other).

organism: Mus musculus

source_name: Xpc-/-, testis, benzo(a)pyrene

label_protocol: Total RNA was labelled by using the Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies according to the manufacturer's protocol.

growth_protocol: Mice were bred and housed under specific pathogen-free conditions in a 12-hour light-dark cycle. They received food and water ad libitum.

extract_protocol: Total RNA was isolated using TRIzol® Reagent according to manufacturer's protocol, with slight modifications.

treatment_protocol: Mice were exposed to a single dose of benzo(a)pyrene (13 mg/kg bw) by oral gavage, and were sacrificed 4 days after exposure. Control mice received the solvent sunflower oil.

tag: strain

value: male

value: whole testis

source_name: common reference pool (3 samples, C57BL/6, testis, control)


title: Xpc-/- testis benzo(a)pyrene 4


title: Control female 4360118017_R004_C004


title: Control male 4360118017_R004_C012


title: Primary progressive male 4360118017_R004_C003


title: Primary progressive male 4360118017_R004_C002


title: Xpc-/- testis benzo(a)pyrene 3


title: Control male 4360118017_R004_C010


title: Secondary progressive female 4360118017_R004_C011


title: Relapsing remitting female 4360118017_R003_C008


title: Primary progressive female 4360118017_R003_C009


title: Secondary progressive female 4360118017_R004_C001


title: Control female 4360118017_R003_C007


title: S.pombe-gH2A-Sphase-Input

type: genomic

city: La Jolla

first: Sophie

last: Rozenzhak

state: CA

address: 10550 N Torrey Pines Rd MB3

institute: The Scripps Research Institute

description: Input on S-phase synchronized S. pombe cells

hyb_protocol: DNA (7.5ug) was hybridized overnight to the S. pombe Tiling 1.0FR Array. Hybridization and scanning of samples was performed using standard Affymetrix protocols and reagents from the GeneChIP Hybridization, Wash and Stain Kit (P/N 900720).

scan_protocol: Chips were screened on the Affymetrix GeneChIP Scanner 30007G with default settings and a target intensity of 250 for scaling

data_processing:
Data analysis was performed using the Model-based Analysis of Tiling arrays (MAT) algorithm (Johnson, WE e al, PNAS,103, 2006). The Input sample was used as a control. Parameters used for analysis were: Bandwidth = 200; MaxGap=200; MinProbe=11; p-value cutoff=1e-5.
SR200.bed file contains the coordinates of all the statistically significant regions called by MAT analysis

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: gH2A ChIP INPUT DNA from Sphase synchronized S. pombe cells

label_protocol: DNA (7.5ug) was fragmented and labeled using the GeneChIP WT Double-Stranded DNA Terminal Kit ( P/N 900812). Samples were checked by gel-shift assay to assess labeling efficiency.

extract_protocol: Wildtype S. pombe cells were synchronized in S phase  by using the cdc25-22 block and release method (Forsburg, SL Curr Protoc Mol Biol Chapter13, 2003).  ChIP experiments were performed as described (Du,L-L et al, Genes Dev, 2006) with the following modifications. Cleared lysates were incubated with protein G Dynabeads (Invitrogen) pre-bound to anti-gammaH2A antibody (Courtesy of C.Redon). For a control sample,  10% of the Input DNA was saved.  DNA was purified using the QIAquick PCR Purification Kit (Quiagen). ChIP enrichment relative to the input was quantitated using qPCR. Chip and Input DNA samples were amplified by random-priming PCR using a standard GeneChIP ChIP-on chip protocol from Affymetrix (available at www.affymetrix.com/support). The linearity of amplification was confirmed by comparing qPCR values with the values from the unamplified samples. DNA was quantitated on the Nanodrop ND-1000.  DNA (7.5ug) was fragmented and labeled using the GeneChIP WT Double-Stranded DNA Terminal Kit ( P/N 900812).

tag: genotype

value: wt with Donorless MT locus:h90 (h+) mat1P mat2,3:leu2  leu1-32  cdc25-22


title: S.pombe-gH2A-Sphase-ChIP

description: gamma H2A ChIP on S-phase synchronized S. pombe cells

source_name: gH2A ChIP DNA from Sphase synchronized S. pombe cells


title: Control female 4360118017_R003_C006


title: Relapsing remitting female 4360118017_R003_C005


title: Xpc-/- testis control 4

source_name: Xpc-/-, testis, control


title: Xpc-/- testis control 5


title: Xpc-/- testis control 3


title: Xpc-/- testis control 2


title: Xpc-/- testis control 1


title: C57BL/6 testis benzo(a)pyrene 3

source_name: C57BL/6, testis, benzo(a)pyrene


title: Control female 4360118017_R003_C004


title: Xpc-/- testis benzo(a)pyrene 1


title: C57BL/6 testis control 5

source_name: C57BL/6, testis, control


title: C57BL/6 testis benzo(a)pyrene 2


title: C57BL/6 testis benzo(a)pyrene 5


title: C57BL/6 testis benzo(a)pyrene 4


title: Control female 4360118017_R003_C003


title: C57BL/6 testis control 4


title: C57BL/6 testis benzo(a)pyrene 1


title: Xpc-/- testis benzo(a)pyrene 2


title: C57BL/6 testis control 3


title: Primary progressive female 4360118017_R003_C002


title: Control female 4360118017_R003_C010


title: Relapsing remitting female 4360118017_R003_C001


title: Relapsing remitting female 4360118017_R003_C012


title: root tip, no treatment, at 246 h, replicate 2

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: Gene expression data from root tips

hyb_protocol: Following fragmentation, 15 µg of biotin-labeled cRNA were hybridized to GeneChip Poplar Genome Array for 16 h at 45°C. GeneChips were then washed using an Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

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

data_processing: The Robust Multichip Average (RMA) summary algorithm as implemented in GeneSpring GX 7.3 (Agilent Technologies Inc.) was used to generate and normalize raw gene expression data from probe intensities. Genespring was also used to filter out normalized expression values when not showing present calls in all replicate measurements of at least one condition. To identify genes whose expression differed upon Al treatment at each time point, a Student’s t-test was performed in R (http://www.r-project.org).

label: Biotin

organism: Populus tremula

source_name: root tips

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 µg total RNA (Affymetrix GeneChip Expression Analysis Technical Manual 2005).

growth_protocol: Aspen cuttings (clone Birmensdorf) were cultivated in solution culture prepared in modified Magenta vessels (GA-7). Teflon-racks, placed on the floor of the vessels, supported a 1190 µm nylon mesh (Sefar) as substrate for the plants and two glass slides with a 5 µm grid (N°5, Boraglas) used as a reference to measure root growth. The modified Magenta vessels were sterilized by autoclaving, and filled with 120 ml of autoclaved 1/6 MS solution (pH 4.0) containing 50 nM indol-3-butyric acid (IBA) to induce and synchronize root formation. In each vessel, four cuttings with 3−4 internodes and 1−2 apical leaves were inserted into the mesh such that the roots formed between the wall of the vessel and the glass slide (slotted 1 cm away of the vessel wall). After one day, the nutrient solution was replaced with fresh 1/6 MS medium (pH 4.0) without IBA. The cuttings were incubated without aeration in a climate chamber maintained at 20 ± 2°C with 16 h light / 8 h darkness period (Osram Dulux L 36W/840 color white, Osram) for 20 d. The nutrient solution was exchanged twice a week.

extract_protocol: Following treatment, the roots were separated from the shoots and rinsed in 1/6 MS pH 4.0. The first centimeter of each root was collected, and all the roots processed per plant were transferred to a sterile 1.5 ml tube, frozen in liquid nitrogen, and stored at −80°C until RNA extraction. Total RNA from the root tips was isolated with the Agilent Total RNA Isolation Mini-Kit (Agilent Technologies) according to the manufacturer’s instructions. The concentration of total RNA was determined with a Nanodrop ND-1000 spectrophotometer and the integrity of the RNA was determined with the Eukaryote Total RNA Nano Assay (Agilent Technologies) using the 2100 Agilent Bioanalyzer. Only RNAs with a 260 nm / 280 nm ratio between 1.8 and 2.1 and a RNA integrity number between 7 and 10 were further processed.

treatment_protocol: After 20 d of incubation, when the cuttings have formed 5−15 adventitious roots, the nutrient solution was replaced with treatment solution composed of autoclaved 1/6 MS medium (pH 4.0) supplemented with no or 500 µM AlCl3 for 6 h, 54 h, and 246 h. For each treatment period, three solution cultures, each containing four plants were established to allow three independent plants per treatment to be sampled.

tag: time point


title: C57BL/6 testis control 1


title: Relapsing remitting female 4360118017_R002_C009


title: Control male 4360118017_R002_C007


title: root tip, no treatment, at 246 h, replicate 1

description: Gene expression data from root tips


title: root tip, no treatment, at 246 h, replicate 3

description: Gene expression data from root tips


title: root tip, no treatment, at 54 h, replicate 1

description: Gene expression data from root tips


title: Secondary progressive female 4360118017_R002_C006


title: root tip, Al treated, at 246 h, replicate 3

description: Gene expression data from root tips

value: 500 µM AlCl3


title: root tip, Al treated, at 54 h, replicate 1

description: Gene expression data from root tips


title: 848 10.1.07 Jejunal Strip

city: Davis

first: William

last: Hu

address: 451 Health Science Dr.

department: Medical Microbiology & Immunology

institute: UC Davis

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: dChip

organism: Macaca mulatta

source_name: Jejunal Strip Post SIVsmE660 Challenge

label_protocol: Affymetrix

extract_protocol: Qiagen

value: Jejunum

tag: status

value: Post SIVsmE660 Challenge


title: C57BL/6 testis control 2


title: root tip, Al treated, at 54 h, replicate 2

description: Gene expression data from root tips


title: Alloxan induced diabetes in heart of conscious dogs_sample 1111

city: Valhalla

first: Caroline

last: Ojaimi

state: NY

institute: New York Medical College

description: Alloxan-induced diabetes in conscious dogs

hyb_protocol: Hybridiation was performed as recommended by affymetrix

scan_protocol: the samples were subsequently processed and scanned according to the Affymetrix instructions

organism: Canis lupus familiaris

source_name: Cardiac tissues

label_protocol: Affymetrix labeling protocol was used.

extract_protocol: RNA isolated using Trizol reagents

tag: weight

value: cardiac cells


title: root tip, no treatment, at 54 h, replicate 2

description: Gene expression data from root tips


title: root tip, Al treated, at 54 h, replicate 3

description: Gene expression data from root tips


title: 870 8.6.07 Jejunal Strip

source_name: Jejunal Strip Pre SIV smE660 Challenge

value: Pre SIV smE660 Challenge


title: 846 10.1.07 Jejunal Strip


title: Control male 4360118017_R002_C005

value: multiple sclerosis

value: whole blood

value: Control


title: 858 8.6.07 Jejunal Strip


title: root tip, no treatment, at 54 h, replicate 3

description: Gene expression data from root tips


title: 847 10.3.07 Jejunal Strip


title: Alloxan induced diabetes in heart of conscious dogs_Sample 0294


title: 848 8.8.07 Jejunal Strip


title: Alloxan induced diabetes in heart of conscious dogs_Sample 1087


title: root tip, no treatment, at 6 h, replicate 3

description: Gene expression data from root tips

value: 6 h


title: root tip, Al treated, at 246 h, replicate 2

description: Gene expression data from root tips


title: Control female 4360118017_R002_C004

value: Female


title: PR male 4360118017_R002_C002

value: PR

value: Male


title: Control male 4360118017_R002_C012


title: root tip, no treatment, at 6 h, replicate 2

description: Gene expression data from root tips


title: Alloxan induced diabetes in heart of conscious dogs_Sample 0292


title: root tip, no treatment, at 6 h, replicate 1

description: Gene expression data from root tips


title: root tip, Al treated, at 6 h, replicate 3

description: Gene expression data from root tips


title: Primary progressive male 4360118017_R002_C010

value: Primary progressive


title: Secondary progressive female 4360118017_R002_C011

value: Secondary progressive


title: Primary progressive male 4360118017_R002_C001


title: Relapsing remitting female 4360118017_R003_C011

value: Relapsing remitting


title: root tip, Al treated, at 6 h, replicate 2

description: Gene expression data from root tips


title: 847 8.8.07 Jejunal Strip


title: Primary progressive male 4360118017_R002_C003


title: RAW_RL_day5

city: Boston

first: Parul

last: Sharma

state: MA

address: 320 Longwood Ave

department: Orthopedic Surgery

institute: Children's Hospital, Boston

description: Gene expression data from RAW cells cultured for 5 days with RANKL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.this was done at the Harvard Microarray core facility.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A at the Harvard Microarray core facility

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

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

growth_protocol: The cells were grown in Alpha MEM medium containing 10%FBS and 100u/ml of pennicilin and streptomycin at 37C, in 5%CO2.

extract_protocol: Total RNA extraction was performed using the Qiagen RNEasy kit.

treatment_protocol: The cells were treated with or without RANKL prepared in serum free alphaMEM on day 0 and day 3 and the RNA extracted on day 1, 2, 3, 4, and 5.

value: multi-nuclear

tag: protocol


title: RAW_RL_day5_rep2

description: Gene expression data from RAW cells cultured for 5 days with RANKL, replicate for 5 days RANKL treatment

tag: cell line


title: A375M2, thick deformable collagen, H1152, rep1

city: London

first: Chris

last: Marshall

address: 237 Fulham Road

department: Cell and Molecular Biology

country: United Kingdom

institute: Institute of Cancer Research

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with H1152
0606_VSM25_H_A375_con_H1152_r1_3.CEL

hyb_protocol: cRNA were hybridized to Affymetrix GeneChip HGU133plus2 arrays using the standard Affymetrix protocol.

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

data_processing: Data were processed using R/Bioconductor.  The RMA (Robust Multichip Average) expression measure was calculated for each probe set using the Affy package's “rma” function with default settings.

source_name: melanoma cells extracted from collagen I

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

growth_protocol: Cells were plated on rigid or deformable matrices.

extract_protocol: Trizol extraction was performed according to the manufacter´s instructions followed by purification with quiagen RNAeasy columns.

treatment_protocol: Rounded cells plated on deformable matrices were treated with actomyosin contractility inhibitors or protease inhibitors that increased contractility.

tag: tumour type

value: melanoma

tag: cell type

tag: cell morphology

value: rounded

tag: matrix

value: thick deformable


title: RAW_RL_day4_rep2

description: Gene expression data from RAW cells cultured for 4 days with RANKL, replicate for 4 day RANKL treatment


title: A375M2, thick deformable collagen, Y27632, rep2

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with Y27632
0506_VSM14_H_A375_con_Y27632_r2.CEL

tag: treatment


title: RAW_RL_day4

description: Gene expression data from RAW cells cultured for 4 days with RANKL


title: Control male 4360118017_R001_C008

tag: disease state

tag: tissue

tag: disease subtype


title: A375M2, thick deformable collagen, Y27632, rep1

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with Y27632
0506_VSM13_H_A375_con_Y27632_r1.CEL


title: Control female 4360118017_R001_C009

tag: gender

tag: age at collection


title: A375M2, thick deformable collagen, H1152, rep3

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with H1152
0606_VSM27_H_A375_con_H1152_r3_2.CEL


title: A375M2, thick deformable collagen, Y27632, rep3

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with Y27632
0506_VSM15_H_A375_con_Y27632_r3.CEL


title: A375M2, thick deformable collagen, blebbistatin, rep3

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with Blebbistatin
0506_VSM12_H_A375_coll_bleb2_r3.CEL

value: blebbistatin


title: Spleen CD8_ID_3wks_rep3

city: Oxford

first: Lian

middle: Ni

last: Lee

address: Peter Medawar Building, South Parks Road

department: Nuffield Dept of Medicine

institute: University of Oxford

description: replicate 3

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value). Both non-normalized and normalized (qspline) data were generated for each sample.

source_name: Spleen CD8 T cells

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

growth_protocol: Groups of 7-8 BalbC mice at 6-8 weeks of age

extract_protocol: CD8 T cells were positively selected from lungs or spleens of each group using CD8 MacBeads (Miltenyi). RNA was extracted in Trizol and purified using Qiagen Rneasy MicroRNA kit according to manufacturer's instructions. Quality control was performed using Agilent Bioanalyzer

treatment_protocol: Mice were vaccinated with single immunization of 50µl containing 2 x 10E9 viral particles of Ad85A per mouse via intransal (IN) or intradermal (ID) route 3 weeks prior to RNA isolation.

tag: strain

value: Balb/c

tag: age

value: 11 weeks

tag: immunization route

value: intra-dermal (ID)

value: Spleen

tag: time post-immunization

value: 3 weeks


title: A375M2, thick deformable collagen, H1152, rep2

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with H1152
0606_VSM26_H_A375_con_H1152_r2_3.CEL


title: A375M2, thick deformable collagen, blebbistatin, rep2

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with Blebbistatin
0506_VSM11_H_A375_coll_bleb2_r2.CEL


title: Spleen CD8_ID_3wks_rep2

description: replicate 2


title: A375M2, thick deformable collagen, blebbistatin, rep1

description:
Gene expression data from A375M2 cells in a thick deformable matrix and treated with Blebbistatin
0506_VSM10_H_A375_coll_bleb2_r1_2.CEL


title: Control female 4360118017_R001_C007

source_name: whole blood

value: multiple sclerosis

value: whole blood

value: Control


title: RAW_RL_day2

description: Gene expression data from RAW cells cultured for 2 days with RANKL

value: mononuclear


title: root tip, Al treated, at 6 h, replicate 1

description: Gene expression data from root tips

value: 500 µM AlCl3

tag: time point

value: 6 h


title: Relapsing remitting female 4360118017_R001_C005

value: Relapsing remitting

value: Female

tag: age at disease onset

tag: edss


title: A375P, thick deformable collagen, rep3

description:
Gene expression data from A375P cells in a thick deformable matrix
0506_VSM9_H_A375_coll_bleb1_r3.CEL

tag: tumour type

value: melanoma

value: elongated


title: Spleen CD8_IN_3wks_rep3

description: replicate 3

value: intranasal (IN)


title: RAW_CTRL_day5

description: Gene expression data from RAW cells cultured for 5 days

tag: cell type

tag: protocol

value: RAW cells cultured for 5 days

tag: cell line


title: Control male 4360118017_R001_C004

value: Male


title: A375P, thick deformable collagen, rep2

description:
Gene expression data from A375P cells in a thick deformable matrix
0506_VSM8_H_A375_coll_bleb1_r2.CEL

tag: cell morphology

tag: treatment

tag: matrix

value: thick deformable


title: Control male 4360118017_R001_C003

tag: disease state

tag: tissue

tag: disease subtype


title: A375P, thick deformable collagen, rep1

description:
Gene expression data from A375P cells in a thick deformable matrix
0506_VSM7_H_A375_coll_bleb1_r1.CEL


title: Control female 4360118017_R002_C008

tag: gender

tag: age at collection


title: Relapsing remitting female 4360118017_R001_C002


title: Control female 4360118017_R001_C006


title: RAW_RL_day1

description: Gene expression data from RAW cells cultured for 1day with RANKL

value: RAW cells cultured for 1 day with RANKL


title: Spleen CD8_ID_3wks_rep1

description: replicate 1

tag: strain

value: Balb/c

tag: age

value: 11 weeks

tag: immunization route

value: intra-dermal (ID)

value: Spleen


title: RAW_CTRL_day4_rep2

description: Gene expression data from RAW cells cultured for 4days, replicate for day4

value: RAW cells cultured for 4 days, replicate for day 4


title: RAW_CTRL_day3_rep2

description: Gene expression data from RAW cells cultured for 3 days, replicate for day 3

value: mononuclear


title: root tip, Al treated, at 246 h, replicate 1

description: Gene expression data from root tips

value: 500 µM AlCl3

tag: time point


title: A375M2, thin rigid collagen, rep3

description:
Gene expression data from a375m2 cells in a thin rigid matrix
0506_VSM6_H_A375_rig_r3.CEL

value: rounded

value: thin rigid


title: A375M2, thin rigid collagen, rep1

description:
Gene expression data from A375M2 cells in a thin rigid matrix
0506_VSM4_H_A375_rig_r1.CEL


title: Control male 4360118017_R001_C012

value: multiple sclerosis

value: whole blood

value: Control


title: Spleen CD8_IN_3wks_rep2

description: replicate 2

value: intranasal (IN)

tag: time post-immunization

value: 3 weeks


title: Lung CD8_ID_3wks_rep2

description: replicate 2

source_name: Lung CD8 T cells

value: Lung


title: Lung CD8_ID_3wks_rep3

description: replicate 3


title: Spleen CD8_IN_3wks_rep1

description: replicate 1


title: A375M2, thin rigid collagen, rep2

description:
Gene expression data from a375m2 cells in a thin rigid matrix
0506_VSM5_H_A375_rig_r2.CEL

tag: tumour type

value: melanoma


title: RAW_CTRL_day3

description: Gene expression data from RAW cells cultured for 3 days

tag: cell type

value: RAW cells cultured for 3 days


title: Lung CD8_ID_3wks_rep1

description: replicate 1

value: Balb/c


title: A375M2, thick deformable collagen, rep3

description:
Gene expression data from A375M2 cells in a thick deformable matrix
0506_VSM3_H_A375_def_r3.CEL

value: thick deformable


title: Lung CD8_IN_3wks_rep3

description: replicate 3

value: 11 weeks


title: Control male 4360118017_R001_C011

value: Male


title: Relapsing remitting male 4360118017_R001_C001

value: Relapsing remitting

tag: age at disease onset

tag: edss


title: Primary progressive female 4360118017_R001_C010

value: Primary progressive

value: Female


title: RAW_CTRL_day2_rep2

description: Gene expression data from RAW cells cultured for 2days, replicate for day2

value: mononuclear

tag: protocol

value: RAW cells cultured for 2 days, replicate for day 2

tag: cell line


title: RAW_CTRL_day2

description: Gene expression data from RAW cells cultured for 2 days

value: RAW cells cultured for 2 days


title: A375M2, thick deformable collagen, rep2

description:
Gene expression data from A375M2 cells in a thick deformable matrix
0506_VSM2_H_A375_def_r2.CEL

tag: cell morphology

value: rounded

tag: treatment

tag: matrix


title: Lung CD8_IN_3wks_rep2

description: replicate 2

tag: tissue


title: Lung CD8_IN_3wks_rep1

description: replicate 1


title: A375M2, thick deformable collagen, rep1

description:
Gene expression data from A375M2 cells in a thick deformable matrix
0506_VSM1_H_A375_def_r1.CEL


title: RAW_CTRL_day1

description: Gene expression data from RAWcells cultured for 1Dayi.e.24 hours

value: RAW cells cultured for 1 day, i.e. 24 hours


title: Fibroblast cell line (NHDF3975)

status: Public on Aug 23 2010

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

description: Gene expression data from NHDF fibroblasts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on human expression arrays

scan_protocol: Gene chips were analyzed using GeneChip® Scanner 3000.

data_processing:
The raw data was processed using the RMA algorithm and was implemented using R (Bioconductor).
The data is presented as a summary of the highest confidence probesets for each given RefSeq identifier. (See Materials and Methods, Chin, et al. Cell Stem Cell, 2009)

source_name: NHDF 3975 fibroblasts

growth_protocol: Cell lines were cultured in hESC cell media for hESC and hiPSC lines (Lowry, et al. PNAS, 2008) and DMEM for the fibroblast line.

extract_protocol: Total RNA was extracted using Stratagene's Lysis Buffer and extracted according to the manufacturer's instructions.

treatment_protocol: Reprogrammed Cell lines were treated as described in Lowry, et al. (PNAS, 2008)

value: fibroblast

value: NHDF 3975


title: fibroblast P4-1

city: Rotterdam

first: W

middle: Edward

last: Visser

address: Dr Molewaterplein 50

department: Internal Medicine

institute: Erasmus Medical Center

description: Gene expression from patients cultured with 1 nM T3

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing

data_processing: Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.

source_name: patient P4 fibroblasts, cultured with 1 nM T3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.

treatment_protocol: Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.

value: skin fibroblasts

tag: condition

value: MCT8 mutation


title: fibroblast P2-1

source_name: patient P2 fibroblasts, cultured with 1 nM T3


title: RAW_RL_day2_rep2

description: Gene expression data from RAW cells cultured for 2 days with RANKL, replicate for 2 day RANKL treatment


title: fibroblast P3-1

source_name: patient P3 fibroblasts, cultured with 1 nM T3


title: fibroblast P4-10

description: Gene expression from patients cultured with 10 nM T3

source_name: patient P4 fibroblasts, cultured with 10 nM T3


title: fibroblast P3-0

description: Gene expression from patients cultured with 0 nM T3

source_name: patient P3 fibroblasts, cultured with 0 nM T3


title: fibroblast P1-1

source_name: patient P1 fibroblasts, cultured with 1 nM T3


title: fibroblast C3-1

description: Gene expression from controls cultured with 1 nM T3

source_name: control C3 fibroblasts, cultured with 1 nM T3

value: normal


title: fibroblast C3-0

description: Gene expression from controls cultured with 0 nM T3

source_name: control C3 fibroblasts, cultured with 0 nM T3


title: fibroblast P2-0

source_name: patient P2 fibroblasts, cultured with 0 nM T3


title: fibroblast P3-10

source_name: patient P3 fibroblasts, cultured with 10 nM T3


title: 24H_PS

city: Marseille

first: Isabelle

last: Lesur Kupin

address: 163 av. de Luminy - case 928

department: Bioinformatics

country: France

institute: INSERM U928

description:
RNA trizol extraction:
Incubate the homogenized samples for 5 minutes at 15 to 30oC to permit the complete dissociation of nucleoprotein complexes.Add 0.2 ml of chloroform per 1 ml of TRIzol® Reagent.Cap sample tubes securely.Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30oC for 2 to 3 minutes.Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8oC.Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase.The volume of the aqueous phase is about 60% of the volume of TRIzol® Reagent used for homogenization.
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired.Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol.Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol® Reagent used for the initial homogenization.Incubate samples at 15 to 30oC for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8oC.The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
Remove the supernatant.Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol® Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8oC.
At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes).Do not dry the RNA by centrifugation under vacuum.It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility.Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10Â minutes at 55 to 60oC.(Avoid SDS when RNA will be used in subsequent enzymatic reactions.) RNA can also be redissolved in 100% formamide (deionized) and stored at -70oC.

hyb_protocol: cDNA were designed and prepared as described in J Immunol. 2004 Nov 15;173(10):6109-18. A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models. Hybridization protocol is also published in DNA microarrays: Gene expression applications » B. Jordan(ed.), Springer-Verlag Berlin Heidelberg Newyork, ISBN: 3-540-41508-4- chapter 4  pp:80-82.

scan_protocol: Image acquisition was performed with a Fuji BAS 1500 system.

data_processing: Hybridation signals were quantified using the Bzscan2 software. All images were carefully inspected and spots with overestimated intensities due to neighborhood effects were manually excluded. We used the NylonArray library for R locally developped by A. Bergon and D. Puthier. This package contains functions to perform diagnosis and normalization of nylon microarray data. The sample datasets were corrected for neighborhood effects and local background as described by F. Lopez et al. Quantile normalization was applied to sample data to correct for global intensity and dispersion. A each time-point, gene expressions in control samples (physiological serum injection) were substracted from  gene expression in OA samples.

label: α-dCTP 33P

source_name: lung, physiological serum , incubation 24H

label_protocol:
cDNA were designed and prepared as described in J Immunol. 2004 Nov 15;173(10):6109-18. A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models.
Labelling protocol is also published in DNA microarrays: Gene expression applications » B. Jordan(ed.), Springer-Verlag Berlin Heidelberg Newyork, ISBN: 3-540-41508-4- chapter 4  pp: 78-80.

growth_protocol: Mices were housed in a specific pathogen-free animal facility. All experimental procedures involving animals were approved by the veterinary office of the Ministry of Agriculture, France (authorization number: 13-27).

extract_protocol: Total RNA from lung was extracted using TRIzol reagent (Invitrogen, #15596-026). The quality of RNA was confirmed on a 1% denaturing agarose gel, and the concentration of RNA was dertermined by reading absorbance at 260/280 nm.

treatment_protocol: Femelle C57Bl/6J mice were anesthetized with 5% Xylazine  20% Ketamine (0,1ml/10g). We injected 20 µl of oleic acid (1,2µl/g body weight, sigma #27728-1L-R) in the mouse. Administration of physiological serum and OA was done through the tail vein with a 0.3-ml insulin syringe (BD #320837).

tag: gender

value: female

value: 7 weeks old

value: a whole lung


title: fibroblast P2-10

source_name: patient P2 fibroblasts, cultured with 10 nM T3


title: 18H_PS

description:
RNA trizol extraction:
Incubate the homogenized samples for 5 minutes at 15 to 30oC to permit the complete dissociation of nucleoprotein complexes.Add 0.2 ml of chloroform per 1 ml of TRIzol® Reagent.Cap sample tubes securely.Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30oC for 2 to 3 minutes.Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8oC.Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase.The volume of the aqueous phase is about 60% of the volume of TRIzol® Reagent used for homogenization.
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired.Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol.Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol® Reagent used for the initial homogenization.Incubate samples at 15 to 30oC for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8oC.The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
Remove the supernatant.Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol® Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8oC.
At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes).Do not dry the RNA by centrifugation under vacuum.It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility.Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10Â minutes at 55 to 60oC.(Avoid SDS when RNA will be used in subsequent enzymatic reactions.) RNA can also be redissolved in 100% formamide (deionized) and stored at -70oC.

This sample consists of two replicates.

source_name: lung, physiological serum , incubation 18H

tag: strain


title: fibroblast C1-1

source_name: control C1 fibroblasts, cultured with 1 nM T3


title: 3H_PS

source_name: lung, physiological serum , incubation 3H

tag: age


title: fibroblast P1-10

source_name: patient P1 fibroblasts, cultured with 10 nM T3


title: fibroblast C2-0

source_name: control C2 fibroblasts, cultured with 0 nM T3


title: fibroblast C2-10

description: Gene expression from controls cultured with 10 nM T3

source_name: control C2 fibroblasts, cultured with 10 nM T3


title: fibroblast P1-0

source_name: patient P1 fibroblasts, cultured with 0 nM T3


title: 1H30_PS

source_name: lung, physiological serum , incubation 1H30


title: fibroblast P4-0

source_name: patient P4 fibroblasts, cultured with 0 nM T3


title: fibroblast C1-10

source_name: control C1 fibroblasts, cultured with 10 nM T3


title: fibroblast C1-0

source_name: control C1 fibroblasts, cultured with 0 nM T3


title: Pglyrp4_DSS_5

city: Gary

first: Roman

last: Dziarski

state: IN

address: 3400 Broadway

institute: Indiana University School of Medicine-Northwest

hyb_protocol: The hybridization was done at the Indiana University School of Medicine Center for Medical Genomics core facility using the protocols provided by Affymetrix GeneChip® Technical Manual. Following fragmentation labeled DNA was hybridized for 17 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The scanning was done at the Indiana University School of Medicine Center for Medical Genomics core facility using standard protocols provided by Affymetrix GeneChip® Technical Manual.

data_processing: The hybridization intensity data were analyzed with Partek Genomics Suite using defaults for RMA, which includes quantile normalization, RMA background correction and Median Polish Probe set Summarization. Only genes reliably expressed (with expression intensity of log2>6) were used for analysis. Genes with average expression signal from all groups of log2<6 are not included in the Matrix templates. Log2 values were used for direct statistical comparisons of expression signals, whereas anti-log2 values were used to calculate fold increases in gene expression between untreated and DSS-treated mice.    Four Matrix templates are provided. In each template induction of gene expression by DSS treatment in mice lacking one Pglyrp gene (Pglyrp1, Pglyrp2, Pglyrp3, or Pglyrp4) is compared to the induction of gene expression by DSS in WT mice.    The fold induction of mRNA in the colon of WT mice treated with DSS to untreated WT mice (column S in each Matrix template) was calculated for each gene on the array as follows: (anti-log2 signal for WT DSS mRNA)/(average anti-log2 signal for untreated WT mRNA). The fold induction of mRNA in the colon of Pglyrp-/- mice treated with DSS to untreated Pglyrp-/- mice (column AL in each Matrix template) was calculated for each gene on the array as follows: (anti-log2 signal for Pglyrp-/- DSS mRNA)/(average anti-log2 signal for untreated Pglyrp-/- mRNA). The significance of differences between the fold induction of mRNA in WT versus Pglyrp-/- mice for each gene on the array was calculated by t-test (column AN in each Matrix template).    The ratio of the fold induction of mRNA in the colon of Pglyrp-/- mice treated with DSS to WT mice treated with DSS (column AT in each Matrix template) was calculated for each gene on the array as follows: [(anti-log2 signal for Pglyrp DSS mRNA)/(average anti-log2 signal for untreated Pglyrp mRNA)] / [(anti-log2 signal for WT DSS mRNA)/(average anti-log2 signal for untreated WT mRNA)].    The genes in each Matrix template are arranged in descending order from the highest to the lowest ratio of gene induction in Pglyrp-/- mice versus WT mice (column AT in each Matrix template).

source_name: Colon RNA, DSS 48 h

label_protocol: Biotinylated sense strand DNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® Whole Ttranscript Sense Target Labeling Assay Manual, Afymetrix) at the Indiana University School of Medicine Center for Medical Genomics core facility.

extract_protocol: Total RNA was isolated from the entire colon from each mouse using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen).

treatment_protocol: Mice (female, 8-9 weeks old) were either untreated or treated with oral solution of 5% dextran sulfate sodium (DSS) in drinking water for 48 hrs.

value: BALB/c Pglyrp4-/-

value: colon


title: fibroblast C3-10

source_name: control C3 fibroblasts, cultured with 10 nM T3


title: 1H_PS

description:
RNA trizol extraction:
Incubate the homogenized samples for 5 minutes at 15 to 30oC to permit the complete dissociation of nucleoprotein complexes.Add 0.2 ml of chloroform per 1 ml of TRIzol® Reagent.Cap sample tubes securely.Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30oC for 2 to 3 minutes.Centrifuge the samples at no more than 12,000Â g for 15 minutes at 2 to 8oC.Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase.The volume of the aqueous phase is about 60% of the volume of TRIzol® Reagent used for homogenization.
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired.Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol.Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol® Reagent used for the initial homogenization.Incubate samples at 15 to 30oC for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8oC.The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
Remove the supernatant.Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol® Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8oC.
At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes).Do not dry the RNA by centrifugation under vacuum.It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility.Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10Â minutes at 55 to 60oC.(Avoid SDS when RNA will be used in subsequent enzymatic reactions.) RNA can also be redissolved in 100% formamide (deionized) and stored at -70oC.

This sample consists of two replicates.

source_name: lung, physiological serum , incubation 1H


title: 95_P16L2_3H_OA

description:
RNA trizol extraction:
Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol® Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 ×  g for 15 minutes at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol® Reagent used for homogenization.
Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol® Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 ×  g for 10 minutes at 2 to 8°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube.
Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol® Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 × g for 5 minutes at 2 to 8°C.
At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes). Do not dry the RNA by centrifugation under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C. (Avoid SDS when RNA will be used in subsequent enzymatic reactions.) RNA can also be redissolved in 100% formamide (deionized) and stored at -70°C.

hyb_protocol: cDNA were designed and prepared as described in J Immunol. 2004 Nov 15;173(10):6109-18. A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models. Hybridization protocol is also published in « DNA microarrays: Gene expression applications » B. Jordan(ed.), Springer-Verlag Berlin Heidelberg Newyork, ISBN: 3-540-41508-4- chapter 4 – pp:80-82.

source_name: lung, oleic acid, incubation 3H

label_protocol:
cDNA were designed and prepared as described in J Immunol. 2004 Nov 15;173(10):6109-18. A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models.
Labelling protocol is also published in  « DNA microarrays: Gene expression applications » B. Jordan(ed.), Springer-Verlag Berlin Heidelberg Newyork, ISBN: 3-540-41508-4- chapter 4 – pp: 78-80.

treatment_protocol: Femelle C57Bl/6J mice were anesthetized with 5% Xylazine – 20% Ketamine (0,1ml/10g). We injected 20 µl of oleic acid (1,2µl/g body weight, sigma #27728-1L-R) in the mouse. Administration of physiological serum and OA was done through the tail vein with a 0.3-ml insulin syringe (BD #320837).


title: 94_P3L2b_1H_OA

source_name: lung, oleic acid, incubation 1H


title: Pglyrp4_DSS_4


title: Pglyrp4_DSS_1


title: 92_P2L1b_3H_OA


title: Pglyrp4_DSS_2


title: Pglyrp4_Untr_4

source_name: Colon RNA, untreated


title: Pglyrp4_Untr_5


title: RAW_CTRL_day4

description: Gene expression data from RAW cells cultured for 4days, replicate for day4

value: RAW cells cultured for 4 days, replicate for day 4


title: Pglyrp4_Untr_3


title: Pglyrp4_Untr_2


title: 88_P5L3_1H30_OA

source_name: lung, oleic acid, incubation 1H30


title: 89_P11L2_4H_OA

source_name: lung, oleic acid, incubation 4H


title: 87_P2L2_1H_OA


title: 79_P12L3b_4H_OA


title: Pglyrp3_DSS_2

value: BALB/c Pglyrp3-/-


title: 78_P6L1_24H_OA

source_name: lung, oleic acid, incubation 24H


title: 80_P4L1_4H_OA


title: Pglyrp3_DSS_3


title: 83_P10L1_18H_OA

source_name: lung, oleic acid, incubation 18H


title: Pglyrp3_DSS_4


title: Pglyrp3_Untr_5


title: 76_P6L2_1H30_OA


title: 81_P4L1_1H30_OA


title: Pglyrp3_DSS_5


title: Pglyrp4_Untr_1


title: Pglyrp3_DSS_1


title: Pglyrp3_Untr_4


title: Pglyrp3_Untr_3


title: 66_P9L3b_3H_OA


title: 84_P1L3_1H30_OA


title: Pglyrp3_Untr_2


title: Pglyrp4_DSS_3


title: Pglyrp3_Untr_1


title: 77_P7L1b_24H_OA


title: 61_P3L2_1H_OA


title: Pglyrp2_DSS_5

value: BALB/c Pglyrp2-/-


title: 47_P2L3b_1H_OA


title: 49_P3L1b_3H_OA


title: 54_P4L2_1H_OA


title: Clone_54_rep1

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

hyb_protocol: Affymetrix Rat Gene 1.0 ST arrays were hybridized with 5 microgramme of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) in Affymetrix Expression Console software.

organism: Rattus norvegicus

source_name: hair follicle cells P5, after first transplanattion into skin, clone 54

label_protocol: 100 nanogram of total RNA were amplified and labeled using Affymetrix whole transcript sense target labeling protocol (kits #900673, #900671)

growth_protocol: Thymic lobes were removed from embryos at E16, and from postnatal rats at P1, P7, and P137. Dissected thymic lobes were harvested and kept in cold Hank’s Balanced Salt Solution (HBSS) complemented with 10% Fetal Bovine Serum during dissection. Single lobes were placed in individual 35 mm size Petri dishes and washed in HBSS without Ca2+ and Mg2+ twice before being dissociated in 0.05% trypsin solution containing 0.1% EDTA at 37°C. Skin grafts containing GFP-positive hair follicles were carefully dissected from the back of recipient nude mice and dissociated in 30 ml of 0.05% trypsin containing 0.1% EDTA at 37°C for 60 to 120 min.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (QIAGEN Inc.)

treatment_protocol: TECs anf hair follicle clones were cultivated on a feeder layer of irradiated 3T3-J2 cells in a 3:1 DMEM F12 medium supplemented as described (Oshima et al., Cell 2001).

value: Sprague-Dawley rats which constitutively express the Enhanced Green Fluorescent protein (EGPF) (green rat CZ-004” SDTgN (act-EGFP)obsCZ-004)


title: 55_P11L1_18H_OA


title: Clone_54_rep2


title: 41_P8L3_3H_OA


title: 60_P15L2_3H_OA


title: Pglyrp2_DSS_3


title: Pglyrp2_DSS_4


title: 44_P13L3_4H_OA


title: MDA-MB-231-Esrp1-4

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon Junction Arrays according to manufacturer’s protocols at the Penn Microarray Core Facility.

scan_protocol: Hybridized Affymetrix Human Exon Junction Arrays were scanned following the manufacturer’s protocols at the Penn Microarrya Core Facility

data_processing: Raw image files were processed using Affymetrix GCOS 1.3 software to generate CEL data files. HJAY array expression indexes were calculated using the ProbeEffects program (Kapur et al., 2007, Genome Biol 8:R82). Briefly, the program employs a sequence-specific background model to correct background intensities of exon-array probes (Kapur et al., 2007, Genome Biol 8:R82), followed by an iterative probe selection procedure (Xing et al., 2006, PLoS ONE 1:e88) that selects a subset of highly correlated probes of a gene for expression index computation. Differential splicing events were detected using the MADS+ algorithm (Shen et al., 2009).

source_name: human breast cancer mesenchymal cell

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix Human Exon Junction arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

growth_protocol: PNT2 cells were grown in RPMI1640 media supplemented with 10% FBS (Thermo Scientific) and Glutamax (Invitrogen).  MDA-MB-231 cells were grown in DMEM media supplemented with 10% FBS (Thermo Scientific), 10ug/ml Insulin (Sigma), and Glutamax (Invitrogen).  Selection for expression of ectopic Esrp1 used 0.5 ug/ml Puromycin (Sigma).

extract_protocol: Total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: siRNA knockdown of ESRP1 and ESRP2 in human prostate epithelial cells PNT2 and ectopic expression of mEsrp1 in human breast cancer cells MDA-MB-231 as described before (Warzecha et al., 2009, Molecular Cell 33:591 - 601).


title: 75_P6L2b_1H30_OA


title: Pglyrp2_DSS_2


title: MDA-MB-231-Esrp1-2


title: YR219P5_RC_rep1

source_name: hair follicle cells P5, after first transplanattion into skin, bulk RC


title: YR219P5_Bulk_V_rep2

source_name: hair follicle cells P5 bulk


title: Pglyrp2_Untr_5


title: Pglyrp2_DSS_1


title: MDA-MB-231-Esrp1-1


title: 36_P4L3b_1H30_OA


title: YR219P5cl7_rep1

source_name: hair follicle cells P5 clonal


title: MDA-MB-231-EV-4


title: YR219P5_RC_rep2


title: Pglyrp2_Untr_4


title: Pglyrp2_Untr_3


title: YR219P5_Bulk_V_rep1


title: MDA-MB-231-Esrp1-3


title: MDA-MB-231-EV-3


title: 38_P7L3b_3H_OA


title: Clone_354_rep2

source_name: thymic epithelial cells 4months after second transplatation into skin, bulk 354


title: 29_P4L1b_4H_AO


title: YR219P5cl7_rep2


title: 26_P3L1_3H_AO


title: 32_P12L1_18H_OA


title: Pglyrp2_Untr_1


title: MDA-MB-231-EV-2


title: 35_P16L2b_3H_OA


title: Pglyrp2_Untr_2


title: MDA-MB-231-EV-1


title: 31_P2L1_3H_AO


title: 24_P7L2b_1H30_AO


title: 23_P11L2b_4H_AO


title: Pglyrp1_DSS_4

value: BALB/c Pglyrp1-/-


title: PNT2-siESRP-4

source_name: human PNT2 prostatic epithelium cells


title: Clone_354_rep1


title: Clone_194_rep1

source_name: thymic epithelial cells P1 after second transplatation into skin, clone 194


title: PNT2-siESRP-3


title: 22_P15L2_3H_AO


title: Pglyrp1_DSS_3

source_name: Colon RNA, DSS 48 h


title: Clone_347_rep2

source_name: thymic epithelial cells E16 after second transplatation into skin, clone 347


title: Pglyrp1_DSS_2


title: 20_P4L2b_1H_AO


title: PNT2-siGFP-4


title: PNT2-siESRP-1


title: Clone_347_rep1


title: PNT2-siGFP-2


title: Pglyrp1_DSS_5


title: 17_P1L3b_1H30_AO


title: 18_P9L3_3H_AO

source_name: lung, oleic acid, incubation 3H


title: PNT2-siESRP-2


title: Clone_907_rep1

source_name: thymic epithelial cells 4months after first transplatation into skin, bulk 907


title: Pglyrp1_DSS_1


title: Clone_287_rep1

source_name: thymic epithelial cells E16 after second transplatation into skin, clone 287


title: Clone_907_rep2


title: PNT2-siGFP-3


title: 21_P6L1b_24H_AO


title: 16_P4L3_1H30_AO

source_name: lung, oleic acid, incubation 1H30


title: Pglyrp1_Untr_3

source_name: Colon RNA, untreated


title: Clone_287_rep2


title: Pglyrp1_Untr_4


title: PNT2-siGFP-1


title: 15_P10L1b_18H_AO


title: Pglyrp1_Untr_1


title: Pglyrp1_Untr_2


title: wild-type strain_45˚C_10 min_2

city: Toyonaka

first: Ryosuke

last: Mega

state: Osaka

address: 1-1 Machikaneyama-cho

department: Biological Sciences

country: Japan

institute: Osaka University

hyb_protocol: 3’-terminal-labeled cDNA (2 mg) was hybridized to a TTHB8401 GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50˚C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix, Santa Clara, CA).

organism: Thermus thermophilus HB8

source_name: wild-type strain at 10 min at 45˚C after cold shock with 4˚C medium

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 35 units of DNase I (GE Healthcare Bio-Science Corp.) at 37˚C for 10 min, and after inactivation at 98˚C for 10 min, the cDNA fragments were labeled with biotin-dideoxy UTP, using terminal transferase according to the manufacturer’s instructions (Affymetrix).

growth_protocol: Wild-type T. thermophilus HB8 strain was pre-cultured at 70˚C for 5 h in 5 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.5 with NaOH.  The cells (5 ml) were inoculated into 300 ml of the same medium and then cultivated at 70˚C. At the Abs600 =0.8 (0min), this culture was divided into two flasks.  Then, equal volume of cold medium (4˚C) was added and the temperature were shifted down to 45˚C.  Hot medium (70˚C) was added to the other flask.  Cells were collected at 0.5 min and 10 min after temperature shift in the equal volume of 100% ice-cold ethanol, and then crude RNA was extracted.

extract_protocol: Crude RNA was extracted by the addition of 1.2 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65˚C for 5 min, chilled on ice for 5 min, and then centrifuged at 4˚C. Then, 0.75 ml of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 20 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37˚C for 40 min in a 25-ml reaction mixture. The reaction was terminated by the addition of 1 ml of 0.5 M EDTA, followed by incubation at 70˚C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M ammonium acetate.

treatment_protocol: The 50 ml of culture was centrifuged by 9,000 x g, 4˚C, and 5 min. After the removal of supernatant, cell pellet was frozen by using liquid nitrogen.

value: wild type


title: Pglyrp1_Untr_5


title: 13_P8L2_1H30_AO


title: wild-type strain_45˚C_10 min_1


title: Clone_57_rep2

source_name: thymic epithelial cells P1 after first transplatation into skin, clone 57


title: Clone_218_rep2

source_name: thymic epithelial cells E16 after first transplatation into skin, clone 218


title: Clone_57_rep1


title: wild-type strain_45˚C_10 min_3


title: 11_P7L1_24H_AO

source_name: lung, oleic acid, incubation 24H


title: wild-type strain_45˚C_0.5 min_3

source_name: wild-type strain at 0 min at 45˚C after cold shock with 4˚C medium


title: WT_DSS_4

value: BALB/c WT


title: Clone_218_rep1


title: WT_DSS_5


title: WT_DSS_3


title: 12_P2L2b_1H_AO

source_name: lung, oleic acid, incubation 1H


title: 10_P8L1b_24H_AO


title: Clone_217_rep1

source_name: thymic epithelial cells E16 after first transplatation into skin, clone 217


title: wild-type strain_45˚C_0.5 min_2


title: 9_P8L1_24H_AO


title: PRP4mo_Cl09_rep2

source_name: thymic epithelial cells 4months clonal


title: wild-type strain_45˚C_0.5 min_1


title: 8_P2L3_1H_AO


title: WT_DSS_1


title: 6_P12L3_4H_AO

source_name: lung, oleic acid, incubation 4H


title: wild-type strain_70˚C_10 min_3

source_name: wild-type strain at 10 min at 70˚C after dilution with 70˚C medium


title: WT_DSS_2

source_name: Colon RNA, DSS 48 h


title: Clone_194_rep2

source_name: thymic epithelial cells P1 after second transplatation into skin, clone 194


title: PRP4mo_bulk_rep2

source_name: thymic epithelial cells 4months bulk


title: 5_P7L3_3H_AO


title: WT_Untr_5


title: Clone_217_rep2


title: wild-type strain_70˚C_10 min_2


title: wild-type strain_70˚C_10 min_1


title: wild-type strain_70˚C_0 min_3

source_name: wild-type strain at 0 min at 70˚C after dilution with 70˚C medium


title: WT_Untr_2


title: PRP1cl11_VII_rep1

source_name: thymic epithelial cells P1 clonal


title: PRP4mo_Cl09_rep1


title: WT_Untr_4


title: WT_Untr_3


title: WT_Untr_1


title: PRP1cl11_VII_rep2


title: PRE16cl11_VII_rep2

source_name: thymic epithelial cells E16 clonal


title: 2_P11L1b_18H_AO

source_name: lung, oleic acid, incubation 18H


title: wild-type strain_70˚C_0 min_2


title: PRP4mo_bulk_rep1


title: wild-type strain_70˚C_0 min_1


title: 3_P13L3b_4H_AO


title: AML sample 214

status: Public on Aug 22 2010

city: New York

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

hyb_protocol: Hybridizations were performed for 18h.

scan_protocol: Slides were scanned using an Axon 4000B scanner. Images were quantified using the SpotReader software.

data_processing: Background intensities given by the SpotReader software were subtracted from foreground intensities. The vsn method (W. Huber et al.; Bioinformatics 2002;18 Suppl 1:S96-104) was then applied separately to each batch of arrays for single color normalization of the green (ChIP) channel across all arrays within that dataset. A model with 48 strata per array according to the print-tips was used. Probes that were flagged by the Spotreader software in more than 25% of the samples as well as empty/blank probes were excluded from the estimation of the model’s parameters. The quantile that is used for the least trimmed sum of squares regression was set to 0.75. After parameter estimation, vsn transformation was applied to all probes. All computations were done within the R-package vsn (ver. 3.6.0).

source_name: pooled AML blasts

label_protocol: DNA was amplified in 2 steps, including a T7 sequenase extension using random primer with a fixed sequence linker and a second step of amplification using the fixed sequence primer and Taq polymerase. The products were purified and labeled with amino-allyl-conjugated dUTP using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) and random primer. Products were purified and crosslinked with monofunctional NHS-ester Cy3 or Cy5 dye.

extract_protocol: DNA was extracted and sonicated to an average DNA length of 500 bp.

tag: batch

value: 2nd batch

source_name: AML blasts

extract_protocol: will update

tag: diagnosis

value: AML


title: AML sample 211

value: male


title: AML sample 212


title: AML sample 213


title: AML sample 215


title: PRE16cl11_VII_rep1


title: AML sample 209


title: AML sample 207


title: AML sample 208


title: AML sample 210


title: AML sample 206


title: AML sample 204


title: AML sample 193


title: AML sample 195


title: AML sample 202


title: AML sample 201


title: AML sample 203


title: AML sample 196


title: AML sample 205


title: AML sample 191


title: AML sample 200


title: 1_P8L2b_1H30_AO

source_name: lung, oleic acid, incubation 1H30


title: AML sample 194


title: AML sample 190


title: AML sample 199


title: ALL sample 168

source_name: ALL blasts

value: ALL


title: AML sample 189


title: AML sample 185


title: AML sample 197


title: AML sample 181


title: ALL sample 171


title: ALL sample 175


title: AML sample 188


title: AML sample 176


title: AML sample 183


title: ALL sample 164


title: ALL sample 170


title: ALL sample 169


title: AML sample 192


title: AML sample 198


title: AML sample 177


title: AML sample 186


title: ALL sample 165


title: ALL sample 163


title: AML sample 178


title: AML sample 182


title: ALL sample 166


title: ALL sample 173


title: AML sample 180


title: ALL sample 167


title: ALL sample 174


title: AML sample 187


title: ALL sample 161


title: ALL sample 160


title: ALL sample 162


title: ALL sample 158


title: ALL sample 159


title: ALL sample 155


title: ALL sample 157


title: ALL sample 151


title: ALL sample 153


title: ALL sample 154


title: ALL sample 146


title: ALL sample 148


title: WBC sample 133

value: 1st batch

source_name: white blood cells

value: WBC


title: AML sample 137


title: WBC sample 134


title: ALL sample 149


title: CD34+ sample 130

source_name: CD34+ progenitor cells


title: ALL sample 152


title: CD34+ sample 135


title: CD34+ sample 138


title: CD34+ sample 131


title: WBC sample 125


title: ALL sample 156


title: AML sample 119

value: female


title: CD34+ sample 126


title: ALL sample 150


title: AML sample 117


title: CD34+ sample 124


title: WBC sample 112


title: WBC sample 104


title: AML sample 105


title: AML sample 121


title: AML sample 097


title: CD34+ sample 128


title: WBC sample 123


title: CD34+ sample 122


title: WBC sample 099


title: AML sample 108


title: WBC sample 129


title: CD34+ sample 111


title: AML sample 095


title: AML sample 116


title: AML sample 091


title: AML sample 106


title: AML sample 092


title: AML sample 107


title: WBC sample 103


title: AML sample 102


title: CD34+ sample 114


title: AML sample 113


title: WBC sample 115


title: CD34+ sample 098


title: AML sample 093


title: AML sample 096


title: CD34+ sample 087


title: WBC sample 088


title: AML sample 086


title: AML sample 090


title: AML sample 081


title: AML sample 085


title: AML sample 082


title: CD34+ sample 077


title: CD34+ sample 075


title: WBC sample 078


title: AML sample 073


title: AML sample 071


title: WBC sample 070


title: AML sample 062


title: AML sample 065


title: CD34+ sample 063


title: WBC sample 076


title: AML sample 074


title: AML sample 072


title: CD34+ sample 067


title: AML sample 080


title: CD34+ sample 061


title: CD34+ sample 069


title: WBC sample 068


title: AML sample 054


title: AML sample 053


title: AML sample 059


title: AML sample 050


title: AML sample 052


title: AML sample 056


title: AML sample 046


title: AML sample 045


title: AML sample 048


title: AML sample 047


title: AML sample 043


title: AML sample 044


title: AML sample 037


title: AML sample 041


title: AML sample 042


title: AML sample 038


title: AML sample 039


title: AML sample 033


title: AML sample 028


title: AML sample 023


title: AML sample 019


title: CD34+ sample 025


title: AML sample 036


title: AML sample 021


title: AML sample 024


title: AML sample 026


title: AML sample 027


title: AML sample 020


title: AML sample 016


title: AML sample 022


title: AML sample 017


title: AML sample 015


title: AML sample 018


title: AML sample 011


title: lung at D5, biological replicate 3

city: Gainesville

first: Amanda

middle: Dawn

last: Rice

email: amandad.rice@gmail.com, amandar@ufl.edu

state: FL

address: 1600 SW Archer Rd

institute: University of Florida

description: Gene expression from lungs during late infection

hyb_protocol: 16hrs at 45C in an Affymetrix 640 GeneChip Hybridization Oven

scan_protocol: Scanned in an Affymetrix GCS 3000 7G scanner

data_processing: CEL files were analyzed using ExpressionStat 5.0 (MAS5). The analysis of the microarray data (CHP files) was performed using BRB Array Tools (NIH). The median probe intensity was used to normalize the arrays, with the median intensity of 84 and the percent call of ~50% across all arrays. The arrays were subjected to an F test with random variance with a significance level of 0.001 in which all arrays were assigned to classes based upon the day post infection the lungs were harvested.

source_name: C57BL/6 mouse lungs, 120 hours post infection with vaccinia virus

label_protocol: 2µg of total purified RNA was used for generation of cRNA for use as probes for the Affymetrix microarrays. The first strand cDNA synthesis was performed using T7-(dT)24 primer and Superscript II RT (Invitrogen). Second strand synthesis was performed using Second Strand Reaction buffer (Invitrogen), of E. coli DNA ligase (NEB), E. coli DNA polymerase I (NEB), E. coli RNase H (NEB), and T4 DNA Polymerase (NEB). cDNA was then purified using GeneChip Sample Cleanup Module (Affymetrix). cRNA was then made using Affymetrix 3’ Labeling IVT kit (Affymextrix) and cleaned up using GeneChip Sample Cleanup Module (Affymetrix). Stained in an Affymetrix GeneChip Fluidics Station 450

growth_protocol: C57BL/6 mice were infected with 10^6 pfu vaccinia virus in PBS via intratracheal route. At hours post infection indicated the mice were euthanized and necropsies performed for tissue harvest.

extract_protocol: Lung tissue was homogenized with Trizol (Invitrogen) and 24 grit silicon carbide (Electro Abrasives, Buffalo NY) In the Mini-Beadbeater 8. RNA isolation was performed with Trizol (Invitrogen) following the manufacturer’s protocol. The resulting RNA pellets were then placed through the Micro-to-Midi Total RNA Purification System (Invitrogen) for the removal of any residual cellular DNA according to the manufacturer’s protocol.

treatment_protocol: Entire lungs without the bronchi were flash frozen in liquid nitrogen and maintained at -80°C were used for RNA isolation.

value: lung

tag: day post infection harvest


title: wild-type (pRK415) vs. wild-type (pHHL)

city: College Station

first: Yunho

state: TX

address: 1501 Harvey Road

department: Chemical engineering

institute: Texas A&M

description: wild-type (pRK415) vs. wild-type (pHHL)

hyb_protocol: Following the method of Mycroarray.com’s Expression Hybridization system

scan_protocol: Following the method of Axon’s GenePix 4000B scanner and GenePix Pro software

data_processing: Agilent's GeneSpring Software

organism: Pseudomonas putida KT2440

source_name: wild-type (pRK415)

label_protocol: Following the method of Invitrogen's Bioprime DNA labeling system

extract_protocol: When grown in M9 medium at the late exponential phase (OD600: ~0.9), total RNA was isolated with a RNeasy Mini kit (Qiagen, Valencia, CA) in accordance with the manufacturer’s recommendations.

treatment_protocol: Cy3 sample

value: Pseudomonas putida KT2440 wild-type harboring empty vector

source_name: wild-type (pHHL)

treatment_protocol: Cy5 sample

value: Pseudomonas putida KT2440 wild-type harboring pHHL


title: lung at D4, biological replicate 3

source_name: C57BL/6 mouse lungs, 96 hours post infection with vaccinia virus


title: lung at D5, biological replicate 1


title: wild-type (pRK415) vs. luxR mutant (pHHL)

value: Pseudomonas putida KT2440 harboring empty vector

source_name: luxR mutant (pHHL)

value: Pseudomonas putida KT2440 luxR mutant harboring pHHL


title: wild-type (pRK415) vs. luxR mutant (pRK415)

source_name: luxR mutant (pRK415)

value: Pseudomonas putida KT2440 luxR mutant harboring empty vector


title: lung at D4, biological replicate 2


title: AML sample 014


title: AML sample 009


title: lung at D3, biological replicate 2

description: Gene expression from lungs during early infection

source_name: C57BL/6 mouse lungs, 72 hours post infection with vaccinia virus


title: lung at D5, biological replicate 2


title: CD34+ sample 004


title: lung at D4, biological replicate 1


title: AML sample 013


title: AML sample 007


title: lung at D2, biological replicate 1

source_name: C57BL/6 mouse lungs, 48 hours post infection with vaccinia virus


title: AML sample 012


title: AML sample 006


title: CD34+ sample 002


title: lung at D2, biological replicate 3


title: lung at D3, biological replicate 1


title: lung at D1, biological replicate 2

source_name: C57BL/6 mouse lungs, 24 hours post infection with vaccinia virus


title: lung at D1, biological replicate 1


title: lung at D2, biological replicate 2


title: AML sample 003


title: lung at D1, biological replicate 3


title: lung at D0, biological replicate 2

description: Gene expression from uninfected mouse lung tissue

source_name: C57BL/6 mouse lungs, normal


title: lung at D0, biological replicate 3


title: lung at D0, biological replicate 1


title: systemic sclerosis fibroblast_50 µg/ml rottlerin_rep 2

city: Philadelphia

first: Peter

middle: Joseph

last: Wermuth

state: PA

address: 233 South 10th Street

department: Dermatology and Cutaneous Biology

institute: Thomas Jefferson University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human Genome HU133A oligonucleotide array. GeneChipwere washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) version 3.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100..  Background correction and normalization were done using a Robust Multichip Average (RMA) with Genespring V 10.0 software.

source_name: Homo sapiens  systemic sclerosis fibroblast_50 µg/ml rottlerin_24 hour

label_protocol: Biotinylated cRNA was prepared using the BioArray High Yield RNA Transcript Labeling Kit according to the manufacturer's instructions

growth_protocol: Human fibroblasts were grown until confluent in 10% DMEM+10% fetal bovine serum, 1% vitamins, 2 mM glutamine, antibiotics, and fungizone in 100 mm plates until confluent, then preincubated for 24 h with 40 μg/ml ascorbic acid phosphate magnesium salt n-hydrate to optimize collagen production.

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

treatment_protocol: Experimental samples were treated with 50 µg/ml rottlerin for 24 hours; control samples were treated with 1xPBS for 24 hours

value: systemic sclerosis fibroblast

tag: sex

value: M

tag: passage #

value: Rottlerin-treated


title: AML sample 066

source_name: pooled AML blasts


title: systemic sclerosis fibroblast_50 µg/ml rottlerin_rep 1

tag: cell type

value: F


title: Jmjd3-/- LPS

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

institute: Kyoto University

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene CHIP scanner 3000.

data_processing: The data were analyzed with RMA using R program.

source_name: Jmjd3-/- macrophages stimulated with LPS for 4 h

label_protocol: Biotinylated cRNA were prepared by NuGEN Ovation system according to the manufactuerer's inscrution.

growth_protocol: Mouse bone marrow cells were cultured with M-CSF for 5 days.

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

treatment_protocol: stimulated with 100 ng/ml LPS for 4 hours

tag: genotype/variation

value: Jmjd3-/- LPS

value: stimulated with LPS for 4 h


title: normal fibroblast_untreated_rep 2

source_name: Homo sapiens  normal fibroblast_untreated

value: normal dermal fibroblast

value: Untreated


title: systemic sclerosis fibroblast_untreated_rep 1

source_name: Homo sapiens  systemic sclerosis fibroblast_untreated


title: normal fibroblast_50 µg/ml rottlerin_rep 2

source_name: Homo sapiens  normal fibroblast_50 µg/ml rottlerin_24 hour


title: systemic sclerosis fibroblast_untreated_rep 3


title: systemic sclerosis fibroblast_50 µg/ml rottlerin_rep 3


title: systemic sclerosis fibroblast_untreated_rep 2


title: normal fibroblast_untreated_rep 3


title: Jmjd3-/- unstimulated

source_name: Jmjd3-/- macrophages unstimulated

value: Jmjd3-/- unstimulated

value: unstimulated


title: normal fibroblast_untreated_rep 1


title: normal fibroblast_50 µg/ml rottlerin_rep 3


title: MCF7-Control-TbetaRIIDN cell line biological rep 2

status: Public on Aug 21 2010

city: Aurora

first: Heide

last: Ford

state: CO

address: 12800 E 19th Ave RC1 North, Room 5102

department: OB/Gyn

institute: University of Colorado at Denver

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix HT Human Genome U133A Array.

scan_protocol: GeneChip scanner 3000

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

source_name: MCF7 mammary carcinoma cell line control clone

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

extract_protocol: Trizol extraction according to the manufacturer's instructions


title: MCF7-Six1-TbetaRIIDN cell line biological rep 1

source_name: MCF7 mammary carcinoma cell line Six1 overexpressing clone


title: MCF7-Six1-GFP cell line biological rep 2


title: MCF7-Six1-GFP cell line biological rep 1


title: normal fibroblast_50 µg/ml rottlerin_rep 1


title: MCF7-Six1-TbetaRIIDN cell line biological rep 2


title: MCF7-Control-GFP cell line biological rep 1

source_name: MCF7 mammary carcinoma cell line control GFP clone


title: MCF7-Control-GFP cell line biological rep 2


title: MCF7-Six1 clone 2 biological rep 2


title: MCF7-Six1 clone 1 biological rep 2


title: MCF7-Six1 clone 3 biological rep 2


title: MCF7-Six1 clone 2 biological rep 1


title: MCF7-Six1 clone 3 biological rep 1


title: MCF7-Control-TbetaRIIDN cell line biological rep 1


title: MCF7-Six1 clone 1 biological rep 1


title: MCF7-Control clone 3 biological rep 1


title: MCF7-Control clone 3 biological rep 2


title: MCF7-Control clone 2 biological rep 2


title: MCF7-Control clone 1 biological rep 2


title: MCF7-Control clone 2 biological rep 1


title: MCF7-Control clone 1 biological rep 1


title: TTF_3factor_4

city: Shinjuku

first: Yumi

last: Matsuzaki

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University, School of Medicine

hyb_protocol: Samples were hybridized to a mouse Oligo Microarray (agilent) according to the manufacturer's protocol.

scan_protocol: Arrays were scanned with a G2565BA Microarray Scanner System (Agilent).

data_processing: Data were analysed using GeneSprings GX software (Agilent).

source_name: TTF (Tail Tip Fibroblast), infected Oct3/4, Sox2, and Klf4

label_protocol: Total RNA from ES cells, PαS cells, OB cells, TTF cells and iPS cells were labelled with Cy3.

extract_protocol: Total RNA was purified with Trizol (invitrogen) and treated with Turbo DNA-free kit (Ambion) to remove genomic DNA contamination.

value: Tail Tip Fibroblast


title: MCF10A-WHSC1L1s line rep 2

city: Detroit

first: Zeng-Quan

last: Yang

address: 4100 John R HWCRC 815

department: Oncology

institute: Karmanos Cancer Institute

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: MCF10A-WHSC1L1s line

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: MCF10A-WHSC1L1s  cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), insulin (5 µg/mL), 10 ng/ml epidermal growth factor (EGF) and 10 µg Blasticidin.

extract_protocol: RNA was extracted  with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

value: MCF10A cells was transduced with WHSC1L1 short isoform lentiviral expression vector


title: ES 2

source_name: Embryonic stem cell (RF 8)

value: ES


title: Breast cancer cell line rep 1

description: replicate 1

source_name: SUM-44 cell line

growth_protocol: SUM-44 cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), and insulin.

value: WHSC1L1 amplified breast cancer cells


title: MCF10A-WHSC1L1s line rep 1

description: replicate 1


title: TTF_4factor_2

source_name: TTF (Tail Tip Fibroblast), infected Oct3/4, Sox2, Klf4, and c-Myc


title: TTF

source_name: Tail Tip Fibroblast


title: ES 1

source_name: Embryonic stem cell (EB-3)


title: TTF_3factor_2


title: TTF_4factor_4


title: TTF_4factor_5


title: PaS

source_name: Bone marrow, PaS (CD45-Ter119-PDGFRa+Sca-1+: MSC)

value: Bone marrow

tag: cell source

value: PaS (MSC)


title: Breast cancer cell line rep 2

description: replicate 2


title: TTF_3factor_3


title: TTF_4factor_3


title: TTF_3factor_1


title: TTF_3factor_5


title: TTF_4factor_1


title: OP_3factor_4

source_name: Bone marrow, OP (Osteo progenitor cell), infected Oct3/4, Sox2, and Klf4

value: OP (Osteo progenitor cell)


title: OP_3factor_3


title: OP

source_name: Bone marrow, OP (CD45-Ter119-PDGFRa-Sca-1-: Osteo progenitor)


title: Placenta_day14.5

city: Izumisano, Osaka

first: Ken

last: Kusakabe

address: 1-58 Rinku-ourai Kita

institute: Osaka Prefecture University

hyb_protocol: Cy3- or Cy5-labeled cRNA targets in hybridization buffer were reacted to microarrays at 60°C for 17h with agitation. After reaction, microarrays were washed with the buffer containing SSC and Triton-X.

scan_protocol: Agilent Technologies Microarray Scanner, G2565BA Type B

data_processing: Data were processed as follows (low-case "g" and "r"  previous data symbol mean Cy3 and Cy5 respectively); A. Calculation of average in the feature (spot) signal from raw data(MeanSignal) B. Calculation of signal background (BGUsed) C. Background correction (MeanSignal - BGUsed) = (BGSubSignal) D. Color collection (DyeNormSignal) E. Application of surrogate values (standard deviation of background) to signal values that became zero after color collection

source_name: Abortion placenta

label_protocol: cDNA synthesis and cRNA labeling were carried out using Low RNA Fluorescent Linear Amplification kit (Agilent). Cy3- or Cy5-labeled cRNA was purified using RNeasy mini spin columns (Qiagen).

growth_protocol: Mice were breed under normal condition. Females were paired with males at evening, and the next day found vaginal plug was confirmed as day 0.5 of pregnancy

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen) from mouse pregnant uterus at day 14.5 of pregnancy,which were divided the normal implantation sites and the abortion ones including dead embryo and shrunk placenta.

value: Placenta

tag: stage

value: Day 14.5 of pregnancy

source_name: Normal placenta


title: LNM35_2nd_GF202

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

description:
compare profiles from N15_2nd
ATCC no. HTB-177

hyb_protocol: Prehybridized for 2 h at 51°C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51°C with the denatured radio-labeled probe. Hybridization of the arrays was followed by two washings with a solution containing 2 M of urea, 0.1 % of SDS, 50 mM of Na phosphate buffer (pH 7.0), 150 mM of NaCl, 1 mM of MgCl2 and 0.2 % of AlkPhos DIRECT blocking reagent (Amersham Bioscience)

scan_protocol: BAS5000 phosphoimager (Fuji Photo Film)

data_processing: Raw data from N15 are used for standard and no normalization were done. 1) Caluculate total intesity of signals from all of spots in both LNM35 and N15. 2) Total intensity of signals of LNM35 was divided by that of N15 (= normalization factor). 3) Intensity of each signal of LNM35 was divided by normalization factor that was calculated at step 2)

label_protocol: 5 mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience)

growth_protocol: RPMI supplemented with 10% FBS

extract_protocol: Total RNA  extracted with RNAeasy (Qiagen) following manufacturer's instructions

tag: cell line


title: N15_2nd_GF202

description:
compare profiles from LNM35_2nd
ATCC no. HTB-177


title: N15_1st_GF202

description:
compare profiles from LNM35_1st
ATCC no. HTB-177