title: H-MS-MSins-2

city: Newark

first: Chaoyang

last: Xue

state: NJ

address: 225 Warren Street

institute: University of Medicine and Dentistry of New Jersey

hyb_protocol: Competitively hybridized to a JEC21 whole-genome array generated previously at Washington University in St. Louis

scan_protocol: After hybridization, arrays were scanned with a GenePix 4000B scanner (Axon Instruments, http://www.axon.com)

data_processing: Analyzed by using GenePix Pro version 4.0 and BRB array tools (developed by Richard Simon and Amy Peng Lam at the National Cancer Institute; http://linus.nci.nih.gov/BRB-ArrayTools.html). Fold changes greater than 2 were considered as significant.

organism: Cryptococcus neoformans

source_name: H99 on SD with 0.1% inositol for 24 hr

label_protocol: Cy3 and Cy5-labeled cDNA were generated by incorporating amino-allyl-dUTP during reverse transcription of 5 µg of total RNA

growth_protocol: H99 was grown on YPD ovrenight at 30 degree with shaking, Cells were washed and transferred to SD without or with 0.1% inositol for 24 hrs with shaking. Cells were collected and RNAs were purified.

extract_protocol: Yeast cells were collected by centrifuge and washed with dH2O twice before RNA extration using Trizol reagents. RNA was purified with kit provided by Clontech. DNA containmination was removed by treating RNA with DNAase I.

treatment_protocol: H99 was grown on SD without or with 0.1% inositol for 24 hrs with shaking. Cells were collected and RNAs were purified.

source_name: H99 on SD without 0.1% inositol for 24 hr


title: H-MS-MSins-1

status: Public on Sep 29 2012

type: RNA

country: USA

molecule: total RNA

tag: strain


title: Seedlings_WT_replicate1

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

description: Expression profiling of lincRNA in WT

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to ATH lincRNA v1 array for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters. We used eBays ANOVA to estimate possibility of differential expression of lincRNA between mutant and WT.

organism: Arabidopsis thaliana

label_protocol: We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: Seedling samples were collected from 2-week-old WT(Col-0) , se-2 and cbp20/cbp80 plants grown on solid MS medium under long-day conditions.

extract_protocol: Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).

tag: tissue

value: 2-week-old Seedlings

tag: genotype/variation


title: Seedlings_se_replicate3

description: Expression profiling of lincRNA in se-2


title: Seedlings_cbp2080_replicate2

description: Expression profiling of lincRNA in cbp20,80 double mutant


title: H-MS-MSins-3


title: Seedlings_WT_replicate2

description: Expression profiling of lincRNA in WT


title: AscarisSuum_FemaleUterus_AvgAcross3rep

status: Public on Sep 30 2012

city: St. Louis

first: Makedonka

last: Mitreva

state: Missouri

address: 4444 Forest Park Ave

institute: The Genome Institute

hyb_protocol: Each cDNA sample was paired and balanced with the common reference, and applied to a single plex of the custom array. Hybridization was carried out at 65 ºC for 20 hours. Washing procedures were carried out according to the Agilent protocols.

scan_protocol: Slides were scanned with an Axon 4000B scanner for the detection of fluorescent signals. Laser power was kept constant and PMT was varied for each slide to ensure optimal signal intensities while maintaining saturation below 0.1%. Images were processed using GenePix v6.1 (Axon) to generate gpr files containing raw intensities, gene information, etc.

data_processing:
Scanned GPR files were first inspected for quality control (QC) using built-in QC tools from the Bioconductor package of R. Inspected microarrays were then analyzed using LIMMA of Bioconductor. After background correction and normalization, gene expression was detected through a linear model fitting which considers both the dye effect and the variation among replications. Differentially expressed genes were defined based on the F test of the linear model fitting. To control the problem of multiple tests, we used false discovery rate (FDR) of 0.01 as a cutoff. The resulting differentially expressed gene set with corrected F-test and FDR was exported for further analysis.
Gene over- and under-expression was determined using the “2 fold” rule based on the linear modeling fitting results. For each gene, if the fitted effect coefficient for one tissue was more than 1 (log-ratio compared with the signal of pooled references), it was recorded as relatively over-expressed in this tissue; if the coefficient was less than -1, it was recorded as relatively under-expressed in that tissue. By this way, each tissue was assessed for its complement of over or under- expressed genes. We further examined the functions of predicted proteins encoded by the genes that were exclusively over-expressed in a specific tissue by GO term enrichment analysis using the Func program.

label: Alexa Fluor 555 succinimidyl ester, Alexa Fluor 647 succinimidyl ester

organism: Ascaris suum

source_name: Tissue from worm uterus

label_protocol: Fluorescence labeled cDNA was prepared from ~10 ug of total RNA using Superscript Plus Indirect labeling system (Invitrogen), with slight modifications. In brief, The anchored oligo(dT)20 primer is a mixture of 12 primers, each consisting of a string of 20 deoxythymidylic acid (dT) residues followed by two additional nucleotides represented by VN, where V is dA, dC, or dG, and N is dA, dC, dG, or dT. The VN “anchor” allows the primer to anneal preferentially at the 5´ end of the poly(A) tail of mRNA, ensuring high specificity, high yields, and longer lengths of cDNA. Two aminoallyl-modified nucleotides were used together with other dNTPs in reverse transcription, for incorporation into the cDNA. After RNA hydrolysis, neutralization, and column purification, the amino-modified cDNA is coupled with a monoreactive, N-hydroxysuccinimide (NHS)-ester fluorescent dye, either Alexa Fluor 555 succinimidyl ester or Alexa Fluor 647 succinimidyl ester. The Alexa dyes provide higher correlation coefficients, signal intensities, and single-to-background ratios. After the final column purification, the fluorescence labeled single-strand cDNA samples are quantified via spectrophotometer.

extract_protocol: Adult worms were collected from infected pigs, and fresh tissues were dissected and snap frozen in liquid nitrogen for subsequent storage at -80 °C. Total RNA of each individual tissue was prepared using TRIzol (Invitrogen) according to the manufacturer’s instruction and treated with Ambion Turbo DNase (Ambion/Applied Biosystems, Austin, TX).  RNA quality and quantity were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Cedar Creek, Texas), and the yield determined using the NanoDrop ND-1000 UV-VIS spectrophotometer v.3.2.1 (NanoDrop Technologies, Wilmington, DE).

tag: species

value: Ascaris suum

value: Uterus

tag: gender

value: Female

source_name: Pooled worm tissue

value: Pooled tissues

value: Pooled genders


title: Seedlings_se_replicate1

description: Expression profiling of lincRNA in se-2


title: Tsu_+Fe_24h_Roots_r1

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

description: gene expression data from Tsu roots on complete media for 24h

hyb_protocol: Done according the manufacturer’s protocol

data_processing: R/Bioconductor.  Normalized with rma

label: biotin

source_name: Tsu roots on complete media for 24h

growth_protocol: Seeds of Arabidopsis thaliana ecotypes Kas-1 and Tsu-1 were imbibed in 0.1% agar at 4°C for 72 h, planted onto rockwool, and grown on hydroponic solution. Lighting was provided at a photoperiod of 16 h of 150 µmol m-2 s-1  4,100K fluorescent light. The ecotypes used are Kas-1 and Tsu-1 for our study, the citation of Schuler (2011) used Columbia-0.

extract_protocol: Total RNA was isolated from whole rosettes using the RNeasy Plant Kit (Qiagen), and quality was assessed using the Agilent Bioanalyzer 2100.

treatment_protocol: 24 d old plants were transferred to treatments of +Fe (50 µM Fe(III)-EDDHA) or -Fe for 24 or 48 h.

tag: genotype

value: Tsu

tag: time

tag: iron

value: Plus


title: HTB58_antiEvi1siRNA_1

city: Pamplona

first: Maria

middle: D

last: Odero

address: Pio XII, 55

country: Spain

institute: University of Navarra

description: Replicate 1 of 3.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA normalization.

organism: Homo sapiens

source_name: Adherent lung cancer cell line, anti-Evi1 siRNA

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS in the case of HTB-58 cells or with 20% FBS and 5-10 ng/ml recombinant GM-CSF in the case of TF-1.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Cell lines were transfected with 1 μg/μl (75 μM) of chemically synthesized anti-EVI1 siRNA or control siRNA.

tag: cell line

value: male

tag: age

value: 65 years

tag: race

value: Caucasian

tag: disease

value: squamous cell carcinoma of the lung

tag: sirna


title: Ctr_PA_92_2

city: Stockholm

first: Annie

last: Pettersson

address: Hälsovägen 7

department: Dept. of medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: Subject 4

hyb_protocol: RNA was prepared and hybridised biotinylated complementary RNA to miRNA 1.0 ST Arrays using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Scanning was performed using Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing:
Data was analysed using QCTool. All microarrays were subjected to an all-probe set scaling to target signal 100.
Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix using default settings i.e. Background Adjustment: BC-CG adjust, Normalization: Quantile: Summarization: Median Polish.

label: Biotin

source_name: Preadipocytes from subcutaneous adipose tissue, fully differentiated and treated for 24 h with DMSO

growth_protocol: Preadipocytes were differentiated as described in PMID: 15925364 and 15492368

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Cells were treated for 24 h with 1 µM GW3965 or DMSO (vehicle)

value: Subcutaneous adipose tissue

tag: cell type

value: in vitro differentiated adipocytes

tag: bmi

tag: subject

value: Subject 4


title: Ctr_PA_5_2

description: Subject 6

label_protocol: RNA was prepared and hybridised biotinylated complementary RNA to miRNA 1.0 ST Arrays using standardized protocols (Affymetrix Inc., Santa Clara, CA).

value: Subject 6


title: GW_PA_5_1

description: Subject 6

source_name: Preadipocytes from subcutaneous adipose tissue, fully differentiated and treated for 24 h with GW3965


title: GW_PA_4_2

description: Subject 5

value: Subject 5


title: GW_PA_5_2

description: Subject 6


title: Ctr_PA_5_1

description: Subject 6


title: Ctr_PA_4_2

description: Subject 5


title: Ctr_PA_92_1

description: Subject 4


title: Ctr_PA_4_1

description: Subject 5


title: GW_PA_74_1

description: Subject 3

value: Subject 3


title: GW_PA_4_1

description: Subject 5


title: Ctr_PA_74_2

description: Subject 3


title: Ctr_PA_74_1

description: Subject 3


title: GW_PA_92_1

description: Subject 4


title: GW_PA_67_1

description: Subject 2

value: Subject 2


title: GW_PA_92_2

description: Subject 4


title: GW_PA_67_2

description: Subject 2


title: GW_PA_74_2

description: Subject 3


title: Ctr_PA_67_2

description: Subject 2


title: GW_PA_62_2

description: Subject 1

value: Subject 1


title: Ctr_PA_67_1

description: Subject 2

value: Female


title: GW_PA_62_1

description: Subject 1


title: Ctr_PA_62_1

description: Subject 1


title: OVCAR 5009 mATF R1

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

description: Mouse Ovarian Cell Line: MOVCAROVCAR 5009 mATF R1

hyb_protocol: Agilent

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

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

organism: Mus musculus

source_name: Stratagene Mouse Universal Reference

label_protocol: Agilent

extract_protocol: Total RNA isolated by Stratagene

tag: reference

value: Mouse Reference

source_name: Cell line generated in the Blancafort Lab

extract_protocol: Qiagen Rneasy Kit

value: Ovarian MOVCAR 5009

tag: treatment

value: mATF


title: OVCAR 5009 IRES R2

description: Mouse Ovarian Cell Line:MOVCAR 5009 Control R2


title: OVCAR 5009 IRES R3

description: Mouse Ovarian Cell Line:MOVCAR5009 Control R3


title: Seedlings_WT_replicate3

description: Expression profiling of lincRNA in WT

tag: tissue

value: 2-week-old Seedlings


title: OVCAR 5009 mATF R2

description: Mouse Ovarian Cell Line:MOVCAR 5009 mATF R2


title: OVCAR 5009 IRES R1

description: Mouse Ovarian Cell Line:MOVCAR 5009 Control R1


title: OVCAR 5009 mATF R3

description: Mouse Ovarian Cell Line:MOVCAR 5009 mATF R3


title: DCIS.05324

city: St Louis

first: Sangjun

last: Lee

state: MO

address: 4940 Parkview Place

department: Pathology

institute: Washington University at St. Louis

description: Gene expression data from DCIS

hyb_protocol: standard Affymetrix protocol using Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were analyzed with dChip software

source_name: Frozen Breast Biopsy

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

growth_protocol: Paired DCIS and IBC samples from same patients

extract_protocol: laser capture microdissection of target cells to estimated >95% total cells using Ambion RNA extraction kit

value: Breast

tag: disease state

value: ductal carcinoma in situ


title: IBC.00333

description: Gene expression data from IBC

value: invasive breast cancer


title: IBC.00425

description: Gene expression data from IBC


title: IBC.00192

description: Gene expression data from IBC


title: DCIS.04031

description: Gene expression data from DCIS


title: IBC.05324

description: Gene expression data from IBC


title: DCIS.03531

description: Gene expression data from DCIS


title: IBC.01428

description: Gene expression data from IBC


title: IBC.04031

description: Gene expression data from IBC


title: DCIS.01745

description: Gene expression data from DCIS


title: IBC.02578

description: Gene expression data from IBC


title: IBC.03412

description: Gene expression data from IBC


title: IBC.03528

description: Gene expression data from IBC


title: DCIS.00333

description: Gene expression data from DCIS


title: Ctr_PA_62_2

description: Subject 1


title: IBC.01286

description: Gene expression data from IBC


title: IBC.01745

description: Gene expression data from IBC


title: DCIS.00126

description: Gene expression data from DCIS


title: DCIS.00425

description: Gene expression data from DCIS


title: IBC.01179

description: Gene expression data from IBC


title: IBC.03531

description: Gene expression data from IBC


title: IBC.02240

description: Gene expression data from IBC


title: DCIS.00192

description: Gene expression data from DCIS


title: IBC.00700

description: Gene expression data from IBC


title: DCIS.03412

description: Gene expression data from DCIS


title: IBC.00126

description: Gene expression data from IBC


title: DCIS3102.2

description: Gene expression data from DCIS


title: IBC2240

description: Gene expression data from IBC

extract_protocol: manual (macro) dissection of tumor epithelium to estimated >75% total cells using Ambion kit


title: IBC2307

description: Gene expression data from IBC


title: DCIS1528.2

description: Gene expression data from DCIS


title: IBC3528

description: Gene expression data from IBC


title: IBC3098

description: Gene expression data from IBC


title: IBC3424

description: Gene expression data from IBC


title: DCIS2921.2

description: Gene expression data from DCIS


title: IBC4699

description: Gene expression data from IBC


title: DCIS2897.2

description: Gene expression data from DCIS


title: IBC2128

description: Gene expression data from IBC


title: IBC2227

description: Gene expression data from IBC


title: IBC2055

description: Gene expression data from IBC


title: IBC4681

description: Gene expression data from IBC


title: IBC1428

description: Gene expression data from IBC


title: IBC2051

description: Gene expression data from IBC


title: IBC1862

description: Gene expression data from IBC


title: IBC4204

description: Gene expression data from IBC


title: DCIS0068.2

description: Gene expression data from DCIS


title: IBC1267

description: Gene expression data from IBC


title: DCIS0011.2

description: Gene expression data from DCIS


title: DCIS0062.2

description: Gene expression data from DCIS


title: IBC1142

description: Gene expression data from IBC


title: IBC2012

description: Gene expression data from IBC


title: IBC1179

description: Gene expression data from IBC


title: IBC1250

description: Gene expression data from IBC


title: IBC0914

description: Gene expression data from IBC


title: IBC3463

description: Gene expression data from IBC


title: IBC1286

description: Gene expression data from IBC


title: IBC0700

description: Gene expression data from IBC


title: IBC1121

description: Gene expression data from IBC


title: DCIS50028

description: Gene expression data from DCIS


title: DCIS50029

description: Gene expression data from DCIS


title: DCIS50023

description: Gene expression data from DCIS


title: DCIS50027

description: Gene expression data from DCIS


title: DCIS50026

description: Gene expression data from DCIS


title: DCIS50021

description: Gene expression data from DCIS


title: DCIS50024

description: Gene expression data from DCIS


title: DCIS50032

description: Gene expression data from DCIS


title: DCIS4899

description: Gene expression data from DCIS


title: DCIS50020

description: Gene expression data from DCIS


title: DCIS50025

description: Gene expression data from DCIS


title: DCIS4160

description: Gene expression data from DCIS


title: DCIS3630

description: Gene expression data from DCIS


title: DCIS4339

description: Gene expression data from DCIS


title: DCIS3794

description: Gene expression data from DCIS


title: DCIS3627

description: Gene expression data from DCIS


title: IBC.S04-16287-Epi

description: Gene expression data from IBC

source_name: FFPE Breast Biopsy

extract_protocol: laser capture microdissection of target cells (Epithelial) to estimated >95% total cells using Ambion RNA extraction kit

value: epithelial


title: IBC.S04-17093-Epi

description: Gene expression data from IBC


title: IBC.S04-13326-Epi

description: Gene expression data from IBC


title: IBC.S05-03468-Epi

description: Gene expression data from IBC


title: IBC.S04-23734-Epi

description: Gene expression data from IBC


title: IBC.S04-19797-Epi

description: Gene expression data from IBC


title: IBC.S04-12043-Epi

description: Gene expression data from IBC


title: DCIS.S05-05886-Epi

description: Gene expression data from DCIS


title: IBC.S04-27640-Epi

description: Gene expression data from IBC


title: DCIS3443

description: Gene expression data from DCIS


title: DCIS3495

description: Gene expression data from DCIS


title: DCIS3102

description: Gene expression data from DCIS


title: DCIS2921

description: Gene expression data from DCIS


title: IBC.S05-11254-Epi

description: Gene expression data from IBC


title: DCIS.S05-15103-Epi

description: Gene expression data from DCIS


title: DCIS.S05-13785-Epi

description: Gene expression data from DCIS


title: DCIS.S04-26857-Epi

description: Gene expression data from DCIS


title: DCIS.S04-22773-Epi

description: Gene expression data from DCIS


title: IBC.S04-12996-Epi

description: Gene expression data from IBC


title: DCIS3340

description: Gene expression data from DCIS


title: IBC.S04-01794-Epi

description: Gene expression data from IBC


title: DCIS0068

description: Gene expression data from DCIS


title: DCIS1528

description: Gene expression data from DCIS


title: DCIS0062

description: Gene expression data from DCIS


title: DCIS.S04-16479-Epi

description: Gene expression data from DCIS


title: DCIS.S04-21947-Epi

description: Gene expression data from DCIS


title: DCIS.S04-27063-Epi

description: Gene expression data from DCIS


title: DCIS2897

description: Gene expression data from DCIS


title: DCIS.S04-18516-Epi

description: Gene expression data from DCIS


title: DCIS0011

description: Gene expression data from DCIS


title: ID 38 DMSO

description: Subject 5

hyb_protocol: RNA was prepared and hybridised biotinylated complementary RNA to Gene 1.0 ST Arrays using standardized protocols (Affymetrix Inc., Santa Clara, CA).

data_processing:
Data was analysed using QCTool. All microarrays were subjected to an all-probe set scaling to target signal 100.
The GeneChip Operating Software Version 1.4 was used for analysis. Arrays were normalized using PLIER and all samples were subjected to an all-probeset scaling-to-target signal of 100.

extract_protocol: Total RNA was extracted as in PMID: 19556420

value: Subcutaneous adipose tissue


title: DCIS.S04-10386-Epi

description: Gene expression data from DCIS


title: IBC.S05-03468-Stroma

description: Gene expression data from IBC

extract_protocol: laser capture microdissection of target cells (Stromal) to estimated >95% total cells using Ambion RNA extraction kit

value: stromal


title: ID 39 GW3967

description: Subject 5

label_protocol: RNA was prepared and hybridised biotinylated complementary RNA to Gene 1.0 ST Arrays using standardized protocols (Affymetrix Inc., Santa Clara, CA).

value: in vitro differentiated adipocytes


title: IBC.S04-23734-Stroma

description: Gene expression data from IBC


title: ID 40 GW3967

description: Subject 5


title: IBC.S04-17093-Stroma

description: Gene expression data from IBC


title: IBC.S04-27640-Stroma

description: Gene expression data from IBC


title: IBC.S04-19797-Stroma

description: Gene expression data from IBC


title: IBC.S05-11254-Stroma

description: Gene expression data from IBC


title: IBC.S04-16287-Stroma

description: Gene expression data from IBC


title: IBC.S04-12996-Stroma

description: Gene expression data from IBC


title: DCIS.S04-22560-Epi

description: Gene expression data from DCIS


title: IBC.S04-01794-Stroma

description: Gene expression data from IBC


title: DCIS.S05-13785-Stroma

description: Gene expression data from DCIS


title: IBC.S04-12043-Stroma

description: Gene expression data from IBC


title: ID 36 GW3967

description: Subject 4

value: Subject 4


title: DCIS.S04-27063-Stroma

description: Gene expression data from DCIS


title: DCIS.S04-22773-Stroma

description: Gene expression data from DCIS


title: DCIS.S04-22560-Stroma

description: Gene expression data from DCIS


title: DCIS.S05-15103-Stroma

description: Gene expression data from DCIS


title: DCIS.S04-21947-Stroma

description: Gene expression data from DCIS


title: DCIS.S04-26857-Stroma

description: Gene expression data from DCIS


title: ID 34 DMSO

description: Subject 4


title: ID 33 DMSO

description: Subject 4


title: ID 35 GW3967

description: Subject 4


title: DCIS.S05-05586-Stroma

description: Gene expression data from DCIS


title: ID 28 GW3966

description: Subject 2


title: ID 29 DMSO

description: Subject 3


title: ID 31 GW3966

description: Subject 3


title: ID 27 GW3966

description: Subject 2


title: ID 37 DMSO

description: Subject 5

value: Subject 5


title: IBC.S04-13326-Stroma

description: Gene expression data from IBC


title: DCIS.S04-16479-Stroma

description: Gene expression data from DCIS


title: ID 26 DMSO

description: Subject 2


title: ID 32 GW3966

description: Subject 3

value: Subject 3


title: DCIS.S04-18516-Stroma

description: Gene expression data from DCIS


title: ID 23 GW3965

description: Subject 1

value: Male


title: ID 30 DMSO

description: Subject 3


title: ID 22 DMSO

description: Subject 1

value: Subject 1


title: ID 21 DMSO

description: Subject 1


title: LCS-CCA-37

status: Public on Sep 28 2012

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: Gene expression data from Non-Tumor Tissue

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip Gene 1_0 st arrays. Arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was perfomed using the GeneChip Operating Software (GCOS, Affymetrix). Background correction, normalization and probe summarization was done with the robust multichip average (RMA) algorithm implemented in the Expression Console software (Affymetrix).

label_protocol: cDNA was labelled with TdT using the WT Terminal Labeling kit (Affymetrix).

extract_protocol: Total RNA was isolated from fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: Liver Non-Tumor Tissue

value: Non-Tumor Tissue


title: LCS-CCA-33


title: ID 24 GW3965

description: Subject 1


title: LCS-CCA-35


title: LCS-CCA-34


title: LCS-CCA-36


title: ID 25 DMSO

description: Subject 2

value: Female

value: Subject 2


title: DCIS.S04-10386-Stroma

description: Gene expression data from DCIS


title: LCS-CCA-32


title: LCS-CCA-31


title: LCS-CCA-25

description: Gene expression data from Hepatic Adenoma

value: Liver Tumor Tissue

value: Hepatic Adenoma


title: LCS-CCA-24


title: LCS-CCA-28

description: Gene expression data from FNH

value: Focal Nodular Hyperplasia (FNH)


title: LCS-CCA-30

description: Gene expression data from FNH


title: LCS-CCA-26

description: Gene expression data from FNH


title: LCS-CCA-29

description: Gene expression data from FNH


title: LCS-CCA-22

description: Gene expression data from CHC

value: Combined Hepatocellular Cholangiocarcinoma (CHC)


title: LCS-CCA-27

description: Gene expression data from FNH


title: LCS-CCA-23

description: Gene expression data from CHC


title: LCS-CCA-15

description: Gene expression data from ICC

value: Intrahepatic Cholangiocarcinoma (ICC)


title: LCS-CCA-18

description: Gene expression data from CHC


title: LCS-CCA-21

description: Gene expression data from CHC


title: LCS-CCA-08

description: Gene expression data from ICC


title: LCS-CCA-19

description: Gene expression data from CHC


title: LCS-CCA-12

description: Gene expression data from ICC


title: LCS-CCA-20

description: Gene expression data from CHC


title: LCS-CCA-10

description: Gene expression data from ICC


title: LCS-CCA-13

description: Gene expression data from ICC


title: LCS-CCA-14

description: Gene expression data from ICC


title: LCS-CCA-16

description: Gene expression data from ICC


title: LCS-CCA-04

description: Gene expression data from ICC


title: LCS-CCA-11

description: Gene expression data from ICC


title: LCS-CCA-06

description: Gene expression data from ICC


title: LCS-CCA-07

description: Gene expression data from ICC


title: LCS-CCA-09

description: Gene expression data from ICC


title: LCS-CCA-02

description: Gene expression data from ICC


title: LCS-CCA-05

description: Gene expression data from ICC


title: LCS-CCA-17

description: Gene expression data from CHC


title: LCS-CCA-03

description: Gene expression data from ICC


title: vol28 pbmc day 2, rep 2

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

country: United Kingdom

institute: Jenner Institute, University of Oxford

description:
12.7
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

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

source_name: frozen human pbmc, MVA85A, d2

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep Kit for Illumina arrays.

extract_protocol: RNA was extracted with the QIAGEN RNeasy Mini Kit including an on-column DNase I digestion in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Volunteers were vaccinated with 1x10^8 pfu MVA85A either intradermally (id) or intramuscularly (im). Blood was taken on the day of vaccination, and 2 and 7 days post-vaccination. PBMCs were separated and frozen down.

tag: volunteer number

value: healthy

value: peripheral blood mononuclear cell (PBMC)

value: MVA85A vaccination

tag: vaccination route

value: intradermal (ID)

tag: days post-vaccination

tag: incubation conditions


title: vol19 pbmc day 0, rep 1

description:
4.8
Replicate 1.

source_name: frozen human pbmc, MVA85A, d0


title: vol28 pbmc day 7, rep 2

description:
12.8
Replicate 2

source_name: frozen human pbmc, MVA85A, d7


title: vol26 6hr mvawt in vitro

description:
11.7
Replicate 1.

source_name: frozen human pbmc, MVA85A, d0, WT MVA incubation

value: intramuscular (IM)

value: 6hrs wild type MVA

tag: sample type

value: control


title: vol29 pbmc day 0, rep 1

description:
7.8
Replicate 1.


title: vol10 pbmc day 2, rep 1

description:
2.8
Replicate 1.


title: vol10 pbmc day 0, rep 1

description:
1.8
Replicate 1.


title: vol26 6hr 85a in vitro

description:
10.7
Replicate 1.

source_name: frozen human pbmc, MVA85A, d0, antigen 85A incubation

value: 6hrs antigen 85A


title: vol28 6hr mvawt in vitro

description:
11.8
Replicate 1.


title: vol19 pbmc day 2, rep 1

description:
5.8
Replicate 1.


title: vol28 6hr 85a in vitro

description:
10.8
Replicate 1.


title: vol28 pbmc day 7, rep 1

description:
9.7
Replicate 1.


title: vol28 pbmc day 2, rep 1

description:
8.7
Replicate 1.


title: vol17 pbmc day 0, rep 1

description:
4.7
Replicate 1.


title: vol17 pbmc day 2, rep 1

description:
5.7
Replicate 1.


title: vol9 pbmc day 0, rep 1

description:
1.7
Replicate 1.


title: vol12 pbmc day 7, rep 2

description:
12.6
Replicate 2


title: vol29 pbmc day 2, rep 1

description:
8.8
Replicate 1.


title: vol28 pbmc day 0, rep 1

description:
7.7
Replicate 1.


title: vol10 pbmc day 7, rep 1

description:
3.8
Replicate 1.


title: vol17 pbmc day 7, rep 1

description:
6.7
Replicate 1.


title: vol17 6hr 85a in vitro

description:
10.6
Replicate 1.


title: vol26 pbmc day 7, rep 1

description:
9.6
Replicate 1.


title: vol17 6hr mvawt in vitro

description:
11.6
Replicate 1.


title: vol29 pbmc day 7, rep 1

description:
9.8
Replicate 1.


title: LCS-CCA-01

description: Gene expression data from ICC


title: vol9 pbmc day 2, rep 1

description:
2.7
Replicate 1.


title: vol26 pbmc day 2, rep 1

description:
8.6
Replicate 1.


title: vol26 pbmc day 0, rep 1

description:
7.6
Replicate 1.


title: vol16 pbmc day 2, rep 1

description:
5.6
Replicate 1.


title: vol16 pbmc day 0, rep 1

description:
4.6
Replicate 1.


title: vol16 pbmc day 7, rep 1

description:
6.6
Replicate 1.


title: vol9 pbmc day 7, rep 1

description:
3.7
Replicate 1.


title: vol7 pbmc day 0, rep 1

description:
1.6
Replicate 1.


title: vol7 pbmc day 7, rep 1

description:
3.6
Replicate 1.


title: vol16 6hr mvawt in vitro

description:
11.5
Replicate 1.


title: vol25 pbmc day 7, rep 1

description:
9.5
Replicate 1.


title: Mammary_tumor_Cebpb_shRNA_rep3

first: Jonas

last: Fuxe

address: Scheeles v. 2, A3:4

department: Department of Medical Biochemistry and Biophysics

description: This sample is of 4T1 tumors expressing Cebpb shRNA. It is the third of five control shRNA replicates used in this experiment, each from separate tumors

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: 4T1 tumors expressing Cebpb shRNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: strain

value: BALB/c

tag: tumor

value: Sc implanted 4T1 mammary tumor

tag: genotype/variation

value: Cebpb shRNA expression


title: Mammary_tumor_control_shRNA_rep1

description: This sample is of 4T1 tumors expressing control shRNA. It is the first of five control shRNA replicates used in this experiment, each from separate tumors

source_name: 4T1 tumors expressing control shRNA


title: vol7 pbmc day 2, rep 1

description:
2.6
Replicate 1.


title: vol25 pbmc day 0, rep 1

description:
7.5
Replicate 1.


title: Mammary_tumor_control_shRNA_rep3

description: This sample is of 4T1 tumors expressing control shRNA. It is the third of five control shRNA replicates used in this experiment, each from separate tumors


title: vol25 pbmc day 2, rep 1

description:
8.5
Replicate 1.


title: vol12 pbmc day 2, rep 2

description:
12.5
Replicate 2


title: Mammary_tumor_control_shRNA_rep5

description: This sample is of 4T1 tumors expressing control shRNA. It is the fifth of five control shRNA replicates used in this experiment, each from separate tumors


title: Mammary_tumor_Cebpb_shRNA_rep1

description: This sample is of 4T1 tumors expressing Cebpb shRNA. It is the first of five control shRNA replicates used in this experiment, each from separate tumors


title: vol16 6hr 85a in vitro

description:
10.5
Replicate 1.


title: Mammary_tumor_Cebpb_shRNA_rep2

description: This sample is of 4T1 tumors expressing Cebpb shRNA. It is the second of five control shRNA replicates used in this experiment, each from separate tumors


title: Mammary_tumor_Cebpb_shRNA_rep4

description: This sample is of 4T1 tumors expressing Cebpb shRNA. It is the fourth of five control shRNA replicates used in this experiment, each from separate tumors


title: Mammary_tumor_Cebpb_shRNA_rep5

description: This sample is of 4T1 tumors expressing Cebpb shRNA. It is the fifth of five control shRNA replicates used in this experiment, each from separate tumors


title: Mammary_tumor_control_shRNA_rep4

description: This sample is of 4T1 tumors expressing control shRNA. It is the fourth of five control shRNA replicates used in this experiment, each from separate tumors


title: vol15 pbmc day 0, rep 1

description:
4.5
Replicate 1.


title: Cancer-associated fibroblast CAF6

city: Chongqing

first: liuyang

last: zhao

address: 1#  Yixueyuan Road, Yuzhong District

institute: Chongqing Medical  University

description: The third passage of primary cancer-associated fibroblast cells was used in the experiments.

hyb_protocol: Cy3-labelled cRNA was hybridized to Homo sapiens Agilent-021827 Human miRNA Microarray G4470C (Feature Number version) using Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: Online Update) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cancer-associated fibroblast

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was isolated using the mir-VanaTM miRNA Isolation Kit (Ambion, Austin, TX, USA) following the manufacturer’s instructions. The RNA quantity was determined using Nanodrop1000 (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). All RNA samples revealed acceptable RNA Integrity Number (RIN) values between 8.8 and 9.6.

treatment_protocol: Tissues were washed 3 times with PBS containing 100U/ml penicillin and 100 ug/ml streptomycin(Sigma, St. Louis, MO, USA), then minced into small pieces and digested for 8 h at 37°C in DMEM containing 10% FBS and 0.5 mg/ml collagenase І (Sigma, St. Louis, MO, USA). After centrifugation and washing with PBS, cells pellets were resuspended in the DMEM with 10% FBS and transfered into 100-mm tissue-culture dishes. CAFs and NFs were routinely maintained in DMEM containing 10% FBS at 37°C in humidified atmosphere containing 5% CO2. The third passage of primary cells was used in the experiments.

value: Cancer-associated fibroblast

tag: gender

value: female

value: breast cancer

tag: source of cells

value: specimen 6


title: Cancer-associated fibroblast CAF4

tag: cell type

value: specimen 4


title: Mammary_tumor_control_shRNA_rep2

description: This sample is of 4T1 tumors expressing control shRNA. It is the second of five control shRNA replicates used in this experiment, each from separate tumors


title: vol15 pbmc day 7, rep 1

description:
6.5
Replicate 1.


title: vol15 pbmc day 2, rep 1

description:
5.5
Replicate 1.


title: Cancer-associated fibroblast CAF5

value: specimen 5


title: vol6 pbmc day 7, rep 1

description:
3.5
Replicate 1.

value: healthy


title: vol19 pbmc day 7, rep 1

description:
6.8
Replicate 1.

value: peripheral blood mononuclear cell (PBMC)


title: Cancer-associated fibroblast CAF3

value: specimen 3


title: vol29 pbmc day 7, rep 2

description:
12.4
Replicate 2

value: MVA85A vaccination


title: Cancer-associated fibroblast CAF2

value: specimen 2


title: Cancer-associated fibroblast CAF1

value: specimen 1


title: Normal fibroblast NF3

description: The third passage of primary normal fibroblast cells was used in the experiments.

source_name: Normal fibroblast

value: Normal fibroblast


title: vol6 pbmc day 0, rep 1

description:
1.5
Replicate 1.

value: intramuscular (IM)


title: Normal fibroblast NF4


title: Normal fibroblast NF2


title: vol24 pbmc day 2, rep 1

description:
8.4
Replicate 1.


title: LCS-CCA-MI35

description: Gene expression data from Cholangiocarcinoma Cell line

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString) with 5 ul of the fivefold diluted sample preparation reaction. All hybridization reactions were incubated at 65ﾂｰC for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer's instructions.  For each assay, a high-density scan (600 fields of view) was performed.

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using code count normalization according to manufacturer's protocol (Nanostring).

value: Cholangiocarcinoma Cell line

value: Cholangiocarcinoma


title: LCS-CCA-MI34


title: Normal fibroblast NF5


title: LCS-CCA-MI33

value: Liver Non-Tumor Tissue

value: Non-Tumor Tissue


title: vol28 6hr mva85a in vitro

description:
11.4
Replicate 1.

source_name: frozen human pbmc, MVA85A, d0, MVA85A incubation

value: intradermal (ID)

value: 6hrs MVA85A

value: control


title: Normal fibroblast NF1

value: female

value: breast cancer


title: vol28 6hr media in vitro

description:
10.4
Replicate 1.

source_name: frozen human pbmc, MVA85A, d0, media incubation

value: healthy

value: 6hrs media


title: vol6 pbmc day 2, rep 1

description:
2.5
Replicate 1.

value: peripheral blood mononuclear cell (PBMC)


title: Normal fibroblast NF6

value: specimen 6


title: LCS-CCA-MI32


title: vol14 pbmc day 2, rep 1

description:
5.4
Replicate 1.

value: MVA85A vaccination


title: Strain I63B rep 2

type: genomic

city: Seattle

first: Weerayuth

last: Kittichotirat

state: WA - Washington

address: 960 Republican st

department: Microbiology

institute: University of Washington

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain I63B

hyb_protocol: 40µl hybridization sample mixture was loaded onto the glass slide and incubated at 65°C for 24 hours with rotation. The arrays were then washed with Agilent CGH wash buffer

scan_protocol: Arrays were scanned using an Agilent scanner 6000C with the manufacturer’s recommended settings for aCGH arrays (scan area 61 x 21.6mm, 5um resolution, 100% PMT R&G). Data was extracted from the scanner using Agilent Feature Extractor v10.5 software using protocol CGH_105_Dec08.

data_processing: The signal data obtained from the Agilent Feature Extraction Software were processed using the following steps. First the gProcessedSignal value, which is a background subtracted signal, for each probe was extracted. Since the labeling process involved incorporating Cyanine 3-dUTP into the genomic sample, it is possible that probes that are rich in nucleotide A have higher signal relative to probes with lower A content and may not accurately reflect the true abundant of the target sequence. For this reason, the signal values were normalized by dividing them with the total number of A nucleotides in the probe sequence. Finally this value was transformed using log2. Processed signal values from probes that are targeting the same gene cluster were consolidated into a single value by averaging the signals.

molecule: genomic DNA

organism: Aggregatibacter actinomycetemcomitans

source_name: Genomic DNA

label_protocol: 0.5µg of genomic DNA was labeled with cyanine3. DNA denaturation and fragmentation was done using a thermocycler by mixing 2.5µl of Random Primers (Agilent) and 13µl of genomic DNA at 94°C for 10 minutes. The mixture was cooled to 4°C degree and 9.5µl of labeling master mix (Agilent) was added to make a total volume of 25µl. DNA labeling was done using a thermocycler following the steps: 37°C for 2 hours, 65°C for 10 minutes, and hold at for 4°C. Labeled genomic DNA was purified using individual Amicon 30kDA filters (Millipore) following manufacturer’s protocol. The yield of labeled DNA was determined by measuring the absorbance at A260nm (DNA) and A550nm (cyanine 3) using Nano-Drop (ND-1000).

growth_protocol: A. actinomycetemcomitans was grown on tryptic soy agar plate with 0.6% yeast extract for two days at 37°C in atmosphere supplemented with 5% CO2, and harvested by washing the bacteria off the plates with PBS buffer.

extract_protocol: Genomic DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA 91355 USA) according the manufacturer’s manual.

tag: serotype

value: d

tag: genotype


title: Strain I63B rep 1


title: Strain D11S-1 rep 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain D11S-1

value: c


title: LCS-CCA-MI31

description: Gene expression data from Non-Tumor Tissue


title: Strain D11S-1 rep 2


title: Strain D41S-1 rep 2_2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain D41S-1

value: b


title: vol24 pbmc day 0, rep 1

description:
7.4
Replicate 1.

value: intramuscular (IM)


title: vol14 pbmc day 7, rep 1

description:
6.4
Replicate 1.


title: Strain D41S-1 rep 1_2


title: vol5 pbmc day 2, rep 1

description:
2.4
Replicate 1.


title: LCS-CCA-MI30


title: LCS-CCA-MI29


title: vol24 pbmc day 7, rep 1

description:
9.4
Replicate 1.


title: Strain G121-2 rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain G121-2


title: LCS-CCA-MI28

description: Gene expression data from FNH

value: Liver Tumor Tissue

value: Focal Nodular Hyperplasia (FNH)


title: LCS-CCA-MI27

description: Gene expression data from FNH


title: vol5 pbmc day 0, rep 1

description:
1.4
Replicate 1.


title: vol5 pbmc day 7, rep 1

description:
3.4
Replicate 1.


title: vol14 pbmc day 0, rep 1

description:
4.4
Replicate 1.


title: vol29 pbmc day 2, rep 2

description:
12.3
Replicate 2


title: Strain G121-2 rep 1


title: LCS-CCA-MI26

description: Gene expression data from FNH


title: vol26 6hr mva85a in vitro

description:
11.3
Replicate 1.


title: vol26 6hr media in vitro

description:
10.3
Replicate 1.


title: Strain G111-1 rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain G111-1


title: LCS-CCA-MI25

description: Gene expression data from Hepatic Adenoma

value: Hepatic Adenoma


title: normal melanocytes patient 5

city: Rome

first: diego

last: arcelli

address: Via delle Messi d'Oro 156

country: Italy

institute: Regina Elena National Cancer Institute

hyb_protocol: The probe array has been first pre-incubated with Pre-Hybridization Mix (Affymetrix) at 45 °C for 10 minutes with rotation. Meanwhile, the hybridization cocktail (containing the labeled and fragmented aRNA) is heated at 99 °C, transferred to 45 °C heat block for 5 minutes, then spun for 5 minutes to collect any insoluble material from the hybridization mixture. Once removed from the hybridization oven, the array has been refilled with the clarified hybridization cocktail, and hybridized at 45 °C, in rotation (60 rpm) for 16 hours

scan_protocol: Scanning has been carried out in a Affymetrix GeneChiP Scanner 3000-6G by GCOS software

data_processing: Data analysis was performed using a customized R language-based script with the Bioconductor packages

source_name: melanocytes from skin

label_protocol: For RNA labeling, the GeneChip® 3’ IVT Express Protocol has been used, according to Affymetrix indications. In brief, total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA (cRNA is also known as amplified RNA or aRNA) and incorporates a biotin-congugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Melanocytes established in culture in Ham's complete (10% FBS) medium containing 16 nM phorbol 12-myristate 13-acetate (PMA). Melanomas grown in RPMI1640 complete (10% FBS) medium, no supplements. Medium in all cultures was replaced with fresh RPMI complete 24 h before RNA extraction.  Barbara?

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Melanin was removed by the c-TAB method (PigmentCell Res 2004; 17: 312-5)

value: normal melanocytes


title: vol22 pbmc day 2, rep 1

description:
8.3
Replicate 1.

value: intradermal (ID)


title: melanoma cells patient 5

source_name: lymph nodal metastasis

value: melanoma


title: vol22 pbmc day 7, rep 1

description:
9.3
Replicate 1.


title: vol13 pbmc day 7, rep 1

description:
6.3
Replicate 1.


title: normal melanocytes patient 4

value: male


title: vol22 pbmc day 0, rep 1

description:
7.3
Replicate 1.


title: melanoma cells patient 4


title: vol13 pbmc day 2, rep 1

description:
5.3
Replicate 1.


title: Strain S067 rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain S067


title: normal melanocytes patient 3


title: Strain 194 rep 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain 194


title: Strain S067 rep 1


title: vol13 pbmc day 0, rep 1

description:
4.3
Replicate 1.


title: Strain ATCC29524 rep 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain ATCC29524


title: Strain ATCC29524 rep 2


title: melanoma cells patient 3


title: vol3 pbmc day 7, rep 1

description:
3.3
Replicate 1.


title: vol24 pbmc day 7, rep 2

description:
12.2
Replicate 2


title: vol 17 6hr mva85a in vitro

description:
11.2
Replicate 1.

value: 6hrs MVA85A

value: control


title: melanoma cells patient 2

value: female


title: Strain A26 rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain A26


title: vol17 6hr media in vitro

description:
10.2
Replicate 1.

value: healthy

value: peripheral blood mononuclear cell (PBMC)

value: 6hrs media


title: vol3 pbmc day 0, rep 1

description:
1.3
Replicate 1.

value: MVA85A vaccination


title: Strain 194 rep 2


title: Strain A26 rep 1


title: vol3 pbmc day 2, rep 1

description:
2.3
Replicate 1.


title: melanoma cells patient 1


title: Strain G104-2 rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain G104-2


title: vol21 pbmc day 7, rep 1

description:
9.2
Replicate 1.


title: Superficial scraping from normal ovary 3

city: Oslo

first: Bente

middle: Vilming

last: Elgaaen

address: Ullernchausseen 70

department: Department of Gynecological Oncology

country: Norway

institute: Oslo University Hospital

description: mRNA from 1 sample

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

scan_protocol: Fluorescent images were captured using gene Array scanner 3000 and Affymetrix GeneChip Operating Software (GCOS)

data_processing: The CEL files from GCOS were imported into Array Assist software (v5.2.0; Iobion Informatics LLC, La Jolla, CA) and normalized using the PLIER algorithm in Array Assist to calculate relative signal values for each probe set.

source_name: Superficial scraping from normal ovary

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Tissue specimens were homogenized directly for 2x2 minutes in 750 µl TRIzol using a Tissuelyzer (Qiagen.com). Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) and further purified by the RNeasy MinElute cleanup kit (Qiagen catalog no. 74204) according to the manufacturer's instructions. The isolated total RNA was quantified (Nano Drop spectrophotometer; Saveen Werner AB) and quality controlled using the Agilent BioAnalyzer 2100 system and the RNA 6000 Nano assay. All samples showed high RNA quality.

treatment_protocol: Immediately after harvesting the tissue samples were snap-frozen in liquid nitrogen, wheras the SNO  samples were transferred to 500 µl TRIzol solution (Invitrogen.com). The samples were stored at -80⁰C until processed.

value: ovary


title: vol21 pbmc day 2, rep 1

description:
8.2
Replicate 1.


title: Superficial scraping from normal ovary 2

description: mRNA from 1 sample


title: Strain G104-2 rep 1

value: b


title: LCS-CCA-MI15

description: Gene expression data from ICC

value: Intrahepatic Cholangiocarcinoma (ICC)


title: LCS-CCA-MI16

description: Gene expression data from ICC

value: Liver Tumor Tissue


title: Superficial scraping from normal ovary 1

description: mRNA from 1 sample


title: LCS-CCA-MI19

description: Gene expression data from CHC

value: Combined Hepatocellular Cholangiocarcinoma (CHC)


title: LCS-CCA-MI18

description: Gene expression data from CHC


title: LCS-CCA-MI22

description: Gene expression data from CHC


title: LCS-CCA-MI20

description: Gene expression data from CHC


title: LCS-CCA-MI24

value: Hepatic Adenoma


title: LCS-CCA-MI23

description: Gene expression data from CHC


title: LCS-CCA-MI17

description: Gene expression data from CHC


title: normal melanocytes patient 1

value: normal melanocytes


title: IStrain 23C rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain I23C


title: LCS-CCA-MI21

description: Gene expression data from CHC


title: normal melanocytes patient 2


title: vol21 pbmc day 0, rep 1

description:
7.2
Replicate 1.

value: intramuscular (IM)


title: Superficial scraping from normal ovary 4

description: mRNA from 1 sample


title: Strain G111-1 rep 1


title: LCS-CCA-MI13

description: Gene expression data from ICC


title: LCS-CCA-MI14

description: Gene expression data from ICC


title: Serous ovarian carcinoma 4

description: mRNA from 2 samples pooled

source_name: Serous ovarian carcinoma


title: LCS-CCA-MI12

description: Gene expression data from ICC


title: LCS-CCA-MI11

description: Gene expression data from ICC


title: vol12 pbmc day 2, rep 1

description:
5.2
Replicate 1.

value: intradermal (ID)


title: Serous ovarian carcinoma 3

description: mRNA from 3 samples pooled


title: Serous ovarian carcinoma 2

description: mRNA from 3 samples pooled


title: vol2 pbmc day 7, rep 1

description:
3.2
Replicate 1.


title: vol12 pbmc day 0, rep 1

description:
4.2
Replicate 1.


title: LCS-CCA-MI10

description: Gene expression data from ICC


title: LCS-CCA-MI09

description: Gene expression data from ICC


title: Strain D18P-1 rep 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain D18P-1

value: f


title: LCS-CCA-MI08

description: Gene expression data from ICC


title: LCS-CCA-MI07

description: Gene expression data from ICC


title: vol12 pbmc day 7, rep 1

description:
6.2
Replicate 1.


title: Strain D17P-2 rep 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain D17P-2

value: c


title: Serous ovarian borderline tumor 4

description: mRNA from 3 samples pooled

source_name: Serous ovarian borderline tumor


title: LCS-CCA-MI06

description: Gene expression data from ICC


title: LCS-CCA-MI05

description: Gene expression data from ICC


title: Serous ovarian carcinoma 1

description: mRNA from 3 samples pooled


title: Serous ovarian borderline tumor 3

description: mRNA from 1 sample


title: Strain D18P-1 rep 2


title: vol2 pbmc day 2, rep 1

description:
2.2
Replicate 1.

source_name: frozen human pbmc, MVA85A, d2


title: Strain ANH9381 rep 2_2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain ANH9381


title: NoL_pool2 [Methylation]

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

description: Methylation profiling of human clinical samples

hyb_protocol: Samples were hybridized to UHN HCGI12K CpG microarrays. After hybridization, microarrays were washed as follows: 3 × 15 min at 55 °C with wash 1 in a rotating oven, then on a gyrating platform 2 × 3 min at room temperature (R.T.) 1x SSC, 2 × 3 min at R.T. Wash 2: 2 × 3 min at R.T. 0.1 × SSC, 2 × 3 min at R.T. Millipore H2O. Finally, slides were rinsed with H2O and centrifuged for 7 min at 370 g to dry.

scan_protocol: Samples were scanned with an Axon GenePix 4400A scanner (MDS Analytical Technologies, Molecular Devices, Sunnyvale, CA, USA) using Genepix Pro 7 software (MDS Analytical Technologies).

data_processing: The output GPR files from Gene Pix Pro 7.15 were imported into the R/Bioconductor Marray program and quality control diagnostic plots were generated and assessed. Poor-quality arrays were removed from the analysis and repeated. The log ratio of median red (Cy5-labeled subject sample) to median green (Cy3-labeled universal control) processed (dye-normalized) signal intensities were computed using the LIMMA R/Bioconductor program. Probes that had been flagged by Gene Pix Pro 7.15 as bad, absent or not found were removed. A genomic smoothing step was then performed in which a weighted average across 1000 bp was calculated for each CpG clone. In order to determine the degree of enrichment, the Partek Genomics Suite ANOVA tool was used and the n-fold change using the geometric mean (for log-transformed data). Probesets that differed significantly (p < 0.10) between the low-risk MDS and control groups were selected for further analysis.

source_name: Bone Marrow mononuclear cells

label_protocol: The methylation assay was done largely as described previously, but with the following modifications: DNA was purified after double digestion, methylated CpG amplification (MCA) reaction and labeling were done using the QIAquick PCR purification kit (Qiagen) without any indicator in the buffer PB. RMCA primers (Eurogentec, Southampton, UK) were used at ligation and MCA reaction stages. The MCA reaction was performed using 5 U HotStarTaq+ (Qiagen) and samples were aliquoted without primers before being heated to 82 °C. The primers were held at 95 °C for 1 min before adding 4 μL to each tube. Cycling conditions were: 95 °C for 10 min before 30 cycles of 95 °C for 1 min, 65 °C for 90 s, 72 °C for 2 min, and finally 72 °C for 10 min, and before holding at 4 °C.

growth_protocol: Human samples obtained from patients and healthy donors

extract_protocol: Genomic DNA from subject samples was isolated using a DNeasy Blood and Tissue kit from QIAGEN, following the manufacturer’s protocol. DNA was eluted in AE buffer (QIAGEN, Hilden, Germany).

tag: disease type

value: Control. Healty. (Pool)

tag: disease subtype

tag: healthy control

value: Control. Healty


title: Strain D17P-2 rep 1


title: Strain ANH9381 rep 1_2


title: LCS-CCA-MI04

description: Gene expression data from ICC

tag: tissue

tag: disease state


title: LCS-CCA-MI03

description: Gene expression data from ICC


title: Serous ovarian borderline tumor 1

description: mRNA from 3 samples pooled


title: Serous ovarian borderline tumor 2

description: mRNA from 1 sample


title: LCS-CCA-MI02

description: Gene expression data from ICC


title: vol2 pbmc day 0, rep 2

description:
1.2
Replicate 2.

source_name: frozen human pbmc, MVA85A, d0

tag: volunteer number

value: healthy

tag: treatment

tag: vaccination route


title: MDS_patient17_RARS [Methylation]

treatment_protocol: Human samples obtained from patients and healthy donors

value: Low-Risk Myelodysplastic Syndrome

value: Refractory anemia with ringed sideroblasts (RARS)


title: vol16 6hr media in vitro

description:
10.1
Replicate 1.

value: peripheral blood mononuclear cell (PBMC)

value: MVA85A vaccination

tag: days post-vaccination

tag: incubation conditions

value: 6hrs media

tag: sample type

value: control


title: vol16 6hr mva85a in vitro

description:
11.1
Replicate 1.

value: 6hrs MVA85A


title: LCS-CCA-MI01

description: Gene expression data from ICC

value: Liver Tumor Tissue

value: Intrahepatic Cholangiocarcinoma (ICC)


title: MDS_patient16_RARS [Methylation]


title: vol20 pbmc day 2, rep 1

description:
8.1
Replicate 1.


title: MDS_patient14 [Methylation]


title: vol24 pbmc day 2 rep 2

description:
12.1
Replicate 2


title: vol20 pbmc day 7, rep 1

description:
9.1
Replicate 1.

source_name: frozen human pbmc, MVA85A, d7


title: MDS_patient15 [Methylation]


title: MDS_patient18_RARS [Methylation]


title: NoL_pool1 [Methylation]


title: Strain D7S-1 rep 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain D7S-1

value: a

tag: strain


title: Strain D7S-1 rep 2


title: vol20 pbmc day 0, rep 1

description:
7.1
Replicate 1.


title: Strain HK1651 rep 2_2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain HK1651

value: b


title: Strain HK1651 rep 1_2


title: MDS_patient12_RA [Methylation]

value: Refractory anemia (RA)


title: vol11 pbmc day 2, rep 1

description:
5.1
Replicate 1.

value: intradermal (ID)


title: MDS_patient11_RA [Methylation]


title: Strain ANH9381 rep 2

description: Gene expression of Aggregatibacter actinomycetemcomitans strain ANH9381

hyb_protocol: The labeled samples were hybridized to the custom Agilent slides following the recommended protocol. A change to the protocol was made to use a nitrogen gun for drying the arrays after washing (instead of centrifugation or drying solution).

scan_protocol: Scans were done using the Agilent Scanner 6000C using manufacturer’s recommended settings for 1-color gene expression (scan area 61 x 21.6mm, 5um resolution, single pass, Green channel only, XDR selected, XDR Hi 100%, XDR Lo 10%). For the 8 x 15K custom arrays we had run, we scanned at 5um resolution, dual pass at 100% and 10% PMT in one channel only (green, or cy-3)

data_processing: The data was then Feature extracted using Agilent's Feature Extractor software v10.5 running the extraction protocol GE1_105_Dec08. Expression data obtained from the Agilent Feature Extraction Software were processed using the following steps. First the gProcessedSignal value for all arrays, which is a background subtracted signal, for each probe was extracted. Quantile normalization was then applied across all the array data being compared to adjust for differences in the probe intensity distribution using limma package. The normalized signal values from probes that are targeting the same gene cluster were finally consolidated into a single value by using median.

source_name: Strain ANH9381 rep 2

label_protocol: WeMessageAmp II-Bacteria kit was used for labeling of the RNA (500 ng for each sample) following the protocol recommended by the manufacturer, with a slight modification in the IVT reaction, in which a combination of 2.6uL T7 CTP and 1.4uL of cy-3 labeled CTP were used for the master mix.

growth_protocol: A starter culture was prepared by inoculating the bacteria in tryptic soy broth with 0.6% yeast extract and incubated overnight at 37°C in atmosphere supplemented with 5% CO2. The starter culture (OD650 of 0.06-0.6) was then diluted with fresh broth to ~OD650=0.1 and incubated further for 4 hours. The OD650 was determined again to assure the continued growth of the bacteria (OD650 in the range of 0.12-0.3). Aliquots of the bacterial cultures were also used to determine colony forming unit/ml and checked for contamination.

extract_protocol: The bacterial RNA was isolated using RiboPure™-Bacteria Kit (Life technology). The resultant RNAs were checked for DNA contamination using the 16S-F and 16S-R as primers and Taq polymerase. The RNAs were then stored at -70o until use.


title: vol11 pbmc day 0, rep 1

description:
4.1
Replicate 1.


title: Strain D41S-1 rep 2

description: Gene expression of Aggregatibacter actinomycetemcomitans strain D41S-1

source_name: Strain D41S-1 rep 2


title: MDS_patient10_RARS [Methylation]


title: Strain ANH9381 rep 1

source_name: Strain ANH9381 rep 1


title: vol11 pbmc day 7, rep 1

description:
6.1
Replicate 1.


title: Strain SCC1398 rep 1

description: Gene expression of Aggregatibacter actinomycetemcomitans strain SCC1398

source_name: Strain SCC1398 rep 1


title: Strain D41S-1 rep 1

source_name: Strain D41S-1 rep 1


title: MDS_patient13_RA [Methylation]


title: Strain SCC1398 rep 2

source_name: Strain SCC1398 rep 2


title: vol1 pbmc day 2, rep 1

description:
2.1
Replicate 1.

value: intramuscular (IM)


title: MDS_patient05 [Methylation]


title: MDS_patient07 [Methylation]


title: GFPKO_rep3

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

description: Spleen and Lymph Node sorted cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression arrays were normalized in Bioconductor, using RMA and median polish settings in the expresso package.

source_name: GFP+ CD4+ T cells from Foxp3GFPKO/WT mice

label_protocol: Affymetrix protocol

growth_protocol: Cells were harvested from 6-8wk old mice.  T cells were purified by Dynal CD4 T cell positive selection kit and double sorted on GFP, etc.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructions.

value: GFP+ CD4+ T cells


title: MDS_patient06 [Methylation]

value: Control. Healty


title: MDS_patient04_RARS [Methylation]


title: MDS_patient08_RARS [Methylation]


title: Treg_rep3

description: Spleen and Lymph Node sorted cells

source_name: Foxp3-positive CD4+ T cells

value: Foxp3-positive CD4+ T cells


title: vol1 pbmc day 0, rep 1

description:
1.1
Replicate 1.

value: healthy


title: vol1 pbmc day 7, rep 1

description:
3.1
Replicate 1.


title: Treg_rep4

description: Spleen and Lymph Node sorted cells


title: GFPKO_rep1

description: Spleen and Lymph Node sorted cells


title: Strain D28S-1 rep 2

description: Gene expression of Aggregatibacter actinomycetemcomitans strain D28S-1

source_name: Strain D28S-1 rep 2


title: Strain HK1651 rep 2

description: Gene expression of Aggregatibacter actinomycetemcomitans strain HK1651

source_name: Strain HK1651 rep 2


title: Strain D28S-1 rep 1

source_name: Strain D28S-1 rep 1


title: Strain HK1651 rep 1

source_name: Strain HK1651 rep 1


title: Treg_rep5

description: Spleen and Lymph Node sorted cells


title: TN_rep3

description: Spleen and Lymph Node sorted cells

source_name: Naïve Foxp3-negative CD4+ T cells

value: Naïve Foxp3-negative CD4+ T cells


title: MDS_patient03_RARS [Methylation]

value: Low-Risk Myelodysplastic Syndrome

value: Refractory anemia with ringed sideroblasts (RARS)


title: Treg_rep1

description: Spleen and Lymph Node sorted cells


title: Treg_rep2

description: Spleen and Lymph Node sorted cells


title: MDS_patient09_RARS [Methylation]


title: MDS_patient02_RA [Methylation]


title: MDS_patient01_RA [Methylation]


title: GFPKO_rep2

description: Spleen and Lymph Node sorted cells


title: ulcerative colitis mucosa 02b (Illumina)

status: Public on Sep 27 2012

city: Kiel

first: Zhe

last: Feng

address: Schittenhelmstr. 12

country: Germany

institute: Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany

description: Genomic DNA extracted from intestinal mucosa was genotyped using The HumanMethylation27 BeadChip (Illumina).

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended scanner setting

data_processing: BeadStudio software v3.2

source_name: ulcerative colitis mucosa

label_protocol: A single base extension was performed using labelled DNP- and biotin labelled dNTPs. See the Illumina Infinium 27k methylation assay protocol.

extract_protocol: DNA was extracted at Tepnel (www.tepnel.com) using a chloroform extraction method and 800ng DNA from each sample was bisulphite converted using the EZ DNA Methylation Kit D5008 (Zymo Research, Orange, CA, USA)

value: Sigmoid colon mucosa

tag: discordant twins id (a&b twins)

tag: diagnosis

value: inflammatory mucosa


title: ulcerative colitis mucosa 07b (Illumina)


title: ulcerative colitis mucosa 08b (Illumina)


title: ulcerative colitis mucosa 12b (Illumina)


title: TN_rep1

description: Spleen and Lymph Node sorted cells

tag: cell type


title: ulcerative colitis mucosa 06b (Illumina)

value: Ileum mucosa


title: Healthy mucosa 10a (Illumina)

source_name: healthy mucosa

value: healthy mucosa


title: ulcerative colitis mucosa 04b (Illumina)


title: ulcerative colitis mucosa 10b (Illumina)


title: Healthy mucosa 03a (Illumina)


title: Healthy mucosa 07a (Illumina)


title: ulcerative colitis mucosa 01b (Illumina)


title: Healthy mucosa 06a (Illumina)


title: Healthy mucosa 09a (Illumina)


title: Healthy mucosa 12a (Illumina)


title: Healthy mucosa 01a (Illumina)


title: ulcerative colitis mucosa 03b (Illumina)


title: ulcerative colitis mucosa 09b (Illumina)


title: Healthy mucosa 08a (Illumina)


title: Healthy mucosa 02a (Illumina)


title: Healthy mucosa 04a (Illumina)


title: TN_rep2

description: Spleen and Lymph Node sorted cells


title: Tumor 10_4C @ 5mins

city: INDIANAPOLIS

first: Nick

last: Liu

state: Indiana

address: 535 Barnhill Drive Suite 420

department: Department of Urology

institute: Indiana University Hospital

description: Gene expression data from tumor 10 at ischemic conditions

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 olgionucleotide array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Each array was  washed, stained and scanned by the Affymetrix GeneChip 3000 Scanner. Raw intensities for each probe were stored as .DAT and .CEL files by the GeneChip Operating Software v1.4 (Affymetrix Inc, Santa Clara, CA USA).

data_processing:
Complete analyses of array data were carried out in BRB-Array Tools v3.7 (http://linus.nci.nih.gov/BRB-ArrayTools.html)
Processed/Filtered and Log2_transformed array intensities

source_name: Tumor 10_4C @ 5mins

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using GeneChip Two-Cycle cDNA Target Synthesis Kit (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: 10 renal tumors were divided and treated under the above listed conditions and snap frozen at 5, 30, 60, 120 and 240 minutes after surgical resection

value: VHL Clear Cell Renal Cell Carcinoma

tag: patient

value: Tumor 10

value: 4C @ 5mins


title: Tumor 10_37C @ 120 mins

source_name: Tumor 10_37C @ 120 mins


title: Tumor 10_22C @ 5 mins

source_name: Tumor 10_22C @ 5 mins

value: 22C @ 5 mins


title: Tumor 10_37C @ 30 mins

source_name: Tumor 10_37C @ 30 mins

value: 37C @ 30 mins


title: Tumor 9_4C @ 60mins

description: Gene expression data from tumor 9 at ischemic conditions

source_name: Tumor 9_4C @ 60mins

value: Tumor 9

value: 4C @ 60mins


title: Tumor 10_22C @ 120 mins

source_name: Tumor 10_22C @ 120 mins


title: Tumor 10_37C @ 5 mins

source_name: Tumor 10_37C @ 5 mins

value: 37C @ 5 mins


title: Tumor 10_4C @ 120 mins

source_name: Tumor 10_4C @ 120 mins

value: 4C @ 120 mins


title: Tumor 9_37C @ 120 mins

source_name: Tumor 9_37C @ 120 mins


title: Tumor 9_22C @ 60 mins

source_name: Tumor 9_22C @ 60 mins

value: 22C @ 60 mins


title: Tumor 10_4C @ 60mins

source_name: Tumor 10_4C @ 60mins


title: Tumor 9_4C @ 120 mins

source_name: Tumor 9_4C @ 120 mins


title: Tumor 9_22C @ 120 mins

source_name: Tumor 9_22C @ 120 mins


title: Tumor 9_22C @ 30 mins

source_name: Tumor 9_22C @ 30 mins

value: 22C @ 30 mins


title: Tumor 10_22C @ 60 mins

source_name: Tumor 10_22C @ 60 mins


title: Tumor 9_4C @ 30mins

source_name: Tumor 9_4C @ 30mins

value: 4C @ 30mins


title: Tumor 9_37C @ 60 mins

source_name: Tumor 9_37C @ 60 mins

value: 37C @ 60 mins


title: Tumor 10_4C @ 240 mins

source_name: Tumor 10_4C @ 240 mins

value: 4C @ 240 mins


title: Tumor 10_37C @ 60 mins

source_name: Tumor 10_37C @ 60 mins


title: Tumor 10_22C @ 30 mins

source_name: Tumor 10_22C @ 30 mins


title: Tumor 10_4C @ 30mins

source_name: Tumor 10_4C @ 30mins


title: Tumor 10_Snap Frozen

source_name: Tumor 10_Snap Frozen

value: Snap Frozen


title: Tumor 9_22C @ 5 mins

source_name: Tumor 9_22C @ 5 mins


title: Tumor 9_4C @ 5mins

source_name: Tumor 9_4C @ 5mins


title: Tumor 9_4C @ 240 mins

source_name: Tumor 9_4C @ 240 mins


title: Tumor 9_37C @ 30 mins

source_name: Tumor 9_37C @ 30 mins


title: Tumor 9_37C @ 5 mins

source_name: Tumor 9_37C @ 5 mins


title: Tumor 9_Snap Frozen

source_name: Tumor 9_Snap Frozen


title: Tumor 8_37C @ 120 mins

description: Gene expression data from tumor 8 at ischemic conditions

source_name: Tumor 8_37C @ 120 mins

value: Tumor 8


title: Tumor 8_37C @ 5 mins

source_name: Tumor 8_37C @ 5 mins


title: Tumor 8_4C @ 120 mins

source_name: Tumor 8_4C @ 120 mins


title: Tumor 8_37C @ 30 mins

source_name: Tumor 8_37C @ 30 mins


title: Tumor 8_22C @ 120 mins

source_name: Tumor 8_22C @ 120 mins


title: Tumor 8_4C @ 60mins

source_name: Tumor 8_4C @ 60mins


title: Tumor 8_22C @ 60 mins

source_name: Tumor 8_22C @ 60 mins


title: Tumor 8_22C @ 5 mins

source_name: Tumor 8_22C @ 5 mins


title: Tumor 8_4C @ 5mins

source_name: Tumor 8_4C @ 5mins


title: Tumor 8_22C @ 30 mins

source_name: Tumor 8_22C @ 30 mins


title: Tumor 7_37C @ 120 mins

description: Gene expression data from tumor 7 at ischemic conditions

source_name: Tumor 7_37C @ 120 mins

value: Tumor 7


title: Tumor 7_37C @ 60 mins

source_name: Tumor 7_37C @ 60 mins

value: VHL Clear Cell Renal Cell Carcinoma


title: Tumor 7_22C @ 60 mins

source_name: Tumor 7_22C @ 60 mins


title: Tumor 7_37C @ 30 mins

source_name: Tumor 7_37C @ 30 mins


title: Tumor 7_Snap Frozen

source_name: Tumor 7_Snap Frozen


title: Tumor 7_4C @ 30mins

source_name: Tumor 7_4C @ 30mins


title: Tumor 7_4C @ 60mins

source_name: Tumor 7_4C @ 60mins


title: Tumor 7_4C @ 240 mins

source_name: Tumor 7_4C @ 240 mins


title: Tumor 7_4C @ 5mins

source_name: Tumor 7_4C @ 5mins


title: Tumor 7_37C @ 5 mins

source_name: Tumor 7_37C @ 5 mins


title: Tumor 7_22C @ 5 mins

source_name: Tumor 7_22C @ 5 mins


title: Tumor 7_22C @ 30 mins

source_name: Tumor 7_22C @ 30 mins


title: Tumor 6_37C @ 60 mins

description: Gene expression data from tumor 6 at ischemic conditions

source_name: Tumor 6_37C @ 60 mins

value: Tumor 6


title: Tumor 7_22C @ 120 mins

source_name: Tumor 7_22C @ 120 mins


title: Tumor 6_37C @ 120 mins

source_name: Tumor 6_37C @ 120 mins


title: Tumor 8_Snap Frozen

source_name: Tumor 8_Snap Frozen


title: Tumor 7_4C @ 120 mins

source_name: Tumor 7_4C @ 120 mins


title: Tumor 6_37C @ 5 mins

source_name: Tumor 6_37C @ 5 mins


title: Tumor 6_22C @ 60 mins

source_name: Tumor 6_22C @ 60 mins


title: Tumor 6_4C @ 120 mins

source_name: Tumor 6_4C @ 120 mins


title: Tumor 6_22C @ 120 mins

source_name: Tumor 6_22C @ 120 mins


title: Tumor 6_22C @ 30 mins

source_name: Tumor 6_22C @ 30 mins


title: Tumor 6_4C @ 30mins

source_name: Tumor 6_4C @ 30mins


title: Tumor 6_Snap Frozen

source_name: Tumor 6_Snap Frozen


title: Tumor 8_4C @ 240 mins

source_name: Tumor 8_4C @ 240 mins


title: Tumor 5_37C @ 120 mins

description: Gene expression data from tumor 5 at ischemic conditions

source_name: Tumor 5_37C @ 120 mins

value: Tumor 5


title: Tumor 6_4C @ 240 mins

source_name: Tumor 6_4C @ 240 mins


title: Tumor 5_37C @ 60 mins

source_name: Tumor 5_37C @ 60 mins


title: Tumor 5_22C @ 30 mins

source_name: Tumor 5_22C @ 30 mins


title: Tumor 5_22C @ 5 mins

source_name: Tumor 5_22C @ 5 mins

value: 22C @ 5 mins


title: Tumor 6_4C @ 60mins

source_name: Tumor 6_4C @ 60mins


title: Tumor 6_37C @ 30 mins

source_name: Tumor 6_37C @ 30 mins

value: 37C @ 30 mins


title: Tumor 5_4C @ 30mins

source_name: Tumor 5_4C @ 30mins


title: Tumor 4_37C @ 30 mins

description: Gene expression data from tumor 4 at ischemic conditions

source_name: Tumor 4_37C @ 30 mins

value: Tumor 4


title: Tumor 6_22C @ 5 mins

source_name: Tumor 6_22C @ 5 mins


title: Tumor 5_4C @ 60mins

source_name: Tumor 5_4C @ 60mins

value: 4C @ 60mins


title: Dll1 GFP high/CD24high 2

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using featuere extraction (V.9.5.3, Agilent Technologies).

source_name: FACS sorted epithelial intestinal cells from Dll1-EGFP-ires-CreERT2 mice

label_protocol: 100 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Cell fractions of intestines from Dll1-EGFP-ires-CreERT2 mice were used, expressing GFP under the control of the Dll1 promoter. RNA was isolated from three FACS sorted cell populations, all expressing GFP at high levels (GFPhi) and three levels of Cd24 (low, medium, high). One additional cell fraction was isolated from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promotor. RNA was isolated from FACS sorted GFP high cells, which constitute intestinal stem cells.

extract_protocol: Rna was isolated using Trizol (Invitrogen)

tag: genotype/variation

value: Dll1-EGFP-ires-CreERT2 mice

tag: promoter

tag: gfp expression

value: high

tag: cd24 expression

source_name: Total RNA from mouse small intestine

tag: source

value: whole small intestine


title: Tumor 5_4C @ 240 mins

source_name: Tumor 5_4C @ 240 mins

tag: tissue


title: Tumor 5_37C @ 30 mins

source_name: Tumor 5_37C @ 30 mins


title: Tumor 5_4C @ 5mins

source_name: Tumor 5_4C @ 5mins

value: 4C @ 5mins


title: Dll1 GFP high/CD24medium 1

value: medium


title: Tumor 5_Snap Frozen

source_name: Tumor 5_Snap Frozen


title: Tumor 6_4C @ 5mins

source_name: Tumor 6_4C @ 5mins


title: Tumor 5_22C @ 120 mins

source_name: Tumor 5_22C @ 120 mins


title: Tumor 5_37C @ 5 mins

source_name: Tumor 5_37C @ 5 mins

value: 37C @ 5 mins


title: Tumor 5_22C @ 60 mins

source_name: Tumor 5_22C @ 60 mins

value: 22C @ 60 mins


title: Tumor 4_22C @ 120 mins

source_name: Tumor 4_22C @ 120 mins


title: Tumor 4_37C @ 60 mins

source_name: Tumor 4_37C @ 60 mins

value: 37C @ 60 mins


title: Dll1 GFP high/CD24low 2

value: low


title: Dll1 GFP high/CD24low 1


title: Dll1 GFP high/CD24medium 2


title: Tumor 4_37C @ 120 mins

source_name: Tumor 4_37C @ 120 mins


title: Dll1 GFP high/CD24high 1


title: Tumor 5_4C @ 120 mins

source_name: Tumor 5_4C @ 120 mins

value: 4C @ 120 mins


title: Tumor 4_22C @ 60 mins

source_name: Tumor 4_22C @ 60 mins

value: VHL Clear Cell Renal Cell Carcinoma


title: Tumor 4_37C @ 5 mins

source_name: Tumor 4_37C @ 5 mins


title: Tumor 4_4C @ 240 mins

source_name: Tumor 4_4C @ 240 mins

value: 4C @ 240 mins


title: Tumor 8_4C @ 30mins

source_name: Tumor 8_4C @ 30mins

value: Tumor 8

value: 4C @ 30mins


title: Lgr5 GFP high

source_name: FACS sorted epithelial intestinal cells from Lgr5-EGFP-ires-CreERT2 mice

value: Lgr5-EGFP-ires-CreERT2 mice

source_name: Total RNA from mouse small intestine


title: T-cell-14h-r3

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: Gene expression data from Con A activated 14hrs T cells

hyb_protocol: Four replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000.

data_processing: CEL files were imported into software affylmGUI (DOI: 10.1093/bioinformatics/btl025), which calls GC-RMA (DOI: 10.1198/016214504000000683) to generated the normalized probset data (default parameters).

source_name: Resting T cells, conconavalin A (conA) activation for 14hrs

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’IVTexpress Labeling kit following manufacturer’s protocol.

growth_protocol: Isolated splenocytes were cultured at 0.5-1 X 106 cells /ml in 37oC and 5% of CO2 incubator with RPMI 1640 (Gibco-Invitrogen) in the presence of Hepes, L-glutamine, sodium pyruvate and 50mM β-mercaptoethanol (SIGMA).

treatment_protocol: B-splenocytes were treated with 25ug/ml of LPS for 0-4hrs.  The T-cells were treated with 7.5ug/ml of ConA for 0, 4 or 14 hrs, respectively.

value: spleen


title: T-cell-4h-r2

description: Gene expression data from Con A activated 4hrs T cells

source_name: Resting T cells, conconavalin A (conA) activation for 4hrs


title: Tumor 8_37C @ 60 mins

source_name: Tumor 8_37C @ 60 mins


title: T-cell-14h-r2


title: T-cell-0h-r1

description: Gene expression data from naïve resting T cells

source_name: Resting T cells


title: B-cell-4h-r1

description: Gene expression data from LPS stimulated 4hrs B cells

source_name: Quiescent B cells, lipopolysaccharide (LPS) treatment for 4hrs


title: Tumor 4_22C @ 5 mins

source_name: Tumor 4_22C @ 5 mins

value: Tumor 4

value: 22C @ 5 mins


title: T-cell-4h-r1


title: T-cell-14h-r1


title: Tumor 3_37C @ 60 mins

description: Gene expression data from tumor 3 at ischemic conditions

source_name: Tumor 3_37C @ 60 mins

value: Tumor 3


title: Tumor 4_22C @ 30 mins

source_name: Tumor 4_22C @ 30 mins

value: 22C @ 30 mins


title: Tumor 3_37C @ 120 mins

source_name: Tumor 3_37C @ 120 mins


title: Tumor 3_22C @ 120 mins

source_name: Tumor 3_22C @ 120 mins


title: T-cell-0h-r3


title: Tumor 4_4C @ 30mins

source_name: Tumor 4_4C @ 30mins


title: Tumor 3_37C @ 5 mins

source_name: Tumor 3_37C @ 5 mins


title: Tumor 4_4C @ 5mins

source_name: Tumor 4_4C @ 5mins

value: 4C @ 5mins


title: T-cell-0h-r2


title: T-cell-4h-r3


title: Tumor 4_Snap Frozen

source_name: Tumor 4_Snap Frozen

value: Snap Frozen


title: Tumor 4_4C @ 60mins

source_name: Tumor 4_4C @ 60mins

value: 4C @ 60mins


title: Tumor 3_4C @ 60mins

source_name: Tumor 3_4C @ 60mins


title: Tumor 3_22C @ 30 mins

source_name: Tumor 3_22C @ 30 mins


title: B-cell-0h-r3

description: Gene expression data from naïve resting B cells

source_name: Quiescent B cells


title: Tumor 3_4C @ 240 mins

source_name: Tumor 3_4C @ 240 mins


title: Tumor 4_4C @ 120 mins

source_name: Tumor 4_4C @ 120 mins


title: B-cell-4h-r3


title: B-cell-0h-r2


title: Airway epithelial cells infected with SIRT1, biological replicate 4

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: SIRT1 activated 4

hyb_protocol: Affymetrix Suggested Protocol

scan_protocol: Affymetrix Suggested Protocol

data_processing:
The CEL files were processed using RMA and the ENTREZ Gene CDF file (version 11.0.1).
probe group file: HuEx10stv2_Hs_ENTREZG_mapping
meta-probeset file: HuEx10stv2_Hs_ENTREZG_probe_tab

label_protocol: Affymetrix Suggested Protocol

growth_protocol: Normal airway epithelial cells were obtained from mainstream bronchial brushings in 3 never smoke smoker volunteers and pooled for the development of the pathway signatures.  Cells were dislodged into bronchial epithelial growth medium (BEGM), and frozen down at -80° C in media (BEGM, serum, and 10% glycerol) after centrifugation.  Cells were subsequently grown on collagen-coated tissue-culture dish in BEGM.

extract_protocol: Qiagen RNeasy kit following manufacturer protocol.

treatment_protocol: Adenoviruses  were used to infect cells with constructs that express key genes from six different smoking related pathways  - ATM, BCL2, GPX1, IKBKB, SIRT1, NOS2, and GFP as the control. RNA was isolated 18 hours after pathway activation.

value: Primary bronchial epithelial cells from 3 never smokers

tag: pathway

tag: batch

tag: included in analysis

value: No


title: Airway epithelial cells infected with SIRT1, biological replicate 3

description: SIRT1 activated 3

value: Yes


title: Tumor 3_22C @ 60 mins

source_name: Tumor 3_22C @ 60 mins

tag: treatment

value: 22C @ 60 mins


title: Tumor 3_4C @ 120 mins

source_name: Tumor 3_4C @ 120 mins

value: VHL Clear Cell Renal Cell Carcinoma

value: 4C @ 120 mins


title: Tumor 3_22C @ 5 mins

source_name: Tumor 3_22C @ 5 mins


title: Tumor 3_37C @ 30 mins

source_name: Tumor 3_37C @ 30 mins

value: 37C @ 30 mins


title: Tumor 3_4C @ 5mins

source_name: Tumor 3_4C @ 5mins


title: B-cell-4h-r2

source_name: Quiescent B cells, lipopolysaccharide (LPS) treatment for 4hrs


title: Airway epithelial cells infected with NOS2, biological replicate 6

description: NOS2 activated 6


title: Airway epithelial cells infected with SIRT1, biological replicate 2

description: SIRT1 activated 2


title: Tumor 3_4C @ 30mins

source_name: Tumor 3_4C @ 30mins

value: 4C @ 30mins


title: Tumor 3_Snap Frozen

source_name: Tumor 3_Snap Frozen


title: Airway epithelial cells infected with SIRT1, biological replicate 1

description: SIRT1 activated 1


title: Airway epithelial cells infected with SIRT1, biological replicate 7

description: SIRT1 activated 7


title: Airway epithelial cells infected with SIRT1, biological replicate 5

description: SIRT1 activated 5


title: Airway epithelial cells infected with SIRT1, biological replicate 6

description: SIRT1 activated 6


title: Airway epithelial cells infected with NOS2, biological replicate 7

description: NOS2 activated 7


title: Airway epithelial cells infected with NOS2, biological replicate 5

description: NOS2 activated 5


title: Airway epithelial cells infected with NOS2, biological replicate 3

description: NOS2 activated 3


title: Tumor 2_37C @ 60 mins

description: Gene expression data from tumor 2 at ischemic conditions

source_name: Tumor 2_37C @ 60 mins

value: Tumor 2

value: 37C @ 60 mins


title: B-cell-0h-r1

value: spleen


title: Airway epithelial cells infected with NOS2, biological replicate 2

description: NOS2 activated 2


title: Airway epithelial cells infected with NOS2, biological replicate 1

description: NOS2 activated 1


title: Tumor 2_37C @ 30 mins

source_name: Tumor 2_37C @ 30 mins


title: Tumor 2_37C @ 5 mins

source_name: Tumor 2_37C @ 5 mins

value: 37C @ 5 mins


title: Airway epithelial cells infected with IKBKB, biological replicate 7

description: IKBKB activated 7

value: IKBKB


title: Tumor 2_22C @ 30 mins

source_name: Tumor 2_22C @ 30 mins

value: 22C @ 30 mins


title: Tumor 2_22C @ 60 mins

source_name: Tumor 2_22C @ 60 mins


title: Tumor 2_22C @ 120 mins

source_name: Tumor 2_22C @ 120 mins


title: Tumor 2_22C @ 5 mins

source_name: Tumor 2_22C @ 5 mins

value: 22C @ 5 mins


title: Tumor 2_37C @ 120 mins

source_name: Tumor 2_37C @ 120 mins


title: Airway epithelial cells infected with NOS2, biological replicate 4

description: NOS2 activated 4


title: Airway epithelial cells infected with IKBKB, biological replicate 4

description: IKBKB activated 4


title: Tumor 1_37C @ 60 mins

description: Gene expression data from tumor 1 at ischemic conditions

source_name: Tumor 1_37C @ 60 mins

value: Tumor 1


title: Tumor 2_4C @ 120 mins

source_name: Tumor 2_4C @ 120 mins


title: Airway epithelial cells infected with IKBKB, biological replicate 5

description: IKBKB activated 5


title: Airway epithelial cells infected with IKBKB, biological replicate 2

description: IKBKB activated 2


title: Airway epithelial cells infected with IKBKB, biological replicate 6

description: IKBKB activated 6


title: Airway epithelial cells infected with IKBKB, biological replicate 3

description: IKBKB activated 3


title: Airway epithelial cells infected with GPX1, biological replicate 6

description: GPX1 activated 6


title: Airway epithelial cells infected with GPX1, biological replicate 7

description: GPX1 activated 7


title: Tumor 2_4C @ 60mins

source_name: Tumor 2_4C @ 60mins

value: 4C @ 60mins


title: Tumor 2_4C @ 30mins

source_name: Tumor 2_4C @ 30mins


title: Tumor 1_37C @ 120 mins

source_name: Tumor 1_37C @ 120 mins


title: Tumor 2_4C @ 5mins

source_name: Tumor 2_4C @ 5mins

value: 4C @ 5mins


title: Airway epithelial cells infected with GPX1, biological replicate 8

description: GPX1 activated 8

value: Primary bronchial epithelial cells from 3 never smokers


title: Tumor 2_4C @ 240 mins

source_name: Tumor 2_4C @ 240 mins

value: 4C @ 240 mins


title: Tumor 2_Snap Frozen

source_name: Tumor 2_Snap Frozen

value: Snap Frozen


title: Airway epithelial cells infected with IKBKB, biological replicate 1

description: IKBKB activated 1

value: Yes


title: Airway epithelial cells infected with GPX1, biological replicate 2

description: GPX1 activated 2


title: Tumor 1_37C @ 30 mins

source_name: Tumor 1_37C @ 30 mins

value: VHL Clear Cell Renal Cell Carcinoma


title: Airway epithelial cells infected with GPX1, biological replicate 1

description: GPX1 activated 1


title: Tumor 1_22C @ 60 mins

source_name: Tumor 1_22C @ 60 mins

value: 22C @ 60 mins


title: Airway epithelial cells infected with GPX1, biological replicate 3

description: GPX1 activated 3


title: Airway epithelial cells infected with GPX1, biological replicate 5

description: GPX1 activated 5

value: No


title: Airway epithelial cells infected with GFP, biological replicate 8

description: GFP control 8

value: GFP


title: Airway epithelial cells infected with GPX1, biological replicate 4

description: GPX1 activated 4


title: Tumor 1_22C @ 5 mins

source_name: Tumor 1_22C @ 5 mins


title: Airway epithelial cells infected with GFP, biological replicate 7

description: GFP control 7


title: Tumor 1_22C @ 30 mins

source_name: Tumor 1_22C @ 30 mins


title: Airway epithelial cells infected with GFP, biological replicate 6

description: GFP control 6


title: Tumor 1_4C @ 60mins

source_name: Tumor 1_4C @ 60mins


title: Tumor 1_37C @ 5 mins

source_name: Tumor 1_37C @ 5 mins


title: Tumor 1_4C @ 240 mins

source_name: Tumor 1_4C @ 240 mins


title: Tumor 1_4C @ 120 mins

source_name: Tumor 1_4C @ 120 mins

value: 4C @ 120 mins


title: Tumor 1_4C @ 5mins

source_name: Tumor 1_4C @ 5mins


title: Tumor 1_Snap Frozen

source_name: Tumor 1_Snap Frozen


title: Airway epithelial cells infected with GFP, biological replicate 1

description: GFP control 1


title: Airway epithelial cells infected with GFP, biological replicate 2

description: GFP control 2


title: Airway epithelial cells infected with GFP, biological replicate 5

description: GFP control 5


title: Airway epithelial cells infected with GFP, biological replicate 3

description: GFP control 3


title: Airway epithelial cells infected with GFP, biological replicate 4

description: GFP control 4


title: Airway epithelial cells infected with BCL2, biological replicate 8

description: BCL2 activated 8


title: Airway epithelial cells infected with BCL2, biological replicate 6

description: BCL2 activated 6


title: Airway epithelial cells infected with BCL2, biological replicate 7

description: BCL2 activated 7


title: AML [ ID_42 ]

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

description: AML [ ID_42 ], ID42_ULM_00085.CEL

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

scan_protocol: The samples were scanned on Affymetrix GeneChip Scanner GCS3000 system using default settings and the software GCOS version 1.2 or newer.

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

source_name: cytogenetically normal AML (CN-AML), CEBPA: n/a, FLT3-ITD: mut, FLT3-TKD: wt, NPM1: wt

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

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

treatment_protocol: Diagnostic samples were collected from untreated patients (de novo AML).

value: Acute myeloid leukemia (AML)

value: mononuclear

tag: cell source

value: bone marrow


title: AML [ ID_33 ]

description: AML [ ID_33 ], ID33_UB_13112006_06KM1590.CEL

source_name: cytogenetically normal AML (CN-AML), CEBPA: wt, FLT3-ITD: mut, FLT3-TKD: wt, NPM1: mut


title: Tumor 1_4C @ 30mins

source_name: Tumor 1_4C @ 30mins

value: 4C @ 30mins


title: Airway epithelial cells infected with BCL2, biological replicate 5

description: BCL2 activated 5


title: AML [ ID_32 ]

description: AML [ ID_32 ], ID32_UB_13112006_06KM1561.CEL

source_name: cytogenetically normal AML (CN-AML), CEBPA: mut, FLT3-ITD: wt, FLT3-TKD: wt, NPM1: wt


title: Airway epithelial cells infected with BCL2, biological replicate 4

description: BCL2 activated 4


title: AML [ ID_31 ]

description: AML [ ID_31 ], ID31_MR_21052006_05KM953.CEL

source_name: cytogenetically normal AML (CN-AML), CEBPA: wt, FLT3-ITD: wt, FLT3-TKD: wt, NPM1: mut


title: Airway epithelial cells infected with BCL2, biological replicate 2

description: BCL2 activated 2


title: AML [ ID_30 ]

description: AML [ ID_30 ], ID30_MR_02062006_05PB1734.CEL

source_name: cytogenetically normal AML (CN-AML), CEBPA: wt, FLT3-ITD: wt, FLT3-TKD: wt, NPM1: wt

value: peripheral blood


title: Airway epithelial cells infected with BCL2, biological replicate 3

description: BCL2 activated 3


title: AML [ ID_23 ]

description: AML [ ID_23 ], ID23_ULM_00044.CEL

source_name: cytogenetically normal AML (CN-AML), CEBPA: wt, FLT3-ITD: wt, FLT3-TKD: mut, NPM1: mut


title: AML [ ID_24 ]

description: AML [ ID_24 ], ID24_ULM_00043.CEL


title: AML [ ID_25 ]

description: AML [ ID_25 ], ID25_ULM_00119.CEL


title: Airway epithelial cells infected with BCL2, biological replicate 1

description: BCL2 activated 1


title: Airway epithelial cells infected with ATM, biological replicate 7

description: ATM activated 7

value: ATM


title: AML [ ID_22 ]

description: AML [ ID_22 ], ID22_ULM_00059.CEL


title: AML [ ID_20 ]

description: AML [ ID_20 ], ID20_ULM_00128.CEL


title: AML [ ID_21 ]

description: AML [ ID_21 ], ID21_UB_110706_05KM3026.CEL


title: Airway epithelial cells infected with ATM, biological replicate 4

description: ATM activated 4


title: Airway epithelial cells infected with ATM, biological replicate 2

description: ATM activated 2


title: Airway epithelial cells infected with ATM, biological replicate 5

description: ATM activated 5


title: AML [ ID_03 ]

description: AML [ ID_03 ], ID03_ULM_00111.CEL


title: Airway epithelial cells infected with ATM, biological replicate 3

description: ATM activated 3


title: AML [ ID_16 ]

description: AML [ ID_16 ], ID16_ULM_00129.CEL


title: AML [ ID_10 ]

description: AML [ ID_10 ], ID10_UB_06KM2582_15052008.CEL


title: Airway epithelial cells infected with ATM, biological replicate 6

description: ATM activated 6


title: AML [ ID_07 ]

description: AML [ ID_07 ], ID07_UB_11102006_05PB4922.CEL

source_name: core binding factor AML, t(8;21), CEBPA: n/a, FLT3-ITD: wt, FLT3-TKD: wt, NPM1: wt


title: Airway epithelial cells infected with ATM, biological replicate 1

description: ATM activated 1


title: CLL with unmutated IgV gene uCLL_4

city: Essen

first: Marc

middle: JS

last: Seifert

state: NRW

address: Virchowstraße 173

department: IFZ

institute: University Hospital Essen

description: batch 3

hyb_protocol: Following fragmentation, cRNA was hybridized on GPL570 Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G and GeneChip Command Console 3.2 software.

data_processing: Data were normalized according to vsn and imported into Gene Spring GX 7.3.1 and filtered according to a minimum amount of 4 present calls (according to GC-RMA normalization and flagging by MAS5) within at least one condition (cell type) and raw signal above 50. Remaining probe sets were exported, processed with ComBat software to compell batch effects and reimported into Gene Spring for further analysis.

source_name: human peripheral blood

label_protocol: Two rounded in vitro transcription protocol with Ambion MessageAmpII kit and MessageAmp Biotin Enhanced-Kit according to manufacturer's instructions.

growth_protocol: cell sorting, see sample title

extract_protocol: 10,000 cell samples sorted into Trizol lysis buffer, hydrous phase mixed with equal volume of 70% EtOH and loaded onto Qiagen RNeasy micro colum. Further processing according to manufacturer's instruction.

tag: tumor stage

value: tumor

value: CLL cell with unmutated IgV gene


title: CLL with unmutated IgV gene uCLL_5

description: batch 3