title: CP106-T

description: cpp

tag: tissue type

value: choroid plexus papillomas

tag: p53 status

tag: tissue source


title: CGD-23

status: Public on Nov 01 2014

type: RNA

city: Turku

first: Tiina

middle: Kelkka

last: Ilona

address: Tykistökatu 6A

department: Medicity

country: Finland

institute: University of Turku

hyb_protocol: 750 ng each cRNA sample was hybridized to Illumina’s HumanHT-12 v3 Expression BeadChip at 58 C overnight (18 h) according to manufacturer's instructions.

scan_protocol: Illumina Bead Array Reader (Factor=1, PMT=521, Filter=100%) and the numerical results were extracted with Bead Studio v3.2.6 without any normalization or background subtraction.

data_processing: Quantile normalized and log2 transformed using Bioconductors LIMMA packages in R.

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: from 250 ng total RNA with Ambion's Illumina Total Prep RNA Amplification kit (cat # AMIL1791).cRNA concentrations where checked with Nanodrop ND-1000 and the quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: Whole blood was used as sample material without any ex vivo treatment

extract_protocol: Blood was stored and RNA isolated using reagents in PAXgene Blood RNA Kit (Qiagen, cat# 762174) according to the manufacturer's instructions. Globin was removed using Ambion’s GLOBINclear™–Human Kit (cat# AM1980) using 1-2 ug of blood RNA as starting material.

tag: group

value: Carrier

tag: mutation

value: CYBB

tag: age

value: Adult

tag: Sex

value: Female

tag: chip number

tag: chip position

value: K


title: CP111-T

type: genomic

city: Toronto

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: cpp

hyb_protocol: Hybridization of genomic DNA to Genome-Wide Human SNP Array 6.0 genotyping microarrays took place at the Toronto Centre of Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto, Canada, according to manufacturer's instructions.

scan_protocol: not provided

data_processing:
Partek® Genomics Suite™ 6.5 (PGS) (Partek Inc. St. Louis, USA) was used for initial copy number analysis. Inferred copy number states (regions of deletion or duplication) were derived from Partek's genomic segmentation algorithm (Partek, St Louis,MO) such that segmented regions were significantly different from neighbouring regions (p<0.001) and contained 10 or more probes, with a signal to noise ratio of 0.3. Diploid samples were those with a copy number between 1.75-2.25. Segmentation assumed all somatic chromosomes were diploid. Annotation file: GenomeWideSNP_6.na33.annot.csv
Copy number (by Genomic Segmentation algorithm) and allele ratio data provided.

label: biotin

molecule: genomic DNA

source_name: brain tumor

label_protocol: not provided

growth_protocol: DNA was isolated from fresh-frozen tumor soon after tumor resection

extract_protocol: Tumor genomic DNA was extracted using standard phenol-chloroform extraction from fresh-frozen samples, and the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion, Carlsbad, USA) from FFPE samples.

treatment_protocol: DNA was isolated from fresh-frozen samples (snapped frozen in liquid nitrogen) (n=46) and optimal cutting temperature compound (OCT)-embedded fresh frozen (n=8),  and formalin-fixed paraffin embedded (FFPE) (1) samples.

value: wt

value: frozen


title: CGD-22

value: Child

value: I


title: NIL-DOG1 at 6 hours imbibed seeds, biological rep1

city: koeln

first: Yong

last: Xiang

address: Carl-von-Linne-Weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Normalization, processing and statistical analysis of the raw data were performed using RankProd in R programming. Background correction, normalization, and summarization of probe sets were based on the Affymetrix AGRONOMICS Tiling Array [CDF: agronomics1attairg version 13.0.0] and RMA implemented in the Aroma.Affymetrix package.

organism: Arabidopsis thaliana

source_name: NIL-DOG1 at 6 hours imbibed seeds

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip HT 3' IVT Express Kit Manual, Affymetrix).

growth_protocol: All plants were sown on soil and grown in a growth chamber with a 16-h-light/8-h-dark cycle (22°C/16°C)

extract_protocol: Total RNA was extracted from developing Arabidopsis siliques or imbibed seeds using RNAqueous columns and RNA isolation aid (Ambion) as described previously (Kushiro et al., 2004)

treatment_protocol: No treament

tag: genotype/varation

value: wildtype


title: NIL-DOG1 at 6 hours imbibed seeds, biological rep3


title: NIL-DOG1 at 6 hours imbibed seeds, biological rep2


title: KTS- rep4

city: Parkville

first: Paul

last: Ekert

state: Vic

address: 1G Royal Parade

department: Cell Signalling and Cell Death

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: MEF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was norm-exp background corrected, quantile normalized and log2 transformed, generated using the Bioconductor package limma

organism: Mus musculus

source_name: Murine embryonic fibroblasts infected with tetracycline repressible EWS/WT1-KTS

label_protocol: Standard Illumina labelling protocol

growth_protocol: Primary freshly generated MEFs, infected tetracycline repressible lentivrial vector expressing EWS/WT1-KTS, EWS/WT1+KTS or eGFP control

extract_protocol: Qiagen RNeasy Mini Kit (Qiagen Sciences, MD, USA Cat number:74104).

treatment_protocol: No tetracycline

tag: cell type

value: murine embryonic fibroblasts

tag: transgene

tag: genetic background


title: CGD-21

value: Healthy control

value: No mutation

value: Male

value: B


title: GFP-rep3

description: MEF

source_name: Murine embryonic fibroblasts infected with GFP

value: GFP


title: KTS+ rep4

description: MEF

source_name: Murine embryonic fibroblasts infected with tetracycline repressible EWS/WT1+KTS


title: Ad8_DC E3_D2

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

country: USA

institute: Case Western Reserve University

description:
4625016055_D
Ad8_DC

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-8 V3 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at CGC.

scan_protocol: The arrays were scanned using an Illumina BeadArray scanner and quantified using Genome Studio software (Illumina).

data_processing: Analysis of the iScan output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center (CGC) at http://www.vgtifl.org. Missing values were imputed using the KNN algorithm from the impute R package. Expression intensity filtering was performed keeping probe sets that have expression higher than log2(40) in at least 2 samples,  Expression variability  filtering was performed using the Inter Quartile Range (IQR) across the samples on the log2 is at least 0.3.  Quantile normalization was applied, followed by a log2 transformation and differential gene expression testing using Limma from Bioconductor.

label: Biotin

source_name: CD4+ Tcell

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: SNARF labelled resting CD4+ T cells were cultured with or without syngeneic DC in the presence or absence of NL(AD8)-nef/EGFP (MOI 5) for 5 days, at which time SNARFhiEGFP- CD4+ T cells were sorted for gene expression analysis.

extract_protocol: totalRNA using Qiagen RNeasy Micro Kit  by the Laboratory of Dr. Sekaly at University of Montreal

treatment_protocol: Sorted SNARFhiEGFP- CD4+ T cells were lysed in RLT buffer and stored at -80oC prior to RNA extraction

tag: donor

tag: treatment

value: DC

tag: coculture

value: NL(AD8)-nef/EGFP (MOI 5)

tag: sorted population

value: SNARFhiEGFP- CD4+ Tcell


title: KTS+ rep2

description: MEF


title: CP103-T

description: cpp

tag: tissue type

value: choroid plexus papillomas

value: mut


title: CP104-T

description: cpp

tag: p53 status


title: Ad8_CCL19_D2

description:
4625016055_C
Ad8_CCL19


title: NIL-DOG1 at dry seeds, biological rep3

source_name: NIL-DOG1 at dry seeds


title: GFP-rep2

description: MEF


title: Mouse tumor cells transduced with 18 ul non-targeting shRNA virus_NTB

city: Westmead

first: Andy

middle: C-M

last: Chang

state: New South Wales

address: 214 Hawkesbury Rd

department: Cancer Unit

institute: Children's Medical Research Institute

description:
NTB
control 2

data_processing: Quantile normalization was performed using the normalization function in R/Bioconductor package called beadarray 2.10.0

source_name: 4T1ch9 cells

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

extract_protocol: RNA was extracted with  QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with agilent Bioanalyser.

tag: strain

value: Balb/c

tag: cell line

value: 4T1ch9 cells

tag: genotype/variation

value: control

tag: transduction

value: 18 ul non-targeting shRNA virus


title: NIL-DOG1 at dry seeds, biological rep2


title: CGD-20

tag: group

tag: mutation

tag: age

value: Adult

tag: Sex

value: Female

value: C


title: CP1-T

description: cpc

value: choroid plexus carcinomas

tag: tissue source

value: frozen


title: CGD-19

value: Chronic granulomatous patient

value: Child

tag: chip number

tag: chip position

value: A


title: Ad8_ctrl_D2

description:
4625016055_B
Ad8_ctrl

tag: donor


title: S_meliloti_rpoH1rpoH2_37C_40min_rep3

city: Sendai

first: Hisayuki

last: Mitsui

address: 2-1-1, Katahira, Aoba-ku

department: Graduate School of Life Sciences

country: Japan

institute: Tohoku University

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the third of four biological replicates of mutant cells with heat shock for 40 min, each from separate cultures.

hyb_protocol: Hybridization was performed by Roche Diagnostics Japan, following their standard operating protocol.

scan_protocol: Scanning was performed with GenePix 4000B Microarray Scanner by Roche Diagnostics Japan, following their standard operating protocol.

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 (Roche NimbleGen, Inc.).

organism: Sinorhizobium meliloti 1021

source_name: rpoH1 rpoH2 mutant cells, with heat shock for 40 min

label_protocol: Labeling was performed by Roche Diagnostics Japan, following their standard operating protocol.

growth_protocol: Sinorhizobium meliloti 1021 was grown to mid-log phase (O.D.660nm 0.3) aerobically at 25°C in LB/MC medium.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and further purified using a RNeasy Midi kit (Qiagen). DNA was removed by DNase digestion with the RNase-Free DNase set (Takara Bio). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: genotype

value: rpoH1 rpoH2 double mutant


title: Mock_DC_D2

description:
4625016055_A
Mock_DC

tag: treatment

value: DC

tag: coculture

value: Mock


title: S_meliloti_rpoH1rpoH2_37C_40min_rep4

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the fourth of four biological replicates of mutant cells with heat shock for 40 min, each from separate cultures.


title: Mock_CCL19_D2

description:
4625016054_H
Mock_CCL19

tag: sorted population

value: SNARFhiEGFP- CD4+ Tcell


title: KTS- rep1

description: MEF

tag: cell type

value: murine embryonic fibroblasts

tag: transgene

tag: genetic background


title: KTS- rep2

description: MEF


title: Mock_ctrl_D2

description:
4625016054_G
Mock_ctrl


title: CGD-17

value: Healthy control

value: No mutation

value: Male

value: D


title: CGD-15

value: E


title: S_meliloti_rpoH1rpoH2_37C_40min_rep2

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the second of four biological replicates of mutant cells with heat shock for 40 min, each from separate cultures.


title: GFP-rep1

description: MEF

value: GFP


title: Ad8_CCL19_D1

description:
4625016054_E
Ad8_CCL19

value: NL(AD8)-nef/EGFP (MOI 5)


title: Ad8_DC_D1

description:
4625016054_F
Ad8_DC


title: S_meliloti_rpoH1rpoH2_37C_40min_rep1

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the first of four biological replicates of mutant cells with heat shock for 40 min, each from separate cultures.


title: KTS+ rep1

description: MEF


title: ALI, S5

city: Madison

first: Yury

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

hyb_protocol: The labeled cDNAs were hybridized to Human Gene ST 1.0 GeneChips (Affymetrix) according to the manufacturer’s protocols.

scan_protocol: GeneChips were scanned using the GC3000 7G scanner (Affymetrix).

data_processing: Raw data (CEL files) were uploaded into ArrayStar software version 4.0 (DNASTAR, Inc., Madison, WI, USA) for normalization and statistical analysis. The robust multichip analysis (RMA) algorithm was used for background correction, quantile normalization and median polish summarization.

source_name: differentiated primary sinus epithelial cells, donor S5

label_protocol: cDNA were prepared using Ambion Whole Transcript Target Labelling Kit according to the manufacturer's instructions. Fragmentation and labeling of the single-stranded cDNA was performed using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Sinus and bronchial epithelial tissue samples were obtained from residual surgical specimens. To isolate primary epithelial cells, the tissue was washed with PBS and digested by pronase (Roche) and DNase (Sigma). Primary airway epithelial cells were cultured submerged for 3-4 days in 12-well plates (undifferentiated monolayers, passage 2) or at air-liquid interface for 2 months in transwell inserts (fully-differentiated, passage 2). HeLa (ATCC# CRL-1958) and WisL (human embryonic lung fibroblast) cells were grown in Eagle's Minimum Essential Medium (Lonza); HEK293T (ATCC# CRL-11268) and NCI-H358 (ATCC# CRL-5807) cells were cultured in Dulbecco's Modified Eagle's Medium (Cellgro). Both culture media were supplemented by non-essential amino acids (Gibco) and 10% fetal bovine serum. The established cell lines were cultured in 12-well plates for 2-4 days until they reached 80-90% confluency.

extract_protocol: Extraction of total RNA from cultured cells and whole tissue samples using TRIzol reagent (Life Technologies) was performed according to the manufacturer's instructions.

treatment_protocol: There was no treatment of cultured cells or tissue samples.

value: differentiated primary sinus epithelial cells, cultured at ALI


title: S_meliloti_rpoH1rpoH2_37C_10min_rep4

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the fourth of four biological replicates of mutant cells with heat shock for 10 min, each from separate cultures.

source_name: rpoH1 rpoH2 mutant cells, with heat shock for 10 min


title: CGD-18

value: Adult

value: Female

value: L


title: S_meliloti_rpoH1rpoH2_37C_10min_rep3

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the third of four biological replicates of mutant cells with heat shock for 10 min, each from separate cultures.


title: CGD-14

value: Child

value: B


title: CGD-13

value: Chronic granulomatous patient

value: CYBA

value: A


title: Ad8_ctrl_D1

description:
4625016054_D
Ad8_ctrl

value: control

value: SNARFhiEGFP- CD4+ Tcell


title: Mock_DC_D1

description:
4625016054_C
Mock_DC

value: DC

value: Mock


title: CGD-16

value: Healthy control

value: No mutation

value: Male

value: F


title: ALI, S33

source_name: differentiated primary sinus epithelial cells, donor S33

value: differentiated primary sinus epithelial cells, cultured at ALI


title: Mock_CCL19_D1

description:
4625016054_B
Mock_CCL19


title: ALI, S35

source_name: differentiated primary sinus epithelial cells, donor S35


title: NIL-DOG1 at dry seeds, biological rep1

tag: genotype/varation

value: wildtype


title: Monolayer, S35

source_name: undifferentiated primary sinus epithelial cells, donor S35

value: undifferentiated primary sinus epithelial cells, cultured in monolayers


title: CGD-12

value: Adult

value: D


title: S_meliloti_rpoH1rpoH2_37C_10min_rep2

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the second of four biological replicates of mutant cells with heat shock for 10 min, each from separate cultures.

value: rpoH1 rpoH2 double mutant


title: S_meliloti_rpoH1rpoH2_37C_10min_rep1

description: This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the first of four biological replicates of mutant cells with heat shock for 10 min, each from separate cultures.


title: CGD-11

value: Female


title: CGD-10

value: Chronic granulomatous patient

value: Unknown mutation

value: Child

value: E


title: S_meliloti_wild-type_37C_40min_rep4

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the fourth of four biological replicates of wild-type cells with heat shock for 40 min, each from separate cultures.

source_name: Wild-type cells, with heat shock for 40 min

value: Wild-type


title: CGD-9

value: C


title: S_meliloti_wild-type_37C_40min_rep3

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the third of four biological replicates of wild-type cells with heat shock for 40 min, each from separate cultures.


title: Mock_ctrl_D1

description:
4625016054_A
Mock_ctrl

value: control

value: Mock

value: SNARFhiEGFP- CD4+ Tcell


title: S_meliloti_wild-type_37C_40min_rep2

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the second of four biological replicates of wild-type cells with heat shock for 40 min, each from separate cultures.


title: S_meliloti_wild-type_37C_40min_rep1

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the first of four biological replicates of wild-type cells with heat shock for 40 min, each from separate cultures.


title: Monolayer, S5

source_name: undifferentiated primary sinus epithelial cells, donor S5


title: CGD-8

source_name: Whole blood

value: Carrier

value: CYBB

value: K


title: CGD-7

value: Male

value: G


title: NCI-H358 monolayer

source_name: NCI_H358 lung carcinoma established cell line

tag: cell line

value: lung carcinoma established cell line, cultured in monolayers


title: Monolayer, S33

source_name: undifferentiated primary sinus epithelial cells, donor S33

value: undifferentiated primary sinus epithelial cells, cultured in monolayers


title: Ovules of fuzzy-lintless mutant (ANOI 1960) of G. arboreum L. cv. at 10 dpa, biological replicate 3

city: New Delhi

first: Mogilicherla

last: Kanakachari

state: Delhi

address: LBS Building, PUSA Campus

department: Molecular Biology and Biotechnology

country: India

institute: National Research Centre on Plant Biotechnology

description: Gene expression profiles of fuzzy-lintless ovules of mutant at 10 dpa , biological replicate 3.

scan_protocol: The cotton GeneChip Genome arrays were scanned on a GeneChip scanner 3000.

data_processing: After scannig CEL files were analyzed using GeneSpring GX 11.5 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

organism: Gossypium arboreum

source_name: ovules of fuzzy-lintless mutant of G. arboreum L. cv. at 10 dpa

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 300ng total RNA Following fragmentation, 12 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

growth_protocol: The Gossypium arboreum L. cv. (wild-type) and its fuzzy-lintless mutant (ANOI 1960) were grown in normal agronomic field.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from fibre bearing ovules of wild-type and fuzzy-lintless ovules of mutant (ANOI 1960) .

treatment_protocol: The Gossypium arboreum L. cv. and its fuzzy-lintless mutant (ANOI 1960) were grown under field condition. Flowers were tagged at the day of anthesis and considered as 0 dpa (days post anthesis). Cotton bolls were collected at fibre initiation ( 0 dpa) and elongation (10 dpa) stages. Harvested cotton bolls were immediately frozen in liquid nitrogen and stored at -70°C until used for total RNA extraction.

value: fuzzy-lintless mutant

tag: tissue

value: ovule

tag: developmental stage

value: 10 dpa


title: Ovules of fuzzy-lintless mutant (ANOI 1960) of G. arboreum L. cv. at 10 dpa, biological replicate 2

description: Gene expression profiles of fuzzy-lintless ovules of mutant at 10 dpa , biological replicate 2.

hyb_protocol: Following fragmentation, 12 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.


title: PBE monolayer

description: PBE

source_name: undifferentiated primary bronchial epithelial cells

value: primary bronchial epithelial cells, cultured in monolayers, passage 3


title: CGD-5

tag: group

value: Healthy control

tag: mutation

value: No mutation

tag: age

value: Adult

value: Female

value: L


title: CGD-6

value: Child

tag: Sex

tag: chip number

value: H


title: Nasal brushing

source_name: nasal mucosa obtained via brushing

value: nasal mucosa obtained via brushing


title: S_meliloti_wild-type_37C_10min_rep3

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the third of four biological replicates of wild-type cells with heat shock for 10 min, each from separate cultures.

source_name: Wild-type cells, with heat shock for 10 min

value: Wild-type


title: Ovules of fuzzy-lintless mutant (ANOI 1960) of G. arboreum L. cv. at 10 dpa, biological replicate 1

description: Gene expression profiles of fuzzy-lintless ovules of mutant at 10 dpa , biological replicate 1.


title: S_meliloti_wild-type_37C_10min_rep2

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the second of four biological replicates of wild-type cells with heat shock for 10 min, each from separate cultures.


title: S_meliloti_wild-type_37C_10min_rep4

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the fourth of four biological replicates of wild-type cells with heat shock for 10 min, each from separate cultures.


title: CGD-4

value: Male

tag: chip position

value: I


title: PSE monolayer

description: PSE

source_name: undifferentiated primary sinus epithelial cells

value: primary sinus epithelial cells, cultured in monolayers, passage 2


title: WisL monolayer

description: WisL

source_name: WisL human embryonic lung fibroblasts

value: WisL

value: human embryonic lung fibroblasts, cultured in monolayers


title: Epi cell suspension, S5

source_name: epithelial cell suspension, donor S5

value: epithelial cell suspension

tag: donor


title: CGD-3

value: Chronic granulomatous patient

value: Unknown mutation

value: J


title: Fibre bearing ovules of G. arboreum L. cv. at 10 dpa, biological replicate 2.

description: Gene expression profiles of fibre bearing ovules of G. arboreum L. cv. at 10 dpa, biological replicate 2.

tag: genotype

value: wild type

value: ovule

value: 10 dpa


title: Fibre bearing ovules of G. arboreum L. cv. at 10 dpa, biological replicate 3.

description: Gene expression profiles of fibre bearing ovules of G. arboreum L. cv. at 10 dpa, biological replicate 3.


title: Fibre bearing ovules of G. arboreum L. cv. at 10 dpa, biological replicate 1.

description: Gene expression profiles of fibre bearing ovules of G. arboreum L. cv. at 10 dpa, biological replicate 1.

value: 0 dpa


title: HeLa monolayer

description: HeLa

source_name: HeLa cervical carcinoma established cell line

value: HeLa

value: cervical carcinoma established cell line, cultured in monolayers


title: S_meliloti_wild-type_37C_10min_rep1

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the first of four biological replicates of wild-type cells with heat shock for 10 min, each from separate cultures.


title: S_meliloti_wild-type_nonstress_25C_rep4

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the fourtht of four biological replicates of unstressed wild-type cells used in this experiment, each from separate cultures.

source_name: Wild-type cells, grown at 25°C


title: Ovules of fuzzy-lintless mutant (ANOI 1960) of G. arboreum L. cv. at 0 dpa, biological replicate 3

description: Gene expression profiles of fuzzy-lintless ovules of mutant at 0 dpa , biological replicate 3.

source_name: ovules of fuzzy-lintless mutant of G. arboreum L. cv. at 0 dpa

value: fuzzy-lintless mutant


title: Whole tissue, S25

source_name: whole-tissue snippet of sinus mucosa, donor S25

value: whole-tissue snippet of sinus mucosa


title: CGD-2

value: Healthy control

value: No mutation

value: Child

value: Male

value: H


title: Ovules of fuzzy-lintless mutant (ANOI 1960) of G. arboreum L. cv. at 0 dpa, biological replicate 2

description: Gene expression profiles of fuzzy-lintless ovules of mutant at 0 dpa , biological replicate 2.


title: Whole tissue, S24

source_name: whole-tissue snippet of sinus mucosa, donor S24


title: S_meliloti_wild-type_nonstress_25C_rep3

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the third of four biological replicates of unstressed wild-type cells used in this experiment, each from separate cultures.

value: Wild-type


title: CGD-1

value: Chronic granulomatous patient

value: CYBB

value: G


title: Whole tissue, S17

source_name: whole-tissue snippet of sinus mucosa, donor S17


title: S_meliloti_wild-type_nonstress_25C_rep2

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the second of four biological replicates of unstressed wild-type cells used in this experiment, each from separate cultures.


title: Fibre bearing ovules of G. arboreum L. cv. at 0 dpa, biological replicate 3.

description: Gene expression profiles of fibre bearing ovules of G. arboreum L. cv. at 0 dpa, biological replicate 3.

value: wild type


title: Fibre bearing ovules of G. arboreum L. cv. at 0 dpa, biological replicate 1.

description: Gene expression profiles of fibre bearing ovules of G. arboreum L. cv. at 0 dpa, biological replicate 1.

value: ovule


title: Whole tissue, S11

source_name: whole-tissue snippet of sinus mucosa, donor S11


title: Fibre bearing ovules of G. arboreum L. cv. at 0 dpa, biological replicate 2.

description: Gene expression profiles of fibre bearing ovules of G. arboreum L. cv. at 0 dpa, biological replicate 2.


title: Whole tissue, S16

source_name: whole-tissue snippet of sinus mucosa, donor S16


title: Ovules of fuzzy-lintless mutant (ANOI 1960) of G. arboreum L. cv. at 0 dpa, biological replicate 1

description: Gene expression profiles of fuzzy-lintless ovules of mutant at 0 dpa , biological replicate 1.


title: S_meliloti_wild-type_nonstress_25C_rep1

description: This sample is of wild-type Sinorhizobium meliloti 1021. It is the first of four biological replicates of unstressed wild-type cells used in this experiment, each from separate cultures.


title: Gli1 loss-of-function mutant regenerating prostate, biological rep 3

status: Public on Oct 31 2014

city: Stanford

first: Agnes

last: Lim

state: CA

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

description: ventral and dorsolateral lobes of the regenerating prostate from one mouse

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were processed using the Partek Genomics Suite software and RMA normalized.
probe group file: MoEx-1_0-st-v1.r2.clf
meta-probeset file: MoEx10stv1_Mm_REFSEQ.cdf

source_name: Gli1-/- prostate

label_protocol: Ambion WT Expression kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Mice were castrated when they were 8 weeks old. 2 weeks after castration, a testosterone pellet was implanted sub-cutaneously, and the ventral and dorsolateral lobes of the prostate harvested 3 days later.

extract_protocol: RNA was extracted using the Qiagen Rneasy Plus Mini kit

treatment_protocol: not applicable

value: 10 weeks

value: regenerating prostate


title: Wild-type regenerating prostate, biological rep 3

source_name: Wild type prostate

value: wild-type


title: Wild-type regenerating prostate, biological rep 2


title: HCT116-nc

city: Spartanburg

first: Timothy

middle: J

last: Yeatman

state: SC

address: 101 E Wood St.

institute: Gibbs Cancer Center & Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scaner.

data_processing: The data were analyzed with the Affymetrix GCOS 1.4 software using the MAS 5.0 alorithm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500.

label_protocol: Biotinylated cRNA was prepared according to the Ambion Message Amp Premier protocol using 100 ng of total RNA (Ambion).

growth_protocol: The cells were cultured in RPMI medium supplemented with 10% FBS, within 5% CO2 incubator.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: Five independent transfections using precursor miR-147 or negative control miR were done with HCT116 cells; RNA was then pooled from all 5 in equimolar amounts prior to analysis.

tag: transfection

value: non-coding miR


title: CD14+ IL3

city: Parma

first: Nicola

last: Giuliani

address: Via Gramsci,14

department: Medicina Clinica e Sperimentale

country: Italy

institute: Università degli Studi di Parma

description: Gene expression profiling data of CD14+ cells from buffy coat from healthy donors

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

scan_protocol: HG-U133 2.0 Plus arrays were scanned using the Scanner G3000 7G (Affymetrix).

data_processing: The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization and log2-transformed.

source_name: Periferal blood CD14+ cells from buffy coat treated with IL3

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

growth_protocol: CD14+ cells from healthy donors were obtained also from peripheral blood buffy-coats. The CD14+ cell fraction was obtained by immunomagnetic cells sorting using anti-CD14 monoclonal antibody-coated microbeads (MACS, Miltenyi Biotec., Bergish-Gladbach, Germany). Samples with a purity of more than 90%, tested via flow-cytometry (BD biosciences, San Josè, CA) were analyzed. These samples were evaluated immediately after purification.

extract_protocol: Total RNA was extracted from CD14+ cells with Rneasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: CD14+ cells from healthy donors and patients were seeded 10*6 cells/ml in RPMI 1640 medium supplemented with 5% heat-inactivated fetal bovine serum (FBS), Penicillin (100U/ml), Streptomycin (100μg/ml), L-Glutamine (2mM) and Fungizone antimycotic (2,5μg/ml), all purchased from Life Technologies (Carlsbad, CA). CD14+ cells were treated with or without IL-3 (recombinant human IL-3, Peprotech, Rocky Hill, NJ), at the concentration of 10ng/ml, for 24 hours.

value: peripheral blood

tag: disease state

value: healthy

tag: treatment


title: Gli1 loss-of-function mutant regenerating prostate, biological rep 2


title: lung-SARS-CoV-mutPBM-REP1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: lung, SARS-CoV-mutPBM infected-REP1

hyb_protocol: The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes.

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Background correction by normexp method (with an offset of 50) and normalization of expression data by adjustment of quantiles were performed using LIMMA package (Smyth, 2004).

source_name: lung, SARS-CoV-mutPBM infected

label_protocol: Preparation of probes and hybridization was performed as described in One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies. Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 μl reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer.

growth_protocol: 8 week-old specific-pathogen-free BALB/c Ola Hsd mice females were purchased from Harlan Laboratories.

extract_protocol: At 2 days post infection, lungs from infected mice were collected and homogenized using the gentleMACS Dissociator (Miltenyibiotec). Then, total RNA was extracted using the RNeasy purification kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: BALB/c mice were infected (or Mock-infected) at the age of 16 weeks with 100000 pfu and all protocols were approved by the Ethical Review Committee at The Center for Animal Health Research (CISA-INIA). Both, Infected and Mock-infected mice were housed in a ventilated rack (Allentown, NJ).

tag: strain

value: BALB/c

value: lung

tag: infection

value: SARS-CoV-mutPBM


title: lung-Mock-REP1

description: lung, Mock infected-REP1

source_name: lung, Mock infected

value: Mock


title: lung-SARS-CoV-mutPBM-REP3

description: lung, SARS-CoV-mutPBM infected-REP3


title: CD14+ Control

source_name: Periferal blood CD14+ cells from buffy coat


title: lung-Mock-REP2

description: lung, Mock infected-REP2


title: lung-Mock-REP3

description: lung, Mock infected-REP3


title: lung-SARS-CoV-mutPBM-REP2

description: lung, SARS-CoV-mutPBM infected-REP2


title: Gli1 loss-of-function mutant regenerating prostate, biological rep 1


title: lung-SARS-CoV-wt-REP3

description: lung, SARS-CoV-wt infected-REP3

source_name: lung, SARS-CoV-wt infected

value: SARS-CoV-wt


title: Wild-type regenerating prostate, biological rep 1


title: lung-SARS-CoV-wt-REP2

description: lung, SARS-CoV-wt infected-REP2


title: lung-SARS-CoV-wt-REP1

description: lung, SARS-CoV-wt infected-REP1


title: TCRneg, biological rep3

status: Public on Oct 21 2014

city: Martinsried

first: Marc

last: Schmidt-Supprian

state: Bavaria

address: Am Klopferspitz 18

department: Molecular Immunology

institute: Max Planck Institute of Biochemistry

description:
Gene expression data from Treg cells
8

hyb_protocol: 7.5 µg biotinylated cRNA was hybridized to an identical lot of Affymetrix GeneChip MOE430 2.0 (16 hours, 45°C) following the manufacturer’s instructions.

scan_protocol: Images were scanned using a GeneChip® Scanner 3000 7G with autoloader and command console software (both Affymetrix).

data_processing: Array normalization and expression value calculation was performed using DNA-Chip Analyzer (www.dchip.org).

source_name: TCRneg Treg cells from lymph nodes and spleen

label_protocol: 50 ng of total RNA were used for biotin labeling (Affymetrix GeneChip whole transcript sense target-labeling kit).

growth_protocol: Organs of 6-8 week old mice were used.

extract_protocol: RNA was extracted using a Qiagen RNAeasy Micro kit according to manufacturer's manual.

treatment_protocol: Mice were given a single dose (400 µg) of poly(I:C) (Amersham) six weeks before analysis.

value: 6-8 weeks

value: lymph node and spleen

tag: cell type

value: Treg

value: Treg cells with induced ablation of TCRalpha-chain


title: TCRpos, biological rep4

description:
Gene expression data from Treg cells
5

source_name: TCRpos Treg cells from lymph nodes and spleen

value: Treg cells with intact TCR expression


title: TCRneg, biological rep5

description:
Gene expression data from Treg cells
10


title: MCF-7 siRNA BIK with TAM

status: Public on Aug 28 2014

city: Estado de Mexico

first: Rubi

last: Viedma

state: Estado de Mexico

address: Av. de los Barrios 1, Los Reyes Ixtacala,  Tlalnepantla,

department: bioquimica

country: Mexico

institute: unam

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Each slide was scanned on two wavelengths (532 and 635 nm) in a confocal scanner. In this equipment the Cy3 and Cy5 molecules are excited by use of a laser, where the emitted fluorescence is captured and converted into an image showing the hybridization sites or specific recognition sequences. For each microarray expression were obtained 2 images, one for flouróforo Cy3 and one for Cy5 fluorophore at this stage should be adjusted laser intensity and sensitivity of the photomultiplier so that both images show values Similar total fluorescence. Scanned images were processed in the reader Virtek Chip using the Array Pro Analyzer software (Media Cybernetics). The program locates each spot or point on the microarray using a programmed pattern (or grid) and calculates the average of each of these signal density as well as the area surrounding each spot. Once the image should consider applying a filter to clean up imperfections or unwanted signals, then a grid in which the areas to be defined is generated quantify. Defined grid, the inclusion or exclusion zone and the area for calculating the background signal of each of the images trying to eliminate points showed no hybridization is determined appropriate. Defined these parameters, the program calculates the mean intensities (density of pixels in the defined area), resulting in a table with the coordinates and values of the density of both the background and each of spots on the microarray. All points and technical replicates are individually evaluated according to some mathematical parameters that allow discriminating unacceptable levels of variability. Items that do not meet these criteria are excluded for statistical analysis. The ratio between the fluorescence levels emitted from Cy3 and Cy5 in each spot or point represents the relative expression of the RNA transcripts that are compared competitively on the microarray that is being analyzed.

data_processing: Data were then normalized and analyzed with genArise software (Institute of Cellular Physiology, UNAM) .Genes with a Z score ≥ 2 or ≤ -2 were considered with altered expression .

source_name: MCF-7 cell

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647. I

growth_protocol: MCF-7 human breast cancer cells (American Type Culture Collection, ATCC, USA) were maintained in Dulbecco Modiﬁed Eagle medium F:12 (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% Fetal Bovine Serum containing penicillin (100 U/ml), and streptomycin (100 µg/ml) (Life Technologies, Inc. BLR, Grand Island, NY, USA). The cells were grown in 75-cm2 tissue culture ﬂasks in a (5% CO2) at 37°C and routinely passaged when conﬂuent. Before each experiment, cells were seeded in 3.5-cm-diameter tissue culture plates (5% CO2).

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

treatment_protocol: Cells were plated in antibiotic-free DMEM- F12 at a density of 2.5 × 105 cells and when 50% confluence was reached, the cells  were transfected with oligofectamine reagent (Invitrogen) and 100 nmol/L BikRNAi  (oligoduplex 5'-AAGACCCCUCUCCAGAGACAU-3',N5′ or AAAUGUCUCUGGAGAGGGGUC-3′) (Labs and Integrated DNA Technologies, IDT) or control sequence-scrambled (Silencer Negative Control #3 siRNA, Ambion) composed of a 19-bp scrambled sequence without significant homology to any known gene sequences from mouse, rat, or human. Briefly, 10-μL oligofectamine was diluted 7.5-fold in Opti-MEM and incubated at room temperature for 10 min. In parallel, a separate tube, 5 μL of 50 μmol/L siRNA, was diluted in 425 μL of Opti-MEM. Diluted oligofectamine (75 μL) was added to the diluted siRNA and the complex was incubated for 20 min at room temperature. Cells were washed with 2 mL of Opti-MEM. siRNA+oligofectamine complex (500 μL) was added gently to the dish. The final concentration of siRNA was 100 mol/L. After 6 h, 1.25 mL of 3X serum medium was added to the dish without removing the transfection mix. The medium was exchanged for serum-containing medium after 6 h and the cells were further cultured for 48 h afterward. The experiments were repeated two to three times.

tag: cell line

value: MCF-7 (American Type Culture Collection, ATCC, USA)

tag: transfected

value: BikRNAi

value: TAM


title: HCT116-147


title: TCRpos, biological rep3

description:
Gene expression data from Treg cells
4

tag: tissue

tag: developmental stage


title: TCRpos, biological rep2

description:
Gene expression data from Treg cells
2


title: TCRneg, biological rep1

description:
Gene expression data from Treg cells
6


title: MCF-7 with TAM (control)


title: TCRneg, biological rep4

description:
Gene expression data from Treg cells
9


title: Normal Fibroblast (NF)

status: Public on Jun 18 2014

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

data_processing: GenomeStudio

source_name: Normal Fibroblast

extract_protocol: RNA was extracted with Trizol reagent

tag: strain background

value: mixed (C57BL/6 and BALB/c)

tag: genotype/variation

value: normal fibroblast


title: TCRpos, biological rep1

description:
Gene expression data from Treg cells
1

tag: age


title: Cancer-Associated Fibroblast (CAF)

source_name: PDAC Fibroblast

value: cancer-associated fibroblast


title: GAPLINC knocking-down human gastric cancer cell line biological rep1

status: Public on Aug 19 2014

city: Shanghai

first: Ye

last: Hu

address: 145 Middle Shandong Rd

country: China

institute: Division of Gastroenterology and Hepatology, Shanghai Jiao-Tong University School of Medicine Renji Hospital

description: Gene expression data from GAPLINC knocking-down MGC803

hyb_protocol: Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip cartridge arrays.

scan_protocol: GeneChips were scanned using the GeneChip® HT Scanner (Affymetrix 00-0172).

data_processing: Affymetrix®Microarray Suite 5.0 statistical algorithm.

source_name: GAPLINC knocking-down human gastric cancer cell line 1

label_protocol: Total RNA is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. The cDNA is converted into double-stranded cDNA template during second strand cDNA synthesis. In vitro transcription synthesizes aRNA that is biotin incorporated and purified.

growth_protocol: MGC803 cells were maintained at 37 °C in an atmosphere of 5% CO2 in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, penicillin and streptomycin (Invitrogen) in 25-ml culture flasks

extract_protocol: High-quality total RNA was isolated using the RNeasy® Mini Kit from QIAGEN

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

value: GAPLINC knockdown


title: GAPLINC knocking-down human gastric cancer cell line biological rep2

source_name: GAPLINC knocking-down human gastric cancer cell line 2


title: TS667_Control shRNA-3_repeat

status: Public on Apr 03 2014

city: Boston

first: Markus

last: Riester

state: MA

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

description:
replicate 3
hGBM_sphere study

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.10.0). It was vst transformed and quantile normalized.

source_name: Human GBM sphere line (TS667) expressing the empty control vector-3_repeat

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: batch

tag: vector constructs

value: pLKO.1-empty vector, SKI-RSI-249999, MSKCC


title: TCRneg, biological rep2

description:
Gene expression data from Treg cells
7


title: TS667_Control shRNA-2_repeat

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the empty control vector-2_repeat


title: TS667_NF1-shRNA #5-2

description:
hybridization duplicate of TS667_Ctrl-2
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5)-2

value: pLKO.1-NF1shRNA (#5), SKI-RSI-192345, MSKCC


title: TS667_Control shRNA-1_repeat

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the empty control vector-1_repeat


title: TS543_Control shRNA-3_repeat

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the empty control vector-3_repeat


title: TS667_NF1-shRNA #5-3

description:
hybridization duplicate of TS667_Ctrl-3
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5)-3


title: GAPLINC knocking-down human gastric cancer cell line biological rep3

source_name: GAPLINC knocking-down human gastric cancer cell line 3


title: TS667_NF1-shRNA #2-3

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2)-3

value: pLKO.1-NF1shRNA (#2), SKI-RSI-192342, MSKCC


title: TS543_NF1-shRNA #5-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5)-1


title: TS543_Control shRNA-1_repeat

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the empty control vector-1_repeat


title: TS667_NF1-shRNA #5-1

description:
hybridization duplicate of TS667_Ctrl-1
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5)-1


title: TS543_NF1-shRNA #2-3

description:
hybridization duplicate of TS543_Ctrl-3
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2)-3


title: TS667_NF1-shRNA #2-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2)-2


title: TS667_NF1-shRNA #2-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2)-1


title: TS543_Control shRNA-2_repeat

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the empty control vector-2_repeat


title: TS543_NF1-shRNA #2-2

description:
hybridization duplicate of TS543_Ctrl-2
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2)-2


title: TS667_Control shRNA-3

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the empty control vector-3


title: Patient 35 - B03-019

status: Public on Mar 31 2014

city: Durham

first: Mark

last: Dewhirst

state: NC

address: Research Dr.

department: Radiation Oncology

institute: Duke University

description: Pretreatment biopsies, collected under ultrasound guidance, were available from 37 patients.  All 37 pretreatment biopsies were confirmed to have at least 60% invasive disease throughout the core sample before RNA harvesting. RNA was prepared, probe generated, and used for hybridization to Affymetrix U133 Plus 2.0 GeneChip arrays

hyb_protocol: Hybridization of samples to Affymetrix U133 Plus 2.0 GeneChip arrays was performed according to Affymetrix manual instructions

scan_protocol: Scanning of Affymetrix U133 Plus 2.0 GeneChip arrays was performed according to the Affmetrix manual instructions

data_processing: Expression was calculated using the robust multiarray average algorithm implemented in the Bioconductor (http://www.bioconductor.org) extensions to the R statistical programming environment. Robust multiarray average generates a background corrected and quantile-normalized measure of expression on the log 2 scale of measurement. Expression estimates from the arrays of 37 tumor samples were then screened to identify genes (in reality, probesets) showing some evidence of more than trivial variation across samples above noise levels. Specifically, probe sets were removed showing normalized expression levels varying at least 1.5-fold across the 37 samples, and whose maximum level among the 37 exceeded the 60% percentile of all data values. Thus, the reduced probe set consisted of 24,134 transcripts that were candidate predictors used in the regression model analysis. Gene expression analysis was done using   Affymetrix U133 Plus 2.0 GeneChip arrays.

source_name: Patients with stage IIB /III breast cancer before neoadjuvant treatment

label_protocol: Affymetrix ENZO labeling kit

extract_protocol: Qiagen mRNA extraction kits. This study involved a total of 37 evaluable patients from which pretreatment biopsies were obtained to allow gene expression analysis. All 37 tissue samples were sectioned and determined to contain at least 60% invasive disease throughout the core sample before RNA harvesting.

value: Fresh frozen pretreatment breast tumor biopsies obtained from patients


title: TS667_Control shRNA-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the empty control vector-1


title: TS543_NF1-shRNA #2-1

description:
hybridization duplicate of TS543_Ctrl-1
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2)-1


title: TS667_Control shRNA-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS667) expressing the empty control vector-2


title: Patient 30 - B01-018


title: Patient 37 - B03-295


title: Patient 31 - B01-027


title: Patient 33 - B03-010


title: Patient 36 - B03-020


title: Patient 34 - B03-018


title: TS543_NF1-shRNA #5-3

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5)-3


title: TS543_NF1-shRNA #5-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5)-2


title: Patient 28 - B01-014


title: Patient 24 - B03-006


title: Patient 23 - B02-017


title: Patient 29 - B01-017


title: Patient 26 - 00-108


title: Patient 27 - 00-058


title: Patient 18 - B00-078


title: Patient 21 - B01-072


title: Patient 32 - B02-012


title: Patient 20 - B03-004


title: Patient 19 - B02-009


title: Patient 25 - B03-015


title: Patient 17 - B02-014


title: Patient 16 - B01-041


title: Patient 15 - B01-053


title: Patient 12 - B01-070


title: Patient 13 - B01-035


title: Patient 14 - CB6132


title: Patient 09 - B02-015


title: Patient 11 - B01-069


title: Patient 04 - B02-003


title: Patient 10 - B02-011


title: Patient 22 - B02-013


title: Patient 06 - B01-060


title: Patient 01- 01-037


title: Patient 05 - B03-012


title: Patient 08 - B01-049


title: Patient 07 - B02-008


title: Patient 03 - B03-011


title: Patient 02 - B01-044


title: ns-siRNA-48h biol. replicate 2

status: Public on Mar 01 2014

city: Oxford

first: Alexander

last: Feuerborn

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology

description:
ns-siRNA-48h rep.2
Gene expression of control-transfected cells

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16hrs at 45◦C on MOE430A mouse GeneChips

scan_protocol: Arrays were scanned using GeneChip™ 3000 7G-scanner

data_processing: The data was analyzed using R(v.3.0.2)/Bioconductor (v.2.13) VSN-normalized

source_name: NM18_non-silencing siRNA for 48hrs

label_protocol: Biotinylated cRNA was generated according to standard Affymetrix protocols from 100ng total RNA (GeneAtlas™ 3'-IVT Express Kit, P/N 702833 Rev. 4)

growth_protocol: Cells were grown under standard cell culture conditions (37◦C, 5%CO2) in ATCC DMEM-media, 10%FCS, 10microgr/ml insulin)

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to manufacturer's instructions (Qiagen), including on-column DNase-digest.

treatment_protocol: Cells were reversed transfected for 24hrs and subsequently treated with 5ng/ml TGF-b1 for another 24hrs or left untreated

value: mammary gland cells line

tag: transfected with

value: non-silencing siRNA for 48hrs


title: ns-siRNA-48h biol. replicate 1

description:
ns-siRNA-48h rep.1
Gene expression of control-transfected cells


title: ns-siRNA-48h biol. replicate 3

description:
ns-siRNA-48h rep.3
Gene expression of control-transfected cells


title: WG1984

status: Public on Dec 10 2013

city: Montreal

first: Stephan

last: Busche

state: Quebec

address: 740 Dr. Penfield Avenue

department: Human Genetics

institute: McGill University

description:
SAMPLE 61
primary skin fibroblast sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software V2011.1

label: Cy5 and Cy3

source_name: genomic DNA from WG1984

label_protocol: standard Illumina protocol

growth_protocol: Cells were grown in alpha MEM Medium (SigmaAldrich, Oakville, ON, Canada) supplemented with 2 mmol/l L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2 to 70-80% confluence, then harvested and stored at -80°C until RNA and DNA was extracted.

extract_protocol: Genomic DNA was extracted from cell pellets using the DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer’s protocol.

tag: gender

value: male

value: skin

value: fibroblast


title: GM00022

description:
SAMPLE 54
primary skin fibroblast sample

source_name: genomic DNA from GM00022

value: female


title: WG1983

description:
SAMPLE 62
primary skin fibroblast sample

source_name: genomic DNA from WG1983


title: GM00016

description:
SAMPLE 53
primary skin fibroblast sample

source_name: genomic DNA from GM00016


title: GM09256

description:
SAMPLE 58
primary skin fibroblast sample

source_name: genomic DNA from GM09256


title: GM00438

description:
SAMPLE 55
primary skin fibroblast sample

source_name: genomic DNA from GM00438


title: GM09255

description:
SAMPLE 57
primary skin fibroblast sample

source_name: genomic DNA from GM09255


title: WG2276

description:
SAMPLE 60
primary skin fibroblast sample

source_name: genomic DNA from WG2276


title: GM00439

description:
SAMPLE 56
primary skin fibroblast sample

source_name: genomic DNA from GM00439


title: WG2275

description:
SAMPLE 59
primary skin fibroblast sample

source_name: genomic DNA from WG2275


title: WG1722

description:
SAMPLE 50
primary skin fibroblast sample

source_name: genomic DNA from WG1722


title: GM00935

description:
SAMPLE 52
primary skin fibroblast sample

source_name: genomic DNA from GM00935


title: GM02149

description:
SAMPLE 36
primary skin fibroblast sample

source_name: genomic DNA from GM02149


title: GM00941

description:
SAMPLE 38
primary skin fibroblast sample

source_name: genomic DNA from GM00941


title: WG2120

description:
SAMPLE 41
primary skin fibroblast sample

source_name: genomic DNA from WG2120


title: WG1310

description:
SAMPLE 44
primary skin fibroblast sample

source_name: genomic DNA from WG1310


title: GM00520

description:
SAMPLE 51
primary skin fibroblast sample

source_name: genomic DNA from GM00520


title: GM00940

description:
SAMPLE 37
primary skin fibroblast sample

source_name: genomic DNA from GM00940


title: WG1514

description:
SAMPLE 48
primary skin fibroblast sample

source_name: genomic DNA from WG1514


title: WG1977

description:
SAMPLE 45
primary skin fibroblast sample

source_name: genomic DNA from WG1977


title: WG1721

description:
SAMPLE 49
primary skin fibroblast sample

source_name: genomic DNA from WG1721


title: WG1978

description:
SAMPLE 46
primary skin fibroblast sample

source_name: genomic DNA from WG1978


title: GM03073

description:
SAMPLE 33
primary skin fibroblast sample

source_name: genomic DNA from GM03073


title: WG1309

description:
SAMPLE 43
primary skin fibroblast sample

source_name: genomic DNA from WG1309


title: GM03075

description:
SAMPLE 34
primary skin fibroblast sample

source_name: genomic DNA from GM03075


title: WG2121

description:
SAMPLE 42
primary skin fibroblast sample

source_name: genomic DNA from WG2121


title: GM02147

description:
SAMPLE 35
primary skin fibroblast sample

source_name: genomic DNA from GM02147


title: WG2193

description:
SAMPLE 39
primary skin fibroblast sample

source_name: genomic DNA from WG2193


title: WG1513

description:
SAMPLE 47
primary skin fibroblast sample

source_name: genomic DNA from WG1513


title: WG2194

description:
SAMPLE 40
primary skin fibroblast sample

source_name: genomic DNA from WG2194


title: GM02456

description:
SAMPLE 31
primary skin fibroblast sample

source_name: genomic DNA from GM02456


title: GM01393

description:
SAMPLE 27
primary skin fibroblast sample

source_name: genomic DNA from GM01393


title: WG2844

description:
SAMPLE 24
primary skin fibroblast sample

source_name: genomic DNA from WG2844


title: WG1283

description:
SAMPLE 22
primary skin fibroblast sample

source_name: genomic DNA from WG1283


title: GM01376

description:
SAMPLE 16
primary skin fibroblast sample

source_name: genomic DNA from GM01376


title: GM01375

description:
SAMPLE 15
primary skin fibroblast sample

source_name: genomic DNA from GM01375


title: GM00289

description:
SAMPLE 25
primary skin fibroblast sample

source_name: genomic DNA from GM00289


title: GM02316

description:
SAMPLE 29
primary skin fibroblast sample

source_name: genomic DNA from GM02316


title: GM02317

description:
SAMPLE 30
primary skin fibroblast sample

source_name: genomic DNA from GM02317


title: WG1282

description:
SAMPLE 21
primary skin fibroblast sample

source_name: genomic DNA from WG1282


title: WG1658

description:
SAMPLE 20
primary skin fibroblast sample

source_name: genomic DNA from WG1658


title: CD8+CD40L+, biological rep5

status: Public on Aug 05 2013

city: Berlin

first: Andreas

last: Thiel

address: Augustenburger Platz 1

institute: Berlin-Brandenburg Center for Regenerative      Therapies, Charite University Medicine

description: Gene expression data of human CD8+CD40L+ stimulated with PMA/Ionomycin for 6 h

hyb_protocol: 15 µg fragmented cRNA was hybridized to the Affymetrix HG-U133Plus2 gene chip in a Hybridization Oven 640, washed and stained in the Fluidics Station 400 (Affymetrix), according to procedure 2 described in the technical manual 'GeneChip Expression Analysis' (Affymetrix, Santa Clara, CA)

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Chip data were analyzed with GeneChip Operating Software (GCOS 1.1; Affymetrix) default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200

source_name: PBMC stimulated with PMA/Ionomycin for 6 h

label_protocol: Biotinylated cRNA were prepared from 3-5 ug total RNA according to the technical manual 'GeneChip Expression Analysis' (Affymetrix, Santa Clara, CA)

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

treatment_protocol: PBMCs were isolated by Ficoll gradient from buffy coat. CD4+ and CD8+ T cells were isolated via MACS, The cells were stimulated with PMA/Ionomycin for 6 h, and subsequently sorted into the CD4+CD45RA-CD40L+, CD8+CD45RA-CD40L-, CD8+CD45RA-CD40L+ populations by FACS-sort

value: Blood

value: Male

tag: cell population


title: GM02173

description:
SAMPLE 17
primary skin fibroblast sample

source_name: genomic DNA from GM02173


title: WG2414

description:
SAMPLE 7
primary skin fibroblast sample

source_name: genomic DNA from WG2414


title: GM01095

description:
SAMPLE 13
primary skin fibroblast sample

source_name: genomic DNA from GM01095


title: GM02175

description:
SAMPLE 18
primary skin fibroblast sample

source_name: genomic DNA from GM02175


title: WG3466

description:
SAMPLE 10
primary skin fibroblast sample

source_name: genomic DNA from WG3466


title: WG2843

description:
SAMPLE 23
primary skin fibroblast sample

source_name: genomic DNA from WG2843


title: GM00031

description:
SAMPLE 12
primary skin fibroblast sample

source_name: genomic DNA from GM00031


title: CD8+CD40L+, biological rep4

value: Female


title: GM01653

description:
SAMPLE 4
primary skin fibroblast sample

source_name: genomic DNA from GM01653


title: WG2415

description:
SAMPLE 8
primary skin fibroblast sample

source_name: genomic DNA from WG2415


title: GM02641

description:
SAMPLE 6
primary skin fibroblast sample

source_name: genomic DNA from GM02641


title: GM00290

description:
SAMPLE 26
primary skin fibroblast sample

source_name: genomic DNA from GM00290


title: CD8+CD40L+, biological rep1


title: WG1657

description:
SAMPLE 19
primary skin fibroblast sample

source_name: genomic DNA from WG1657


title: CD8+CD40L+, biological rep2


title: WG3465

description:
SAMPLE 9
primary skin fibroblast sample

source_name: genomic DNA from WG3465


title: GM01392

description:
SAMPLE 28
primary skin fibroblast sample

source_name: genomic DNA from GM01392


title: CD8+CD40L-, biological rep3

description: Gene expression data of human CD8+CD40L- stimulated with PMA/Ionomycin for 6 h


title: CD8+CD40L+, biological rep3


title: CD8+CD40L-, biological rep5


title: CD8+CD40L-, biological rep2


title: GM02704

description:
SAMPLE 1
primary skin fibroblast sample

source_name: genomic DNA from GM02704


title: GM01650

description:
SAMPLE 3
primary skin fibroblast sample

source_name: genomic DNA from GM01650


title: GM02640

description:
SAMPLE 5
primary skin fibroblast sample

source_name: genomic DNA from GM02640


title: GM00042

description:
SAMPLE 11
primary skin fibroblast sample

source_name: genomic DNA from GM00042


title: CD4+CD40L+, biological rep5

description: Gene expression data of human CD4+CD40L+ stimulated with PMA/Ionomycin for 6 h

source_name: PBMC stimulated with PMA/Ionomycin for 6 h


title: GM02555

description:
SAMPLE 32
primary skin fibroblast sample

source_name: genomic DNA from GM02555


title: CD8+CD40L-, biological rep1


title: GM01096

description:
SAMPLE 14
primary skin fibroblast sample

source_name: genomic DNA from GM01096


title: GM02706

description:
SAMPLE 2
primary skin fibroblast sample

source_name: genomic DNA from GM02706


title: Histone H3 density normal growth

status: Public on Jul 22 2013

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Histone H3 density under normal growth compared to input control

hyb_protocol: According to the Affymetrix manufacturer's manual.

data_processing:
The file is processed from the bar files. Gcn5 enrichment at normal conditions is provided for each gene in separate files. Each genes are provided with 38 data points, with the first 9 points show the equal bins of 5'IGR region (start s from the milddle of upstream intergenic regions and end before the starting code),  20 equal bins of ORF region, and 9 equal bins of 3'IGR region (starts after the stop code and end at the middle of the intergenic region).
Raw data from Affymetrix (CEL format) were analyzed using Tiling Analysis software (TAS) from affymetrix to find the enrichment for whole genome regions (bar file). The  data for the 5 conditions are normalized to the have the same medium value. Average gene analysis was done using a procedure modified from Pokholok et al (2005) and Li et al (2007). Briefly, the ORF region of each gene in S. cerevisiae was divided into 20 equally sized bins. while the of upstream 5´IGR region starts from the milddle of upstream intergenic regions and end before the starting code and and downstream 3ÍGR region starts after the stop code and end at the middle of the intergenic region. Both 5’IGR and 3’IGR are divided in to 9 equal sized bins. The java code for average gene analysis is in the supplementary filesX and with a 2-clause BSD license.

organism: Saccharomyces cerevisiae

source_name: Histone H3 density normal growth

growth_protocol: Gcn5-myc tagged strain is from (ref) and is used for stress adaptation and recovery model. The cells are cultivated at 30°C in YPD medium (1% yeast extract, 2% bacto peptone and 2% glucose)

extract_protocol: Extraction and Chromatin IP procedures refers to Johnsson etc. EMBO reports (2009) 10, 1009. acH3K18 (ab1191) and acH4K16(ab61240) and Histone3  antibody are from Abcam and are used with 1:100 dilution for Chromatin Immuno-precipitation experiment, Gcn5-myc are from Sigma (M5546) and 1:50 dilution are used in ChIP experiment.

treatment_protocol: Cells grow to log phase at a density of 1 × 107 to 2 × 107 cells/ml (sample collection A: normal growth), then and dilute to 5X106 cells/ml and subjected to stress condition by adding a equal amount of YPD medium containing 2 M KCl, making a final concentration of 1 M KCl with cell number around 2.5X106 cells/ml.  (sample collection B 1hr after medium change B: during stress adaptation). When cell numbers reach to a concentration to 1X107 cells/ml (sample collected C: after stress adaptation). Cells are spanned down and medium is replaced with YPD without KCl for stress recovery with a start concentration around 2.5X106 cells/ml  (Sample collection D after 1hr of medium changes: during stress recovery). After 2-3 generations, final samples are collected.(sample collection E: after recovery) . Cell number is counted every hour.  Replicates are cultured as different batches.

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

value: Normal growth

tag: genetic background

value: BQS1350 (Rosaleny LE etc. Biol 2007, 8(6):R119)

source_name: Input

tag: control

value: input control


description: Histone H3 density after stress recovery compared to input control

scan_protocol: According to the Affymetrix manufacturer's manual.

tag: treatment

value: After stress (KCL) recovery


description: Histone H3 density after stress adaptation compared to input control

label_protocol: According to the Affymetrix manufacturer's manual.

value: After stress (KCL) adaptation


title: acH4K16 after stress recovery

description: H4K16 acetylation level after stress recovery compared to input control

tag: chip antibody catalog #


description: Histone H3 density during stress adaptation growth compared to input control

value: During stress (KCL) adpatation


title: acH4K16 during stress recovery

description: H4K16 acetylation level during stress recovery compared to input control

value: During stress (KCL) recovery


title: acH4K16 after stress adaptation

description: H4K16 acetylation level after stress adaptation compared to input control


title: acH4K16 during stress adaptation

description: H4K16 acetylation level during stress adaptation growth compared to input control


title: acH4K16 normal growth

description: H4K16 acetylation level under normal growth compared to input control

source_name: acH4K16 normal growth


title: acH3K18 after stress recovery

description: H3K18 acetylation level after stress recovery compared to input control


title: acH3K18 during stress recovery

description: H3K18 acetylation level during stress recovery compared to input control


title: after stress adaptation 1

description: Gene expression profile after stress adaptation compared to input control

data_processing: Data processed with RMA method using Affymetrix Expression Console software.

source_name: after stress adaptation replicate1

growth_protocol: The yeast cells are cultivated at 30°C in YPD medium (1% yeast extract, 2% bacto peptone and 2% glucose)

extract_protocol: RNA is prepared by hot phenol method as describe in Xue etc. Yeast, 21:25-39.2003

value: after stress (KCL) adaptation


description: Histone H3 density during stress recovery compared to input control


title: acH3K18 during stress adaptation

description: H3K18 acetylation level during stress adaptation growth compared to input control


title: acH3K18 after stress adaptation

description: H3K18 acetylation level after stress adaptation compared to input control


title: during stress recovery 1

description: Gene expression profile during stress recovery compared to input control

source_name: during stress recovery replicate1

value: during stress (KCL) recovery


title: acH3K18 normal growth

description: H3K18 acetylation level under normal growth compared to input control

source_name: acH3K18 normal growth


title: after stress recovery 2

description: Gene expression profile after stress recovery compared to input control

source_name: after stress recovery replicate2

value: after stress (KCL) recovery


title: during stress adaptation 2

description: Gene expression profile during stress adaptation growth compared to input control

source_name: during stress adaptation replicate2

value: during stress (KCL) adaptation


title: during stress recovery 2

source_name: during stress recovery replicate2


title: CD4+CD40L+, biological rep3

description: Gene expression data of human CD4+CD40L+ stimulated with PMA/Ionomycin for 6 h


title: CD4+CD40L+, biological rep1


title: normal growth 1

description: Gene expression profile under normal growth compared to input control

source_name: normal growth replicate1

value: normal growth


title: Gcn5 enrichment after stress

description: Gcn5 enrichment after stress adaptation compared to input control

value: Sigma


title: Gcn5 enrichment after recovery

description: Gcn5 enrichment after stress recovery compared to input control


title: Gcn5 enrichment normal

description: Gcn5 enrichment under normal growth compared to input control


title: Gcn5 enrichment during recovery

description: Gcn5 enrichment during stress recovery compared to input control


title: Gcn5 enrichment during stress

description: Gcn5 enrichment during stress adaptation growth compared to input control


title: during stress adaptation 1

source_name: during stress adaptation replicate1


title: after stress recovery 1

source_name: after stress recovery replicate1


title: CD4+CD40L+, biological rep2

value: Blood


title: normal growth 2

source_name: normal growth replicate2


title: CD4+CD40L+, biological rep4

source_name: PBMC stimulated with PMA/Ionomycin for 6 h


title: cholangiocarcinoma surgical sample NO.5

status: Public on Jun 10 2013

city: Wuhan

first: Feng

last: Peng

state: Hubei

address: 1095 Jiefang Ave

department: Department of Biliary-Pancreatic Surgery

institute: Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
5B_NS
normal bile duct obtained from patient #5

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: cholangiocarcinoma surgical sample

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The samples were obtained 20 minutes after operation and treated with RNAlater(AM7024,Ambion)

tag: patient

value: cholangiocarcinoma (distal biliary)

value: female

tag: modus operandi

value: Whipple


title: corresponding normal bile duct tissues NO.2

description:
2A_NS
cholangiocarcinoma tissue obtained from patient #2

source_name: corresponding normal bile duct tissues

tag: tissue

value: normal bile duct


title: cholangiocarcinoma surgical sample NO.2

description:
2B_NS
normal bile duct obtained from patient #2


title: corresponding normal bile duct tissues NO.5

description:
5A_NS
cholangiocarcinoma tissue obtained from patient #5


title: cholangiocarcinoma surgical sample NO.1

description:
1B_NS
normal bile duct obtained from patient #1

value: male


title: corresponding normal bile duct tissues NO.1

description:
1A_NS
cholangiocarcinoma tissue obtained from patient #1


title: after stress adaptation 2

description: Gene expression profile after stress adaptation compared to input control

source_name: after stress adaptation replicate2

value: BQS1350 (Rosaleny LE etc. Biol 2007, 8(6):R119)


title: Gastrointestinal stromal tumor 20

status: Public on Apr 10 2013

city: Stockholm

first: Pinar

last: Akcakaya

address: CCK R8:04

department: Oncology-Pathology

institute: Karolinska Institutet

description: miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470A) for 18-20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v1.0. Images obtained after scanning were processed with Feature Extraction Software 9.5.3.1 (Agilent, Santa Clara, CA)

data_processing: Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 20% missing values across the samples were included in the further analysis.

source_name: Imatinib-sensitive GIST tissue

label_protocol: 100 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.Labeled RNA was purified using Micro Bio Spin 6 Columns (Bio-Rad, 732-6221)

extract_protocol: Total RNA was extracted using mirVana miRNA Isolation Kit (Applied Biosystem/Ambion, Austin, TX) according to the protocol recommended by the manufacturer.

value: Fresh frozen tissue

tag: phenotype

value: Imatinib-sensitive


title: Gastrointestinal stromal tumor 11

description: miRNA expression profile


title: Gastrointestinal stromal tumor 12

description: miRNA expression profile


title: Gastrointestinal stromal tumor 19

description: miRNA expression profile


title: Gastrointestinal stromal tumor 15

description: miRNA expression profile


title: Gastrointestinal stromal tumor 16

description: miRNA expression profile


title: Gastrointestinal stromal tumor 3

description: miRNA expression profile

source_name: Imatinib-resistant GIST tissue

value: Imatinib-resistant


title: Gastrointestinal stromal tumor 17

description: miRNA expression profile


title: Gastrointestinal stromal tumor 1

description: miRNA expression profile


title: Gastrointestinal stromal tumor 4

description: miRNA expression profile


title: Gastrointestinal stromal tumor 7

description: miRNA expression profile


title: Gastrointestinal stromal tumor 2

description: miRNA expression profile


title: Gastrointestinal stromal tumor 13

description: miRNA expression profile


title: Gastrointestinal stromal tumor 18

description: miRNA expression profile


title: Gastrointestinal stromal tumor 9-4

description: miRNA expression profile


title: Gastrointestinal stromal tumor 14

description: miRNA expression profile


title: Gastrointestinal stromal tumor 5

description: miRNA expression profile


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 124

status: Public on Sep 28 2012

city: Toronto

first: Igor

last: Jurisica

state: ON

address: 101 College St.

institute: Princess Margaret Cancer Center

description: SAMPLE 124

hyb_protocol: 300 ng of sample and reference DNA from pre-treatment prostate biopsies were differentially labeled in a random priming reaction with Cyanine 3–dCTP and Cyanine 5–dCTP (Perkin Elmer Life Sciences). DNA samples were then combined and mixed with 100 μg of human Cot-1 DNA (Invitrogen) followed by removal of unincorporated nucleotides using microcon YM-30 columns (Millipore). Sample mixtures were denatured at 85°C for 10 min, and repetitive sequences were blocked at 45°C for 1 hr before hybridization. The mixture was then applied onto arrays containing 26,819 bacterial artificial chromosome (BAC) derived amplified fragment pools spotted in duplicate on aldehyde coated glass slides (SMRT v.2, BC Cancer Research Centre Array Facility). Array hybridization was performed in the dark at 45°C for 36 hr inside a hybridization chamber, rinsed four times in 0.1X SSC at room temperature and dried by centrifugation at 1,000g before imaging.

scan_protocol: Slides were scanned using a dual laser array scanner (Axon) and spot signal intensities determined using the SoftWoRx Tracker Spot Analysis software (Applied Precision).

data_processing: Normalized using algorithm by Khojasteh et al (PMID: 16297240) : A three-step normalization procedure, including LOWESS fitting, spatial, and median normalization.

source_name: Biopsy Tumor Tissue

label_protocol: Random-primer labelling reaction  1. For each slide combine: (1 reaction tube for reference & 1 reaction tube for sample)  a) DNA (200ng)  b) 5uL of 5X (PB) random primers buffer (Final concentration: 5X Promega Klenow buffer and 7ug/ul random octomers)  c) Dilute to 16.5uL total volume with ddH2O    2. Boil for 10 min at 100°C in PCR machine. Transfer immediately to ice for 2 min  3. Add 4ul of 10X dNTP mix (2mM each dATP, dGTP, dTTP, 1.2mM dCTP) - Vortex very well  4. Add CyeDyes: Vortex and spin prior to adding  • Add 2uL (2nmoles) of Cy3 labelled dCTP to Reference DNA (Novagen Male Genomic)  • Add 2uL (2nmoles) of Cy5 labelled dCTP to sample DNA   5. Add 2.5uL of Klenow (9U/uL) and mix by pipetting   6. Incubate 37oC overnight (~18hours).

extract_protocol: Genomic DNA was extracted by the standard phenol-chloroform extraction protocol.

value: Prostate cancer biopsy

tag: relapse rate (bf=biochemical failure, ned = no evidence of disease)

value: NED

source_name: Normal male

value: Pooled male genomic DNA [Novegen]


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 123

description: SAMPLE 123


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 120

description: SAMPLE 120


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 121

description: SAMPLE 121

value: BF


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 119

description: SAMPLE 119


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 122

description: SAMPLE 122


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 118

description: SAMPLE 118


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 116

description: SAMPLE 116


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 115

description: SAMPLE 115


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 126

description: SAMPLE 126


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 125

description: SAMPLE 125


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 111

description: SAMPLE 111


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 104

description: SAMPLE 104


title: CD8+CD40L-, biological rep4

description: Gene expression data of human CD8+CD40L- stimulated with PMA/Ionomycin for 6 h

value: Female


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 114

description: SAMPLE 114


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 110

description: SAMPLE 110


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 99

description: SAMPLE 99


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 105

description: SAMPLE 105


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 109

description: SAMPLE 109


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 113

description: SAMPLE 113


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 117

description: SAMPLE 117


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 101

description: SAMPLE 101


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 106

description: SAMPLE 106


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 100

description: SAMPLE 100


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 108

description: SAMPLE 108


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 107

description: SAMPLE 107


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 103

description: SAMPLE 103


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 102

description: SAMPLE 102


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 98

description: SAMPLE 98


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 112

description: SAMPLE 112


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 92

description: SAMPLE 92


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 90

description: SAMPLE 90


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 96

description: SAMPLE 96


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 97

description: SAMPLE 97


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 93

description: SAMPLE 93


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 91

description: SAMPLE 91


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 87

description: SAMPLE 87


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 95

description: SAMPLE 95


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 89

description: SAMPLE 89


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 94

description: SAMPLE 94


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 82

description: SAMPLE 82


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 86

description: SAMPLE 86


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 83

description: SAMPLE 83


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 85

description: SAMPLE 85


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 81

description: SAMPLE 81


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 78

description: SAMPLE 78


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 74

description: SAMPLE 74


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 73

description: SAMPLE 73


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 75

description: SAMPLE 75


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 76

description: SAMPLE 76


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 84

description: SAMPLE 84


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 79

description: SAMPLE 79


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 80

description: SAMPLE 80


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 77

description: SAMPLE 77


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 88

description: SAMPLE 88


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 71

description: SAMPLE 71


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 70

description: SAMPLE 70


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 69

description: SAMPLE 69


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 68

description: SAMPLE 68


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 72

description: SAMPLE 72


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 67

description: SAMPLE 67


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 61

description: SAMPLE 61


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 64

description: SAMPLE 64


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 65

description: SAMPLE 65


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 62

description: SAMPLE 62


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 59

description: SAMPLE 59


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 58

description: SAMPLE 58


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 54

description: SAMPLE 54


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 56

description: SAMPLE 56


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 66

description: SAMPLE 66


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 57

description: SAMPLE 57


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 55

description: SAMPLE 55


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 52

description: SAMPLE 52


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 48

description: SAMPLE 48


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 53

description: SAMPLE 53


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 51

description: SAMPLE 51


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 44

description: SAMPLE 44


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 41

description: SAMPLE 41


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 47

description: SAMPLE 47


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 40

description: SAMPLE 40


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 42

description: SAMPLE 42


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 49

description: SAMPLE 49


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 34

description: SAMPLE 34


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 45

description: SAMPLE 45


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 50

description: SAMPLE 50


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 43

description: SAMPLE 43


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 37

description: SAMPLE 37


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 36

description: SAMPLE 36


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 35

description: SAMPLE 35


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 32

description: SAMPLE 32


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 39

description: SAMPLE 39


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 38

description: SAMPLE 38


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 46

description: SAMPLE 46


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 33

description: SAMPLE 33


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 60

description: SAMPLE 60


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 30

description: SAMPLE 30


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 29

description: SAMPLE 29


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 63

description: SAMPLE 63


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 28

description: SAMPLE 28


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 20

description: SAMPLE 20


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 22

description: SAMPLE 22


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 27

description: SAMPLE 27


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 21

description: SAMPLE 21


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 24

description: SAMPLE 24


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 23

description: SAMPLE 23


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 25

description: SAMPLE 25


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 19

description: SAMPLE 19


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 26

description: SAMPLE 26


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 17

description: SAMPLE 17


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 14

description: SAMPLE 14


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 31

description: SAMPLE 31


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 18

description: SAMPLE 18


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 13

description: SAMPLE 13


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 12

description: SAMPLE 12


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 10

description: SAMPLE 10


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 9

description: SAMPLE 9


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 11

description: SAMPLE 11


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 8

description: SAMPLE 8


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 7

description: SAMPLE 7


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 15

description: SAMPLE 15


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 5

description: SAMPLE 5


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 6

description: SAMPLE 6


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 4

description: SAMPLE 4


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 3

description: SAMPLE 3


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 2

description: SAMPLE 2


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 1

description: SAMPLE 1


title: Biofilm WT8-10mM sucrose/3h 10 mM glucose

status: Public on Sep 01 2012

city: Miami

first: Dragana

last: Ajdic

state: Florid

address: 1600 NW 10th Ave, RMSB 2023

department: Dermatology

institute: University of Miami

description: Gene transcription data from 48h biofilm

hyb_protocol: Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 47C on GeneChip S. mutans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix)

data_processing: Data were analyzed with Gene Chip Operating Software version 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Streptococcus mutans UA159

source_name: Biofilm WT8-10mM sucrose/3h glucose

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown in defined medium with specific sugars (sucrose, glucose or nigerose). Planktonic and aggregarion cultures were grown to mid-log (OD600=0.6) phase in 0.5% sugar. Biofilm cultures were grown for 48h in 10 mM sugar.

extract_protocol: Extraction of total RNA was performed using Ambion RiboPure Bacteria kit according to the manufacturers protocol.

treatment_protocol: Cells were harvested by centrifugation lysed using beat-beater.

tag: genotype

value: wild type

value: 10mM sucrose then 3h 10mM glucose

tag: cell type

value: biofilm cells


title: Aggregation WT1 0.5% sucrose

description: Gene transcription data from aggregation culture OD600=0.6

source_name: Aggregation WT1 0.5% sucrose

value: 0.5% sucrose

value: aggregation cells


title: Biofilm gtfB1 10mM sucrose

source_name: Biofilm gtfB1 10mM sucrose

value: 10mM sucrose


title: Planktonic WT1 0.5% nigerose

description: Gene transcription data from planktonic culture OD600=0.6

source_name: Planktonic WT1 0.5% nigerose

value: 0.5% nigerose

value: planktonic cells


title: Planktonic WT2 0.5% nigerose

source_name: Planktonic WT2 0.5% nigerose


title: Biofilm gtfC2 10mM sucrose

source_name: Biofilm gtfC2 10mM sucrose


title: Biofilm gtfB2 10mM sucrose

source_name: Biofilm gtfB2 10mM sucrose


title: Biofilm gtfC1 10mM sucrose

source_name: Biofilm gtfC1 10mM sucrose


title: Aggregation WT2 0.5% sucrose

source_name: Aggregation WT2 0.5% sucrose


title: Biofilm WT7-10mM sucrose/3h 10 mM glucose

source_name: Biofilm WT7-10mM sucrose/3h glucose


title: Aggregation gtfB1 0.5% sucrose

source_name: Aggregation gtfB1 0.5% sucrose


title: Aggregation gtfBC1 0.5% sucrose

source_name: Aggregation gtfBC1 0.5% sucrose


title: Aggregation gtfC1 0.5% sucrose

source_name: Aggregation gtfC1 0.5% sucrose


title: Aggregation gtfC2 0.5% sucrose

source_name: Aggregation gtfC2 0.5% sucrose


title: Tissue Biopsy of Intermediate Risk Prostate Cancer Patient 16

description: SAMPLE 16


title: Biofilm WT6-10mM sucrose

source_name: Biofilm WT6-10mM sucrose


title: Aggregation gtfB2 0.5% sucrose

source_name: Aggregation gtfB2 0.5% sucrose


title: Biofilm WT5-10mM sucrose

source_name: Biofilm WT5-10mM sucrose


title: Biofilm WT2-10mM sucrose

source_name: Biofilm WT2-10mM sucrose