title: Ewing's Sarcoma Cell Line VH64


title: Ewing's Sarcoma Cell Line STAET10

status: Public on Aug 01 2011

type: genomic

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

country: Spain

institute: Centro de Investigación del Cáncer

hyb_protocol: Labeled DNA was purified through Illustra G-50 Microspin Columns (Amersham, GE), mixed and then precipitated along with Cot Human DNA (Roche). Hybridization was performed for 48 hours at 42°C and excess probe was removed.

scan_protocol: Data were acquired using an Axon 4000B scanner and GenePix software (Axon Laboratories).

data_processing: Normalization was carried out with GenePix software using the mean of the median of ratios of all the autosomal features in the array.

molecule: genomic DNA

organism: Homo sapiens

source_name: Ewing's Sarcoma Cell Line

label_protocol: Tumor and reference DNA was Cy5/Cy3-dCTP-labelled (Amersham, GE) using a non-commercial Random Priming kit composed of random octamers dissolved in Exo-Minus Klenow buffer (Eppicentre), a dNTPs mix depleted in dCTP (Eppendorf), and Exo-Minus Klenow enzyme (Eppicentre).

growth_protocol: In case of cell lines, they were cultured in their corresponding mediums, most of them in RPMI supplemented with 10% FBS. SKES1 in McCoy's 15% FBS and TC71 in IMDM 20% FBS

extract_protocol: Cell lines: DNA was extracted using QIAamp DNA Mini Kit (Qiagen) following manufacturer's instructions for extracting DNA from cell lines; Tumors: Genomic DNA was extracted from frozen tumor biopsies containing at least 70% of tumor cells. Tissue samples containing less than 80% of tumor cells, as quantified by histological examination, were microdissected from unstained glass slides prior to DNA extraction. DNA was isolated using the Qiagen DNA Extraction kit (Qiagen) or the High Pure PCR Template Preparation kit (Roche) following the manufacturer’s recommendations.

treatment_protocol: no treatment was applied to samples before DNA extraction

tag: sample type

value: DNA sample from cell line

tag: sex

tag: age

tag: primary tumor/metas

tag: overall metastasis

source_name: DNA pooled from 100 healthy donors

tag: source

value: Spanish National Tumor Bank


title: HEK, ligand and radiation treated, rep3A

type: RNA

city: Delhi

first: Vibha

last: Tandon

state: Delhi

address: Department of Chemistry

department: Department of Chemistry

country: India

institute: University of Delhi

hyb_protocol: 20µg of the labeled aRNA in 200µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins, and 100µl was used for hybridization with the Human 40KA and Human 40KB chips separately printed at Ocimum Biosolutions, Hyderabad. Hybridization was performed at 50°C for two hours on Tecan HS4800 automated Hyb station.

scan_protocol: Hybridized chips were scanned using the Affymetrix 428 Array scanner at three different PMT gains.

data_processing: Initial data (chip A and B combined for each) consisted of 40,320 probes. Probes with 'not detected' value were removed. For each replicate, the respective chips were separately normalized using Quantile method implemented in the R language. This was followed by combining chip A and B for each of the replicates and then applying a final normalization step across the three replicates on the common set of probes. Before testing for differential expression, the different set of control probes were removed.

molecule: total RNA

source_name: Human embryonic kidney, ligand and radiation treated

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

extract_protocol: RNA was extracted using TriReagent and further purified using the Qiagen RNeasy mini kit according to the manufacturer's protocol. RNA quality was checked by agarose gel electrophoresis and spectrophotometry.

treatment_protocol: The HEK human embryonic kidney cell line was plated 24 hrs prior to the experiment. The treatment conditions followed were: control (untreated), DNA minor groove binding ligand (50uM treated), radiation (2 Gy treated), and ligand+radiation (50uM+2Gy treated). Cells were then incubated further for 4 hrs following these treatment conditions and RNA samples were prepared.

tag: cell line

value: HEK

tag: cell type

value: human embryonic kidney

tag: treatment

value: DNA minor groove binding ligand and radiation


title: G361 cells, untreated, 0h, rep1

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: Expression data from untreated G361 cells, 0h

hyb_protocol: Five ug of fragmented cRNAs were hybridized  for 16 hr at 45°C  to Affymetrix Human Genome U133A 2.0 Arrays; Arrays were washed and stained in the Affymetrix Fluidics Station 450. Hybridization and downstream processing of the arrays were performed as recommended by the manufacturer.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000.

data_processing: CEL files were processed using Affy Eexpression Console Tool (rma method).

label: biotin

source_name: G361 cells, untreated, 0h

label_protocol: Biotinylated cRNAs were prepared according to Affymetrix standard GeneChip® Array Protocols, as instructed in the Affymetrix  GeneChip® Expression analysis technical manual.

growth_protocol: Cells were grown  in DMEM which was routinely supplemented with 10% FCS; Cells were maintained in a humidified, 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted from cells using the RNeasyÒ Plus mini kit (Qiagen), in combination with QIAshredderTM columns (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Cells were irradiated at 63.25 R/min to a dose of either 5 Gy, using a Keithly model 96035 (15 cc) ion chamber accompanied with a Keithly model 35050A electrometer. Irradiated cells were incubated for selected time periods at 37°C. Mock-irradiated controls were treated identically, excluding the IR treatment.

tag: stress

value: untreated

tag: time


title: HEK, radiation treated, rep3A

source_name: Human embryonic kidney, radiation treated

value: radiation


title: liver_10 mg/kg SP70_6h_biological rep4

city: Hangzhou

first: Xiaoyan

last: Lu

address: Yuhang Road 866

country: China

institute: Zhejiang University

description:
SP70-10-4
Gene expression data from the liver of 10 mg/kg SP70-treated mouse

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: GeneChips were scanned by GeneChip® Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method in ArrayTrack. Raw microarray intensity data were normalized per chip to the same median intensity value of 1000.

organism: Mus musculus

source_name: left lateral liver of the 10 mg/kg SP70-treated mouse, 6 h after injection

label_protocol: Total RNA were amplified, labeled and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The mice were randomly assigned to one of the following seven treatment groups (5 mice per group): vehicle control (deionized water at 0.1 ml/10 g), SP30 at 10 mg/kg, SP70 at 10 mg/kg, SP70 at 20 mg/kg, SP70 at 40 mg/kg, SP300 at 10 mg/kg, and SP300 at 200 mg/kg. The mice were intravenously injected with the silica particles at 10–200 mg/kg body weight as described above, and sacrificed at 6 h after injection.

extract_protocol: Total RNA was collected using TRIZol Reagent (Invitrogen) for extraction and RNeasy Mini kits (QIAGEN) for purification, in accordance with the manufacturer’s protocols.

treatment_protocol: After 6 h post-injection, an aliquot of the sample for RNA analysis was obtained from the left lateral lobe of the liver in each animal immediately after sacrifice.The excised samples were immediately flash frozen in liquid nitrogen, and stored at -80 °C for microarray analysis.

tag: strain

value: BALB/c

tag: tissue

value: left lateral liver


title: HEK, untreated, rep3A

source_name: Human embryonic kidney, untreated


title: G361 cells, untreated, 0h, rep2


title: HEK, ligand treated, rep3A

source_name: Human embryonic kidney, ligand treated

value: DNA minor groove binding ligand


title: liver_10 mg/kg SP70_6h_biological rep3

description:
SP70-10-3
Gene expression data from the liver of 10 mg/kg SP70-treated mouse


title: G361 cells, untreated, 3h, rep3

description: Expression data from untreated G361 cells, 3h

source_name: G361 cells, untreated, 3h


title: Ewing's Sarcoma Cell Line STAET2.1


title: Ewing's Sarcoma Cell Line STAET1


title: h+22-11

city: Wuerzburg

first: Burkhard

middle: Gerhard

last: Kneitz

address: Oberdürrbacher Str. 6

department: Klinik und Poliklinik für Urologie und Kinderurologie

country: Germany

institute: University of Wuerzburg

description: Gene expression data from a high risk prostate carcinoma h+22-11

hyb_protocol: hybridization for 16 hr at 42C using a Agilent hybridization oven, labeled targets from 15ug total RNA were used for hybridization

scan_protocol: Arrays were scanned using the ScanArray 4000 (PerkinElmer)

data_processing: The data were analyzed with Bioconductor packages (under R) 1st median value of 4 replicates (flaged spots excluded) was calculated,  2nd vsn normalization, 3rd gene finding using the Limma-package

source_name: prostate carcinoma

label_protocol: labeling according to the Applied Biosystems mirVana™ manual without deviation from the original protocol

extract_protocol: purification from formalin-fixed paraffin embedded (FFPE) material (RecoverAll™ Total Nucleic Acid Isolation Kit), subsequent miRNA purification (flashPAGE™ Fractionator) without deviation from the original protocol

tag: disease state

value: high risk prostate carcinoma


title: G361 cells, untreated, 0h, rep3


title: HEK, radiation treated, rep2A


title: liver_10 mg/kg SP70_6h_biological rep1

description:
SP70-10-1
Gene expression data from the liver of 10 mg/kg SP70-treated mouse


title: HEK, ligand and radiation treated, rep2A


title: TALL-1 Mig-ICN GSI treated 12hrs

city: Vancouver

first: Andrew

middle: P

last: Weng

state: BC

address: 675 West 10th Ave

department: Pathology

country: Canada

institute: BC Cancer Agency

description:
TALL-1 Mig-ICN CmpdE
YF060509H133P22.CEL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: dChip software was used to perform interarray brightness normalization by the invariant set method followed by calculation of PM/MM difference model-based expression values.

source_name: TALL-1 cell line

label_protocol: Ten micrograms of total RNA was used to generate biotin labeled cRNA according to standard Affymetrix protocols.

growth_protocol: Cells were cultured in RPMI 1640 media supplemented with 10% fetal bovine serum, sodium pyruvate, pen/strep, and L-glutamine in a humidified 5% CO2 atmosphere at 37C.

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

treatment_protocol: Mock-treated cultures included DMSO vehicle at 0.01% final concentration for 12 hours. Gamma-secretase inhibitor (GSI)-treated cultures included compound E (CmpdE; (S,S)- 2-[2-(3,5-Difluorophenyl)-acetylamino]-N-(1-methyl-2-oxo-5-phenyl-2,3-dihydro-1H-benzo[e][1,4]diazepin-3-yl)-propionamide) (Calbiochem) at 1.0uM final concentration for 12 hours.

tag: tumor type

value: T-cell acute lymphoblastic leukemia

tag: transduction

value: ICN

tag: agent post-transduction

value: CmpdE


title: TALL-1 Mig-cMyc mock treated 12hrs

description:
TALL-1 Mig-cMyc DMSO
YF060509H133P23.CEL

value: cMyc

value: DMSO


title: liver_control_6h_biological rep4

description:
Control-4
Gene expression data from the liver of control mouse

source_name: left lateral liver of the control mouse, 6 h after injection


title: HEK, ligand treated, rep2A


title: liver_10 mg/kg SP70_6h_biological rep2

description:
SP70-10-2
Gene expression data from the liver of 10 mg/kg SP70-treated mouse


title: liver_control_6h_biological rep5

description:
Control-5
Gene expression data from the liver of control mouse


title: HEK, ligand and radiation treated, rep1A


title: HEK, untreated, rep2A


title: liver_control_6h_biological rep3

description:
Control-3
Gene expression data from the liver of control mouse


title: Ewing's Sarcoma Cell Line SKNMC

description: SKNMC

tag: sample type


title: Ewing's Sarcoma Cell Line SKES1

tag: sex


title: Ewing's Sarcoma Cell Line RM82

tag: age


title: TALL-1 GSI treated 12hrs

description:
TALL-1 CmpdE
YF060509H133P20.CEL

tag: agent


title: TALL-1 mock treated 12hrs

description:
TALL-1 DMSO
YF060509H133P19.CEL


title: TALL-1 Mig-cMyc GSI treated 12hrs

description:
TALL-1 Mig-cMyc CmpdE
YF060509H133P24.CEL


title: liver_control_6h_biological rep1

description:
Control-1
Gene expression data from the liver of control mouse


title: Ewing's Sarcoma Cell Line RDES

description: RDES

tag: primary tumor/metas

tag: overall metastasis


title: KOPTK1 Mig-cMyc GSI treated 12hrs

description:
KOPTK1 Mig-cMyc CmpdE
CP060329H133P10.CEL

source_name: KOPTK1 cell line

tag: cell line


title: HEK, radiation treated, rep1A

tag: cell type


title: KOPTK1 Mig-cMyc mock treated 12hrs

description:
KOPTK1 Mig-cMyc DMSO
CP060329H133P09.CEL


title: TALL-1 Mig-ICN mock treated 12hrs

description:
TALL-1 Mig-ICN DMSO
YF060509H133P21.CEL


title: KOPTK1 Mig-ICN mock treated 12hrs

description:
KOPTK1 Mig-ICN DMSO
CP060329H133P07.CEL


title: liver_control_6h_biological rep2

description:
Control-2
Gene expression data from the liver of control mouse


title: U87, ligand and radiation treated, rep3A

source_name: glioma, ligand and radiation treated

treatment_protocol: The U87 human glioma cell line was plated 24 hrs prior to the experiment. The treatment conditions followed were: control (untreated), DNA minor groove binding ligand (50uM treated), radiation (8.5 Gy treated), and ligand+radiation (50uM+8.5Gy treated). Cells were then incubated further for 4 hrs following these treatment conditions and RNA samples were prepared.

value: glioma cells

tag: treatment


title: Lif-WD ES cells, rep2

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

country: USA

institute: National Institutes of Health

hyb_protocol: 20 micrograms of biotin labeled RNA was fragmented to ~100 bp fragments by incubating in a buffer containing 200 mM Tris-Acetate pH 8.2, 500 mM Potassium Acetate and 500 Magnesium Acetate for 35 minutes at 95C. Fragments were hybridized to Affymetrix 430 2.0 chips for 16 hrs, washed and stained on an Affymetrix fluidics station.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: Raw signal values were normalized using RMAExpress.

source_name: Brg(lox/lox);Actin-CreER mice

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), followed by RNeasy kit with DNaseI digestion to eliminate genomic DNA

value: Brg conditional ES cells prepared from Brg(lox/lox);Actin-CreER mice that allow conditional deletion of Brg upon addition of 4-hydroxytamoxifen (4OHT, Sigma)

value: starved of LIF for 48 hours


title: KOPTK1 GSI treated 12hrs

description:
KOPTK1 CmpdE
CP060329H133P06.CEL


title: Ewing's Sarcoma Cell Line ESCADO1

value: DNA sample from cell line

tag: source

value: Spanish National Tumor Bank


title: Lif-WD ES cells, rep3


title: Lif-WD ES cells, rep1


title: Ewing's Sarcoma Cell Line A4573


title: Ewing's Sarcoma Cell Line CHP100


title: Ewing's Sarcoma Cell Line EW3


title: HEK, untreated, rep1A

value: HEK

value: human embryonic kidney


title: HEK, ligand treated, rep1A


title: U87, untreated, rep3A

source_name: glioma, untreated


title: KOPTK1 Mig-ICN GSI treated 12hrs

description:
KOPTK1 Mig-ICN CmpdE
CP060329H133P08.CEL


title: U87, ligand treated, rep3A

source_name: glioma, ligand treated


title: KOPTK1 mock treated 12hrs

description:
KOPTK1 DMSO
CP060329H133P05.CEL


title: U87, ligand and radiation treated, rep2A

value: DNA minor groove binding ligand and radiation


title: Ewing's Sarcoma Tumor Sample WIL_W

source_name: Ewing's Sarcoma Tumor Sample

value: DNA sample from tumor biopsy

value: male

value: primary tumor

value: yes


title: U87, radiation treated, rep3A

source_name: glioma, radiation treated

value: radiation


title: HPBALL Mig-cMyc GSI treated 12hrs

description:
HPBALL Mig-cMyc CmpdE
YF060509H133P18.CEL

source_name: HPBALL cell line

value: HPBALL

value: T-cell acute lymphoblastic leukemia


title: Ewing's Sarcoma Tumor Sample TIL_M

value: female

value: no

source_name: DNA pooled from 100 healthy donors


title: HPBALL Mig-ICN GSI treated 12hrs

description:
HPBALL Mig-ICN CmpdE
YF060509H133P16.CEL

value: ICN

value: CmpdE


title: U87, ligand treated, rep2A

value: glioma cells

value: DNA minor groove binding ligand


title: U87, ligand and radiation treated, rep1A


title: Ewing's Sarcoma Tumor Sample WYS_T

value: Spanish National Tumor Bank


title: Ewing's Sarcoma Tumor Sample SZE_A


title: U87, untreated, rep2A


title: HPBALL Mig-ICN mock treated 12hrs

description:
HPBALL Mig-ICN DMSO
YF060509H133P15.CEL

value: DMSO


title: HPBALL Mig-cMyc mock treated 12hrs

description:
HPBALL Mig-cMyc DMSO
YF060509H133P17.CEL

value: cMyc


title: HPBALL GSI treated 12hrs

description:
HPBALL CmpdE
YF060509H133P14.CEL


title: Ewing's Sarcoma Tumor Sample STU_A


title: U87, radiation treated, rep1A


title: U87, ligand treated, rep1A


title: SG200 biological rep2

city: Sevilla

first: Jose

middle: I

last: Ibeas

address: Carretera de Utrera Km 1

department: Biolgía Molecular e Ingeniería Bioquímica

institute: Universidad Pablo de Olavide

hyb_protocol: Affymetrix EukGE-WS2 on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GCS2500

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: U. maydis strain SG200  grown for 48 h in Charcoal minimal media

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: SG200 and SG200deltatup1 were grown to an OD600 of 0.5 at 28°C in YEPSL (0.4% peptone, 1% yeast extract, 0.4% sucrose). Then, cells were washed twice with sterile water and spread out on charcoal array plates (6.25 % (w/v) Holiday salt solution, 1% vitamin solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized) and mixed with 2% agar, 1% charcoal sterile solution) at a concentration of OD600 of 0.1 per cm2 and grown for 48 hours at 22ºC.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer’s instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

value: SG200 is a FB1 derivative with the insertion of a compatible b-mating locus

tag: genetic background

tag: genotype

value: wild type


title: HPBALL mock treated 12hrs

description:
HPBALL DMSO
YF060509H133P13.CEL


title: SG200 dtup1 biological rep1

source_name: U. maydis strain SG200 delta tup1 grown for 48 h in Charcoal minimal media

tag: strain

value: SG200 delta tup1 is a SG200 derivative with the deletion of Tup1 gene (carboxine replacement)

value: tup1 deletion


title: SG200 dtup1 biological rep2

source_name: U. maydis strain SG200 delta tup1  grown for 48 h in Charcoal minimal media


title: Ewing's Sarcoma Tumor Sample STR_J

value: DNA sample from tumor biopsy

value: male

value: primary tumor

value: yes


title: U87, untreated, rep1A


title: HEK, ligand and radiation treated, rep3B

source_name: Human embryonic kidney, ligand and radiation treated

value: HEK

value: human embryonic kidney

value: DNA minor groove binding ligand and radiation


title: DND41 Mig-cMyc GSI treated 12hrs

description:
DND41 Mig-cMyc CmpdE
YF060509H133P12.CEL

source_name: DND41 cell line

value: T-cell acute lymphoblastic leukemia

value: CmpdE


title: Ewing's Sarcoma Tumor Sample SCH_Y

value: female


title: Ewing's Sarcoma Tumor Sample SCH_P

value: no

value: Spanish National Tumor Bank


title: DND41 Mig-cMyc mock treated 12hrs

description:
DND41 Mig-cMyc DMSO
YF060509H133P11.CEL

value: cMyc

value: DMSO


title: HEK, radiation treated, rep3B

source_name: Human embryonic kidney, radiation treated

value: radiation


title: Ewing's Sarcoma Tumor Sample THO_C


title: U87, radiation treated, rep2A

value: glioma cells


title: HEK, ligand treated, rep3B

source_name: Human embryonic kidney, ligand treated

value: DNA minor groove binding ligand


title: SG200 biological rep 1

value: SG200 is a FB1 derivative with the insertion of a compatible b-mating locus

value: wild type


title: Tet1 KO #22

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression profile of Tet1 KO #22

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 1.65ug cy3-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetronitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing: Arrays were normalized using limma R package with across-array quantile normalization for one-color arrays

source_name: mouse ESC

label_protocol: Cy3-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 0.5 µg total RNA.

growth_protocol: All mouse ESCs were cultured on irridiated feeders in LIF contianing media.

extract_protocol: RNA used for microarray was extracted from preplated mESCs using RNAeasy Kit (Qaigen).

value: mix 129 C57BL6 backgound

tag: genotype/variation

value: Tet1 KO


title: Ewing's Sarcoma Tumor Sample SCH_B

value: DNA sample from tumor biopsy

value: primary tumor

value: yes


title: Ewing's Sarcoma Tumor Sample ROU_J

value: male


title: Tet1 KO #4

description: Gene expression profile of Tet1 KO #4


title: DND41 Mig-ICN GSI treated 12hrs

description:
DND41 Mig-ICN CmpdE
YF060509H133P10.CEL

tag: tumor type

value: T-cell acute lymphoblastic leukemia

value: ICN

value: CmpdE


title: DND41 GSI treated 12hrs

description:
DND41 CmpdE
YF060509H133P08.CEL


title: DND41 Mig-ICN mock treated 12hrs

description:
DND41 Mig-ICN DMSO
YF060509H133P09.CEL

tag: transduction


title: Ewing's Sarcoma Tumor Sample PRE_D

value: female

value: no

value: Spanish National Tumor Bank


title: HEK, untreated, rep3B

source_name: Human embryonic kidney, untreated

value: HEK

value: human embryonic kidney


title: Tet1 WT

description: Gene expression profile of Tet1 WT

value: Tet1 WT


title: DND41 mock treated 12hrs

description:
DND41 DMSO
YF060509H133P07.CEL

value: DMSO


title: HP1 gamma -/-_E11.5_PGCs_rep2

city: Kanazawa

first: Masahide

last: Asano

state: Ishikawa

department: Advanced Science Research Center,

country: Japan

institute: Kanazawa University

description: Gene expression of HP1g-/- PGCs at E11.5

hyb_protocol: 0.9 ug of Cy3-labelled cRNA (specific activity >7.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 4x44K (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20100617) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HP1g-/-, E11.5, PGCs, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions with some changes. 4th Spike mix was made by diluted 3rd Spike-Mix 20 times, and 1.6 ul of 4th Spike-Mix was added to samples. Cy3 labeled cRNA was synthesized at 40°C for 20 hours and purified by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HP1g mutant mice were generated by a modified gene-trap method. To mark the PGCs by fluorescence, HP1g+/- mice were mated with Blimp1-mVenus transgenic mice and HP1g+/-; Blimp1-mVenus tg mice were backcrossed to HP1g+/- mice to make HP1g-/-; Blimp1-mVenus tg mice that were used.

extract_protocol: The total RNA was extracted from these sorted cells by an RNeasy micro kit (Qiagen). RNA was quantified and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The genital ridges of  HP1g-/-; Blimp1-mVenus tg mice and  wild-type; Blimp1-mVenus tg mice were dissected from embryos and singly cells were suspended in FACS solution (2% FCS and 0.01% NaN3 in Hank’s solution). The mVenus-positive cells were isolated by a flow cytometer (JSAN, Bay Bioscience)

value: primordial germ cells (PGCs)

tag: Stage

value: embryonic day 11.5 (E11.5)

value: HP1 gamma -/-


title: HEK, radiation treated, rep2B

value: radiation


title: ALLSIL Mig-cMyc mock treated 12hrs

description:
ALLSIL Mig-cMyc DMSO
YF060509H133P05.CEL

source_name: ALLSIL cell line

value: ALLSIL

value: cMyc

tag: agent post-transduction


title: Ewing's Sarcoma Tumor Sample PEE_L

tag: sample type

value: DNA sample from tumor biopsy

tag: sex

value: primary tumor


title: HEK, ligand and radiation treated, rep2B

value: DNA minor groove binding ligand and radiation


title: wild-type_E11.5_PGCs_rep2

description: Gene expression of wild-type PGCs at E11.5

source_name: wild-type, E11.5, PGCs, replicate 2

value: wild-type


title: HP1 gamma -/-_E11.5_PGCs_rep1

source_name: HP1g-/-, E11.5, PGCs, replicate 1


title: ALLSIL Mig-cMyc GSI treated 12hrs

description:
ALLSIL Mig-cMyc CmpdE
YF060509H133P06.CEL

value: T-cell acute lymphoblastic leukemia

value: CmpdE


title: Ewing's Sarcoma Tumor Sample MEU_A

source_name: Ewing's Sarcoma Tumor Sample

value: male

tag: age

value: yes

value: Spanish National Tumor Bank


title: HEK, ligand treated, rep2B

value: HEK

value: human embryonic kidney

value: DNA minor groove binding ligand


title: HEK, untreated, rep2B


title: Ewing's Sarcoma Tumor Sample MER_J

tag: primary tumor/metas

value: no


title: HEK, ligand and radiation treated, rep1B


title: Ewing's Sarcoma Tumor Sample OZC_B

value: female

tag: overall metastasis


title: HEK, radiation treated, rep1B

tag: cell line

value: radiation


title: wild-type_E11.5_PGCs_rep1

source_name: wild-type, E11.5, PGCs, replicate 1

tag: cell type

value: primordial germ cells (PGCs)

value: embryonic day 11.5 (E11.5)


title: ALLSIL Mig-ICN GSI treated 12hrs

description:
ALLSIL Mig-ICN CmpdE
YF060509H133P04.CEL

value: ALLSIL

value: ICN


title: ALLSIL GSI treated 12hrs

description:
ALLSIL CmpdE
YF060509H133P02.CEL

tag: agent


title: ALLSIL Mig-ICN mock treated 12hrs

description:
ALLSIL Mig-ICN DMSO
YF060509H133P03.CEL

value: DMSO


title: Ewing's Sarcoma Tumor Sample NOO_F

value: DNA sample from tumor biopsy

value: primary tumor

tag: source


title: Ewing's Sarcoma Tumor Sample MBA_M


title: Ewing's Sarcoma Tumor Sample LIN_N


title: ALLSIL mock treated 12hrs

description:
ALLSIL DMSO
YF060509H133P01.CEL

value: T-cell acute lymphoblastic leukemia


title: HEK, ligand treated, rep1B

tag: treatment


title: HEK, untreated, rep1B


title: U87, radiation treated, rep3B

source_name: glioma, radiation treated

value: glioma cells


title: Ewing's Sarcoma Tumor Sample HUW_L

value: male

source_name: DNA pooled from 100 healthy donors


title: Ewing's Sarcoma Cell Line A673

source_name: Ewing's Sarcoma Cell Line

value: DNA sample from cell line

value: Spanish National Tumor Bank


title: Ewing's Sarcoma Tumor Sample HOO_C

value: yes


title: 46_D

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed (Fluidics Scripts FS450_001) and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: Cell intensity files were generated using GCOS (Affymetrix). The probe set data was generated using R/BioConductor (version 2.12.0) packages affy (version 1.28.0), gcrma (version 2.22.0).

source_name: lymph node

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit, 2005-2009, Affymetrix).

extract_protocol: Extraction of total RNA was performed using the RNeasy Plus Mini Kit (cat. 74134) according to Qiagen's instructions.

tag: status

value: negative

tag: Sex


title: 61_D


title: U87, ligand and radiation treated, rep3B

source_name: glioma, ligand and radiation treated

value: DNA minor groove binding ligand and radiation


title: Ewing's Sarcoma Tumor Sample HOE_K


title: U87, ligand treated, rep3B

source_name: glioma, ligand treated

value: DNA minor groove binding ligand


title: SKES1_Nsp1

description: Hybridized to 500K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the the Gene Array reader (Affymetrix)

data_processing:
CEL files were processed to study copy number alterations using GTYPE 4.1 and CNAT 4.0 software (Affymetrix), smoothing = 0.1, using the Mapping 500K Sample Data Set (http://www.affymetrix.com/support/technical/sample_data/500k_data.affx) which includes CEL files from 48 samples (96 hybridizations, considering both Nsp and Sty arrays) belonging to the International Hap Map project, as healthy references.
Sample tables are the CNAT output, which includes the log2ratio and the results of the HMM segmentation algorithm.

label: Biotin

source_name: SKES1 Ewing's Sarcoma cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: The SKES1 cell lines was cultured in McCoy's medium supplemented with 15% FBS

extract_protocol: DNA was extracted using QIAamp DNA Mini Kit (Qiagen) following manufacturer's instructions for extracting DNA from cell lines

treatment_protocol: no treatment was applied, the cell line was used in normal growing conditions.

value: cell line

value: Ewing's Sarcoma


title: 61_B

value: metastatic

value: female


title: Ewing's Sarcoma Tumor Sample HER_M

value: no


title: 46_B


title: U87, ligand and radiation treated, rep2B


title: Ewing's Sarcoma Tumor Sample HEN_F


title: 21_E


title: U87, untreated, rep3B

source_name: glioma, untreated


title: 15_E


title: Ewing's Sarcoma Tumor Sample HAE_R


title: U87, radiation treated, rep2B

value: radiation


title: 21_D


title: Ewing's Sarcoma Tumor Sample HAE_L

value: DNA sample from tumor biopsy


title: 15_D


title: U87, untreated, rep2B


title: U87, ligand treated, rep2B


title: Ewing's Sarcoma Tumor Sample GYP_V

value: primary tumor


title: Ewing's Sarcoma Tumor Sample GYS_B


title: polysomal RNA_treat insulin_biological replicate 2

type: other

city: Mexico City

first: Laura

last: Uribe

state: DF

address: Periferico Sur 4124 Col. Ex rancho de Anzaldo

department: Research

country: Mexico

institute: INMEGEN

hyb_protocol: 10 micrograms of  fragmented and labeled cRNA were hybridized for 16 hr at 45C to the Maize GeneChip Genome array.   Microarrays were washed and stained in the Affymetrix Fluidics Station 450 with the Midi_euk2v3 protocol.

scan_protocol: Genechips were scanned using the Affymetrix GCOS software  and the Affymetrix Genechip Scanner 3000  7G.

data_processing: The data was analyzed using R and Bioconductor softwares. Two normalization processes were performed: quantile normalization and Loess normalization .To identify differentially expressed genes, a linear model with the empirical Bayes approach was implemented using the Limma package (Smyth, 2004 and 2005).

molecule: other

organism: Zea mays

source_name: polysomal, germinated embryonic axes, insulin treatment

label_protocol: 4 ug of total RNA as starting material were used for the preparation of biotinylated cRNA , according to the standard IVT Labeling Affymetrix protocol ( GeneChip Expression Analysis Technical Manual 2005-2006, Affymetrix).

growth_protocol: Maize seeds were germinated in a Griffin incubator for 24 hrs on a water moisturized cotton at  27°± 1°C. Embryonic axes were manually exceded for both the quiescent and germinated seeds and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted  from 1 g of  quiescent or germinated embryonic axes using the TRIzol reagent as per  manufacturers instructions.  Polysomal RNA was extracted from 2 g of  germinated embryonic axes after a sucrose cushion polysome concentration step. The polysomal fraction was resuspended in 500 µL of buffer B3 (200 mM Tris-HCI pH 8.4, 200 mM KCl, 25 mM EGTA, 36 mM MgC12, 5 mM DTT, 50 mg/mL cycloheximide, 25 mL of SDS 10% and 1 mL of proteinase K [1 mg/mL]), mixed and incubated at 37°C for 30 min. Then TRIzol reagent and chloroform were added. Isopropanol was added to the aqueous phase to precipitate the RNA.

treatment_protocol: Dissected maize embryonic axes from seeds imbibed during 22 h at  27°± 1°C in darkness were incubated in nutrient-complete MS medium (Murashige and Skoog, 1962) for an additional 2 h, in the presence or absence of 200 µU/mL of bovine insulin (Sigma-Aldrich).

tag: developmental stage

value: germinated

value: insulin


title: Ewing's Sarcoma Tumor Sample ENC_R

value: male


title: total RNA_treat insulin biological replicate 1

source_name: total RNA, germinated embryonic axes, insulin treatment


title: U87, radiation treated, rep1B

value: glioma cells


title: Ewing's Sarcoma Tumor Sample DRY_S

value: Spanish National Tumor Bank


title: U87, ligand and radiation treated, rep1B


title: polysomal RNA_treat insulin_biological replicate 1


title: polysomal RNA_biological replicate 3

source_name: polysomal, germinated embryonic axes

value: no insulin


title: total RNA_treat insulin_technical replicate 1-R


title: polysomal RNA_treat insulin_biological replicate 3


title: U87, ligand treated, rep1B


title: polysomal RNA_biological replicate 2


title: U87, untreated, rep1B


title: Ewing's Sarcoma Tumor Sample DON_J


title: polysomal RNA_biological replicate 1


title: Ewing's Sarcoma Tumor Sample DER_S

value: yes


title: muscle_control_rep8

city: Bar Harbor

first: Roger

last: Sher

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: log2-transformed Illumina average intensity data followed by quantile normalization

source_name: muscle

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

extract_protocol: Total RNA was extracted with Trizol Reagent, followed by Qiagen DNAse1 treatment according to manufacturer's protocol.  Quality control was performed with Agilent Bioanalyser.

value: M

tag: strain

value: A/J

tag: tumor

value: control


title: Ewing's Sarcoma Tumor Sample DED_C


title: total RNA_time24_biological replicate RB

source_name: germinated embryonic axes excised after 24 hrs

tag: time


title: total RNA_time24_technical replicate M4-R


title: total RNA_time0_biological replicate 1

source_name: quiescent embryonic axes

value: quiescent


title: total RNA_time24_biological replicate M4


title: total RNA_time0_biological replicate 2


title: muscle_control_rep5

value: BALB/cByJ


title: muscle_control_rep4


title: Ewing's Sarcoma Tumor Sample DAA_I


title: total RNA_time0_technical replicate 1


title: Ewing's Sarcoma Tumor Sample BUS_C

value: female


title: Ewing's Sarcoma Tumor Sample CLE_S

value: no


title: muscle_control_rep6


title: muscle_control_rep7


title: Ewing's Sarcoma Tumor Sample BLO_D


title: muscle_control_rep3


title: Ewing's Sarcoma Tumor Sample DEK_M


title: muscle_control_rep2


title: muscle_rhabdo_rep4

value: rhabdo


title: Abcb4 liver_rep8

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: Abcb4-/- liver, mouse ID: 30082706

label_protocol: For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye. HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: gender

value: 17 weeks

value: Balb/cByJ

tag: genotype/variation

tag: tissue

value: liver

tag: mouse id

source_name: Wt RNA pool liver

value: wild type

tag: mouse ids


title: Ewing's Sarcoma Tumor Sample BIE_E

source_name: Ewing's Sarcoma Tumor Sample

tag: sample type

value: DNA sample from tumor biopsy

tag: sex

tag: age

tag: primary tumor/metas

value: primary tumor

tag: overall metastasis


title: Abcb4 liver_rep7

value: male


title: Abcb4 liver_rep5

source_name: Abcb4-/- liver, mouse ID: 30082701


title: Ewing's Sarcoma Tumor Sample BEN_A

source_name: DNA pooled from 100 healthy donors

tag: source

value: Spanish National Tumor Bank


title: Abcb4 liver_rep6


title: muscle_rhabdo_rep3


title: Ewing's Sarcoma Tumor Sample 93_03

value: yes


title: Abcb4 liver_rep3

source_name: Abcb4-/- liver, mouse ID: 30082704


title: Ewing's Sarcoma Tumor Sample 96_03


title: Ewing's Sarcoma Tumor Sample 91_03


title: Ewing's Sarcoma Tumor Sample 98_05


title: Abcb4 liver_rep2

source_name: Abcb4-/- liver, mouse ID: 30082705


title: Abcb4 liver_rep4


title: Ewing's Sarcoma Tumor Sample 92_04


title: Ewing's Sarcoma Tumor Sample 88_03

value: metastasis


title: Ewing's Sarcoma Tumor Sample 63_04


title: muscle_rhabdo_rep2

value: M

value: A/J


title: Abcb4 liver_rep1


title: Human blood_Chronic ITP_Pt36

city: Palo Alto

first: Bing

last: Zhang

state: CA

address: 3373 Hillview Ave

institute: Stanford University

description: Peripheral blood from ITP Pt#36. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

hyb_protocol: For each experimental sample, Cy5- and Cy3-labeled samples were co-hybridized to a Stanford cDNA microarray at 65°C for 14 hours.  After hybridization, arrays were washed before scanning.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 36_SHGO.gpr (see below for link to file)

data_processing:
Normalization performed with GenePix Pro software version is 5.0.  The fluorescence ratios were normalized by mean-centering genes for each array (that is, 'global' normalization), and then by mean centering each gene across all arrays.
The reason for the discrepancy between the array description and the platform data table is mainly due to the filters we set up for data retrieval from SMD:  Select only features with no flag (include only features that have not been designated as unreliable either by the scanning software or by the array/hybridization owner); Regression correlation>0.6;median fluorescent hybridization signal intensity divided by median background intensity >1.5 in both the sample and reference channels for at least 80% of the samples analyzed. The controls account for a relatively small portion of the missing data.

source_name: ITP patient peripheral blood (test)

label_protocol: The total RNA from ITP paitents and Universal Human Reference RNA was first linerly amplified for one round using MessageAmp aRNA Amplification Kit(Ambion) following manufacturer's protocol, then 6µg of amplified aRNA was mixed with 10µg of pdN6 hexamer primer, incubate at 65°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 200 µM dTTP, 100 µM Cy3 or Cy5-labeled (Amersham) dUTP.

extract_protocol: Total RNA was extracted using PAXgene Blood RNA Kit following manufacturer's instructions.

tag: patient

value: Whole blood

tag: disease

value: ITP

tag: disease state

value: Chronic ITP

source_name: Universal Human Reference RNA, Stratagene

tag: reference

value: Total RNA from 10 pooled cell lines


title: Human blood_Chronic ITP_Pt33

description: Peripheral blood from ITP Pt#33. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 33_SHGO.gpr (see below for link to file)


title: Untreated_AntiSense-array_biological-rep2

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

institute: CSIR-Institute Of Genomics and Integrative Biology

description:
Anti-Sense transcript detecting array.
Compared with the standard protocol, this protocol skips the first cycle cDNA synthesis and the IVT amplification process, and starts directly from the second cycle cDNA synthesis.

hyb_protocol: Exon array Affy chip is a 49/64 Format array. It has 5 micron feature. Samples were hybridized as per Affymetrix Exon 1.0 ST array protocol.

scan_protocol: Washing, staining, & scanning of array was done using GeneChip Fluidics Station 450/250. Before this, an experiment must first be registered in GeneChip Operating Software (GCOS).

data_processing:
Exon array CEL files were processed in 'Expression Console' software from Affymetrix. For analysis at 'Full' level (i.e. using exons derived from sets of ab-initio gene predictions in addition to the 'Core' and 'Extended' exons), signal intensities were summarized using RMA and including DABG (detection above background) levels. The Probe Group File (.pgf) is HuEx-1_0-st-v2.r2.pgf.
For normalization across the arrays Sketch-Quantile method was used.

source_name: HeLa cell line, untreated control

label_protocol: The labeling was done using standard protocol and kit from Affymetrix, called GeneChip Whole Transcript (WT) Sense Target Labeling Assay.

growth_protocol: Cells were cultured in DMEM-High Glucose (SIGMA) supplemented with heat-inactivated 10% FCS and antibiotic mix (HiMedia)

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). Purification was done using RNeasy Kit (Qiagen) to remove aromatic remnants.

treatment_protocol: Heat-shock treatment was given at 45 degree Celsius for 30 min. in water bath. This was followed by incubation of 2 hours for heat-shock recovery and response, at 37 degree Celsius and 5% CO2.

tag: cell line

value: HeLa

value: Cervix

value: Female


title: Human blood_Chronic ITP_Pt32

description: Peripheral blood from ITP Pt#32. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 32_SHGO.gpr (see below for link to file)


title: muscle_control_rep1

tag: Sex

tag: strain

tag: tumor

value: control


title: Human blood_Chronic ITP_Pt31

description: Peripheral blood from ITP Pt#31. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 31_SHGO.gpr (see below for link to file)

tag: tissue


title: muscle_rhabdo_rep1

value: rhabdo


title: Human blood_Chronic ITP_Pt34

description: Peripheral blood from ITP Pt#34. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 34_SHGO.gpr (see below for link to file)


title: Ewing's Sarcoma Tumor Sample 335_05

hyb_protocol: Labeled DNA was purified through Illustra G-50 Microspin Columns (Amersham, GE), mixed and then precipitated along with Cot Human DNA (Roche). Hybridization was performed for 48 hours at 42°C and excess probe was removed.

scan_protocol: Data were acquired using an Axon 4000B scanner and GenePix software (Axon Laboratories).

label_protocol: Tumor and reference DNA was Cy5/Cy3-dCTP-labelled (Amersham, GE) using a non-commercial Random Priming kit composed of random octamers dissolved in Exo-Minus Klenow buffer (Eppicentre), a dNTPs mix depleted in dCTP (Eppendorf), and Exo-Minus Klenow enzyme (Eppicentre).

extract_protocol: Cell lines: DNA was extracted using QIAamp DNA Mini Kit (Qiagen) following manufacturer's instructions for extracting DNA from cell lines; Tumors: Genomic DNA was extracted from frozen tumor biopsies containing at least 70% of tumor cells. Tissue samples containing less than 80% of tumor cells, as quantified by histological examination, were microdissected from unstained glass slides prior to DNA extraction. DNA was isolated using the Qiagen DNA Extraction kit (Qiagen) or the High Pure PCR Template Preparation kit (Roche) following the manufacturer’s recommendations.

value: DNA sample from tumor biopsy

value: female


title: Untreated_Sense-array_biological-rep1

description: Sense transcript detecting array.

tag: gender


title: Ewing's Sarcoma Tumor Sample 322_04

value: male

value: primary tumor

value: no


title: Untreated_AntiSense-array_biological-rep1


title: Heat-shock_AntiSense-array_biological-rep1

source_name: HeLa cell line, Heat-shock treated


title: Ewing's Sarcoma Tumor Sample 313_04

value: Spanish National Tumor Bank


title: Heat-shock_AntiSense-array_biological-rep2


title: Human blood_Chronic ITP_Pt30

description: Peripheral blood from ITP Pt#30. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 30_SHGO.gpr (see below for link to file)


title: Ewing's Sarcoma Tumor Sample 03_05

value: yes


title: Ewing's Sarcoma Tumor Sample 28_07


title: Granulosa_cells Replicate 2

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description: Biological replicate 2 of 3.

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.) Images were quantified using ArrayPro 6.4 software (Media Cybernetics).

data_processing: LOESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Bos taurus

source_name: granulosa cells

label_protocol: Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

extract_protocol:
In_vitro_Blastocyst_protocol: Bovine ovaries were collected from a local abattoir and oocytes were aspirated from healthy 3 to 6 mm follicles. Oocytes with a dark uniform cytoplasm surrounded by at least five layers of cumulus cells, referred to as healthy cumulusâ€“oocyte complexes, were selected for culture in SOF using our defined protocols. Oocytes were fertilized using frozen semen from a mixture of three different bulls and embryos were also cultured using our standard protocols in SOF medium supplemented with 0.8% BSA. Blastocyst-stage embryos were collected 7 days post-fertilization. All the embryos were washed three times with RNAse-free PBS, frozen, and stored at -80°C
GC_collection protocol: Granulosa cells were collected on day 8 to 11 post-oestrus of lactating cows, from follicles with a diameter higher than 5 mm. Administration of FSH started 36 h after the aspiration of those follicles. 6 injections of 40 mg, twice a day, were administrated for a total of 240 mg of FSH. Granulosa cell harvest procedure was done 44h after the last injection of FSH, under epidural using ultrasound examination with a 18G needle and COOK aspiration unit. Cells were collected in warm Hepes buffered Tyrodeâ€™s media (TLH) containing Hepalean (10 UI/mL) and transferred to the lab. They were placed in Hepes buffered Tyrodeâ€™s media (TLH) solution (supplemented with 10% bovine serum, 0.2 mM pyruvate and 50 ug/ml gentamicin). Granulosa cells were selected under binocular observation and  washed 3 times with sterile PBS.
Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturerâ€™s instructions. RNA was eluted in 11 Âµl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

tag: breed

value: Holstein

tag: developemental stage

source_name: in-vitro Blastocyst

value: blastocyst day 7


title: Granulosa_cells Replicate 3

description: Biological replicate 3 of 3.

value: day 8 to 11 post-oestrus of lactating cows


title: DAY 30 (IRI)

city: Boston

first: John

last: Iacomini

address: 800 Washington st

institute: Tufts University/ Medical Center

description: Sample 8_Cy3

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by LC sciences by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: Mus musculus kidney IRI

label_protocol: The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments

growth_protocol: Kidney tissue was extracted directly from treated mice

extract_protocol: Total RNA was extracted from kidney tissue using the miRNeasy kit

treatment_protocol: Mice were either 1)untreated naïve, 2) sham operated controls or 3) 30 minutes warm ischemia.  Tissue was harvested from groups 2 and 3 on days 1,3,5,7,10,14,21 and 30

value: kidney

value: 10-12 weeks

tag: stress

value: ischemia reperfusion injury

tag: time

value: day 30


title: DAY 30 (sham)

description: Sample 8_Cy5

source_name: Mus musculus kidney sham

tag: age

value: Female

value: sham operated control


title: Human blood_Chronic ITP_Pt29

description: Peripheral blood from ITP Pt#29. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 29_SHGO.gpr (see below for link to file)

value: Whole blood

value: ITP

value: Chronic ITP

value: Total RNA from 10 pooled cell lines


title: Ewing's Sarcoma Tumor Sample 307_04

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

institute: Centro de Investigación del Cáncer

data_processing: Normalization was carried out with GenePix software using the mean of the median of ratios of all the autosomal features in the array.

tag: sample type

value: DNA sample from tumor biopsy

tag: sex

value: male

tag: primary tumor/metas

value: primary tumor

tag: overall metastasis


title: DAY 21  (sham)

description: Sample 7_Cy5

value: day 21


title: NAÏVE

description: Sample 9_Cy3 (single channel hybridization)

source_name: Mus musculus kidney naive

value: untreated naïve


title: Granulosa_cells Replicate 1

description: Biological replicate 1 of 3.

value: Holstein

value: blastocyst day 7


title: Ewing's Sarcoma Tumor Sample 31_07

value: yes

tag: source

value: Spanish National Tumor Bank


title: In-vitro_Blastocyst Replicate 2

description: Biological replicate 2 of 3.

value: day 8 to 11 post-oestrus of lactating cows


title: In-vitro_Blastocyst Replicate 3

description: Biological replicate 3 of 3.


title: Heat-shock_Sense-array_biological-rep2

description: Sense transcript detecting array

value: HeLa

value: Cervix


title: Ewing's Sarcoma Tumor Sample 26_05

value: no


title: Human blood_Chronic ITP_Pt24

description: Peripheral blood from ITP Pt#24. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 24_SHEB.gpr (see below for link to file)

tag: patient

value: Whole blood

tag: disease

tag: disease state

tag: reference


title: Human blood_Chronic ITP_Pt25

description: Peripheral blood from ITP Pt#25. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 25_SHEB.gpr (see below for link to file)

value: ITP


title: Untreated_Sense-array_biological-rep2

description: Sense transcript detecting array.

tag: cell line

value: Female


title: DAY 21  (IRI)

description: Sample 7_Cy3

tag: strain

tag: tissue

value: kidney

value: 10-12 weeks

value: ischemia reperfusion injury


title: Human blood_Chronic ITP_Pt28

description: Peripheral blood from ITP Pt#28. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 28_SHGO.gpr (see below for link to file)

value: Chronic ITP

value: Total RNA from 10 pooled cell lines


title: Ewing's Sarcoma Tumor Sample 173_07

value: DNA sample from tumor biopsy

value: male

value: primary tumor


title: Human blood_Chronic ITP_Pt26

description: Peripheral blood from ITP Pt#26. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 26_SHEB.gpr (see below for link to file)


title: Human blood_Chronic ITP_Pt27

description: Peripheral blood from ITP Pt#27. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 27_SHEB.gpr (see below for link to file)


title: Ewing's Sarcoma Tumor Sample 167_04

value: female


title: DAY 14 (sham)

description: Sample 6_Cy5

tag: gender

value: sham operated control

value: day 14


title: Human blood_Chronic ITP_Pt23

description: Peripheral blood from ITP Pt#23. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 23_SHEB.gpr (see below for link to file)


title: DAY 14 (IRI)

description: Sample 6_Cy3


title: DAY 10  (sham)

description: Sample 5_Cy5

value: day 10


title: DAY 10  (IRI)

description: Sample 5_Cy3


title: Ewing's Sarcoma Tumor Sample 166_04

value: Spanish National Tumor Bank


title: Heat-shock_Sense-array_biological-rep1

description: Sense transcript detecting array

value: HeLa

value: Cervix


title: Human blood_Progression to chronic ITP_Pt12

description: Peripheral blood from ITP Pt#12. Collected within 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 12_SHEB.gpr (see below for link to file)

value: Whole blood

value: ITP

value: Progression-to-chronic ITP


title: Ewing's Sarcoma Tumor Sample 164_07

value: no


title: Ewing's Sarcoma Tumor Sample 164_04

value: yes


title: Human blood_Progression to chronic ITP_Pt11

description: Peripheral blood from ITP Pt#11. Collected within 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 11_SHEB.gpr (see below for link to file)


title: Ewing's Sarcoma Tumor Sample 120_06


title: Human blood_Chronic ITP_Pt22

description: Peripheral blood from ITP Pt#22. Collected after 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 22_SHEB.gpr (see below for link to file)

value: Chronic ITP


title: DAY 7 (sham)

description: Sample 4_Cy5

value: kidney

value: 10-12 weeks

value: Female

value: day 7


title: DAY 7 (IRI)

description: Sample 4_Cy3

value: ischemia reperfusion injury


title: IP-PUM2, biological rep 2

city: Curitiba

first: PATRICIA

last: SHIGUNOV

state: Paraná

address: Rua Prof. Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas - FIOCRUZ-PR

description:
11_2_09_9
mRNAs associated with human PUM2 protein.

hyb_protocol: RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), in accordance with the manufacturer’s instructions. After purification and fragmentation, cRNA (1µg) was hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Data was imported into Partek software using the GCRMA protocol (Partek Incorporated, St. Louis, MO). Differentially enriched RNAs were found comparing immunoprecipitated samples against control samples. Final lists of genes were obtained by filtering the data where enrichment was more than 2-fold (ratio IP-PUM2/IP-control).

source_name: adipose tissue stem cells, PUM2 IP

label_protocol: cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second-strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Adipose tissue was obtained from donors who were undergoing elective bariatric surgery and dermolipectomy procedures. Typically, 100 ml of adipose tissue was processed. ADSCs were isolated by using enzymatic digestion. The cell suspension was centrifuged at 800 g for 10 mins, and contaminating erythrocytes were removed by erythrocyte lysis buffer, pH 7.3. The cells were washed and then cultivated in T75 culture flasks in DMEM-F12 (Gibco Invitrogen) supplemented with 10% FCS, penicillin (100 units/ml), and streptomycin (100 lg/ml). The medium was changed 2 days after the initial plating. The culture medium was then replaced twice each week.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Immunoprecipitation (IP) reactions were performed with 2 µg of anti-Pum2 antibody (SC-31536 -lot#k1405, goat polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein G-agarose beads (Sigma, Deisenhofen, Germany). ADSCs were lysed in polysome lysis buffer (Tris-HCl pH 7.4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U/ml RNase Out, PMSF 1mM and E64 10uM) for 1 hat 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 h at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer, and then the RNA was extracted for microarray and RT-PCR experiments. Identical IPs were performed with beads precoated with preimmune goat serum as a negative control.

tag: cell type

value: adipose tissue stem cells

tag: donor

tag: ip antibody

value: goat anti-Pum2 polyclonal

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number

tag: antibody lot number


title: Human blood_Progression to chronic ITP_Pt10

description: Peripheral blood from ITP Pt#10. Collected within 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 10_SHGO.gpr (see below for link to file)

value: Total RNA from 10 pooled cell lines


title: IP-control, biological rep 2

description:
11_2_09_10
Non-specifically enriched RNAs.

source_name: adipose tissue stem cells, control IP

value: preimmune goat serum


title: In-vitro_Blastocyst Replicate 1

description: Biological replicate 1 of 3.

tag: breed

value: Holstein

tag: developemental stage

value: blastocyst day 7

value: day 8 to 11 post-oestrus of lactating cows


title: DAY 5 (sham)

description: Sample 3_Cy5

tag: age

tag: stress

value: sham operated control

tag: time

value: day 5


title: Ewing's Sarcoma Tumor Sample 105_07

tag: sample type

value: DNA sample from tumor biopsy

tag: sex

value: male

tag: primary tumor/metas

value: primary tumor

tag: overall metastasis

value: yes

tag: source

value: Spanish National Tumor Bank


title: IP-PUM2, biological rep 1

description:
11_2_09_7
mRNAs associated with human PUM2 protein.


title: Human blood_Progression to chronic ITP_Pt9

description: Peripheral blood from ITP Pt#9. Collected within 6 months of dx during active disease, the pt did not recover by 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 9_SHEB.gpr (see below for link to file)

tag: patient

tag: tissue

value: Whole blood

tag: disease

value: ITP

tag: disease state

value: Progression-to-chronic ITP

tag: reference


title: STAET10 cell line, shRNA-construction sh280

description: DTL silenced ES-cell line

hyb_protocol: cRNAs was fragmented by alkaline digestion and used in hybridizations with Affymetrix Human Genome U133 Plus 2.0. The hybridizations were performed according to the GeneChip System (Affymetrix) in a GeneChip Fluidics Station, model 450

scan_protocol: GeneChips were scanned using the Gene Array reader (Affymetrix).

data_processing: The raw data was processed (background substraction and normalization) with BioC package affy using the RMA method.

source_name: STAET10 cell line transduced with pLKO.1-280_s1c1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix). This and the latter process required a total of 5 µg of RNA.

growth_protocol: ES cell lines were cultered in RPMI 10% FBS (RM82) or in RPMI 20% FBS (TC32, STAET10), onto gelatin coated plates

extract_protocol: 72 hours after transduction, total RNA from DTL-silenced cell lines was extracted with Trizol (Invitrogen). RNA integrity and pureness (degree of contamination by DNA) were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: pLKO.1-shRNA constructions were transfected separately in the 293T packaging cell line along with the pMD.G and pCMV-dR8.91 vectors, following a typical lipofectamine 2000 (Invitrogen) protocol. At 48 hours after transfection, 12ml-viral supernatants were collected, fresh medium added (8ml), passed through a 0.44 µm-polysulfonate filter (PALL), polybrene-added to a final 8 µg/ml concentration (SIGMA Aldrich) and used to transduce (1'5ml per well) the target ES cell lines that were plated in 6-well plates 24-hours before (RM82, TC32: 400000 cells per well; STAET10: 600000 cells per well). 6-well plates were centrifuged at 2000 rpm, 32 ºC for 1 hour. pLKO.1-non-targeting control is used as a control.

value: cell line

tag: cell line

value: Ewing's sarcoma


title: IP-control, biological rep 1

description:
11_2_09_8
Non-specifically enriched RNAs.

tag: cell type

value: adipose tissue stem cells

tag: donor

tag: ip antibody


title: STAET10 cell line, shRNA-construction sh2495

description: DTL silenced ES-cell line

source_name: STAET10 cell line transduced with pLKO.1-2495_s1c1


title: DAY 5 (IRI)

description: Sample 3_Cy3

tag: strain

value: kidney

tag: age

value: 10-12 weeks

tag: gender

value: Female

value: ischemia reperfusion injury


title: STAET10 cell line, non-targeting control

description: Non-targeting control ES-cell line

source_name: STAET10 cell line transduced with pLKO.1-non-targeting control

tag: sample type


title: TC32 cell line, shRNA-construction sh2495

description: DTL silenced ES-cell line

source_name: TC32 cell line transduced with pLKO.1-2495_s1c1


title: Human blood_Acute ITP_Pt7

description: Peripheral blood from ITP Pt#7. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 7_SHGO.gpr (see below for link to file)

value: Self-limited acute ITP

value: Total RNA from 10 pooled cell lines


title: Ewing's Sarcoma Tumor Sample 104_07

scan_protocol: Data were acquired using an Axon 4000B scanner and GenePix software (Axon Laboratories).

source_name: Ewing's Sarcoma Tumor Sample

value: DNA sample from tumor biopsy

tag: sex

source_name: DNA pooled from 100 healthy donors


title: Ewing's Sarcoma Tumor Sample 12_06

value: female

tag: primary tumor/metas

value: no


title: DAY 1 (sham)

description: Sample 1_Cy5

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

tag: stress

value: sham operated control

tag: time

value: day 1


title: Ewing's Sarcoma Tumor Sample 06_03

value: male

value: primary tumor

tag: overall metastasis

value: yes

tag: source

value: Spanish National Tumor Bank


title: DAY 3 (sham)

description: Sample 2_Cy5

tag: tissue

value: day 3


title: DAY 3 (IRI)

description: Sample 2_Cy3


title: Ewing's Sarcoma Tumor Sample 05_03


title: AcH3

status: Public on Jul 30 2011

middle: Jonghan

last: Woo

address: 1 Blackfan Circle, Karp Res Bldg

department: Hematology / Oncology

institute: Children's Hospital Boston / Harvard Medical School

hyb_protocol: According to standard Affymetrix protocols.

data_processing: MAT (Johnson et al., 2006) was used to process the raw CEL files. The following settings; Bandwith = 300, MaxGap = 300, MinProbe = 10 were used. BAR and BED files were generated by using Mm_PromPR_v02-1_NCBIv36.NR.bpmap.

source_name: AcH3 ChIP DNA from human Erythroblasts

label_protocol: Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.

growth_protocol: De-identified cryogenically preserved primary human CD34+  (hCD34+) cells were obtained from the Yale Center of Excellence in Molecular Hematology (New Haven, Connecticut).  They were prepared by magnetically sorting mononuclear samples of G-CSF mobilized peripheral blood from donors.  For erythroid ex vivo differentiation, hCD34+ progenitor stem cells were expanded for 6 days in StemSpan SFEM Medium with 1X CC100 cytokine mix (StemCell Technologies Inc.) and 2% P/S.  On day 6 of expansion, cells were reseeded into erythroid differentiation medium (StemSpan SFEM Medium containing 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM β-estradiol).

extract_protocol: Approximately, 5 × 10^7 of day 5 differentiated erythroid cells were used. Briefly, cells were cross-linked by addition of final 1% formaldehyde for 7 min at room temperature. Cross-linking was terminated by adding final 125 mM glycine and cells were washed with cold phosphate-buffered saline (PBS) containing protease inhibitor cocktail, collected by centrifugation and washed again. Collected cell pellet was resuspended in SDS ChIP buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, and protease inhibitors). Cells were sonicated and fragmented DNA was visualized on an agarose gel (average size 0.5-1 kb). The sample was centrifuged at 12000 rpm at 4°C for 10 min and supernatant was collected. Sample was pre-cleared with protein A beads at 4°C for 1 hr and incubated with antibody (or PBS for reference sample) at 4°C overnight. Following day samples were immunoprecipitated with protein A beads.  The IP complexes were successively washed with low salt (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), high salt (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), buffer LiCl (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). All washes were for 8 min at room temperature. SDS elution buffer was added and incubated at 65°C overnight to reverse crosslink protein-DNA complexes. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25μl of water.

treatment_protocol: No other treatments

value: Day5 Differentiated Erythroid Cells

tag: antibody

tag: antibody vendor

value: Millipore

tag: antibody lot/batch number

tag: antibody catalog number

source_name: Mock ChIP DNA from human Erythroblasts


title: Ewing's Sarcoma Tumor Sample 05_04


title: Human blood_Acute ITP_Pt8

description: Peripheral blood from ITP Pt#8. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 8_SHGO.gpr (see below for link to file)

source_name: ITP patient peripheral blood (test)

tag: patient

value: Whole blood

tag: disease

value: ITP

tag: disease state

source_name: Universal Human Reference RNA, Stratagene

tag: reference


title: Human blood_Acute ITP_Pt4

description: Peripheral blood from ITP Pt#4. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 4_SHEB.gpr (see below for link to file)


title: RM82 cell line, shRNA-construction sh2495

description: DTL silenced ES-cell line

source_name: RM82 cell line transduced with pLKO.1-2495_s1c1

value: cell line

tag: cell line

value: Ewing's sarcoma


title: RM82 cell line, shRNA-construction sh280

description: DTL silenced ES-cell line

source_name: RM82 cell line transduced with pLKO.1-280_s1c1

tag: sample type


title: RM82 cell line, non-targeting control

description: Non-targeting control ES-cell line

source_name: RM82 cell line transduced with pLKO.1-non-targeting control


title: TC32 cell line, non-targeting control

description: Non-targeting control ES-cell line

source_name: TC32 cell line transduced with pLKO.1-non-targeting control


title: Human blood_Acute ITP_Pt5

description: Peripheral blood from ITP Pt#5. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 5_SHGO.gpr (see below for link to file)

value: Self-limited acute ITP

value: Total RNA from 10 pooled cell lines


title: LcL, starvation, centenarian 3

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

hyb_protocol: HG-U133A GeneChip Plus 2.0 arrays hybridization and staining were performed according to the GeneChip One-Cycle Target Labeling and Control Reagents protocol, supplied by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed according to the GeneChip One-Cycle Target Labeling and Control Reagents protocol, supplied by the manufacturer (Affymetrix, Santa Clara, CA, USA).

data_processing: RMA using Partek Genomics Suite.

source_name: LcL, starvation, centenarian

label_protocol: Biotin-labeled target synthesis was performed according to the GeneChip One-Cycle Target Labeling and Control Reagents protocol, supplied by the manufacturer (Affymetrix, Santa Clara, CA, USA).

growth_protocol: The Lcs were cultured in RPMI medium supplemented with 2 mM L-Glutamine, penicillin/streptomycin (100 mg/ml) in the presence or absence of 10% fetal bovine serum (FBS) for 48 hours.

extract_protocol: Cells were collected and total cellular RNA was isolated by means of the Qiagen RNeasy Micro Kit following the manifacturer's instructions (Qiagen, Valencia, CA). Quantity and purity/integrity of each sample was quantified using the Nanodrop 1000 (Thermo Fisher Scientific, Freemont, CA, USA) and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Starvation was performed by cultivating the cells in the absence of FBS for 48h.

tag: cell type

value: cultured lymphoblastoid cells

tag: gender

tag: age

value: 106 years

tag: culture condition

value: starvation

tag: subject identifier


title: Human blood_Acute ITP_Pt6

description: Peripheral blood from ITP Pt#6. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 6_SHGO.gpr (see below for link to file)


title: LcL, starvation, young 2

source_name: LcL, starvation, young

value: 28 years


title: Human blood_Acute ITP_Pt3

description: Peripheral blood from ITP Pt#3. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 3_SHEB.gpr (see below for link to file)


title: LcL, basal, young 1

source_name: LcL, basal, young

value: male

value: 40 years

value: basal


title: Human blood_Acute ITP_Pt2

description: Peripheral blood from ITP Pt#2 Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 2_SHEB.gpr (see below for link to file)


title: LcL, starvation, young 1


title: LcL, basal, centenarian 3

source_name: LcL, basal, centenarian


title: LcL, basal, young 2


title: ZBP89

scan_protocol: According to standard Affymetrix protocols.

source_name: ZBP89 ChIP DNA from human Erythroblasts

value: ZBP89 N14 (Rabbit polyclonal)

value: Generated in the lab of Alan B. Cantor.


title: TC32 cell line, shRNA-construction sh280

description: DTL silenced ES-cell line

source_name: TC32 cell line transduced with pLKO.1-280_s1c1


title: Human blood_Acute ITP_Pt1

description: Peripheral blood from ITP Pt#1. Collected within 6 months of dx during active disease, the pt recovered within 6 months of dx.

scan_protocol: Microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments) and fluorescence ratios for array elements were extracted using GenePix software. GPR file:  ITP 1_SHEB.gpr (see below for link to file)


title: DAY 1 (IRI)

description: Sample 1_Cy3

source_name: Mus musculus kidney IRI

tag: strain

value: kidney

value: 10-12 weeks

value: Female

tag: stress

value: ischemia reperfusion injury

tag: time

value: day 1


title: LcL, starvation, young 3

value: female

value: 37 years


title: LcL, basal, young 3


title: LcL, basal, centenarian 2

value: 100 years


title: LcL, starvation, centenarian 1

value: cultured lymphoblastoid cells

value: 104 years


title: LcL, starvation, centenarian 2

value: starvation


title: NC-4

status: Public on Jul 28 2011

city: Taoyuan

first: Kuo Hsuan

last: Chang

address: No. 5,  No.5, Fusing Street, Gueishan Township

department: Department of Neurology

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Gene expression data from peripheral leukocytes

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
We use Genespring default protocol to normalize our raw data. The protocol is listed below:
Summarization Algorithm: RMA
Technology: Affymetrix.GeneChip.HG-U133A
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: Peripheral leukocytes from a normal control

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

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

tag: tissue

value: Blood

value: peripheral leukocyte

tag: ethnicity

value: Chinese


title: NC-3

value: Male


title: NC-5


title: NC-2


title: GBS-6

source_name: Peripheral leukocytes from a GBS patient


title: NC-6


title: GBS-7


title: GBS-5


title: LcL, basal, centenarian 1

value: basal


title: GBS-3


title: NC-1


title: NC-7


title: GBS-4


title: GBS-2


title: GBS-1


title: GCSF

status: Public on Jul 25 2011

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: GCSF

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Partek Genomics Suite.

source_name: Purified neutrophils, control mice, in vitro culture, GCSF

label_protocol: Standard Illumina labeling protocol.

growth_protocol: Samples 5-10 were cultured for 2 hours in OptiMEM media supplemented with 0.5% FBS.

extract_protocol: RNA was extracted using Trizol reagent.

treatment_protocol: Cultured neutrophils were treated with chemokines (20ng/ml) for 2 hours.

value: nude NCR

tag: 4t1 tumor bearing

value: no

value: neutrophils

tag: treatment

value: rhGCSF


title: GCSF+CCL2

source_name: Purified neutrophils, control mice, in vitro culture, GCSF+CCL2


title: GCSF+CCL5

source_name: Purified neutrophils, control mice, in vitro culture, GCSF+CCL5


title: Control+CCL5

source_name: Purified neutrophils, control mice, in vitro culture, CCL5


title: TENs, rep 1

source_name: Purified neutrophils, tumor-bearing mice

value: yes


title: Control neutrophils, rep 2

source_name: Purified neutrophils, control mice


title: TENs, rep 2


title: Control

description: Cont

source_name: Purified neutrophils, control mice, in vitro culture


title: Control lung 1

description:
ZG_MOE430A_2_Lung10
Gene expression data from control lung, rep1 of 3.

hyb_protocol: Standard Affymetrix hybridization protocol.

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

data_processing: R/Bioconductor through gcRMA normalization and LIMMA.

source_name: Lung sample from mouse orthotopically injected with PBS day 7 post injection

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

value: lung

value: control


title: Control lung 2

description:
ZG_MOE430A_2_Lung11
Gene expression data from control lung, rep2 of 3.

value: female


title: Control neutrophils, rep 1


title: Control+CCL2

source_name: Purified neutrophils, control mice, in vitro culture, CCL2


title: Control lung 3

description:
ZG_MOE430A_2_Lung12
Gene expression data from control lung, rep3 of 3.


title: Pre-metastatic lung 3

description:
ZG_MOE430A_2_Lung9
Gene expression data from pre-metastatic lung, rep3 of 3.

source_name: Lung sample from mouse bearing an orthotopic 4T1 tumor day 7 post tumor engraftment

value: pre-metastatic


title: Control liver 2

description:
ZG_MOE430A_2_Liver11
Gene expression data from control liver, rep2 of 3.

source_name: Liver sample from mouse orthotopically injected with PBS day 7 post injection

value: liver


title: Pre-metastatic lung 1

description:
ZG_MOE430A_2_Lung7
Gene expression data from pre-metastatic lung, rep1 of 3.


title: Pre-metastatic liver 3

description:
ZG_MOE430A_2_Liver9
Gene expression data from pre-metastatic liver, rep3 of 3.

source_name: Liver sample from mouse bearing an orthotopic 4T1 tumor day 7 post tumor engraftment


title: Pre-metastatic lung 2

description:
ZG_MOE430A_2_Lung8
Gene expression data from pre-metastatic lung, rep2 of 3.


title: Control liver 3

description:
ZG_MOE430A_2_Liver12
Gene expression data from control liver, rep3 of 3.


title: Control liver 1

description:
ZG_MOE430A_2_Liver10
Gene expression data from control liver, rep1 of 3.


title: Pre-metastatic liver 2

description:
ZG_MOE430A_2_Liver8
Gene expression data from pre-metastatic liver, rep2 of 3.


title: hybrid_FlowerBud_RNA1

status: Public on Jul 27 2011

city: Münster

first: Fei

last: He

address: Hüfferstr. 1

department: Münster University

institute: Institute for Evolution and Biodiversity

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G

data_processing:
GeneChip Operating Software Version 1.4 (GCOS)
primary_data_description: raw intensity was read from .CEL file, log transformed, background corrected, quantile normalzied, then convert back to normal scale

organism: Arabidopsis thaliana x Arabidopsis lyrata

source_name: flower bud

label_protocol: Biotin, Invitrogen Bioprime random labeling

growth_protocol: stratifying for 7 days at 4°C and growing in the greenhouse under 16h cool white light supplemented with red light at 20°C

extract_protocol: Qiagen RNeasy Plant Mini Kit

treatment_protocol: 3 four-weeks-old leaves, 3-4 open flowers and 3-4 flower buds

tag: ecotype

value: Be-0 x LF10

value: flower bud


title: hybrid_leaf_RNA3

source_name: 4-weeks-old leaf

value: 4-weeks-old leaf


title: hybrid_leaf_RNA2


title: hybrid_leaf_RNA4


title: Pre-metastatic liver 1

description:
ZG_MOE430A_2_Liver7
Gene expression data from pre-metastatic liver, rep1 of 3.


title: hybrid_FlowerBud_RNA3


title: Control (22 WPI), 1

status: Public on Jul 21 2011

city: NEW YORK

first: TAMAS

middle: A

last: GONDA

address: 161 FT WASHINGTON

department: MEDICINE

institute: COLUMBIA UNIVERSITY

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

source_name: stomach, control, 22 WPI

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

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

tag: background strain

value: FVB

tag: genotype

value: INS-GAS transgenic

tag: phenotype

value: hypergastrinemic

value: stomach

tag: infection

value: Helicobacter felis

tag: dysplasia score

value: normal folate diet


title: hybrid_leaf_RNA1


title: Control (22 WPI), 2


title: LF10_DNA1

organism: Arabidopsis lyrata

source_name: seedling

extract_protocol: Qiagen DNeasy Plant Mini Kit

value: seedling


title: hybrid_Openflower_RNA1

source_name: open flower

value: open flower


title: F1_DNA4


title: hybrid_Openflower_RNA4


title: F1_DNA3


title: F1_DNA1


title: hybrid_Openflower_RNA3


title: Be_DNA1

organism: Arabidopsis thaliana


title: Be_DNA3


title: hybrid_Openflower_RNA2


title: F1_DNA2


title: LF10_DNA3


title: hybrid_FlowerBud_RNA2


title: LF10_DNA4


title: Human pancreatic beta cell-enriched cell, biological replicate 2

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

country: Belgium

institute: Vrije Universiteit Brussel

description:
Beta cell-b1
each biological replicate obtained from pooled cultures of 3-4 human organs, 10 donor organs in total
Beta Cell Bank at Diabetes Research Center, Brussels, Belgium

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to the Affymetrix HG133A

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 400, and scanned in the Affymetrix GeneArray2500scanner.

data_processing: Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity. Using the PM-MM model with mismatch correction, a 90% confidence interval was calculated for the fold change in gene expression in each comparison, and the lower limit of this interval (LCB) was used as a measure of differential gene expression.

source_name: Pool of pancreatic beta cell-enriched fractions, obtained from 3 non-selected adult human pancreases (Beta Cell Bank at Diabetes Research Center, Brussels, Belgium)

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

growth_protocol: We hybridized 3 different pools of 6 µg RNA obtained from 10 human organs in total: pool 1 (45% insulin+, from n=3 donor organs), pool 2 (65% ins+, from n=3 donor organs) and pool 3 (55% insulin+, from n=4 donor organs). Average donor age and BMI were 47±10 yrs and 26±4, respectively.  Pancreatic duct cells-enriched preparations contained 85±7% cytokeratin 19+ cells with 4±1% insulin+ cells and 6±4% glucagon+ cells and were isolated as described by Heimberg H. et al.( Diabetes 2001,49: 571-579 ).

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

treatment_protocol: Suspensions of human beta and duct cells were maintained 2-3w in culture as described ( Diabetes 2001,49: 571-579 ) with no specific treatment.

tag: tissue source

value: 3 non-selected adult human pancreases

tag: pancreatic cell type

value: adult pancreatic endocrine cells


title: Folate - 16 wks, 2

source_name: stomach, folate, 16 wks

value: folate-supplemented diet

tag: time of treatment

value: 16 wks after H. felis infection


title: Human pancreatic duct cells, biological replicate 2

description:
Duct cell-b1
each biological replicate obtained from pooled cultures of 3 human organs, 6 donor organs in total
Beta Cell Bank at Diabetes Research Center, Brussels, Belgium

source_name: Pool of pancreatic duct cell-enriched fractions, obtained from 3 non-selected adult human pancreases (Beta Cell Bank at Diabetes Research Center, Brussels, Belgium)

value: adult pancreatic exocrine-duct cells


title: Human pancreatic beta cell-enriched cell, biological replicate 1

description:
Beta cell-a1
each biological replicate obtained from pooled cultures of 3-4 human organs, 10 donor organs in total
Beta Cell Bank at Diabetes Research Center, Brussels, Belgium


title: Control (28 WPI), 2

source_name: stomach, control, 28 WPI


title: Control (28 WPI), 3


title: Human pancreatic duct cells, biological replicate 1

description:
Duct cell-a1
each biological replicate obtained from pooled cultures of 3 human organs, 6 donor organs in total
Beta Cell Bank at Diabetes Research Center, Brussels, Belgium


title: Folate - 16 wks, 1


title: Human pancreatic beta cell-enriched cell, biological replicate 3

description:
Beta cell-c1
each biological replicate obtained from pooled cultures of 3-4 human organs, 10 donor organs in total
Beta Cell Bank at Diabetes Research Center, Brussels, Belgium

source_name: Pool of pancreatic beta cell-enriched fractions, obtained from 4 non-selected adult human pancreases (Beta Cell Bank at Diabetes Research Center, Brussels, Belgium)

value: 4 non-selected adult human pancreases


title: Folate - 8 wks, 1

source_name: stomach, folate, 8 wks

value: 8 wks after H. felis infection


title: Folate - 4 wks

source_name: stomach, folate, 4 wks

value: 4 wks after H. felis infection


title: Be_DNA2