title: wt-P4 1

status: Public on Dec 01 2010

type: other

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: miRNA profiling

hyb_protocol: miRNA Complete Labeling and Hyb Kit (Agilent)

scan_protocol: Agilent scanner.

data_processing: The scanned images were processed with algorithms specified by the Agilent Feature Extraction software 10.5.1.1. Data has been further processed (i.e.,  quantile normalized across arrays ) in R/Bioconductor.

molecule: total RNA

organism: Mus musculus

source_name: sciatic nerves

growth_protocol: Mice were housed under SPF (specific pathogen free) conditions

extract_protocol: miRNeasy (Qiagen)

treatment_protocol: mice analyzed are offsprings of the crossing tgDhh-Cre+ Dicerwt/flox x Dicerflox/flox

tag: strain

tag: genotype

value: Dicer1 wt/fl Dhh-Cre pos

tag: developmental stage

value: postnatal day 4 (P4)


title: fl-E17 1

description: miRNA profiling

label_protocol: miRNA Complete Labeling and Hyb Kit (Agilent)

value: Dicer1 fl/fl Dhh-Cre pos

value: embryonal day 17 (E17)


title: wt-P4 4

description: miRNA profiling


title: wt-E17 4

description: miRNA profiling


title: wt-P4 2

description: miRNA profiling


title: fl-P4 1

description: miRNA profiling


title: fl-E17 4

description: miRNA profiling


title: fl-P4 4

description: miRNA profiling


title: wt-P4 3

description: miRNA profiling


title: fl-E17 2

description: miRNA profiling


title: fl-E17 3

description: miRNA profiling


title: wt-E17 3

description: miRNA profiling


title: fl-P4 2

description: miRNA profiling


title: Karenia brevis_60 µM H2O2_5min_dye swap_ 251377210020-

type: RNA

city: Charleston

first: Frances

middle: M

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

country: USA

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

description: Karenia brevis exposed to 60 µM H2O2 for 5 min v Karenia brevis untreated control culture harvested at time 0 of 60 µM H2O2 treatment

hyb_protocol: 500 ng each of Cy3 and Cy5 labeled targets were combined and hybridized to a custom K. brevis oligonucleotide microarray (Agilent) for 17 hours at 60°C in an Agilent DNA microarray hybridization oven. After hybridization, arrays were washed consecutively in solutions of 6X SSPE and 0.005% N-laurylsarcosine and 0.06X SSPE and 0.005% N-laurylsarcosine for 1 minute each at room temperature, followed by a 30 second wash in a stabilization and drying solution (Agilent, Palo Alto, CA).

scan_protocol: Microarrays were imaged on an Agilent microarray scanner at 10 µm scan resolution.  Concurrent scans of the red and green PMT were performed

data_processing: Images were extracted with Agilent Feature Extraction software version A7.5.1 using Agilent Design File 013772_D_F_20050913.

organism: Karenia brevis

source_name: Karenia brevis, log phase culture, exposed to 60 µM H2O2

label_protocol: Total RNA (500 ng) from pooled cultures at each timepoint was labeled with Cy3 or Cy5 dye using an Agilent low input linear RNA amplification kit according to manufacturers recommendations (Agilent, Palo Alto, CA).  Following cleanup, labeled cRNA was quantified by UV spectroscopy and 500 ng each of Cy3 and Cy5 labeled targets were hybridized to the array for 17 hours at 60°C.

growth_protocol: Karenia brevis Wilson isolate grown in 25 mL batch cultures in autoclaved, 20 µm filtered seawater at 36‰ enriched with f/2 medium, 25 ± 1°C on a 16h:8h light:dark cycle with illumination from cool white lights at 150μE m-2 sec-1

extract_protocol: Five replicate cultures at each time-point were pooled and harvested by centrifugation. Total RNA from each pooled sample was prepared using TriReagent. Following precipitation in isopropanol, the RNA was resuspended and purified using a Qiagen RNeasy column.  Total RNA was quantified by UV spectroscopy and qualified on an Agilent 2100 Bioanalyzer.

treatment_protocol: Replicate 25 mL cultures grown at to mid-log phase were exposed to 60 µM H2O2. Samples were collected at 5, 15, 30, 60, and 240 min.

tag: Wilson isolate, log phase culture, exposed to 60 µM H2O2

source_name: Karenia brevis, log phase culture

treatment_protocol: Replicate 25 mL cultures grown to mid-log phase

tag: Wilson isolate, log phase culture


title: fl-P4 3

description: miRNA profiling


title: wt-E17 1

description: miRNA profiling


title: Karenia brevis_60 µM H2O2_5min_251377210020+

description: Karenia brevis untreated control culture harvested at time 0 of 60 µM H2O2 treatment v Karenia brevis exposed to 60 µM H2O2 for 5 min

treatment_protocol: Replicate 25 mL cultures grown to mid-log phase.

treatment_protocol: Replicate 25 mL cultures grown at to mid-log phase were exposed to 60 µM H2O2.  Samples were collected at 5, 15, 30, 60, and 240 min.


title: wt-E17 2

description: miRNA profiling


title: Karenia brevis_5°C heat shock_30min_dye swap_251377210008-

description: Karenia brevis exposed to 5°C heat shock for 30 min v Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment

scan_protocol: Microarrays were imaged on an Agilent microarray scanner at 10 µm scan resolution.  Concurrent scans of the red and green PMT were performed.

source_name: Karenia brevis, log phase culture, exposed to 5°C heat shock

treatment_protocol: Replicate 25 mL cultures grown at 25°C were placed in a waterbath maintained at 30°C.  Samples were collected at 5, 15, 30, 60, or 240 min.

tag: Wilson isolate, log phase culture, exposed to 5°C heat shock

treatment_protocol: Replicate 25 mL cultures grown at 25°C to mid-log phase


title: Karenia brevis_5°C heat shock_240min_dyeswap_251377210019-

description: Karenia brevis exposed to 5°C heat shock for 240 min v Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment

extract_protocol: Five replicate cultures at each time-point were pooled and harvested by centrifugation. Total RNA from each pooled sample was prepared using TriReagent. Following precipitation in isopropanol, the RNA was resuspended and purified using a Qiagen RNeasy column.  Total RNA was quantified by UV spectroscopy and qualified on an Agilent 2100 Bioanalyzer

treatment_protocol: Replicate 25 mL cultures grown at 25°C to mid-log phase.


title: Karenia brevis_10°C heat shock_60min_dye swap_251377210083-

description: Karenia brevis exposed to 10°C heat shock for 60 min v Karenia brevis untreated control culture harvested at time 0 of 10°C heat shock treatment

source_name: Karenia brevis, log phase culture, exposed to 10°C heat shock

treatment_protocol: Replicate 25 mL cultures grown at 25°C were placed in a waterbath maintained at 35°C.  Samples were collected at 60 min.

tag: Wilson isolate, log phase culture, exposed to 10°C heat shock


title: Karenia brevis_5°Cheat shock_5min_dye swap_251377210005-

description: Karenia brevis exposed to 5°C heat shock for 5 min v Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment


title: Karenia brevis_60 µM H2O2_15min_251377210028+

description: Karenia brevis untreated control culture harvested at time 0 of 60 µM H2O2 treatment v Karenia brevis exposed to 60 µM H2O2 for 15 min


title: Karenia brevis_5°C heat shock_240min_251377210019+

description: Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment v Karenia brevis exposed to 5°C heat shock for 240 min


title: Karenia brevis_5°C heat shock_60min_251377210009+

description: Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment v Karenia brevis exposed to 5°C heat shock for 60 min


title: Karenia brevis_12 µM PbCl2_1hour _dye swap_251377210081-

description: Karenia brevis exposed to 12 µM PbCl2 for 1 hour v Karenia brevis untreated control culture harvested at time 0 of 12 µM PbCl2 treatment

source_name: Karenia brevis, log phase culture, exposed to 12 µM PbCl2

treatment_protocol: Replicate 25 mL cultures grown at to mid-log phase were exposed to 12 µM PbCl2. Samples were collected at 1, 4, and 7 hours.

tag: Wilson isolate, log phase culture, exposed to 12 µM PbCl2


title: Karenia brevis_5°C heat shock_15min_251377210007+

description: Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment v Karenia brevis exposed to 5°C heat shock for 15 min


title: Karenia brevis_10°C heat shock_60min_251377210083+

description: Karenia brevis untreated control culture harvested at time 0 of 10°C heat shock treatment v Karenia brevis exposed to 10°C heat shock for 60 min


title: Karenia brevis_12 µM PbCl2_4hour_dye swap_251377210082-

description: Karenia brevis exposed to 12 µM PbCl2 for 4 hours v Karenia brevis untreated control culture harvested at time 0 of 12 µM PbCl2 treatment.


title: Karenia brevis_5°C heat shock_15min_dye swap_251377210007-

description: Karenia brevis exposed to 5°C heat shock for 15 min v Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment


title: Karenia brevis_5°C heat shock_60min_dye swap_251377210009-

description: Karenia brevis exposed to 5°C heat shock for 60 min v Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment


title: Karenia brevis_5°C heat shock_30min_251377210008+

description: Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment v Karenia brevis exposed to 5°C heat shock for 30 min


title: Karenia brevis_5°C heat shock_5min_251377210005+

description: Karenia brevis untreated control culture harvested at time 0 of 5°C heat shock treatment vs Karenia brevis exposed to 5°C heat shock for 5 min


title: Karenia brevis_10 mM NaNO2_4hours_dye swap_251377210075-

description: Karenia brevis exposed to 10 mM NaNO2 for 4 hours v Karenia brevis untreated control culture harvested at time 0 of 10 mM NaNO2 treatment.

source_name: Karenia brevis, log phase culture, exposed to 10 mM NaNO2

treatment_protocol: Replicate 25 mL cultures grown at to mid-log phase were exposed to 10 mM NaNO2. Samples were collected at 1, 4, and 7 hours.

tag: Wilson isolate, log phase culture, exposed to 10 mM NaNO2


title: Karenia brevis_10 mM NaNO2_7hours_dye swap_251377210077-

description: Karenia brevis exposed to 10 mM NaNO2 for 7 hours v Karenia brevis untreated control culture harvested at time 0 of 10 mM NaNO2 treatment.


title: Karenia brevis_12 µM PbCl2_1hour_251377210081+

description: Karenia brevis untreated control culture harvested at time 0 of 12 µM PbCl2 treatment v Karenia brevis exposed to 12 µM PbCl2 for 1 hour


title: RKO_BSA pretreatment_microZnO

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description: CaCo2 BSA and microZnO comparison to BSA control

hyb_protocol: Agilent two-color GE hyb/wash protocol

scan_protocol: Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505B US45102802

data_processing: Feature extraction and processing - Agilent FE 9.5.1.1 protocol, lowess normaliztion and background subtracted

organism: Homo sapiens

source_name: RKO; BSA pretreatment; 5 μg/cm2 microZnO

label_protocol: Agilent two-color LRILAK labeling protocol

growth_protocol: All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Advanced DMEM media (supplemented with 2% FBS, and glutamax) and allowed to begin growing overnight.

extract_protocol: Total RNA was collected using Qiagen RNeasy Mini kits.

treatment_protocol: Cells were then pretreated with 100 ng/ml BSA or TNF for 1 hr, then media was removed and replaced with 2 ml of media with the nanoparticulate material for 4 hrs prior to RNA collection..

tag: cell line

value: RKO

source_name: RKO; BSA pretreatment


title: CaCo2_BSA pretreatment_microZnO

source_name: CaCo-2; BSA pretreatment; 5 μg/cm2 microZnO

source_name: CaCo-2; BSA pretreatment


title: Karenia brevis_60 µM H2O2_60min_251377210036+

description: Karenia brevis untreated control culture harvested at time 0 of 60 µM H2O2 treatment v Karenia brevis exposed to 60 µM H2O2 for 60 min


title: CaCo2_TNFα pretreatment_microZnO

description: CaCo2 TNF and microZnO comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 5 μg/cm2 microZnO


title: Karenia brevis_12 µM PbCl2_7hour_dye swap_251377210080-

description: Karenia brevis exposed to 12 µM PbCl2 for 7 hours v Karenia brevis untreated control culture harvested at time 0 of 12 µM PbCl2 treatment.


title: Karenia brevis_12 µM PbCl2_7hour_251377210080+

description: Karenia brevis untreated control culture harvested at time 0 of 12 µM PbCl2 treatment v Karenia brevis exposed to 12 µM PbCl2 for 7 hours.


title: Karenia brevis_10 mM NaNO2_1hour_dye swap_251377210076-

description: Karenia brevis exposed to 10 mM NaNO2 for 1 hour v Karenia brevis untreated control culture harvested at time 0 of 10 mM NaNO2 treatment.


title: Karenia brevis_12 µM PbCl2_4hour_251377210082+

description: Karenia brevis untreated control culture harvested at time 0 of 12 µM PbCl2 treatment v Karenia brevis exposed to 12 µM PbCl2 for 4 hours


title: Karenia brevis_60 µM H2O2_240min_251377210036+

description: Karenia brevis untreated control culture harvested at time 0 of 60 µM H2O2 treatment v Karenia brevis exposed to 60 µM H2O2 for 240 min

treatment_protocol: Replicate 25 mL cultures grown at to mid-log phase were exposed to 60 µM H2O2. Samples were collected at 5, 15, 30, 60, and 240 min


title: Karenia brevis_60 µM H2O2_15min_dye swap_251377210028-

description: Karenia brevis exposed to 60 µM H2O2 for 15 min v Karenia brevis untreated control culture harvested at time 0 of 60 µM H2O2 treatment


title: RKO_TNFα pretreatment_microZnO

source_name: RKO; TNFα pretreatment; 5 μg/cm2 microZnO


title: Karenia brevis_10 mM NaNO2_ 4hours_251377210075+

description: Karenia brevis untreated control culture harvested at time 0 of 10 mM NaNO2 treatment v Karenia brevis exposed to 10 mM NaNO2 for 4 hours


title: Karenia brevis_10 mM NaNO2_1hour_251377210076+

description: Karenia brevis untreated control culture harvested at time 0 of 10 mM NaNO2 treatment v Karenia brevis exposed to 10 mM NaNO2 for 1 hour


title: Karenia brevis_10 mM NaNO2_7hours_251377210077+

description: Karenia brevis untreated control culture harvested at time 0 of 10 mM NaNO2 treatment v Karenia brevis exposed to 10 mM NaNO2 for 7 hours.


title: CaCo2_TNFα pretreatment_nano-carbon black

description: CaCo2 TNF and nano-carbon black comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 50 μg/cm2 nano-carbon black


title: CaCo2_BSA pretreatment_nano-carbon black

description: CaCo2 BSA and nano-carbon black comparison to BSA control

source_name: CaCo-2; BSA pretreatment; 50 μg/cm2 nano-carbon black


title: CaCo2_BSA pretreatment_nanoAl2O3

description: CaCo2 BSA and nanoAl2O3 comparison to BSA control

source_name: CaCo-2; BSA pretreatment; 50 μg/cm2 nanoAl2O3


title: CaCo2_TNFα pretreatment_nanoSiO2

description: CaCo2 TNF and nanoSiO2 comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 50 μg/cm2 nanoSiO2


title: RKO_TNFα pretreatment_nanoTiO2

description: RKO TNF and nanoTiO2 comparison to BSA control

source_name: RKO; TNFα pretreatment; 50 μg/cm2 nanoTiO2


title: CaCo2_TNFα pretreatment

description: CaCo2 TNF comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; media


title: CaCo2_BSA pretreatment_nanoTiO2

description: CaCo2 BSA and nanoTiO2 comparison to BSA control

source_name: CaCo-2; BSA pretreatment; 50 μg/cm2 nanoTiO2


title: CaCo2_TNFα pretreatment_nanoAl2O3

description: CaCo2 TNF and nanoAl2O3 comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 50 μg/cm2 nanoAl2O3


title: CaCo2_BSA pretreatment_nanoSiO2

description: CaCo2 BSA and nanoSiO2 comparison to BSA control

source_name: CaCo-2; BSA pretreatment; 50 μg/cm2 nanoSiO2


title: CaCo2_BSA pretreatment_nanoZnO

description: CaCo2 BSA and nanoZnO comparison to BSA control

source_name: CaCo-2; BSA pretreatment; 5 μg/cm2 nanoZnO


title: CaCo2_TNFα pretreatment_nanoTiO2

description: CaCo2 TNF and nanoTiO2 comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 50 μg/cm2 nanoTiO2


title: CaCo2_TNFα pretreatment_nanoFe2O3

description: CaCo2 TNF and nanoFe2O3 comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 10 μg/cm2 nanoFe2O3


title: CaCo2_TNFα pretreatment replicate

description: CaCo2 TNF comparison to BSA control


title: RKO_BSA pretreatment_nanoFe2O3

description: RKO BSA and nanoFe2O3 comparison to BSA control

source_name: RKO; BSA pretreatment; 10 μg/cm2 nanoFe2O3

source_name: RKO; BSA pretreatment


title: RKO_BSA pretreatment_nano-carbon black

description: RKO BSA and nano-carbon black comparison to BSA control

source_name: RKO; BSA pretreatment; 50 μg/cm2 nano-carbon black


title: CaCo2_TNFα pretreatment_nanoZnO

description: CaCo2 TNF and nanoZnO comparison to BSA control

source_name: CaCo-2; TNFα pretreatment; 5 μg/cm2 nanoZnO

source_name: CaCo-2; BSA pretreatment


title: RKO_TNFα pretreatment_nano-carbon black

description: RKO TNF and nano-carbon black comparison to BSA control

source_name: RKO; TNFα pretreatment; 50 μg/cm2 nano-carbon black


title: RKO_TNFα pretreatment_nanoSiO2

description: RKO TNF and nanoSiO2 comparison to BSA control

source_name: RKO; TNFα pretreatment; 50 μg/cm2 nanoSiO2


title: CaCo2_BSA pretreatment_nanoFe2O3

description: CaCo2 BSA and nanoFe2O3 comparison to BSA control

source_name: CaCo-2; BSA pretreatment; 10 μg/cm2 nanoFe2O3


title: RKO_BSA pretreatment_nanoSiO2

description: RKO BSA and nanoSiO2 comparison to BSA control

source_name: RKO; BSA pretreatment; 50 μg/cm2 nanoSiO2


title: RKO_TNFα pretreatment_nanoFe2O3

description: RKO TNF and nanoFe2O3 comparison to BSA control

source_name: RKO; TNFα pretreatment; 10 μg/cm2 nanoFe2O3


title: RKO_TNFα pretreatment_nanoZnO

description: RKO TNF and nanoZnO comparison to BSA control

source_name: RKO; TNFα pretreatment; 5 μg/cm2 nanoZnO


title: RKO_TNFα pretreatment_nanoAl2O3

description: RKO TNF and nanoAl2O3 comparison to BSA control

source_name: RKO; TNFα pretreatment; 50 μg/cm2 nanoAl2O3


title: RKO_BSA pretreatment_nanoAl2O3

description: RKO BSA and nanoAl2O3 comparison to BSA control

source_name: RKO; BSA pretreatment; 50 μg/cm2 nanoAl2O3


title: RKO_BSA pretreatment_nanoTiO2

description: RKO BSA and nanoTiO2 comparison to BSA control

source_name: RKO; BSA pretreatment; 50 μg/cm2 nanoTiO2


title: RKO_TNFα pretreatment replicate

description: RKO TNF comparison to BSA control

source_name: RKO; TNFα pretreatment; media


title: RKO_TNFα pretreatment

description: RKO TNF comparison to BSA control


title: NB1852

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

description: primary untreated neuroblastoma tumour

hyb_protocol: Following fragmentation, ~5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Human Exon 1.0 ST Arrays (Affymetrix Part No. 900 651). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update

data_processing: In order to obtain expression information per gene, exon data was merged by transcript clusters (hg18/core exons). Exon array data was normalized according to the RMA-sketch algorithm using Affymetrix Power Tools (Affymetrix).

label: Biotin

source_name: neuroblastoma tumour, fresh frozen

label_protocol: Biotinylated cDNA was prepared according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Rev. 5) from 1000 ng total RNA, including the rRNA reduction step

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

tag: tissue type

value: primary untreated neuroblastoma tumour

tag: genomic mycn status

value: normal

tag: stage


title: NB1851

description: primary untreated neuroblastoma tumour

value: amplified


title: NB1855

description: primary untreated neuroblastoma tumour


title: NB1792

description: primary untreated neuroblastoma tumour


title: NB1821

description: primary untreated neuroblastoma tumour


title: NB1827

description: primary untreated neuroblastoma tumour


title: NB1795

description: primary untreated neuroblastoma tumour


title: NB1820

description: primary untreated neuroblastoma tumour


title: RKO_BSA pretreatment_nanoZnO

description: RKO BSA and nanoZnO comparison to BSA control

source_name: RKO; BSA pretreatment; 5 μg/cm2 nanoZnO


title: NB1777

description: primary untreated neuroblastoma tumour


title: NB1784

description: primary untreated neuroblastoma tumour


title: NB1829

description: primary untreated neuroblastoma tumour


title: Cohybridization_PBL_B

type: genomic

city: Houston

first: Robert

middle: A

last: Waterland

state: TX

address: 1100 Bates St.,

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out  according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and LOWESS normalization. Probe ratios within one SmaI interval were averaged and the median of the P value log10 ratios of the probes within one SmaI interval was calculated.

molecule: genomic DNA

source_name: genomic DNA extracted from PBL of Caucasian B1 subject

label_protocol: 0.5ug of the digested and amplified DNA was labelled from each sample with either Cy3 or Cy5 according to the Agilent Chip-on-chip mammalian protocol (version 9.1, 2006)

extract_protocol: Total DNA was extracted by standard phenol-chloroform isolation

tag: race

value: Caucasian

tag: gender

value: female

tag: age

value: 38 years

source_name: genomic DNA extracted from PBL of Caucasian B2 subject

value: 34 years


title: Cohybridization_PBL_C

source_name: genomic DNA extracted from PBL of Caucasian C1 subject

value: male

value: 42 years

source_name: genomic DNA extracted from PBL of Caucasian C2 subject


title: NB1776

description: primary untreated neuroblastoma tumour


title: NB1824

description: primary untreated neuroblastoma tumour


title: Cohybridization_PBL_A

source_name: genomic DNA extracted from PBL of Caucasian A1 subject

value: 29 years

source_name: genomic DNA extracted from PBL of Caucasian A2 subject

value: 37 years


title: Cohybridization_HF_A

source_name: genomic DNA extracted from HF of Caucasian A1 subject

source_name: genomic DNA extracted from HF of Caucasian A2 subject


title: Cohybridization_HF_D

source_name: genomic DNA extracted from HF of Caucasian D1 subject

value: 46 years

source_name: genomic DNA extracted from HF of Caucasian D2 subject


title: normal colonic mucosa_familial_proximal, rep2

city: Lisboa

first: Cristina

last: Albuquerque

address: Rua Professor Lima Basto

department: Centro de Investigação de Patobiologia Molecular (CIPM)

country: Portugal

institute: Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE

description:
Gene expression data from samples of patients with HPPS.
A478MNP2

hyb_protocol: RNA hybridization was performed according to Affymetrix recommendations. Briefly, cRNA was hybridized in the GeneChip array (Human Genome U133 Plus 2.0, Affymetrix) for 16 hours.

scan_protocol: The intensity was measured using the GeneChip scanner 3000 (Affymetrix).

data_processing: Microarray data analysis was performed with Partek Genomics Suite software. For the identification of differentially expressed genes, we used ANOVA.

label: biotin

source_name: Normal colonic mucosa located in proximal colon from a familial HPPS patient

label_protocol: cRNA was labelled with biotin according to Affymetrix instructions.

growth_protocol: Fresh colorectal lesions were obtained from surgical or colectomy specimens from patients who underwent surgery or colonoscopy in the Portuguese Institute of Oncology Francisco Gentil in Lisbon.

extract_protocol: Total RNA was isolated from each tissue sample using RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The lesions were maintained in liquid nitrogen until the RNA extraction.

tag: tissue

value: colon

tag: histology

value: normal colonic mucosa

tag: colon location

value: proximal

tag: disease

value: hyperplastic polyposis syndrome (HPPS)

tag: hereditary nature of hpps

value: familial


title: Cohybridization_HF_C

source_name: genomic DNA extracted from HF of Caucasian C1 subject

source_name: genomic DNA extracted from HF of Caucasian C2 subject


title: hyperplastic polyp_sporadic_proximal, rep2

description:
Gene expression data from samples of patients with HPPS.
A500PB

source_name: Hyperplastic polyp located in proximal colon from a sporadic HPPS patient

value: hyperplastic polyp

value: sporadic


title: NB1822

description: primary untreated neuroblastoma tumour

value: primary untreated neuroblastoma tumour

value: amplified


title: normal colonic mucosa_familial_distal, rep1

description:
Gene expression data from samples of patients with HPPS.
A643MND1

source_name: Normal colonic mucosa located in distal colon from a familial HPPS patient

value: distal


title: normal colonic mucosa_familial_proximal, rep1

description:
Gene expression data from samples of patients with HPPS.
A643MNP1


title: hyperplastic polyp_sporadic_distal

description:
Gene expression data from samples of patients with HPPS.
A983PC

source_name: Hyperplastic polyp located in distal colon from a sporadic HPPS patient


title: hyperplastic polyp_sporadic_proximal, rep1

description:
Gene expression data from samples of patients with HPPS.
A500PA


title: Cohybridization_PBL_D

source_name: genomic DNA extracted from PBL of Caucasian D1 subject

value: Caucasian

value: female

source_name: genomic DNA extracted from PBL of Caucasian D2 subject


title: hyperplastic polyp_familial_distal

description:
Gene expression data from samples of patients with HPPS.
A686P1A

source_name: Hyperplastic polyp located in distal colon from a familial HPPS patient


title: CANCER - 17 (gastric cancer study)

status: Public on Nov 30 2010

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

description: no additional information

hyb_protocol: The Cy3 and Cy5 labeled aRNA was used for hybridization onto the microarray chips from Stanford Functional Genomics Facility (SFGF) containing 44,544 spots, for 16 hrs in Lucidea SlidePro hybridization chamber (GE Health care) at 420C . After hybridization, slides were washed in 0.1X SSC,1X SSC  followed by 0.1X SSC and dried.

scan_protocol: The slides were scanned in ProScanArray (Perklin Elmer) . Gridding was done using Scan array Express software package (version -4). The integrated or mean intensity of signal within the spot was calculated. The files were saved as GPR files

data_processing: The Foreground Median intensity for Cy3 and Cy5, Background Median intensity for Cy3 and Cy5, spot size data were imported into BRB-ArrayTools software using the Import wizard function. Background correction was not done. Global normalization was used to median center the log-ratios on each array in order to adjust for differences in labeling intensitites of the Cy3 and Cy5 dyes

source_name: gastric cancer

label_protocol: 1µg of total RNA from tumor sample and universal RNA (Stratagene Cat No: – 740000-41) was reverse transcribed using array script  at 420C for 2 hrs to obtain cDNA using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion,AM1797). The cDNA was amplified by invitro transcription in the presence of T7 RNA polymerase; aRNA thus obtained was purified and quantitated in NanoDrop. 20 µg of tumor aRNA was labeled using NHS ester of Cy5 dye and control universal aRNA was labeled using NHS ester of Cy3 dye.

extract_protocol: RNA isolation was done from all the samples using the RNeasy RNA extraction kit  (Qiagen) as per manufacturer’s instructions. RNA obtained was quantitated using Nanodrop and quality checked using Agilent Bioanalyser.

treatment_protocol: Surgery

value: stomach

tag: disease state

value: CANCER

tag: cancer stage

tag: cancer histopathological examination (hpe)

value: Adenocarcinoma

tag: cancer nuclear grade

value: III

source_name: Universal Reference RNA

tag: reference

value: Stratagene's universal RNA obtained from multiple cell lines


title: Cohybridization_HF_B

source_name: genomic DNA extracted from HF of Caucasian B1 subject

value: 38 years

source_name: genomic DNA extracted from HF of Caucasian B2 subject

value: 34 years


title: CANCER - 23 (gastric cancer study)

description: no additional information


title: hyperplastic polyp_familial_unknown

description:
Gene expression data from samples of patients with HPPS.
A478PA2

source_name: Hyperplastic polyp of unknown colon location from a familial HPPS patient

value: colon

value: not available


title: PN - 20 (gastric cancer study)

description: no additional information

source_name: paired normal

value: Paired Normal (PN)

value: Normal


title: CANCER - 19 (gastric cancer study)

description: no additional information

tag: no evidence of disease (ned) or failed

value: NED


title: CANCER - 22 (gastric cancer study)

description: no additional information

value: FAILED


title: PN - 19 (gastric cancer study)

description: no additional information


title: CANCER - 18 (gastric cancer study)

description: no additional information


title: CANCER - 16 (gastric cancer study)

description: no additional information

value: II


title: CANCER - 20 (gastric cancer study)

description: no additional information


title: CANCER - 21 (gastric cancer study)

description: no additional information

treatment_protocol: Surgery initially + Palliative Chemotherapy after relapse


title: CANCER - 24 (gastric cancer study)

description: no additional information


title: CANCER - 12 (gastric cancer study)

description: no additional information


title: CANCER - 15 (gastric cancer study)

description: no additional information


title: PN - 18 (gastric cancer study)

description: no additional information


title: CANCER - 14 (gastric cancer study)

description: no additional information

value: failed


title: CANCER - 13 (gastric cancer study)

description: no additional information


title: CANCER - 8 (gastric cancer study)

description: no additional information


title: PN - 16 (gastric cancer study)

description: no additional information


title: PN - 15 (gastric cancer study)

description: no additional information


title: CANCER - 10 (gastric cancer study)

description: no additional information


title: CANCER - 6 (gastric cancer study)

description: no additional information


title: CANCER - 11 (gastric cancer study)

description: no additional information

value: Poorly diff. (Neuro Endocrine diff)


title: PN - 17 (gastric cancer study)

description: no additional information


title: CANCER - 9 (gastric cancer study)

description: no additional information


title: normal colonic mucosa_familial_distal, rep2

description:
Gene expression data from samples of patients with HPPS.
A478MND2

value: normal colonic mucosa

value: distal

value: hyperplastic polyposis syndrome (HPPS)

value: familial


title: CANCER - 7 (gastric cancer study)

description: no additional information

value: stomach

value: CANCER

value: Adenocarcinoma

value: III


title: AN - 5 (gastric cancer study)

description: no additional information

source_name: apparently normal

value: Apparently Normal (AN)

value: Stratagene's universal RNA obtained from multiple cell lines


title: PN - 14 (gastric cancer study)

description: no additional information

value: Paired Normal (PN)


title: CANCER - 5 (gastric cancer study)

description: no additional information


title: PN - 10 (gastric cancer study)

description: no additional information

value: Normal


title: CANCER - 2 (gastric cancer study)

description: no additional information

value: NED


title: CANCER - 4 (gastric cancer study)

description: no additional information


title: PN - 8 (gastric cancer study)

description: no additional information


title: PN - 13 (gastric cancer study)

description: no additional information


title: PN - 9 (gastric cancer study)

description: no additional information


title: CANCER - 3 (gastric cancer study)

description: no additional information


title: PN - 11 (gastric cancer study)

description: no additional information


title: PN - 12 (gastric cancer study)

description: no additional information


title: AN - 4 (gastric cancer study)

description: no additional information


title: PN - 6 (gastric cancer study)

description: no additional information


title: PN - 2 (gastric cancer study)

description: no additional information


title: PN - 5 (gastric cancer study)

description: no additional information


title: PN - 3 (gastric cancer study)

description: no additional information


title: PN - 7 (gastric cancer study)

description: no additional information


title: B.subtilis strain DS901 GFP+ amplified_rep2

status: Public on Nov 29 2010

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

country: Netherlands

institute: TNO

description: This sample is collected from the GFP+ population which is obtained by cell sorting. The RNA is amplified before hybridisation. It is the second of two technical replicates used in this experiment.

hyb_protocol: The NimbleGen hybridization system was used to hybridize the probes to the oligos on the array. First was 4 μl of yeast tRNA supplemented to each sample prior to the drying step. The pellets were suspended in 11.5 μl DIG Easyhyb hybridization buffer (Roche) and 0.5 μl of the 50mM C3-CPK6-48mer suspension (NimbleGen). The mixture was incubated for 5’ at 95°C,  transferred to the 42°C block and hybridized on 60-mer B.subtilis subsp. subtilis strain NC_000964 microarray slides (Roche NimbleGen, Inc.). Hybridization is performed overnight at 42ºC in a Nimblegen hybridization system 4 (Roche NimbleGen, Inc.) according to the manufacturer's protocol. Microarray slides were washed for 10 sec in 1x SSC/0.2% SDS at 37 ºC, 10 sec in 0.5x SSC at 37 ºC, and twice for 10 min in 0.2x SSC at room temperature. Slides were dried by the use of a nitrogen flow.

scan_protocol: Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences).

data_processing: The TIFF-images were quantified with the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).The raw data (.pair file) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Bacillus subtilis

source_name: B.subtilis strain DS901 GFP+ amplified

label_protocol:
without_amplification: From the isolated RNA was 30-50 ng vacuum dried and incubated in 5 µl Random primer mix (3 µl 5U/µl RNAsin (Promega) and 2 µl 2 µg/µl P(dN6) random primer (Roche)) for 5’ at 70°C. After cooling down for 10’, 8.5 µl RT mix was supplemented: 1 µl RNAsin (10 U/µl, Promega); 2.5 µl First Strand Buffer 5X (Invitrogen); 1 µl 0,1 M DTT(Invitrogen); 3 µl dNTP’s (2 mM dATP, 2mM dGTP, 2 mM dCTP, 1.2 mM dTTP (Roche) and 0.8 mM aa-dUTP (Sigma)) and 1 µl Superscript II enzyme (200U/µl, Invitrogen). The RT reaction was performed for 60’ at 42°C. Subsequently, for RNA hydrolysis 2.5 µl of 2.5M NaOH was suspended to the reaction mix and incubated for 15’ at 65°C, followed by the addition of 2.5 µl from 2.5M HAc and 10 µl MQ. The cDNA suspension was purified with QIAquick®Spin colomns (QIAGen) by addition of 5X reaction volume binding PB1 Buffer (Qiagen supplied). The suspension was washed twice with the QIAquick®Spin at 13000 rpm for 1’ and three times with 500 µl NaBO2 pH 8.5 (80% ethanol). In a new tube the cDNA was washed off from the column with 30 μl MQ and vacuum dried. For coupling of the Cy3 dye ester DNA samples were suspended in 4.5 μl 0.1 M Na3CO3 pH 9.0 buffer for 10’ at RT. The Cy3 ester was added in a final concentration of 0.1mM (Amersham Pharmica) and incubated for 1 hour at RT in the dark. 15 μl MQ was appended prior to purification using the G50 autoseq column . Quality and incorporation of the Cy3 dye were checked with the NanoDrop® ND-1000 UV Spectrophotometer.
with_amplification: Approximately 30-50 ng RNA was vacuum dried and incubated in 5 µl Random primer mix (3 µl 5U/µl RNAsin (Promega) and 2 µl 2 µg/µl P(dN6) random primer (Roche)) for 5’ at 70°C. After cooling down for 10’, 8.5 µl RT mix was supplemented: 1 µl RNAsin (10 U/µl, Promega); 2.5 µl First Strand Buffer 5X (Invitrogen); 1 µl 0,1 M DTT(Invitrogen); 3 µl dNTP’s (2 mM  Invitrogen) and 1 µl Superscript II enzyme (200U/µl, Invitrogen). The RT reaction was performed for 60’ at 42°C. Subsequently, 2.5 µl of 2.5M NaOH was suspended to the reaction mix and incubated for 15’ at 65°C, followed by the addition of 2.5 µl from 2.5M HAc and 10 µl MQ. The cDNA in the suspension was washed in a G50 Autoseq (GE Healthcare) column by centrifugation for 1’ at 2000g. The cDNA was vacuum dried and dissolved in 5.25 μl MQ supplemented with 5 μl 2,5X random primer (Bioprime Kit), the mix was incubated for 5’ at 96°C and directly chilled on ice. After 30’’ centrifugation was each sample supplemented with: 0.25 μl 50X aa dNTP mix (25mM dATP/dCTP,dGTP, 15mM dTTP, (Life Technologies) and 10mM aa-dUTP (Sigma)); 1,75μl MQ and 0,25 μl klenow Fragment (Bioprime Kit). Amplification occurred at 37°C for 1 hour. Subsequently, the samples were purified with QIAquick®Spin columns and vacuum dried. For coupling of the Cy3 dye ester DNA samples were suspended in 4.5 μl 0.1 M Na3CO3 pH 9.0 buffer for 10’ at RT. The Cy3 ester was added in a final concentration of 0.1mM (Amersham Pharmica) and incubated for 1 hour at RT in the dark. 15 μl MQ was appended prior to purification using the G50 autoseq column . Quality and incorporation of the Cy3 dye were checked with the NanoDrop® ND-1000 UV Spectrophotometer.

growth_protocol: cells of strain DS901 (Phag-gfp) provided by Kearns and Losick (Kearns DB, Losick R. 2005. Cell population heterogeneity during growth of Bacillus subtilis. Genes and development. 19:3083-3094) were cultured to an OD660 of 0.5 and quickly quenched on ice

extract_protocol:
cell sort protocol:  B. subtilis strain DS901 GFP+ and GFP- cells were separated from each other by use of the Cytopeia Influx cell sorter  Settings for separation of the GFP+ and GFP- population were obtained by the use of the mother strain, B.subtilis strain 168, as a GFP- control. During cell sorting the samples were kept at 4°C in the water cooling holder and sorted cells were directly quenched with RNA Protect (Qiagen).
The cells were sorted directly in 10 ml tubes containing 6 ml RNA (Qiagen) Protect to quench the metabolic activity. The filled tubes were centrifuged for 20’ at RT and 10000g. The pellets of the GFP-, GFP+ and Total unsorted populations were eventually stored on dry ice. Each collected pellet was supplemented with: 1/3 volume of zirconium beads, 350 µl TEMS buffer (TE including 5% βmercapto-ethanol (JT Baker) and 0.01% SDS) and 800 µl phenol chloroform pH 4.8 (Fluka). Subsequently the cells were perished by the bead beat method with the BIO101 Fast prep FP120. Once for 45’’ and twice for 35’’ at setting 6.5. After centrifugation for 10’ at RT and 10000g the supernatant was transferred to a new tube and two extractions were performed: first with 300 µl phenol-chloroform: isoamylalcohol (25:24:1, pH 8.05-8.35, Invitrogen), next with chloroform-isoamylalcohol (24:1). Between both steps a 5’ centrifugation step at RT was performed and the supernatant was transferred to a new tube. In the last step 1/20 volume 3M NaOAc pH 5.4 and an equal volume of isopropanol (Merck) was added to each tube o/n at -20°C. After centrifugation for 20’ at 4°C and 14000rpm the pellet was washed with -20°C 96% ethanol and taken up in 50 ul MQ. An extra extraction with the Total RNA Cell Kit from Invitrogen was performed including DNA-se treatment but without the lysozyme treatment. The RNA yield was measured with the RNA 6000 Nano Assay kit combined to the 2100 Bioanalyzer from Agilent Technologies.

tag: population

value: GFP+

tag: amplified cdna/ not amplified cdna

value: amplified


title: B.subtilis strain DS901 GFP- amplified_rep1

description: This sample is collected from the GFP- population which is obtained by cell sorting. The RNA is amplified before hybridisation. It is the first of two technical replicates used in this experiment.

source_name: B.subtilis strain DS901 GFP- amplified

value: GFP-


title: B.subtilis strain DS901 GFP+ amplified_rep1

description: This sample is collected from the GFP+ population which is obtained by cell sorting. The RNA is amplified before hybridisation. It is the first of two technical replicates used in this experiment.


title: B.subtilis strain DS901 GFP+ not amplified

description: This sample is collected from the GFP+ population which is obtained by cell sorting. The RNA is not amplified before hybridisation

value: not amplified


title: AN - 3 (gastric cancer study)

description: no additional information


title: PN - 4 (gastric cancer study)

description: no additional information


title: B.subtilis strain DS901 GFP- amplified_rep2

description: This sample is collected from the GFP- population which is obtained by cell sorting. The RNA is amplified before hybridisation. It is the second of two technical replicates used in this experiment.


title: Suma Bac D10 0.0106mM_rep2

status: Public on Nov 27 2010

description: This sample is treated with 0.0106 Suma Bac D10. It is the second of two biological replicates used in this experiment.

hyb_protocol: The Cy3-labeled cDNA was mixed with 0.1 mg yeast tRNA and 10 fmol Cy3 CPK6-48mer control oligo. After drying, samples were dissolved in 15 ul EasyHyb buffer (Roche, Mannheim, Germany) and denatured for 2 min at 95 ºC and hybridized on 60-mer L.monocytogenes str. 4b F2365 NC_002973 microarray slides (Roche NimbleGen, Inc.). Hybridization is performed overnight at 42ºC in a Nimblegen hybridization system 4 (Roche NimbleGen, Inc.) according to the manufacturer's protocol. Microarray slides were washed for 10 sec in 1x SSC/0.2% SDS at 37 ºC, 10 sec in 0.5x SSC at 37 ºC, and twice for 10 min in 0.2x SSC at room temperature. Slides were dried by the use of a nitrogen flow.

organism: Listeria monocytogenes serotype 4b str. F2365

source_name: Suma Bac D10 0.0106mM

label_protocol: fluorescent labeled cDNA was prepared by indirect labeling from 1ug of total RNA by random hexamer pd(N)6-primer (Roche, Mannheim, Germany) polymerization using Superscript II reverse transcriptase (Invitrogen, Breda, NL). Concentrations of nucleotides in Reverse Transcription reaction mixture were 0.6 mM dATP, dGTP, dCTP, 0.36 mM dTTP and 0.24mM of AA-dUTP (Sigma-Aldrich Chemie BV). Unincorporated AA-dUTP, dNTP’s, primers and salts were removed by purification with Qiaquick columns (Qiagen Benelux BV). After dissolving cDNA in 0.1M bi-Sodium carbonate buffer pH9, Cy3 monofunctional reactive dye (GE healthcare) which is dissolved in DMSO (Sigma-Aldrich Chemie BV) is coupled to the cDNA. Unincorporated dye is removed with AutoSeq G50 columns (GE Healthcare).

growth_protocol: An overnight culture of L.monocytogenes (strain F2365) was diluted in TSB to an OD600 of 0.073 and incubated at 30°C at 150 rpm till OD600 reached 0.575.

extract_protocol: Immediate quenching of metabolic activity in the samples was performed with liquid nitrogen. Before cell disruption Samples are kept cold on dry-ice. Cells were disrupted in a 2-ml screw-cap tube in the presence of 100-um zirconium beads and  SDS, phenol, chloroform/isoamylalcohol and b-mercapto-ethanol for two times 90 seconds in the Minibeadbeater 8TM (Biospec Products). After phenol, chloroform extraction, nucleic acids are further purified with ChargeSwitch RNA isolation kit (Invitrogen). DNA is removed by DNAse I (Qiagen Benelux BV) treatment. The purified RNA is verified by absorption properties in the 200-300 nm region by the use of the ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA).

treatment_protocol: portions of 4-ml of the pre-culture of L.monocytogenes were exposed to five different detergents at three concentrations for one hour. T=0 Control is before adding detergent and t=1 control is untreated after one hour.

tag: compound

value: Suma Bac D10

tag: active compound

value: Alkyldimethylbenzyl Ammoniumchloride

tag: supplier

value: JohnsonDiversey

tag: concentration compound

tag: dose general application (mm)

tag: concentration treatment micro-array analysis (mm)

tag: strain


title: B.subtilis strain DS901 GFP- not amplified

description: This sample is collected from the GFP- population which is obtained by cell sorting. The RNA is not amplified before hybridisation


title: AN - 1 (gastric cancer study)

description: no additional information

tag: tissue


title: AN - 2 (gastric cancer study)

description: no additional information


title: CANCER - 1 (gastric cancer study)

description: no additional information


title: B.subtilis strain DS901 total not amplified

description: This sample is collected from an unsorted culture. The RNA is not amplified before hybridisation

value: total, unsorted_cells


title: B.subtilis strain DS901 total amplified

description: This sample is collected from an unsorted culture. The RNA is amplified before hybridisation

source_name: B.subtilis strain DS901 total amplified


title: Herlisil 87.8mM_rep2

description: This sample is treated with 87.8mM Herlisil. It is the second of two biological replicates used in this experiment.

source_name: Herlisil 87.8mM

value: Herlisil

value: Hydrogen peroxide

value: Tevan


title: Herlisil 87.8mM_rep1

description: This sample is treated with 87.8mM Herlisil. It is the first of two biological replicates used in this experiment.


title: Herlisil 35.1mM_rep2

description: This sample is treated with 35.1mM Herlisil. It is the second of two biological replicates used in this experiment.

source_name: Herlisil 35.1mM


title: Suma Bac D10 0.0053mM_rep2

description: This sample is treated with 0.0053 Suma Bac D10. It is the second of two biological replicates used in this experiment.

source_name: Suma Bac D10 0.0053mM


title: Suma Bac D10 0.0106mM_rep1

description: This sample is treated with 0.0106 Suma Bac D10. It is the first of two biological replicates used in this experiment.


title: Suma Bac D10 0.0021mM_rep2

description: This sample is treated with 0.0021 Suma Bac D10. It is the second of two biological replicates used in this experiment.

source_name: Suma Bac D10 0.0021mM


title: Suma Bac D10 0.0021mM_rep1

description: This sample is treated with 0.0021 Suma Bac D10. It is the first of two biological replicates used in this experiment.


title: Herlisil 35.1mM_rep1

description: This sample is treated with 35.1mM Herlisil. It is the first of two biological replicates used in this experiment.


title: Suma Bac D10 0.0053mM_rep1

description: This sample is treated with 0.0053 Suma Bac D10. It is the first of two biological replicates used in this experiment.


title: PN - 1 (gastric cancer study)

description: no additional information

value: stomach


title: Herlisil 17.6mM_rep1

description: This sample is treated with 17.6mM Herlisil. It is the first of two biological replicates used in this experiment.

source_name: Herlisil 17.6mM


title: CPC 0.003mM_rep2

description: This sample is treated with 0.003mM CPC. It is the second of two biological replicates used in this experiment.

source_name: CPC 0.003mM

value: CPC

value: Cetylpyridinium Chloride

value: Safe Foods Corporation


title: Halamid-d 5.6mM_rep1

description: This sample is treated with 5.6mM Halamid-d. It is the first of two biological replicates used in this experiment.

source_name: Halamid-d 5.6mM

value: Halamid-d

value: N-chloro-p-toluene Sulfonamide sodium

value: Veip bv

value: 81% = 2.9M (of which 25%  is active chloor)


title: Halamid-d 5.6mM_rep2

description: This sample is treated with 5.6mM Halamid-d. It is the second of two biological replicates used in this experiment.


title: Halamid-d 14mM_rep1

description: This sample is treated with 14mM Halamid-d. It is the first of two biological replicates used in this experiment.

source_name: Halamid-d 14mM


title: Halamid-d 14mM_rep2

description: This sample is treated with 14mM Halamid-d. It is the second of two biological replicates used in this experiment.


title: CPC 0.006mM_rep2

description: This sample is treated with 0.006mM CPC. It is the second of two biological replicates used in this experiment.

source_name: CPC 0.006mM


title: CPC 0.003mM_rep1

description: This sample is treated with 0.003mM CPC. It is the first of two biological replicates used in this experiment.


title: Herlisil 17.6mM_rep2

description: This sample is treated with 17.6mM Herlisil. It is the second of two biological replicates used in this experiment.


title: CPC 0.006mM_rep1

description: This sample is treated with 0.006mM CPC. It is the first of two biological replicates used in this experiment.


title: Halamid-d 2.8mM_rep1

description: This sample is treated with 2.8mM Halamid-d. It is the first of two biological replicates used in this experiment.

source_name: Halamid-d 2.8mM


title: Halamid-d 2.8mM_rep2

description: This sample is treated with 2.8mM Halamid-d. It is the second of two biological replicates used in this experiment.


title: CPC 0.0015mM_rep1

description: This sample is treated with 0.0015mM CPC. It is the first of two biological replicates used in this experiment.


title: Actisan 5L 1.2mM_rep2

description: This sample is treated with 1.2mM Actisan 5L. It is the second of two biological replicates used in this experiment.

source_name: Actisan 5L 1.2mM

value: Actisan 5L

value: Sodium dichloro Isocyanurate


title: CPC 0.0015mM_rep2

description: This sample is treated with 0.0015mM CPC. It is the second of two biological replicates used in this experiment.


title: untreated t=0_rep2

description: This sample is untreated and collected before adding detergent. It is the second of two biological replicates used in this experiment

source_name: untreated t=0

value: untreated


title: Actisan 5L 1.2mM_rep1

description: This sample is treated with 1.2mM Actisan 5L. It is the first of two biological replicates used in this experiment.


title: Actisan 5L 0.48mM_rep2

description: This sample is treated with 0.48mM Actisan 5L. It is the second of two biological replicates used in this experiment.

source_name: Actisan 5L 0.48mM


title: Actisan 5L 0.24mM_rep1

description: This sample is treated with 0.24mM Actisan 5L. It is the first of two biological replicates used in this experiment.

source_name: Actisan 5L 0.24mM


title: untreated t=0_rep1

description: This sample is untreated and collected before adding detergent. It is the first of two biological replicates used in this experiment


title: untreated t=1_rep1

description: This sample is untreated and collected after one hour. It is the first of two biological replicates used in this experiment

source_name: untreated t=1


title: untreated t=1_rep2

description: This sample is untreated and collected after one hour. It is the second of two biological replicates used in this experiment


title: Actisan 5L 0.48mM_rep1

description: This sample is treated with 0.48mM Actisan 5L. It is the first of two biological replicates used in this experiment.


title: Actisan 5L 0.24mM_rep2

description: This sample is treated with 0.24mM Actisan 5L. It is the second of two biological replicates used in this experiment.


title: 4021 R vs SAvr- 4hpi biorep2 dye-swap

status: Public on Nov 21 2010

city: Beijing

first: Guozhen

last: Liu

address: Beijing Airport Industrial Zone B-6

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: Inoculated leaves with Xoo Philippine race 6 vs. Xoo Philippine race 10 at 4 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

hyb_protocol: Microarray slides were hybridized for 12h to 18h in 42°C water bath.

scan_protocol: Each microarray slide was scanned  at 5-nm resolution using the ScanArray Lite (Perkin-Elmer). Photomultiplier tube (PMT) voltages were adjusted manually to minimize background interference and to reduce the percentage of spots on the microarray with saturated signal values.

data_processing: The pre-processed data were normalized using scale LOWESS (Locally Weighted Linear Regression) implemented in R package limma 2.0 (http://bioinf.wehi.edu.au). All spots from each microarray were included in the analysis, but zero weight was given to all the spots whose Genepix flags were less than 0.

organism: Oryza sativa

source_name: Inoculated 4021 leaves with Xoo Philippine race 6 at 4 hours post inoculation.

label_protocol: Indirect incorporation of amino-allyl-dUTP during reverse transcription followed by coupling with either Cy5.

growth_protocol: Rice seeds were imbibed in water overnight at 30°C and placed on moist filter paper. After germination, the seeds were grown in soil in a green house until the seedling stage. The seedlings were transferred to experimental field plots located at the Institute of Genetics and Developmental Biology in Beijing.

extract_protocol: Total RNA was isolated using a QIAGEN RNeasy Plant Mini Kit, following the manufacturer’s protocols.

tag: line

value: 4021 expressing Xa21

tag: cultivar

value: japonica

tag: developmental stage

value: about nine weeks

value: inoculated leaves, approximately 1cm from the inoculation site

source_name: Inoculated 4021 leaves with Xoo Philippine race 10 at 4 hours post inoculation.

label_protocol: Indirect incorporation of amino-allyl-dUTP during reverse transcription followed by coupling with either Cy3.


title: 4021 R vs TP309 SR- 4hpi biorep2 dye-swap

description: Inoculated 4021 leaves with Xoo Philippine race 6 vs. inoculated TP309 leaves with Xoo Philippine race 6 at 4 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated TP309 leaves with Xoo Philippine race 6 at 4 hours post inoculation.


title: 4021 R vs TP309 SR- 4hpi biorep2


title: 4021 R vs M 120hpi biorep2 dye-swap

description: Inoculated leaves with Xoo Philippine race 6 vs. sterile distilled water at 120 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated 4021 leaves with Xoo Philippine race 6 at 120 hours post inoculation.

source_name: Inoculated 4021 leaves with sterile distilled water at 120 hours post inoculation.


title: 4021 R vs TP309 SR- 4hpi biorep1


title: 4021 R vs SAvr- 4hpi biorep2


title: 4021 R vs M 72hpi biorep2 dye-swap

description: Inoculated leaves with Xoo Philippine race 6 vs. sterile distilled water at 72 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated 4021 leaves with sterile distilled water at 72 hours post inoculation.

source_name: Inoculated 4021 leaves with Xoo Philippine race 6 at 72 hours post inoculation.


title: 4021 R vs M 120hpi biorep1


title: 4021 R vs SAvr- 4hpi biorep1


title: 4021 R vs M 72hpi biorep2


title: Wild type MEFs Replicate 2

status: Public on Nov 25 2010

city: Atlanta

first: Engda

last: Hagos

state: GA

address: 615 Michael Street

department: Digestive Diseases

institute: Emory University

description: Replicate 2 of 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genome StudioV1.0.2 (Illumina)

label: Cy3 and Cy5

source_name: MEFs, wild type

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

growth_protocol: MEFs were maintained in DMEM, supplemented with 10% FBS, 1% penicillin-streptomycin at 37OC in atomosphere containing 5% CO2

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

tag: genotype/variation

tag: cell type

value: mouse embryonic fibroblast

tag: age

value: 13 days


title: 4021 R vs M 24hpi biorep1 dye-swap

description: Inoculated leaves with Xoo Philippine race 6 vs. sterile distilled water at 24 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated 4021 leaves with sterile distilled water at 24 hours post inoculation.

source_name: Inoculated 4021 leaves with Xoo Philippine race 6 at 24 hours post inoculation.


title: Klf4 null MEFs Replicate 3

description: Replicate 3 of 3

source_name: MEFs, Klf4 null


title: Wild type MEFs Replicate 3

description: Replicate 3 of 3


title: 4021 R vs M 120hpi biorep2


title: 4021 R vs M 8hpi biorep1

description: Inoculated leaves with Xoo Philippine race 6 vs. sterile distilled water at 8 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated 4021 leaves with sterile distilled water at 8 hours post inoculation.

source_name: Inoculated 4021 leaves with Xoo Philippine race 6 at 8 hours post inoculation.


title: 4021 R vs M 0hpi biorep2

description: Inoculated leaves with Xoo Philippine race 6 vs. sterile distilled water at 0 hour post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated 4021 leaves with sterile distilled water at 0 hour post inoculation.

source_name: Inoculated 4021 leaves with Xoo Philippine race 6 at 0 hour post inoculation.


title: Klf4 null MEFs Replicate 1

description: Replicate 1 of 3


title: Klf4 null MEFs Replicate 2

description: Replicate 2 of 3


title: 4021 R vs M 8hpi biorep2


title: 4021 R vs M 8hpi biorep2 dye-swap


title: 4021 R vs M 4hpi biorep2

description: Inoculated leaves with Xoo Philippine race 6 vs. sterile distilled water at 4 hours post inoculation. To minimize biological variation, five independent rice leaves were pooled together for each biological replication.

source_name: Inoculated 4021 leaves with sterile distilled water at 4 hours post inoculation.


title: 4021 R vs M 4hpi biorep1


title: Wild type MEFs Replicate 1

description: Replicate 1 of 3


title: 4021 R vs M 24hpi biorep1


title: 4021 R vs M 72hpi biorep1


title: 4021 R vs TP309 SR- 4hpi biorep2


title: 4021 R vs M 4hpi biorep1 dye-swap


title: 4021 R vs M 24hpi biorep2


title: 4021 R vs M 0hpi biorep1


title: 4021 R vs SAvr- 4hpi biorep2 dye-swap


title: 4021 R vs SAvr- 4hpi biorep2


title: 4021 R vs M 72hpi biorep2 dye-swap


title: 4021 R vs SAvr- 4hpi biorep1


title: 4021 R vs M 24hpi biorep1 dye-swap


title: 4021 R vs TP309 SR- 4hpi biorep1


title: 4021 R vs M 120hpi biorep1


title: 4021 R vs M 120hpi biorep1 dye-swap


title: 4021 R vs M 0hpi biorep2


title: 4021 R vs M 4hpi biorep2


title: 4021 R vs M 8hpi biorep2 dye-swap


title: 4021 R vs M 8hpi biorep1


title: 4021 R vs M 72hpi biorep2


title: 4021 R vs M 4hpi biorep1


title: 4021 R vs M 8hpi biorep2


title: 4021 R vs M 120hpi biorep2


title: CAF11untreated

status: Public on Nov 20 2010

city: Baltimore

first: Kim

last: Walter

state: MD

address: 1550 Orleans St.

institute: Johns Hopkins University

description: RMA expression value derived from Expression Console software; core-exon analysis; Partek version 6.3beta

hyb_protocol: Samples were hybridized with the GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the JHMI Microarray Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative gene expression values were obtained after using the RMA method to normalize the raw intensity measurements of all probe sets. Partek version 6.3beta was used.

source_name: Untreated pancreatic cancer associated fibroblasts

label_protocol: Single stranded cDNA was generated from the amplified cRNA using the WT cDNA Synthesis kit (Affymetrix) and then fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were maintained in culture at 37degrees C in DMEM containing 10% FBS and 2% penicillin-streptomycin.

extract_protocol: RNA was isolated from fibroblast cultures using the Ambion mirVana RNA extraction kit, according to the manufacturer's instructions

treatment_protocol: Untreated or treated with 1uM 5-aza-dC as indicated

tag: gender

value: male

value: pancreas

tag: disease status

value: pancreatic cancer

value: fibroblasts

tag: treatment group


title: CAF16untreated

value: female


title: CAF13untreated


title: CAF15untreated


title: CAF16 5AZA

source_name: 5-aza-dC treated fibroblasts

value: 5-aza-dC treated


title: CAF12untreated


title: CAF15 5AZA


title: CAF12 5AZA


title: CAF13 5AZA


title: CAF11 5AZA


title: Stomach_HpWT_rep3

status: Public on Nov 13 2010

city: blacksburg

first: Saroj

middle: K

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

hyb_protocol: The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

scan_protocol: The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

data_processing: The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Gene set enrichment analysis was applied using bioconductor packages GSEABase and Category.

source_name: Gastric mucosa

label_protocol: RNA was processed and labeled according to the standard target labeling protocols.

growth_protocol: Gastric mucosa were obtained from uninfected mice or those infected with one of the two isogenic strains of H. pylori (cagA+, cagA-)

extract_protocol: After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

value: gastric mucosa

tag: infection

value: H. pylori strain 98-325 (wild-type, HpcagA+)


title: Stomach_control_rep1

value: uninfected


title: Stomach_HpWT_rep1


title: Stomach_Hpmutant_rep1

value: H. pylori strain 99-305 (mutant, HpcagA-)


title: Stomach_control_rep3


title: Stomach_Hpmutant_rep3


title: NHEK_DUOX1-siRNA-IL-4/IL-13_3

status: Public on Oct 31 2010

city: Yokohama

first: Satoshi

last: Hirakawa

address: 560 Kashio-cho, Totsuka-ku,

country: Japan

institute: POLA CHEMICAL INDUSTRIES, INC.

description: Gene expression in NHEK transfected with DUOX1 siRNA before treatment with IL-4 and IL-13

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containig 10 X Blocking Agent, Nuclease-free water, and 25 X Fragmentation Buffer following the manufature's instructions. On completion of the fragmentation reaction, 55 ul of 2 X GE Hybridization Buffer (HI-RPM) was added to the fragmentation mixture and hybridized to 44K Agilent Whole Human Genome Oligo Microarays (G4112F) containing 45015 features representing 41000 biological probes for 17 hours at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minutes at room temparature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: After washing according to manufacture's instructions, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1 X 44K array slides (Scan Area 61 X 21.6 mm, Scan resolution 5 um, Dye channel is set to Green, and eXtended Dynamic Range Scan Mode (Hi; 100%, Low;10%)).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent Technologies) using default parameters (protocol GE1-v1_95 and Grid: 014850_D_F_20060807). The data from all microarrays were analyzed using GeneSpringGX 10.0.2 (Agilent Technologies). After data transformation (to convert any negative value to 0.01), normalization was performed by using a per-chip 75th percentile method that normalizes each chip on its median.  On the basis of accumulated experimental results, probes were excluded because of extremely low intensity or poorly-reproducible. As a result, 37055 probes were used for analysis.

source_name: Epidermal keratinocyte, 48hr, DUOX1-siRNA knockdown and then IL4/IL-13 treatment, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the Nanodrop spectrophotometer.

extract_protocol: Total RNA was extracted from NHEK using RNeasy Mini Kits accoriding to the manufacture's instructions (Qiagen, Valecia, CA, USA). The concentration of the obtained total RNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA quality was determined using the RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies), and RNA was stored in RNase-free water at -80ºC. RNA with an RNA Integrity Number (RIN) of nine or more was used for experiments.

treatment_protocol: NHEK derived from neonatal foreskin were purchased from Kurabo and were cultured in serum-free keratinocyte growth medium (HuMedia-KB2) (Kurabo) containing 0.15 mM calcium and supplemented with human epidermal growth factor (0.1 ng/ml), insulin (10 μg/ml), hydrocortisone (0.5 μg/ml), gentamycin (50 μg/ml), amphotericin B (50μg/ml) and bovine brain pituitary extract (0.4% vol/vol), at 37ºC under 5% CO2/ 95% air. THe medium was replaced every 2 days. The second-passage NHEK was used for all experiments. When the cells reached approximately 80% confluence (0 hr), they were incubated in the presence or absence of IL-4 (100 ng/ml) and/or IL-13 (100 ng/ml).

value: epidermal keratinocyte

tag: cell line

value: NHEK


title: NHEK_IL-4/IL-13-treatment_3

description: Gene expression after 48 hr in IL-4/IL-13-treatment of NHEK

source_name: Epidermal kertinocyte, 48hr, IL4/IL13-treatment, replicate 3


title: Stomach_control_rep2


title: Stomach_Hpmutant_rep2


title: Stomach_HpWT_rep2


title: NHEK_IL-4/IL-13-treatment_2

source_name: Epidermal kertinocyte, 48hr, IL4/IL13-treatment, replicate 2


title: NHEK_DUOX1-siRNA-IL-4/IL-13_2

source_name: Epidermal keratinocyte, 48hr, DUOX1-siRNA knockdown and then IL4/IL-13 treatment, replicate 2


title: NHEK_IL-4/IL-13-treatment_1

source_name: Epidermal kertinocyte, 48hr, IL4/IL13-treatment, replicate 1


title: NHEK_no-treatment_2

description: Gene expression after 48 hr in no-treatment of NHEK

source_name: Epidermal keratinocyte, 48hr, no-treatment, replicate 2


title: NHEK_no-treatment_1

source_name: Epidermal keratinocyte, 48hr, no-treatment, replicate 1


title: NHEK_no-treatment_3

source_name: Epidermal keratinocyte, 48hr, no-treatment, replicate 3


title: NHEK_DUOX1-siRNA-IL-4/IL-13_1

source_name: Epidermal keratinocyte, 48hr, DUOX1-siRNA knockdown and then IL4/IL-13 treatment, replicate 1


title: blastomere from 8-cell embryos E11.M4

status: Public on Oct 30 2010

city: Valencia

first: Amparo

last: Galan

address: Avda Autopista del Saler 16, 3

country: Spain

institute: Prince Felipe Research Centre (CIPF)

description:
Amplified cDNA from single blastomere
Global gene expression of single blastomere from 8-cell embryos

hyb_protocol: Up to 3000 ng of Cy3 labeled cRNA were hybridised for 20 hours to the Whole Human Genome Oligo Microarray Kit.

scan_protocol: Arrays were scanned in an Agilent microarray Scanner (Agilent G2565BA) according to the manufacturer´s protocol.

data_processing: Data were extracted using Agilent Feature Extraction Software 9.5.3, grid template 014850_D_F_20080627, following the Agilent Protocol GE1-v5_95_Feb07.Samples were first filterd by comparison to the negative sample microarray and those considered not to have signal were excluded from teh analysis. Agilent Processed Signals were standardized across arrays usign quantile normalization.

source_name: Blastomere 4. Embryo 11

label_protocol: 300 ng of cDNA were used to produce Cyanin 3-CTP-labeled cRNA using the Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-0442). "One-Color Microarray-Based Gene Expression Analysis" protocol Version 5.7 (Agilent p/n G4140-90040) was followedfor 16 hours in the IVT reaction and the resulting cRNA purified. Yield and Cy3 specific activity were measured by spectrometry (Nanodrop, DW, USA) and cRNA length evaluated by the mRNA 6000 Nano Bioanalyzer assay.

extract_protocol: The biopsied single blastomeres, inner cell masses and trophectoderms were collected in cell lysis buffer for RNA denaturalization. First-strand cDNAs were synthesized by retro-transcription with the SSIII (Invitrogen) and were then tailed with poly(dA) by TdT (Invitrogen, CA, USA). The cDNA products were divided and the second strand synthesized with another oligo(dT)-tagged primers and amplified. PCR products were purified with the DNA Clean & Concentrator™ Kit (Zymo Research, CA, USA),and subjected to another PCR amplification reaction containing the primers bearing the T7 promoter. PCR products were then purified with the DNA Clean & Concentrator™ Kit (Zymo Research, CA, USA) and electrophoresed and gel purified with the ZymoClean™ Gel DNA Recovery Kit (Zymo Research, CA, USA). Purified products were divided and subjected to a final PCR cycle and purified with the DNA Clean & Concentrator™ Kit (Zymo Research, CA, USA).

treatment_protocol: Single blastomeres from 5- to 8- cell human embryos, and inner cell mass and trophectoderm from blastocysts were biopsied and transferred to lysis buffer for later cDNA amplification protocol

value: blastomere

value: 8-cell embryos


title: trophectoderm from blastocyst TFE2

description:
Amplified cDNA from the trophectoderm from blastocyst
Global gene expression of Trophectoderm from blastocyst

source_name: Trophectoderm. Embryo 13

tag: sample type

value: trophectoderm

value: blastocyst


title: blastomere from 8-cell embryos E11.M8

source_name: Blastomere 8. Embryo 11


title: blastomere from 8-cell embryos E11.M5

source_name: Blastomere 5. Embryo 11


title: inner cell mass from blastocysts ICM2

description:
Amplified cDNA from the inner cell mass from blastocyst
Global gene expression of inner cell mass from blastocysts

source_name: Inner Cell Mass. Embryo 13

value: inner cell mass


title: inner cell mass from blastocysts ICM1

source_name: Inner Cell Mass. Embryo 12


title: trophectoderm from blastocyst TFE1

source_name: Trophectoderm. Embryo 12


title: blastomere from 8-cell embryos E10.M5

source_name: Blastomere 5. Embryo 10


title: blastomere from 8-cell embryos E11.M2

source_name: Blastomere 2. Embryo 11


title: blastomere from 8-cell embryos E10.M8

source_name: Blastomere 8. Embryo 10


title: blastomere from 8-cell embryos E10.M7

source_name: Blastomere 7. Embryo 10


title: blastomere from 8-cell embryos E11.M3

source_name: Blastomere 3. Embryo 11


title: blastomere from 8-cell embryos E10.M2

source_name: Blastomere 2. Embryo 10


title: blastomere from 8-cell embryos E10.M1

source_name: Blastomere 1. Embryo 10


title: blastomere from 8-cell embryos E10.M4

source_name: Blastomere 4. Embryo 10


title: blastomere from 8-cell embryos E9.M8

source_name: Blastomere 8. Embryo 9


title: blastomere from 8-cell embryos E10.M3

source_name: Blastomere 3. Embryo 10


title: blastomere from 8-cell embryos E10.M6

source_name: Blastomere 6. Embryo 10


title: blastomere from 8-cell embryos E9.M7

source_name: Blastomere 7. Embryo 9


title: blastomere from 8-cell embryos E11.M6

source_name: Blastomere 6. Embryo 11


title: blastomere from 8-cell embryos E9.M6

source_name: Blastomere 6. Embryo 9


title: blastomere from 8-cell embryos E9.M4

source_name: Blastomere 4. Embryo 9


title: blastomere from 8-cell embryos E9.M3

source_name: Blastomere 3. Embryo 9


title: blastomere from 6-cell embryo E8.M2

description:
Amplified cDNA from single blastomere
Global gene expression of single blastomere from 6-cell embryo

source_name: Blastomere 2. Embryo 8

value: 6-cell embryo


title: blastomere from 6-cell embryo E8.M6

source_name: Blastomere 6. Embryo 8


title: blastomere from 6-cell embryo E8.M3

source_name: Blastomere 3. Embryo 8


title: blastomere from 8-cell embryos E9.M5

source_name: Blastomere 5. Embryo 9


title: blastomere from 6-cell embryo E7.M3

source_name: Blastomere 3. Embryo 7


title: blastomere from 8-cell embryos E9.M2

source_name: Blastomere 2. Embryo 9


title: blastomere from 6-cell embryo E8.M5

source_name: Blastomere 5. Embryo 8


title: blastomere from 6-cell embryo E7.M4

source_name: Blastomere 4. Embryo 7


title: blastomere from 6-cell embryo E6.M4

source_name: Blastomere 4. Embryo 6


title: blastomere from 5-cell embryo E4.M5

description:
Amplified cDNA from single blastomere
Global gene expression of single blastomere from 5-cell embryo

source_name: Blastomere 5. Embryo 4

value: 5-cell embryo


title: blastomere from 6-cell embryo E6.M1

source_name: Blastomere 1. Embryo 6


title: blastomere from 6-cell embryo E5.M6

source_name: Blastomere 6. Embryo 5


title: blastomere from 6-cell embryo E8.M1

source_name: Blastomere 1. Embryo 8


title: blastomere from 6-cell embryo E6.M3

source_name: Blastomere 3. Embryo 6


title: blastomere from 8-cell embryos E9.M1

source_name: Blastomere 1. Embryo 9


title: blastomere from 6-cell embryo E6.M2

source_name: Blastomere 2. Embryo 6


title: blastomere from 6-cell embryo E5.M1

source_name: Blastomere 1. Embryo 5


title: blastomere from 6-cell embryo E5.M3

source_name: Blastomere 3. Embryo 5


title: blastomere from 5-cell embryo E4.M4

source_name: Blastomere 4. Embryo 4


title: blastomere from 6-cell embryo E5.M4

source_name: Blastomere 4. Embryo 5


title: blastomere from 5-cell embryo E4.M3

source_name: Blastomere 3. Embryo 4


title: blastomere from 6-cell embryo E5.M2

source_name: Blastomere 2. Embryo 5


title: blastomere from 6-cell embryo E7.M1

source_name: Blastomere 1. Embryo 7


title: blastomere from 5-cell embryo E4.M2

source_name: Blastomere 2. Embryo 4


title: blastomere from 5-cell embryo E3.M1

source_name: Blastomere 1. Embryo 3


title: blastomere from 6-cell embryo E7.M2

source_name: Blastomere 2. Embryo 7


title: blastomere from 5-cell embryo E4.M1

source_name: Blastomere 1. Embryo 4


title: E4 -O2 1

status: Public on Oct 15 2010

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: Respiratory defecient E. coli mutant (ECOM4), M9 media with 4 g/L glucose, aerobic, log phase

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

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

data_processing: The data were analyzed with ArrayStar 3 (DNASTAR) using RMA normalization method. Genes with at least two-fold expression level change and FDR-adjusted P-value (T-test) of less than 0.05 were considered significant.

organism: Escherichia coli str. K-12 substr. MG1655

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

growth_protocol: Wild type and the mutant were grown on minimal M9 media with 4 g/L glucose as a sole carbon source at 37C with aeration (+O2) or nitrogen sparging (-O2)

extract_protocol: total RNA was extreacted using Quagen RNA mini kit. DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000.

treatment_protocol: No specific treatment was done. Samples were collected in the mid-log growth phase for expression analysis


title: Affected individual

status: Public on Nov 01 2010

city: Madrid

first: Victor

last: Martinez-Glez

address: Paseo la Castellana 261

department: INGEMM

institute: HULP

description: Genomic DNA extracted from peripheral blood

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed (XC1, XC2, TEM, STM, ATM, XC3, PB1) on a Teflow chamber rack system.

scan_protocol: After allele-specific staining BeadChip arrays were coated with PB1/XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (Illumina).

source_name: Peripheral blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37ºC using amplification master mix (WG-MSM) and primer/neutralization mix (WG-MA2). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitate

extract_protocol: Extraction of genomic DNA from peripheral blood was performed by standard phenol-chlorophorm method

value: Male

value: Peripheral blood

tag: histological type

tag: disease state

value: OI


title: blastomere from 5-cell embryo E2.M1

source_name: Blastomere 1. Embryo 2


title: WT +O2 3

description: E. coli MG1655, M9 media with 4 g/L glucose, aerobic, log phase


title: E4 -O2 3

source_name: Respiratory defecient E. coli mutant (ECOM4), M9 media with 4 g/L glucose, aerobic, log phase


title: blastomere from 5-cell embryo E1.M1

source_name: Blastomere 1. Embryo 1


title: WT -O2 1

description: E. coli MG1655, M9 media with 4 g/L glucose, anaerobic, log phase


title: WT -O2 3

source_name: E. coli MG1655, M9 media with 4 g/L glucose, anaerobic, log phase


title: E4 +O2 3


title: WT +O2 1

source_name: E. coli MG1655, M9 media with 4 g/L glucose, aerobic, log phase


title: Replicate 1, 0.04% bile (+) vs. (-) in vtrA-null

status: Public on Oct 10 2010

city: Suita

first: Toshio

last: Kodama

state: Osaka

address: 3-1 Yamadaoka

institute: OSAKA university

hyb_protocol: Cy3- or Cy5-labeled probes (approximately 20 µl for each) were mixed, and 3 µl of 10% SDS, 6 µl of 1 mg/ml human Cot-1 DNA (Invitrogen) and 15 µl of 20X SSC (3 M NaCl, 0.3 M trisodium citrate 2H2O, pH 7.0) were added to the mixture. After incubation at 96˚C for 2 min, the denatured sample was applied to a microarray slide and incubated on an MAUI hybridization chamber at 60˚C for 16h. The slide was then washed twice in 2X SSC/0.1% SDS solution at 60˚C for 10 min, twice in 0.2X SSC/0.1% SDS solution at room temperature for 10 min, and twice in 0.2X SSC solution at room temperature for another 10 min. Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.

scan_protocol: Arrays were scanned with a ScanArrayExpress scanner (PerkinElmer).  The obtained data were analyzed by the ScanArrayExpress software ver. 3.0.

data_processing: LOWESS normalized using ScanArrayExpress software ver. 3.0 (PerkinElmer), background subtracted data obtained from log2 of processed Cy3 signal/processed Cy5 signal. Finally, the fault spot data indicated as '0 or 1' in the flags column in the raw data table were filtered.

organism: Vibrio parahaemolyticus

source_name: vtrA-null with 0.04% bile

label_protocol: First, 20 µg of total RNA were primed with 2 µl of 5 µg/µl random hexamer at 70˚C for 5 min then reversed transcribed at 46˚C for 2 h in the presence of 800 U SuperScript III RTase (Invitrogen), and 5 mM each dATP, dTTP, dCTP, with 2 mM dTTP, 3 mM aminoallyl-modified dUTP (Sigma). The aminoallyl-labeled cDNA was purified by phenol-chloroform extraction and ethanol precipitation. Precipitated cDNA was dried and resuspended in 10 µl of 50 mM NaHCO3. After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (GE healthcare), the sample was incubated at room temperature in the dark for 1h to allow the dye to couple with DNA. The fluorescently labeled DNA was finally purified by the CentriCep spin column (Princeton Sepatations Inc.).

growth_protocol: Cells were vigorously shaken at 37˚C in Luria-Bertani medium containing 0.3 M NaCl to an OD600 = 0.6.

extract_protocol: Total RNA was purified using Trizol (Invitrogen), and DNA was digested with TURBO DNA-free (Ambion). Then, RNeasy mini Kit (Qiagen) was carried out according to the manufacturer's instructions.

treatment_protocol: Crude bile was added to 0.04%, and the cells were continuously shaken for 30 minutes and harvested by centrifugation. No bile was added to control cells.

tag: genotype

value: vtrA-null

tag: treatment

source_name: vtrA-null without 0.04% bile

value: no bile


title: E4 +O2 1

tag: strain


title: Replicate 3, 0.04% bile (+) vs. (-) in vtrA-null


title: Replicate 2, 0.04% bile (+) vs. (-) in vtrA-null


title: WT +O2 2


title: blastomere from 6-cell embryo E5.M5

source_name: Blastomere 5. Embryo 5


title: WT -O2 2


title: E4 +O2 2


title: Replicate 3, 0.04% bile (+) vs. (-) in WT

source_name: WT with 0.04% bile

value: WT

source_name: WT without 0.04% bile


title: E4 -O2 2


title: Replicate 2, 0.04% bile (+) vs. (-) in WT


title: Non-affected sibling

value: Female

tag: tissue

value: healthy


title: BMM untreated Exp.A

status: Public on Oct 01 2010

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: Gene expression analysis in bone marrow-derived macrophages

hyb_protocol: Labelled cRNA was then purified using Qiagen’s RNease mini spin columns (Qiagen) and 1.65 µg from each sample were fragmented for 30 min and mixed with a 2xGExHybridization Buffer HI-RPM according to the manufacturer’s instructions (Agilent Technologies). The resulting mixture was applied to a Whole Mouse Genome (4x44k) Oligo Microarray (Agilent Technologies Inc.) and the hybridization followed at 65°C for 17 h.

scan_protocol: Arrays were then washed and scanned according to Agilent protocols with the Agilent Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters. Extracted data were further processed with GeneSpring GX 11. Data were normalized to the 75th percentile and baseline transformed to the median of untreated BMM samples.

source_name: Bone marrow-derived macrophages

label_protocol: Agilent’s Low RNA Input Linear Amplification One-Color kit (Agilent Technologies, Inc. Wimmington, DE, USA) was used to label the target RNA for hybridization following the manufacturer instructions. Briefly, 1 µg total RNA was reverse transcribed using a T7 promoter Primer. The resulting cDNAs were then in vitro transcribed followed by reverse transcription in the presence of Cyanin 3-CTP.

growth_protocol: To generate bone marrow-derived macrophages (BMM), bone marrow cells were flushed from femurs and tibias of 8 to 12 weeks old mice using cold PBS. Cells from several animals were pooled and plated on bacteriological 100 mm square plastic plates (Bibby Sterilin, Staffordshire, UK Ltd) at 0.5 Mio cells/ml in 20 ml endotoxin-free RPMI 1640 medium (Biochrom KG, Berlin, Germany) supplemented with glutamine, vitamins, pyruvate, nonessential amino acids, β-mercaptoethanol (all purchased from Invitrogen, Germany), 10% FCS (PAA Laboratories GmbH, Austria), and 200 ng/ml human rCSF1 (Cetus) per plate for 5 days. Complete medium was replaced on day 5, cells were harvested on day 6 and seeded with rCSF1 at a density of 10 Mio cells/10 ml medium on 10 cm tissue culture dishes (Falcon).

extract_protocol: Cells were collected, pelleted and used for total RNA preparation with the RNeasy midi kit (Qiagen).

treatment_protocol: On day 7, cells were incubated for 18 h with or without IL4 (10 ng/ml) or IFNγ (100 U/ml). During the last 4 h of incubation, cells were incubated with LPS (10 ng/ml) for 4h (in the absence or presence of IL4, or IFNγ).

tag: experiment

value: A

value: 8 to 12 weeks

tag: sex

value: 2 males and 1 female

value: Bone marrow


title: BMM untreated Exp.F

value: F


title: BMM untreated Exp.C

value: C


title: BMM treated with LPS Exp.E

value: LPS (4h)

value: E


title: BMM untreated Exp.E


title: BMM untreated Exp.G

value: G


title: BMM treated with LPS Exp.B

value: B


title: BMM treated with LPS Exp.D

value: D


title: BMM untreated Exp.D


title: BMM treated with LPS Exp.C


title: Liver_TAK1KO_Rep5

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5).  The resulting data were imported into Rosetta Resolver (v7.1) and log2 intensities were exported.

source_name: Liver from 1 year old- TAK1 KO mice

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

value: 1 year old

value: liver


title: Liver_TAK1KO_Rep2


title: Liver_TAK1KO_Rep4


title: BMM treated with LPS Exp.A


title: Liver_TAK1KO_Rep3


title: BMM treated with IFNgamma Exp.F

value: IFNgamma (18h)


title: BMM treated with LPS Exp.G


title: BMM treated with IFNgamma-LPS Exp.F

value: IFNgamma (18h) - LPS (4h)


title: Liver_TAK1KO_Rep1


title: BMM treated with IL4-LPS Exp.A


title: BMM untreated Exp.B


title: BMM treated with IFNgamma Exp.E


title: Liver_WT_Rep5

source_name: Liver from 1 year old- WT mice


title: BMM treated with LPS Exp.F


title: BMM treated with IL4-LPS Exp.G


title: BMM treated with IL4 Exp.B


title: Liver_WT_Rep4


title: BMM treated with IL4 Exp.C


title: BMM treated with IFNgamma-LPS Exp.E


title: BMM treated with IL4 Exp.A


title: BMM treated with IFNgamma-LPS Exp.G


title: Liver_WT_Rep3


title: BMM treated with IL4-LPS Exp.B


title: Liver_WT_Rep1


title: Liver_WT_Rep2


title: BMM treated with IL4-LPS Exp.C


title: Replicate 1, 0.04% bile (+) vs. (-) in WT

value: WT

value: no bile


title: Irf4+/- IL4 18h C

description: Gene expression analysis in Irf4+/- BMM after 18h IL-4 stimulation

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters. Extracted data were further processed with GeneSpring GX 11. Data were normalized to the 75th percentile and baseline transformed to the median of untreated Irf4+/- samples. The Feature Extraction Software values are in the Sample data tables. The additional processed data are on the Series record.

treatment_protocol: On day 7, cells were incubated for 4 or 18 h with or without IL4 (10 ng/ml).

tag: il4 stimulation time


title: Irf4+/- IL4 4h B

description: Gene expression analysis in Irf4+/- BMM after 4h IL-4 stimulation


title: BMM treated with IL4 Exp.G


title: Irf4-/- IL4 18h A

description: Gene expression analysis in Irf4-/- BMM after 18h IL-4 stimulation


title: Irf4+/- IL4 4h C


title: Irf4+/- Mock B

description: Gene expression analysis in Irf4+/- BMM in the absence of IL-4


title: BMM treated with IFNgamma Exp.G


title: Irf4+/- IL4 18h A


title: Irf4-/- Mock B

description: Gene expression analysis in Irf4-/- BMM in the absence of IL-4


title: Irf4-/- Mock C


title: Irf4-/- IL4 4h C

description: Gene expression analysis in Irf4-/- BMM after 4h IL-4 stimulation


title: Irf4+/- Mock C


title: Irf4+/- IL4 18h B


title: Irf4-/- IL4 4h A


title: Irf4-/- IL4 18h B


title: Irf4-/- Mock A


title: Irf4-/- IL4 4h B


title: Irf4-/- IL4 18h C


title: Irf4+/- Mock A


title: Irf4+/- IL4 4h A


title: Mouse liver_C3H_PD32_2

first: Hongzu

last: Ren

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

description: samples were obtained from 7 age groups with 4 samples each

hyb_protocol: Samples were hybridized according to the Affymetrix protocol

scan_protocol: Affymetrix protocol using a GeneChip scanner 3000

data_processing: Probe set expression levels were normalized using the Rosetta Resolver (version 7.1) gene-specific error model. Differentially expressed genes were identified using an error-weighted one-way ANOVA with a Benjamini-Hochberg FDR of 0.05  followed by a post-hoc test for significance.

source_name: liver sample from a PD32 C3H mouse

label_protocol: Samples were labeled according to the Affymetrix protocol

extract_protocol: Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)

treatment_protocol: Timed-pregnant C57BL/6 or C3H dams were purchased from Charles River Laboratory (Raleigh, NC) and acclimated for 1 week.  Mice were housed (1 per cage) in polycarbonate cages on Alpha Dry bedding with a 12 hour light/dark cycle.  Room temperature was 70 ± 2° F with a relative humidity of 50%. The basal diet was Ralston Purina 5001 (Ralston Purina Co., St. Louis, MO) and water was provided ad libitum.  Pregnant dams were sacrificed at GD19 and male pups were sacrificed by decapitation.  Mice from additional litters at ages PND7, PND32, and PND67 were sacrificed using CO2 asphyxiation.  Studies with the C3H mice have been described previously (Ahlborn, Nelson et al. 2009).  Male C57BL/6 mice, at approximately 6, 12, 18 and 24 months of age, were obtained from Charles River Laboratory (Raleigh) and acclimated for 1 week.  Mice were housed in polycarbonate cages on Alpha Dry bedding with a 12-hour light/dark cycle.  Room temperature was 70 ± 2° F with a relative humidity of 50%.  The basal diet was Ralston Purina 5001 and water was provided ad libitum.  Control animals at 6, 12, 18 and 24 months of age were sacrificed using CO2 asphyxiation.  Only male mice were used in this study.  Livers were removed, weighed and sections from the left and median lobes were fixed in formalin, embedded, sectioned, and stained with H&E.  The remainder of the liver was cubed and stored at -80°C until RNA isolation.

value: male


title: Mouse liver_C3H_PD67_2

source_name: liver sample from a PD67 C3H mouse


title: Mouse liver_C3H_PD67_1


title: Mouse liver_C3H_PD67_4


title: Mouse liver_12month_6

source_name: liver sample from a 12 month C57Bl6/J mouse

value: 12 month


title: Mouse liver_C3H_GD19_1

source_name: liver sample from a GD19 C3H mouse


title: Mouse liver_18month_14

source_name: liver sample from a 18 month C57Bl6/J mouse

value: 18 month


title: Mouse liver_C3H_PD32_1


title: Mouse liver_C3H_PD67_3


title: Mouse liver_C3H_GD19_2


title: Mouse liver_24month_33

source_name: liver sample from a 24 month C57Bl6/J mouse

value: 24 month


title: Mouse liver_18month_9


title: Mouse liver_C3H_PD32_4


title: Mouse liver_C3H_GD19_4


title: Mouse liver_12month_17


title: Mouse liver_C3H_GD19_3


title: Mouse liver_12month_13


title: Mouse liver_C3H_PD32_3


title: Mouse liver_18month_4


title: Mouse liver_6month_16

source_name: liver sample from a 6 month C57Bl6/J mouse

value: 6 month


title: Mouse liver_24month_25


title: Mouse liver_24month_29


title: Mouse liver_24month_34


title: Mouse liver_6month_21


title: Mouse liver_18month_19


title: Mouse liver_12month_3


title: Mouse liver_6month_11


title: Mouse liver_6month_2


title: 32Dcl3 Xbp1U

city: Tokyo

first: Morito

last: Kurata

address: bunkyo-ku yusima1-5-45

department: Comprehensive Patho.

institute: Tokyo Med. & Dent. univ.

description: in situ oligonucleotide

hyb_protocol: 5ug of cRNA was hybridized for 16 hours using standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol (Gene Chip Scanner 3000) was used.

data_processing: MAS5 Statistical Algorithm

source_name: pMY-Xbp1U retrovirus vector transfected 32Dcl3 cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: Cells were grown in DMEM medium with 2 mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, 10 mM HEPES, 1.0 mM sodium pyruvate, 10% heat-inactivated fetal bovine serum, 10% mouse Interleukin-3 (10ng/ml) at 37.0°C.

extract_protocol: Total RNA was obtained using the RNeasy kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: The retrovirus vector-plasmid was transfected into Plat-E packaging cells (a gift from Dr. Toshio Kitamura) using lipofectamine 2000 (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. 1 x 10e6 32Dcl3 cells were added to retroviral stock with 6 ug/ml of polybrene (Sigma) and spun at 1,400 g for 2 hours. After 24 hours, cells were harvested.

tag: cell type

tag: transfectant type

value: pMY-Xbp1U retrovirus vector

tag: genome/variation

value: Xbp1U (unspliced form)


title: 32Dcl3 Xbp1S

description: in situ oligonucleotide

source_name: pMY-Xbp1S retrovirus transfected 32Dcl3 cells

value: pMY-Xbp1S retrovirus vector

value: Xbp1S (spliced form)


title: 32Dcl3 pMIG

description: in situ oligonucleotide

source_name: pMIG retorovirus vector transfected 32Dcl3 cells

value: pMIG (pMY) retrovirus vector


title: DRG_DR_7d_rep_3

status: Public on Sep 01 2010

city: Amsterdam

first: Harold

middle: D

last: MacGillavry

address: De Boelelaan 1087

department: Center for neurogenomics and cognitive research

institute: Vrije Universiteit

description: gene expression data of regenerating dorsal root ganglion neurons

hyb_protocol: According to manufacturers instructions.

scan_protocol: Agilent scanner

data_processing: The data were analyzed with the R packages 'bioconductor' and 'limma'. Raw spot intensities were background corrected using Edwards method, loess normalized within arrays and normalized between arrays using Aquantile method.

organism: Rattus norvegicus

source_name: L4, L5 and L6 dorsal root ganglia

label_protocol: Agilent labeling kit, according to manufacturers instructions.

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

value: dorsal root ganglia

tag: time

value: 7 days after dorsal root crush

value: unlesioned dorsal root ganglia pooled from 3 animals


title: DRG_DR_24h_rep3

value: 24h after dorsal root crush


title: DRG_DR_72h_rep3

value: 72h after dorsal root crush


title: DRG_DR_72h_rep1


title: DRG_SN_12h_rep3

value: 12h after sciatic nerve crush


title: DRG_SN_12h_rep2


title: DRG_DR_24h_rep1


title: DRG_SN_72h_rep1

value: 72h after sciatic nerve crush


title: DRG_SN_24h_rep1

value: 24h after sciatic nerve crush


title: DRG_SN_24h_rep2


title: DRG_DR_12h_rep1

value: 12h after dorsal root crush


title: DRG_SN_7d_rep_1

value: 7 days after sciatic nerve crush


title: DRG_DR_72h_rep2


title: DRG_SN_24h_rep3


title: DRG_SN_12h_rep1


title: DRG_DR_7d_rep_1


title: DRG_SN_72h_rep3


title: DRG_SN_72h_rep2


title: DRG_DR_12h_rep3


title: DRG_SN_7d_rep_2


title: DRG_SN_7d_rep_3


title: DRG_DR_24h_rep2


title: DRG_DR_12h_rep2


title: DRG_DR_7d_rep_2


title: Wild type, left ventricle, 4 TAM injection, rep3

city: Oslo

first: Karina

last: Hougen

address: Kirkeveien 166

country: Norway

institute: University of Oslo

description: left ventricle, 4 TAM injection, rep3

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 450C in the hybridization oven at 60 rpm, as described by manufacturer (Affymetrix).

scan_protocol: Gene Chips were scanned using the Hewlett Packard GeneArray Scanner 3000 7G.

data_processing: The data were preprocessed using the robust multi-array average (RMA) package in R with default settings, i.e. quantile normalization and RMA background correction

source_name: left ventricle, 4 TAM injection

label_protocol: According to standard Affymetrix protocol (FS450_00007).

extract_protocol: Total RNA was isolated with an RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Mice were anesthetized with isoflurane and sacrificed by cervical dislocation. Left ventricle was quickly excised and immediately frozen in liquid nitrogen.

tag: time point

value: 4 days

tag: agent

value: tamoxifen

tag: gender

value: female

value: Wild type

tag: age

value: 9-13 weeks

value: left ventricle myocardium


title: Wild type, left ventricle, 4 TAM injection, rep2

description: left ventricle, 4 TAM injection, rep2


title: Wild type, left ventricle, 4 TAM injection, rep1

description: left ventricle, 4 TAM injection, rep1

value: male


title: Wild type, left ventricle, 4 ctrl injection, rep3

description: left ventricle, 4 ctrl injection, rep3

source_name: left ventricle, 4 ctrl injection

value: control


title: Wild type, left ventricle, 4 ctrl injection, rep6

description: left ventricle, 4 ctrl injection, rep6


title: Wild type, left ventricle, 4 ctrl injection, rep5

description: left ventricle, 4 ctrl injection, rep5


title: Tg(αMHC-MerCreMer), left ventricle, 4 TAM injection, rep2

description: left ventricle, 4 TAM injection, rep2

value: Tg(αMHC-MerCreMer)


title: Wild type, left ventricle, 4 ctrl injection, rep4

description: left ventricle, 4 ctrl injection, rep4


title: Wild type, left ventricle, 4 ctrl injection, rep1

description: left ventricle, 4 ctrl injection, rep1


title: Tg(αMHC-MerCreMer), left ventricle, 4 ctrl injection, rep3

description: left ventricle, 4 ctrl injection, rep3


title: Wild type, left ventricle, 4 ctrl injection, rep2

description: left ventricle, 4 ctrl injection, rep2


title: Tg(αMHC-MerCreMer), left ventricle, 1 TAM injection, rep2

description: left ventricle, 1 TAM injection, rep2

source_name: left ventricle, 1 TAM injection

value: 1 day