title: Retinoic Acid treated mouse embryonic stem cells TT2  Replicate 2


title: alphaTC cell line

status: Public on Feb 05 2014

type: genomic

city: Jerusalem

first: guy

last: ludwig

address: Ein Kerem

country: Israel

institute: Hebrew University

hyb_protocol: The labeled Input and Bound DNAs were combined and hybridized for 60 h at 67°C in 15% deionized formamide to a CpG island microarray using the Agilent aCGH hybridization buffer and protocol.

scan_protocol: Arrays were washed according to the Agilent aCGH protocol, immediately scanned on an Agilent microarray scanner and processed using Agilent Feature extraction software version 9.5.

data_processing: Probe log ratio signals were Loess normalized and transformed into Z-scores according to their Tm using Agilent Feature extraction software version 9.5.

molecule: genomic DNA

organism: Mus musculus

label_protocol: The Input and Bound DNAs were labeled using the Agilent Technologies Genomic Labeling kit Plus according to the manufacturer’s instructions. Briefly, 300ng of each sample was labeled with Cyanine-3 or Cyanine-5 dUTP and purified using microcon YM 30 columns.

extract_protocol: mouse (40µg) DNA was sonicated to an average fragment size of 300–1000 bp, precipitated with  400 mM NaCl, 2 volumes of ethanol and 1 µl glycogen. 1.5 µg were set aside as the Input fraction. DNA was denatured and anti-5-methylcytidine  monoclonal antibody (10 µl for 5 µg) was added and incubated on a rotator at 4°C overnight. 40 µl Dynabeads (Sheep anti-Mouse IgG) were prewashed  with 0.1% BSA/PBS and added to the DNA. The DNA was then washed 3 times and Ab-bound DNA resuspended and extracted with proteinase K,  phenol-chloroform and ethanol precipitation.

tag: cell line

value: alphaTC


title: purified natural  β cells from pancreatic tissue

description: Beta

tag: cell type


title: Placenta 14.5

tag: strain background

tag: gender

value: Female

tag: age

tag: tissue

value: Placenta


title: P61S2L10H3: ChronicLocalizedAffected

type: RNA

city: New York

first: Paolo

last: Guarnieri

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

country: USA

institute: Columbia University

hyb_protocol: Labeled RNA hybridized with microarrays carrying probes for 1,205 human and 144 human viral miRNAs (SurePrint G3 Human v16 miRNA 8x60K Microarray Kit).

scan_protocol: Array images were scanned with Agilent Technologies Scanner G2505C US83000178 using grid 031181_D_F_20110707 and protocol miRNA_105_Dec08.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using  031181_D_F_20110707.xml as design file to obtain background subtracted and Processed Signal intensities. Subsequent data analysis and normalization was performed within R/Bioconductor. Data was normalized and background corrected using rmaMicroRna function with background and normalize set to TRUE. Filtering was performed according to the recommended AgiMicroRna documentation having the following filterMicroRna parameters:
control = TRUE,
IsGeneDetected = TRUE,
wellaboveNEG = FALSE,
limIsGeneDetected = 75,
limNEG = 25

label: cyanine 3-pCp

molecule: total RNA

organism: Homo sapiens

source_name: periodontal tissue

label_protocol: miRNA profiling was carried out using the Agilent platform (Agilent Technologies). Total RNA (100 ng/specimen) was labeled to generate fluorescent miRNA by ligation of cyanine 3-pCp to the 3’end

extract_protocol: Tissue samples were stored in liquid RNA stabilization reagent (RNAlater, Austin, TX) overnight at 4°C, snap-frozen and stored in liquid nitrogen. Specimens were homogenized in Trizol (Invitrogen Life Technologies, Carlsbad, CA), incubated with chloroform and centrifuged at 12,000g. RNA collected in the upper aqueous phase was precipitated by mixing with 75% isopropyl-alcohol and additional centrifugation and washings, and was quantified spectrophotometrically. RNA quality was assessed by determining the RNA Integrity Number (RIN).

treatment_protocol: Gingival tissue samples comprising pocket/sulcus epithelium and the underlying connective tissue were obtained from patients with chronic or aggressive periodontitis in conjunction with periodontal surgery

tag: patient

tag: specimen

tag: biopsyid

tag: diagnosis

value: Chronic

tag: extent

value: Localized

tag: condition

value: Affected

tag: labelbatch

tag: hybridizebatch


title: P60S2L10H3: ChronicLocalizedAffected


title: P61S1L10H3: ChronicLocalizedAffected


title: Min6 cell line


title: teratoma C4 Replicate 1

value: teratoma C4


title: Mesoderm differentiated from EB5

description: Mesoderm

value: mesoderm differentiated from EB5


title: P60S1L10H3: ChronicLocalizedAffected


title: Retinoic Acid treated mouse embryonic stem cells TT2  Replicate 1


title: mouse embryonic stem cells C4 Replicate 2

value: mouse embryonic stem cells


title: Endoderm Replicate 2 differentiated from EB5

value: Endoderm differentiated from EB5


title: P59S2L10H3: AggressiveGeneralizedAffected

value: Aggressive

value: Generalized


title: P58S2L24H7: ChronicGeneralizedAffected


title: P58S3L10H3: ChronicGeneralizedControl

value: Control


title: Endoderm Replicate 1 differentiated from EB5


title: P56S4L24H7: ChronicLocalizedControl


title: P58S1L24H7: ChronicGeneralizedAffected


title: mouse embryoid bodies from es TT2

description: EB


title: P56S2L24H7: ChronicLocalizedAffected


title: mouse embryonic stem cells C4 Replicate 1


title: mouse embryonic stem cells D3


title: mouse embryonic stem cells J1


title: Embryo 12.5 days

value: Embryo


title: mouse embryonic stem cells TT2


title: spleen Replicate 2

value: Male

value: 3 months

value: spleen


title: Embryo 10.5 days


title: muscle Replicate 2

value: muscle


title: P53S2L23H7: ChronicLocalizedAffected


title: P55S3L24H7: ChronicLocalizedControl


title: P52S2L23H7: ChronicLocalizedAffected


title: P50S2L22H6: ChronicLocalizedAffected


title: P56S1L24H7: ChronicLocalizedAffected


title: P50S1L22H6: ChronicLocalizedAffected


title: P55S2L23H7: ChronicLocalizedAffected


title: P53S3L23H7: ChronicLocalizedAffected


title: P52S1L22H6: ChronicLocalizedAffected


title: P54S2L23H7: ChronicGeneralizedAffected


title: P54S3L23H7: ChronicGeneralizedControl


title: P54S1L23H7: ChronicGeneralizedAffected


title: P55S1L23H7: ChronicLocalizedAffected


title: lung Replicate 2

value: Female

value: lung


title: liver Replicate 2

value: liver


title: kidney Replicate 2

value: kidney


title: brain Replicate 2

value: brain


title: Embryo 8.5 days


title: brain Replicate 1


title: mouse embryonic stem cells EB5


title: muscle Replicate 1


title: Embryo 11.5 days


title: spleen Replicate 1


title: lung Replicate 1


title: kidney Replicate 1


title: Embryo 9.5 days


title: liver Replicate 1


title: P49S2L22H6: ChronicLocalizedAffected

value: Chronic

value: Localized

value: Affected


title: P48S1L21H6: ChronicLocalizedAffected


title: P48S2L22H6: ChronicLocalizedAffected


title: P48S3L22H6: ChronicLocalizedControl


title: P49S3L22H6: ChronicLocalizedControl


title: P49S1L22H6: ChronicLocalizedAffected


title: P47S3L21H6: ChronicLocalizedControl


title: P46S3L21H6: ChronicLocalizedControl


title: P47S2L21H6: ChronicLocalizedAffected


title: P46S2L21H6: ChronicLocalizedAffected


title: P47S1L21H6: ChronicLocalizedAffected


title: P45S2L21H6: ChronicGeneralizedAffected


title: pancreas Replicate 2

value: pancreas


title: P45S3L21H6: ChronicGeneralizedControl


title: P46S1L21H6: ChronicLocalizedAffected


title: pancreas Replicate 1


title: colon Replicate 2

value: colon


title: P45S1L25H8: ChronicGeneralizedAffected

value: Generalized


title: colon Replicate 1


title: P43S1L9H3: ChronicGeneralizedAffected


title: P44S2L9H3: ChronicGeneralizedAffected


title: P44S1L9H3: ChronicGeneralizedAffected


title: P42S4L9H3: ChronicLocalizedAffected


title: P43S4L9H3: ChronicGeneralizedControl

value: Control


title: P42S2L9H3: ChronicLocalizedAffected


title: P42S1L8H3: ChronicLocalizedAffected


title: P42S3L9H3: ChronicLocalizedControl


title: P43S2L9H3: ChronicGeneralizedAffected


title: P40S1L8H3: AggressiveGeneralizedAffected

value: Aggressive


title: P40S2L8H3: AggressiveGeneralizedAffected


title: ecoli_del.rpoS_stationary_glucose_2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

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

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

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

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

source_name: E. coli ΔrpoS, stationary phase, M9 glucose 2

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

growth_protocol: E. coli ΔrpoS was grown to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: genotype

value: K-12 MG1655 ΔrpoS


title: ecoli_del.rpoS_stationary_glucose_1

source_name: E. coli ΔrpoS, stationary phase, M9 glucose 1


title: P41S2L8H3: AggressiveLocalizedAffected


title: E. Coli Heatshock RpoD ChIP DNA 2

hyb_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

data_processing: The raw pair data (.txt file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com).

source_name: E. Coli Heatshock RpoD ChIP DNA 2

growth_protocol: E. coli strains  were grown in minimal M9 medium supplemented with glucose (2 g/L) to mid-exponential phase with heatshock for 10 min

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. 6 uL of mouse antibody (NT63, Neoclone) was used to immunoprecipitate the chromatin complex of RNA polymerase subunit and DNA. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR.

treatment_protocol: Cross-linked and sonicated chromatin complex of RNAP and DNA was immunoprecipitated by anti-RpoB antibody.

value: wild type

tag: chip antibody

value: anti-RpoD antibody

source_name: E. Coli Heatshock RpoD ChIP DNA Mock 2

treatment_protocol: Cross-linked and sonicated chromatin complex of RNAP and DNA was immunoprecipitated by using normal mouse IgG for the control.

value: normal mouse IgG (Upstate)

tag: chip antibody manufacturer

value: Upstate


title: ecoli_del.rpoS_stationary_glucose_3

source_name: E. coli ΔrpoS, stationary phase, M9 glucose 3


title: E. Coli Glutamine RpoD ChIP DNA 2

scan_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

source_name: E. Coli Glutamine RpoD ChIP DNA 2

growth_protocol: E. coli strains  were grown in minimal W2 medium supplemented with glucose (2 g/L) and glutamine (2 g/L) to mid-exponential phase

source_name: E. Coli Glutamine RpoD ChIP DNA Mock 2


title: E. Coli Iron RpoD ChIP DNA 1

source_name: E. Coli Iron RpoD ChIP DNA 1

label_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

growth_protocol: E. coli strains  were grown in minimal M9 medium supplemented with glucose (2 g/L) and additional iron to mid-exponential phase

source_name: E. Coli Iron RpoD ChIP DNA Mock 1


title: P38S3L16H7: AggressiveGeneralizedControl


title: E. Coli Stationary RpoD DelS ChIP DNA 2

source_name: E. Coli Stationary RpoD DelS ChIP DNA 2

growth_protocol: E. coli strains  were grown in minimal M9 medium supplemented with glucose (2 g/L) to stationary phase

value: ΔrpoS

source_name: E. Coli Stationary RpoD DelS ChIP DNA Mock 2


title: E. Coli Stationary RpoD ChIP DNA 2

source_name: E. Coli Stationary RpoD ChIP DNA 2

source_name: E. Coli Stationary RpoD ChIP DNA Mock 2


title: P38S3L8H3: AggressiveGeneralizedControl

description: P38S3L8H3 (this sample failed QC and was excluded from the final analysis)


title: P39S1L8H3: ChronicLocalizedAffected


title: E. Coli Glutamine RpoD ChIP DNA 1

source_name: E. Coli Glutamine RpoD ChIP DNA 1

source_name: E. Coli Glutamine RpoD ChIP DNA Mock 1


title: E. Coli Stationary RpoD DelS ChIP DNA 1

source_name: E. Coli Stationary RpoD DelS ChIP DNA 1

source_name: E. Coli Stationary RpoD DelS ChIP DNA Mock 1


title: E. Coli Exponential RpoN ChIP DNA 1

source_name: E. Coli Exponential RpoN ChIP DNA 1

growth_protocol: E. coli strains  were grown in minimal M9 medium supplemented with glucose (2 g/L) to mid-exponential phase

value: anti-RpoN antibody

source_name: E. Coli Exponential RpoN ChIP DNA Mock 1


title: E. Coli Exponential RpoD DelN ChIP DNA 2

value: ΔrpoN

source_name: E. Coli Exponential RpoD DelN ChIP DNA Mock 2


title: E. Coli Exponential RpoD ChIP DNA 1

source_name: E. Coli Exponential RpoD ChIP DNA 1

source_name: E. Coli Exponential RpoD ChIP DNA Mock 1


title: E. Coli Exponential RpoD ChIP DNA 2

source_name: E. Coli Exponential RpoD ChIP DNA 2

source_name: E. Coli Exponential RpoD ChIP DNA Mock 2


title: E. Coli Exponential RpoN ChIP DNA 3

source_name: E. Coli Exponential RpoN ChIP DNA 3

source_name: E. Coli Exponential RpoN ChIP DNA Mock 3


title: E. Coli Stationary RpoD ChIP DNA 1

source_name: E. Coli Stationary RpoD ChIP DNA 1

source_name: E. Coli Stationary RpoD ChIP DNA Mock 1


title: E. Coli Glutamine RpoN ChIP DNA 2

source_name: E. Coli Glutamine RpoN ChIP DNA 2

source_name: E. Coli Glutamine RpoN ChIP DNA Mock 2


title: E. Coli Exponential RpoD DelN ChIP DNA 1

source_name: E. Coli Exponential RpoD DelN ChIP DNA Mock 1


title: P38S2L8H3: AggressiveGeneralizedAffected

source_name: periodontal tissue


title: E. Coli Stationary RpoS ChIP DNA 3

source_name: E. Coli Stationary RpoS ChIP DNA 3

value: anti-RpoS antibody

source_name: E. Coli Stationary RpoS ChIP DNA Mock 3


title: E. Coli Exponential RpoN ChIP DNA 2

source_name: E. Coli Exponential RpoN ChIP DNA 2

source_name: E. Coli Exponential RpoN ChIP DNA Mock 2


title: Peritoneal_macrophages_4%_thioglycollate_with_IL-4C_rep4

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

description:
THIO+IL-4C_4
Gene expression of inflammatory monocyte-derived macrophages.

hyb_protocol: Equal amount of Cy3-labeled target was hybridized to Agilent-028005 Sureprint G3 Mouse GE 8x60k array for 15 hours according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using Agilent microarray scanner.

data_processing:
Raw signal intensities were extracted with Feature Extraction v11.5 software.
Expression intensities of each chip were background corrected using the limma package by normal-exponential convolution method, resulting in log2-transformed expression values. To correct for systematic differences in expression levels between arrays, we scaled the expression values of each array so that the median-absolute-values are equal for all arrays.

source_name: Peritoneal macrophages, 4% thioglycollate with IL-4C

label_protocol: Labeling was performed with Cy3 according to the manufacturer protocol for one color microarray based gene expression analysis (Agilent).

growth_protocol: C57BL/6 mice were maintained in specific-pathogen-free facility at NYU and University of Edinburgh.

extract_protocol: RNA was isolated from FACS-sorted cells (positive for both CD11b and F4/80), stored in Trizol using chloroform purification and isopropanol extraction and purified using QIAgen RNeasy Mini Kit.

treatment_protocol: Intra-peritoneal injection of mice with either PBS vehicle control, IL-4c (i.e. 5μg of IL-4 and 25μg of 11B11), 2ml of 4% thioglycollate medium, or 2ml of 4% thioglycollate in combination with IL-4c.

tag: strain/background

tag: treatment

value: 4% thioglycollate with IL-4C

value: sorted cells (CD11b and F4/80 positive)


title: E. Coli Exponential RpoS ChIP DNA 2

source_name: E. Coli Exponential RpoS ChIP DNA 2

source_name: E. Coli Exponential RpoS ChIP DNA Mock 2


title: E. Coli Stationary RpoS ChIP DNA 1

source_name: E. Coli Stationary RpoS ChIP DNA 1

source_name: E. Coli Stationary RpoS ChIP DNA Mock 1


title: Peritoneal_macrophages_4%_thioglycollate_with_IL-4C_rep2

description:
THIO+IL-4C_2
Gene expression of inflammatory monocyte-derived macrophages.

tag: cell type


title: E. Coli Heatshock RpoD ChIP DNA 1

source_name: E. Coli Heatshock RpoD ChIP DNA 1

source_name: E. Coli Heatshock RpoD ChIP DNA Mock 1


title: E. Coli Glutamine RpoN ChIP DNA 1

source_name: E. Coli Glutamine RpoN ChIP DNA 1

source_name: E. Coli Glutamine RpoN ChIP DNA Mock 1


title: Peritoneal_macrophages_4%_thioglycollate_with_IL-4C_rep3

description:
THIO+IL-4C_3
Gene expression of inflammatory monocyte-derived macrophages.


title: E. Coli Stationary RpoS ChIP DNA 2

source_name: E. Coli Stationary RpoS ChIP DNA 2

source_name: E. Coli Stationary RpoS ChIP DNA Mock 2


title: Peritoneal_macrophages_4%_thioglycollate_rep3

description:
THIO_3
Gene expression of monocytes.

source_name: Peritoneal macrophages, 4% thioglycollate

value: 4% thioglycollate


title: Peritoneal_macrophages_4%_thioglycollate_with_IL-4C_rep1

description:
THIO+IL-4C_1
Gene expression of inflammatory monocyte-derived macrophages.


title: P37S2L7H2: AggressiveLocalizedAffected

source_name: periodontal tissue

value: Localized

value: Affected


title: E. Coli Iron RpoD ChIP DNA 2

source_name: E. Coli Iron RpoD ChIP DNA 2

source_name: E. Coli Iron RpoD ChIP DNA Mock 2


title: Peritoneal_macrophages_4%_thioglycollate_rep2

description:
THIO_2
Gene expression of monocytes.


title: P36S3L7H2: ChronicGeneralizedControl

value: Chronic

value: Generalized


title: E. Coli Exponential RpoD ChIP DNA 3

source_name: E. Coli Exponential RpoD ChIP DNA 3

source_name: E. Coli Exponential RpoD ChIP DNA Mock 3


title: E. Coli Exponential RpoH ChIP DNA 2

source_name: E. Coli Exponential RpoH ChIP DNA 2

value: anti-c-myc antibody

source_name: E. Coli Exponential RpoH ChIP DNA Mock 2


title: Peritoneal_macrophages_IL-4C_rep3

description:
IL-4C_3
Gene expression of proliferating tissue macrophages.

source_name: Peritoneal macrophages, IL-4C


title: Peritoneal_macrophages_4%_thioglycollate_rep1

description:
THIO_1
Gene expression of monocytes.


title: Peritoneal_macrophages_IL-4C_rep4

description:
IL-4C_4
Gene expression of proliferating tissue macrophages.


title: P36S2L7H2: ChronicGeneralizedAffected


title: P35S4L7H2: ChronicGeneralizedControl

value: Control


title: Peritoneal_macrophages_untreated_rep2

description:
control_2
Gene expression of resident macrophages.

source_name: Peritoneal macrophages, untreated

value: PBS vehicle control


title: Peritoneal_macrophages_untreated_rep3

description:
control_3
Gene expression of resident macrophages.


title: Peritoneal_macrophages_IL-4C_rep2

description:
IL-4C_2
Gene expression of proliferating tissue macrophages.


title: P35S2L7H2: ChronicGeneralizedAffected


title: Peritoneal_macrophages_IL-4C_rep1

description:
IL-4C_1
Gene expression of proliferating tissue macrophages.


title: Peritoneal_macrophages_untreated_rep1

description:
control_1
Gene expression of resident macrophages.


title: E. Coli Exponential RpoH ChIP DNA 1

source_name: E. Coli Exponential RpoH ChIP DNA 1

source_name: E. Coli Exponential RpoH ChIP DNA Mock 1


title: P36S1L7H2: ChronicGeneralizedAffected


title: E. Coli Heatshock RpoH ChIP DNA 1

source_name: E. Coli Heatshock RpoH ChIP DNA 1

source_name: E. Coli Heatshock RpoH ChIP DNA Mock 1


title: P35S1L6H2: ChronicGeneralizedAffected


title: E. Coli Exponential RpoS ChIP DNA 1

source_name: E. Coli Exponential RpoS ChIP DNA 1

value: wild type

source_name: E. Coli Exponential RpoS ChIP DNA Mock 1


title: E. Coli Heatshock RpoH ChIP DNA 3

source_name: E. Coli Heatshock RpoH ChIP DNA 3

source_name: E. Coli Heatshock RpoH ChIP DNA Mock 3

value: normal mouse IgG (Upstate)


title: P37S1L7H2: AggressiveLocalizedAffected

source_name: periodontal tissue

value: Aggressive


title: P34S1L6H2: ChronicLocalizedAffected


title: P34S2L6H2: ChronicLocalizedAffected


title: P34S3L6H2: ChronicLocalizedControl


title: P38S1L8H3: AggressiveGeneralizedAffected


title: P33S1L6H2: ChronicGeneralizedAffected


title: P32S2L6H2: ChronicGeneralizedAffected


title: P33S2L6H2: ChronicGeneralizedAffected


title: P31S2L6H2: ChronicLocalizedAffected


title: P30S2L5H2: AggressiveGeneralizedAffected


title: E. Coli Exponential RpoF ChIP DNA 3

source_name: E. Coli Exponential RpoF ChIP DNA 3

value: anti-RpoF antibody

source_name: E. Coli Exponential RpoF ChIP DNA Mock 3

value: Upstate


title: E. Coli Exponential FecI ChIP DNA 3

source_name: E. Coli Exponential FecI ChIP DNA 3

value: anti-FecI antibody

source_name: E. Coli Exponential FecI ChIP DNA Mock 3


title: P30S1L5H2: AggressiveGeneralizedAffected


title: E. Coli Exponential RpoF ChIP DNA 1

source_name: E. Coli Exponential RpoF ChIP DNA 1

source_name: E. Coli Exponential RpoF ChIP DNA Mock 1


title: E. Coli Exponential RpoF ChIP DNA 2

source_name: E. Coli Exponential RpoF ChIP DNA 2

source_name: E. Coli Exponential RpoF ChIP DNA Mock 2


title: E. Coli Heatshock RpoH ChIP DNA 2

source_name: E. Coli Heatshock RpoH ChIP DNA 2

source_name: E. Coli Heatshock RpoH ChIP DNA Mock 2


title: E. Coli Exponential FecI ChIP DNA 1

source_name: E. Coli Exponential FecI ChIP DNA 1

source_name: E. Coli Exponential FecI ChIP DNA Mock 1


title: P37S3L7H2: AggressiveLocalizedControl


title: P29S2L5H2: AggressiveGeneralizedAffected


title: P29S1L5H2: AggressiveGeneralizedAffected


title: P29S3L5H2: AggressiveGeneralizedControl


title: P24S1L5H2: ChronicGeneralizedAffected


title: E. Coli Exponential FecI ChIP DNA 2

source_name: E. Coli Exponential FecI ChIP DNA 2

source_name: E. Coli Exponential FecI ChIP DNA Mock 2


title: P23S2L5H2: ChronicGeneralizedAffected


title: E. Coli Heatshock RpoB ChIP DNA 1

source_name: E. Coli Heatshock RpoB ChIP DNA 1

growth_protocol: E. coli strains  were grown in minimal M9 medium supplemented with glucose (2 g/L) to mid-exponential phase and treated with heatshock for 10 min

value: anti-RpoB antibody

source_name: E. Coli Heatshock RpoB ChIP DNA Mock 1


title: clbn 108hpf rep 3

city: Parkville

first: Joan

middle: Kathleen

last: Heath

state: Victoria

address: 1G Royal Parade

department: Development and Cancer

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Labeled material was hydrolyzed and used for hybridization to Agilent Zebrafish V2 Gene Expression arrays. Hybridization to each array was performed for 16 h at 45°C

scan_protocol: Hybridized microarrays were scanned on a 600B Scanner (Agilent). The images were analyzed using Imagene 5.6.0 (BioDiscovery) to determine mean foreground and background signal intensities

data_processing: Data was extracted using Agilent Feature Extraction software and analyzed using the Linear Models for Microarray Data (LIMMA) software package via the R Project for Statistical Computing (www.r-project.org). Data was background-corrected and normalized both within and between arrays. Differential expression was defined using a robust statistical method rather than simple fold change. Genes were ranked using the B-statistic method, where both the fold change and variance of signals in replicates are used to determine the likelihood that expression of a gene is truly differential. A linear model of the data was fitted to the experimental design matrix and used to calculate Bayesian statistics (B statistics; posterior log odds) adjusted for multiple testing using Benjamini-Hochberg analysis. A threshold in the B statistic of 0.0 was adopted.

organism: Danio rerio

source_name: clbns841_whole larvae

label_protocol: Microarrays were performed as one-color experiments. Total RNA was linearly amplified from 1µg of total RNA per each sample using the messageAMP amplified RNA (aRNA) kit (Ambion), yielding a minimum of 20µg of amino-allyl-labeled antisense aRNA. Quantity and integrity of aRNAs were compared by running each sample on a bioanalyzer RNA microfluidic chip (Agilent) before labeling. Five micrograms of each aRNA sample were then labeled by covalent linking of Cy3-labeled UTP (Amersham).

growth_protocol: Embryos for all experiments were produced by natural spawning, transferred into petri dishes with pre-warmed egg water (60mg of sea salt/1L ddH20) and placed in a 28.5°C incubator on a 12h light/dark cycle.

extract_protocol: Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate-phenol-chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first, and aqueous phases of all homozygous wildtype and mutant larvae, respectively, were pooled prior to RNA precipiation with isopropanol. For microarray analysis, RNA was extracted from 3 biologically independent pools of approximately 20 genotyped larvae for each genetic condition.

treatment_protocol: Starting at 24 hpf, embryos were transferred into egg water containing 0.003% 1-Phenyl-2-thiourea (PTU) to prevent pigmentation

tag: genotype/variation

tag: developmental stage

value: 108 hours post-fertilization (hpf)

value: whole larvae


title: clbn 108hpf rep 1

tag: tissue


title: P22S2L4H2: AggressiveGeneralizedAffected

source_name: periodontal tissue

tag: patient


title: wt 108hpf rep3

source_name: wildtype_whole larvae

value: wildtype


title: E. Coli Heatshock RpoB ChIP DNA 2

source_name: E. Coli Heatshock RpoB ChIP DNA 2

source_name: E. Coli Heatshock RpoB ChIP DNA Mock 2


title: R15-Mature-2-Rep1

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Research

description: Global gene expression

hyb_protocol: The resulting Cy3 dye incorporated aRNA was quantified using ND-1000 spectrophotometer (Nano Dro Technologies) and 1.65 ug of labeled aRNA was hybridized onto Agilent’s 4x44k format arrays (Agilent Technologies).

scan_protocol: After hybridization, the arrays were washed following the manufacturer’s protocol using Gene Expression Wash Pack (Agilent Technologies) and scanned using the Agilent C Scanner. The intensities of the scanned fluorescence images were extracted with Agilent Feature Extrcaction software ver 10.7.3.1.

data_processing: The mean signals were background corrected and transformed to the log2 scale.  The data were normalized between arrays by quantile approach.  The empirical Bayes moderated t-statistics implemented in the limma Bioconductor package were used for differential expression detection.  The Benjamini and Hochberg’s approach was used to control for false discovery.  Genes with at least 2-fold changes at the 95% confidence level were considered as significant.  The hierarchical clustering and other statistical analyses were performed using R/Bioconductor.  Principal component analysis (PCA) was performed with Partek Genomics Suite (Partek Inc. St. Louis, MO).

organism: Aplysia californica

source_name: Abdominal ganglia, mature, biological replicate 2, technical replicate 1

label_protocol: The total RNA was subjected to two rounds of linear IVT-amplification and labeled with Cy3-labeled CTP using Amino Allyl MessageAmp II Amplification kits (Ambion).

growth_protocol: Aplysia were maintained in an aquarium at 16 °C under 12:12 light-dark conditions in the Instant Ocean artificial seawater (ASW).

extract_protocol: Total RNA was prepared using theTrizol-chloroform (Invitrogen) method and quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Aanimals were anaesthetized by injecting 380 mM MgCl2 solution with 30-35% of the animal’s body weight for 5-10 minutes.  The abdominal ganglion (AG) was removed by surgical operation and treated with 0.1% protease for 30 minutes. AG was desheathed and individual neurons were isolated with micro scissors and placed in 500 ul of Trizol.

value: Single neuron

tag: gender

tag: age

value: 6 months


title: P22S1L4H2: AggressiveGeneralizedAffected

tag: specimen

tag: biopsyid

tag: diagnosis

value: Affected


title: clbn 108hpf rep 2


title: Dhc195/DVH/PF (-) B12_rep3

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using Affymetrix GeneChip software and the MAS5 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays. Analysis limited to Dhc195 probe sets.

label: biotin

organism:
Nitratidesulfovibrio vulgaris str. Hildenborough
Dehalococcoides mccartyi 195
Pelosinus fermentans DSM 17108

source_name: tri-culture without exogenous cobalamin

label_protocol: cDNA was synthesized using 9 µg total RNA according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).~3-4 µg of cDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: Dhc195/DVH (+) B12 and Dhc195/DVH/PF (+) B12 were grown in defined medium with the amendement of 0.7mmol lactate, 100 µg/L vitamin B12 and ~77 µmol TCE; Dhc195/DVH/PF (-) B12 was grown in the same medium except that no vitamin B12 was added.

extract_protocol: Total RNA was extracted using a acdic phenol-chloroform method.

treatment_protocol: cell samples were taken when 70-80% TCE is degraded.

tag: consortia

value: Dehalococcoides mccartyi strain 195; Desulfovibrio vulgaris Hildenborough; Pelosinus fermentans strain R7


title: Dhc195/DVH/PF (-) B12_rep2

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: E. Coli Stationary RpoB ChIP DNA 2

source_name: E. Coli Stationary RpoB ChIP DNA 2

source_name: E. Coli Stationary RpoB ChIP DNA Mock 2


title: E. Coli Glutamine RpoB ChIP DNA 1

source_name: E. Coli Glutamine RpoB ChIP DNA 1

source_name: E. Coli Glutamine RpoB ChIP DNA Mock 1


title: R15-Mature-3

description: Global gene expression

source_name: Abdominal ganglia, mature, biological replicate 3


title: P23S1L4H2: ChronicGeneralizedAffected

value: Chronic

tag: extent

value: Generalized

tag: condition

tag: labelbatch

tag: hybridizebatch


title: Dhc195/DVH/PF (-) B12_rep1


title: P20S3L4H2: ChronicLocalizedAffected

value: Localized


title: E. Coli Glutamine RpoB ChIP DNA 2

source_name: E. Coli Glutamine RpoB ChIP DNA 2

tag: genotype

value: wild type

tag: chip antibody

source_name: E. Coli Glutamine RpoB ChIP DNA Mock 2

tag: chip antibody manufacturer


title: Dhc195/DVH/PF (+) B12_rep3

source_name: tri-culture with exogenous cobalamin


title: E. Coli Exponential RpoB ChIP DNA 3

source_name: E. Coli Exponential RpoB ChIP DNA 3

source_name: E. Coli Exponential RpoB ChIP DNA Mock 3

value: normal mouse IgG (Upstate)


title: E. Coli Stationary RpoB ChIP DNA 1

source_name: E. Coli Stationary RpoB ChIP DNA 1

source_name: E. Coli Stationary RpoB ChIP DNA Mock 1


title: P24S2L5H2: ChronicGeneralizedAffected

source_name: periodontal tissue


title: wt 108hpf rep1

source_name: wildtype_whole larvae

tag: genotype/variation


title: E. Coli Exponential RpoB ChIP DNA 2

source_name: E. Coli Exponential RpoB ChIP DNA 2

source_name: E. Coli Exponential RpoB ChIP DNA Mock 2


title: R15-Mature-2

description: Global gene expression

source_name: Abdominal ganglia, mature, biological replicate 2


title: R15-Mature-1

description: Global gene expression

source_name: Abdominal ganglia, mature, biological replicate 1


title: Dhc195/DVH (+) B12 cDNA_rep3

organism:
Nitratidesulfovibrio vulgaris str. Hildenborough
Dehalococcoides mccartyi 195

source_name: co-culture with exogenous cobalamin

value: Dehalococcoides mccartyi strain 195; Desulfovibrio vulgaris Hildenborough


title: Dhc195/DVH/PF (+) B12_rep2


title: P20S2L4H2: ChronicLocalizedAffected


title: Dhc195/DVH/PF (+) B12_rep1


title: P17S2L4H2: AggressiveGeneralizedAffected

value: Aggressive


title: P17S1L4H2: AggressiveGeneralizedAffected


title: Dhc195/DVH (+) B12 cDNA_rep2


title: P20S1L4H2: ChronicLocalizedControl

value: Control


title: R15-Old-3-Rep1

description: Global gene expression

source_name: Abdominal ganglia, old, biological replicate 3, technical replicate 1

value: 1 year


title: Dhc195/DVH (+) B12 cDNA_rep1


title: E. Coli Exponential RpoB ChIP DNA 1

source_name: E. Coli Exponential RpoB ChIP DNA 1

value: anti-RpoB antibody

source_name: E. Coli Exponential RpoB ChIP DNA Mock 1

value: Upstate


title: R15-Old-3

description: Global gene expression

source_name: Abdominal ganglia, old, biological replicate 3


title: H1299_Ad-p73b

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

description:
Gene expression after Ad-p73b infection
H1299_6

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction.
The values in the data matrix (log2) were calculated by Limma (R package) for the normalization using all probes and then the values for lincRNAs were selected for further analysis.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: H1299 were cultured in RPMI1640 medium with 10% FCS.

extract_protocol: 24h after infection, total RNA was extracted by RNeasy mini kit (QIAGEN) according to manufacturer's protocol. RNA was quantified using the NanoDrop spectrophotometer.

treatment_protocol: H1299 cells were infected with adenoviruses expressing LacZ, p53, p63a, p63g, p73a or p73b at 25 moi.

tag: cell line

tag: cell type

value: human lung carcinoma cells

tag: infected with

value: adenoviruses expressing p73b


title: P12S4L3H1: ChronicLocalizedControl

tag: patient


title: H1299_Ad-p63g

description:
Gene expression after Ad-p63g infection
H1299_4

value: adenoviruses expressing p63g


title: wt 108hpf rep2

value: wildtype

tag: developmental stage

value: 108 hours post-fertilization (hpf)

tag: tissue

value: whole larvae


title: P13S1L3H1: ChronicLocalizedAffected

tag: specimen

tag: biopsyid

value: Chronic

value: Affected


title: P14S1L16H2: AggressiveLocalizedAffected

tag: diagnosis

value: Localized


title: P15S2L3H1: ChronicLocalizedAffected

tag: extent


title: P14S3L3H1: AggressiveLocalizedControl

tag: condition


title: P15S1L3H1: ChronicLocalizedAffected

tag: labelbatch


title: H1299_Ad-p73a

description:
Gene expression after Ad-p73a infection
H1299_5

value: adenoviruses expressing p73a


title: R15-Old-2

description: Global gene expression

source_name: Abdominal ganglia, old, biological replicate 2

value: Single neuron

tag: gender

tag: age


title: P12S2L3H1: ChronicLocalizedAffected

tag: hybridizebatch


title: P12S1L1H1: ChronicLocalizedAffected


title: H1299_Ad-p53

description:
Gene expression after Ad-p53 infection
H1299_2

value: adenoviruses expressing p53


title: R15-Old-1

description: Global gene expression

source_name: Abdominal ganglia, old, biological replicate 1


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Saline 3

first: Li

last: Shen

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
D2_381_Mut_Sal
Gene expression from Drd2 MSNs

hyb_protocol: See Schaefer, A. et al. Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron 64, 678-91 (2009), Heiman, M. et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738-48 (2008), and Doyle, J.P. et al. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135, 749-62 (2008) for experimental details.

scan_protocol: Mouse Genome 430 2.0 arrays were scanned using the GeneChip Scanner 3000 (Affymetrix) and globally scaled to 150 using the Affymetrix GeneChip Operating Software (GCOS v1.4).

data_processing:
Affymetrix Probe Sets Summarization: Probe level intensity files (CEL) were imported into Affymetrix’s Expression Console (v1.1) program for analysis. The RMA algorithm was used for normalization and probe level summarization files (CHP) were then exported for further analysis. Only 1 of 30 files was filtered out, as it failed default quality thresholds. Two negative control files were also removed, leaving 27 files remaining across the three design factors.
Differential Analysis: Two-way ANOVAs among different genotypes and experimental treatments were performed for each cell type individually to identify genes displaying differential expression. For each gene, three F-tests were performed for genotype, treatment and their interaction. All F-test results were subjected to multiple testing corrections using the Benjamini-Hochberg procedure. FDR < 15% was used as a cutoff to select genes for the heatmaps displayed. Pairwise comparisons were performed between two groups of any combination of the three factors using student t-tests. A p-value of < 0.005 was used as a cutoff. This approach was first used to compare compiled data sets: 1) control-saline-Drd1 vs. control-saline-Drd2 from our bacTRAP arrays; 2) control-saline-Drd1 vs. control-saline-Drd2 from Heiman et al.; and 3) Drd1 vs. Drd2 FACS arrays from Lobo et al. to identify cell-type specific gene expression enrichment under basal conditions. It was then used to compare the effects of cocaine treatment, G9a KO, or a combination of the two with respective cell-type specific saline controls. These comparisons were performed to identify genes displaying increased expression of Drd1 enriched genes or decreased expression of Drd2 enriched genes in Drd2 MSNs following different perturbations.

source_name: D2 G9a Mutant adult mouse striatum saline

treatment_protocol: Polyribosome associated mRNAs from 2–5 month old, age and sex matched Drd1-Cre; Drd1-TRAP; G9afl/fl and Drd1-TRAP; G9afl/fl, Drd2-Cre; Drd2-TRAP; G9afl/fl and Drd2-TRAP; G9afl/fl mice (n = 2–4 mice/genotype/drug treatment, 2 hours after the last of eight repeated saline or cocaine injections of 20 mg/kg/day) were obtained.

tag: strain background

value: Mix between C57BL/6 (G9a line) and 129/Sv (BAC line); 2 generations of C57BL/6 backcrossing

value: Drd-TRAP; Drd2-Cre; G9a fl/fl

value: male

value: 2-5 month old

tag: tag

value: TRAP (L10a-GFP)

tag: treated with

value: saline

value: Striatum(Drd2 MSNs)

tag: molecule subtype

value: polyribosome associated mRNA


title: Drd2-TRAP; G9a fl/fl Cocaine 4

description:
D2_374_Con_Coc
Gene expression from Drd2 MSNs

source_name: D2 G9a Control adult mouse striatum cocaine

label_protocol: See Schaefer, A. et al. Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron 64, 678-91 (2009), Heiman, M. et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738-48 (2008), and Doyle, J.P. et al. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135, 749-62 (2008) for experimental details.

tag: genotype/variation

value: Drd2-TRAP; G9a fl/fl

value: 20 mg/kg/day cocaine


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Cocaine 4

description:
D2_380_Mut_Coc
Gene expression from Drd2 MSNs

extract_protocol: See Schaefer, A. et al. Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron 64, 678-91 (2009), Heiman, M. et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738-48 (2008), and Doyle, J.P. et al. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135, 749-62 (2008) for experimental details.


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Saline 2

description:
D2_375_Mut_Sal
Gene expression from Drd2 MSNs


title: Fkh2Myc_anti_Myc_rep_2

city: Los Angeles

first: Andrew

middle: Zachary

last: Ostrow

state: California

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

description: α-Myc (9E10) ChIP-chip of Fkh2-Myc

hyb_protocol: Nimblegen standard protocol

scan_protocol: Genepix Personal 4100A Scanner (Axon Instruments).

data_processing: We used RINGO package (http://www.biomedcentral.com/1471-2105/8/221) in BIOCONDUCTOR suite to perform normalization.

organism: Saccharomyces cerevisiae

source_name: 9E10 ChIP DNA from FKH2-MYC cells

label_protocol: Nimblegen standard protocol

growth_protocol: cells were grown in YEPD

extract_protocol: Genomic DNA was extracted as described in as described in Viggiani CJ, Aparicio JG, Aparicio OM (2009) ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays. Methods Mol Biol 521: 255-278.

tag: genotype

value: FKH2::13MYC (TRP1) bar1Δ::URA3

tag: strain

tag: chip antibody

value: 9E10 monoclonal

source_name: Total DNA from FKH2-MYC cells


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Cocaine 2

description:
D2_370_Mut_Coc
Gene expression from Drd2 MSNs

source_name: D2 G9a Mutant adult mouse striatum cocaine

tag: tissue


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Cocaine 3

description:
D2_371_Mut_Coc
Gene expression from Drd2 MSNs


title: P10S2L2H1: ChronicLocalizedAffected

source_name: periodontal tissue

tag: patient

tag: specimen

tag: biopsyid

value: Chronic

value: Affected


title: H1299_Ad-LacZ

description:
Gene expression after Ad-LacZ infection
H1299_1

tag: cell line

tag: cell type

value: human lung carcinoma cells

tag: infected with

value: adenoviruses expressing LacZ


title: P11S1L2H1: AggressiveGeneralizedAffected

tag: diagnosis

value: Aggressive

tag: extent

value: Generalized

tag: condition

tag: labelbatch


title: H1299_Ad-p63a

description:
Gene expression after Ad-p63a infection
H1299_3

value: adenoviruses expressing p63a


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Saline 1

description:
D2_372_Mut_Sal
Gene expression from Drd2 MSNs

tag: strain background

value: Mix between C57BL/6 (G9a line) and 129/Sv (BAC line); 2 generations of C57BL/6 backcrossing

value: Drd-TRAP; Drd2-Cre; G9a fl/fl

tag: gender

value: male

tag: age

tag: tag

tag: treated with


title: Fkh2Myc_anti_Myc_rep_1

description: α-Myc (9E10) ChIP-chip of Fkh2-Myc

tag: genotype

tag: strain

tag: chip antibody


title: P10S4L2H1: ChronicLocalizedControl

tag: patient

tag: specimen

value: Localized

value: Control

tag: hybridizebatch


title: Fkh2Myc_anti_Myc_rep_3

description: α-Myc (9E10) ChIP-chip of Fkh2-Myc


title: P11S2L2H1: AggressiveGeneralizedAffected

tag: biopsyid


title: Fkh1Myc_anti_Myc_rep_3

description: α-Myc (9E10) ChIP-chip of Fkh1-Myc

source_name: 9E10 ChIP DNA from FKH1-MYC cells

value: FKH1::9MYC (TRP1) bar1Δ::URA3

source_name: Total DNA from FKH1-MYC cells


title: Drd2-TRAP; G9a fl/fl Saline 3

description:
D2_365_Con_Sal
Gene expression from Drd2 MSNs

source_name: D2 G9a Control adult mouse striatum saline

tag: genotype/variation

value: Drd2-TRAP; G9a fl/fl

value: 2-5 month old

value: TRAP (L10a-GFP)

value: saline

tag: tissue

value: Striatum(Drd2 MSNs)

tag: molecule subtype

value: polyribosome associated mRNA


title: Drd2-TRAP; G9a fl/fl Cocaine 3

description:
D2_348_Con_Coc
Gene expression from Drd2 MSNs

value: 20 mg/kg/day cocaine


title: P9S3L2H1: ChronicGeneralizedControl

tag: diagnosis

value: Chronic

tag: extent

tag: condition


title: Fkh1Myc_anti_Myc_rep_2

description: α-Myc (9E10) ChIP-chip of Fkh1-Myc

value: 9E10 monoclonal


title: Fkh1Myc_anti_Myc_rep_1

description: α-Myc (9E10) ChIP-chip of Fkh1-Myc


title: P10S1L2H1: ChronicLocalizedAffected

value: Affected

tag: labelbatch


title: WT_anti_Myc_rep_1

description: α-Myc (9E10) ChIP-chip of WT; no-epitope control

source_name: 9E10 ChIP DNA from WT cells

value: ura3::BrdU‐Inc (URA3) bar1Δ::hisG

source_name: Total DNA from WT cells


title: P9S1L2H1: ChronicGeneralizedAffected

value: Generalized


title: P8S2L2H1: ChronicGeneralizedAffected


title: P9S2L2H1: ChronicGeneralizedAffected


title: P7S3L1H1: AggressiveGeneralizedAffected

value: Aggressive


title: Drd-TRAP; Drd2-Cre; G9a fl/fl Cocaine 1

description:
D2_347_Mut_Coc
Gene expression from Drd2 MSNs

tag: strain background

value: Mix between C57BL/6 (G9a line) and 129/Sv (BAC line); 2 generations of C57BL/6 backcrossing

value: Drd-TRAP; Drd2-Cre; G9a fl/fl

tag: gender

value: male

tag: age


title: Drd2-TRAP; G9a fl/fl Cocaine 1

description:
D2_245_Con_Coc
Gene expression from Drd2 MSNs

tag: tag

tag: treated with


title: Drd2-TRAP; G9a fl/fl Saline 1

description:
D2_246_Con_Sal
Gene expression from Drd2 MSNs


title: Drd2-TRAP; G9a fl/fl Cocaine 2

description:
D2_344_Con_Coc
Gene expression from Drd2 MSNs


title: Drd2-TRAP; G9a fl/fl Saline 2

description:
D2_345_Con_Sal
Gene expression from Drd2 MSNs


title: WT_G1_anti_Fkh_rep_3

description: α-Fkh ChIP-chip of G1-phase arrested WT cells

source_name: Fkh ChIP DNA from α-factor-arrested WT cells

treatment_protocol: incubated with α-factor for 3hrs

tag: genotype

tag: strain

tag: chip antibody

value: anti-Fkh polyclonal

source_name: Total DNA from α-factor-arrested WT cells


title: P7S2L1H1: AggressiveGeneralizedAffected

tag: patient

tag: specimen

tag: hybridizebatch


title: P14S1L3H1: AggressiveLocalizedAffected

description: P14S1L3H1 (this sample failed QC and was excluded from the final analysis)

tag: biopsyid

value: Localized


title: WT_anti_Myc_rep_2


title: WT_anti_Myc_rep_3


title: WT_G1_anti_Fkh_rep_1


title: Drd1-TRAP; G9a fl/fl Saline 2

description:
D1_257_Con_Sal
Gene expression from Drd1 MSNs

source_name: D1 G9a Control adult mouse striatum saline

tag: genotype/variation

value: Drd1-TRAP; G9a fl/fl

value: 2-5 month old

tag: tissue

value: Striatum (Drd1 MSNs)

tag: molecule subtype


title: Drd1-TRAP; Drd1-Cre; G9a fl/fl Cocaine 4

description:
D1_255_Mut_Coc
Gene expression from Drd1 MSNs

source_name: D1 G9a Mutant adult mouse striatum cocaine

value: Drd1-TRAP; Drd1-Cre; G9a fl/fl

value: TRAP (L10a-GFP)


title: WT_G1_anti_Fkh_rep_2


title: P5S3L1H1: ChronicLocalizedAffected

tag: diagnosis

tag: extent

tag: condition


title: Drd1-TRAP; G9a fl/fl Cocaine 4

description:
D1_256_Con_Coc
Gene expression from Drd1 MSNs

source_name: D1 G9a Control adult mouse striatum cocaine

tag: strain background

tag: gender

value: 20 mg/kg/day cocaine

value: polyribosome associated mRNA


title: Drd1-Trap; Drd1-Cre; G9a fl/fl Saline 3

description:
D1_246_Mut_Sal
Gene expression from Drd1 MSNs

source_name: D1 G9a Mutant adult mouse striatum saline

value: Drd1-Trap; Drd1-Cre; G9a fl/fl

tag: age

tag: tag

value: saline


title: Drd1-TRAP; Drd1-Cre; G9a fl/fl Cocaine 3

description:
D1_244_Mut_Coc
Gene expression from Drd1 MSNs

tag: treated with


title: P7S1L1H1: AggressiveGeneralizedAffected

value: Affected

tag: labelbatch


title: P5S2L1H1: ChronicLocalizedAffected

value: Chronic


title: doxycycline replicate C, card A

city: Boston

first: Michael

last: Xiang

state: MA

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: SAMPLE 6

data_processing:
Non-normalized data consist of raw Ct values that were reported for each miRNA assayed. Ct values above 30 are considered unreliable, according to the experience of the Molecular Diagnostics Laboratory, due to high intra-sample variability in this regime. Samples that did not show any amplification up to 40 cycles were labeled 'Undetermined'.  Normalized data were generated by subtracting the average Ct values of the housekeeping genes RNU44 and RNU48 in the sample from the Ct value of each miRNA. Fold-change data were calculated using the delta-delta Ct value method and are shown relative to untreated sample replicate A.
Normalized data report miRNA Ct values normalized against housekeeping genes (average Ct values of RNU44 and RNU48 for a particular sample). Fold-change data are relative to sample 1 (untreated condition, replicate A).

label: FAM

source_name: MCF-10A Dox-on cells_test

label_protocol: Generation of cDNA and TaqMan qRT-PCR reactions were performed by the Dana-Farber Cancer Institute Molecular Diagnostics Laboratory as specified by the manufacturer. Briefly, 60ng of input RNA was reverse-transcribed using miRNA-specific stem-loop primers. Next, 12 cycles of pre-amplification reactions were performed using miRNA-specific forward primers and a universal reverse primer. Finally, the pre-amplification reactions were diluted, transferred to 384-well plates via microfluidic channels, and subjected to TaqMan miRNA amplification reactions using miRNA-specific FAM-labeled TaqMan probes.

extract_protocol: Total RNA was harvested using the MicroRNeasy Mini Kit (Qiagen).

tag: cell type

value: Doxycycline-inducible MCF-10A cells

value: 2μg/ml doxycycline for 48hr


title: Drd1-TRAP; Drd1-Cre; G9a fl/fl Cocaine 2

description:
D1_239_Mut_Coc
Gene expression from Drd1 MSNs

value: Mix between C57BL/6 (G9a line) and 129/Sv (BAC line); 2 generations of C57BL/6 backcrossing


title: doxycycline replicate B, card A

description: SAMPLE 5


title: WT_S_anti_Fkh_rep_2

description: α-Fkh ChIP-chip of S-phase arrested WT cells

source_name: Fkh ChIP DNA from Hydroxyurea-arrested WT cells

treatment_protocol: incubated with hydroxyurea for 3hrs

tag: genotype

value: ura3::BrdU‐Inc (URA3) bar1Δ::hisG

tag: strain

tag: chip antibody

source_name: Total DNA from Hydroxyurea-arrested WT cells


title: WT_S_anti_Fkh_rep_3

value: anti-Fkh polyclonal


title: P5S1L1H1: ChronicLocalizedControl

tag: patient

tag: specimen

tag: biopsyid

value: Localized

value: Control

tag: hybridizebatch


title: WT_G2M_anti_Fkh_rep_3

description: α-Fkh ChIP-chip of G2/M-phase arrested WT cells

source_name: Fkh ChIP DNA from Nocodazole-arrested WT cells

treatment_protocol: incubated with nocodazole for 3hrs

source_name: Total DNA from Nocodazole-arrested WT cells


title: WT_S_anti_Fkh_rep_1


title: Drd1-TRAP; G9a fl/fl Saline 1

description:
D1_203_Con_Sal
Gene expression from Drd1 MSNs

tag: genotype/variation

value: Drd1-TRAP; G9a fl/fl

value: male

value: 2-5 month old

tag: tissue

tag: molecule subtype


title: Drd1-TRAP; G9a fl/fl Cocaine 3

description:
D1_226_Con_Coc
Gene expression from Drd1 MSNs

tag: strain background

value: TRAP (L10a-GFP)

value: Striatum (Drd1 MSNs)


title: WT_G2M_anti_Fkh_rep_1


title: doxycycline replicate A, card A

description: SAMPLE 4


title: WT_G2M_anti_Fkh_rep_2


title: untreated replicate B, card A

description: SAMPLE 2

source_name: MCF-10A Dox-on cells_control

value: none (untreated control)


title: fkh2D_anti_Fkh_rep_3

description: α-Fkh ChIP-chip of fkh2Δ

source_name: Fkh ChIP DNA from fkh2Δ cells

value: ura3::BrdU-Inc (URA3) bar1Δ::hisG fkh2Δ::HIS3

source_name: Total DNA from fkh2Δ cells


title: untreated replicate C, card A

description: SAMPLE 3


title: doxycycline replicate C, card B

description: SAMPLE 6

data_processing:
Non-normalized data consist of raw Ct values that were reported for each miRNA assayed. Ct values above 30 are considered unreliable, according to the experience of the Molecular Diagnostics Laboratory, due to high intra-sample variability in this regime. Samples that did not show any amplification up to 40 cycles were labeled “Undetermined.” Normalized data were generated by subtracting the average Ct values of the housekeeping genes RNU44 and RNU48 in the sample from the Ct value of each miRNA. Fold-change data were calculated using the delta-delta Ct value method and are shown relative to untreated sample replicate A.
Normalized data report miRNA Ct values normalized against housekeeping genes (average Ct values of RNU44 and RNU48 for a particular sample). Fold-change data are relative to sample 1 (untreated condition, replicate A).


title: doxycycline replicate B, card B

description: SAMPLE 5


title: fkh2D_anti_Fkh_rep_2

description: α-Fkh ChIP-chip of fkh2Δ


title: untreated replicate A, card A

description: SAMPLE 1


title: doxycycline replicate A, card B

description: SAMPLE 4


title: fkh2D_anti_Fkh_rep_1

description: α-Fkh ChIP-chip of fkh2Δ


title: fkh1D_anti_Fkh_rep_2

description: α-Fkh ChIP-chip of fkh1Δ

source_name: Fkh ChIP DNA from fkh1Δ cells

value: ura3::BrdU-Inc (URA3) bar1Δ::hisG fkh1Δ::KanMX

source_name: Total DNA from fkh1Δ cells


title: fkh1D_anti_Fkh_rep_3

description: α-Fkh ChIP-chip of fkh1Δ


title: P8S1L1H1: ChronicGeneralizedAffected

source_name: periodontal tissue

tag: diagnosis

tag: extent

value: Generalized

tag: condition

value: Affected


title: untreated replicate C, card B

description: SAMPLE 3

value: Doxycycline-inducible MCF-10A cells

tag: treated with


title: Drd1-Trap; Drd1-Cre; G9a fl/fl Saline 2

description:
D1_164_Mut_Sal
Gene expression from Drd1 MSNs

value: Drd1-Trap; Drd1-Cre; G9a fl/fl

tag: gender

tag: age

tag: tag

value: saline

value: polyribosome associated mRNA


title: Drd1-TRAP; G9a fl/fl Cocaine 2

description:
D1_150_Con_Coc
Gene expression from Drd1 MSNs

value: Mix between C57BL/6 (G9a line) and 129/Sv (BAC line); 2 generations of C57BL/6 backcrossing

value: 20 mg/kg/day cocaine


title: untreated replicate B, card B

description: SAMPLE 2

tag: cell type


title: Drd1-TRAP; Drd1-Cre; G9a fl/fl Cocaine 1

description:
D1_200_Mut_Coc
Gene expression from Drd1 MSNs

value: Drd1-TRAP; Drd1-Cre; G9a fl/fl


title: S. pombe  cells, lacking  isp7+ - replicate 3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

institute: Tel Aviv University

description:
Cells lacking isp7+ were grown to mid-log phase in minimal medium, replicate 3
Gene expression of Cells lacking isp7+

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.5) Copyright © 2010).

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: S. pombe strains were grown  to mid-log phase at  30 degree in Edinburgh minimal medium (EMM, 5 g/L NH4Cl).

extract_protocol: RNA was prepared using the hot phenol method. RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

treatment_protocol: WT and cells lacking isp7+ were grown as described above/

tag: genotype

value: isp7+ null


title: fkh1D_anti_Fkh_rep_1

description: α-Fkh ChIP-chip of fkh1Δ

tag: strain

tag: chip antibody

value: anti-Fkh polyclonal


title: S. pombe  cells, lacking  isp7+ - replicate 1

description:
Cells lacking isp7+ were grown to mid-log phase in minimal medium, replicate 1
Gene expression of Cells lacking isp7+

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: S. pombe  cells, lacking  isp7+ - replicate 2

description:
Cells lacking isp7+ were grown to mid-log phase in minimal medium, replicate 2
Gene expression of Cells lacking isp7+


title: untreated replicate A, card B

description: SAMPLE 1


title: Control Human Serum 3

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

description: miRNA expression

hyb_protocol: The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately cooled to 0 °C. Each 45 mL sample was hybridized onto a microarray at 55 °C for 21 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C, followed by an acetonitrile wash for 10 sec at RT to dry the slides completely.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, No XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid:029297_D_F_20101116) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human serum

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 6 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 h. The labeled samples were dried completely in a vaccum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: RNA from serum was isolated using the mirVana PARIS RNA Isolation Kit (Ambion). In all instances RNA isolation was performed according to the manufacturer’s instructions using 300 ml serum.

tag: sample type

value: serum

tag: disease state

value: control


title: Drd1-TRAP; G9a fl/fl Cocaine 1

description:
D1_112_Con_Coc
Gene expression from Drd1 MSNs

tag: genotype/variation

value: Drd1-TRAP; G9a fl/fl

value: male

value: 2-5 month old

value: TRAP (L10a-GFP)

value: Striatum (Drd1 MSNs)


title: Control Human Serum 5

description: miRNA expression


title: Control Human Serum 2

description: miRNA expression


title: Ovarian Cancer Human Serum 2

description: miRNA expression

value: ovarian cancer


title: Control Human Serum 4

description: miRNA expression


title: Ovarian Cancer Human Serum 1

description: miRNA expression


title: S. pombe  wild type cells, control - replicate 3

description:
Wild type cells were grown to mid-log phase in minimal medium, replicate 3
Gene expression of WT

value: wild type


title: Ovarian Cancer Human Serum 4

description: miRNA expression


title: fkh1Dfkh2D_anti_Fkh_rep_3

description: α-Fkh ChIP-chip of fkh1Δfkh2Δ; no-epitope control

source_name: Fkh ChIP DNA from fkh1Δfkh2Δ cells

value: ura3::BrdU-Inc (URA3) bar1Δ::hisG fkh1Δ::KanMX fkh2Δ::HIS3

source_name: Total DNA from fkh1Δfkh2Δ cells


title: WT_anti_Fkh_rep_3

description: α-Fkh ChIP-chip of WT

source_name: Fkh ChIP DNA from WT cells

value: ura3::BrdU‐Inc (URA3) bar1Δ::hisG

source_name: Total DNA from WT cells


title: Ovarian Cancer Human Serum 5

description: miRNA expression


title: Drd1-TRAP; Drd1-Cre; G9a fl/fl Saline 1

description:
D1_111_Mut_Sal
Gene expression from Drd1 MSNs

source_name: D1 G9a Mutant adult mouse striatum saline

value: saline

tag: tissue

value: polyribosome associated mRNA


title: S. pombe  wild type cells, control - replicate 2

description:
Wild type cells were grown to mid-log phase in minimal medium, replicate 2
Gene expression of WT


title: fkh1Dfkh2D_anti_Fkh_rep_2


title: S. pombe  wild type cells, control - replicate 1

description:
Wild type cells were grown to mid-log phase in minimal medium, replicate 1
Gene expression of WT


title: genomic DNA from Tregs Purified WBC subtype (Treg2280)

status: Public on Feb 04 2014

first: William

middle: P

last: Accomando

address: Kresge Bldg 911, 677 Huntington Ave

department: Epidemiology

institute: Harvard School of Public Health

description:
Treg2280
Tregs Purified WBC subtype Treg2280
Illumina VeraCode GGMA

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
Illumina GenomeStudio v2010.3
Unmethylated and methylated signal intensities are reported in a supplementary file on the Series record.

label: Cy5 and Cy3

source_name: Tregs Purified WBC subtype Treg2280

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted using QIAGEN Dneasy blood and tissue kit according to standard instructions

treatment_protocol: Leukocyte subtypes were purified via magnetic activated cell sorting (MACS) using kits from Miltenyi Biotec

value: Purified WBC subtype

value: normal

tag: sample subtype

value: Tregs


title: genomic DNA from Citrate, o/n at room temp Human whole blood (3082CitRt)

description:
3082CitRt
Citrate, o/n at room temp Human whole blood 3082CitRt
Illumina VeraCode GGMA

value: Human whole blood

value: Citrate, o/n at room temp


title: genomic DNA from CD16+ NK cells Purified WBC subtype (NK16p2589)

description:
NK16p2589
CD16+ NK cells Purified WBC subtype NK16p2589
Illumina VeraCode GGMA

value: CD16+ NK cells


title: fkh1Dfkh2D_anti_Fkh_rep_1

value: anti-Fkh polyclonal


title: genomic DNA from Heparin, o/n at 4C Human whole blood (3093Hep4C)

description:
3093Hep4C
Heparin, o/n at 4C Human whole blood 3093Hep4C
Illumina VeraCode GGMA

value: Heparin, o/n at 4C


title: Control Human Serum 1

description: miRNA expression

value: serum

value: control


title: WT_anti_Fkh_rep_2

description: α-Fkh ChIP-chip of WT


title: genomic DNA from Citrate, o/n at -80C Human whole blood (3159Cit80)

description:
3159Cit80
Citrate, o/n at -80C Human whole blood 3159Cit80
Illumina VeraCode GGMA

value: Citrate, o/n at -80C


title: genomic DNA from Heparin, o/n at 4C Human whole blood (3021Hep4C)

description:
3021Hep4C
Heparin, o/n at 4C Human whole blood 3021Hep4C
Illumina VeraCode GGMA


title: WT_anti_Fkh_rep_1

description: α-Fkh ChIP-chip of WT


title: genomic DNA from Pan-NK cells Purified WBC subtype (NKpan2503)

description:
NKpan2503
Pan-NK cells Purified WBC subtype NKpan2503
Illumina VeraCode GGMA

value: Pan-NK cells


title: genomic DNA from Heparin, Fresh Human whole blood (3021HepFr)

description:
3021HepFr
Heparin, Fresh Human whole blood 3021HepFr
Illumina VeraCode GGMA

value: Heparin, Fresh


title: genomic DNA from Heparin, Fresh Human whole blood (3082HepFr)

description:
3082HepFr
Heparin, Fresh Human whole blood 3082HepFr
Illumina VeraCode GGMA


title: genomic DNA from Granuloctyes Purified WBC subtype (Gran2271)

description:
Gran2271
Granuloctyes Purified WBC subtype Gran2271
Illumina VeraCode GGMA

value: Granuloctyes


title: genomic DNA from Citrate, o/n at 4C Human whole blood (3177Cit4C)

description:
3177Cit4C
Citrate, o/n at 4C Human whole blood 3177Cit4C
Illumina VeraCode GGMA

value: Citrate, o/n at 4C


title: genomic DNA from Heparin, o/n at 4C Human whole blood (3045Hep4C)

description:
3045Hep4C
Heparin, o/n at 4C Human whole blood 3045Hep4C
Illumina VeraCode GGMA


title: genomic DNA from Pan-T cells Purified WBC subtype (Tpan1795)

description:
Tpan1795
Pan-T cells Purified WBC subtype Tpan1795
Illumina VeraCode GGMA

value: Pan-T cells


title: genomic DNA from Heparin, o/n at 4C Human whole blood (3177Hep4C)

description:
3177Hep4C
Heparin, o/n at 4C Human whole blood 3177Hep4C
Illumina VeraCode GGMA


title: genomic DNA from Monocytes Purified WBC subtype (Mono1827)

description:
Mono1827
Monocytes Purified WBC subtype Mono1827
Illumina VeraCode GGMA

source_name: Monocytes Purified WBC subtype Mono1827

value: Monocytes


title: genomic DNA from CD16- NK cells Purified WBC subtype (NK16m2577)

description:
NK16m2577
CD16- NK cells Purified WBC subtype NK16m2577
Illumina VeraCode GGMA

value: Purified WBC subtype

value: CD16- NK cells


title: genomic DNA from CD8+ NK cells Purified WBC subtype (NK8p2614)

description:
NK8p2614
CD8+ NK cells Purified WBC subtype NK8p2614
Illumina VeraCode GGMA

value: normal

value: CD8+ NK cells


title: genomic DNA from EDTA, o/n at 4C Human whole blood (3093EDTA4C)

description:
3093EDTA4C
EDTA, o/n at 4C Human whole blood 3093EDTA4C
Illumina VeraCode GGMA

value: Human whole blood

value: EDTA, o/n at 4C


title: genomic DNA from Basophils Purified WBC subtype (Baso2492)

description:
Baso2492
Basophils Purified WBC subtype Baso2492
Illumina VeraCode GGMA

source_name: Basophils Purified WBC subtype Baso2492

value: Basophils


title: genomic DNA from EDA, o/n at -80C Human whole blood (3021EDTA80)

description:
3021EDTA80
EDA, o/n at -80C Human whole blood 3021EDTA80
Illumina VeraCode GGMA

value: EDA, o/n at -80C


title: genomic DNA from Granulocytes Purified WBC subtype (Gran1150)

description:
Gran1150
Granulocytes Purified WBC subtype Gran1150
Illumina VeraCode GGMA

value: Granulocytes


title: genomic DNA from Eosinophils Purified WBC subtype (Eos2042)

description:
Eos2042
Eosinophils Purified WBC subtype Eos2042
Illumina VeraCode GGMA

value: Eosinophils


title: genomic DNA from Pan-NK cells Purified WBC subtype (NKpan2510)

description:
NKpan2510
Pan-NK cells Purified WBC subtype NKpan2510
Illumina VeraCode GGMA


title: genomic DNA from Citrate, o/n at 4C Human whole blood (3093Cit4C)

description:
3093Cit4C
Citrate, o/n at 4C Human whole blood 3093Cit4C
Illumina VeraCode GGMA


title: Ovarian Cancer Human Serum 3

description: miRNA expression

value: serum

value: ovarian cancer


title: genomic DNA from Citrate, o/n at room temp Human whole blood (3093CitRt)

description:
3093CitRt
Citrate, o/n at room temp Human whole blood 3093CitRt
Illumina VeraCode GGMA

value: Citrate, o/n at room temp


title: genomic DNA from Citrate, o/n at room temp Human whole blood (3159CitRt)

description:
3159CitRt
Citrate, o/n at room temp Human whole blood 3159CitRt
Illumina VeraCode GGMA


title: genomic DNA from EDTA, o/n at 4C Human whole blood (3159EDTA4C)

description:
3159EDTA4C
EDTA, o/n at 4C Human whole blood 3159EDTA4C
Illumina VeraCode GGMA


title: genomic DNA from Monocytes Purified WBC subtype (Mono1993)

description:
Mono1993
Monocytes Purified WBC subtype Mono1993
Illumina VeraCode GGMA

source_name: Monocytes Purified WBC subtype Mono1993


title: genomic DNA from CD8+ T-cells Purified WBC subtype (Tc2007)

description:
Tc2007
CD8+ T-cells Purified WBC subtype Tc2007
Illumina VeraCode GGMA

value: CD8+ T-cells


title: genomic DNA from EDTA, o/n at room temp Human whole blood (3177EDTARt)

description:
3177EDTARt
EDTA, o/n at room temp Human whole blood 3177EDTARt
Illumina VeraCode GGMA

value: EDTA, o/n at room temp


title: genomic DNA from Heparin, o/n at room temp Human whole blood (3082HepRt)

description:
3082HepRt
Heparin, o/n at room temp Human whole blood 3082HepRt
Illumina VeraCode GGMA

value: Heparin, o/n at room temp


title: genomic DNA from CD8- NK cells Purified WBC subtype (NK8m2631)

description:
NK8m2631
CD8- NK cells Purified WBC subtype NK8m2631
Illumina VeraCode GGMA

value: CD8- NK cells


title: genomic DNA from Citrate, o/n at room temp Human whole blood (3177CitRt)

description:
3177CitRt
Citrate, o/n at room temp Human whole blood 3177CitRt
Illumina VeraCode GGMA


title: genomic DNA from Granulocytes Purified WBC subtype (Gran1149)

description:
Gran1149
Granulocytes Purified WBC subtype Gran1149
Illumina VeraCode GGMA

value: Purified WBC subtype


title: genomic DNA from Pan-NK cells Purified WBC subtype (NKpan1869)

description:
NKpan1869
Pan-NK cells Purified WBC subtype NKpan1869
Illumina VeraCode GGMA

value: Pan-NK cells


title: genomic DNA from Granulocytosis Reconstruction mixture

description:
X8942297054_R04C01
Infinium Type I and Type II Probes
Granulocytosis Reconstruction mixture Gosis

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

data_processing:
Unmethylated and methylated signal intensities generated using methylumi in R (see supplementary file on the Series record).
Average Betas (not normalized) generated using GenomeStudio v2010.3

treatment_protocol: Leukocyte subtypes were purified via magnetic activated cell sorting (MACS) using kits from Miltenyi Biotec; venous whole blood was collected into Heparin

value: Reconstruction mixture

value: normal

value: Granulocytosis


title: genomic DNA from Citrate, Fresh Human whole blood (3045CitFr)

description:
3045CitFr
Citrate, Fresh Human whole blood 3045CitFr
Illumina VeraCode GGMA

value: Human whole blood

value: Citrate, Fresh


title: genomic DNA from Heparin, o/n at -80C Human whole blood (3045Hep80)

description:
3045Hep80
Heparin, o/n at -80C Human whole blood 3045Hep80
Illumina VeraCode GGMA

value: Heparin, o/n at -80C


title: genomic DNA from Citrate, o/n at -80C Human whole blood (3021Cit80)

description:
3021Cit80
Citrate, o/n at -80C Human whole blood 3021Cit80
Illumina VeraCode GGMA

value: Citrate, o/n at -80C


title: genomic DNA from EDTA, o/n at 4C Human whole blood (3177EDTA4C)

description:
3177EDTA4C
EDTA, o/n at 4C Human whole blood 3177EDTA4C
Illumina VeraCode GGMA

value: EDTA, o/n at 4C


title: genomic DNA from CD8+ NK cells Purified WBC subtype (NK8p2623)

description:
NK8p2623
CD8+ NK cells Purified WBC subtype NK8p2623
Illumina VeraCode GGMA

value: CD8+ NK cells


title: genomic DNA from Neutrophils Purified WBC subtype (Neut1147)

description:
Neut1147
Neutrophils Purified WBC subtype Neut1147
Illumina VeraCode GGMA

value: Neutrophils


title: genomic DNA from Monocytes Purified WBC subtype (Mono2639)

description:
Mono2639
Monocytes Purified WBC subtype Mono2639
Illumina VeraCode GGMA

source_name: Monocytes Purified WBC subtype Mono2639

value: Monocytes


title: genomic DNA from Heparin, Fresh Human whole blood 3177

description:
X8942297054_R06C02
Infinium Type I and Type II Probes
Heparin, Fresh Human whole blood 3177HepFr

value: Heparin, Fresh


title: genomic DNA from Granulocytopenia Reconstruction mixture

description:
X8942297054_R03C01
Infinium Type I and Type II Probes
Granulocytopenia Reconstruction mixture Gpen

value: Granulocytopenia


title: genomic DNA from NKT cells Purified WBC subtype (NKT2616)

description:
NKT2616
NKT cells Purified WBC subtype NKT2616
Illumina VeraCode GGMA

source_name: NKT cells Purified WBC subtype NKT2616

value: NKT cells


title: genomic DNA from Heparin, Fresh Human whole blood 3082

description:
X8942297054_R03C02
Infinium Type I and Type II Probes
Heparin, Fresh Human whole blood 3082HepFr


title: genomic DNA from Heparin, Fresh Human whole blood 3159

description:
X8942297054_R05C02
Infinium Type I and Type II Probes
Heparin, Fresh Human whole blood 3159HepFr


title: genomic DNA from Heparin, Fresh Human whole blood 3093

description:
X8942297054_R04C02
Infinium Type I and Type II Probes
Heparin, Fresh Human whole blood 3093HepFr


title: genomic DNA from Monocytosis Reconstruction mixture

description:
X8942297054_R06C01
Infinium Type I and Type II Probes
Monocytosis Reconstruction mixture Mosis

value: Monocytosis


title: genomic DNA from Heparin, Fresh Human whole blood 3045

description:
X8942297054_R02C02
Infinium Type I and Type II Probes
Heparin, Fresh Human whole blood 3045HepFr


title: genomic DNA from Normal Reconstruction mixture Reconstruction mixture

description:
X8942297054_R01C01
Infinium Type I and Type II Probes
Normal Reconstruction mixture Reconstruction mixture NormMix

value: Normal Reconstruction mixture


title: genomic DNA from EDA, o/n at -80C Human whole blood (3159EDTA80)

description:
3159EDTA80
EDA, o/n at -80C Human whole blood 3159EDTA80
Illumina VeraCode GGMA

value: EDA, o/n at -80C


title: genomic DNA from B-cells Purified WBC subtype (B1877)

description:
B1877
B-cells Purified WBC subtype B1877
Illumina VeraCode GGMA

source_name: B-cells Purified WBC subtype B1877

value: Purified WBC subtype

value: B-cells


title: genomic DNA from Heparin, Fresh Human whole blood 3021

description:
X8942297054_R01C02
Infinium Type I and Type II Probes
Heparin, Fresh Human whole blood 3021HepFr

value: normal


title: genomic DNA from B-cell Lymphopenia Reconstruction mixture

description:
X8942297054_R05C01
Infinium Type I and Type II Probes
B-cell Lymphopenia Reconstruction mixture Bpen

value: Reconstruction mixture

value: B-cell Lymphopenia


title: genomic DNA from B-cells Purified WBC subtype (B1690)

description:
B1690
B-cells Purified WBC subtype B1690
Illumina VeraCode GGMA

source_name: B-cells Purified WBC subtype B1690


title: genomic DNA from Citrate, o/n at room temp Human whole blood (3021CitRt)

description:
3021CitRt
Citrate, o/n at room temp Human whole blood 3021CitRt
Illumina VeraCode GGMA

value: Human whole blood

value: Citrate, o/n at room temp


title: genomic DNA from Citrate, o/n at -80C Human whole blood (3045Cit80)

description:
3045Cit80
Citrate, o/n at -80C Human whole blood 3045Cit80
Illumina VeraCode GGMA

value: Citrate, o/n at -80C


title: genomic DNA from Neutrophils Purified WBC subtype (Neut2270)

description:
Neut2270
Neutrophils Purified WBC subtype Neut2270
Illumina VeraCode GGMA


title: genomic DNA from Heparin, o/n at room temp Human whole blood (3177HepRt)

description:
3177HepRt
Heparin, o/n at room temp Human whole blood 3177HepRt
Illumina VeraCode GGMA

value: Heparin, o/n at room temp


title: genomic DNA from Monocytosis Reconstruction mixture (Mosis)

description:
Mosis
Monocytosis Reconstruction mixture Mosis
Illumina VeraCode GGMA


title: genomic DNA from NKT cells Purified WBC subtype (NKT2572)

description:
NKT2572
NKT cells Purified WBC subtype NKT2572
Illumina VeraCode GGMA

source_name: NKT cells Purified WBC subtype NKT2572


title: genomic DNA from Heparin, o/n at -80C Human whole blood (3177Hep80)

description:
3177Hep80
Heparin, o/n at -80C Human whole blood 3177Hep80
Illumina VeraCode GGMA

value: Heparin, o/n at -80C


title: genomic DNA from Heparin, o/n at room temp Human whole blood (3159HepRt)

description:
3159HepRt
Heparin, o/n at room temp Human whole blood 3159HepRt
Illumina VeraCode GGMA


title: genomic DNA from Pan-T cells Purified WBC subtype (Tpan1612)

description:
Tpan1612
Pan-T cells Purified WBC subtype Tpan1612
Illumina VeraCode GGMA

value: Pan-T cells


title: genomic DNA from Neutrophils Purified WBC subtype (Neut0612)

description:
Neut0612
Neutrophils Purified WBC subtype Neut0612
Illumina VeraCode GGMA

value: Neutrophils


title: genomic DNA from Moderate T-cell Lymphopenia Reconstruction mixture (MTpen)

description:
MTpen
Moderate T-cell Lymphopenia Reconstruction mixture MTpen
Illumina VeraCode GGMA

value: Moderate T-cell Lymphopenia


title: genomic DNA from Citrate, Fresh Human whole blood (3177CitFr)

description:
3177CitFr
Citrate, Fresh Human whole blood 3177CitFr
Illumina VeraCode GGMA

value: Citrate, Fresh


title: genomic DNA from Granulocytosis Reconstruction mixture (Gosis)

description:
Gosis
Granulocytosis Reconstruction mixture Gosis
Illumina VeraCode GGMA

value: Granulocytosis


title: genomic DNA from Pan-T cells Purified WBC subtype (Tpan2294)

description:
Tpan2294
Pan-T cells Purified WBC subtype Tpan2294
Illumina VeraCode GGMA


title: genomic DNA from CD8+ T-cells Purified WBC subtype (Tc2636)

description:
Tc2636
CD8+ T-cells Purified WBC subtype Tc2636
Illumina VeraCode GGMA

value: CD8+ T-cells


title: genomic DNA from CD8- NK cells Purified WBC subtype (NK8m2641)

description:
NK8m2641
CD8- NK cells Purified WBC subtype NK8m2641
Illumina VeraCode GGMA

value: CD8- NK cells


title: genomic DNA from Heparin, o/n at 4C Human whole blood (3082Hep4C)

description:
3082Hep4C
Heparin, o/n at 4C Human whole blood 3082Hep4C
Illumina VeraCode GGMA

value: Heparin, o/n at 4C


title: genomic DNA from Normal Reconstruction mixture Reconstruction mixture (NormMix)

description:
NormMix
Normal Reconstruction mixture Reconstruction mixture NormMix
Illumina VeraCode GGMA

value: Normal Reconstruction mixture


title: genomic DNA from Eosinophils Purified WBC subtype (Eos2275)

description:
Eos2275
Eosinophils Purified WBC subtype Eos2275
Illumina VeraCode GGMA

value: Purified WBC subtype

value: normal

value: Eosinophils


title: genomic DNA from Tregs Purified WBC subtype (Treg21692)

description:
Treg21692
Tregs Purified WBC subtype Treg21692
Illumina VeraCode GGMA

source_name: Tregs Purified WBC subtype Treg21692

value: Tregs


title: genomic DNA from Severe T-cell Lymphopenia Reconstruction mixture (STpen)

description:
STpen
Severe T-cell Lymphopenia Reconstruction mixture STpen
Illumina VeraCode GGMA

value: Reconstruction mixture

value: Severe T-cell Lymphopenia


title: genomic DNA from Granulocytes Purified WBC subtype (Gran1146)

description:
Gran1146
Granulocytes Purified WBC subtype Gran1146
Illumina VeraCode GGMA

value: Granulocytes


title: genomic DNA from Heparin, Fresh Human whole blood (3045HepFr)

description:
3045HepFr
Heparin, Fresh Human whole blood 3045HepFr
Illumina VeraCode GGMA

value: Human whole blood

value: Heparin, Fresh


title: genomic DNA from Tregs Purified WBC subtype (Treg1782)

description:
Treg1782
Tregs Purified WBC subtype Treg1782
Illumina VeraCode GGMA

source_name: Tregs Purified WBC subtype Treg1782


title: genomic DNA from Heparin, o/n at -80C Human whole blood (3021Hep80)

description:
3021Hep80
Heparin, o/n at -80C Human whole blood 3021Hep80
Illumina VeraCode GGMA

value: Heparin, o/n at -80C


title: genomic DNA from Heparin, o/n at room temp Human whole blood (3093HepRt)

description:
3093HepRt
Heparin, o/n at room temp Human whole blood 3093HepRt
Illumina VeraCode GGMA

value: Heparin, o/n at room temp


title: genomic DNA from Pan-T cells Purified WBC subtype (Tpan1779)

description:
Tpan1779
Pan-T cells Purified WBC subtype Tpan1779
Illumina VeraCode GGMA

value: Pan-T cells


title: genomic DNA from Heparin, o/n at room temp Human whole blood (3045HepRt)

description:
3045HepRt
Heparin, o/n at room temp Human whole blood 3045HepRt
Illumina VeraCode GGMA


title: genomic DNA from Basophils Purified WBC subtype (Baso1889)

description:
Baso1889
Basophils Purified WBC subtype Baso1889
Illumina VeraCode GGMA

source_name: Basophils Purified WBC subtype Baso1889

value: Basophils


title: genomic DNA from CD8- NK cells Purified WBC subtype (NK8m4229)

description:
NK8m4229
CD8- NK cells Purified WBC subtype NK8m4229
Illumina VeraCode GGMA


title: genomic DNA from Citrate, o/n at 4C Human whole blood (3159Cit4C)

description:
3159Cit4C
Citrate, o/n at 4C Human whole blood 3159Cit4C
Illumina VeraCode GGMA

value: Citrate, o/n at 4C


title: genomic DNA from EDTA, o/n at room temp Human whole blood (3021EDTARt)

description:
3021EDTARt
EDTA, o/n at room temp Human whole blood 3021EDTARt
Illumina VeraCode GGMA

value: EDTA, o/n at room temp


title: genomic DNA from EDTA, Fresh Human whole blood (3082EDTAFr)

description:
3082EDTAFr
EDTA, Fresh Human whole blood 3082EDTAFr
Illumina VeraCode GGMA

value: EDTA, Fresh


title: genomic DNA from CD16+ NK cells Purified WBC subtype (NK16p2297)

description:
NK16p2297
CD16+ NK cells Purified WBC subtype NK16p2297
Illumina VeraCode GGMA

value: CD16+ NK cells


title: genomic DNA from Severe T-cell Lymphopenia Reconstruction mixture

description:
X8942297054_R02C01
Infinium Type I and Type II Probes
Severe T-cell Lymphopenia Reconstruction mixture STpen


title: genomic DNA from Citrate, Fresh Human whole blood (3082CitFr)

description:
3082CitFr
Citrate, Fresh Human whole blood 3082CitFr
Illumina VeraCode GGMA

value: Citrate, Fresh


title: genomic DNA from CD8+ NK cells Purified WBC subtype (NK8p2619)

description:
NK8p2619
CD8+ NK cells Purified WBC subtype NK8p2619
Illumina VeraCode GGMA

value: Purified WBC subtype

value: normal

value: CD8+ NK cells


title: genomic DNA from CD8+ T-cells Purified WBC subtype (Tc1547)

description:
Tc1547
CD8+ T-cells Purified WBC subtype Tc1547
Illumina VeraCode GGMA

value: CD8+ T-cells


title: genomic DNA from CD16- NK cells Purified WBC subtype (NK16m2606)

description:
NK16m2606
CD16- NK cells Purified WBC subtype NK16m2606
Illumina VeraCode GGMA

value: CD16- NK cells


title: genomic DNA from CD4+ T-cells Purified WBC subtype (Th2611)

description:
Th2611
CD4+ T-cells Purified WBC subtype Th2611
Illumina VeraCode GGMA

value: CD4+ T-cells


title: genomic DNA from Citrate, Fresh Human whole blood (3159CitFr)

description:
3159CitFr
Citrate, Fresh Human whole blood 3159CitFr
Illumina VeraCode GGMA

value: Human whole blood


title: genomic DNA from EDTA, o/n at room temp Human whole blood (3093EDTARt)

description:
3093EDTARt
EDTA, o/n at room temp Human whole blood 3093EDTARt
Illumina VeraCode GGMA


title: genomic DNA from EDTA, o/n at 4C Human whole blood (3021EDTA4C)

description:
3021EDTA4C
EDTA, o/n at 4C Human whole blood 3021EDTA4C
Illumina VeraCode GGMA

value: EDTA, o/n at 4C


title: genomic DNA from Heparin, o/n at room temp Human whole blood (3021HepRt)

description:
3021HepRt
Heparin, o/n at room temp Human whole blood 3021HepRt
Illumina VeraCode GGMA


title: genomic DNA from CD4+ T-cells Purified WBC subtype (Th2546)

description:
Th2546
CD4+ T-cells Purified WBC subtype Th2546
Illumina VeraCode GGMA


title: genomic DNA from CD16- NK cells Purified WBC subtype (NK16m2578)

description:
NK16m2578
CD16- NK cells Purified WBC subtype NK16m2578
Illumina VeraCode GGMA


title: genomic DNA from Eosinophils Purified WBC subtype (Eos2063)

description:
Eos2063
Eosinophils Purified WBC subtype Eos2063
Illumina VeraCode GGMA

value: Eosinophils


title: genomic DNA from EDTA, o/n at room temp Human whole blood (3159EDTARt)

description:
3159EDTARt
EDTA, o/n at room temp Human whole blood 3159EDTARt
Illumina VeraCode GGMA


title: genomic DNA from NKT cells Purified WBC subtype (NKT2613)

description:
NKT2613
NKT cells Purified WBC subtype NKT2613
Illumina VeraCode GGMA

source_name: NKT cells Purified WBC subtype NKT2613

value: NKT cells


title: genomic DNA from CD4+ T-cells Purified WBC subtype (Th1831)

description:
Th1831
CD4+ T-cells Purified WBC subtype Th1831
Illumina VeraCode GGMA


title: genomic DNA from Basophils Purified WBC subtype (Baso1915)

description:
Baso1915
Basophils Purified WBC subtype Baso1915
Illumina VeraCode GGMA

source_name: Basophils Purified WBC subtype Baso1915


title: genomic DNA from Eosinophils Purified WBC subtype (Eos2272)

description:
Eos2272
Eosinophils Purified WBC subtype Eos2272
Illumina VeraCode GGMA


title: genomic DNA from Citrate, o/n at -80C Human whole blood (3093Cit80)

description:
3093Cit80
Citrate, o/n at -80C Human whole blood 3093Cit80
Illumina VeraCode GGMA

value: Citrate, o/n at -80C


title: genomic DNA from Pan-NK cells Purified WBC subtype (NKpan1850)

description:
NKpan1850
Pan-NK cells Purified WBC subtype NKpan1850
Illumina VeraCode GGMA

value: Pan-NK cells


title: genomic DNA from EDTA, Fresh Human whole blood (3093EDTAFr)

description:
3093EDTAFr
EDTA, Fresh Human whole blood 3093EDTAFr
Illumina VeraCode GGMA


title: genomic DNA from CD4+ T-cells Purified WBC subtype (Th2535)

description:
Th2535
CD4+ T-cells Purified WBC subtype Th2535
Illumina VeraCode GGMA


title: genomic DNA from Granulocytopenia Reconstruction mixture (Gpen)

description:
Gpen
Granulocytopenia Reconstruction mixture Gpen
Illumina VeraCode GGMA

value: Reconstruction mixture

value: Granulocytopenia


title: genomic DNA from Basophils Purified WBC subtype (Baso2477)

description:
Baso2477
Basophils Purified WBC subtype Baso2477
Illumina VeraCode GGMA

source_name: Basophils Purified WBC subtype Baso2477

value: Basophils


title: genomic DNA from Citrate, o/n at room temp Human whole blood (3045CitRt)

description:
3045CitRt
Citrate, o/n at room temp Human whole blood 3045CitRt
Illumina VeraCode GGMA

value: Citrate, o/n at room temp


title: genomic DNA from Citrate, Fresh Human whole blood (3093CitFr)

description:
3093CitFr
Citrate, Fresh Human whole blood 3093CitFr
Illumina VeraCode GGMA

value: Citrate, Fresh


title: genomic DNA from CD16- NK cells Purified WBC subtype (NK16m2640)

description:
NK16m2640
CD16- NK cells Purified WBC subtype NK16m2640
Illumina VeraCode GGMA

value: Purified WBC subtype


title: genomic DNA from CD16- NK cells Purified WBC subtype (NK16m2608)

description:
NK16m2608
CD16- NK cells Purified WBC subtype NK16m2608
Illumina VeraCode GGMA

value: normal


title: genomic DNA from Citrate, o/n at -80C Human whole blood (3177Cit80)

description:
3177Cit80
Citrate, o/n at -80C Human whole blood 3177Cit80
Illumina VeraCode GGMA


title: genomic DNA from EDA, o/n at -80C Human whole blood (3082EDTA80)

description:
3082EDTA80
EDA, o/n at -80C Human whole blood 3082EDTA80
Illumina VeraCode GGMA

value: EDA, o/n at -80C


title: genomic DNA from Heparin, o/n at -80C Human whole blood (3093Hep80)

description:
3093Hep80
Heparin, o/n at -80C Human whole blood 3093Hep80
Illumina VeraCode GGMA

value: Heparin, o/n at -80C


title: genomic DNA from EDTA, Fresh Human whole blood (3177EDTAFr)

description:
3177EDTAFr
EDTA, Fresh Human whole blood 3177EDTAFr
Illumina VeraCode GGMA

value: EDTA, Fresh


title: genomic DNA from EDA, o/n at -80C Human whole blood (3093EDTA80)

description:
3093EDTA80
EDA, o/n at -80C Human whole blood 3093EDTA80
Illumina VeraCode GGMA


title: genomic DNA from Tregs Purified WBC subtype (Treg21691)

description:
Treg21691
Tregs Purified WBC subtype Treg21691
Illumina VeraCode GGMA

source_name: Tregs Purified WBC subtype Treg21691

value: Tregs


title: genomic DNA from CD8+ NK cells Purified WBC subtype (NK8p2621)

description:
NK8p2621
CD8+ NK cells Purified WBC subtype NK8p2621
Illumina VeraCode GGMA

value: CD8+ NK cells


title: genomic DNA from CD16+ NK cells Purified WBC subtype (NK16p2594)

description:
NK16p2594
CD16+ NK cells Purified WBC subtype NK16p2594
Illumina VeraCode GGMA

value: CD16+ NK cells


title: genomic DNA from EDTA, o/n at 4C Human whole blood (3082EDTA4C)

description:
3082EDTA4C
EDTA, o/n at 4C Human whole blood 3082EDTA4C
Illumina VeraCode GGMA

value: Human whole blood

value: EDTA, o/n at 4C


title: genomic DNA from Heparin, Fresh Human whole blood (3159HepFr)

description:
3159HepFr
Heparin, Fresh Human whole blood 3159HepFr
Illumina VeraCode GGMA

value: Heparin, Fresh


title: genomic DNA from Heparin, o/n at 4C Human whole blood (3159Hep4C)

description:
3159Hep4C
Heparin, o/n at 4C Human whole blood 3159Hep4C
Illumina VeraCode GGMA

value: Heparin, o/n at 4C


title: genomic DNA from B-cell Lymphopenia Reconstruction mixture (Bpen)

description:
Bpen
B-cell Lymphopenia Reconstruction mixture Bpen
Illumina VeraCode GGMA

value: Reconstruction mixture

value: B-cell Lymphopenia


title: genomic DNA from Heparin, o/n at -80C Human whole blood (3159Hep80)

description:
3159Hep80
Heparin, o/n at -80C Human whole blood 3159Hep80
Illumina VeraCode GGMA


title: genomic DNA from B-cells Purified WBC subtype (B1681)

description:
B1681
B-cells Purified WBC subtype B1681
Illumina VeraCode GGMA

source_name: B-cells Purified WBC subtype B1681

value: B-cells


title: genomic DNA from Heparin, o/n at -80C Human whole blood (3082Hep80)

description:
3082Hep80
Heparin, o/n at -80C Human whole blood 3082Hep80
Illumina VeraCode GGMA


title: genomic DNA from Monocytes Purified WBC subtype (Mono1775)

description:
Mono1775
Monocytes Purified WBC subtype Mono1775
Illumina VeraCode GGMA

source_name: Monocytes Purified WBC subtype Mono1775

value: Monocytes


title: genomic DNA from NKT cells Purified WBC subtype (NKT2584)

description:
NKT2584
NKT cells Purified WBC subtype NKT2584
Illumina VeraCode GGMA

source_name: NKT cells Purified WBC subtype NKT2584

value: NKT cells


title: genomic DNA from Heparin, Fresh Human whole blood (3177HepFr)

description:
3177HepFr
Heparin, Fresh Human whole blood 3177HepFr
Illumina VeraCode GGMA


title: genomic DNA from B-cells Purified WBC subtype (B2005)

description:
B2005
B-cells Purified WBC subtype B2005
Illumina VeraCode GGMA

source_name: B-cells Purified WBC subtype B2005

value: Purified WBC subtype


title: genomic DNA from EDTA, Fresh Human whole blood (3021EDTAFr)

description:
3021EDTAFr
EDTA, Fresh Human whole blood 3021EDTAFr
Illumina VeraCode GGMA

value: normal


title: genomic DNA from CD16+ NK cells Purified WBC subtype (NK16p2590)

description:
NK16p2590
CD16+ NK cells Purified WBC subtype NK16p2590
Illumina VeraCode GGMA


title: genomic DNA from EDA, o/n at -80C Human whole blood (3177EDTA80)

description:
3177EDTA80
EDA, o/n at -80C Human whole blood 3177EDTA80
Illumina VeraCode GGMA

value: EDA, o/n at -80C


title: genomic DNA from CD8- NK cells Purified WBC subtype (NK8m2299)

description:
NK8m2299
CD8- NK cells Purified WBC subtype NK8m2299
Illumina VeraCode GGMA

value: CD8- NK cells


title: STOSE cell line, biological replicate 3

city: Ottawa

first: Barbara

middle: C.

last: Vanderhyden

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

description: Gene expression data from STOSE cell line biological replicate 3

hyb_protocol: Labeled target cDNA was hybridized to the Affymetrix Genechip Mouse Gene 2.0 array at 45C for 17 hours.  GeneChips were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Gene Expression Console using Affymetrix default analysis settings for RMA processing.

label: Biotin

source_name: Transformed M0505 murine ovarian surface epithelial cell line.

label_protocol: cDNA was prepared according to the standard Affymetrix protocol using the Ambion WT Expression kit (Life Technologies) from 300 ng total RNA.  cDNA was biotinilated and fragmented using the Affymetrix GeneChip Wt Terminal Labeling kit.

growth_protocol: M0505 and STOSE cells were grown in murine OSE (MOSE) media (α-Minimal Essential Medium, 4% fetal calf serum, 0.002μg/mL EGF, 1μg/mL ITSS, 0.1μg/ml Gentamicin, 0.005mg/mL Streptomycin, 5U/mL Penicillin)

extract_protocol: RNA was extracted using the Qiagen RNAeasy Mini Kit according to the manufacterers directions.

value: FVB/N

value: ovarian surface epithelium


title: genomic DNA from EDA, o/n at -80C Human whole blood (3045EDTA80)

description:
3045EDTA80
EDA, o/n at -80C Human whole blood 3045EDTA80
Illumina VeraCode GGMA


title: genomic DNA from Citrate, o/n at -80C Human whole blood (3082Cit80)

description:
3082Cit80
Citrate, o/n at -80C Human whole blood 3082Cit80
Illumina VeraCode GGMA

value: Citrate, o/n at -80C


title: genomic DNA from CD8+ T-cells Purified WBC subtype (Tc2637)

description:
Tc2637
CD8+ T-cells Purified WBC subtype Tc2637
Illumina VeraCode GGMA

value: CD8+ T-cells


title: genomic DNA from NKT cells Purified WBC subtype (NKT2574)

description:
NKT2574
NKT cells Purified WBC subtype NKT2574
Illumina VeraCode GGMA

source_name: NKT cells Purified WBC subtype NKT2574


title: genomic DNA from Neutrophils Purified WBC subtype (Neut1145)

description:
Neut1145
Neutrophils Purified WBC subtype Neut1145
Illumina VeraCode GGMA

value: Neutrophils


title: genomic DNA from EDTA, o/n at 4C Human whole blood (3045EDTA4C)

description:
3045EDTA4C
EDTA, o/n at 4C Human whole blood 3045EDTA4C
Illumina VeraCode GGMA

value: Human whole blood

value: EDTA, o/n at 4C


title: genomic DNA from Neutrophils Purified WBC subtype (Neut1148)

description:
Neut1148
Neutrophils Purified WBC subtype Neut1148
Illumina VeraCode GGMA


title: genomic DNA from Pan-NK cells Purified WBC subtype (NKpan2241)

description:
NKpan2241
Pan-NK cells Purified WBC subtype NKpan2241
Illumina VeraCode GGMA

value: Pan-NK cells


title: genomic DNA from Citrate, Fresh Human whole blood (3021CitFr)

description:
3021CitFr
Citrate, Fresh Human whole blood 3021CitFr
Illumina VeraCode GGMA

value: Citrate, Fresh


title: genomic DNA from Basophils Purified WBC subtype (Baso1832)

description:
Baso1832
Basophils Purified WBC subtype Baso1832
Illumina VeraCode GGMA

source_name: Basophils Purified WBC subtype Baso1832

value: Basophils


title: M0505 cell line, biological replicate 2

description: Gene expression data from M0505 cell line biological replicate 2

source_name: Murine ovarian surface epithelial cell line established in May 2005


title: STOSE cell line, biological replicate 2

description: Gene expression data from STOSE cell line biological replicate 2


title: M0505 cell line, biological replicate 3

description: Gene expression data from M0505 cell line biological replicate 3


title: CD34 Transwell Mono-culture - 24 hr - repeat 3

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: No additional information.

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Images of the arrays were acquired using a microarray scanner Scan G2505B and image analysis was performed using Scan Control software version 9.5 (Agilent Technologies). The images were extracted using the Feature Extraction Software (Agilent Technologies).

data_processing:
Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Agilent Technologies). Spot values were normalized using the default linear-lowess normalization. Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) and Ingenuity Pathway Analysis website (http://www.ingenuity.com, Ingenuity System Inc., Redwood City, CA, USA) were used for further data analysis.

source_name: Universal Human Reference RNA

label_protocol:
Cy3 Labeling Protocol
Other: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit.

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: other

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: CD34 Transwell Mono-culture - 24 hr

label_protocol:
Cy5 Labeling Protocol
Other: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was purified using miRNA Easy Kit (Qiagen). The RNA concentration was measured using a Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: In-vitro treatment: CD34+ cells isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). CD34+ cells were harvested and RNA extracted.

value: Blood

value: CD34+ cells

value: Cells were harvested after 24 hours of mono-culture.


title: BMSC Transwell Co-cultured with CD34 - 24 hr - repeat 3

description: No additional information.

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were co-cultured with CD34+ cells isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and CD34+ cell populations separate from each other. BMSC cells were harvested and RNA extracted.

value: Bone marrow

value: Bone marrow derived stromal cells (BMSC)

value: Cells were harvested after 24 hours of co-culture.


title: STOSE cell line, biological replicate 1

description: Gene expression data from STOSE cell line biological replicate 1

value: FVB/N


title: CD34 Transwell Co-cultured with BMSC - 10 hr - repeat 3

description: No additional information.

treatment_protocol: In-vitro treatment: CD34+ cells isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors were co-cultured with BMSCs from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and CD34+ cell populations separate from each other. CD34+ cells were harvested and RNA extracted.

value: Cells were harvested after 10 hours of co-culture.


title: CD34 Transwell Co-cultured with BMSC - 24 hr - repeat 3

description: No additional information.


title: M0505 cell line, biological replicate 1

description: Gene expression data from M0505 cell line biological replicate 1

value: ovarian surface epithelium