title: SS_P1 cells_SAHA_rep.3

description:
P1_3_S
US83700202_252800415433_S01_GE1_107_Sep09_2_4


title: SS_P2 cells_Ctrl_rep.2

status: Public on Dec 12 2016

type: RNA

city: MARSEILLE

first: CHELBI

last: RABIE

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

description:
P2_2_C
US83700202_252800415373_S01_GE1_107_Sep09_1_4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: SS cells_no drug

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PBMC were collected from 4 Sézary Syndrome (SS) patients and were put in culture without prior further purification because of the high percentage of T lymphocytes and the great majority of CD4+ among them. Cells were expanded for seven days in RPMI medium in the presence of IL-7 (10 ng/ml) and anti-CD28 (mAb ascites 1/400).

extract_protocol: Cells were recovered after drug treatment and RNA was extracted with Qiagen RNeasy® mini Kit. On column DNA digestion was done with Qiagen Rnase-free Dnase set.

treatment_protocol: Expanded cells were treated, or not, with SAHA (2.6 µM) and MitA (223 nM) for 24 h.

tag: subject status

value: Sézary Syndrome (SS) patient

tag: gender

value: female

tag: age (yrs)

tag: cell type

value: peripheral blood tumor cells

tag: tumor stage

value: III

tag: treatment

tag: % cd3+ in pbmc

tag: cd4+/cd8+ ratio


title: SS_P2 cells_MitA_rep.2

description:
P2_2_M
US83700202_252800415373_S01_GE1_107_Sep09_1_2

source_name: SS cells_MitA_24 h


title: SS_P1 cells_Ctrl_rep.3

description:
P1_3_C
US83700202_252800415433_S01_GE1_107_Sep09_2_1

value: male

value: eECPx1/ Roferon CHOPx6


title: SS_P2 cells_Ctrl_rep.3

description:
P2_3_C
US83700202_252800415433_S01_GE1_107_Sep09_2_2


title: SS_P4 cells_Ctrl_rep.2

description:
P4_2_C
US83700202_252800415374_S01_GE1_105_Dec08_1_4


title: SS_P2 cells_Ctrl_rep.1

description:
P2_1_C
US83700202_252800415391_S01_GE1_107_Sep09_1_2


title: SS_P1 cells_Ctrl_rep.1

description:
P1_1_C
US83700202_252800415375_S01_GE1_107_Sep09_2_4


title: SS_P3 cells_Ctrl_rep.3

description:
P3_3_C
US83700202_252800415383_S01_GE1_107_Sep09_2_3


title: SS_P3 cells_Ctrl_rep.1

description:
P3_1_C
US83700202_252800415374_S01_GE1_105_Dec08_2_4


title: SS_P3 cells_Ctrl_rep.2

description:
P3_2_C
US83700202_252800415382_S01_GE1_107_Sep09_1_2


title: CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [CFTRinh172 rep 1-1]

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

description: Technical replicate 1 of 2 of biological replicate 1 of 2. CFTR inhibitor 172 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.

hyb_protocol: Whole Human Genome 44K arrays (Agilent Technologies, product G4112A) were used for all experiments. RNA samples (825 ng/each) were subjected to fragmentation, followed by 16 h hybridization, washing.

scan_protocol: Agilent Technologies, model G2505B according to the manufacturer’s protocol (manual ID #G4140-90030)

data_processing: Agilent dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantiﬁed using Agilent’s Feature Extraction software (v.7.11) with the default parameters.

source_name: Cystic fibrosis bronchial epithelial cells (CFBE41o−)

label_protocol: Total RNA (1 µg) was subjected to two rounds of ampliﬁcation using the Amino Allyl MessageAMP II aRNA ampliﬁcation kit (Ambion, Applied Biosystems, USA). The integrity and quantity of the aRNA was revaluated by Nanodrop and Agilent Bioanalyzer, and coupled to Cy3 and Cy5 (Amersham Biosciences, UK).

growth_protocol:
CFBE41o− cell lines transduced with TranzVector lentivectors containing ΔF508 CFTR (CFBE41o-ΔF508CFTR) or wildtype CFTR (CFBE41o−CFTR) cells were kindly provided by J.P. Clancy. Cells were maintained in Eagle’s minimum essential medium (EMEM, Wisent, St-Bruno, QC, Canada) plus 10% fetal bovine serum (FBS) in a 5% CO2, 95% air incubator at 37 °C.
polarized_protocol: Cells were seeded at a density of 3 × 105 cells/cm2 on cell culture inserts (Transwell-clear, diameter 12 mm, 0.4 μm pores; Corning, Acton, MA, USA) in multi-well plates and kept submerged (i.e. under liquid–liquid conditions) until they were conﬂuent, after which the apical medium was removed from the upper compartment to allow polarisation at the air–liquid interface.

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

tag: cell line

value: polarized CFBE41o-cell line

tag: transduction

value: TranzVector lentivectors containing deltaF508 CFTR (CFBE41o-deltaF508CFTR)

source_name: untreated HeLa cells

value: HeLa cells


title: 124-Frozen-Nugen_FFPE-rep1

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

description: The fragmented, biotin-labeled RNA sample was combined with the hybridization mix and loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with streptavidine/phycoerythrin conjugate and biotinylated antibody and scanned according to the manufacturer’s recommendation.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were normalized in R using the Bioconductor package frma v1.9.3

label: biotin

source_name: Primary HNSCC tumor

label_protocol: standard Affymetrix protocol

extract_protocol: Nugen FFPE

value: M

tag: ethnicity

value: O

tag: tissue

value: Primary HNSCC

tag: research number

tag: procurement

value: Frozen

tag: rna isolation

value: Invitrogen PureLink

tag: amplification

value: Nugen FFPE

tag: hpv

value: Neg

tag: smoking

value: 50 pyr

tag: alcohol

value: Y

tag: pathology state at diagnosis

tag: pathology tnm at diagnosis

tag: subsite

value: HP

tag: recurrence location

value: Primary

tag: disease state

value: DOD


title: 182-Frozen-Nugen_FFPE-rep1

tag: gender

value: W

value: Pos

value: 80 pyr

value: L

value: Lung


title: VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs [VRT-325 rep 2-2]

description: Technical replicate 2 of 2 of biological replicate 2 of 3.VRT-325 10 µM CFBE41o-ΔF508CFTR of treated cells 24 hrs.

tag: cell line

value: polarized CFBE41o-cell line

value: TranzVector lentivectors containing deltaF508 CFTR (CFBE41o-deltaF508CFTR)

value: HeLa cells


title: 62-Frozen-Nugen_FFPE-rep1

value: M

value: Primary HNSCC

value: Frozen

value: 0 pyr

value: N

value: OP

value: NED


title: 365-Frozen-Nugen_FFPE-rep1

value: F

value: B

value: Invitrogen PureLink

value: Nugen FFPE

value: Neg

value: 40 cans

value: OC

value: Lung, Liver


title: 369-Frozen-Nugen_FFPE-rep1

value: W

value: Pos

value: 40 pyr


title: 372-Frozen-Nugen_FFPE-rep1

value: Primary HNSCC


title: 644-FFPE-Nugen_FFPE-rep1

extract_protocol: Nugen FFPE beta

value: M

value: FFPE

value: Ambion RecALL

value: Nugen FFPE beta

value: 60 pyr

value: Y

value: Skin

value: DOD


title: 1186-FFPE-Nugen_FFPE-rep1

value: F

value: 0.5 pyr

value: bone


title: SS_P1 cells_Ctrl_rep.2

description:
P1_2_C
US83700202_252800415391_S01_GE1_107_Sep09_1_1

tag: subject status

value: Sézary Syndrome (SS) patient

value: male

tag: age (yrs)

tag: cell type

value: peripheral blood tumor cells

tag: tumor stage

value: III

tag: treatment

value: eECPx1/ Roferon CHOPx6

tag: % cd3+ in pbmc

tag: cd4+/cd8+ ratio


title: 1247-Frozen-Nugen_FFPE-rep1

tag: ethnicity

value: W

tag: tissue

value: Primary HNSCC

tag: research number

tag: procurement

value: Frozen

tag: rna isolation

value: Invitrogen PureLink

tag: amplification

value: Nugen FFPE

tag: hpv

value: Pos

value: OP

value: NED


title: 670-Frozen-Nugen_FFPE-rep1

value: Neg

tag: smoking

value: 45 pyr

tag: alcohol

value: N

tag: pathology state at diagnosis

tag: pathology tnm at diagnosis

tag: subsite

tag: recurrence location

value: Primary

tag: disease state

value: DOD


title: 1610-FFPE-Nugen_FFPE-rep1

tag: gender

value: M

value: FFPE

value: Ambion RecALL

value: 165 pyr

value: L

value: lung


title: 549-Frozen-Nugen_FFPE-rep1

value: W

value: Primary HNSCC

value: Frozen

value: 100 pyr

value: Y


title: 767-FFPE-Nugen_FFPE-rep1

value: B

value: Nugen FFPE beta

value: 128 pyr

value: OP

value: rec lung met and locoregional


title: 1657-Frozen-Nugen_FFPE-rep1

value: Invitrogen PureLink

value: Nugen FFPE

value: Pos

value: 0 pyr

value: NED


title: 1831-FFPE-Nugen_FFPE-rep1

value: M

value: FFPE

value: Ambion RecALL

value: Neg

value: 180 pyr

value: OC

value: DOD


title: 1389-FFPE-Nugen_FFPE-rep1

value: W

value: Primary HNSCC

value: 20 pyr

value: Y

value: Primary


title: 1756-FFPE-Nugen_FFPE-rep1

value: Nugen FFPE beta

value: 60 pyr

value: L

value: skin


title: 1955-Frozen-Nugen_FFPE-rep1

value: Frozen

value: Invitrogen PureLink

value: Nugen FFPE

value: 100 pyr

value: HP

value: DOC


title: 1756-Frozen-Nugen_FFPE-rep1

value: M

value: Neg


title: 1767-FFPE-Nugen_FFPE-rep1

value: W

value: FFPE

value: Ambion RecALL

value: 52 pyr

value: OP

value: LN, primary

value: DOD


title: 2412-Frozen-Nugen_FFPE-rep2

value: Primary HNSCC

value: 28 pyr

value: N

value: L

value: NED


title: 1831-Frozen-Nugen_FFPE-rep1

value: Frozen

value: Invitrogen PureLink

value: Nugen FFPE

value: 180 pyr

value: Y

value: OC

value: lung


title: 2412-FFPE-Nugen_FFPE-rep1

value: M

value: W

value: FFPE

value: Ambion RecALL

value: Neg


title: 2233-Frozen-Nugen_FFPE-rep1

value: Primary HNSCC

value: Pos

value: 40 pyr

value: OP


title: 376-Frozen-Nugen_FFPE-rep1

value: Primary

value: DOD


title: 1936-FFPE-Nugen_FFPE-rep1

value: Nugen FFPE beta

value: 35 cans


title: 2458-Frozen-Nugen_FFPE-rep1

value: Frozen

value: Invitrogen PureLink

value: Nugen FFPE

value: 7 pyr

value: DOC


title: 2469-Frozen-Nugen_FFPE-rep2

value: M

value: W

value: 60 pyr

value: N

value: LN

value: AWD


title: 2396-FFPE-Nugen_FFPE-rep1

value: Primary HNSCC

value: FFPE

value: Ambion RecALL

value: Pos

value: 138 pyr

value: Y


title: 2412-Frozen-Nugen_FFPE-rep1

value: Frozen

value: Neg

value: 28 pyr

value: L

value: NED


title: 2649-Frozen-Nugen_FFPE-rep1

value: M

value: Invitrogen PureLink

value: Nugen FFPE

value: 0 pyr

value: OP


title: control 3

city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

country: South Korea

institute: Korea University

description: Streptococcus pneumoniae biofilms control 3

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing:
Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used Global normalization.
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).

organism: Streptococcus pneumoniae D39

source_name: Streptococcus pneumoniae in-vitro biofilm grown with DMSO (control)

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for all)

growth_protocol: 1.5 mL (1:100 diluted) bacteria cell suspension was inoculated in 24-well microtiter plate, supplied with 7µm/ml DMSO and incubated in 5% CO2 for 15 hrs at 37° C. Thereafter plates were washed 3 times to remove planktonic cells and RNA was extracted.

extract_protocol: After washing cells were scraped, treated with 100 µl (3mg/ml) lysozyme and incubation for 4 min. Subsequently, total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Biofilm grown in 24-well plate with 7µm/ml DMSO (control biofilms) for 15 hours. Washed three times with PBS to remove growth medium and planktonic cells.

tag: strain


title: 2549-FFPE-Nugen_FFPE-rep1

value: W


title: 152-Frozen-Nugen_FFPE-rep1

value: Primary HNSCC

value: OC


title: Control_sample1

city: New Orleans

first: Patricia

middle: E.

last: Molina

state: LA

address: 1901 Perdido Street

department: Physiology

institute: LSU Health Sciences Center

description: SAMPLE 1

hyb_protocol: Hybridization using standard hybridization protocols from Illumina for 14h at 58°C

scan_protocol: Standard Illumina protocols for HumanWG6_v3 chips from Illumina using the Illumina BeadArray Reader

data_processing: Background signal was removed using the Detection P value algorithm. Signals were normalized using the cubic spline algorithm. Differential expression was determined using the Illumina Custom Algorithm. Ratios were determined as the fraction between the treatments and the Control group

organism: Macaca mulatta

source_name: Hippocampal brain tissue

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX),

growth_protocol: Animals [SIV- (N=2), isocaloric sucrose SIV infected (SUC/SIV+; N=2), and CBA SIV infected (CBA/SIV+; N=2)]

extract_protocol: RNA was extracted using TRIzol (LifeTechnologies)

treatment_protocol: Animals were treated with 19 months of chronic binge alcohol administration, during which 30% ethanol was infused intragastrically, 4 consecutive days per week. Blood alcohol levels were kept at 50-60 mMol during each 5 hour infusion period. Animals were inoculated with 10,000 TCID50 of SIV mac251 by i.v. injection. Animals were euthanized 16 months after SIV inoculation.

value: hippocampus


title: 2480-FFPE-Nugen_FFPE-rep1

value: FFPE

value: Ambion RecALL

value: 15 pyr

value: lung

value: DOD


title: control 2

description: Streptococcus pneumoniae biofilms control 2


title: 2660-FFPE-Nugen_FFPE-rep1

value: Pos

value: Y


title: SIV+Ethanol treated_sample1

description: SAMPLE 5


title: 291-Frozen-Nugen_FFPE-rep1

value: B

value: Frozen

value: Neg

value: L

value: LN, primary


title: 2469-Frozen-Nugen_FFPE-rep1

value: M

value: Invitrogen PureLink

value: Nugen FFPE

value: 60 pyr

value: N

value: OP

value: LN

value: AWD


title: SIV treated_sample1

description: SAMPLE 3

value: hippocampus


title: SIV treated_sample2

description: SAMPLE 4


title: SIV+Ethanol treated_sample2

description: SAMPLE 6


title: 2469-FFPE-Nugen_FFPE-rep1

value: W

value: Primary HNSCC

value: FFPE

value: Ambion RecALL


title: mol-1-3

description: Streptococcus pneumoniae Pyrimidinediones biofilm 3

source_name: Streptococcus pneumoniae in-vitro biofilm grown with 7µm/ml Pyrimidinediones small molecule

growth_protocol: 1.5 mL (1:100 diluted) bacteria cell suspension was inoculated in 24-well microtiter plate, supplied with 7µm/ml pyrimidine-diones small molecule and incubated in 5% CO2 for 15 hrs at 37° C. Thereafter plates were washed 3 time to remove planktonic cells and RNA was extracted.

treatment_protocol: Biofilm grown in 24-well plate with 7µm/ml pyrimidine-diones small molecule for 15 hours. Washed three times with PBS to remove growth medium and planktonic cells.


title: mol-1-2

description: Streptococcus pneumoniae Pyrimidinediones biofilm 2


title: 454-Frozen-Nugen_FFPE-rep1

value: Frozen

value: Y

value: NED


title: ENT Biofilm Control

description: Streptococcus pneumoniae biofilms control 1


title: 478-Frozen-Nugen_FFPE-rep1

value: Pos

value: LN, primary


title: SS_P2 cells_SAHA_rep.1

description:
P2_1_S
US83700202_252800415391_S01_GE1_107_Sep09_2_1

source_name: SS cells_SAHA_24 h

tag: subject status

value: Sézary Syndrome (SS) patient

value: female

tag: age (yrs)

tag: cell type

value: peripheral blood tumor cells

tag: tumor stage

value: III

tag: treatment

tag: % cd3+ in pbmc

tag: cd4+/cd8+ ratio


title: 394-Frozen-Nugen_FFPE-rep1

value: M

tag: ethnicity

tag: tissue

tag: research number

tag: procurement

tag: rna isolation

value: Invitrogen PureLink

tag: amplification

value: Nugen FFPE

tag: hpv

value: OP


title: Control_sample2

description: SAMPLE 2

value: hippocampus


title: Balb/c Neonate mouse Epidermis Stem cell control group

city: Lucknow

first: Shiv

last: Poojan

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: CSIR-Indian Institute of Toxicology Research

description:
EPSC(A)
Pregnant Balb/c mice exposed to vehicle drinking water ad libitum during the gestation period of 8-18 days.

hyb_protocol: 1650ng of the labeled cRNA samples were hybridized on to an Agilent Custom Mouse Whole Genome 4x44k Gene expression designed by Genotypic Technology Private Limited.  (AMADID No:14868). Cy3 labeled samples were fragmented and hybridized on the array.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent Microarray G2600D at 5 micron resolution and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX  Software using 75th Percentile Shift Normalization

organism: Mus musculus

source_name: transplacental exposure to vehicle_EpiSC

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Label retaining cells (LRC, Epidermal stem cell, EpSC) samples from control and exposed neonate mouse skin epidermis were obtained. BrdU labelling, FACS based sorting, and collagen-fibronectin adhesion based method provided selective EpSC enrichment. Dose of 85 ppm and 42.5ppm sodium arsenite as per the relevant literature was administered to the pregnant mice during the gestation period of 8-18days. Epidermal stem cells were isolated from neonate skin sampled from all the groups and were cultured in growth promoting medium till attaining confluence. One million cells wer used for microarray study. RNA was extracted from these LRCs. Samples with RIN value more than 7 were used for the cytogenomics analyses using 4*44 Agilent microarray based genome. The cytokeratin expression profile of stem cells was used as the biomarker of internal exposure to the toxicant.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit  following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Epidermal stem cells were grown as described earlier (Poojan and Kumar 2010).

value: Balb/c

tag: age

value: neonate (0-3days old)

tag: exposed to

value: vehicle drinking water

value: skin epidermis

value: skin epidermal stem cells (EpiSCs)


title: 458-Frozen-Nugen_FFPE-rep1

tag: gender

value: W

value: Primary HNSCC

value: Frozen

tag: smoking

value: Y

tag: alcohol

tag: pathology state at diagnosis

tag: pathology tnm at diagnosis

tag: subsite

tag: recurrence location

tag: disease state

value: NED


title: ENT Biofilm mgl-1

description: Streptococcus pneumoniae Pyrimidinediones biofilm 1

tag: strain


title: Balb/c Neonate mouse Epidermis Stem cell exposed with 85ppm As [III] set2

description:
Set3_EpiSC(85)_II
Pregnant Balb/c mice exposed to sodium arsnite at 42.5ppm in drinking water ad libitum during the gestation period of 8-18 days.

source_name: transplacental exposure to Arsenic_EpiSC

tag: tissue

tag: cell type


title: Balb/c Neonate mouse Epidermis Stem cell exposed with 42.5ppm As[III] set2

description:
Set2_EpiSC (42.5)
Pregnant Balb/c mice exposed to sodium arsnite at 85ppm in drinking water ad libitum during the gestation period of 8-18 days.


title: OCD Sample 1650

status: Public on Dec 11 2016

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: mother

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions.

scan_protocol: The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek.
Genotype Call (SNP call): AA, AB, BB, and NoCall

molecule: genomic DNA

source_name: Saliva

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Oragene saliva kits were heated o/n (5pm - 9am) at 50C in an air oven. OG500 saliva kits collected from adults were extracted using Puregene chemistry on an AutopureLS automated DNA extractor. Saliva lysates were RNase a treated prior to extracting using either a 5.0ml or 2.5ml lysate protocol depending on collected saliva volume. OG575 saliva kits collected from children were extracted manually using same Puregene chemistry and RNase A treatment. Pelleted DNA was rehydrated in TE overnight and quantitated next day using Hoescht dye and FLX800 Flurometer.

tag: diagnosis

value: obsessive-compulsive disorder

value: Saliva

value: Female


title: OCD Sample 1525

description: mother


title: OCD Sample 1580

description: proband


title: OCD Sample 1398

description: proband

value: Male


title: OCD Sample 896513

description: proband


title: OCD Sample 1649

description: father


title: 671-Frozen-Nugen_FFPE-rep1

value: M

tag: ethnicity

value: B

tag: research number

tag: procurement

tag: rna isolation

value: Invitrogen PureLink

value: Nugen FFPE

value: Neg

value: OC


title: QM-24-2

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

growth_protocol: Huh-7 cells were culture with either fetal bovine serum (FBS) or human serum (HS).

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Differentiated Huh-7 cells were infected with hepatitis C virus (HCV) clones with (Q70/M91) or without (R70/L91) oncogenic mutations and treated with interferon for 24h.

tag: culture medium

value: with human serum (HS)

tag: infected hvc clone

tag: interferon treatment

value: yes

tag: cell line


title: Balb/c Neonate mouse Epidermis Stem cell exposed with 85ppm As [III]

description:
EpiSC (85 P)
Pregnant Balb/c mice exposed to sodium arsnite at 42.5ppm in drinking water ad libitum during the gestation period of 8-18 days.

value: Balb/c

tag: age

value: neonate (0-3days old)

tag: exposed to

value: skin epidermis

value: skin epidermal stem cells (EpiSCs)


title: FBS-2

scan_protocol: Refer to the Illumina beadarray Assay System Manual

value: with fetal bovine serum (FBS)

value: no


title: RL-0-2

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: 79-Frozen-Nugen_FFPE-rep1

tag: gender

value: W

value: Primary HNSCC

value: Frozen

tag: amplification

tag: hpv

tag: smoking

value: Y

tag: alcohol

tag: pathology state at diagnosis

tag: pathology tnm at diagnosis

tag: subsite

value: LN, primary

value: DOD


title: QM-0-1


title: HS-1


title: OCD Sample 1633

description: mother

tag: diagnosis

value: obsessive-compulsive disorder

tag: tissue

value: Saliva

value: Female


title: OCD Sample 1635

description: father

value: Male


title: OCD Sample 1636

description: mother


title: Balb/c Neonate mouse Epidermis Stem cell exposed with 42.5ppm As[III]

description:
EpiSC (42.5)
Pregnant Balb/c mice exposed to sodium arsnite at 85ppm in drinking water ad libitum during the gestation period of 8-18 days.

tag: strain

tag: cell type


title: RL-24-1

tag: culture medium

value: with human serum (HS)

tag: infected hvc clone

value: yes


title: QM-24-1

tag: interferon treatment

tag: cell line


title: RL-24-2


title: RL-0-1


title: FBS-1


title: HS-2


title: QM-0-2


title: OCD Sample 1609

description: father


title: OCD Sample 1608

description: mother


title: OCD Sample 1718

description: father


title: OCD Sample 1584

description: mother


title: OCD Sample 1594

description: mother


title: OCD Sample 1581

description: mother


title: OCD Sample 1648

description: proband


title: OCD Sample 1617

description: mother


title: OCD Sample 1632

description: father


title: OCD Sample 1582

description: father


title: OCD Sample 1579

description: father


title: OCD Sample 1551

description: father


title: OCD Sample 1550

description: mother


title: OCD Sample 1549_293

description: proband


title: OCD Sample 1400-2

description: mother


title: OCD Sample 1526

description: father


title: OCD Sample 1524

description: proband


title: OCD Sample 1399-2

description: father


title: OCD Sample 1054

description: father


title: OCD Sample 8961113

description: proband


title: OCD Sample 1053

description: proband


title: OCD Sample 8961112

description: mother


title: OCD Sample 8961111

description: father


title: OCD Sample 8961052

description: mother


title: OCD Sample 8961081

description: father


title: OCD Sample 8961083

description: proband


title: OCD Sample 8961073

description: proband


title: OCD Sample 8961053

description: proband


title: OCD Sample 8961082

description: mother


title: OCD Sample 8961051

description: father


title: OCD Sample 1651

description: mother


title: OCD Sample 8961093

description: proband


title: OCD Sample 8961043

description: proband


title: OCD Sample 8961042

description: mother


title: OCD Sample 8961041

description: father


title: OCD Sample 8961013

description: proband


title: OCD Sample 8961012

description: mother


title: OCD Sample 8961011

description: father


title: OCD Sample 896913

description: proband


title: OCD Sample 896973

description: proband


title: OCD Sample 896953

description: proband


title: OCD Sample 896971

description: father


title: OCD Sample 896902

description: mother


title: OCD Sample 896972

description: mother


title: OCD Sample 896901

description: father


title: OCD Sample 896903

description: proband


title: OCD Sample 1055

description: mother


title: OCD Sample 896993

description: proband


title: OCD Sample 896992

description: mother


title: OCD Sample 896991

description: father


title: OCD Sample 7542

description: proband


title: OCD Sample 8818

description: proband


title: OCD Sample 5884

description: proband


title: OCD Sample 8473

description: proband


title: OCD Sample 8771

description: proband


title: OCD Sample 5813

description: proband


title: OCD Sample 8961003

description: proband


title: OCD Sample 5766

description: proband


title: OCD Sample 5299

description: proband


title: OCD Sample 715

description: proband


title: OCD Sample 944

description: proband


title: OCD Sample 1479

description: father


title: OCD Sample 2206

description: proband


title: OCD Sample 253

description: proband


title: OCD Sample 1463

description: father


title: OCD Sample 7286

description: proband


title: OCD Sample 896621

description: father


title: OCD Sample 896622

description: mother


title: OCD Sample 896623

description: proband


title: OCD Sample 140-1366

description: proband


title: OCD Sample 1337_188601

description: father


title: OCD Sample 1440

description: mother


title: OCD Sample 1480

description: mother


title: OCD Sample 106

description: proband


title: OCD Sample 1244

description: proband


title: OCD Sample 1487

description: father


title: OCD Sample 1295

description: proband


title: OCD Sample 1347

description: proband


title: OCD Sample 1488

description: mother


title: OCD Sample 273

description: proband


title: OCD Sample 1431

description: father


title: OCD Sample 1388_189277

description: mother


title: OCD Sample 0625-7951-3

description: proband


title: OCD Sample 1387

description: father


title: OCD Sample 1432

description: mother


title: OCD Sample 1430

description: proband


title: OCD Sample 0625-7951-1

description: father


title: OCD Sample 0625-7951-2

description: mother


title: OCD Sample 0625-7948-3

description: proband


title: OCD Sample 0625-7948-2

description: mother


title: OCD Sample 1348

description: father


title: OCD Sample 0625-7921-3

description: proband


title: OCD Sample 161

description: proband


title: OCD Sample 0625-7921-1

description: father


title: OCD Sample 0625-4194-2

description: mother


title: OCD Sample 0625-7921-2

description: mother


title: OCD Sample 0625-4194-1

description: father


title: OCD Sample 0625-2972-2

description: mother


title: OCD Sample 0625-3695-1

description: father


title: OCD Sample 0625-3695-2

description: mother


title: OCD Sample 0625-3695-3

description: proband


title: OCD Sample 0625-2972-1

description: father


title: OCD Sample 896483

description: proband


title: OCD Sample 896462

description: mother


title: OCD Sample 896461

description: father


title: OCD Sample 896481

description: father


title: OCD Sample 896463

description: proband


title: OCD Sample 896203

description: proband


title: OCD Sample 896842

description: mother


title: OCD Sample 0625-2318-2

description: mother


title: OCD Sample 896822

description: mother


title: OCD Sample 896823

description: proband


title: OCD Sample 896813

description: proband


title: OCD Sample 0625-0648-3

description: proband


title: OCD Sample 896053

description: proband


title: OCD Sample 896013

description: proband


title: OCD Sample 896863

description: proband


title: OCD Sample 0625-4194-3

description: proband


title: OCD Sample 0625-0648-1

description: father


title: OCD Sample 896033

description: proband


title: OCD Sample 0625-7618-3

description: proband


title: OCD Sample 0625-7618-2

description: mother


title: OCD Sample 896851

description: father


title: OCD Sample 896783

description: proband


title: OCD Sample 0625-7618-1

description: father


title: OCD Sample 0625-5214-3

description: proband


title: OCD Sample 0625-2668-2

description: mother


title: OCD Sample 0625-2318-3

description: proband


title: OCD Sample 0625-2668-1

description: father


title: OCD Sample 896482

description: mother


title: OCD Sample 896763

description: proband


title: OCD Sample 896881

description: father


title: OCD Sample 0625-2668-3

description: proband


title: OCD Sample 896883

description: proband


title: OCD Sample 0625-0648-2

description: mother


title: OCD Sample 896103

description: proband


title: OCD Sample 896852

description: mother


title: OCD Sample 896841

description: father


title: OCD Sample 896812

description: mother


title: OCD Sample 896793

description: proband


title: OCD Sample 896853

description: proband


title: OCD Sample 896301

description: father


title: OCD Sample 896041

description: father


title: OCD Sample 896811

description: father


title: OCD Sample 896821

description: father


title: OCD Sample 896792

description: mother


title: OCD Sample 896563

description: proband


title: OCD Sample 896791

description: father


title: OCD Sample 896843

description: proband


title: OCD Sample 896771

description: father


title: OCD Sample 896773

description: proband


title: OCD Sample 896071

description: father


title: OCD Sample 896741

description: father


title: OCD Sample 896882

description: mother


title: OCD Sample 896743

description: proband


title: OCD Sample 896303

description: proband


title: OCD Sample 896742

description: mother


title: OCD Sample 896721

description: father


title: OCD Sample 896711

description: father


title: OCD Sample 896772

description: mother


title: OCD Sample 896712

description: mother


title: OCD Sample 896713

description: proband


title: OCD Sample 896722

description: mother


title: OCD Sample 896702

description: mother


title: OCD Sample 896703

description: proband


title: OCD Sample 896701

description: father


title: OCD Sample 896682

description: mother


title: OCD Sample 896681

description: father


title: OCD Sample 896292

description: mother


title: OCD Sample 896302

description: mother


title: OCD Sample 896553

description: proband


title: OCD Sample 896562

description: mother


title: OCD Sample 896561

description: father


title: OCD Sample 896552

description: mother


title: OCD Sample 896683

description: proband


title: OCD Sample 896293

description: proband


title: OCD Sample 896072

description: mother


title: OCD Sample 896803

description: proband


title: OCD Sample 896042

description: mother


title: OCD Sample 1015-3

description: proband


title: OCD Sample 896043

description: proband


title: OCD Sample 0625-1325-3

description: proband


title: OCD Sample 896291

description: father


title: OCD Sample 896023

description: proband


title: OCD Sample 896063

description: proband


title: OCD Sample 896283

description: proband


title: OCD Sample 896723

description: proband


title: OCD Sample 896073

description: proband


title: OCD Sample 0625-9794-3

description: proband


title: OCD Sample 0625-4081-2

description: mother


title: OCD Sample 0625-2200-3

description: proband


title: OCD Sample 896263

description: proband


title: OCD Sample 0625-4081-1

description: father


title: OCD Sample 37

description: proband


title: OCD Sample 0625-4081-3

description: proband


title: OCD Sample 0625-3790-2

description: mother


title: OCD Sample 0625-3790-1

description: proband


title: OCD Sample 0625-3790-3

description: father


title: OCD Sample 0625-9923-2

description: mother


title: OCD Sample 0625-9698-1

description: father


title: OCD Sample 0625-9698-3

description: proband


title: OCD Sample 0625-9391-1

description: father


title: OCD Sample 0625-9391-2

description: mother


title: OCD Sample 0625-9923-1

description: father


title: OCD Sample 0625-9698-2

description: mother


title: OCD Sample 0625-6323-3

description: proband


title: OCD Sample 0625-8740-3

description: proband


title: OCD Sample HAM493

description: proband


title: OCD Sample 1681

description: mother


title: OCD Sample 8961123

description: proband


title: OCD Sample 896372

description: mother


title: OCD Sample 896511

description: father


title: OCD Sample HAM533

description: proband


title: OCD Sample 8961133

description: proband


title: OCD Sample 0625-7269-1

description: father


title: OCD Sample 0625-6223-3

description: proband


title: OCD Sample 0625-6107-1

description: father


title: OCD Sample 0625-6107-3

description: proband


title: OCD Sample 0625-6045-2

description: mother


title: OCD Sample 0625-6045-1

description: father


title: OCD Sample 0625-6045-3

description: proband


title: OCD Sample 0625-5375-1

description: father


title: OCD Sample 0625-8346-2

description: mother


title: OCD Sample 1015-2

description: mother


title: OCD Sample 0625-9391-3

description: proband


title: OCD Sample 0625-8219-2

description: mother


title: OCD Sample 0625-8740-1

description: father


title: OCD Sample 0625-8219-1

description: father


title: OCD Sample 0625-7269-2

description: mother


title: OCD Sample 0625-7445-1

description: father


title: OCD Sample 0625-7114-1

description: father


title: OCD Sample 0625-7445-3

description: proband


title: OCD Sample 0625-7114-2

description: mother


title: OCD Sample 0625-8346-1

description: father


title: OCD Sample 0625-8346-3

description: proband


title: OCD Sample 0625-7269-3

description: proband


title: OCD Sample 0625-7114-3

description: proband


title: OCD Sample 0625-6223-2

description: mother


title: OCD Sample 0625-5986-1

description: father


title: OCD Sample 0625-5986-3

description: proband


title: OCD Sample 0625-5706-2

description: mother


title: OCD Sample 0625-5706-3

description: proband


title: OCD Sample 0625-5986-2

description: mother


title: OCD Sample 0625-7445-2

description: mother


title: OCD Sample 0625-5375-2

description: mother


title: OCD Sample 0625-4262-2

description: mother


title: OCD Sample 0625-4262-3

description: father


title: OCD Sample 0625-3682-3

description: proband


title: OCD Sample 0625-4262-1

description: proband


title: OCD Sample 0625-2765-1

description: father


title: OCD Sample 0625-2765-3

description: proband


title: OCD Sample 0625-2251-2

description: mother


title: OCD Sample 0625-8219-3

description: proband


title: OCD Sample 0625-2251-1

description: father


title: OCD Sample 0625-1428-2

description: mother


title: OCD Sample 0625-2251-3

description: proband


title: OCD Sample 0625-1428-3

description: proband


title: OCD Sample 0625-1127-1

description: mother


title: OCD Sample 0625-1152-1

description: father


title: OCD Sample 0625-1127-3

description: proband


title: OCD Sample 0625-1152-2

description: mother


title: OCD Sample 0625-5375-3

description: proband


title: OCD Sample 0625-0144-3

description: proband


title: OCD Sample 0625-0201-1

description: father


title: OCD Sample 0555-6300-2

description: mother


title: OCD Sample 0625-0144-1

description: father


title: OCD Sample 0625-1152-3

description: proband


title: OCD Sample 0625-0201-3

description: proband


title: OCD Sample 0555-6300-1

description: father


title: OCD Sample 0625-0144-2

description: mother


title: OCD Sample 896673

description: proband


title: OCD Sample 0555-6300-3

description: proband


title: OCD Sample 0625-2765-2

description: mother


title: OCD Sample 896592

description: mother


title: OCD Sample 896593

description: proband


title: OCD Sample 896583

description: proband


title: OCD Sample 896581

description: father


title: OCD Sample 0625-1428-1

description: father


title: OCD Sample 896582

description: mother


title: OCD Sample 896572

description: mother


title: OCD Sample 896571

description: father


title: OCD Sample 896573

description: proband


title: OCD Sample 0625-1127-2

description: father


title: OCD Sample 0625-0201-2

description: mother


title: OCD Sample 1689

description: father


title: OCD Sample 896241

description: father


title: OCD Sample 1638

description: father


title: OCD Sample 4121

description: proband


title: OCD Sample 896672

description: mother


title: OCD Sample 896671

description: father


title: OCD Sample 1737

description: mother


title: OCD Sample 1736

description: proband


title: OCD Sample 1733

description: mother


title: OCD Sample 1713

description: mother


title: OCD Sample 1697

description: proband


title: OCD Sample 1725

description: proband


title: OCD Sample 1693

description: proband


title: OCD Sample 1690

description: mother


title: OCD Sample 1694

description: father


title: OCD Sample 896591

description: father


title: OCD Sample 1682

description: proband


title: OCD Sample 1666

description: mother


title: OCD Sample 1665

description: father


title: OCD Sample 1657

description: father


title: OCD Sample 1658

description: mother


title: OCD Sample 1653

description: father


title: OCD Sample 1639

description: mother


title: OCD Sample 896382

description: mother


title: OCD Sample 1741

description: father


title: OCD Sample 896373

description: proband


title: OCD Sample 1712

description: father


title: OCD Sample 896353

description: proband


title: OCD Sample 896392

description: mother


title: OCD Sample 896391

description: father


title: OCD Sample 896393

description: proband


title: OCD Sample 896351

description: father


title: OCD Sample 896371

description: father


title: OCD Sample 896381

description: father


title: OCD Sample 896321

description: father


title: OCD Sample 896352

description: mother


title: OCD Sample 896323

description: proband


title: OCD Sample 896893

description: proband


title: OCD Sample 1688

description: proband


title: OCD Sample 896542

description: mother


title: OCD Sample 896543

description: proband


title: OCD Sample 896541

description: father


title: OCD Sample 896532

description: mother


title: OCD Sample 1656

description: proband


title: OCD Sample 896533

description: proband


title: OCD Sample 896531

description: father


title: OCD Sample 896502

description: mother


title: OCD Sample 896501

description: father


title: OCD Sample 896512

description: mother


title: OCD Sample 896503

description: proband


title: OCD Sample 1652

description: proband


title: OCD Sample 896322

description: mother


title: OCD Sample 896442

description: mother


title: OCD Sample 896441

description: father


title: OCD Sample 896432

description: mother


title: OCD Sample 896412

description: mother


title: OCD Sample 896433

description: proband


title: OCD Sample 896431

description: father


title: OCD Sample 896413

description: proband


title: OCD Sample 896383

description: proband


title: OCD Sample 0625-8925-1

description: father


title: OCD Sample 896443

description: proband


title: OCD Sample 896411

description: father


title: OCD Sample 0625-8972-1

description: father


title: OCD Sample 0625-8972-2

description: mother


title: OCD Sample 0625-9550-2

description: mother


title: OCD Sample 0625-8925-3

description: proband


title: OCD Sample 0625-6323-2

description: mother


title: OCD Sample 0625-0832-1

description: father


title: OCD Sample 0625-2207-3

description: proband


title: OCD Sample 0625-2207-2

description: mother


title: OCD Sample HAM553

description: proband


title: OCD Sample HAM503

description: proband


title: OCD Sample HAM513

description: proband


title: OCD Sample HAM563

description: proband


title: OCD Sample HAM483

description: proband


title: OCD Sample 8961103

description: proband


title: OCD Sample HAM473

description: proband


title: OCD Sample HAM523

description: proband


title: OCD Sample 896273

description: proband


title: OCD Sample 896271

description: father


title: OCD Sample 896272

description: mother


title: OCD Sample 896221

description: father


title: OCD Sample 896243

description: proband


title: OCD Sample 0625-8972-3

description: proband


title: OCD Sample 896222

description: mother


title: OCD Sample 896143

description: proband


title: OCD Sample 896172

description: mother


title: OCD Sample 896192

description: mother


title: OCD Sample 896223

description: proband


title: OCD Sample 896191

description: father


title: OCD Sample 896242

description: mother


title: OCD Sample 0625-9550-3

description: proband


title: OCD Sample 896173

description: proband


title: OCD Sample 896193

description: proband


title: OCD Sample 896171

description: father


title: OCD Sample 896253

description: proband


title: OCD Sample 896152

description: mother


title: OCD Sample 896153

description: proband


title: OCD Sample HAM543

description: proband


title: OCD Sample 896151

description: father


title: OCD Sample 896142

description: mother


title: OCD Sample 896873

description: proband


title: OCD Sample 896141

description: father


title: OCD Sample 896132

description: mother


title: OCD Sample 896131

description: father


title: OCD Sample 896121

description: father


title: OCD Sample 896133

description: proband


title: OCD Sample 896122

description: mother


title: OCD Sample 896113

description: proband


title: OCD Sample 896123

description: proband


title: OCD Sample 896092

description: mother


title: OCD Sample 896091

description: father


title: OCD Sample 896111

description: father


title: OCD Sample 896082

description: mother


title: OCD Sample 896112

description: mother


title: OCD Sample 896093

description: proband


title: OCD Sample 896081

description: father


title: OCD Sample 1827

description: mother


title: OCD Sample 896083

description: proband


title: OCD Sample 8961181

description: father


title: OCD Sample 8961151

description: father


title: OCD Sample 374_1805

description: proband


title: OCD Sample 1762

description: mother


title: OCD Sample 1761

description: father


title: OCD Sample 896282

description: mother


title: OCD Sample 8961182

description: mother


title: OCD Sample 356-1756

description: proband


title: OCD Sample 8961153

description: proband


title: OCD Sample 1754

description: father


title: OCD Sample 358-1760

description: proband


title: OCD Sample 1807

description: mother


title: OCD Sample 896281

description: father


title: OCD Sample 1222

description: mother


title: OCD Sample 1806

description: father


title: OCD Sample 1227

description: father


title: OCD Sample 8961183

description: proband


title: OCD Sample 379-1818

description: proband


title: OCD Sample 8961152

description: mother


title: OCD Sample 1809

description: father


title: OCD Sample 1826

description: father


title: OCD Sample 384-1825

description: proband


title: OCD Sample 1776

description: mother


title: OCD Sample 364_1774

description: proband


title: OCD Sample 1812

description: father


title: OCD Sample 1775

description: father


title: OCD Sample 1813

description: mother


title: OCD Sample 375_1808

description: proband


title: OCD Sample 8961251

description: father


title: OCD Sample 1773

description: mother


title: OCD Sample 8961253

description: proband


title: OCD Sample 8961232

description: mother


title: OCD Sample 1772

description: father


title: OCD Sample 363_1771

description: proband


title: OCD Sample 1810

description: mother


title: OCD Sample 8961172

description: mother


title: OCD Sample 8961212

description: mother


title: OCD Sample 8961213

description: proband


title: OCD Sample 8961211

description: father


title: OCD Sample 8961233

description: proband


title: OCD Sample 8961171

description: father


title: OCD Sample 8961173

description: proband


title: OCD Sample 8961162

description: mother


title: OCD Sample 8961161

description: father


title: OCD Sample 8961163

description: proband


title: OCD Sample 8961142

description: mother


title: OCD Sample 896473

description: proband


title: OCD Sample 896471

description: father


title: OCD Sample 896472

description: mother


title: OCD Sample 8961143

description: proband


title: OCD Sample 896232

description: mother


title: OCD Sample 896231

description: father


title: OCD Sample 8961231

description: father


title: OCD Sample 896233

description: proband


title: OCD Sample 8961252

description: mother


title: OCD Sample 376_1811

description: proband


title: OCD Sample 0625-4932-3

description: proband


title: OCD Sample 1338_188608

description: mother


title: OCD Sample 1449

description: proband


title: OCD Sample 0625-2972-3

description: proband


title: OCD Sample 0625-4932-1

description: father


title: OCD Sample 0625-2318-1

description: father


title: OCD Sample 1596

description: proband

source_name: Blood

extract_protocol: DNA was extracted from whole blood using Qiagen genomic DNA extraction kit following manufacturer's specifications

value: Blood


title: OCD Sample 0625-9923-3

description: proband


title: OCD Sample 1634

description: proband


title: OCD Sample 0625-4932-2

description: mother


title: OCD Sample 896511_b

description: father


title: OCD Sample 1588_1450

description: father


title: OCD Sample 1607_313

description: proband


title: OCD Sample 0625-8740-2

description: mother


title: OCD Sample 1015-1

description: father


title: OCD Sample 1593

description: proband


title: OCD Sample 8961141

description: father


title: OCD Sample 1595

description: father


title: OCD Sample 1583

description: proband


title: OCD Sample 1585

description: father


title: OCD Sample 1578

description: proband


title: OCD Sample 1239_190116

description: father


title: OCD Sample 1263_189803

description: mother


title: OCD Sample 1262_188515

description: father


title: OCD Sample 204_189717

description: proband


title: OCD Sample 224_188564

description: proband


title: OCD Sample 1284_190127

description: mother


title: OCD Sample 1283_190122

description: father


title: OCD Sample 1464_188576

description: mother


title: OCD Sample 1279_189807

description: mother


title: OCD Sample 1282_190114

description: proband


title: OCD Sample 1232_189802

description: proband


title: OCD sample 1257

description: proband

hyb_protocol: Standard Illumina protocol for Omni2.5M

scan_protocol: Standard Illumina protocol for Omni2.5M

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. We detected CNVs from OMNI2.5M microarray data using iPattern, PennCNV, CNVPartition, and QuantiSNP. We defined a stringent set of variants when each variant was called by at least by two algorithms
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: Cy3 and Cy5

source_name: saliva

label_protocol: Standard Illumina protocol for Illumina Omni2.5M

value: saliva


title: OCD sample 151

description: proband


title: OCD Sample 1238_190120

description: proband


title: OCD sample 270

description: proband


title: OCD Sample 1297_190321

description: mother


title: OCD sample 1427

description: proband


title: OCD sample 1453

description: proband


title: OCD Sample 1240_189982

description: mother


title: OCD sample 145_b

description: proband


title: OCD Sample 1296_188614

description: father


title: OCD Sample 1367_188568

description: father


title: OCD Sample 1368_189719

description: mother


title: OCD Sample 1439_189732

description: father


title: OCD Sample 188610

description: father


title: OCD sample 9740

description: proband


title: OCD Sample 1245_188603

description: father


title: OCD Sample 189806

description: mother


title: OCD sample 8060

description: proband


title: OCD sample 6795

description: proband


title: OCD Sample 1254_188613

description: proband


title: OCD Sample 1246_189249

description: mother


title: OCD Sample 1349_188527

description: mother


title: OCD sample 9196

description: proband


title: OCD sample 6676

description: proband


title: OCD sample 2427

description: proband


title: OCD Sample 1300_189271

description: mother


title: OCD sample 4859

description: proband


title: OCD Sample 1299_189273

description: father


title: OCD Sample 1298_189711NF

description: proband


title: OCD sample 1888

description: proband


title: OCD sample 1209

description: proband


title: OCD Sample 1413

description: mother


title: OCD sample 1707

description: proband


title: OCD Sample 1411

description: proband


title: OCD sample 108_B

description: proband


title: OCD sample 1339

description: proband


title: OCD Sample 1491

description: mother


title: OCD Sample 1313

description: father


title: OCD sample 1446

description: proband


title: OCD Sample 1490

description: father


title: OCD Sample 267

description: proband


title: OCD sample 207

description: proband


title: OCD Sample 1314

description: mother


title: OCD Sample 1312

description: proband


title: OCD Sample 1215

description: mother


title: OCD sample 30

description: proband


title: OCD sample 108_A

description: proband


title: OCD Sample 1214

description: father


title: OCD sample 1402

description: proband


title: OCD Sample 1213

description: proband


title: OCD Sample 1412

description: father


title: OCD sample 1264

description: proband


title: OCD sample 1306

description: proband


title: OCD sample 120_a

description: proband


title: OCD Sample 1473

description: father


title: OCD sample HAM383

description: proband


title: OCD Sample 249

description: proband


title: OCD sample 1203

description: proband


title: OCD sample 199

description: proband


title: OCD Sample 1229

description: father


title: GFP-PRDM1 transduced cells on days 17, biological rep2

city: Taipei

first: I-Ying

last: Lin

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

description: Gene expression data from GFP-PRDM1 transduced cells on days 17

hyb_protocol: After converting linear RNA into 35-200 nt biotin-labeled fragments, samples were then hybridized to GeneChip® Human Genome U133 array.

scan_protocol: The array data were acquired with GeneChip® Scanner 3000 using AGCC software.

data_processing: The data from GFP control and GFP-PRDM1 transduced H9 hESCS were analyzed with GeneSpring GX.

source_name: H9 hESCs were transduced with GFP-PRDM1 vector and collected at days 17

label_protocol: 1 ug of total RNA was subjected to reverse transcription and biotin-conjugated nucleotide incorporation by using GeneChip ® 3' IVT Express Kit (Affymetrix).

growth_protocol: H9 hESCs were maintained in DMEM/F12 supplemented with 20% KnockOut serum and 5 ng/ml bFGF on MEF feeders.

extract_protocol: Total RNA was isolated according to the manufacturer's instructions by an RNeasy spin column (Qiagen).

treatment_protocol: H9 hESCs were transduced with GFP control and GFP-PRDM1 vectors and maintained in ES culture medium. The transduced cells were collected on days 7 and 17.

tag: time

value: Days 17

tag: ectopic expression


title: GFP-PRDM1 transduced cells on days 17, biological rep1


title: GFP transduced cells on days 17, biological rep3

description: Gene expression data from GFP transduced cells on days 17

source_name: H9 hESCs were transduced with GFP vector and collected at days 17

value: GFP


title: OCD sample HAM373

description: proband

tag: gender


title: OCD sample HAM363

description: proband


title: GFP-PRDM1 transduced cells on days 7, biological rep2

description: Gene expression data from GFP-PRDM1 transduced cells on days 7

source_name: H9 hESCs were transduced with GFP-PRDM1 vector and collected at days 7

value: Days 7


title: GFP-PRDM1 transduced cells on days 7, biological rep1


title: GFP-PRDM1 transduced cells on days 17, biological rep3


title: OCD Sample 1249

description: mother


title: GFP transduced cells on days 7, biological rep2

description: Gene expression data from GFP transduced cells on days 7

source_name: H9 hESCs were transduced with GFP vector and collected at days 7


title: OCD sample HAM353

description: proband


title: OCD Sample 1248

description: father


title: GFP transduced cells on days 17, biological rep1


title: OCD Sample 1247

description: proband


title: OCD Sample 1422

description: mother


title: 62_RNA

type: SRA

city: Chapel Hill

first: Shehzad

last: Sheikh

state: NC

address: 5023A Genetic Medicine Building

institute: University of North Carolina - Chapel Hill

library_source: transcriptomic

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained. High quality reads were aligned to their respective personalized genomes using the SNP-tolerant GSNAP software (Wu and Nacu 2010).
Transcript abundance was estimated by computing RPKM (Mortazavi et al. 2008) using RefSeq gene models aggregated by gene symbol.
genome build: hg19
processed data file format and content: Raw abundance matrix

molecule: polyA RNA

source_name: Colonic mucosa

growth_protocol: CD patients from the adult IBD Center at University of North Carolina were included in this study.

extract_protocol:
RNA was isolated as described in Peck et al, Inflamm Bowel Dis, 2015
TruSeq libraries were constructed as per manufacturer's recommendations.

value: Colonic mucosa

tag: disease status

value: CD

tag: molecular subtype

value: Colon-like


title: 63_RNA


title: OCD Sample 1474

description: mother


title: 64_RNA

value: Ileum-like


title: OCD sample HAM333

description: proband


title: OCD Sample 1421

description: father


title: OCD Sample 1420

description: proband


title: 50_RNA

value: nonIBD


title: 51_RNA


title: OCD sample HAM313

description: proband


title: OCD sample HAM343

description: proband


title: OCD sample HAM303

description: proband


title: GFP transduced cells on days 7, biological rep1


title: GFP transduced cells on days 17, biological rep2


title: OCD Sample 1228

description: proband


title: OCD sample HAM253

description: proband


title: OCD Sample 1457

description: father


title: 48_RNA


title: 49_RNA


title: 54_RNA


title: OCD sample HAM223

description: proband


title: OCD Sample 1458

description: mother


title: OCD sample HAM323

description: proband


title: 450_RNA


title: 440_RNA


title: OCD Sample 218

description: proband


title: OCD sample HAM173

description: proband


title: 43_RNA


title: OCD sample HAM193

description: proband


title: OCD Sample 1272

description: father


title: OCD sample 124_1351

description: proband


title: OCD sample 1291

description: proband


title: OCD sample 155

description: proband


title: 431_RNA


title: OCD Sample 1271-51

description: proband


title: 434_RNA


title: OCD sample 1328

description: proband


title: OCD Sample 1376

description: mother


title: OCD sample 86

description: proband


title: OCD Sample 1375

description: father


title: OCD Sample 1374

description: proband


title: 422_RNA


title: OCD sample 1468

description: proband


title: 413_RNA


title: OCD sample 1275

description: proband


title: OCD Sample 1237

description: mother


title: OCD Sample 1273

description: mother


title: 420_RNA


title: OCD sample 191

description: proband


title: 408_RNA


title: OCD Sample 1236

description: father


title: 405_RNA


title: OCD sample 206

description: proband


title: 407_RNA


title: OCD Sample 0625-1111-2-2222-2

description: mother


title: OCD Sample 1241

description: proband


title: 39_RNA


title: OCD Sample 1243

description: mother


title: 36_RNA


title: 429_RNA


title: 424_RNA


title: OCD sample 263

description: proband


title: 32_RNA


title: OCD Sample 1726

description: father


title: OCD sample 210

description: proband


title: OCD sample 1390_a

description: proband


title: OCD Sample 188563

description: mother


title: 29_RNA


title: OCD sample 252

description: proband


title: OCD Sample 1234

description: proband


title: OCD sample 1333

description: proband


title: OCD Sample 1242

description: father


title: OCD sample AD_CAMH

description: proband


title: OCD Sample 188609

description: father


title: 30_RNA


title: 25_RNA


title: OCD sample 262

description: proband


title: OCD sample 896693_b

description: proband


title: OCD Sample 1637

description: proband


title: 23_RNA


title: OCD sample 134_a

description: proband


title: 22_RNA


title: OCD Sample 1731

description: proband


title: OCD sample 896673_a

description: proband


title: OCD Sample 1727

description: mother


title: OCD sample 896653_b

description: proband


title: OCD sample 896633_b

description: proband


title: 21_RNA


title: OCD Sample 1711

description: proband


title: 20_RNA


title: OCD Sample 1699

description: mother


title: OCD sample 896633_a

description: proband


title: 63_FAIRE

library_source: genomic

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained. High quality reads were aligned to their respective personalized genomes using the SNP-tolerant GSNAP software (Wu and Nacu 2010).
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
genome build: hg19
processed data file format and content: bigWig of raw FAIRE-seq signal

extract_protocol:
FAIRE was performed as described previously (Simon 2012).
TruSeq libraries were constructed as per manufacturer's recommendations.


title: 27_RNA


title: OCD Sample 1628

description: proband


title: OCD sample 896623_a

description: proband


title: 62_FAIRE


title: OCD sample 896603_b

description: proband


title: OCD Sample 1680

description: father


title: 54_FAIRE


title: OCD Sample 1732

description: father


title: OCD sample 0625-7518-3

description: proband


title: OCD Sample 1695

description: mother


title: OCD Sample 1664

description: proband


title: OCD sample 1014-3

description: proband


title: OCD sample 0625-2289-3

description: proband


title: OCD Sample 1465

description: proband


title: 434_FAIRE


title: 450_FAIRE


title: OCD Sample 1426

description: mother


title: OCD sample 0625-4889-3

description: proband


title: OCD Sample 1654

description: mother


title: 433_FAIRE


title: OCD sample 896493

description: proband


title: OCD sample 896733

description: proband


title: OCD Sample 1425

description: father


title: 440_FAIRE


title: OCD sample 896423

description: proband


title: OCD Sample 1424

description: proband


title: 431_FAIRE


title: 429_FAIRE


title: OCD sample 896403

description: proband


title: OCD Sample 1698

description: father


title: OCD Sample 1467

description: mother


title: 424_FAIRE


title: OCD sample 896363

description: proband


title: 51_FAIRE


title: OCD Sample 1466

description: father


title: 422_FAIRE


title: OCD sample 896343

description: proband


title: OCD Sample 0625-1111-3

description: proband


title: OCD Sample 0625-1111-1-2222-1

description: father


title: OCD Sample 1288

description: mother


title: 420_FAIRE


title: 408_FAIRE


title: OCD Sample 1287

description: father


title: OCD Sample 1286

description: proband


title: 407_FAIRE


title: OCD Sample 1755

description: mother


title: 405_FAIRE


title: 29_FAIRE


title: 25_FAIRE


title: OCD Sample 1278_190003

description: father


title: OCD Sample 1587_1451

description: mother


title: 21_FAIRE


title: OCD Sample 1631

description: proband


title: 20_FAIRE


title: 413_FAIRE


title: CD34-enriched HSPC_S3_rep1

city: Navi Mumbai

first: Jyoti

middle: Anand

last: Kode

state: Maharashtra

address: Kharghar

department: Kode Lab

institute: Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre

description: Gene expression in CD34-enriched G-CSF mobilized human periheral blood from cancer patient

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Human 8x60k (AMADID No: 027114). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software Version 10.5 and 75th Percentile shift Normalization of the data was done in GeneSpring GX V 11.0

source_name: CD34-enriched HSPC

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit as per the manufacturer’s protocol

treatment_protocol: Nucleated cells were isolated from mobilized peripheral blood stem cell harvests obtained during  hematopoietic stem cell transplantation (Allogenic transplantation, n=4; Autologous transplantation, n=1). CD34+ hematopoietic stem and progenitor cells (HSPC) were enriched from PBSC harvests by immunomagnetic  separation using negative selection method. Enriched CD34+ cells  at 2.5 x 104/ ml were cultured in IMDM containing 10%FCS in a 96-well plate culture plate. The cultures were treated with recombinant TPO (50 ng/ml, Stem Cell Technology, Canada), SCF (50ng/ml), Flt3L (50 ng/ml) and SDF1 peptide (10ng/ml; A gift from Prof Nobukata Fujii and Dr Shinya Oishi, Kyoto University, Japan) for 4 days. Medium alongwith factors was replenished after 4 days. After 8 days of stimulation, cells were counted for total nucleated cell count and stored in RNAlater for microarray experiments .

value: Immunomagentically separated CD34+ HSPC from mobilized whole blood

value: male

tag: donor

value: Cancer patient


title: ExVivoExpanded GF stimulated HSPC_S5_rep1

description: Gene expression after ex-vivo expansion after stimulation of CD34-enriched HSPC with GF (SCF+TPO+FLT3)

source_name: ExVivoExpanded GF-stimulated HSPC

value: Ex Vivo expanded HSPC

value: Healthy Donor


title: Mobilized PBSC_S3_rep1

description: Gene expression in G-CSF mobilized human periheral blood from cancer patient

source_name: Mobilized PBSC

value: Mobilized whole blood


title: ExVivoExpanded GF+SDF1 stimulated HSPC_S4_rep1

description: Gene expression after ex-vivo expansion after stimulation of CD34-enriched HSPC with GF (SCF+TPO+FLT3) + homing

source_name: ExVivoExpanded GF+SDF1-stimulated HSPC

value: female


title: TMEV 16hr

status: Public on Dec 10 2016

city: Nakahara-ku, Kawasaki-shi

first: Nobuyuki

last: Tanaka

state: Kanagawa

address: 1-356, Kosugi-cho

department: Department of Molecular Oncology

country: Japan

institute: Institute for Advanced Medical Sciences, Nippon Medical School

description: 16 hours after TMEV infection

hyb_protocol: See hybridization protocol described in the manual of the Affymetrix GeneChip® WT PLUS Reagent Kit. cDNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Data Analysis Tool Ver3.2 (Filogen).

source_name: Cochlear sensory epithelia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA as described in GeneChip® WT Terminal Labeling Kit (Affymetorix).

growth_protocol: Cochlear sensory epithelia were resected and cultured as previously described (Hayashi, Y. et al. Microbes Infect 15, 592-598, 2013). All experiments began after an overnight incubation of each cochlea with 300 µl DMRM medium to stabilize the explants.

extract_protocol: RNeasy Micro Kit of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Each cochlea was then transferred to 400 µl medium containing 3.0x10 7 pfu/ml TMEV or 1000 ng/ml LPS (Sigma-Aldrich), and incubated for indicated time.

value: ICR

value: cochlear sensory epithelia

tag: treatment

value: TMEV 16hr


title: TMEV 9hr

description: 9 hours after TMEV infection

value: TMEV 9hr


title: Mobilized PBSC_S1_rep1

description: Gene expression in G-CSF mobilized human periheral blood from healthy donor


title: CD34-enriched HSPC_S5_rep1

description: Gene expression in CD34-enriched G-CSF mobilized human periheral blood from healthy donor


title: MCI_36-18

city: Obu

first: SAYURI

last: HIGAKI

state: Aichi

address: 7-430 Morioka-cho

department: Medical Genome Center

institute: National Center for Geriatrics and Gerotology

description: MCI

data_processing:
The raw data was extracted from the Light cycler 480 software. The GenEx software (Exiqon) was used for data filtering analysis. Any assay data value must be detected below Cp <37 or at least 3 Cp lower than negative control value to be included in the data analysis. Data that did not pass these criteria were omitted from any further analysis.
The amplification efficiency was calculated using the LinRegPCR software. Reactions with amplification efficiency below 1.6 were also removed.
Fold Change worksheet reports MCI/Control ratio of normalized values detected (not null) in over 80% samples in either MCI or Control [2^(-ddCp) = 2^(MCI average (-dCp) - Control average (-dCp)] .

label: SYBR Green

source_name: Plasma

label_protocol: For reverse transcription, 19.2 μL of RNA eluate was used in total 80 μL reactions with the miRCURY LNA™ Universal RT cDNA synthesis kit (Exiqon). The cDNA products were diluted 57.25 fold (80 μL cDNA reactions + 4500 μL water) and assayed in 10 μL PCR reactions according to the protocol for the miRCURY LNA™ Universal RT microRNA PCR System; each microRNA was assayed once by qPCR on the microRNA Ready-to-Use PCR, Human panel I and panel II, V2. Negative controls excluding template from the reverse transcription reaction were assayed and profiled in the same manner of the other samples. The amplification was performed in a LightCycler® 480 Real-Time PCR System (Roche) in 384 well plates. The amplification curves were analyzed using the Roche LC software (ver. 1.5), both for determination of Cp (by the second derivative method) and for melting curve analysis.

extract_protocol: Total RNA was extracted from plasma using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions with the following modifications. Plasma was thawed on ice and centrifuged at 3000×g for 5 min in a 4 ◦C microcentrifuge. An aliquot of 200 μL of plasma per sample was transferred to a new tube and 750 μL of Qiazol mixture containing 1.25 μg/mL of MS2 bacteriophage RNA (Roche Applied Science) was added to the plasma. The tube was mixed and incubated for 5 min followed by the addition of 200 μL chloroform. The tube was mixed, incubated for 2 min and centrifuged at 12,000×g for 15 min in a 4 ◦C microcentrifuge. The upper aqueous phase was transferred to a new microcentrifuge tube and 1.5 volume of 100% ethanol was added. The contents were mixed thoroughly and 750 μL of the sample was transferred to a Qiagen RNeasy Mini spin column in a collection tube followed by centrifugation at 15,000×g for 30 sec at room temperature. The process was repeated until all remaining sample had been loaded. The spin column was rinsed with 700 μL Qiagen RWT buffer and centrifuged at 15,000×g for 1 min at room temperature followed by another rinse with 500 μL Qiagen RPE buffer and centrifuged at 15,000×g for 1 min at room temperature. A rinse step (500 μL Qiagen RPE buffer) was repeated twice. The spin column was transferred to a new collection tube and centrifuged at 15,000×g for 2 min at room temperature. The spin column was transferred to a new microcentrifuge tube and the lid was left open for 1 min to allow the column to dry. Total RNA was eluted by adding 50 μL of RNase-free water to the membrane of the spin column and incubating for 1 min before centrifugation at 15,000×g for 1 min at room temperature. The RNA was stored in a -80 ◦ C freezer.

tag: sample type

value: MCI

tag: age


title: MCI_36-17

description: MCI


title: MCI_36-19

description: MCI


title: MCI_36-20

description: MCI


title: ExVivoExpanded GF stimulated HSPC_S2_rep1


title: LPS 9hr

description: 9 hours after LPS stimulation

value: LPS 9hr


title: Mobilized PBSC_S5_rep1


title: ExVivoExpanded GF+SDF1 stimulated HSPC_S2_rep1

description: Gene expression after ex-vivo expansion after stimulation of CD34-enriched HSPC with GF (SCF+TPO+FLT3) + homing factor SDF1


title: Smooth chorion cytotrophoblasts from second trimester 3

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

hyb_protocol: Sample processing and hybridization were done according to protocols that were devised by the UCSF Gladstone (NHLBI) Genomics Core Facility.

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: Gene level expression data quality was confirmed, normalized (RMA) and summarized (Affymetrix Expression Console Software). Significant differential expression was determined by statistical analysis of false discovery rate (FDR < 0.05) and absolute linear fold change >2 (Affymetrix Transcriptome Analysis Console Software).

source_name: human placenta

label_protocol: Samples were prepared using the Ambion Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix GeneChip  WT Terminal Labeling and Controls Reagent kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus Micro

treatment_protocol: Portions of the smooth chorion were washed repeatedly in cold PBS to remove blood. Unfixed  specimens were rolled end-to-end, placed in cryomolds containing OCT, frozen over a  dry ice/ethanol slurry, and stored at -80C. The blocks were sectioned at 20 μm by using  a Leica CM3050 cryostat, mounted on UV treated PEN-membrane slides and stored under dry ice prior to laser capture microdissection later that day.  Immediately prior to the procedure, sections were immersed in cold PBS until the OCT  dissolved (~1 min), dipped in 0.1% toluidine blue for 30 s, washed in cold PBS,  dehydrated (30 s/treatment) in a graded ethanol series (75%, 95%, 100%), then rapidly  dried with compressed nitrogen. All solutions were made with nuclease-free water.  schCTBs were laser dissected (Leica LMD 7000) and collected directly into RLT Plus  Buffer.

value: smooth chorion cytotrophoblasts


title: Smooth chorion cytotrophoblasts from normal preterm birth 2


title: Smooth chorion cytotrophoblasts from severe preeclampsia 3


title: Smooth chorion cytotrophoblasts from normal preterm birth 3


title: Smooth chorion cytotrophoblasts from second trimester 1


title: LPS 16hr

description: 16 hours after LPS stimulation

value: LPS 16hr


title: Smooth chorion cytotrophoblasts from normal preterm birth 4


title: Smooth chorion cytotrophoblasts from normal preterm birth 1


title: Mock

description: mock

value: mock


title: Smooth chorion cytotrophoblasts from severe preeclampsia 1


title: Smooth chorion cytotrophoblasts from severe preeclampsia 4


title: Smooth chorion cytotrophoblasts from severe preeclampsia 2


title: Smooth chorion cytotrophoblasts from second trimester 2


title: Smooth chorion cytotrophoblasts from second trimester 4


title: MCI_36-16

description: MCI


title: MCI_36-15

description: MCI


title: MCI_36-13

description: MCI


title: MCI_36-14

description: MCI


title: MCI_36-12

description: MCI


title: MCI_22-16

description: MCI


title: MCI_22-13

description: MCI


title: MCI_36-10

description: MCI


title: MCI_36-09

description: MCI


title: MCI_36-06

description: MCI


title: MCI_36-08

description: MCI


title: MCI_22-14

description: MCI


title: MCI_36-07

description: MCI


title: MCI_22-15

description: MCI


title: MCI_22-11

description: MCI


title: MCI_22-12

description: MCI


title: MCI_22-10

description: MCI


title: Cont_36-04

description: Control

value: normal


title: Cont_36-03

description: Control


title: Cont_36-05

description: Control


title: Cont_36-02

description: Control


title: MCI_22-9

description: MCI


title: MCI_36-11

description: MCI


title: Cont_36-01

description: Control


title: Cont_34-11

description: Control


title: Cont_34-09

description: Control


title: Cont_34-06

description: Control


title: Cont_34-04

description: Control


title: Cont_34-03

description: Control


title: Cont_34-02

description: Control


title: Cont_34-01

description: Control


title: SEA treated CD11b+CD103- lymph DCs, biological rep3

city: Glasgow

first: Simon

last: Milling

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

hyb_protocol: Following fragmentation, 5.5ug ss-cDNA were hybridized for 16hr at 45C on Mouse Transcriptome Array 1.0 (Affymetrix) in the Affymetrix GeneChip® Hybridization Oven 645. Microarrays were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G according to the manufacturers’ instructions.

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.3.1.187
program-company = Affymetrix

source_name: FACS purified lymph migrating DC subset incubated with SEA for 18 hours

label_protocol: RNA samples were amplified from 20-30 ng total RNA using the Affymetrix WT Pico kit according to the manufacturers’ instructions.

growth_protocol: DC subsets were FACS purified from the lymph of C57BL/6 MLNx mice.

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

treatment_protocol: 30,000 cells of each subset (three replicates) were incubated with or without 15 µg/ml SEA in X-vivo 15 media (Lonza) supplemented with 1% L-glutamine (Invitrogen) and 0.1% 2-mercaptoethanol (Sigma-Aldrich) for 18 hours at 37C and 5% CO2.

value: intestinal lymph from MLNx animals

value: CD11b+CD103- lymph DCs

value: SEA


title: Cont_34-07

description: Control


title: Cont_34-05

description: Control

value: male


title: Cont_34-08

description: Control


title: CP161_4

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: mRNA expression profiles from primary tissue

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: gdT-cells stimulated with bromohydrin pyrophosphate  + IL-15 + TGF-b

extract_protocol: RNA extracted using miRVana (Ambion) according to the manufacturers guidelines

treatment_protocol: samples origin from primary human tissue

tag: tissue type

value: primary tissue

value: gamma delta T cells


title: untreated CD11b+CD103+ lymph DCs, biological rep2

source_name: FACS purified lymph migrating DC subset incubated with media for 18 hours

tag: tissue

value: CD11b+CD103+ lymph DCs

value: control


title: SEA treated CD11b+CD103+ lymph DCs, biological rep2

tag: strain


title: untreated CD11b+CD103- lymph DCs, biological rep2

tag: cell type


title: CP161_6

source_name: gdT-cells stimulated with activation/expander beads + IL-15 + TGF-b

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: SEA treated CD11b+CD103- lymph DCs, biological rep2


title: untreated CD11b+CD103+ lymph DCs, biological rep1


title: CP161_1

source_name: unstimulated gdT-cells


title: CP161_2

source_name: unstimulated Vd2-gdT-cells

value: Vd2 gamma delta T cells


title: CP161_7

source_name: Vd2-gdT-cells stimulated with activation/expander beads + IL-2


title: CP161_8

source_name: Vd2-gdT-cells stimulated with activation/expander beads + IL-15 + TGF-b


title: SEA treated CD11b+CD103+ lymph DCs, biological rep1


title: SEA treated CD11b+CD103- lymph DCs, biological rep1


title: untreated CD11b+CD103- lymph DCs, biological rep1


title: SEA treated CD11b+CD103+ lymph DCs, biological rep3


title: CP161_3

source_name: gdT-cells stimulated with bromohydrin pyrophosphate  + IL-2


title: untreated CD11b+CD103+ lymph DCs, biological rep3


title: untreated CD11b+CD103- lymph DCs, biological rep3


title: CP161_5

source_name: gdT-cells stimulated with activation/expander beads + IL-2


title: Cont_22-8

description: Control

value: female


title: Cont_22-7

description: Control


title: Cont_22-5

description: Control


title: Cont_22-4

description: Control


title: Cont_22-2

description: Control


title: Cont_22-3

description: Control


title: Cont_22-1

description: Control


title: Cont_22-6

description: Control


title: Cont_07-13

description: Control


title: Cont_07-14

description: Control


title: CP160_7


title: CP160_5


title: C57BL6/J mouse mock)-infected, biological rep2

city: Galveston

first: Slobodan

last: Paessler

address: 301 University Blvd

department: Pathology

institute: UTMB

description: Gene expression data from brain of  wild-type mice (strain C57BL6/J) mock-infected i.n. with PBS

hyb_protocol: Total fragmented cRNA was hybridized to the Affymetrix Gene Chip Mouse Genome 430A 2.0 Array using the GeneChip Hybridization Oven 640. The chips were washed and stained in a GeneChip Fluidics Station 450.

scan_protocol: Fluorescence was detected with an Affymetrix-GS3000 Gene Array scanner using the GeneChip Operating System software (GCOS1.4)

data_processing: Microarrays quality assessment (affy, affyPLM and QCReport, affycoretools packages), preprocessing (gcrma package) and differential expression analysis (limmapackage) were performed with Bioconductor software packages in R programming environment.  Hierarchical clustering of differentially expressed genes was performed in the Spotfire Decision Site 9.0 for Functional Genomics (Spotfire Inc., Somerville, MA) using Unweighted Pair-Group with Arithmetic Mean and Euclidian distance method.  Differentially expressed genes were associated with biological functions and/or diseases or with canonical pathways in Ingenuity’s Knowledge Base of the Ingenuity Pathways Analysis (Ingenuity Systems, http://www.ingenuity.com). Right-tailed Fisher’s exact test was used to calculate a p-value determining the probability that the association between the genes in the dataset and the canonical pathway or biological function and/or disease is caused by chance.

source_name: Mice, strain C57BL6/J, mock-infected

label_protocol: Total RNA was subjected to GeneChip Expression Analysis (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions [Expression Analysis Technical Manual, Section 2: Eukaryotic Sample and Array Processing, Alternative protocol for One-Cycle cDNA synthesis followed by synthesis of biotin-labeled cRNA with MessageAmp Premier RNA Amplification Kit (Ambion Inc., Austin, TX)]

growth_protocol: At day 0, mice were challenged with PBS (mock-infection) or vaccine strain of VEEV (TC83) intranasally (i.n.) with 1 × 10^7 plaque forming units of VEEV (TC83) per animal in 40 μl of PBS administering approximately 20 μl per nare.

extract_protocol: DNase-treated total RNA was isolated using TRIZOL Reagent followed by the RNAqueous Mini and RNeasy-Free DNAase Set according to the protocols adapted from the manufacturer’s instructions.

treatment_protocol: At 6 days post infection mice were humanely sacrificed and midline saggital sections of brain was removed

value: brain

tag: age/gender

value: 4 to 8 week old

tag: genotype/variation

value: wildtype

tag: infection

value: mock-infection


title: C57BL6/J mouse VEEV (TC83)-infected, biological rep3

description: Gene expression data from brain of wild-type mice (strain C57BL6/J) infected i.n. with VEEV (TC83)

source_name: Mice, strain C57BL6/J, VEEV (TC83)-infected

value: VEEV (TC83)


title: CP160_8


title: Cont_07-11

description: Control


title: CP156_6


title: αβ-TCR -/- mouse mock-infected, biological rep2

description: Gene expression data from brain of mice (strain αβ-TCR -/-) mock-infected i.n. with PBS

source_name: Mice, strain αβ-TCR -/-, mock-infected

value: alphabeta-TCR -/-


title: CP160_6


title: C57BL6/J mouse VEEV (TC83)-infected, biological rep2


title: C57BL6/J mouse VEEV (TC83)-infected, biological rep1


title: CP160_2


title: CP160_1


title: CP160_3


title: C57BL6/J mouse mock)-infected, biological rep1

description: Gene expression data from brain of wild-type mice (strain C57BL6/J) mock-infected i.n. with PBS


title: αβ-TCR -/- mouse mock-infected, biological rep1


title: Cont_07-10

description: Control

value: normal


title: CP160_4


title: αβ-TCR -/- mouse VEEV (TC83)-infected, biological rep2

description: Gene expression data from brain of mice (strain αβ-TCR -/-) infected i.n. with VEEV (TC83)

source_name: Mice, strain αβ-TCR -/-, VEEV (TC83)-infected


title: Cont_07-9

description: Control


title: Cont_07-12

description: Control


title: CP156_5


title: αβ-TCR -/- mouse VEEV (TC83)-infected, biological rep3


title: αβ-TCR -/- mouse VEEV (TC83)-infected, biological rep1


title: CP156_4


title: C3H/HeN mouse mock-infected, biological rep2

description: Gene expression data from brain of mice (strain C3H/HeN) mock-infected i.n. with PBS

source_name: Mice, strain C3H/HeN, mock-infected


title: C3H/HeN mouse mock-infected, biological rep1


title: CP156_1


title: C3H/HeN mouse VEEV (TC83)-infected, biological rep3

description: Gene expression data from brain of mice (strain C3H/HeN) infected i.n. with VEEV (TC83)

source_name: Mice, strain C3H/HeN, VEEV (TC83)-infected


title: Cont_07-8

description: Control

source_name: Plasma


title: CP156_2


title: C3H/HeN mouse VEEV (TC83)-infected, biological rep2


title: A_276

status: Public on Dec 09 2016

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

hyb_protocol: Standard procedure for Affymetrix® GeneTitan™ running Affymetrix GeneChip® Command Console 2.0.

data_processing: Scans were imported into ArrayStudio V8.0 and pre-processed using the default RMA pipeline

source_name: Blood

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: RNA was extracted from blood collected in PAXgene tubes using the PAXgene blood miRNA kit

tag: cohort

value: Severe asthma, non-smoking

tag: race

value: blood


title: A_663

scan_protocol: Standard procedure for Affymetrix® GeneTitan™ running Affymetrix GeneChip® Command Console 2.0.


title: A_189


title: A_400

value: Healthy, non-smoking


title: A_460

value: male


title: A_433

value: Severe asthma, smoking


title: A_406


title: A_625

value: Moderate asthma, non-smoking


title: A_543


title: A_577


title: A_585


title: A_649


title: A_421


title: A_219


title: A_586


title: C3H/HeN mouse VEEV (TC83)-infected, biological rep1


title: A_128


title: CP156_3

value: primary tissue

value: gamma delta T cells


title: A_145


title: A_389


title: A_014


title: A_023


title: A_197


title: A_436


title: A_368


title: A_391


title: A_482


title: A_631


title: A_149


title: A_257


title: A_253


title: A_071


title: A_267


title: A_699


title: A_217


title: A_058


title: A_592


title: A_712


title: A_239


title: A_620


title: A_623


title: A_470


title: A_512


title: A_144


title: A_492


title: A_377


title: A_729


title: A_587


title: A_245


title: A_615


title: A_531


title: A_336


title: A_230


title: A_312


title: A_241


title: A_509


title: A_383


title: A_233


title: A_437


title: A_037


title: A_576


title: A_107


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title: A_517


title: A_212


title: A_466


title: A_006


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title: A_684


title: A_299


title: A_650


title: A_250


title: A_658


title: A_629


title: A_290


title: A_347


title: A_416


title: A_476


title: A_124


title: A_029


title: A_448


title: A_271


title: A_123


title: A_656


title: A_413


title: A_105


title: A_052


title: A_206


title: A_655


title: A_578


title: A_122


title: A_687


title: A_666


title: A_379


title: A_647


title: A_365


title: A_183


title: A_083


title: A_359


title: A_039


title: A_380


title: A_613


title: A_274


title: A_041


title: A_028


title: A_340


title: A_329


title: A_131


title: A_343


title: A_560


title: A_583


title: A_007


title: A_405


title: A_461


title: A_714


title: A_525


title: A_061


title: A_032


title: A_143


title: A_301


title: A_692


title: A_572


title: A_284


title: A_367


title: A_237


title: A_305


title: A_713


title: A_497


title: A_214


title: A_203


title: A_181


title: A_455


title: A_165


title: A_705


title: A_354


title: A_298


title: A_180


title: A_709


title: A_342


title: A_568


title: A_707


title: A_719


title: A_648


title: A_544

value: other


title: A_469

value: female


title: A_557


title: A_556


title: A_321


title: A_374


title: A_633


title: A_269


title: A_654


title: A_319


title: A_635


title: A_018


title: A_045


title: A_575


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title: A_378


title: A_574


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title: A_225


title: A_177


title: A_597


title: A_171


title: A_685


title: A_409


title: A_044


title: A_099


title: A_163


title: A_341


title: A_038


title: A_363


title: A_590


title: A_025


title: A_060


title: A_275


title: A_050


title: A_527


title: A_364


title: A_213


title: A_308


title: A_695


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title: A_550


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title: A_287


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title: A_659


title: A_146


title: A_446


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title: A_067


title: A_072


title: A_652


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title: A_327


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title: A_595


title: A_010


title: A_514


title: A_573


title: A_486


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title: A_677


title: A_689


title: A_031


title: A_040


title: A_104


title: A_609


title: A_035


title: A_580


title: A_154


title: A_208


title: A_559


title: A_080


title: A_358


title: A_288


title: A_680


title: A_345


title: A_415


title: A_614


title: A_558


title: A_091


title: A_101


title: A_619


title: A_394


title: A_524


title: A_027


title: A_155


title: A_095


title: A_030


title: A_369


title: A_630


title: A_199


title: A_581


title: A_306


title: A_505


title: A_679


title: A_172


title: A_244


title: A_382


title: A_111


title: A_387


title: A_530


title: A_335


title: A_715


title: A_360


title: A_500


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title: A_386


title: A_278


title: A_093


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title: A_268


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title: A_216


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title: A_496


title: A_019


title: A_533


title: A_110


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title: A_346


title: A_066


title: A_449


title: A_273


title: A_098


title: A_419


title: A_059


title: A_311


title: A_674


title: A_646


title: A_152


title: A_643


title: A_328


title: A_481


title: A_005


title: A_055


title: A_254


title: A_407


title: A_513


title: A_467


title: A_682


title: A_593


title: A_385


title: A_215


title: A_431


title: A_087


title: A_004


title: A_632


title: A_458


title: A_324


title: A_353


title: A_442


title: A_510


title: A_256


title: A_147


title: A_332


title: A_634


title: A_396


title: A_320


title: A_723


title: A_526


title: A_381


title: A_176


title: A_205


title: A_314


title: A_053


title: A_286


title: A_338


title: A_552


title: A_430


title: A_097


title: A_535


title: A_555


title: A_236


title: A_384


title: A_453


title: A_247


title: A_211


title: A_637


title: A_698


title: A_720


title: A_033


title: A_289


title: A_488


title: A_502


title: A_638


title: A_351


title: A_594


title: A_100


title: A_333


title: A_255


title: A_507


title: A_108


title: A_561


title: A_291


title: A_653


title: A_722


title: A_447


title: A_627


title: A_070


title: A_204


title: A_417


title: A_454


title: A_252


title: A_142


title: A_292


title: A_611


title: A_553


title: A_313


title: A_003


title: A_085


title: A_602


title: A_537


title: A_702


title: A_020


title: A_444


title: A_450


title: A_700


title: A_209


title: A_371


title: A_562


title: A_673


title: A_487


title: A_129


title: A_175


title: A_036


title: A_182


title: A_133


title: A_069


title: A_418


title: A_296


title: A_234


title: A_263


title: A_536


title: A_639


title: A_528


title: A_150


title: A_302


title: A_210


title: A_249


title: A_690


title: A_119


title: A_491


title: A_167


title: A_616


title: A_564


title: A_115


title: A_410


title: A_427


title: A_190


title: A_191


title: A_248


title: A_624


title: A_156


title: A_376


title: A_642


title: A_200


title: A_607


title: A_484


title: A_137


title: A_518


title: A_598


title: A_588


title: A_300


title: A_174


title: A_089


title: A_498


title: A_361


title: A_463


title: A_539


title: A_662


title: A_140


title: A_541


title: A_135


title: A_294


title: A_002


title: A_591


title: A_096


title: A_640


title: A_516


title: A_283


title: A_026


title: A_589


title: A_024


title: A_545


title: A_399


title: A_608


title: A_366


title: A_227


title: A_708


title: A_310


title: A_457


title: A_717


title: A_515


title: A_395


title: A_494


title: A_325


title: A_198


title: topal-00039: US82800149_251643612332_S01_miRNA-v1_10_Apr08_2_3

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Primary solid_tumor

tag: diseasestate

value: Untreated primary (de novo) GBM

tag: organismpart

value: Brain

tag: Sex

value: Male

tag: clinical diagnosis

tag: individual

tag: pathologic status

tag: tissue anatomic site

tag: histologic diagnosis


title: topal-00039: US45102955_251643612232_S01_miRNA-v1_95_May07_2_2

scan_protocol: See mage-tab files linked to series entry for additional details

tag: age


title: topal-00039: US82800149_251643612378_S01_miRNA_105_Dec08_1_3

data_processing: See mage-tab files linked to series entry for additional details


title: topal-00039: US45102955_251643612131_S01_miRNA-v1_95_May07_2_1

label_protocol: See mage-tab files linked to series entry for additional details

value: Female

value: GBM

value: MALIGNANT

value: PARIETAL LOBE

value: GLIOBLASTOMA MULTIFORME


title: A_596

tag: gender

tag: tissue

value: blood


title: topal-00039: US82800149_251643612343_S01_miRNA_105_Dec08_1_2

extract_protocol: See mage-tab files linked to series entry for additional details


title: A_617

value: Healthy, non-smoking


title: A_243

value: male


title: A_282


title: topal-00039: US45102955_251643612134_S01_miRNA-v1_95_May07_2_1

value: FRONTAL LOBE


title: A_483


title: topal-00039: US82800149_251643612335_S01_miRNA_105_Dec08_2_2


title: topal-00039: US45102955_251643610869_S01_miRNA-v1_95_May07_1_4

value: NOT SPECIFIED


title: topal-00039: US45102955_251643610869_S01_miRNA-v1_95_May07_1_2

value: TEMPORAL LOBE


title: A_021