title: OX2-28

first: Sally

last: Cowley

address: South Parks Road

institute: University of Oxford

description: single replicate

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file and manifest HumanCytoSNP-12v2-1_H provided by Illumina for GPL13829, and humanomniexpress_24v1-1_a for GPL22678. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor OX2, clone 28

value: male

value: control donor

value: mTeSR-1 + matrigel

value: induced pluripotent stem cells derived from dermal fibroblasts


title: 1660

status: Public on Jun 01 2017

type: protein

city: Tempe

first: Benjamin

middle: A

last: Katchman

state: AZ

address: 727 E. Tyler St.

country: USA

institute: Arizona State University

description: The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

hyb_protocol: Plasma hybridization was performed on TECAN HS 4800 Pro. 1. Protein arrays were blocked with 5% milk PBST (0.2% Tween) for 1 hour at RT; 2. 150ul 1:50 diluted serum was applied to each slide with medium agitation 16 hours at 4oC; 3. Slides were incubated with 150ul 1:500 dilution of Dylight 649-linked anti-human secondary antibodies (Jackson Immunoresearch) in milk PBST.

scan_protocol: Slides were scanned by TECAN PowerScanner at 50% gain, 50% laser and 10µm resolution.

data_processing: 1. The background signal estimated by the 25th percentile of the negative control; 2. Normalize the array by the median.

label: Serum samples are not labeled

molecule: protein

organism: Homo sapiens

source_name: Peripheral Blood

label_protocol: No lable was performed on the serum sample

extract_protocol: Peripheral blood samples were drawn from the antecubital vein and serum was prepared according to a standardized protocol before freezing serum aliquots at -80oC

tag: tissue

value: Serum

tag: type

value: Serous Ovarian Cancer

tag: array batch

value: GST1 - 4; FLAG


title: 80148

value: Benign Ovarian Disease


title: DNAN-62.5ppm-4

type: RNA

city: Vicksburg

first: Ping

last: Gong

state: Mississippi

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: U.S Army Engineer Research and Development Center

description: Labeled cRNA was hybridized to the genome-wide microarray to profile global gene expression.

hyb_protocol: The labeled cDNA was hybridized to the C. elegans-specific 44K-olig array (one sample/array) at 65°C for 17 hrs using Agilent’s Gene Expression Hybridization Kits. A total of 48 samples (3 chemicals × 4 treatments per chemical × 4 replicates per treatment) were hybridized to six 8 × 44K-array slides in a randomized fashion to reduce systematic errors.

scan_protocol: An Agilent high-resolution DNA Microarray Scanner Model G2565CA was used to scan microarray images (resolution = 3 microns per pixel).

data_processing: Raw microarray gene expression data were extracted from acquired array images as spot and background signal intensity using Agilent’s Feature Extraction software v10.7. A spot was flagged out if its raw signal intensity was below its background level, or if it was saturated. A gene was flagged out if over 50% of the 48 samples had missing values for this gene. The filtered data was background subtracted and log-transformed. The spike-in RNA mix with known composition and RNA copy numbers was used to construct standard linear regression curves, from which the unknown worm RNA concentrations were derived. The derived RNA concentrations were normalized to the median value per array (sample).

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Wild type C. elegans var. Bristol strain N2

label_protocol: One hundred ng of total RNA was first reverse-transcribed into cDNA, followed by cDNA labeling using Low Input Quick Amp Labeling Kits (Agilent, Palo Alto, CA) in the presence of cyanine 3-CTP dye.

growth_protocol: The wild-type C. elegans var. Bristol, strain N2, was maintained at 20°C on NGM agar plates seeded with Escherichia coli OP50 bacteria. The culture was synchronized at the first larval stage (L1) by bleaching with a 5% sodium hypochlorite solution. Worms were harvested by gentle rinsing with K Medium in late L3 stage which were determined by both length and age (Donkin and Williams 1995; Altun and Hall 2005).

extract_protocol: After the 24-hr exposure, all 400 worms per well were collected into a cryogenic vial and spun at 1150 x g for 2.5 min. Supernatant was removed and the vial were flash frozen in liquid nitrogen and stored at -80°C.  Total RNA was extracted from each vial using RNeasy mini kits (Qiagen, Valencia, CA) and treated as one biological replicate. Four of the five replicates (total RNA samples) per treatment were chosen for further microarray hybridization.

treatment_protocol: After harvesting from agar plates, worms were spun at 1150 x g for 2.5 min and re-suspended in a given volume of K Medium. Twenty µL of worms were deposited on a microscope slide containing a grid sticker and worms were counted. The number of worms/mL was then calculated. Wide-bore pipet tips or transfer pipets were always used to avoid shearing of worms. Worms were exposed in 24-well tissue-culture treated (TC) plates for 24 hours to DNAN, NTO, or NQ. All test solutions were prepared in K medium except that acetone was used to dissolve DNAN, resulting in 5% carrier in the final solution. Each weel in the TC plates contained 400 worms and 1 ml of K medium or test solution. The nominal concentrations were: Vehicle control, 1.9, 15.5, 62 mg DNA/L, Blank control, 187, 750, 3000 mg NTO/L, and Blank control, 83, 666, 2667 mg NQ/L. Each treatment had 5 replicates.

value: Pooled somatic tissue of approx. 400 nematodes

tag: gender

value: hermaphrodite

tag: developmental stage

value: Late L3 stage grown from synchronized culture

tag: 24-hr acute treatment

value: DNAN

tag: concentration

tag: replicate


title: DNAN-Control-1

value: Control


title: 2585


title: NTO-750ppm-5

value: NTO


title: NQ-2667ppm-2

value: NQ


title: Oral epithelial cells-non-infected-1 [exon-level]

city: Shenyang

first: Fengxue

last: Geng

state: Liaoning

address: Nanjing North St. 117, Heping District

department: Periodontics

country: China

institute: China Medical University

description:
RNA1-1
control-1
Gene expression data from cells without bacterial infection.

hyb_protocol: Preprocessed hybridization solution (the final dilution of DNA was 25ng/μl) was added on the GeneChip and centrifuged for 16 h at 45℃ (60 rpm).

scan_protocol: GeneChip was scanned with Affymetrix scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Expression Console (version 1.3.1, Affymetrix) software offered RMA normalization for both gene- and exon-level analysis. Differential exon or junction identified through splicing index as well as P value calculated with One-Way Between-Subject ANOVA (Unpaired). The threshold was splicing index >= 2.0 or < = -2.0 and a P value<= 0.05.

label: biotin

source_name: immortalized oral epithelial cells, not infected

label_protocol: Biotinylated cDNAs were prepared according to the manufacturer's standard protocols (Ambion® WT Expression Kit).

growth_protocol: Human immortalized oral epithelial cells (HIOECs) were cultured in Defined Keratinocyte-SFM (GibcoTM, Thermo Fisher Scientific Inc., MA, USA) with growth supplement; P. gingivalis ATCC 33277 (American Type Culture Collection, Manassas, VA, USA) was routinely cultured.

extract_protocol: Total RNAs of HIOECs and HIOECs infected for 15 weeks were extracted with RNAiso Plus kit (TaKaRa, Dalian, China).

treatment_protocol: HIOECs were persistently infected with Porphyromonas gingivalis for up to 15 weeks. Cells without infection were cultured as the control.

tag: cell line

value: HIOEC

tag: cell type

value: human immortalized oral epithelial cells

tag: treatment


title: 1494


title: 1547


title: SFC848-03-02

type: genomic

city: Oxford

department: Sir William Dunn School of Pathology

country: United Kingdom

description: single replicate

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

label: Biotin (C, G), Dinitrophenyl (A, T)

molecule: genomic DNA

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 848, clone 2

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: male

tag: donor

tag: culture conditions


title: 1571


title: SFC871-03-09

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 871, clone 9

value: female

value: control donor


title: Oral epithelial cells-non-infected-3 [exon-level]

description:
RNA1-3
control-3
Gene expression data from cells without bacterial infection.


title: 80135


title: DNAN-15.5ppm-5


title: 1885


title: 2613


title: Oral epithelial cells-15-week-1 [exon-level]

description:
RNA2-1-1
test-1
Gene expression data from cells with bacterial infection.

source_name: immortalized oral epithelial cells infected with P. gingivalis for 15 wks

value: Porphyromonas gingivalis infection for 15 weeks


title: SF871

description: single replicate

source_name: human dermal fibroblasts, GBA N370S donor 871

value: GBA N370S donor

value: ADMEM + 10% FCS

value: dermal fibroblasts


title: Oral epithelial cells-non-infected-2 [exon-level]

description:
RNA1-2
control-2
Gene expression data from cells without bacterial infection.


title: 1066

value: Serum

value: Benign Ovarian Disease


title: recurrent ovarian cancer [R6]

city: Seoul

first: Eun Ji

last: Nam

address: 50 Yonsei-ro

department: Obstetrics and Gynecology

country: South Korea

institute: Yonsei University College of Medicine

hyb_protocol: Desalted labeled RNA was reaction volume of 45 ul containing 10x GE blocking agent and 2x Hi-RPM Agilent hybridization buffer following the manufacturers instructions. Hybridized to Human miRNA Microarray Kit Release 16.0, 8x60K  (G4872A) for 20 hours at 55Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on theAgilent Technologies Scanner C (G2505C)  using one color scan setting for AgilentG3_miRNA (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 031181_D_F_20111226) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: recurrent ovarian cancer [R6]

label_protocol: Cyanine3-pCp (Cy3) labeled dephosphorylated RNA was prepared from using the Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions, followed by Micro Bio-Spin 6 column purification (Bio-RAD).  Dry the samples was using a vacuum concentrator at 45 to 55°C or on the medium-high heat setting.

extract_protocol: FFPE specimens were deparaffinized overnight in xylene. Total RNA isolation was performed using RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion Inc., Austin, TX) for FFPE following the manufacturer's recommendations.

value: paraffin-embedded tissue

tag: age


title: recurrent ovarian cancer [R7]

source_name: recurrent ovarian cancer [R7]


title: recurrent ovarian cancer [R8]

source_name: recurrent ovarian cancer [R8]


title: 2562


title: 1545

value: Serous Ovarian Cancer

value: GST1 - 4; FLAG


title: 2390


title: 1614


title: 1521


title: 2169


title: primary ovarian cancer [P7]

source_name: primary ovarian cancer [P7]


title: NQ-2667ppm-4

value: Pooled somatic tissue of approx. 400 nematodes

value: hermaphrodite

value: Late L3 stage grown from synchronized culture


title: NQ-2667ppm-3

value: NQ


title: DNAN-15.5ppm-2

value: DNAN


title: NQ-83ppm-5


title: NTO-187ppm-3

value: NTO


title: recurrent ovarian cancer [R5]

source_name: recurrent ovarian cancer [R5]

value: female


title: DNAN-15.5ppm-4


title: primary ovarian cancer [P6]

source_name: primary ovarian cancer [P6]


title: 1607


title: SF848

description: single replicate

source_name: human dermal fibroblasts, GBA N370S donor 848

value: male


title: primary ovarian cancer [P5]

source_name: primary ovarian cancer [P5]


title: 1676


title: 1017


title: recurrent ovarian cancer [R4]

source_name: recurrent ovarian cancer [R4]

value: fresh frozen tissue


title: 973


title: NQ-666ppm-1


title: recurrent ovarian cancer [R3]

source_name: recurrent ovarian cancer [R3]


title: 1588

source_name: Peripheral Blood


title: 1461


title: 80253


title: recurrent ovarian cancer [R2]

source_name: recurrent ovarian cancer [R2]


title: NTO-3000ppm-1

source_name: Wild type C. elegans var. Bristol strain N2


title: primary ovarian cancer [P8]

source_name: primary ovarian cancer [P8]


title: 2443


title: recurrent ovarian cancer [R1]

source_name: recurrent ovarian cancer [R1]


title: DNAN-1.9ppm-5


title: primary ovarian cancer [P4]

source_name: primary ovarian cancer [P4]


title: DNAN-62.5ppm-1


title: NQ-83ppm-1


title: NQ-666ppm-4


title: 1739


title: primary ovarian cancer [P3]

source_name: primary ovarian cancer [P3]


title: NQ-83ppm-2


title: NQ-Control-1

value: Control


title: NTO-3000ppm-5


title: NQ-666ppm-5


title: NTO-750ppm-3


title: NTO-3000ppm-4


title: primary ovarian cancer [P1]

source_name: primary ovarian cancer [P1]


title: primary ovarian cancer [P2]

source_name: primary ovarian cancer [P2]


title: 1472


title: DNAN-1.9ppm-1


title: 2608


title: 80059


title: 2301


title: 1780


title: normal ovarian tissue [N4]

source_name: normal ovarian tissue [N4]


title: 80321


title: normal ovarian tissue [N2]

source_name: normal ovarian tissue [N2]


title: normal ovarian tissue [N1]

source_name: normal ovarian tissue [N1]


title: normal ovarian tissue [N3]

source_name: normal ovarian tissue [N3]


title: DNAN-15.5ppm-1


title: 984


title: NTO-187ppm-5


title: RKOp53wt control rep 1

status: Public on May 31 2017

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Hybriddized biotinylated-aRNA accordig to the manufacturer prorocol.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix GCOS software. Data processing and analysis was done using ROOT frameworks, and xps, lumi, et al R/Bioconductor packages. In the xps, for probeset selection options,  ‘metacore’ + ‘affx’ was used in the analysis, which selects core meta probesets and standard AFFX control probesets (resulting in 37,270 data rows).

source_name: RKOp53wt control

label_protocol: Biotin labelled accordig to the manufacturer prorocol.

growth_protocol: HCT116 cells were cultured in DMEM with 10% FBS, at 37oC, 5%CO2

extract_protocol: Total RNA from thyroids was isolated using TRIzol (Invitrogen, Carlsbad, CA) as indicated by the protocol of the manufacturer.

treatment_protocol: HCT116 p53 WT, SW48 p53 WT and RKO p53 WT cells were kept untreated or treated with 10µM Nutlin-3a for 8 hr.

value: RKO

tag: treated with

value: none (untreated control)


title: SW48p53wt control rep 1

source_name: SW48p53wt control


title: DNAN-62.5ppm-3


title: RKOp53wt treated with Nutlin-3a rep 2

source_name: RKOp53wt treated with Nutlin-3a

value: 10µM Nutlin-3a for 8 hr


title: RKOp53wt treated with Nutlin-3a rep 1


title: SW48p53wt treated with Nutlin-3a rep 2

source_name: SW48p53wt treated with Nutlin-3a


title: HCT116p53wt treated with Nutlin-3a rep 2

source_name: HCT116p53wt treated with Nutlin-3a


title: DNAN-Control-3


title: HCT116p53wt control rep 1

source_name: HCT116p53wt control


title: Experiment S UT7 pMGp8 diff baso

city: BORDEAUX

first: Bruno

last: CARDINAUD

address: 146 rue Leo Saignat

department: INSERM U1035

country: France

institute: Bordeaux University

description: Gene expression of MYB-GATA1 + GATA1 shRNA differentiated UT7 cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity 11-18 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Hi-RPM Agilent hybridization buffe was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression v2 Microarrays (G4845A) for 16 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 B DNA Microarray Scanner using settings for 4x44k one color slides (eXtended Dynamic Range, scan area 61x21.6 mm, Scan resolution 5um, dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Differentiated UT7 cells, MYB-GATA1 + shGATA1 lentiviruses, experiment S

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the LIQA Gene Expression One-Color v6.0 kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: UT7 cells were grown at 37°C in IMDM containing 50 μM β-mercaptoethanol, 10mM Hepes, 10% fetal calf serum, 2mM L-Glutamine, 100 U/mL penicillin- streptomycin. They were transduced (MOI=10) with a combination of 2 different lentiviruses. The first one allowed the expression of both MYB-GATA1 and TdTomato and the second one carried a GATA1 shRNA and GFP cds as well. Control lentiviruses (empty vector for MYB-GATA1, and shRNA directed against the Luciferase cds for GATA1 shRNA) were also used in combination. TdTomato+/GFP+ cells were selected using FACS.

extract_protocol: RNA was prepared using the Trizol kit ThermoFisher). The first steps of the extraction were performed following the manufacturer's recommendations. After Ethanol addition (1.5volume), the aqueous phase was deposited onto a RNeasy column (Qiagen) and RNA were purified following the RNA cleanup protocol supplied by the manufacturer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored usinf agarose gel electrophoresis.

treatment_protocol: For maintenance of undifferentiated cells, 1 U/mL EPO was added to the growth medium. For basophilic differentiation, 100 ng/mL IL-3 and 2.5 ng/mL GM-CSF were used.

tag: lentiviruses

value: MYB-GATA1 + shGATA1

tag: differentiation

value: Differentiated


title: SW48p53wt control rep 2


title: HCT116p53wt treated with Nutlin-3a rep 1


title: HCT116p53wt control rep 2


title: SW48p53wt treated with Nutlin-3a rep 1


title: RKOp53wt control rep 2


title: Experiment S UT7 p252pLuc non diff

description: Gene expression of Control undifferentiated UT7 cells

source_name: Undifferentiated UT7 cells, control lentiviruses, experiment S

value: Undifferentiated


title: Experiment S UT7 p252pLuc diff baso

description: Gene expression of Control differentiated UT7 cells

source_name: Differentiated UT7 cells, control lentiviruses, experiment S


title: Experiment S UT7 pMGp8 non diff

description: Gene expression of MYB-GATA1 + GATA1 shRNA undifferentiated UT7 cells

source_name: Undifferentiated UT7 cells, MYB-GATA1 + shGATA1 lentiviruses, experiment S


title: NanoString counts for prostate tumour sample CPCG0455-F1-M2

status: Public on May 27 2017

city: Toronto

first: Dorota

last: Sendorek

state: ON

address: 661 University Ave, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: Prostate cancer tissue evaluated for Gleason Score (3+3 or 3+4 or 4+3) and cellularity (>= 70%)

hyb_protocol: Hybridization was carried out according to the NanoString protocol.

scan_protocol: Scan was carried out according to the NanoString protocol.

data_processing: Sample content normalization was performed on endogenous and invariant probe counts using invariant probe information, as outlined in NanoString guidelines. Control probes (positive, negative, restriction site) were not normalized.

label: biotiin

source_name: fresh frozen prostate tumour tissue

label_protocol: DNA was not labelled.

extract_protocol: Genomic DNA was tested according to the NanoString protocol.

tag: patient

tag: fragmentation method

value: AluI Digestion

tag: cartridge

tag: lane

tag: matched normal sample

value: missing

tag: replicate sample


title: NanoString counts for prostate tumour sample CPCG0462-F1-M2

tag: concentration


title: Experiment A UT7 pMGp8 non diff

source_name: Undifferentiated UT7 cells, MYB-GATA1 + shGATA1 lentiviruses, experiment A


title: Experiment A UT7 p252pLuc diff baso

source_name: Differentiated UT7 cells, control lentiviruses, experiment A


title: NanoString counts for prostate tumour sample CPCG0459-F1-M2


title: NanoString counts for prostate tumour sample CPCG0457-F1-M1


title: Experiment A UT7 p252pLuc non diff

source_name: Undifferentiated UT7 cells, control lentiviruses, experiment A


title: NanoString counts for prostate tumour sample CPCG0448-F1-M2


title: NanoString counts for prostate tumour sample CPCG0455-F1-M1

value: Sonication


title: NanoString counts for prostate tumour sample CPCG0410-F1-M2


title: NanoString counts for prostate tumour sample CPCG0388-F1-M2


title: NanoString counts for prostate tumour sample CPCG0382-F1-M2


title: NanoString counts for prostate tumour sample CPCG0402-F1-M2


title: NanoString counts for prostate tumour sample CPCG0392-F1-M2


title: NanoString counts for prostate tumour sample CPCG0395-F1-M2


title: NanoString counts for prostate tumour sample CPCG0382-F1-M1


title: NanoString counts for prostate tumour sample CPCG0379-F1-M2


title: NanoString counts for blood normal sample CPCG0334-B-M1

description: Whole blood samples collected during follow-up

source_name: matched blood normal


title: NanoString counts for blood normal sample CPCG0334-B-M2


title: NanoString counts for blood normal sample CPCG0345-B-M2


title: NanoString counts for blood normal sample CPCG0335-B-M1


title: NanoString counts for prostate tumour sample CPCG0335-F1-M2


title: NanoString counts for blood normal sample CPCG0345-B-M1


title: NanoString counts for blood normal sample CPCG0349-B-M1


title: NanoString counts for prostate tumour sample CPCG0346-F1-M2

value: CPCG0346B M2_01.RCC


title: NanoString counts for prostate tumour sample CPCG0345-F1-M2


title: NanoString counts for blood normal sample CPCG0335-B-M2


title: NanoString counts for blood normal sample CPCG0346-B-M1


title: NanoString counts for prostate tumour sample CPCG0334-F1-M2


title: NanoString counts for blood normal sample CPCG0346-B-M2


title: NanoString counts for prostate tumour sample CPCG0345-F1-M1


title: NanoString counts for prostate tumour sample CPCG0379-F1-M1


title: NanoString counts for prostate tumour sample CPCG0349-F1-M2


title: NanoString counts for prostate tumour sample CPCG0366-F1-M2


title: NanoString counts for prostate tumour sample CPCG0357-F1-M2


title: NanoString counts for prostate tumour sample CPCG0333-F1-M2


title: NanoString counts for prostate tumour sample CPCG0266-F1-M2


title: NanoString counts for blood normal sample CPCG0266-B-M1


title: NanoString counts for prostate tumour sample CPCG0249-F1-M2


title: NanoString counts for blood normal sample CPCG0233-B-M2


title: NanoString counts for blood normal sample CPCG0248-B-M2


title: NanoString counts for prostate tumour sample CPCG0248-F1-M2


title: NanoString counts for prostate tumour sample CPCG0232-F1-M2


title: NanoString counts for blood normal sample CPCG0249-B-M1


title: NanoString counts for blood normal sample CPCG0249-B-M2


title: NanoString counts for prostate tumour sample CPCG0184-P1-M1

source_name: FFPE prostate tumour tissue


title: NanoString counts for blood normal sample CPCG0232-B-M2


title: NTO-Control-5

source_name: Wild type C. elegans var. Bristol strain N2

tag: tissue

value: Pooled somatic tissue of approx. 400 nematodes

tag: gender

value: hermaphrodite

tag: developmental stage

value: Late L3 stage grown from synchronized culture

tag: 24-hr acute treatment

tag: replicate


title: NanoString counts for blood normal sample CPCG0233-B-M1


title: NanoString counts for prostate tumour sample CPCG0398-F1-M2


title: NanoString counts for blood normal sample CPCG0232-B-M1


title: NanoString counts for blood normal sample CPCG0266-B-M2


title: NanoString counts for prostate tumour sample CPCG0184-P2-M1


title: NanoString counts for blood normal sample CPCG0248-B-M1


title: NanoString counts for prostate tumour sample CPCG0236-F1-M2


title: NanoString counts for blood normal sample CPCG0235-B-M2


title: NanoString counts for prostate tumour sample CPCG0233-F1-M2


title: NanoString counts for blood normal sample CPCG0236-B-M2


title: NanoString counts for blood normal sample CPCG0235-B-M1


title: NanoString counts for blood normal sample CPCG0236-B-M1


title: NanoString counts for prostate tumour sample CPCG0235-F1-M2


title: NanoString counts for prostate tumour sample CPCG0184-F1-M2


title: NanoString counts for prostate tumour sample CPCG0184-F1-M1


title: NanoString counts for prostate tumour sample CPCG0183-F1-M2


title: NanoString counts for prostate tumour sample CPCG0103-P7-M1


title: NanoString counts for prostate tumour sample CPCG0103-P3-M1


title: NanoString counts for prostate tumour sample CPCG0103-P5-M1


title: NanoString counts for prostate tumour sample CPCG0183-F1-M1


title: 2067143-M, at 32-38 weeks of gestation

status: Public on Feb 09 2017

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

scan_protocol: Standard Illumina scanning protocol

data_processing: All 60 samples were standard background adjusted, logarithm base 2 transformed and quantile normalized using the R Bioconductor package lumi. Gene probes with empty gene symbols or unspecified chromosome locations were remove beforehand.

label: Biotin

source_name: whole blood_at 32-38 weeks of gestation

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

extract_protocol: Total RNA was isolated from whole blood using the PAXgene Blood RNA Kit (Qiagen®) according to manufacturers protocol. The Ambion Globin Clear kit (Ambion®) was used to remove alpha and beta globin mRNA from the sample to increase the sensitivity of gene expression assays through improving the detection rate of expressed genes. The RNA was quantified using the Nanodrop 8000 and checked for high integrity before preparation of cDNA. The integrity of RNA samples was assessed using the Agilent 2100 Bioanalyzer.  Sample purity was confirmed using the NanoDrop spectrophotometer and RNA Integrity Number (RIN ≥ 8).

tag: study center

value: WU - Washington University

tag: Sex

value: Female

tag: ethnicity

value: African American (Hispanic and Non-Hispanic)

tag: age at enrollment

tag: gestational day at enrollment

tag: treatment group

value: Intervention group, 4400 IU vitamin D supplementation

tag: pregnancy condition

value: Normal

tag: sex of child

tag: vitamin d level at enrollment (nmol/l)

tag: vitamin d level at 32-38 weeks of gestation (nmol/l)

value: PAXgene whole blood

tag: microarray hybridization date


title: 5028464-M, at enrollment

source_name: whole blood_at enrollment

value: Male


title: 7052439-M, at enrollment

value: Caucasian (Non-Hispanic)

value: Control group, 400 IU vitamin D supplementation


title: 6058718-M, at enrollment


title: 6058718-M, at 32-38 weeks of gestation


title: 7063614-M, at enrollment

value: Preeclampsia


title: 8057224-M, at 32-38 weeks of gestation


title: 7063614-M, at 32-38 weeks of gestation


title: 4018451-M, at 32-38 weeks of gestation


title: 8057224-M, at enrollment


title: 5098874-M, at enrollment


title: 1086430-M, at enrollment


title: 5098874-M, at 32-38 weeks of gestation


title: 3095286-M, at 32-38 weeks of gestation


title: 7052439-M, at 32-38 weeks of gestation


title: 5028464-M, at 32-38 weeks of gestation


title: 9028555-M, at enrollment


title: 3019680-M, at 32-38 weeks of gestation


title: 9028555-M, at 32-38 weeks of gestation


title: 4018451-M, at enrollment


title: 3019680-M, at enrollment


title: 2067143-M, at enrollment


title: Experiment A UT7 pMGp8 diff baso

source_name: Differentiated UT7 cells, MYB-GATA1 + shGATA1 lentiviruses, experiment A

tag: lentiviruses

value: MYB-GATA1 + shGATA1

tag: differentiation

value: Differentiated


title: 4031682-M, at 32-38 weeks of gestation

tag: tissue


title: 3095286-M, at enrollment


title: 1086430-M, at 32-38 weeks of gestation


title: 4031682-M, at enrollment


title: 6057756-M, at 32-38 weeks of gestation


title: NanoString counts for blood normal sample CPCG0349-B-M2

tag: patient

tag: fragmentation method

value: AluI Digestion

tag: concentration

tag: cartridge

tag: lane

tag: matched normal sample

tag: replicate sample


title: 6057756-M, at enrollment

tag: study center

tag: Sex

tag: ethnicity

tag: age at enrollment

tag: gestational day at enrollment


title: 3012659-M, at 32-38 weeks of gestation

tag: treatment group

tag: pregnancy condition

tag: sex of child

tag: vitamin d level at enrollment (nmol/l)

tag: vitamin d level at 32-38 weeks of gestation (nmol/l)


title: 2067862-M, at 32-38 weeks of gestation

tag: tissue

tag: microarray hybridization date


title: 4041035-M, at enrollment

value: BU - Boston University


title: 1086584-M, at enrollment


title: 3045067-M, at 32-38 weeks of gestation


title: 4001301-M, at enrollment


title: 3012659-M, at enrollment


title: 2006605-M, at enrollment


title: 1086584-M, at 32-38 weeks of gestation


title: 2067862-M, at enrollment


title: 2006605-M, at 32-38 weeks of gestation


title: 5037279-M, at enrollment


title: 4041035-M, at 32-38 weeks of gestation


title: 6041552-M, at 32-38 weeks of gestation

value: KP - Kaiser Permanente


title: 1027224-M, at enrollment


title: 5037279-M, at 32-38 weeks of gestation


title: 3045067-M, at enrollment


title: 1044556-M, at 32-38 weeks of gestation


title: 6041552-M, at enrollment


title: 1027224-M, at 32-38 weeks of gestation


title: 2066267-M, at 32-38 weeks of gestation


title: 5025572-M, at enrollment


title: 2093964-M, at enrollment


title: 4001301-M, at 32-38 weeks of gestation


title: 2093964-M, at 32-38 weeks of gestation


title: 2066267-M, at enrollment


title: 1044556-M, at enrollment


title: 5025572-M, at 32-38 weeks of gestation


title: 8082231-M, at enrollment


title: HCV-specific CD8 T cells, r-21, p01

status: Public on Jan 18 2017

first: David

last: Wolski

address: 55 Fruit Street

department: Gastrointestinal Unit

institute: Massachusetts General Hospital

description: Gene expression data from HCV-specific CD8 T cells from subjects with resolving infection targeting non-escaped viral epitope

hyb_protocol: Hybridization to Affymetrix GeneChip Human Genome U133A 2.0 microarrays was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform at the Dana-Farber Cancer Institute Molecular Biology core facility.

scan_protocol: Arrays were scanned using an Affymettrix GeneChip® Scanner 3000.

data_processing: A custom HG_U133A2_ENTREZG (v20) chip definition file from the MBNI Microarray Lab was used in Robust Multichip Averaging (RMA) and log2 transformation of data with the affy package for R/Bioconductor.

source_name: HCV-specific CD8+ T cells from human PBMC

label_protocol: cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.

growth_protocol: HCV-specific CD8 T cells were sorted at multiple time points during the early and late acute phase of infection (≤36 weeks) using MHC-I multimers.

extract_protocol: RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer. RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: PBMC were isolated via density centrifugation and stained for viability as well as CD4, CD14, CD16, CD19, and CD56 antibodies chosen to exclude irrelevant lineages and dead cells. Anti-CD8 and MHC Class I multimers were used to identify and sort the antigen-specific populations using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).

value: pbmc

tag: cell type

value: CD8+ T cells

tag: infection outcome

value: resolver

tag: viral escape

value: non-escape

tag: subject id

tag: time point

tag: time from infection

tag: viral load

tag: alt

tag: cd4 help

tag: sample source

value: boston

value: nonhispanic

tag: age

value: female

tag: array batch

tag: rna processing batch


title: HCV-specific CD8 T cells, r-20, p01

value: high

tag: ethnicity

tag: Sex


title: HCV-specific CD8 T cells, r-16, p03

tag: tissue


title: HCV-specific CD8 T cells, r-20, p02


title: HCV-specific CD8 T cells, r-14, p02


title: HCV-specific CD8 T cells, r-21, p02


title: HCV-specific CD8 T cells, r-15, p01


title: HCV-specific CD8 T cells, r-13, p03


title: HCV-specific CD8 T cells, r-13, p02


title: HCV-specific CD8 T cells, r-19, p01


title: 8082231-M, at 32-38 weeks of gestation

tag: study center

value: Female

tag: age at enrollment

tag: gestational day at enrollment

tag: treatment group

value: Intervention group, 4400 IU vitamin D supplementation

tag: pregnancy condition

value: Normal

tag: sex of child

tag: vitamin d level at enrollment (nmol/l)

tag: vitamin d level at 32-38 weeks of gestation (nmol/l)

value: PAXgene whole blood

tag: microarray hybridization date


title: HCV-specific CD8 T cells, r-16, p01

tag: cell type

tag: infection outcome

tag: viral escape

tag: subject id

tag: time point

tag: time from infection

tag: viral load

tag: alt

tag: cd4 help


title: HCV-specific CD8 T cells, r-12, p02

tag: tissue

tag: sample source

tag: ethnicity

tag: age

tag: Sex

tag: array batch

tag: rna processing batch


title: HCV-specific CD8 T cells, r-12, p01


title: HCV-specific CD8 T cells, r-18, p01

value: male


title: HCV-specific CD8 T cells, r-13, p01


title: 9061441-M, at 32-38 weeks of gestation

tag: study center

value: African American (Hispanic and Non-Hispanic)

tag: age at enrollment

tag: gestational day at enrollment

tag: treatment group

value: Control group, 400 IU vitamin D supplementation

tag: pregnancy condition

tag: sex of child

tag: vitamin d level at enrollment (nmol/l)

tag: vitamin d level at 32-38 weeks of gestation (nmol/l)

tag: microarray hybridization date


title: HCV-specific CD8 T cells, r-17, p01

tag: cell type

tag: infection outcome

tag: viral escape

tag: subject id

tag: time point

tag: time from infection

tag: viral load

tag: alt

tag: cd4 help


title: HCV-specific CD8 T cells, r-11, p01b

tag: tissue

tag: sample source

tag: ethnicity

tag: age

tag: Sex

tag: array batch

tag: rna processing batch


title: HCV-specific CD8 T cells, r-11, p01a


title: HCV-specific CD8 T cells, r-16, p02


title: HCV-specific CD8 T cells, r-15, p02


title: HCV-specific CD8 T cells, r-14, p01


title: HCV-specific CD8 T cells, r-03, p03

value: brazil

value: brazilwhite


title: HCV-specific CD8 T cells, r-08, p02

value: pbmc


title: HCV-specific CD8 T cells, r-08, p01

value: CD8+ T cells


title: HCV-specific CD8 T cells, r-09, p01

value: resolver


title: HCV-specific CD8 T cells, r-02, p01

value: non-escape

value: brazilbrown


title: HCV-specific CD8 T cells, r-07, p01


title: HCV-specific CD8 T cells, e-06, p02

description: Gene expression data from HCV-specific CD8 T cells from subjects with chronic infection targeting escaped viral epitope

value: chronic

value: escape

value: boston

value: nonhispanic


title: HCV-specific CD8 T cells, e-07, p01

value: female


title: HCV-specific CD8 T cells, r-06, p01

value: high


title: HCV-specific CD8 T cells, r-01, p01


title: HCV-specific CD8 T cells, r-10, p01


title: HCV-specific CD8 T cells, r-05, p01

value: brazilblack


title: HCV-specific CD8 T cells, e-04, p02

value: male


title: HCV-specific CD8 T cells, e-04, p01


title: HCV-specific CD8 T cells, r-03, p02


title: HCV-specific CD8 T cells, r-05, p02


title: HCV-specific CD8 T cells, r-02, p02


title: HCV-specific CD8 T cells, r-09, p02


title: HCV-specific CD8 T cells, e-03, p01

value: low


title: HCV-specific CD8 T cells, e-03, p03


title: HCV-specific CD8 T cells, r-03, p01


title: HCV-specific CD8 T cells, e-03, p02


title: HCV-specific CD8 T cells, e-06, p01


title: HCV-specific CD8 T cells, e-02, p01


title: HCV-specific CD8 T cells, e-05, p01


title: HCV-specific CD8 T cells, r-04, p01


title: HCV-specific CD8 T cells, e-06, p03


title: HCV-specific CD8 T cells, e-05, p02


title: 9061441-M, at enrollment

tag: study center

value: KP - Kaiser Permanente

value: Female

value: African American (Hispanic and Non-Hispanic)

tag: age at enrollment

tag: gestational day at enrollment

tag: treatment group

value: Control group, 400 IU vitamin D supplementation

tag: pregnancy condition

value: Normal

tag: sex of child

tag: vitamin d level at enrollment (nmol/l)

tag: vitamin d level at 32-38 weeks of gestation (nmol/l)

value: PAXgene whole blood

tag: microarray hybridization date


title: HCV-specific CD8 T cells, c-15, p01

description: Gene expression data from HCV-specific CD8 T cells from subjects with chronic infection targeting non-escaped viral epitope

value: pbmc

tag: cell type

value: CD8+ T cells

tag: infection outcome

tag: viral escape

value: non-escape

tag: subject id

tag: time point

tag: time from infection

tag: viral load

tag: alt

tag: cd4 help


title: HCV-specific CD8 T cells, e-01, p01

tag: tissue

value: chronic

value: escape

tag: sample source

value: brazil

tag: ethnicity

value: brazilbrown

tag: age

tag: Sex

tag: array batch

tag: rna processing batch


title: HCV-specific CD8 T cells, e-01, p02


title: HCV-specific CD8 T cells, c-10, p02

value: boston

value: nonhispanic


title: HCV-specific CD8 T cells, c-10, p03

value: male


title: HCV-specific CD8 T cells, c-09, p01

value: high


title: HCV-specific CD8 T cells, c-11, p01

value: female


title: HCV-specific CD8 T cells, c-08, p02


title: HCV-specific CD8 T cells, c-10, p01


title: HCV-specific CD8 T cells, c-06, p03


title: HCV-specific CD8 T cells, c-06, p02


title: HCV-specific CD8 T cells, c-07, p01


title: HCV-specific CD8 T cells, c-14, p01

value: hispanic


title: HCV-specific CD8 T cells, c-13, p01


title: HCV-specific CD8 T cells, c-07, p02


title: HCV-specific CD8 T cells, c-08, p01

value: low


title: HCV-specific CD8 T cells, c-09, p03


title: HCV-specific CD8 T cells, c-02, p02


title: HCV-specific CD8 T cells, c-06, p01


title: HCV-specific CD8 T cells, c-02, p01


title: HCV-specific CD8 T cells, c-12, p01


title: HCV-specific CD8 T cells, c-03, p01

value: brazilwhite


title: HCV-specific CD8 T cells, c-04, p01


title: HCV-specific CD8 T cells, c-09, p02


title: HCV-specific CD8 T cells, c-05, p02


title: HCV-specific CD8 T cells, vr-02, p01

description: Gene expression data from HCV-specific CD8 T cells from subjects with resolving infection

hyb_protocol: Hybridization to Affymetrix GeneChip HT Human Genome U133A Array plate set was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform at the Dana-Farber Cancer Institute Molecular Biology core facility.

scan_protocol: Arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: A custom HTHGU133A_Hs_ENTREZG (v20) chip definition file from the MBNI Microarray Lab was used in Robust Multichip Averaging (RMA) and log2 transformation of data with the affy package for R/Bioconductor.

growth_protocol: HCV-specific CD8 T cells from the early acute phase of infection (≤21 weeks) were sorted using MHC-I multimers.

value: resolver


title: HCV-specific CD8 T cells, c-05, p03


title: HCV-specific CD8 T cells, vr-01, p01


title: HCV-specific CD8 T cells, c-05, p01


title: HCV-specific CD8 T cells, vr-03, p01


title: HCV-specific CD8 T cells, vc-07, p01

description: Gene expression data from HCV-specific CD8 T cells from subjects with chronic infection


title: HCV-specific CD8 T cells, c-01, p02


title: HCV-specific CD8 T cells, vc-05, p01


title: HCV-specific CD8 T cells, c-01, p01


title: HCV-specific CD8 T cells, vc-04, p01


title: HCV-specific CD8 T cells, vc-03, p01


title: HCV-specific CD8 T cells, vc-06, p01


title: H12_VTA

status: Public on Jan 10 2017

city: Austin

first: Laura

last: Ferguson

state: TX

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

institute: Dell Medical School, University of Texas at Austin

hyb_protocol: We sent 1.5 µg cRNA to The Microarray Resource at Yale University where it was hybridized to Illumina Mouse WG-6 v2.0 Expression BeadChips (Illumina, San Diego, CA, USA).

data_processing:
The data were preprocessed using the Bioconductor lumi package in the R programming environment.  A total of 168 samples across 7 brain regions were used for data analysis. Variance-stabilizing transformation and quantile normalization were applied. Outlier detection was performed within brain region and samples were considered as outliers when their distances to the average of all samples were larger than the threshold (2*median distances to the center). The normalized data for all 168 samples is available in the file GSE93311_HDID_QNORM_168samples.txt on the series record.
Two control samples, one from AcbC (rep 5), the other from BNST  (rep 5) were removed for final analysis. Variance-stabilizing transformation and quantile normalization were reapplied to the raw data of the remaining 166 samples. These data are available in the sample tables and on the series record in the file GSE93311_HDID_QNORM_WGCNA.txt.
Differential expression analysis was conducted within brain area. Thus, the samples from each brain area were normalized together (separately from the other brain areas). For each brain region, only genes that were significantly expressed (detection threshold 0.05) in at least 75% of samples were selected. Grubb's test (p < 0.05) was performed within group to remove outliers for each gene. These brain-area-specific normalized data sets are available in the tar archive brain_region_normalized.tar on the series record.

organism: Mus musculus

label_protocol: Total RNA was amplified using Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Austin, TX, USA). The cRNA was quantified using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Eilmington, DE, USA) and the size was analyzed using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). Using 30 ng of RNA as input yielded at least 4 µg of amplified biotinylated cRNA, with most of them distributing between 800 and 1500 nt, indicating an expected yield and size.

extract_protocol: Lysis solution from RNAqueous-Micro Kit (Ambion, Austin, TX, USA) was added to the microdissected samples. The samples were incubated at 42°C for 30 minutes and stored at -80°C until processed. RNA was isolated following the manufacturer's instructions for LCM samples, and then quantified using Quant-iT RiboGreen RNA Assay Kit (Invitrogen, Carlsbad, CA, USA) and qualified using Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA). In our study, the average RNA integrity number was 6.77 ± 0.58, indicating that the samples are of good quality.

treatment_protocol: No treatments. Mice were naïve. All differences reflect the baseline genetic differences between HDID-1 and HS/Npt control mice (the founding population of HDID-1 mice).

value: ventral tegmental area

tag: strain

value: 2-3 months


title: C10_VTA

value: HS/Npt


title: C11_VTA


title: H9_VTA


title: C9_VTA


title: HCV-specific CD8 T cells, vc-01, p01

value: pbmc

tag: cell type

value: CD8+ T cells


title: HCV-specific CD8 T cells, vc-02, p01

tag: infection outcome

value: chronic


title: H10_VTA


title: H11_VTA


title: C5_VTA


title: H5_VTA


title: C12_VTA


title: H8_VTA


title: C8_VTA


title: H3_VTA


title: H4_VTA


title: C6_VTA


title: H7_VTA


title: C4_VTA


title: H6_VTA


title: C7_VTA


title: C3_VTA


title: H2_VTA


title: C2_VTA


title: H1_VTA


title: C10_CeA

value: central nucleus of the amygdala


title: H10_CeA


title: C1_VTA


title: C7_CeA


title: C5_CeA


title: H9_CeA


title: C12_CeA


title: H4_CeA


title: H2_CeA


title: H12_CeA


title: C4_CeA


title: H11_CeA


title: H5_CeA


title: C3_CeA


title: C11_CeA


title: C8_CeA


title: C9_CeA


title: H8_CeA


title: H6_CeA


title: H10_BLA

value: basolateral amygdala


title: C1_CeA


title: C6_CeA


title: H1_CeA


title: H7_CeA


title: C10_BLA


title: C11_BLA


title: H3_CeA


title: C2_CeA


title: H9_BLA


title: H11_BLA


title: H12_BLA


title: C12_BLA


title: C9_BLA


title: H8_BLA


title: C6_BLA


title: H4_BLA


title: C7_BLA


title: H5_BLA


title: C4_BLA


title: H1_BLA


title: C8_BLA


title: C2_BLA


title: H2_BLA


title: H3_BLA


title: C3_BLA


title: C10_BNST

value: bed nucleus of the stria terminalis


title: C5_BLA


title: H10_BNST


title: H11_BNST


title: H6_BLA


title: H9_BNST


title: C11_BNST


title: C9_BNST


title: H12_BNST


title: H7_BLA


title: C12_BNST


title: H7_BNST


title: H8_BNST


title: C8_BNST


title: C7_BNST


title: C5_BNST


title: C4_BNST


title: H4_BNST


title: C12_AcbSh

value: nucleus accumbens, shell


title: H6_BNST

value: male


title: C2_BNST


title: H11_AcbSh


title: H4_AcbSh


title: H3_BNST


title: C5_AcbSh


title: H5_BNST


title: C6_BNST


title: C11_AcbSh


title: C3_BNST


title: H10_AcbSh


title: H2_BNST


title: C7_AcbSh


title: H8_AcbSh


title: H12_AcbSh


title: C9_AcbSh


title: C10_AcbSh


title: H7_AcbSh


title: C6_AcbSh


title: H9_AcbSh


title: C1_BNST


title: H5_AcbSh


title: C8_AcbSh


title: H2_AcbSh


title: C10_AcbC

value: nucleus accumbens, core


title: H9_AcbC


title: C3_AcbSh


title: C1_AcbSh


title: H12_AcbC


title: C4_AcbSh


title: C5_AcbC


title: C8_AcbC


title: H7_AcbC


title: H6_AcbSh


title: C11_AcbC


title: H11_AcbC


title: C4_AcbC


title: C9_AcbC


title: H8_AcbC


title: C12_AcbC


title: H3_AcbSh


title: H10_AcbC


title: C2_AcbSh


title: C7_AcbC


title: H4_AcbC


title: H1_BNST


title: H1_AcbSh


title: H5_AcbC


title: C6_AcbC


title: C1_BLA


title: H6_AcbC


title: H3_AcbC


title: C10_PFC

value: prefrontal cortex


title: H2_AcbC


title: H12_PFC


title: C3_AcbC


title: H1_AcbC


title: H10_PFC


title: H9_PFC


title: C2_AcbC


title: H11_PFC


title: C12_PFC


title: C4_PFC


title: C11_PFC


title: H7_PFC


title: H5_PFC


title: C2_PFC


title: C5_PFC


title: H8_PFC


title: H3_PFC


title: 20273331

status: Public on Aug 01 2016

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

description: case blood

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Genomic DNA was extracted from frozen whole blood samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

source_name: case blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

tag: sentrixids

value: M


title: H4_PFC


title: H6_PFC


title: C8_PFC


title: 12765075

description: case blood

extract_protocol: Genomic DNA was extracted from frozen whole blood samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.


title: C7_PFC


title: 33248141

description: case blood


title: C6_PFC


title: 8568276

description: case blood

value: F


title: 12764479

description: case blood


title: C3_PFC


title: 12763907

description: case blood


title: C1_AcbC


title: 33262073

description: case blood


title: 8568215

description: case blood


title: H2_PFC


title: 12764504

description: case blood


title: 12764440

description: case blood


title: 20273335

description: case blood


title: 33262599

description: case blood


title: C9_PFC


title: 33262414

description: case blood


title: 33248151

description: case blood


title: 33262648

description: case blood


title: H1_PFC


title: 8567854

description: case blood


title: 12763931

description: case blood


title: 12764422

description: case blood


title: C1_PFC


title: 12818097

description: case blood


title: 12778822

description: case blood


title: 33262228

description: case blood


title: 33262066

description: case blood


title: 8567905

description: case blood


title: 33262427

description: case blood


title: 8602049

description: case blood


title: 20273874

description: case blood


title: 12765123

description: case blood


title: 8567828

description: case blood


title: 12764540

description: case blood


title: 8643193

description: case blood


title: 12763908

description: case blood


title: 8567827

description: case blood


title: 12764548

description: case blood


title: 12763892

description: case blood


title: 33262401

description: case blood


title: 8568256

description: case blood


title: 20273891

description: case blood


title: 12763895

description: case blood


title: 33262510

description: case blood


title: 33262259

description: case blood


title: 33262225

description: case blood


title: 8567863

description: case blood


title: 12778811

description: case blood


title: 33262625

description: case blood


title: 12764464

description: case blood


title: 8568250

description: case blood


title: 8567869

description: case blood


title: 12764544

description: case blood


title: 33261627

description: case blood


title: 8568238

description: case blood


title: 33262282

description: case blood


title: 12764451

description: case blood


title: 8567847

description: case blood


title: 33262500

description: case blood


title: 8567817

description: case blood


title: 33261677

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title: 12771005

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title: 33248145

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title: 33262249

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title: 8936849

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title: 10139255

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title: 12769553

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title: 33262310

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title: 20273369

description: control blood


title: 10139252

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title: 33262057

description: control blood


title: 33261968

description: control blood


title: 33262065

description: control blood


title: 33262293

description: control blood


title: 33262304

description: control blood


title: 33262634

description: control blood


title: 12766303

description: control blood


title: 12772334

description: control blood


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description: control blood


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description: control blood


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description: control blood


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description: control blood


title: 33262071

description: control blood


title: 8916121

description: control blood


title: 10139310

description: control blood


title: 12785465

description: control blood


title: 33262475

description: control blood


title: 12778768

description: control blood


title: 33262257

description: control blood


title: 20273301

description: control blood


title: 12769636

description: control blood


title: 8918120

description: control blood


title: 20273830

description: control blood


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description: control blood


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description: control blood


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description: control blood


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description: control blood


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title: 20273370

description: control blood


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description: control blood


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description: control blood


title: 33262040

description: control blood


title: 33261717

description: control blood


title: 20274206

description: control blood


title: 33248125

description: control blood


title: 12777682

description: control blood


title: 33261658

description: control blood


title: 33262069

description: control blood


title: 33262608

description: control blood


title: 10139268

description: control blood


title: 12785410

description: control blood


title: 12785387

description: control blood


title: 10136936

description: control blood


title: 33262493

description: control blood


title: 12781107

description: control blood


title: 10139305

description: control blood


title: 33262430

description: control blood


title: 20273849

description: control blood


title: 20273821

description: control blood


title: 33261640

description: control blood


title: 33248152

description: control blood


title: 7466509

description: control blood


title: 33262369

description: control blood


title: 20273351

description: control blood


title: 33262509

description: control blood


title: 33261759

description: control blood


title: 33262240

description: control blood


title: 12785441

description: control blood


title: 12816901

description: control blood


title: 12817976

description: control blood


title: 20274205

description: control blood


title: 10139317

description: control blood


title: 12781119

description: control blood


title: 20274231

description: control blood


title: 12574190

description: control blood


title: 33261646

description: control blood


title: 33262490

description: control blood


title: 33262352

description: control blood


title: 33262454

description: control blood


title: 12785470

description: control blood


title: 8918147

description: control blood


title: 12771031

description: control blood


title: 33262498

description: control blood


title: 12777684

description: control blood


title: 12786472

description: control blood


title: 12781071

description: control blood


title: 33262502

description: control blood


title: 33262292

description: control blood


title: 33262445

description: control blood


title: 33261971

description: control blood


title: 33262345

description: control blood


title: 33261644

description: control blood


title: 33261610

description: control blood


title: 33261685

description: control blood


title: 33262209

description: control blood


title: 7466544

description: control blood


title: 33248135

description: control blood


title: 33262630

description: control blood


title: 33262056

description: control blood


title: 12786515

description: control blood


title: 33262450

description: control blood


title: 33261671

description: control blood


title: 20274219

description: control blood


title: 33262239

description: control blood


title: 12781114

description: control blood


title: 20273904

description: control blood


title: 12574632

description: control blood


title: 33262326

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title: 33262220

description: control blood


title: 12765313

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description: control blood


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title: 12781138

description: control blood


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title: 33261744

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title: 33262598

description: control blood


title: 12772415

description: control blood


title: 12574641

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title: 33262307

description: control blood


title: 12771053

description: control blood


title: 12776426

description: control blood


title: 12776096

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title: 12785402

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title: 33262262

description: control blood


title: 33262300

description: control blood


title: 20274218

description: control blood


title: 12778775

description: control blood


title: 8917399

description: control blood


title: 20273918

description: control blood


title: 33261934

description: control blood


title: 33261651

description: control blood


title: 12781088

description: control blood


title: 20274244

description: control blood


title: 20273365

description: control blood


title: 8917438

description: control blood


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description: control blood


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description: control blood


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description: control blood


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description: control blood


title: 33261964

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description: control blood


title: 20274153

description: control blood


title: 33262035

description: control blood


title: 12769545

description: control blood


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description: control blood


title: 33261623

description: control blood


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description: control blood


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description: control blood


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description: control blood


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description: control blood


title: 33261959

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title: 33262635

description: control blood


title: 12781066

description: control blood


title: 33262452

description: control blood


title: 7466568

description: control blood


title: 33262570

description: control blood


title: 33262211

description: control blood


title: 10139312

description: control blood


title: 12781095

description: control blood


title: 33262203

description: control blood


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description: control blood


title: 8936874

description: control blood


title: 33262614

description: control blood


title: 33262321

description: control blood


title: Ly49E-CD8aa+ cells, biological replicate 3

status: Public on Jul 08 2016

city: Ghent

first: Georges

last: Leclercq

address: De Pintelaan 185 (MRB2 building)

department: Department of Clinical chemistry, microbiology and immunology

country: Belgium

institute: Ghent University

description: Ly49E-CD8aa+ small intestinal intraepithelial lymphocytes, biological replicate 3

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps
All samples passed quality control, and the Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization).

source_name: small intestinal intraepithelial lymphocytes, Ly49E-CD8aa+

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Small intestine dissected from 8-10 week old NOD-SCID mice

extract_protocol: Isolation of Intestinal Intraepithelial Lymphocytes, protocol according to M. Kronenberg (The Journal of Immunology, 2007, 178: 4230-4239)

treatment_protocol: Not applicable

value: NOD SCID

value: 8-10 weeks old

value: small intestine

value: intraepithelial lymphocytes

tag: markers


title: Ly49E+CD8aa- cells, biological replicate 2

description: Ly49E+CD8aa- small intestinal intraepithelial lymphocytes, biological replicate 2

source_name: small intestinal intraepithelial lymphocytes, Ly49E+CD8aa-


title: Ly49E-CD8aa+ cells, biological replicate 2

description: Ly49E-CD8aa+ small intestinal intraepithelial lymphocytes, biological replicate 2


title: Ly49E+CD8aa- cells, biological replicate 1

description: Ly49E+CD8aa- small intestinal intraepithelial lymphocytes, biological replicate 1


title: Ly49E+CD8aa+ cells, biological replicate 1

description: Ly49E+CD8aa+ small intestinal intraepithelial lymphocytes, biological replicate 1

source_name: small intestinal intraepithelial lymphocytes, Ly49E+CD8aa+


title: Ly49E-CD8aa+ cells, biological replicate 1

description: Ly49E-CD8aa+ small intestinal intraepithelial lymphocytes, biological replicate 1


title: Ly49E+CD8aa+ cells, biological replicate 3

description: Ly49E+CD8aa+ small intestinal intraepithelial lymphocytes, biological replicate 3


title: Cont-Ter-AGA, rep13

status: Public on May 10 2016

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

description:
SAMPLE_7994
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

hyb_protocol: Hybridization was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

data_processing:
Data was processed, normalized, and converted into log2 values in R 3.0.1 using the Affy library from Bioconductor.
The file complete_dataset.csv contains the expression information for 14,651 genes found in common across the different array platforms analyzed. Row names contain gene symbols.

source_name: Human placenta from Cont-Ter-AGA pregnancy

label_protocol: Biotinylated cDNA was prepared by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

extract_protocol: To control for batch affect, samples were randomized into groups of 20 for processing. A 100 mg aliquot was used to prepare an mRNA extract using Trizol followed by RNAeasy spin columns. RNA purity and integrity were determined using 28S to 18S rRNA ratio (Agilent Bioanalyzer).

treatment_protocol: Four tissue biopsies (one sample/quadrant, excluding the chorionic plate) are collected per placenta, rinsed in PBS to remove contaminating maternal blood, pooled, crushed into a powder, and snap-frozen in liquid nitrogen.

tag: diagnosis

value: non-PE

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: East Indian

tag: maternal blood type

value: O

tag: previous nulliparity

value: Yes

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

value: No

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: Vaginal

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Ly49E+CD8aa- cells, biological replicate 3

description: Ly49E+CD8aa- small intestinal intraepithelial lymphocytes, biological replicate 3

tag: strain

tag: age

tag: tissue

tag: cell type

tag: markers


title: Ly49E+CD8aa+ cells, biological replicate 2

description: Ly49E+CD8aa+ small intestinal intraepithelial lymphocytes, biological replicate 2


title: Cont-Ter-AGA, rep28

description:
SAMPLE_9933
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery


title: Retentostat run time 545 h replicate 2 dye swap

city: Wien

first: Alexandra

middle: Bettina

last: Graf

address: Muthgasse 18

department: Applied Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.11.5.1.1).

data_processing: Raw data was loaded into R, the limma package was used to normalize (LOESS, Aquantile) the data, summarize, and calculate differential expression. The multiple testing adjustment method was Benjamini and Yekutieli.

organism: Komagataella phaffii CBS 7435

source_name: Retentostat run time 545 h

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Precultures for shake-flask and bioreactor experiments were inoculated from cryo stocks and cultivated in YPD and YPD-Geneticin, respectively at 25 °C and 180 rpm overnight. The prefilled bioreactors were inoculated with precultures.  After completion of the batch phase, chemostat cultivation was initiated at the respective dilution rate. A working volume of 400 mL was kept steady and the dissolved oxygen concentration was kept above 20%, cultures were stirred at 450 rpm and sparged by a constant air flow of 0.2 L min-1. Culture temperature was controlled at 25 °C and the pH was kept at 5.85 by automated addition of 10% ammonia solution. Chemostat media contained per liter: 10 g glucose, 5 g (NH4)2SO4, 3 g KH2PO4, 0.5 g MgSO4 7H2O, 1.5 mL trace metals solution (31), 0.4 mL of a 0.2 g L-1 biotin solution (Sigma-Aldrich, USA) and 0.25 g Pluronic 6100 PE antifoaming agent (BASF, Germany). After reaching a steady-state in chemostat cultures, the retentostat phase was started by switching the reactor effluent to an outflow port equipped with an autoclavable Applisense filter assembly (Applikon, The Netherlands). To control biomass accumulation, the medium reservoir connected to the mixing vessel was exchanged for a reservoir containing chemostat medium supplemented with 5 g L-1 instead of 10 g L-1 glucose (CS,MR). Consequently, the concentration of the growth-limiting substrate glucose entering the bioreactor (CS,in in [g L-1]) decreased over time.

extract_protocol: Total RNA extracted using TRI reagent following manufacturer's instructions

tag: strain

source_name: mixed pool of Pichia pastoris cells sampled from various conditions including cells grown on glycerine, glucose and methanol, on full andminimal medium, in stationary and exponential growth phase, and in different stress states


title: Retentostat run time 380 h replicate 3 dye swap

source_name: Retentostat run time 380 h


title: Retentostat run time 545 h replicate 2

description: Retentostat run time 545 h replicate 2


title: Retentostat run time 116 h replicate 3

description: Retentostat run time 116 h replicate 3

source_name: Retentostat run time 116 h


title: Retentostat run time 380 h replicate 1

description: Retentostat run time 380 h replicate 1


title: Retentostat run time 545 h replicate 3

description: Retentostat run time 545 h replicate 3


title: Retentostat run time 380 h replicate 2

description: Retentostat run time 380 h replicate 2


title: Retentostat run time 545 h replicate 1 dye swap


title: Retentostat run time 116 h replicate 2 dye swap


title: Retentostat run time 545 h replicate 1

description: Retentostat run time 545 h replicate 1


title: Retentostat run time 380 h replicate 1 dye swap


title: Retentostat run time 380 h replicate 2 dye swap


title: Retentostat run time 380 h replicate 3

description: Retentostat run time 380 h replicate 3


title: Retentostat run time 116 h replicate 2

description: Retentostat run time 116 h replicate 2


title: Retentostat run time 116 h replicate 1 dye swap