title: Cont-Term-CH, rep8

description:
SAMPLE_3931
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.

source_name: Human placenta from Cont-Term-CH pregnancy

tag: diagnosis

tag: tissue

tag: mode of delivery

value: C-Section

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: Retentostat run time 65 h replicate 3 dye swap

status: Public on May 10 2016

type: RNA

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.

molecule: total RNA

organism: Komagataella phaffii CBS 7435

source_name: Retentostat run time 65 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: 12778791

status: Public on Aug 01 2016

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

description: control 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.

molecule: genomic DNA

organism: Homo sapiens

source_name: control 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

tag: Sex

value: M

tag: age


title: Retentostat run time 65 h replicate 2 dye swap


title: Retentostat run time 116 h replicate 1

description: Retentostat run time 116 h replicate 1

source_name: Retentostat run time 116 h


title: Retentostat run time 65 h replicate 3

description: Retentostat run time 65 h replicate 3


title: Retentostat run time 116 h replicate 3 dye swap


title: Retentostat run time 65 h replicate 1 dye swap


title: Retentostat run time 65 h replicate 2

description: Retentostat run time 65 h replicate 2


title: Retentostat run time 21 h replicate 1 dye swap

source_name: Retentostat run time 21 h


title: Retentostat run time 21 h replicate 3

description: Retentostat run time 21 h replicate 3


title: Retentostat run time 21 h replicate 2 dye swap


title: Retentostat run time 65 h replicate 1

description: Retentostat run time 65 h replicate 1


title: Retentostat run time 21 h replicate 1

description: Retentostat run time 21 h replicate 1


title: Retentostat run time 21 h replicate 3 dye swap


title: Retentostat run time 21 h replicate 2

description: Retentostat run time 21 h replicate 2


title: Chemostat growth rate 0.1 replicate 3

description: Chemostat growth rate 0.1 replicate 3

source_name: Chemostat growth rate 0.1


title: Chemostat growth rate 0.1 replicate 2 dye swap


title: Chemostat growth rate 0.1 replicate 2

description: Chemostat growth rate 0.1 replicate 2


title: Chemostat growth rate 0.1 replicate 1 dye swap


title: Chemostat growth rate 0.1 replicate 1

description: Chemostat growth rate 0.1 replicate 1


title: Chemostat growth rate 0.075 replicate 1

description: Chemostat growth rate 0.075 replicate 1

source_name: Chemostat growth rate 0.075


title: Chemostat growth rate 0.05 replicate 2 dye swap

source_name: Chemostat growth rate 0.05


title: Chemostat growth rate 0.075 replicate 2 dye swap


title: Chemostat growth rate 0.075 replicate 1 dye swap


title: Chemostat growth rate 0.05 replicate 3 dye swap


title: Chemostat growth rate 0.1 replicate 3 dye swap


title: Chemostat growth rate 0.05 replicate 1

description: Chemostat growth rate 0.05 replicate 1


title: Chemostat growth rate 0.025 replicate 3 dye swap

source_name: Chemostat growth rate 0.025


title: Chemostat growth rate 0.075 replicate 3

description: Chemostat growth rate 0.075 replicate 3


title: Chemostat growth rate 0.025 replicate 3

description: Chemostat growth rate 0.025 replicate 3


title: Chemostat growth rate 0.075 replicate 2

description: Chemostat growth rate 0.075 replicate 2


title: Chemostat growth rate 0.05 replicate 3

description: Chemostat growth rate 0.05 replicate 3


title: Chemostat growth rate 0.025 replicate 2 dye swap


title: Chemostat growth rate 0.025 replicate 2

description: Chemostat growth rate 0.025 replicate 2


title: Chemostat growth rate 0.075 replicate 3 dye swap


title: Chemostat growth rate 0.025 replicate 1 dye swap


title: Chemostat growth rate 0.05 replicate 2

description: Chemostat growth rate 0.05 replicate 2


title: meningioma sample Jed58_MN

status: Public on Apr 20 2016

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description:
Jed58_MN
Gene expression data from brain tumor tissue.

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings.
Meningioma and control data were RMA normalized and analyzed with Partek Genomics Suite 6.6. The RMA-normalized data for the control samples are available in 'GSE77259_normalized_data_for_normal_brain_controls.txt', which is linked to the GSE77259 record as a supplementary file.

label: biotin

source_name: meningioma, grade II, atypical histology

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Total RNA from biospecimens was extracted using the Qiagen RNeasy mini kit according to the manufacturer's instructions. Integrity of RNA was checked by using the Agilent Bioanalyzer.

value: meningioma

tag: tumor grade

value: II

tag: tumor location

value: right falcine

tag: histology

value: atypical

tag: gender

value: male


title: meningioma sample Jed13_MN

description:
Jed13_MN
Gene expression data from brain tumor tissue.

source_name: meningioma, grade I, meningothelial histology

tag: tissue

value: I

value: left frontal

value: meningothelial

value: female


title: meningioma sample Jed53_MN

description:
Jed53_MN
Gene expression data from brain tumor tissue.

source_name: meningioma, grade II, transitional histology with brain invasion

value: right sphenoid wing

value: transitional with brain invasion


title: meningioma sample Jed64_MN

description:
Jed64_MN
Gene expression data from brain tumor tissue.

source_name: meningioma, grade I, fibroblastic histology

value: right frontal

value: fibroblastic


title: meningioma sample Jed04_MN

description:
Jed04_MN
Gene expression data from brain tumor tissue.

source_name: meningioma, grade I, transitional histology

value: left tentorial

value: transitional


title: meningioma sample Jed40_MN

description:
Jed40_MN
Gene expression data from brain tumor tissue.

value: cerebellopontine angle


title: Chemostat growth rate 0.05 replicate 1 dye swap


title: meningioma sample Jed57_MN

description:
Jed57_MN
Gene expression data from brain tumor tissue.

value: right parasagittal


title: Breast cancer 26

status: Public on Apr 15 2014

first: Manikandan

last: Jayapal

address: King Fahd Medical Research Center | King Abdulaziz University | PO BOX 80216, Jeddah 21589. KSA.

description: Fresh Tissue

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.

source_name: Breast cancer fresh tissue

label_protocol: 1ng total RNA was used as input for the Pico amplification and 4ug of amplified cDNA was used for Exon Module amplification. cDNA amplification products were fragmented and labeled with biotin using the NuGEN FL module, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit. And washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol: RNA samples for amplification with the Pico kit were isolated from fresh tissues using the RNeasy Micro Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA amplifications were carried out using Nugen Pico WTA amplification system according to the manufacturersâ€™ suggestions followed by an additional amplification step using Nugen Exon Module.

value: breast cancer tumor

tag: histological type

value: IDC

tag: age (y)

tag: grade

tag: site

value: R

tag: er   (1= positive, 0=nagative)

tag: pr   (1= positive, 0= negative)

tag: her2  (1=positive, 0=negative)

tag: triple negative (1= yes, 0= no)


title: Breast cancer 31

description: Fresh Tissue

value: L


title: Breast cancer 34

description: Fresh Tissue


title: Breast cancer 35

description: Fresh Tissue


title: Breast cancer 15

description: Fresh Tissue


title: Breast cancer 40

description: Fresh Tissue


title: Breast cancer 23

description: Fresh Tissue


title: Breast cancer 3

description: Fresh Tissue


title: Breast cancer 45

description: Fresh Tissue


title: Breast cancer 38

description: Fresh Tissue

value: Mixed


title: Breast cancer 29

description: Fresh Tissue

value: ILC


title: Breast cancer 22

description: Fresh Tissue


title: Breast cancer 4

description: Fresh Tissue


title: Breast cancer 19

description: Fresh Tissue


title: Breast cancer 20

description: Fresh Tissue


title: Memory Ly6c Int Cxcr5 pos 3

status: Public on Apr 22 2013

city: Atlanta

first: Rama

middle: S

last: Akondy

state: GA

address: 1462 CLifton Rd

department: Emory Vaccine Center

country: USA

institute: Emory University

description: Gene expression data from FACS isolated memory Lyc6c nt Cxcr5 pos

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Genepattern 2.0 and RMA as a normalization method. Data was preprocessed to exclude probesets intensities or delta less than 100 and a fold change cutoff of at least 1.5. This prepocessed dataset was collapsed such that of mutiple probesets for a gene, the one with maximum intensity was used (see linked GSE43863_Norm_Preproc_Data.txt file containing RMA normalized intensity of preprocessed collapsed probesets). Statistical analysis was done in Excel using a 2-tailed t test of unequal variance.

organism: Mus musculus

source_name: Memory Lyc6c nt Cxcr5 pos

label_protocol: The amplified cDNA was fragmented and labeled using the Encore Biotin Module

growth_protocol: Congenically labeled (CD45.1) transgenic CD4 T cell splenocytes specific to the gp66-77 epitope of the lymphocytic choriomeningitis virus (LCMV) were obtained from naïve SMARTA TCR transgenic mice (Oxenius et al., 1998). For generation of SMARTA chimeric mice,naïve SMARTA CD4 T cell splenocytes were intravenously transferred into naïve C57BL/6 (CD45.2) mice. ~24 hours post-transfer, chimeric mice were infected i.p. with 2x10e5 PFU of LCMV Armstrong to establish an acute infection.  For adoptive transfer of memory SMARTA cells, CD4+ splenocytes from chimeric mice (between 56 and 101 days post-LCMV infection) were enriched using a MACS CD4+ T cell Isolation Kit II (Miltenyi). Enriched CD4 T cells were then stained and sorted to isolate CD45.2- (CD45.1 SMARTA) Ly6chi CXCR5- and CXCR5hi Ly6clo populations to greater than 98% purity.  8x10e3 sorted memory SMARTA cells were adoptively transferred into naïve C57BL/6 mice (CD45.2)  mice that were subsequently infected 24 hours post transfer with 2x105 PFU of LCMV Armstrong i.p.

extract_protocol: Extraction of total RNA was performed using the Qiagen RNA-mini kit according to the manufacturer's instructions. Genomic DNA was removed using DNAse treatment for some samples and qiagen RNA-mini plus columns for others. For RNA amplification, Ovation Pico WTA System (Nugen) for Affymetrix GeneChip® Arrays was used.

tag: cell type

value: CD4 T cells

tag: cell subtype

value: Memory Lyc6c nt Cxcr5 pos

tag: day after lcmv(arm) infection

value: Day 119

tag: phenotype

value: Ly6c Int Cxcr5 pos


title: Breast cancer 5

description: Fresh Tissue


title: Memory Ly6c lo Cxcr5 pos 3

description: Gene expression data from FACS isolated memory Tfh

source_name: Memory Tfh

value: Memory Tfh

value: Day 68

value: Ly6c lo Cxcr5 pos


title: Memory Ly6c hi Cxcr5 neg 4

description: Gene expression data from FACS isolated memory Th1

source_name: Memory Th1

value: Memory Th1

value: Ly6c hi Cxcr5 neg


title: Memory Ly6c Int Cxcr5 pos 2


title: Memory Ly6c Int Cxcr5 pos 1

value: Day 70


title: Memory Ly6c lo Cxcr5 pos 1

value: Day 147


title: Memory Ly6c hi Cxcr5 neg 2


title: Memory Ly6c lo Cxcr5 pos 4


title: Day6 Ly6c int Cxcr5 pos 1

description: Gene expression data from FACS isolated effector Ly6c int Cxcr5 pos CD4 T cells

source_name: Effector Ly6c int Cxcr5 pos CD4 T cells

value: Effector Ly6c int Cxcr5 pos CD4 T cells

value: Day 6

value: Ly6c int Cxcr5 pos


title: Day6 Ly6c lo Cxcr5 neg 1

description: Gene expression data from FACS isolated effector Ly6c lo Cxcr5 neg CD4 T cells

source_name: Effector Ly6c lo Cxcr5 neg CD4 T cells

value: Effector Ly6c lo Cxcr5 neg CD4 T cells

value: Ly6c lo Cxcr5 neg


title: Naïve Smarta3

description: Gene expression data from FACS isolated naive SMARTA CD4 T cells

source_name: Naive SMARTA CD4 T cells

value: Naive SMARTA CD4 T cells

value: Naïve

value: CD44 lo


title: Day6 Ly6c int Cxcr5 pos 2

value: CD4 T cells


title: Day6 Ly6c lo Cxcr5 neg 2


title: Memory Ly6c hi Cxcr5 neg 3


title: Day6 Ly6c lo Cxcr5 pos 2

description: Gene expression data from FACS isolated effector Tfh

source_name: Effector Tfh

value: Effector Tfh


title: Memory Ly6c lo Cxcr5 pos 2

value: Memory Tfh


title: Naïve Smarta2


title: Memory Ly6c hi Cxcr5 neg 1


title: Day6 Ly6c hi Cxcr5 neg 2

description: Gene expression data from FACS isolated effector Th1

source_name: Effector Th1

value: Effector Th1


title: Day6 Ly6c lo Cxcr5 pos 1

value: Ly6c lo Cxcr5 pos


title: Naïve Smarta1


title: Day6 Ly6c hi Cxcr5 neg 1


title: Retentostat run time 545 h replicate 3 dye swap

source_name: Retentostat run time 545 h

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: Chemostat growth rate 0.025 replicate 1

description: Chemostat growth rate 0.025 replicate 1

source_name: Chemostat growth rate 0.025


title: meningioma sample Jed26_MN

description:
Jed26_MN
Gene expression data from brain tumor tissue.

value: meningioma

tag: tumor grade

value: I

tag: tumor location

value: occipital

value: meningothelial

value: male

tag: age


title: Monocytes_32

status: Public on Mar 14 2013

city: Stockholm

first: Francesco

last: Marabita

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

description:
SAMPLE_91
CD14+ monocytes

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Beachips were scanned using an iScan

data_processing: Raw intesities exported from GenomeStudio software were imported into R and analyzed with the Bioconductor lumi package. Probes on chromosomes X and Y were removed. Probes with a detection P-value > 0.01 exceeding 5% of the samples were also filtered out. Color-bias adjustment and quantile normalization were performed as implemented in lumi. BMIQ correction was applied to beta values to correct for probe type bias.

label: Cy3 and Cy5

source_name: CD14+ monocytes

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted with the Sigma Gene Elute Mammalian Genomic DNA miniprep Kit, according to standard instructions.

treatment_protocol: Monocytes were purified with MACS CD14 Microbeads from Miltenyi.

tag: gender

value: female

tag: slide

tag: array


title: PB_22

description:
SAMPLE_93
Peripheral blood

source_name: Peripheral blood

value: MS

value: N

value: NS

value: case

tag: py


title: PB_49

description:
SAMPLE_89
Peripheral blood

value: E


title: Monocytes_20

description:
SAMPLE_96
CD14+ monocytes


title: PB_25

description:
SAMPLE_94
Peripheral blood


title: 12777651

description: control blood

source_name: control 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.

tag: sentrixids

tag: Sex

value: M


title: PB_3

description:
SAMPLE_88
Peripheral blood


title: Monocytes_28

description:
SAMPLE_87
CD14+ monocytes


title: PB_46

description:
SAMPLE_86
Peripheral blood


title: PB_21

description:
SAMPLE_79
Peripheral blood


title: PB_34

description:
SAMPLE_84
Peripheral blood


title: PB_38

description:
SAMPLE_85
Peripheral blood


title: PB_33

description:
SAMPLE_71
Peripheral blood


title: Monocytes_18

description:
SAMPLE_83
CD14+ monocytes


title: PB_43

description:
SAMPLE_72
Peripheral blood


title: Monocytes_7_r

description:
SAMPLE_82
CD14+ monocytes


title: Monocytes_31

description:
SAMPLE_78
CD14+ monocytes


title: Monocytes_8

description:
SAMPLE_95
CD14+ monocytes


title: PB_11

description:
SAMPLE_80
Peripheral blood


title: PB_44

description:
SAMPLE_73
Peripheral blood


title: PB_19

description:
SAMPLE_81
Peripheral blood


title: PB_24

description:
SAMPLE_92
Peripheral blood


title: Monocytes_16

description:
SAMPLE_70
CD14+ monocytes


title: Monocytes_30_r

description:
SAMPLE_76
CD14+ monocytes


title: Monocytes_39_r

description:
SAMPLE_77
CD14+ monocytes


title: Monocytes_35

description:
SAMPLE_75
CD14+ monocytes


title: Monocytes_26

description:
SAMPLE_74
CD14+ monocytes


title: Monocytes_6

description:
SAMPLE_69
CD14+ monocytes


title: Monocytes_7

description:
SAMPLE_90
CD14+ monocytes


title: PB_10

description:
SAMPLE_67
Peripheral blood


title: Monocytes_38

description:
SAMPLE_63
CD14+ monocytes


title: Monocytes_4_r

description:
SAMPLE_62
CD14+ monocytes


title: PB_17

description:
SAMPLE_68
Peripheral blood


title: Monocytes_30

description:
SAMPLE_65
CD14+ monocytes


title: Monocytes_15_r

description:
SAMPLE_57
CD14+ monocytes


title: Monocytes_24_r

description:
SAMPLE_60
CD14+ monocytes


title: PB_12

description:
SAMPLE_42
Peripheral blood


title: Monocytes_37

description:
SAMPLE_50
CD14+ monocytes


title: PB_48

description:
SAMPLE_51
Peripheral blood


title: Monocytes_29

description:
SAMPLE_52
CD14+ monocytes


title: PB_32

description:
SAMPLE_58
Peripheral blood


title: PB_29

description:
SAMPLE_45
Peripheral blood


title: PB_42

description:
SAMPLE_59
Peripheral blood


title: PB_40

description:
SAMPLE_46
Peripheral blood


title: Monocytes_15

description:
SAMPLE_48
CD14+ monocytes


title: Monocytes_34

description:
SAMPLE_49
CD14+ monocytes


title: Monocytes_5

description:
SAMPLE_56
CD14+ monocytes


title: PB_50

description:
SAMPLE_64
Peripheral blood


title: PB_18

description:
SAMPLE_53
Peripheral blood


title: PB_7

description:
SAMPLE_41
Peripheral blood


title: Monocytes_4

description:
SAMPLE_43
CD14+ monocytes


title: PB_20

description:
SAMPLE_66
Peripheral blood


title: Monocytes_25

description:
SAMPLE_61
CD14+ monocytes


title: PB_16

description:
SAMPLE_40
Peripheral blood


title: Monocytes_14

description:
SAMPLE_44
CD14+ monocytes


title: PB_14

description:
SAMPLE_55
Peripheral blood


title: Monocytes_24

description:
SAMPLE_47
CD14+ monocytes


title: PB_8

description:
SAMPLE_54
Peripheral blood


title: PB_9

description:
SAMPLE_39
Peripheral blood


title: Monocytes_23

description:
SAMPLE_34
CD14+ monocytes


title: PB_28

description:
SAMPLE_32
Peripheral blood


title: PB_45

description:
SAMPLE_36
Peripheral blood


title: PB_47

description:
SAMPLE_38
Peripheral blood


title: Monocytes_36

description:
SAMPLE_37
CD14+ monocytes


title: PB_5

description:
SAMPLE_28
Peripheral blood


title: Monocytes_3

description:
SAMPLE_30
CD14+ monocytes


title: PB_15

description:
SAMPLE_27
Peripheral blood


title: Monocytes_39

description:
SAMPLE_23
CD14+ monocytes


title: PB_35

description:
SAMPLE_35
Peripheral blood


title: PB_13_r

description:
SAMPLE_14
Peripheral blood


title: Monocytes_10

description:
SAMPLE_24
CD14+ monocytes


title: PB_13

description:
SAMPLE_25
Peripheral blood


title: PB_4

description:
SAMPLE_15
Peripheral blood


title: Monocytes_2

description:
SAMPLE_17
CD14+ monocytes


title: Monocytes_39_r2

description:
SAMPLE_12
CD14+ monocytes


title: PB_6

description:
SAMPLE_16
Peripheral blood


title: Monocytes_12

description:
SAMPLE_18
CD14+ monocytes


title: Monocytes_22

description:
SAMPLE_21
CD14+ monocytes


title: PB_41

description:
SAMPLE_26
Peripheral blood


title: HCmel3_relapse_rep4

status: Public on Oct 10 2012

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital Bonn

description:
excised_tumour_skin
8294816100_D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Variance stabilization and normalisation using vsn2 package from bioconductor in R without background correction.

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase.

extract_protocol: Total RNA was isolated using TRI Reagent and purified using Rneasy columns (Quiagen).  RNA quality was assayed using Agilent Bioanalyzer.

tag: adoptive cell therapies (act)

tag: recipient strain

tag: hcmel3 strain

tag: material


title: Monocytes_13

description:
SAMPLE_31
CD14+ monocytes


title: PB_39

description:
SAMPLE_10
Peripheral blood


title: Monocytes_33

description:
SAMPLE_13
CD14+ monocytes


title: HCmel3_ctrl_rep4

description:
excised_tumour_skin
8294816100_A


title: PB_31

description:
SAMPLE_22
Peripheral blood


title: HCmel3_relapse_rep5

description:
excised_tumour_skin
8294816100_E


title: PB_36

description:
SAMPLE_20
Peripheral blood


title: HCmel3_ctrl_rep3

description:
excised_tumour_skin
8294816099_C


title: HCmel3_relapse_rep2

description:
excised_tumour_skin
8294816099_E


title: PB_27

description:
SAMPLE_19
Peripheral blood


title: HCmel3_ctrl_rep5

description:
excised_tumour_skin
8294816100_B


title: PB_26

description:
SAMPLE_9
Peripheral blood


title: HCmel3_relapse_rep3

description:
excised_tumour_skin
8294816099_F


title: HCmel3_ctrl_rep2

description:
excised_tumour_skin
8294816099_B


title: PB_30

description:
SAMPLE_7
Peripheral blood


title: PB_23

description:
SAMPLE_6
Peripheral blood


title: HCmel3_ctrl_rep1

description:
excised_tumour_skin
8294816099_A


title: Monocytes_11

description:
SAMPLE_5
CD14+ monocytes


title: PB_1

description:
SAMPLE_1
Peripheral blood


title: PB_2

description:
SAMPLE_2
Peripheral blood


title: PB_3_r

description:
SAMPLE_3
Peripheral blood


title: OV_FFPE_56

status: Public on Aug 21 2012

city: Tampa

first: Youngchul

last: Kim

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

description:
S0456F098.CEL
Gene expression data from stage III-IV ovarian cancer patients

hyb_protocol: Punches of FFPE tumor tissue blocks and gene expression profiling were performed in a standard procedure by Almac Dignostics, Inc. (Durham, NC).

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

data_processing: Data normalization and quality control assessment of the hybridization results were performed with the RMA Bioconductor package (http://www.bioconductor.org)

source_name: formalin-fixed paraffin embedded (FFPE) tissue, ovarian cancer cells

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

extract_protocol: RNA extraction and amplification was performed with the NuGen WT-Ovation™ FFPE RNA Amplification kit.

tag: cell type

value: ovarian cancer cell

tag: dob

tag: race

value: White

tag: histo

value: Serous

tag: grade

value: Poor

tag: Stage

value: IIIC

tag: surgtype

value: Primary Surgery

tag: datedx

tag: surgdate

tag: optimal

value: Sub-optimal

tag: chemtype

value: Adjuvant

tag: chemoresponse

value: CR (completely response)

tag: chemo agent

value: Carboplatin/Taxol

tag: pfi days

tag: relapse(1=yes, 0=no)

tag: overall survival days


title: OV_FFPE_52

description:
S0456F092.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: age

value: Mod

value: PR (partial response)

value: Cisplatin/Taxol


title: Monocytes_21

description:
SAMPLE_8
CD14+ monocytes

tag: gender

value: male

tag: slide

tag: array


title: PB_9_r

description:
SAMPLE_29
Peripheral blood

value: female

value: MS

value: case

tag: py


title: OV_FFPE_49

description:
S0456F087.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: cell type

value: ovarian cancer cell

tag: dob

tag: race

tag: histo

value: Mucinous

tag: grade


title: OV_FFPE_53

description:
S0456F093.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: White

value: Serous

tag: Stage

value: IIIB

tag: surgtype

tag: datedx

tag: surgdate

tag: optimal

value: Optimal


title: OV_FFPE_55

description:
S0456F096.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: IIIC

value: Primary Surgery

tag: chemtype

tag: chemoresponse

tag: chemo agent

tag: pfi days

tag: relapse(1=yes, 0=no)


title: OV_FFPE_51

description:
S0456F090.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: age

value: Sub-optimal

value: Adjuvant

tag: overall survival days


title: Monocytes_9

description:
SAMPLE_11
CD14+ monocytes

tag: gender

tag: slide

tag: array


title: Monocytes_1

description:
SAMPLE_4
CD14+ monocytes


title: OV_FFPE_46

description:
S0456F081.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: cell type

tag: dob

tag: race

tag: histo

value: Mod

value: Carboplatin/Taxol


title: OV_FFPE_54

description:
S0456F095.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: grade

value: Poor

tag: Stage

tag: surgtype

tag: datedx

value: CR (completely response)


title: OV_FFPE_48

description:
S0456F083.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Black

value: IVA

tag: surgdate

tag: chemtype

tag: chemoresponse

value: PR (partial response)


title: OV_FFPE_47

description:
S0456F082.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: ovarian cancer cell

tag: optimal

tag: chemo agent

tag: pfi days

tag: relapse(1=yes, 0=no)


title: OV_FFPE_57

description:
S0456F099.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: age

value: Unknown

value: UNKnown

tag: overall survival days


title: OV_FFPE_40

description:
S0456F065.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: cell type

value: White

value: Serous


title: OV_FFPE_44

description:
S0456F074.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: dob


title: OV_FFPE_43

description:
S0456F072.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: race

value: Well

value: IIIA

value: Optimal


title: OV_FFPE_58

description:
S0456F100.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: histo

value: IIIC

value: Primary Surgery

value: Sub-optimal


title: OV_FFPE_41

description:
S0456F069.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Endometrioid

tag: grade

value: IIIB

value: Adjuvant

value: Carboplatin/Taxol


title: OV_FFPE_42

description:
S0456F070.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Poor

tag: Stage

value: CR (completely response)


title: OV_FFPE_39

description:
S0456F064.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: ovarian cancer cell

tag: surgtype


title: OV_FFPE_37

description:
S0456F062.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Mod

tag: datedx

value: Cisplatin/Taxol


title: OV_FFPE_38

description:
S0456F063.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: White

tag: surgdate

value: Carboplatin/Cytoxan


title: OV_FFPE_35

description:
S0456F060.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Black

value: Serous

value: IVA

tag: chemtype


title: OV_FFPE_34

description:
S0456F059.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Clear

value: Unk

value: IIIC

value: Optimal

tag: chemoresponse

value: PR (partial response)


title: OV_FFPE_50

description:
S0456F088.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: IIIB

value: Primary Surgery

tag: optimal

value: Sub-optimal

value: Adjuvant


title: OV_FFPE_36

description:
S0456F061.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: ovarian cancer cell

value: Unknown

value: Poor

value: CR (completely response)

tag: chemo agent

value: Carboplatin


title: OV_FFPE_33

description:
S0456F058d.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: White

value: Carboplatin/Taxol

tag: pfi days


title: OV_FFPE_32

description:
S0456F057.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Black

value: Serous

tag: relapse(1=yes, 0=no)


title: OV_FFPE_31

description:
S0456F056.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: age

value: Mod


title: HCmel3_relapse_rep1

description:
excised_tumour_skin
8294816099_D

tag: adoptive cell therapies (act)

tag: recipient strain

tag: hcmel3 strain

tag: material


title: OV_FFPE_30

description:
S0456F054.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: cell type

tag: dob

tag: race

tag: histo

value: IIIA

tag: overall survival days


title: OV_FFPE_28

description:
S0456F051.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Undiff

tag: grade

tag: Stage

tag: surgtype

tag: datedx

tag: surgdate

value: Optimal


title: OV_FFPE_27

description:
S0456F050.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: IIIC

tag: optimal

tag: chemtype

tag: chemoresponse

value: PD (progress of disease)

tag: chemo agent

tag: pfi days


title: OV_FFPE_25

description:
S0456F048.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: age

value: IIIB

value: Primary Surgery

value: Cisplatin/Cytoxan

tag: relapse(1=yes, 0=no)


title: OV_FFPE_24

description:
S0456F047.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: cell type

value: ovarian cancer cell

value: Well

value: Adjuvant

value: PR (partial response)


title: OV_FFPE_21

description:
S0456F039.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: dob

value: White

value: Transitional

value: Poor

value: IVA

value: Sub-optimal

value: CR (completely response)


title: OV_FFPE_18

description:
S0456F034.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: race

value: Serous

value: unknown

value: Carboplatin/Taxol

value: UNKnown


title: OV_FFPE_6

description:
S0456F014.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: histo

value: Mod

value: IIIA

value: Optimal

value: Cisplatin/Taxol


title: OV_FFPE_22

description:
S0456F044.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: ovarian cancer cell

value: IIIB

value: Primary Surgery

tag: overall survival days


title: OV_FFPE_19

description:
S0456F036.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: White

tag: grade

value: Adjuvant


title: OV_FFPE_5

description:
S0456F010.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Clear

value: Poor

tag: Stage


title: OV_FFPE_17

description:
S0456F033.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: IVA

tag: surgtype

value: Sub-optimal

value: PR (partial response)


title: OV_FFPE_11

description:
S0456F022.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Serous

value: IIIC

tag: datedx

value: CR (completely response)


title: OV_FFPE_15

description:
S0456F030.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: surgdate

value: Carboplatin/Taxol

value: UNKnown


title: OV_FFPE_13

description:
S0456F027.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: optimal


title: OV_FFPE_12

description:
S0456F025.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: chemtype


title: OV_FFPE_16

description:
S0456F032.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Mod

tag: chemoresponse


title: OV_FFPE_9

description:
S0456F019.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: chemo agent


title: OV_FFPE_3

description:
S0456F008.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: pfi days


title: OV_FFPE_26

description:
S0456F049.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: age

value: Black


title: OV_FFPE_20

description:
S0456F037.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: ovarian cancer cell

tag: relapse(1=yes, 0=no)


title: OV_FFPE_23

description:
S0456F045a.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: cell type

value: Unk

value: Optimal


title: OV_FFPE_10

description:
S0456F021.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: dob

value: White

value: Primary Surgery


title: OV_FFPE_8

description:
S0456F018.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: race

value: Adjuvant


title: OV_FFPE_14

description:
S0456F028.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: histo

value: Clear

value: IIIB


title: OV_FFPE_45

description:
S0456F076.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Poor

value: Sub-optimal

tag: overall survival days


title: OV_FFPE_29

description:
S0456F053.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: Serous

tag: grade


title: OV_FFPE_7

description:
S0456F017.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: Stage

value: IIIC


title: OV_FFPE_2

description:
S0456F005.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: surgtype

value: CR (completely response)


title: OV_FFPE_4

description:
S0456F009.CEL
Gene expression data from stage III-IV ovarian cancer patients

tag: datedx

value: PR (partial response)

value: Carboplatin/Taxol


title: OV_FFPE_1

description:
S0456F001.CEL
Gene expression data from stage III-IV ovarian cancer patients

value: IVA

tag: surgdate


title: RIT6_6MOS_SD0510B

status: Public on Mar 23 2012

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: RIT6_6MOS_B, Rituximab Patient tissue

hyb_protocol: Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.

data_processing: Data for both channels were lowess-normalized and then log(2) ratio was taken. As for lowess program, we download from BASE.

source_name: RIT6_6MOS_B, Rituximab Patient tissue

label_protocol: Agilent Low RNA Input Linear Amplification protocol: 100 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).

extract_protocol: Total RNA extract using Qiagen Rneasy Tissuekit

treatment_protocol: 3 - 6 mm punch biopsy stored in RNA later

tag: biopsy

value: skin

source_name: Universal Human Reference

extract_protocol: Total RNA isolated by stratagene

tag: reference

value: Stratagene's Universal Human Reference (RNA pool from 10 different human cell lines; http://www.ncbi.nlm.nih.gov/pubmed/15113400)


title: RIT7_PREBASE_SD0411A

description: RIT7_PREBASE_FA, Rituximab Patient tissue


title: RIT7_6MOS_SD0511A

description: RIT7_6MOS_FA, Rituximab Patient tissue

source_name: RIT7_6MOS_FA, Rituximab Patient tissue


title: RIT7_6MOS_SD0511B

description: RIT7_6MOS_B, Rituximab Patient tissue

source_name: RIT7_6MOS_B, Rituximab Patient tissue


title: NONRIT_SD0707A

description: dSSc_8_FA, Non Rituximab Patient tissue

source_name: dSSc_8_FA, Non Rituximab Patient tissue


title: RIT6_BASE_SD0501B

description: RIT6_BASE_B, Rituximab Patient tissue

source_name: RIT6_BASE_B, Rituximab Patient tissue


title: RIT13_BASE_SD517A

description: RIT13_BASE_FA, Rituximab Patient tissue

source_name: RIT13_BASE_FA, Rituximab Patient tissue


title: RIT7_PREBASE_SD0411B

description: RIT7_PREBASE_B, Rituximab Patient tissue


title: RIT7_BASE_SD0503A

description: RIT7_BASE_FA, Rituximab Patient tissue

source_name: RIT7_BASE_FA, Rituximab Patient tissue


title: RIT6_BASE_SD0501B_replicate

description: RIT6_BASE_B_r, Rituximab Patient tissue, replicate


title: RIT15_BASE_SD0519A_replicate

description: RIT15_BASE_FA_r, Rituximab Patient tissue, replicate


title: RIT5_BASE_SD0415B

description: RIT5_BASE_B, Rituximab Patient tissue

source_name: RIT5_BASE_B, Rituximab Patient tissue


title: RIT6_6MOS_SD0510A

description: RIT6_6MOS_FA, Rituximab Patient tissue

source_name: RIT6_6MOS_FA, Rituximab Patient tissue


title: RIT15_6MOS_SD064A

description: RIT15_6MOS_FA, Rituximab Patient tissue

source_name: RIT15_6MOS_FA, Rituximab Patient tissue


title: RIT5_6MOS_SD0507A

description: RIT5_6MOS_FA, Rituximab Patient tissue

source_name: RIT5_6MOS_FA, Rituximab Patient tissue


title: NONRIT_1_SD0704A

description: dSSc_1_FA, Non Rituximab Patient tissue

source_name: dSSc_1_FA, Non Rituximab Patient tissue


title: RIT15_BASE_SD0519A

description: RIT15_BASE_FA, Rituximab Patient tissue

source_name: RIT15_BASE_FA, Rituximab Patient tissue


title: NONRIT_1_SD0805A

description: dSSc_1_10MOS_FA, Non Rituximab Patient tissue


title: RIT5_BASE_SD0415A

description: RIT5_BASE_FA, Rituximab Patient tissue

source_name: RIT5_BASE_FA, Rituximab Patient tissue


title: RIT13_6MOS_SD063A

description: RIT13_6MOS_FA, Rituximab Patient tissue

source_name: RIT13_6MOS_FA, Rituximab Patient tissue


title: NONRIT_2_SD0803A

description: dSSc_2_6MOS_FA, Non Rituximab Patient tissue


title: RIT10_6MOS_SD0516A

description: RIT10_6MOS_FA, Rituximab Patient tissue

source_name: RIT10_6MOS_FA, Rituximab Patient tissue


title: RIT8_6MOS_SD0512B

description: RIT8_6MOS_B, Rituximab Patient tissue

source_name: RIT8_6MOS_B, Rituximab Patient tissue


title: RIT8_6MOS_SD0512A

description: RIT8_6MOS_FA, Rituximab Patient tissue

source_name: RIT8_6MOS_FA, Rituximab Patient tissue

source_name: Universal Human Reference


title: NONRIT_2_SD0705A

description: dSSc_2_FA, Non Rituximab Patient tissue

source_name: dSSc_2_FA, Non Rituximab Patient tissue


title: RIT10_36MOS_SD0801A

description: RIT10_36MOS_FA, Rituximab Patient tissue


title: RIT6_BASE_SD0501A

description: RIT6_BASE_FA, Rituximab Patient tissue

source_name: RIT6_BASE_FA, Rituximab Patient tissue


title: RIT8_BASE_SD0504B

description: RIT8_BASE_B, Rituximab Patient tissue

source_name: RIT8_BASE_B, Rituximab Patient tissue


title: RIT15_BASE_SD0519A_TB_SAPgrid

description: RIT15_BASE_FA_r, Rituximab Patient tissue


title: RIT5_6MOS_SD0507B

description: RIT5_6MOS_B, Rituximab Patient tissue

source_name: RIT5_6MOS_B, Rituximab Patient tissue


title: NONRIT_SD0703A_replicate

description: dSSc_6_FA_r, Non Rituximab Patient tissue, replicate


title: NONRIT_SD0412A_TB_SAPscan

description: dSSc_3_FA_r, Non Rituximab Patient tissue


title: NONRIT_SD0703A_TB_SAPgrid

description: dSSc_6_FA_r, Non Rituximab Patient tissue


title: NONRIT_SD0412B_SAP_SAPscan

description: dSSc_3_B_r, Non Rituximab Patient tissue


title: NONRIT_SD0412A_TB_SAPgrid

source_name: dSSc_3_FA_r, Non Rituximab Patient tissue


title: NONRIT_SD0412B_SAP_SAPgrid

description: dSSc_3_B, Non Rituximab Patient tissue

source_name: dSSc_3_B, Non Rituximab Patient tissue


title: NONRIT_SD0412A_SAP_SAPscan


title: RIT14_BASE_SD0518A_TB_SAPscan

description: RIT14_BASE_FA_r, Rituximab Patient tissue


title: RIT2_6MOS_SD0502B

description: RIT2_6MOS_B, Rituximab Patient tissue

source_name: RIT2_6MOS_B, Rituximab Patient tissue


title: RIT14_6MOS_SD0605A

description: RIT14_6MOS_FA, Rituximab Patient tissue

source_name: RIT14_6MOS_FA, Rituximab Patient tissue


title: RIT12_6MOS_SD0602A

description: RIT12_6MOS_FA, Rituximab Patient tissue

source_name: RIT12_6MOS_FA, Rituximab Patient tissue


title: RIT14_6MOS_SD0605A_TB_SAPscan

description: RIT14_6MOS_FA_r, Rituximab Patient tissue


title: RIT17_6MOS_SD071A

description: RIT17_6MOS_FA, Rituximab Patient tissue

source_name: RIT17_6MOS_FA, Rituximab Patient tissue


title: RIT17_BASE_SD0606A

description: RIT17_BASE_FA, Rituximab Patient tissue

source_name: RIT17_BASE_FA, Rituximab Patient tissue


title: RIT14_6MOS_SD0605A_SAP_SAPscan

source_name: RIT14_6MOS_FA_r, Rituximab Patient tissue


title: RIT12_BASE_SD0515A

description: RIT12_BASE_FA, Rituximab Patient tissue

source_name: RIT12_BASE_FA, Rituximab Patient tissue


title: RIT3_6MOS_SD0506B

description: RIT3_6MOS_B, Rituximab Patient tissue

source_name: RIT3_6MOS_B, Rituximab Patient tissue


title: RIT3_BASE_SD0413B

description: RIT3_BASE_B, Rituximab Patient tissue

source_name: RIT3_BASE_B, Rituximab Patient tissue


title: NONRIT_SD0412B_TB_SAPscan

source_name: dSSc_3_B_r, Non Rituximab Patient tissue


title: NONRIT_SD0703A

description: dSSc_6_FA, Non Rituximab Patient tissue

source_name: dSSc_6_FA, Non Rituximab Patient tissue

source_name: Universal Human Reference


title: RIT14_BASE_SD0518A_SAP_SAPscan

source_name: RIT14_BASE_FA_r, Rituximab Patient tissue


title: RIT11_6MOS_SD0601B

description: RIT11_6MOS_B, Rituximab Patient tissue

source_name: RIT11_6MOS_B, Rituximab Patient tissue


title: RIT14_BASE_SD0518A

description: RIT14_BASE_FA, Rituximab Patient tissue

source_name: RIT14_BASE_FA, Rituximab Patient tissue


title: RIT12_6MOS_SD0602A_replicate

description: RIT12_6MOS_FA_r, Rituximab Patient tissue, replicate


title: RIT17_25MOS_SD0806A

description: RIT17_25MOS_FA, Rituximab Patient tissue


title: RIT11_BASE_SD0509A

description: RIT11_BASE_FA, Rituximab Patient tissue

source_name: RIT11_BASE_FA, Rituximab Patient tissue


title: RIT11_6MOS_SD0601A

description: RIT11_6MOS_FA, Rituximab Patient tissue

source_name: RIT11_6MOS_FA, Rituximab Patient tissue


title: NONRIT_SD0513B_replicate

description: dSSc_4_B_r, Non Rituximab Patient tissue, replicate


title: RIT3_6MOS_SD0506A

description: RIT3_6MOS_FA, Non Rituximab Patient tissue


title: NONRIT_SD0513B

description: dSSc_4_B, Non Rituximab Patient tissue

source_name: dSSc_4_B, Non Rituximab Patient tissue


title: NONRIT_SD0513A

description: dSSc_4_FA, Non Rituximab Patient tissue

source_name: dSSc_4_FA, Non Rituximab Patient tissue


title: RIT3_6MOS_SD0506A_replicate

description: RIT3_6MOS_FA_r, Non Rituximab Patient tissue, replicate


title: NONRIT_SD0520A

description: dSSc_5_FA, Non Rituximab Patient tissue

source_name: dSSc_5_FA, Non Rituximab Patient tissue


title: NormalRIT_NO7-1_replicate

description: NormalRIT_5_r, Normal Non-SSc Patient, replicate


title: RIT3_BASE_SD0413A_SAP_SAPgrid

description: RIT3_BASE_FA_r, Rituximab Patient tissue


title: NormalRIT_NO7-1

description: NormalRIT_5, Normal Non-SSc Patient

source_name: NormalRIT_5, Normal Non-SSc Patient


title: NONRIT_SD0706A

description: dSSc_7_FA, Non Rituximab Patient tissue

source_name: dSSc_7_FA, Non Rituximab Patient tissue


title: NONRIT_SD0520A_replicate

description: dSSc_5_FA_r, Non Rituximab Patient tissue, replicate


title: NormalRIT_NO8-03

description: NormalRIT_7, Normal Non-SSc Patient

source_name: NormalRIT_7, Normal Non-SSc Patient


title: NormalRIT_NO8-04_replicate

description: NormalRIT_8_r, Normal Non-SSc Patient, replicate


title: NormalRIT_NO8-02_replicate

description: NormalRIT_6_r, Normal Non-SSc Patient, replicate


title: NONRIT_SD0706A_replicate

description: dSSc_7_FA_r, Non Rituximab Patient tissue, replicate


title: NormalRIT_NO8-02

description: NormalRIT_6, Normal Non-SSc Patient

source_name: NormalRIT_6, Normal Non-SSc Patient


title: RIT11_BASE_SD0509A_replicate

description: RIT11_BASE_FA_r, Rituximab Patient tissue, replicate


title: RIT11_6MOS_SD0601B_replicate

description: RIT11_6MOS_B_r, Rituximab Patient tissue, replicate


title: NormalRIT_NO5-3

description: NormalRIT_3, Normal Non-SSc Patient

source_name: NormalRIT_3, Normal Non-SSc Patient


title: NONRIT_SD0412A_SAP_SAPgrid

description: dSSc_3_FA, Non Rituximab Patient tissue

source_name: dSSc_3_FA, Non Rituximab Patient tissue


title: NormalRIT_NO5-4

description: NormalRIT_4, Normal Non-SSc Patient

source_name: NormalRIT_4, Normal Non-SSc Patient


title: NormalRIT_NO5-2_SAP_SAPgrid

description: NormalRIT_2_r, Normal Non-SSc Patient

source_name: NormalRIT_2_r, Normal Non-SSc Patient


title: NormalRIT_N08-05

description: NormalRIT_9, Normal Non-SSc Patient

source_name: NormalRIT_9, Normal Non-SSc Patient

source_name: Universal Human Reference


title: NormalRIT_N08-05_replicate

description: NormalRIT_9_r, Normal Non-SSc Patient, replicate


title: NormalRIT_NO5-3_replicate

description: NormalRIT_3_r, Normal Non-SSc Patient, replicate


title: NormalRIT_NO5-1_TB_SAPgrid

description: NormalRIT_1_r, Normal Non-SSc Patient

source_name: NormalRIT_1_r, Normal Non-SSc Patient


title: NormalRIT_NO5-1_replicate

description: NormalRIT_1_r, Normal Non-SSc Patient, replicate


title: NormalRIT_NO5-2_replicate

description: NormalRIT_2, Normal Non-SSc Patient, replicate


title: NormalRIT_NO8-04

description: NormalRIT_8, Normal Non-SSc Patient

source_name: NormalRIT_8, Normal Non-SSc Patient


title: Fetal growth restriction (FGR) _3

status: Public on Sep 15 2010

city: Toyoake

first: Haruki

last: Nishizawa

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Obstetrics and Gynecology

country: Japan

institute: Fujita Health University

description: Unexplained FGR was defined by exclusion of known maternal and fetal factors including maternal systemic diseases, multiple gestation, fetal congenital infection, structural abnormalities and chromosomal abnormalities.

hyb_protocol: Samples were hybridized to Affymetrix Human Exon 1.0 ST Array kit.

scan_protocol: Signal intensities were amplified using a second staining with a biotin-labeled anti-streptavidin antibody followed by phycoerythrin-streptavidin staining. Array fluorescent images were obtained using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
Microarray experiment data analyses were performed using Microsoft Excel (Microsof t, Redmond, WA), Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) and Genespring GX11 (Silicon Genetics, Redwood City, CA). All data were subjected to per chip and per gene normalization, intensity dependent normalization and quality control.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0st-v2.r2.dt.hg18.core.mps

source_name: Human placenta (Pla92a)

label_protocol: After fragmentation into ~200 bp with uracil DNA glycosylase, , synthesized sense-strand cDNAs were end-labeled with biotin.

growth_protocol: All of the placental biopsies both from pre-eclampsia and normal normotensive pregnancies with or without FGR pregnancy were obtained after Caesarean sections. To avoid the effect of labor to the expression profile further, only placental samples that were obtained from the women who had not undergone labor were included to the study

extract_protocol: Total RNA was extracted from the chorionic villous tissues with an RNeasy mini-kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions. The quality of the RNA samples was determined by electrophoresis through denaturing agarose gels and staining with ethidium bromide. The RNA was quantified and evaluated for purity by UV spectrophotometry. Approximately 1 ug of each total RNA sample was used for double strand cDNA synthesis. Then cRNA was synthesized with in vitro transcription followed by sense-strand cDNA synthesis using the Ambion Whole Transcript Expression Kit (Applied Biosystems, Foster City, CA).

treatment_protocol: not applicable

tag: tissue

value: Placenta

tag: disease state

value: Fetal growth restriction (FGR)


title: NormalRIT_NO5-1

description: NormalRIT_1, Normal Non-SSc Patient

source_name: NormalRIT_1, Normal Non-SSc Patient


title: NONRIT_SD0802A

description: dSSc_9_FA, Non Rituximab Patient tissue

source_name: dSSc_9_FA, Non Rituximab Patient tissue


title: Fetal growth restriction (FGR) _1

source_name: Human placenta (Pla91)


title: Fetal growth restriction (FGR) _8

source_name: Human placenta (Pla97)


title: Fetal growth restriction (FGR) _5

source_name: Human placenta (Pla99)


title: Normotensive control pregnancy_6

description: All of the placental biopsies were obtained after Caesarean sections.

source_name: Human placenta (Pla78b)

value: Normotensive control pregnancy


title: Normotensive control pregnancy_8

source_name: Human placenta (Pla9b)


title: Fetal growth restriction (FGR) _4

source_name: Human placenta (Pla94)


title: Fetal growth restriction (FGR) _7

source_name: Human placenta (Pla96)


title: Normotensive control pregnancy_7

source_name: Human placenta (Pla79b)


title: Normotensive control pregnancy_4

source_name: Human placenta (Pla61)


title: Fetal growth restriction (FGR) _6

source_name: Human placenta (Pla90a)


title: Fetal growth restriction (FGR) _2

source_name: Human placenta (Pla98a)


title: Normotensive control pregnancy_3

source_name: Human placenta (Pla1)


title: RIT11_BASE_SD0509B

description: RIT11_BASE_B, Rituximab Patient tissue

source_name: RIT11_BASE_B, Rituximab Patient tissue

source_name: Universal Human Reference


title: Normotensive control pregnancy_1

source_name: Human placenta (Pla11a)


title: Normotensive control pregnancy_5

source_name: Human placenta (Pla77)


title: Normotensive control pregnancy_2

source_name: Human placenta (Pla12b)


title: dSSc9-FA

status: Public on Jul 15 2008

scan_protocol: Microarrays were scanned using a dual laser GenePix 4000B scanner (Axon Instruments). The pixel intensities of the acquired images were then quantified using GenePix Pro 5.0 software.

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis.  Only spots with fluorescent signal at least twofold greater than local background in both Cy3- and Cy5- channels were included in the analysis.  Genes missing more than 20% of their data points were excluded, resulting in 28,495 probes that passed the filtering criteria.

source_name: patient SS1-forearm biopsy

label_protocol: Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).

growth_protocol: 5mm punch biopsies frozen in RNAlater

extract_protocol: Qiagen RNeasy for fibrous tissue

treatment_protocol: 5mm punch biopsies frozen in RNAlater

tag: 58 yo WF, 20 years of dSSc

source_name: Universal Human Reference RNA

tag: pool of RNA from 10 different human cell lines


title: Nor6-B

source_name: normal control G6-back biopsy

tag: 29 yo WF, normal control


title: dSSc17-B

source_name: patient SS4-back biopsy

tag: 56 yo WF, 8 years of dSSc


title: dSSc18-FA

source_name: patient SD-forearm biopsy

tag: 42 yo WF with Eosinophilic Fasciitis


title: dSSc15-FA

source_name: patient SS2-forearm biopsy

tag: 65 yo WF, 10 years of dSSc


title: Nor5-FA

source_name: normal control G5-forearm biopsy

tag: 45 yo WM, normal control


title: dSSc16-FA

source_name: patient SS3-forearm biopsy

tag: 40 yo AF, 20 years of dSSc


title: Nor6-FA

source_name: normal control G6-forearm biopsy


title: Nor4-FA(a)

source_name: normal control G4-forearm biopsy

tag: 26 yo WF, normal control


title: Nor4-B

source_name: normal control G4-back biopsy


title: Nor3-B

source_name: normal control G3-back biopsy

tag: 41 yo WF, normal control


title: Nor5-B

source_name: normal control G5-back biopsy


title: Nor2-FA(b)

source_name: normal control G2-forearm biopsy

tag: 47 yo WF, normal control


title: Nor3-FA

source_name: normal control G3-forearm biopsy


title: Nor1-FA

source_name: normal control G1-forearm biopsy

tag: 53 yo WF, normal control


title: lSSc7-FA(a)

source_name: patient D4-forearm biopsy

tag: 67 yo WF, 5 years of lSSc/CREST


title: Nor1-B

source_name: normal control G1-back biopsy


title: Morph3

source_name: patient E2-back biopsy

tag: 49 yo WF, 4 years of morphea, back biopsy

source_name: Universal Human Reference RNA


title: Morph1( c)

source_name: patient F1-leg biopsy

tag: 49 yo WF, 16 years of morphea, leg biopsy


title: Nor4-FA(b)


title: lSSc7-FA(b)


title: Morph2

source_name: patient F2-abdomen biopsy

tag: 54 yo WF, 7 years of disease, abdomen biopsy


title: Nor2-FA( c)


title: Nor2-FA(a)


title: Nor2-B

source_name: normal control G2-back biopsy


title: Morph1(b)


title: lSSc7-B

source_name: patient D4-back biopsy


title: Morph1(a)


title: lSSc6-B

source_name: patient D3-back biopsy

tag: 55 yo WF, 17 years od lSSc/CREST


title: lSSc6-FA

source_name: patient D3-forearm biopsy


title: lSSc5-FA

source_name: patient D2-forearm biopsy

tag: 60 yo AAF, 28 years of lSSc/CREST


title: lSSc5-B

source_name: patient D2-back biopsy

tag: pool of RNA from 10 different human cell lines


title: lSSc3-FA

source_name: patient C3-forearm biopsy

tag: 35 yo WF, 3 years of lSSc/CREST


title: lSSc4-FA

source_name: patient D1-forearm biopsy

tag: 63 yo WF, 12.5 years of lSSc/CREST


title: lSSc2-FA

source_name: patient C2-forearm biopsy

tag: 57 yo WM, 2 years of lSSc/CREST


title: lSSc2-B

source_name: patient C2-back biopsy


title: lSSc1-FA(a)

source_name: patient C1-forearm biopsy

tag: 67 yo WF, 3 years of lSSc/CREST


title: dSSc14-FA(a)

source_name: patient B6-forearm biopsy

tag: 49 yo WF, 10 years of dSSc


title: lSSc1-B

source_name: patient C1-back biopsy


title: lSSc4-B

source_name: patient D1-back biopsy


title: lSSc1-FA(b)

source_name: Universal Human Reference RNA


title: lSSc3-B

source_name: patient C3-back biopsy


title: dSSc13-B(b)

source_name: patient B5-back biopsy

tag: 47 yo WF, 6 years of dSSc


title: dSSc11-FA

source_name: patient B3-forearm biopsy

tag: 47 yo WF, 8.5 years of dSSc


title: dSSc14-FA(b)


title: dSSc12-B(a)

source_name: patient B4-back biopsy

tag: 58 yo WM, 9 years of dSSc


title: dSSc13-B(a)


title: dSSc13-FA

source_name: patient B5-forearm biopsy


title: dSSc10-FA

source_name: patient B2-forearm biopsy

tag: 35 yo AAF, 7 years of dSSc


title: dSSc7-B

source_name: patient A7-back biopsy

tag: 43 yo WF, 2.5 years of dSSc


title: dSSc11-B

source_name: patient B3-back biopsy


title: dSSc12-FA(b)

source_name: patient B4-forearm biopsy


title: dSSc6-B

source_name: patient A6-back biopsy

tag: 63 yo WF, 6 months of dSSc


title: dSSc10-B

source_name: patient B2-back biopsy


title: dSSc12-B(b)


title: dSSc8-B

source_name: patient A8-back biopsy

tag: 58 yo AM, 2.5 years of dSSc


title: dSSc8-FA(b)

source_name: patient A8-forearm biopsy


title: dSSc12-FA(a)


title: dSSc14-B

source_name: patient B6-back biopsy


title: dSSc4-FA

source_name: patient A4-forearm biopsy

tag: 47 yo WF, 3 years of dSSc


title: dSSc6-FA

source_name: patient A6-forearm biopsy


title: dSSc7-FA

source_name: patient A7-forearm biopsy

source_name: Universal Human Reference RNA


title: dSSc5-B

source_name: patient A5-back biopsy

tag: 52 yo WF, 1 years od dSSc


title: dSSc5-FA

source_name: patient A5-forearm biopsy


title: dSSc8-FA(a)


title: dSSc4-B

source_name: patient A4-back biopsy


title: dSSc3-FA

source_name: patient A3-forearm biopsy

tag: 33 yo HF, 2.5 years of dSSc


title: dSSc2-B(b)

source_name: patient A2-back biopsy

tag: 49 yo WM, 2.5 years of dSSc


title: dSSc2-FA(b)

source_name: patient A2-forearm biopsy

tag: pool of RNA from 10 different human cell lines


title: dSSc2-FA( c)


title: dSSc3-B

source_name: patient A3-back biopsy


title: dSSc2-FA(a)


title: dSSc2-B(a)


title: dSSc1-FA

source_name: patient A1-forearm biopsy

tag: 41yo WF, 2 years of dSSc