title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group6_2_WT_col_CD64+Ly-6Clo

description:
Group6 chip2: WT colonic lamina propria CD64+Ly-6Chi macrophages from WT Th cell-induced colitis without restimulation
Group6_2_WT_col_CD64+Ly-6Clo

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group4_2_WT_col_CD64+Ly-6Chi

status: Public on Feb 04 2016

type: RNA

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
Group4 chip2: WT colonic lamina propria CD64+Ly-6Chi monocytes from WT Th cell-induced colitis without restimulation
Group4_2_WT_col_CD64+Ly-6Chi

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing:
Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the BioRetis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the BioRetis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 2 chips of one group (Experiment group) were compared to the 2 chips of any other group (Baseline group) and chips within one group were compared to each other in both directions. This results in 15 different comparisons of 6 groups. Of relevance for this publication were the comparisons of groups 1 vs. 2, groups 3 vs. 4, and groups 5 vs. 6. The following parameters of absolute and comparative analysis were included in the BioRetis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 4 SLR values of Experiment group vs. Baseline group and 4 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.385E-07) or more than 50% of non-parametrically calculated Change calls (one-sided Wilcoxon’s signed rank test after Tukey-Biweight reduction of outliers, calculated by GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction and not No Changed. Significantly differentially expressed genes were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chips comparisons (one direction).
ABS_CALL: A: gene is detected as Absent, M: as Marginal present, or P: as Present
DETECTION P-VALUE: Non-parametrical p-value for generation of detection call

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Group 4: monocytes from WT Th cell-induced colitis

growth_protocol: Colitis was induced by i.v. transfer of 4E05 naïve CD4+CD45RBhiCD25- Th cells from WT C57BL/6 or Tbx21-/- mice into congenic Rag1-/- recipients. When signs of colitis became apparent (day 15-17), mice were sacrificed and the inflamed colons were harvested. The epithelial layer was stripped off by 2 rounds of incubation in HBSS with 5 mM EDTA and 10 mM HEPES at 37 °C for 20 minutes with 100 RPM shaking. Lamina propria leukocytes were isolated by 3 rounds of incubation in HBSS containing Ca and Mg with 0.5 µg/ml DNase I (Sigma), 0.5 µg/ml Collagenase D (Roche) and 0.5 U/ml Dispase (BD Biosciences) for 20 minutes at 37 °C with 100 RPM shaking. For sorting, electronic gates were set to identify viable, single leukocytes (FSC/SSC, DAPI-, FSC-height vs. FSC-area). Th cells (CD3+CD4+), monocytes (CD64+Ly-6Chi) and macrophages (CD64+Ly-6Clow) were sorted. Th cells were stimulated for 3 hours in IMDM with 10% FCS containing PMA (10 ng/ml) and ionomycin (1 µg/ml).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: cell type

value: colonic lamina propria leukocytes from colitis

tag: genotype of sorted cells

tag: genotype of th cells for colitis induction

tag: activation

tag: flow cytometric cell sorting


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group5_2_Tbx21ko_col_CD64+Ly-6Clo

description:
Group5 chip2: WT colonic lamina propria CD64+Ly-6Chi macrophages from Tbx21-/- Th cell-induced colitis without restimulation
Group5_2_Tbx21ko_col_CD64+Ly-6Clo

source_name: Group 5: macrophages from Tbx21-/- Th cell-induced colitis


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group5_1_Tbx21ko_col_CD64+Ly-6Clo

description:
Group5 chip1: WT colonic lamina propria CD64+Ly-6Chi macrophages from Tbx21-/- Th cell-induced colitis without restimulation
Group5_1_Tbx21ko_col_CD64+Ly-6Clo


title: Unmethylated human DNA [Unmethylated_2]

status: Public on Feb 29 2016

type: genomic

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description:
Zymo Research Cat no D5014
Unmethylated_2

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116 DNMT1 (-/-) and DNMT3b (-/-) cell line

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA was obtained from commercial sources except for the two normal breast tissue samples for which genomic DNA was isolated from fresh frozen breast tissues in a three-step procedure. Tumour cells were pre-treated with Proteinase K (20 mg/ml) at 55C over-night, DNA was further purified using the Promega Wizard Genomic DNA Purification kit (Promega Corporation, Madison, Wisconsin) and finally DNA was purified by phenol/chloroform treatment in phase-lock tubes.

tag: cell line


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group4_1_WT_col_CD64+Ly-6Chi

description:
Group4 chip1: WT colonic lamina propria CD64+Ly-6Chi monocytes from WT Th cell-induced colitis without restimulation
Group4_1_WT_col_CD64+Ly-6Chi


title: Human mammary fibroblast genomic DNA [HMF_2]

description:
ScienCell Research Laboratories Cat no 7639
HMF_2

source_name: mammary fibroblast

value: mammary fibroblast


title: Human mammary epithelial cell genomic DNA [HMEpiC_2]

description:
ScienCell Research Laboratories Cat no 7619
HMEpiC_2

source_name: mammary epithelial cell

value: mammary epithelial cell


title: Human Genomic DNA Male [Blood]

description:
Promega Cat no G1471
Blood

source_name: peripheral blood leukocytes

value: peripheral blood leukocytes


title: Human epidermal melanocyte-light genomic DNA [HEM-l_2]

description:
ScienCell Research Laboratories Cat no 2209
HEM-l_2

source_name: epidermal melanocyte

value: epidermal melanocyte


title: Human mesenchymal stem cell-bone marrow genomic DNA [HMSC-bm_2]

description:
ScienCell Research Laboratories Cat no 7509
HMSC-bm_2

source_name: bone marrow

value: bone marrow


title: Human normal breast tissue [TAX577589]

description:
Lund University Hospital
TAX577589

source_name: normal breast tissue

value: normal breast tissue


title: Human epidermal keratinocyte-adult genomic DNA [HEK-a_2]

description:
ScienCell Research Laboratories Cat no 2119
HEK-a_2

source_name: epidermal keratinocyte

value: epidermal keratinocyte


title: Human epidermal melanocyte-dark genomic DNA [HEM-d_2]

description:
ScienCell Research Laboratories Cat no 2229
HEM-d_2


title: Human mammary epithelial cell genomic DNA [HMEpiC_1]

description:
ScienCell Research Laboratories Cat no 7619
HMEpiC_1


title: Human epidermal melanocyte-medium genomic DNA [HEM-m_2]

description:
ScienCell Research Laboratories Cat no 2219
HEM-m_2


title: Human normal breast tissue [TAX577591]

description:
Lund University Hospital
TAX577591


title: Human mesenchymal stem cell-bone marrow genomic DNA [HMSC-bm_1]

description:
ScienCell Research Laboratories Cat no 7509
HMSC-bm_1


title: Human dermal fibroblast-adult genomic DNA [HDF-a_1]

description:
ScienCell Research Laboratories Cat no 2329
HDF-a_1

source_name: dermal fibroblast

value: dermal fibroblast


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group1_1_CD4_Tbx21ko_PMAIono

description:
Group1 chip1: Tbx21-/- colonic lamina propria CD3+CD4+ Th cells from Tbx21-/- Th cell-induced colitis restimulated for 3h with PMA/ionomycin
Group1_1_CD4_Tbx21ko_PMAIono

source_name: Group 1: Th cells from Tbx21-/- Th cell-induced colitis

value: 3h PMA and ionomycin


title: Control 3 (Biological Replicate 3)

status: Public on Feb 01 2016

city: Baltimore

first: Angelika

last: Doetzlhofer

state: MD

address: 855 North Wolfe St.

department: Neuroscience

country: USA

institute: The Johns Hopkins University School of Medicine

description: After 24 hours of culture, DMSO treated cochlear explants were pooled and cochlear epithelial tissue was isolated from cochlear explants using collagenase/ dispase treatment.

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

label: biotin

source_name: Cultured Control Cochlear Epithelium

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: Embryonic Day 15.5 (E15.5) mouse cochlear tissue was isolated from wild type embryos. Cochlear explants including cochlear duct and innervating neurons were cultured in DMEM-F12 with 1X N2 supplement, 2.5 ng/ml EGF, 2.2ng/ml FGF, 100 U/ml Penicillin.

extract_protocol: Total RNA was purified from enzymatically purified cochlear epithelia using the RNeasy Micro kit (QIAGEN).

treatment_protocol: Tissue for control sample was cultured in the presence of 0.013% DMSO for 24 hours.

tag: developmental stage

tag: tissue

value: cochlear epithelium

tag: culture time

value: 24 hours

tag: treatment

tag: strain

value: wild-type


title: Unmethylated human DNA [Unmethylated_1]

description:
Zymo Research Cat no D5014
Unmethylated_1

value: HCT116 DNMT1 (-/-) and DNMT3b (-/-) cell line


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group2_2_CD4_WT_PMAIono

description:
Group2 chip2: WT colonic lamina propria CD3+CD4+ Th cells from WT Th cell-induced colitis restimulated for 3h with PMA/ionomycin
Group2_2_CD4_WT_PMAIono

source_name: Group 2: Th cells from WT Th cell-induced colitis

value: Wildtype (WT, C57BL/6)


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group1_2_CD4_Tbx21ko_PMAIono

description:
Group1 chip2: Tbx21-/- colonic lamina propria CD3+CD4+ Th cells from Tbx21-/- Th cell-induced colitis restimulated for 3h with PMA/ionomycin
Group1_2_CD4_Tbx21ko_PMAIono


title: Human mammary endothelial cell genomic DNA [HMMEC_1]

description:
ScienCell Research Laboratories Cat no 7609
HMMEC_1

source_name: mammary endothelial cell

value: mammary endothelial cell


title: Human dermal fibroblast-adult genomic DNA [HDF-a_2]

description:
ScienCell Research Laboratories Cat no 2329
HDF-a_2


title: Human epidermal melanocyte-medium genomic DNA [HEM-m_1]

description:
ScienCell Research Laboratories Cat no 2219
HEM-m_1


title: Human epidermal keratinocyte-adult genomic DNA [HEK-a_1]

description:
ScienCell Research Laboratories Cat no 2119
HEK-a_1


title: Control 2 (Biological Replicate 2)

description: After 19 hours of culture, cochlear epithelial tissue was isolated from cochlear explants using collagenase/ dispase treatment

growth_protocol: Embryonic Day 15.5 (E15.5) mouse cochlear tissue was isolated from wild type embryos. Cochlear explants including cochlear duct and innervating neurons were cultured in DMEM-F12 with 1X N2 supplement, 2.5 ng/ml EGF, 2.2ng/ml FGF, 100 U/ml Penicillin

extract_protocol: Total RNA was purified from enzymatically purified cochlear epithelia using the RNeasy Micro kit (QIAGEN)

treatment_protocol: E15.5 cochlear explants were cultured in the presence of 0.013% DMSO for 19 hours

value: Cochlear Epithelium

value: 19 hours

value: DMSO control


title: Human mammary endothelial cell genomic DNA [HMMEC_2]

description:
ScienCell Research Laboratories Cat no 7609
HMMEC_2


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group2_1_CD4_WT_PMAIono

description:
Group2 chip1: WT colonic lamina propria CD3+CD4+ Th cells from WT Th cell-induced colitis restimulated for 3h with PMA/ionomycin
Group2_1_CD4_WT_PMAIono

value: colonic lamina propria leukocytes from colitis


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group3_2_Tbx21ko_col_CD64+Ly-6Chi

description:
Group3 chip2: WT colonic lamina propria CD64+Ly-6Chi monocytes from Tbx21-/- Th cell-induced colitis without restimulation
Group3_2_Tbx21ko_col_CD64+Ly-6Chi

source_name: Group 3: monocytes from Tbx21-/- Th cell-induced colitis


title: Human epidermal melanocyte-dark genomic DNA [HEM-d_1]

description:
ScienCell Research Laboratories Cat no 2229
HEM-d_1


title: Human mammary fibroblast genomic DNA [HMF_1]

description:
ScienCell Research Laboratories Cat no 7639
HMF_1

value: mammary fibroblast


title: Human epidermal melanocyte-light genomic DNA [HEM-l_1]

description:
ScienCell Research Laboratories Cat no 2209
HEM-l_1

value: epidermal melanocyte


title: Th cells, macrophages, monocytes derived from WT or Tbx21-/- Th cell-induced colitis; Group3_1_Tbx21ko_col_CD64+Ly-6Chi

description:
Group3 chip1: WT colonic lamina propria CD64+Ly-6Chi monocytes from Tbx21-/- Th cell-induced colitis without restimulation
Group3_1_Tbx21ko_col_CD64+Ly-6Chi


title: FT85_v

status: Public on Jan 23 2016

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

description:
source: FT85
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922117
450k Sentrix_Position: R04C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

source_name: genomic DNA from FT85 control chorionic villi

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: ntd status

value: control

tag: fetal sex

value: F

tag: sample tissue

value: chorionic villi

tag: fetal gestational age (weeks)


title: FT78_v

description:
source: FT78
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922117
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT78 spina bifida chorionic villi

value: spina bifida


title: NTD2_v

description:
source: NTD2
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R06C01

source_name: genomic DNA from NTD2 spina bifida chorionic villi

value: M


title: NTD16_v

description:
source: NTD16
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922117
450k Sentrix_Position: R04C02

source_name: genomic DNA from NTD16 spina bifida chorionic villi


title: FT72_kid

description:
source: FT72
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT72 spina bifida kidney

value: kidney


title: FT54_kid

description:
source: FT54
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922117
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT54 spina bifida kidney


title: FT82_v

description:
source: FT82
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT82 control chorionic villi


title: FT27_kid

description:
source: FT27
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT27 spina bifida kidney


title: FT78_kid

description:
source: FT78
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922117
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT78 spina bifida kidney


title: FT3_kid

description:
source: FT3
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT3 control kidney


title: FT82_kid

description:
source: FT82
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT82 control kidney


title: FT47_v

description:
source: FT47
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT47 spina bifida chorionic villi


title: NTD17_sc

description:
source: NTD17
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R06C01

source_name: genomic DNA from NTD17 spina bifida spinal cord

value: spinal cord


title: FT75_v

description:
source: FT75
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT75 anencephaly chorionic villi

value: anencephaly


title: FT84_v

description:
source: FT84
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT84 anencephaly chorionic villi


title: FT18_sc

description:
source: FT18
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT18 control spinal cord


title: FT85_mus

description:
source: FT85
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT85 control muscle

value: muscle


title: FT73_sc

description:
source: FT73
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT73 control spinal cord


title: PL149_v

description:
source: PL149
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R03C02

source_name: genomic DNA from PL149 control chorionic villi


title: FT73_mus

description:
source: FT73
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT73 control muscle


title: FT27_v

description:
source: FT27
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT27 spina bifida chorionic villi


title: NTD16_sc

description:
source: NTD16
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R05C01

source_name: genomic DNA from NTD16 spina bifida spinal cord


title: NTD6_sc

description:
source: NTD6
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R02C01

source_name: genomic DNA from NTD6 spina bifida spinal cord


title: FT22_kid

description:
source: FT22
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT22 spina bifida kidney


title: FT22_v

description:
source: FT22
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT22 spina bifida chorionic villi


title: FT54_v

description:
source: FT54
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922026
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT54 spina bifida chorionic villi


title: FT67_v

description:
source: FT67
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT67 spina bifida chorionic villi


title: NTD14_v

description:
source: NTD14
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930155
450k Sentrix_Position: R06C02

source_name: genomic DNA from NTD14 anencephaly chorionic villi


title: FT18_mus

description:
source: FT18
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9406922117
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT18 control muscle


title: NTD17_v

description:
source: NTD17
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R02C02

source_name: genomic DNA from NTD17 spina bifida chorionic villi


title: FT79_v

description:
source: FT79
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT79 anencephaly chorionic villi


title: FT4_br

description:
source: FT4
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT4 control brain

value: brain


title: FT18_kid

description:
source: FT18
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT18 control kidney


title: FT4_mus

description:
source: FT4
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930154
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT4 control muscle


title: FT54_sc

description:
source: FT54
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT54 spina bifida spinal cord


title: FT72_sc

description:
source: FT72
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT72 spina bifida spinal cord


title: FT47_sc

description:
source: FT47
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT47 spina bifida spinal cord


title: FT47_kid

description:
source: FT47
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT47 spina bifida kidney


title: NTD6_v

description:
source: NTD6
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R05C01

source_name: genomic DNA from NTD6 spina bifida chorionic villi


title: FT28_v

description:
source: FT28
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT28 control chorionic villi


title: NTD17_kid

description:
source: NTD17
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R03C02

source_name: genomic DNA from NTD17 spina bifida kidney


title: NTD16_kid

description:
source: NTD16
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R02C02

source_name: genomic DNA from NTD16 spina bifida kidney


title: FT28_kid

description:
source: FT28
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT28 control kidney


title: FT73_v

description:
source: FT73
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT73 control chorionic villi


title: FT3_v

description:
source: FT3
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT3 control chorionic villi


title: FT67_kid

description:
source: FT67
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT67 spina bifida kidney


title: NTD6_kid

description:
source: NTD6
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R03C02

source_name: genomic DNA from NTD6 spina bifida kidney


title: PL118_v

description:
source: PL118
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R01C02

source_name: genomic DNA from PL118 spina bifida chorionic villi


title: FT74_v

description:
source: FT74
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT74 anencephaly chorionic villi


title: FT72_v

description:
source: FT72
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT72 spina bifida chorionic villi


title: NTD1_v

description:
source: FT83
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT83 anencephaly chorionic villi


title: FT73_kid

description:
source: FT73
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930124
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT73 control kidney


title: FT73_br

description:
source: FT73
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT73 control brain


title: FT85_kid

description:
source: FT85
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT85 control kidney


title: FT59_v

description:
source: FT59
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT59 spina bifida chorionic villi


title: FT64_kid

description:
source: FT64
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT64 spina bifida kidney


title: FT36_mus

description:
source: FT36
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT36 control muscle


title: FT4_kid

description:
source: FT4
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT4 control kidney


title: FT57_br

description:
source: FT57
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT57 spina bifida brain


title: FT67_sc

description:
source: FT67
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930114
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT67 spina bifida spinal cord


title: FT39_sc

description:
source: FT39
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT39 control spinal cord


title: FT65_mus

description:
source: FT65
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT65 anencephaly muscle


title: FT34_v

description:
source: FT34
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT34 control chorionic villi


title: FT57_kid

description:
source: FT57
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT57 spina bifida kidney


title: FT33_br

description:
source: FT33
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT33 control brain


title: PL148_v

description:
source: PL148
450k plate ID: WG0011603-MSA4
450k Sentrix_ID: 9296930117
450k Sentrix_Position: R06C01

source_name: genomic DNA from PL148 control chorionic villi


title: FT23_v

description:
source: FT23
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT23 spina bifida chorionic villi


title: NTD9_mus

description:
source: NTD9
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R06C01

source_name: genomic DNA from NTD9 spina bifida muscle


title: FT41_v

description:
source: FT41
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT41 control chorionic villi


title: NTD8_mus

description:
source: NTD8
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R05C01

source_name: genomic DNA from NTD8 spina bifida muscle


title: FT42_v

description:
source: FT42
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT42 control chorionic villi


title: FT35_kid

description:
source: FT35
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT35 anencephaly kidney


title: FT57_mus

description:
source: FT57
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT57 spina bifida muscle


title: FT42_br

description:
source: FT42
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT42 control brain


title: FT62_kid

description:
source: FT62
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT62 spina bifida kidney


title: NTD9_kid

description:
source: NTD9
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R02C01

source_name: genomic DNA from NTD9 spina bifida kidney


title: FT13_mus

description:
source: FT13
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201038
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT13 control muscle


title: FT30_mus

description:
source: FT30
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368082
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT30 anencephaly muscle


title: FT58_mus

description:
source: FT58
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT58 anencephaly muscle


title: FT38_br

description:
source: FT38
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368082
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT38 control brain


title: NTD3_v

description:
source: NTD3
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R05C01

source_name: genomic DNA from NTD3 spina bifida chorionic villi


title: FT23_br

description:
source: FT23
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT23 spina bifida brain


title: FT42_kid

description:
source: FT42
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT42 control kidney


title: FT41_br

description:
source: FT41
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368082
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT41 control brain


title: FT58_sc

description:
source: FT58
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT58 anencephaly spinal cord


title: FT58_kid

description:
source: FT58
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368082
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT58 anencephaly kidney


title: FT22_br

description:
source: FT22
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368082
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT22 spina bifida brain


title: FT60_kid

description:
source: FT60
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368082
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT60 spina bifida kidney


title: FT16_v

description:
source: FT16
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368062
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT16 anencephaly chorionic villi


title: FT41_sc

description:
source: FT41
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT41 control spinal cord


title: FT65_v

description:
source: FT65
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT65 anencephaly chorionic villi


title: FT29_kid

description:
source: FT29
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368100
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT29 anencephaly kidney


title: FT30_kid

description:
source: FT30
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT30 anencephaly kidney


title: FT60_sc

description:
source: FT60
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7973201026
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT60 spina bifida spinal cord


title: FT62_sc

description:
source: FT62
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368062
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT62 spina bifida spinal cord


title: mt4-5_br

description:
source: mt4-5
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368062
450k Sentrix_Position: R02C02

source_name: genomic DNA from mt4-5 control brain


title: FT62_v

description:
source: FT62
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368062
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT62 spina bifida chorionic villi


title: FT62_mus

description:
source: FT62
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368062
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT62 spina bifida muscle


title: FT33_kid

description:
source: FT33
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368062
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT33 control kidney


title: FT27_sc

description:
source: FT27
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368023
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT27 spina bifida spinal cord


title: FT38_kid

description:
source: FT38
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT38 control kidney


title: FT39_mus

description:
source: FT39
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT39 control muscle


title: FT39_v

description:
source: FT39
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT39 control chorionic villi


title: FT60_mus

description:
source: FT60
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT60 spina bifida muscle


title: FT64_v

description:
source: FT64
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT64 spina bifida chorionic villi


title: FT38_v

description:
source: FT38
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT38 control chorionic villi


title: FT60_v

description:
source: FT60
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT60 spina bifida chorionic villi


title: FT64_sc

description:
source: FT64
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368142
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT64 spina bifida spinal cord


title: NTD8_br

description:
source: NTD8
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368023
450k Sentrix_Position: R02C01

source_name: genomic DNA from NTD8 spina bifida brain


title: NTD9_sc

description:
source: NTD9
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368023
450k Sentrix_Position: R05C01

source_name: genomic DNA from NTD9 spina bifida spinal cord


title: FT29_sc

description:
source: FT29
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368023
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT29 anencephaly spinal cord


title: mt4-5_v

description:
source: mt4-5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R06C01

source_name: genomic DNA from mt4-5 control chorionic villi


title: FT16_kid

description:
source: FT16
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT16 anencephaly kidney


title: FT52_sc

description:
source: FT52
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT52 anencephaly spinal cord


title: NTD3_mus

description:
source: NTD3
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R03C02

source_name: genomic DNA from NTD3 spina bifida muscle


title: FT35_mus

description:
source: FT35
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368023
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT35 anencephaly muscle


title: FT35_sc

description:
source: FT35
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT35 anencephaly spinal cord


title: NTD9_v

description:
source: NTD9
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R01C02

source_name: genomic DNA from NTD9 spina bifida chorionic villi


title: FT59_kid

description:
source: FT59
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT59 spina bifida kidney


title: FT64_mus

description:
source: FT64
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT64 spina bifida muscle


title: NTD8_sc

description:
source: NTD8
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R04C02

source_name: genomic DNA from NTD8 spina bifida spinal cord


title: FT23_sc

description:
source: FT23
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368050
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT23 spina bifida spinal cord


title: FT29_v

description:
source: FT29
450k plate ID: WG000907-MSA4
450k Sentrix_ID: 7970368023
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT29 anencephaly chorionic villi


title: FT42_sc

description:
source: FT42
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368112
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT42 control spinal cord


title: mt4-5_kid

description:
source: mt4-5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R06C02

source_name: genomic DNA from mt4-5 control kidney


title: FT59_br

description:
source: FT59
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT59 spina bifida brain


title: FT40_v

description:
source: FT40
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT40 anencephaly chorionic villi


title: FT40_mus

description:
source: FT40
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT40 anencephaly muscle


title: FT52_mus

description:
source: FT52
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT52 anencephaly muscle


title: FT57_sc

description:
source: FT57
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT57 spina bifida spinal cord


title: FT5_mus

description:
source: FT5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT5 control muscle


title: FT42_mus

description:
source: FT42
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT42 control muscle


title: FT57_v

description:
source: FT57
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT57 spina bifida chorionic villi


title: FT36_sc

description:
source: FT36
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT36 control spinal cord


title: FT64_br

description:
source: FT64
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT64 spina bifida brain


title: FT13_v

description:
source: FT13
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT13 control chorionic villi


title: FT33_sc

description:
source: FT33
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT33 control spinal cord


title: FT58_v

description:
source: FT58
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT58 anencephaly chorionic villi


title: FT38_sc

description:
source: FT38
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368066
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT38 control spinal cord


title: FT23_mus

description:
source: FT23
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368066
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT23 spina bifida muscle


title: FT36_br

description:
source: FT36
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368066
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT36 control brain


title: FT59_sc

description:
source: FT59
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT59 spina bifida spinal cord


title: FT39_br

description:
source: FT39
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368066
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT39 control brain


title: FT52_v

description:
source: FT52
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368076
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT52 anencephaly chorionic villi


title: FT38_mus

description:
source: FT38
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368066
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT38 control muscle


title: FT5_v

description:
source: FT5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT5 control chorionic villi


title: FT29_mus

description:
source: FT29
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368066
450k Sentrix_Position: R05C01

source_name: genomic DNA from FT29 anencephaly muscle


title: FT39_kid

description:
source: FT39
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT39 control kidney


title: FT52_kid

description:
source: FT52
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT52 anencephaly kidney


title: FT28_sc

description:
source: FT28
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT28 control spinal cord


title: FT65_kid

description:
source: FT65
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT65 anencephaly kidney


title: NTD3_kid

description:
source: NTD3
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368097
450k Sentrix_Position: R06C01

source_name: genomic DNA from NTD3 spina bifida kidney


title: FT59_mus

description:
source: FT59
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT59 spina bifida muscle


title: NTD8_v

description:
source: NTD8
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R04C02

source_name: genomic DNA from NTD8 spina bifida chorionic villi


title: FT41_kid

description:
source: FT41
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT41 control kidney


title: FT35_v

description:
source: FT35
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT35 anencephaly chorionic villi


title: FT33_mus

description:
source: FT33
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R06C01

source_name: genomic DNA from FT33 control muscle


title: FT21_kid

description:
source: FT21
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT21 spina bifida kidney


title: FT26_v

description:
source: FT26
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R05C02

source_name: genomic DNA from FT26 anencephaly chorionic villi


title: FT13_br

description:
source: FT13
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368054
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT13 control brain


title: FT41_mus

description:
source: FT41
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT41 control muscle


title: Genomic DNA from miscarriage placental chorionic villus 9

status: Public on Jan 02 2016

description:
N31
Recurrent miscarriage patient.

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation27 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan using the standard recommended Illumina scanner setting.

data_processing: Data in the table were processed by background normalization using GenomeStudio v1.0.5 that subtracts a background value derived by averaging the signals of built-in negative control bead types. Probes with detection p-value less than 0.01 in at least one sample were eliminated.

source_name: placental whole villus, miscarriage

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using standard techniques and purified using the Qiagen DNeasy Kit according to standard instructions.

treatment_protocol: Bisulfite conversion using the Zymo EZ DNA Methylation Gold Kit.

value: first-trimester placental whole villus

tag: karyotype

value: normal

tag: pregnancy outcome

value: miscarriage

tag: gender

value: male

tag: gestational age

value: 12 weeks


title: mt4-5_mus

description:
source: mt4-5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R04C02

source_name: genomic DNA from mt4-5 control muscle


title: FT40_kid

description:
source: FT40
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R04C01

source_name: genomic DNA from FT40 anencephaly kidney


title: Genomic DNA from miscarriage placental chorionic villus 8

description:
N28
Recurrent miscarriage patient.

value: female

value: 8 weeks


title: FT21_mus

description:
source: FT21
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT21 spina bifida muscle


title: FT40_sc

description:
source: FT40
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT40 anencephaly spinal cord


title: Genomic DNA from miscarriage placental chorionic villus 5

description:
N19
Recurrent miscarriage patient.

value: 9 weeks


title: Genomic DNA from miscarriage placental chorionic villus 3

description:
N90
Recurrent miscarriage patient.

value: 6 weeks


title: Genomic DNA from miscarriage placental chorionic villus 4

description:
N99
Recurrent miscarriage patient.

value: 11.5 weeks


title: NTD8_kid

description:
source: NTD8
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368036
450k Sentrix_Position: R01C01

source_name: genomic DNA from NTD8 spina bifida kidney

value: spina bifida


title: Genomic DNA from miscarriage placental chorionic villus 7

description:
N25
Recurrent miscarriage patient.


title: Genomic DNA from elective termination placental chorionic villus 9

source_name: placental whole villus, elective termination

value: elective termination


title: Genomic DNA from miscarriage placental chorionic villus 10

description:
N3
Recurrent miscarriage patient.

value: 14 weeks


title: Genomic DNA from miscarriage placental chorionic villus 1

description:
N45
Recurrent miscarriage patient.

value: 11.4 weeks


title: Genomic DNA from elective termination placental chorionic villus 10


title: FT21_v

description:
source: FT21
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT21 spina bifida chorionic villi

value: M

value: chorionic villi


title: FT13_kid

description:
source: FT13
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R01C01

source_name: genomic DNA from FT13 control kidney

value: control

value: F

value: kidney


title: Genomic DNA from elective termination placental chorionic villus 4

value: first-trimester placental whole villus

value: normal


title: Genomic DNA from elective termination placental chorionic villus 5

value: male


title: Genomic DNA from elective termination placental chorionic villus 7

value: female


title: Genomic DNA from elective termination placental chorionic villus 6


title: Genomic DNA from miscarriage placental chorionic villus 2

description:
N89
Recurrent miscarriage patient.

value: miscarriage


title: Genomic DNA from elective termination placental chorionic villus 2


title: FT21_br

description:
source: FT21
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT21 spina bifida brain

value: brain


title: NTD3_br

description:
source: NTD3
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R05C01

source_name: genomic DNA from NTD3 spina bifida brain


title: Genomic DNA from miscarriage placental chorionic villus 6

description:
N22
Recurrent miscarriage patient.

value: 6 weeks


title: FT5_br

description:
source: FT5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R04C02

source_name: genomic DNA from FT5 control brain


title: NTD9_br

description:
source: NTD9
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R06C01

source_name: genomic DNA from NTD9 spina bifida brain


title: FT36_kid

description:
source: FT36
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT36 control kidney


title: FT36_v

description:
source: FT36
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R03C01

source_name: genomic DNA from FT36 control chorionic villi


title: FT21_sc

description:
source: FT21
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R02C02

source_name: genomic DNA from FT21 spina bifida spinal cord

value: spinal cord


title: FT26_mus

description:
source: FT26
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R02C01

source_name: genomic DNA from FT26 anencephaly muscle

value: anencephaly

value: muscle


title: Genomic DNA from elective termination placental chorionic villus 8

value: elective termination


title: FT5_kid

description:
source: FT5
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368015
450k Sentrix_Position: R03C02

source_name: genomic DNA from FT5 control kidney


title: FT23_kid

description:
source: FT23
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R06C02

source_name: genomic DNA from FT23 spina bifida kidney

value: spina bifida


title: FT30_sc

description:
source: FT30
450k plate ID: WG0009065-MSA4
450k Sentrix_ID: 7970368014
450k Sentrix_Position: R01C02

source_name: genomic DNA from FT30 anencephaly spinal cord


title: Genomic DNA from elective termination placental chorionic villus 3


title: Genomic DNA from elective termination placental chorionic villus 1


title: NKcell_stringent_FACS_ind10

status: Public on Oct 02 2015

hyb_protocol: Illumina HumanMethylation450 BeadChip protocol

scan_protocol: Arrays were imaged using Illumina HiScan on a two-colour channel

data_processing:
GenomeStudio 2011.1 software and R version 3.1.1.
Normalized by background subtraction in GenomeStudio, red-green colour bias correction (lumi, Bioconductor package), subset within-array quantile normalization (minfi, Bioconductor package); correction for surrogate variables (sva, Bioconductor package).
Unmethylated and methylated signal intensities are available in the .idat files.

source_name: term cord blood 10

extract_protocol: Genomic DNA was purified using Qiagen's DNeasy Blood and Tissue kit followed by bisulphite conversion using Zymo's EZ DNA Methylation Kit following manufacturer's protocols

value: blood

tag: cell type

value: NK cell

tag: Sex

tag: facs strategy

value: Stringent (formal exclusion of erythroid lineage marker CD235)


title: CD8Tcell_stringent_FACS_ind10

label_protocol: Illumina HumanMethylation450 BeadChip protocol

value: CD8 T cell

value: F


title: Bcell_stringent_FACS_ind10

value: B cell


title: Monocyte_stringent_FACS_ind12

source_name: term cord blood 12

value: Monocyte


title: nRBC_stringent_FACS_ind10

value: RBC nRBC


title: nRBC_stringent_FACS_ind9

source_name: term cord blood 9


title: CD8Tcell_stringent_FACS_ind11

source_name: term cord blood 11


title: Monocyte_stringent_FACS_ind10


title: NKcell_stringent_FACS_ind12


title: Granulocyte_stringent_FACS_ind11

value: Granulocyte


title: CD4Tcell_stringent_FACS_ind11

value: CD4 T cell


title: Bcell_stringent_FACS_ind9


title: Monocyte_stringent_FACS_ind8

source_name: term cord blood 8

value: M


title: CD8Tcell_stringent_FACS_ind12


title: Granulocyte_stringent_FACS_ind10


title: CD4Tcell_stringent_FACS_ind10


title: NKcell_stringent_FACS_ind9


title: Granulocyte_stringent_FACS_ind12


title: Bcell_stringent_FACS_ind12


title: nRBC_stringent_FACS_ind8


title: Bcell_stringent_FACS_ind11


title: CD4Tcell_stringent_FACS_ind9


title: Monocyte_stringent_FACS_ind9


title: nRBC_stringent_FACS_ind12


title: Granulocyte_stringent_FACS_ind9


title: CD4Tcell_stringent_FACS_ind12


title: nRBC_stringent_FACS_ind11


title: Granulocyte_stringent_FACS_ind8


title: Monocyte_stringent_FACS_ind11


title: CD8Tcell_stringent_FACS_ind8


title: NKcell_stringent_FACS_ind8


title: CD4Tcell_stringent_FACS_ind8


title: Bcell_stringent_FACS_ind8


title: nRBC_stringent_FACS_ind7

source_name: term cord blood 7


title: CD8Tcell_stringent_FACS_ind7


title: CD4Tcell_stringent_FACS_ind7


title: Monocyte_standard_FACS_ind5

source_name: term cord blood 5

value: Standard (no erythroid marker exclusion)


title: CD4Tcell_stringent_FACS_ind6

source_name: term cord blood 6


title: Tcell_standard_FACS_ind5

value: T cell


title: Bcell_stringent_FACS_ind6


title: T-cell acute lymphoblastic leukemia diagnostic sample-FR5

status: Public on Jul 30 2015

city: Rio de Janeiro

first: Marcela

middle: B.

last: Mansur

state: Rio de Janeiro

address: Rua André Cavalcanti, 37, 2º floor

department: Division of Clinical Research, Research Centre

country: Brazil

institute: Instituto Nacional de Câncer - INCA

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL and CHP files (generated using Affymetrix Genotyping Console) were processed using CNAG 3.3.0 beta.

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: T-cell acute lymphoblastic leukemia


title: CD8Tcell_stringent_FACS_ind6


title: Monocyte_standard_FACS_ind2

source_name: term cord blood 2


title: T-cell acute lymphoblastic leukemia diagnostic sample-FR3


title: T-cell acute lymphoblastic leukemia diagnostic sample-FR2


title: Monocyte_stringent_FACS_ind7


title: nRBC_standard_FACS_ind5

value: nRBC


title: Monocyte_standard_FACS_ind4

source_name: term cord blood 4


title: NKcell_stringent_FACS_ind6


title: Tcell_standard_FACS_ind3

source_name: term cord blood 3


title: nRBC_standard_FACS_ind4


title: T-cell acute lymphoblastic leukemia diagnostic sample-UK1


title: nRBC_stringent_FACS_ind6


title: KPC

status: Public on Sep 03 2015

first: Lei

last: Zheng

address: 1650 Orleans Street, CRB1 Rm 488

institute: Johns Hopkins University School of Medicine

description: KPC Tumor

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: pancreas tumor

growth_protocol: cells were grown as a monolayer in a T175 flask to confluence prior to harvesting for RNA extraction

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions. Total RNA was converted to cDNA using the Invitrogen SuperScript III First-Strand Synthesis kit according to the manufacturer's instructions.

treatment_protocol: no treatments were given to the cells

tag: strain background

tag: genotype/variation

value: KrasG12D, p53R172H, Pdx-1 Cre

value: male

tag: annexin a2 status

value: WT

value: pancreas tumor

value: primary pancreatic tumor cell line


title: Monocyte_standard_FACS_ind3

tag: tissue

value: blood


title: T-cell acute lymphoblastic leukemia diagnostic sample-FR4


title: Granulocyte_stringent_FACS_ind6

value: F

value: Stringent (formal exclusion of erythroid lineage marker CD235)


title: NKcell_stringent_FACS_ind7

value: NK cell


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR7


title: nRBC_standard_FACS_ind2


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR4


title: Tcell_standard_FACS_ind4


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR3


title: Tcell_standard_FACS_ind2


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR2


title: nRBC_standard_FACS_ind3


title: nRBC_standard_FACS_ind1

source_name: term cord blood 1


title: Monocyte_stringent_FACS_ind6

value: Monocyte


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR1


title: Tcell_standard_FACS_ind1


title: Granulocyte_stringent_FACS_ind7

value: Granulocyte


title: Monocyte_standard_FACS_ind1


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR5


title: Primary tumor breast - BCPT0156

status: Public on Jul 08 2015

city: Stockholm

first: Alexandra

last: Jauhiainen

address: PO Box 281

department: Medical Epidemiology and Biostatistics

institute: Karolinska Institutet

description: Some arrays correspond to multiple study subjects, which is indicated by the setnr/case-control status

hyb_protocol: Fragmented and biotinylated cRNA (10 μg) was hybridized at 45C for 16 h to a high density oligonucleotide custom made Affymetrix array chip (Human Cancer G110 Array). The arrays were then washed, stained with streptavidin-phycoerythrin (SAPE, final concentration of 10 μg/ml).

scan_protocol: The arrays were scanned according to the manufacturer’s instructions (Affymetrix Genechip® Technical Manual, 2001). The scanned images were inspected for the presence of obvious defects (artifacts or scratches) on the array. In case of visible microarray artifacts, the sample was rehybridized and rescanned on new chips using the same fragmented probe.

data_processing: The microarray analysis was done in the open source software R using the aroma.affymetrix package. Each array was individually background corrected and normalized using robust multichip averaging (RMA). The arrays were then quantile normalized for comparability. Only perfect match (PM) probes were used in the normalization steps. The signals from multiple PM probes targeting the same transcript were summarized using a probe level model adjusting for chip effects. A variance filter was employed and probes with inter-quartile-range less than 0.5 were excluded, resulting in 28449 retained probes.

source_name: Primary tumor breast

label_protocol: Preparation of in vitro transcription (IVT) products and oligonucleotide array hybridization and scanning were performed according to the Affymetrix protocol (Santa Clara, CA, USA). In brief, the amount of starting total RNA for each probe preparation varied between 2 and 5 μg. IVT reactions were performed in batches to generate biotinylated cRNA targets, which were subsequently chemically fragmented at 95C for 35 min.

extract_protocol: Extraction of total RNA from frozen tumors was carried out using the Qiagen RNeasy Mini Kit (Qiagen, Germany). The integrity of the RNA extracts was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies, Rockville, MD), measuring the 28S: 18S ribosomal RNA ratio. RNA extracts of high quality were stored at -70C until microarray analyses.

treatment_protocol: The fresh frozen tumor samples were collected from liquid nitrogen and cryosectioning was performed on a Cryo-Star HM 560 M. Five μm sections were cut from the surface of the same tumor sample that was used for isolation of RNA and DNA. The section was counterstained with hematoxylin and eosin and dehydrated through graded concentrations of ethanol to xylene before mounting. The percentage of tumor cells, as well as the percentage of epithelial cancer cells in relation to stroma, was quantified in the frozen tumor sections by a breast cancer pathologist.

tag: sample group

value: discovery

tag: setnr

tag: case-control status

value: Primary tumor breast


title: Bcell_stringent_FACS_ind7

value: B cell

value: M


title: Primary tumor breast - BCPT0456

value: validation


title: Primary tumor breast - BCPT0685


title: Primary tumor breast - BCPT0736


title: Primary tumor breast - BCPT0732


title: Primary tumor breast - BCPT0848


title: Primary tumor breast - BCPT0830


title: Primary tumor breast - BCPT0628


title: Primary tumor breast - BCPT0978


title: Primary tumor breast - BCPT0597


title: Primary tumor breast - BCPT0263


title: Primary tumor breast - BCPT0209


title: Primary tumor breast - BCPT0328


title: Primary tumor breast - BCPT0412


title: Primary tumor breast - BCPT0777


title: Primary tumor breast - BCPT0135


title: Primary tumor breast - BCPT0487


title: Primary tumor breast - BCPT0267


title: Primary tumor breast - BCPT0436


title: KPCA-/-

description: KPCA

value: KrasG12D, p53R172H, Pdx-1 Cre, AnxA2-/-

value: female

value: KO


title: Primary tumor breast - BCPT0029


title: T-cell acute lymphoblastic leukemia diagnostic sample-FR1

value: T-cell acute lymphoblastic leukemia


title: Primary tumor breast - BCPT0260


title: Primary tumor breast - BCPT0535


title: Primary tumor breast - BCPT0889


title: Primary tumor breast - BCPT0409


title: Primary tumor breast - BCPT0247


title: Primary tumor breast - BCPT0382


title: Primary tumor breast - BCPT0446


title: Primary tumor breast - BCPT0803


title: Primary tumor breast - BCPT0520


title: Primary tumor breast - BCPT0886


title: Primary tumor breast - BCPT0997


title: Primary tumor breast - BCPT0186


title: Primary tumor breast - BCPT0211


title: Primary tumor breast - BCPT0492


title: Primary tumor breast - BCPT0422


title: Primary tumor breast - BCPT0169


title: Primary tumor breast - BCPT0026


title: Primary tumor breast - BCPT0315


title: Primary tumor breast - BCPT0025


title: Primary tumor breast - BCPT0972


title: Primary tumor breast - BCPT0460


title: Primary tumor breast - BCPT0512


title: Primary tumor breast - BCPT0573


title: Primary tumor breast - BCPT0536


title: Primary tumor breast - BCPT0006


title: Primary tumor breast - BCPT0488


title: Primary tumor breast - BCPT0741


title: Primary tumor breast - BCPT0753


title: Primary tumor breast - BCPT0296


title: Primary tumor breast - BCPT0203


title: Primary tumor breast - BCPT0950


title: T-cell acute lymphoblastic leukemia diagnostic sample-BR6


title: Primary tumor breast - BCPT0541


title: Primary tumor breast - BCPT0727


title: Primary tumor breast - BCPT0146


title: Primary tumor breast - BCPT0569


title: Primary tumor breast - BCPT0879


title: Primary tumor breast - BCPT0013


title: Primary tumor breast - BCPT0884


title: Primary tumor breast - BCPT0904


title: Primary tumor breast - BCPT0102


title: Primary tumor breast - BCPT0703


title: Primary tumor breast - BCPT0893


title: Primary tumor breast - BCPT0704


title: Primary tumor breast - BCPT0983


title: Primary tumor breast - BCPT0550


title: Primary tumor breast - BCPT0786


title: Primary tumor breast - BCPT0595


title: Primary tumor breast - BCPT0044


title: Primary tumor breast - BCPT0916


title: Primary tumor breast - BCPT0414


title: Primary tumor breast - BCPT0423


title: Primary tumor breast - BCPT0823


title: Primary tumor breast - BCPT0885


title: Primary tumor breast - BCPT0177


title: Primary tumor breast - BCPT0970


title: Primary tumor breast - BCPT0249


title: Primary tumor breast - BCPT0620


title: UM-UC-12_copy_number_variation

status: Public on Jun 19 2015

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.

scan_protocol: After allele-specific staining BeadChip arrays were scanned on a BeadArray Reader

data_processing:
Data processing was carried out with GenomeStudio software v2011.1 (Genotyping v1.9.4) provided by Illumina
Genotype: AA,AB,BB, or - - (no call)
GSE64572_cell_line_calls_with_annotation.txt: The Illumina 1 M Duo array includes 902,103 autosomal probes and 39,779 probes from sex chromosomes. A total of 43 different cell lines were hybridized to the arrays (GSE64572) Genotypes and R values were extracted using the beadstudio software (version 3.1.3.0) and R values were normalized using the method described by Pounds and co-workers. Log R ratios were calculated using as reference the average R value from 200 blood leukocyte samples from control subjects included in the EPICURO study with the R program version 2.8. Copy number calls were obtained using the waviCGH software. Gene copy number changes were called as follows: -1 = loss (hemi or homozygous), 0 = copy number neutral, 1 = gain.

source_name: Bladder Cell Line_UM-UC-12

label_protocol: 400ng of genomic DNA was whole-genome amplified, fragmented , precipitated and resuspended in hybridization buffer

growth_protocol: Cells were cultured in RPMI supplemented with 10-20% FBS and were harvested at 70-90% confluence.

extract_protocol: Extraction of genomic DNA using the DNAeasy blood and tissue kit (Qiagen)

tag: cell line

value: bladder cancer


title: UM-UC-17_copy_number_variation_2

source_name: Bladder Cell Line_UM-UC-17


title: Primary tumor breast - BCPT0681


title: Primary tumor breast - BCPT0469


title: Primary tumor breast - BCPT0540


title: 97-24_rep_2_copy_number_variation

source_name: Bladder Cell Line_97-24_rep_2


title: UM-UC-11_copy_number_variation

source_name: Bladder Cell Line_UM-UC-11


title: Primary tumor breast - BCPT0591


title: 92-1_rep_2_copy_number_variation

source_name: Bladder Cell Line_92-1_rep_2


title: UM-UC-14_rep_2_copy_number_variation

source_name: Bladder Cell Line_UM-UC-14_rep_2


title: Primary tumor breast - BCPT0919


title: UM-UC-14_copy_number_variation

source_name: Bladder Cell Line_UM-UC-14


title: 92-1_copy_number_variation

source_name: Bladder Cell Line_92-1


title: Primary tumor breast - BCPT0363


title: Primary tumor breast - BCPT0817


title: Primary tumor breast - BCPT0020


title: Primary tumor breast - BCPT0276


title: Primary tumor breast - BCPT0075


title: 639V_rep_2_copy_number_variation

source_name: Bladder Cell Line_639V_rep_2


title: Primary tumor breast - BCPT0534


title: VM-CUB-2_copy_number_variation

source_name: Bladder Cell Line_VM-CUB-2


title: Primary tumor breast - BCPT0220


title: Primary tumor breast - BCPT0779


title: Primary tumor breast - BCPT0397


title: 97-24_copy_number_variation

source_name: Bladder Cell Line_97-24


title: Primary tumor breast - BCPT0309


title: Primary tumor breast - BCPT0774


title: Primary tumor breast - BCPT0744


title: Primary tumor breast - BCPT0867


title: RT112_rep_2_copy_number_variation

source_name: Bladder Cell Line_RT112_rep_2


title: VM-CUB-3_copy_number_variation

source_name: Bladder Cell Line_VM-CUB-3


title: J82_copy_number_variation

source_name: Bladder Cell Line_J82


title: 96-1_copy_number_variation

source_name: Bladder Cell Line_96-1


title: 575A_copy_number_variation

source_name: Bladder Cell Line_575A


title: 253J_rep_2_copy_number_variation

source_name: Bladder Cell Line_253J_rep_2


title: 5637_copy_number_variation

source_name: Bladder Cell Line_5637


title: MGH-U3_copy_number_variation

source_name: Bladder Cell Line_MGH-U3


title: LGWO1 G600_copy_number_variation

source_name: Bladder Cell Line_LGWO 1 G600

value: LGWO 1 G600


title: RT4_copy_number_variation

source_name: Bladder Cell Line_RT4


title: T24_copy_number_variation

source_name: Bladder Cell Line_T24


title: UM-UC-3_copy_number_variation

source_name: Bladder Cell Line_UM-UC-3


title: UM-UC-4_rep_2_copy_number_variation

source_name: Bladder Cell Line_UM-UC-4_rep_2


title: BC61_copy_number_variation

source_name: Bladder Cell Line_BC61


title: UM-UC-7_copy_number_variation

source_name: Bladder Cell Line_UM-UC-7


title: UM-UC-4_copy_number_variation

source_name: Bladder Cell Line_UM-UC-4


title: UM-UC-9_copy_number_variation

source_name: Bladder Cell Line_UM-UC-9


title: UM-UC-13_copy_number_variation

source_name: Bladder Cell Line_UM-UC-13


title: UM-UC-6_copy_number_variation

source_name: Bladder Cell Line_UM-UC-6


title: SCaBER_copy_number_variation

source_name: Bladder Cell Line_SCaBER

value: SCaBER


title: UM-UC-5_copy_number_variation

source_name: Bladder Cell Line_UM-UC-5


title: SW-780_copy_number_variation

source_name: Bladder Cell Line_SW-780


title: UM-UC-18_copy_number_variation

source_name: Bladder Cell Line_UM-UC-18


title: SW-800_copy_number_variation

source_name: Bladder Cell Line_SW-800


title: SW-1710_copy_number_variation

source_name: Bladder Cell Line_SW-1710


title: UM-UC-1_copy_number_variation

source_name: Bladder Cell Line_UM-UC-1


title: TCCSUP_copy_number_variation

source_name: Bladder Cell Line_TCCSUP

value: TCCSUP


title: 97-18_copy_number_variation

source_name: Bladder Cell Line_97-18


title: 639V_copy_number_variation

source_name: Bladder Cell Line_639V


title: HT1376_copy_number_variation

source_name: Bladder Cell Line_HT1376


title: KK47_copy_number_variation

source_name: Bladder Cell Line_KK47


title: MGH-U4_copy_number_variation

source_name: Bladder Cell Line_MGH-U4


title: 253J_copy_number_variation

source_name: Bladder Cell Line_253J


title: VM-CUB-1_copy_number_variation

source_name: Bladder Cell Line_VM-CUB-1


title: HU456_copy_number_variation

source_name: Bladder Cell Line_HU456


title: 97-7_copy_number_variation

source_name: Bladder Cell Line_97-7


title: 97-1_copy_number_variation

source_name: Bladder Cell Line_97-1


title: UM-UC-17_copy_number_variation_1

source_name: Bladder Cell Line_UM-UC-17


title: Primary tumor breast - BCPT0151

source_name: Primary tumor breast


title: RT112_copy_number_variation

source_name: Bladder Cell Line_RT112


title: Group2-1 immunized iDCs

status: Public on Apr 20 2015

description: Gene expression profiles of iDCs isolated from the spleens and draining lymph nodes of immunized mice were compared using Affymetrix MG430 2.0 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the two groups to the GeneChip arrays. For quality reasons only five of these six chips were analyzed: 3 times Group1 tolerized, and 2 times Group2 immunized iDCs.

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Affymetrix Mouse Genome 430 2.0 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software 1.4 from Affymetrix.

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 + 2 chips were compared to each other (tolerized vs. immunized group, 6 comparisons, and all chips within the groups, 6 comparisons for tolerized and 2 comparisons for immunized group), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 6 SLR values of tolerized vs. immunized group and 8 SLR values within both groups (the latter 8 giving a mean SLR value of zero; p-value had to be <= 7.919E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 4 or more of all 6 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).

source_name: MOG35-55-immunized (immunized) mice

growth_protocol: For isolation of iDCs, dLNs and spleens were digested with Collagenase D (2 mg/ml; Roche) for 30 min at 37 °C. For the purification of total DCs, single cell suspensions were incubated with Pan DC MicroBeads (Miltenyi), and then positively selected on a magnetic field according to the manufacturer’s instruction (Miltenyi). For the purification of iDCs, positively selected DCs were stained with monoclonal antibodies against CD11c, CD11b, and Gr-1. CD11c+CD11b+Gr-1+ cells were sorted on a high speed MoFlo (Dako). Cell purity was about 85–95%.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was detected with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: strain

value: lymph nodes and spleen

value: iDCs, isolated from immunized mice


title: Group2-3 immunized iDCs

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Affymetrix Mouse Genome 430 2.0 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

treatment_protocol: For isolation of iDCs, dLNs and spleens were digested with Collagenase D (2 mg/ml; Roche) for 30 min at 37 °C. For the purification of total DCs, single cell suspensions were incubated with Pan DC MicroBeads (Miltenyi), and then positively selected on a magnetic field according to the manufacturer’s instruction (Miltenyi). For the purification of iDCs, positively selected DCs were stained with monoclonal antibodies against CD11c, CD11b, and Gr-1. CD11c+CD11b+Gr-1+ cells were sorted on a high speed MoFlo (Dako). Cell purity was about 85–95%.


title: Group1-2 tolerized iDCs

description: Gene expression profiles of iDCs isolated from the spleens and draining lymph nodes of tolerized mice were compared using Affymetrix MG430 2.0 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the two groups to the GeneChip arrays. For quality reasons only five of these six chips were analyzed: 3 times Group1 tolerized, and 2 times Group2 immunized iDCs.

value: iDCs, isolated from tolerized mice


title: Group1-3 tolerized iDCs


title: Grp4_Chip3_CD44posCD127pos_spl_stim

status: Public on Feb 05 2015

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine spleen, in vitro activated with α-CD3 and α-CD28; group 4, chip 3

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG_U430_2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

data_processing:
Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the BioRetis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMed ID: 19265543). Chip data included in the BioRetis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All five groups were compared to every other group to obtain 10 lists of significant differentially regulated genes. All 3 chips of every group (Experiment group) were compared to the 3 chips of one of the other groups (Baseline group) and chips within one group were compared to each other in both directions. The following parameters of absolute and comparative analysis were included in the BioRetis database for all 10 comparisons: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 2 times 6 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls of Experiment vs. Baseline group have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria. These are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets, respectively and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (in one direction only; 65 true positive IDs in average).
Data tables contain the following: Probe Set ID; VALUE: GCOS Signal, i.e. gene expression height; Detection call: A: gene is detected as Absent, M: as Marginal present, or P: as Present; P-value: Non-parametrical p-value for generation of detection call

source_name: Group 4: activated spleen memory CD8 T cells

growth_protocol: Ex-breeder female mice were purchased from Charles-River laboratories, Sulzfeld,Germany. Single cell suspension from the spleen and bones (tibiae, femur, hips and sternum) of aged C57BL/6 mice were prepared. CD8+ T cells were first enriched with α-CD8 α microbeads (Miltenyi). Naive (CD44-CD127+) and memory (CD44+CD127+) CD8+CD3+ T cells were then cytometrically sorted with FACS Aria or Influx (BD Biosciences). The cells of 3-12 mice were pooled. Sorted cells were then either immediately lysed with RA-1 buffer (Macherey-Nagel) for RNA preparation or were activated with α-CD3 and α-CD28. For this, wells of a 96-well plate were coated with α-CD3 (2.5 µg/ml) and α-CD28 (2.5 µg/ml) at 37 °C for 2-3 hours. After the excess antibody was washed away, approximately 2.0E05 cells were plated per well. Cells were cultured in RPMI 1640 medium supplemented with 10% FCS, 1% Streptomycin, 1% Penicillin and 0.1% β-mercaptoethanol. 42-44 hours later, activated cells were lysed with RA-1 buffer.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA (Macherey-Nagel) according to the manufacturer’s instruction, including the recommended DNase digestion. Contaminating genomic DNA was removed by an on-column DNA digestion step (Macherey-Nagel). The amount of RNA was checked with a NanoDrop ND-1000 spectrophotometer.

value: Spleen

tag: cells

value: CD8+CD3+ T cells; Memory (CD44+CD127+); 3-12 mice were pooled

tag: magnetic cell sorting

tag: flow cytometric cell sorting

value: Memory (CD44+CD127+) CD8+CD3+ T cells were cytometrically sorted with FACS Aria or Influx (BD Biosciences)

tag: activation

tag: cell cultivation

value: Cultured in RPMI 1640 medium with 10% FCS, 1% Streptomycin, 1% Penicillin, and 0.1% β-mercaptoethanol. 42-44 h later, lysed with RA-1 buffer (Macherey-Nagel)


title: Grp4_Chip1_CD44posCD127pos_spl_stim

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine spleen, in vitro activated with α-CD3 and α-CD28; group 4, chip 1

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG_U430_2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

tag: gender

value: CD8+ T cells were first enriched with α-CD8 α microbeads (Miltenyi)


title: Grp5_Chip2_CD44posCD127pos_bm_stim

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine bone marrow, in vitro activated with α-CD3 and α-CD28; group 5, chip 2

source_name: Group 5: activated bone marrow memory CD8 T cells

value: Bone marrow


title: Group2-2 immunized iDCs not used in HPCDA

tag: cell type


title: Group1-1 tolerized iDCs


title: Grp5_Chip3_CD44posCD127pos_bm_stim

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine bone marrow, in vitro activated with α-CD3 and α-CD28; group 5, chip 3


title: Grp5_Chip1_CD44posCD127pos_bm_stim

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine bone marrow, in vitro activated with α-CD3 and α-CD28; group 5, chip 1


title: Grp4_Chip2_CD44posCD127pos_spl_stim

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine spleen, in vitro activated with α-CD3 and α-CD28; group 4, chip 2


title: Primary tumor breast - BCPT0164

value: validation

value: Primary tumor breast


title: Hollow Fibre 7

status: Public on Apr 07 2015

hyb_protocol: Illumina HumanMethylation450 BeadChip Protocol

scan_protocol: Arrays were imaged using Illumina iScan on a two-color channel

data_processing: GenomeStudio 2011.1 software and R version 2.14.0; Normalization using SWAN; The file Unmethylated_and_methylated_signal.txt is available on the series record and contains the raw data.

source_name: Cultured Placenta Villous explant exposed to decidua natural killer cells trapped in a hollow fiber

label_protocol: Cy5 and Cy3

growth_protocol: Placental tissues were collected from consenting healthy women undergoing elective pregnancy termination at gestational ages between 7-9 weeks.  dNK were isolated from decidua after collagenase and hyaluronidase digestion, depletion of attached cells, and were then enriched by human NK cell enrichment cocktail following the manufacturer’s instructions. The percentage of CD56+/CD16- dNK reached ~87%, CD16+ cells were < 2.1% (Hu et al., 2006). The dNK were trapped inside of hollow fiber (Spectrum Laboratories, Inc., Rancho Dominquez, CA, USA) (HF-dNK) and used for co-culturing with explants in order to eliminate trophoblast cell contamination from dNK when performing EVT DNA extraction. HF permits soluble factors with molecular weight below 500 kDa to be exchanged freely. For each placental specimen, villous explant cultures were set up in 12 well plates on collagen gel. After overnight incubation, explant cultures with EVT outgrowth on villous tips were identified and exposed to medium control (DMEM/F12 supplemented with 10% FBS), or IL-15 alone, or concordant HF-dNK plus IL-15 for a total of 96 hours. 6-8 explants were used for each treatment group in each placental specimen.

extract_protocol: For each of the explant cultures, EVT were harvested from collagen gel after dissecting villi tissue and pooled from each treatment group. Previous study has shown that the EVT forming the cell column and migrating on collagen were cytokeratin positive and vimentin negative cells and purity was high (Hu et al., 2006; Hu et al., 2008). Five placental specimens in total were used for global DNA methylation array and Bisulfite pyrosequencing validation. Genomic DNA from EVT was purified using QIAamp DNA mini kit  according to the manufacturer’s instructions (Qiagen Inc. Mississauga, ON, Canada).

value: Placenta villous explant

tag: trimester

value: First Trimester


title: IL-15 7

source_name: Cultured Placenta Villous explant exposed to media supplemented with IL-15


title: IL-15 8


title: Grp2_Chip2_CD44posCD127pos_bm_exvivo

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine bone marrow, ex vivo isolated; group 2, chip 2

source_name: Group 2: resting bone marrow memory CD8 T cells

value: female

value: not activated; ex vivo isolated

value: No cultivation, immediately lysed with RA-1 buffer (Macherey-Nagel) for RNA preparation


title: Grp1_Chip3_CD44posCD127pos_spl_exvivo

description: Memory (CD44+CD127+) CD8+CD3+ T cells from murine spleen, ex vivo isolated; group 1, chip 3

source_name: Group 1: resting spleen memory CD8 T cells


title: IL-15 4