title: peripheral blood-T1DControl18_3

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (cat. no 901530).

scan_protocol: GeneTitan MC Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control GeneTitan hybridization process and in summarizing probe cell intensity data (.CEL file generation).

data_processing: Sample T1DControl7_4 was excluded from the final analysis as an outlier.  The CEL file and a readme for T1DControl7_4 containing the Metadata are provided as supplementary files on the Series record. The intensities were RMA normalized and log2-transformed using R/Bioconductor.

source_name: peripheral blood

label_protocol: 50 ng of total RNA was processed to cDNA with Nugen Ovation RNA Amplification System V2 (cat. no 3100-60) and subsequently biotin-labelled and fragmented with Nugen Encore Biotin Module (cat. no 4200-A01) according to manufacture’s protocol.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70C until analyzed.

tag: t1dcase/t1dcontrol pair

value: no T1D diagnosis


title: T1DControl15_2

status: Public on Feb 20 2014

type: RNA

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: 750 ng each cDNA was hybridized to Human HT-12 Expression BeadChips, version 3 (Illumina, cat. no BD-103-0603) at 58 °C overnight (18 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridizations were detected with 1 ug/ml Cyanine3-streptavidine (GE Healthcare Biosciences cat. no PA43001).

scan_protocol: Chips were scanned with Illumina Bead Array Reader, BeadScan software version 3.5. The numerical results were extracted with GenomeStudio2008 v1 without any normalization or background subtraction.

data_processing: The intensities were quantile normalized and log2-transformed using R/Bioconductor.

molecule: total RNA

organism: Homo sapiens

label_protocol: 100 ng total RNA was amplified to cDNA with Ovation RNA Amplification System V2 (NuGEN, cat. no 3100-60), including Ovation Whole Blood Reagent (cat. no 1300-60). The amplified cDNA was labelled according to NuGEN’s Illumina Solution protocol, Application Note #2.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70 °C until analyzed.

extract_protocol: Total whole-blood RNA was extracted from the samples using PAX gene RNA Blood RNA kit (Qiagen, Germany) according to manufacturer's instructions. RNA quality and quantity was determined using Nano Drop ND-1000 (Nano Drop Technologies, USA) and Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).

tag: case/control pair

tag: age at sample (months)

tag: time from seroconversion (months)

value: no seroconversion

tag: time from t1d diagnosis (months)

value: no diagnosis

tag: gender

value: female

tag: tissue

value: peripheral blood

tag: hla-dqb1 genotype


title: T1DCase15_7


title: HUVEC_SFO_6h

city: Jinan

first: Jing

last: Zhao

address: Shanda nan road 27#

country: China

institute: Shandong University

description: SFO treatment group compared to control group, SFO/Ctrl

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Cells treated with vehicle, 6h (ctrl)

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: Primary HUVECs were isolated by using the method of Jaffe et al and cultured in Medium 199 supplemented with 10% heat-inactivated fetal bovine serum in a 5% CO2 incubator

extract_protocol: Cells was centrifuged (1,500 rpm) for 10 min and the cell pellet was kept in frozen. Total RNA was extracted with Trizol Reagent (BD Biosciences Clontech, Palo Alto, CA) and ethanol precipitation

treatment_protocol: Cells were divided into two groups when the cultures of cells reached sub-confluence: control group, the cells were cultured in the normal medium with 10% serum and 5 ng/ml ﬁbroblast growth factor-2 (FGF-2); SFO-treated group, the cells were treated with normal medium (10% serum, 5 ng/ml FGF-2) and  50 µg/ml SFO for 6 h. SFO was dissolved in ethanol as previously report

tag: cell type

value: primary HUVEC

tag: treatment

value: control

source_name: Cells treated with safrole oxide (SFO), 6h

value: SFO


title: peripheral blood-T1DCase18_5

label: biotin

value: male


title: T1DCase15_6


title: peripheral blood-T1DControl18_1


title: peripheral blood-T1DCase18_4


title: peripheral blood-T1DCase18_3


title: T1DCase15_5


title: peripheral blood-T1DControl17B_3


title: T1DCase15_4


title: T1DCase15_2


title: peripheral blood-T1DCase18_2


title: peripheral blood-T1DControl17B_2


title: peripheral blood-T1DControl17B_4


title: peripheral blood-T1DCase18_1


title: peripheral blood-T1DControl18_2


title: peripheral blood-T1DControl17A_4


title: T1DControl14_5


title: peripheral blood-T1DControl17A_5


title: peripheral blood-T1DControl17B_1


title: peripheral blood-T1DControl17A_6


title: T1DControl14_2


title: T1DCase15_3


title: T1DCase14_5


title: T1DControl14_4


title: T1DControl14_1


title: T1DControl14_3


title: peripheral blood-T1DControl17A_2


title: T1DCase14_4


title: peripheral blood-T1DControl17A_3


title: T1DCase14_2


title: T1DCase15_1


title: T1DCase14_3


title: peripheral blood-T1DCase17_4


title: T1DControl13B_4


title: peripheral blood-T1DControl17A_1


title: peripheral blood-T1DCase17_3


title: T1DCase14_1


title: T1DControl13B_3


title: peripheral blood-T1DCase17_1


title: T1DControl13B_2


title: peripheral blood-T1DControl16_8


title: peripheral blood-T1DCase17_2


title: T1DCase13_4


title: peripheral blood-T1DControl16_9


title: T1DControl13A_5


title: peripheral blood-T1DControl16_6


title: T1DControl13A_3


title: peripheral blood-T1DControl16_4


title: peripheral blood-T1DControl16_3


title: T1DCase13_5


title: T1DControl13A_4


title: peripheral blood-T1DControl16_7


title: peripheral blood-T1DControl16_1


title: T1DControl13A_1


title: peripheral blood-T1DControl16_5


title: T1DControl13B_1


title: T1DControl13A_2


title: T1DCase13_3


title: T1DCase13_1


title: T1DControl12_2


title: peripheral blood-T1DControl16_2


title: T1DControl12_3


title: T1DControl12_1


title: peripheral blood-T1DCase16_9


title: T1DCase13_2


title: peripheral blood-T1DCase16_8


title: T1DCase12_6


title: peripheral blood-T1DCase16_5


title: peripheral blood-T1DCase16_7


title: peripheral blood-T1DCase16_3


title: T1DCase12_2


title: peripheral blood-T1DCase16_2


title: T1DControl11_5


title: peripheral blood-T1DCase15_8


title: peripheral blood-T1DCase15_5


title: peripheral blood-T1DCase16_1


title: T1DControl11_7


title: peripheral blood-T1DCase15_4


title: peripheral blood-T1DCase15_6


title: peripheral blood-T1DCase16_4


title: T1DControl11_6


title: peripheral blood-T1DCase15_3


title: T1DControl11_2


title: T1DCase12_5


title: T1DCase12_3


title: T1DCase11_8

value: unknown


title: peripheral blood-T1DControl14_4


title: T1DControl11_3


title: T1DControl11_1


title: peripheral blood-T1DCase15_1


title: T1DControl11_4


title: peripheral blood-T1DControl14_5


title: peripheral blood-T1DCase15_7


title: peripheral blood-T1DCase15_2


title: T1DCase11_7


title: peripheral blood-T1DControl14_3


title: T1DCase12_1


title: T1DCase11_6


title: peripheral blood-T1DCase16_6


title: peripheral blood-T1DCase14_4


title: T1DCase11_5


title: peripheral blood-T1DControl14_2


title: peripheral blood-T1DCase14_5


title: T1DCase11_3


title: peripheral blood-T1DControl14_1


title: T1DCase11_2


title: T1DControl10_7


title: T1DCase11_4


title: T1DCase11_1


title: peripheral blood-T1DCase14_3


title: peripheral blood-T1DControl13B_1


title: peripheral blood-T1DCase14_2


title: T1DControl10_8


title: T1DControl10_3


title: T1DControl10_6


title: T1DControl10_4


title: peripheral blood-T1DControl13B_3


title: T1DControl10_2


title: peripheral blood-T1DControl13B_4


title: T1DControl10_5


title: peripheral blood-T1DControl13A_5


title: peripheral blood-T1DCase14_1


title: peripheral blood-T1DControl13A_4


title: peripheral blood-T1DControl13B_2


title: peripheral blood-T1DControl13A_3


title: T1DControl10_1


title: T1DCase10_6


title: peripheral blood-T1DCase13_5


title: peripheral blood-T1DControl13A_2


title: peripheral blood-T1DControl13A_1


title: peripheral blood-T1DCase13_3


title: T1DCase12_4


title: T1DControl9_6


title: T1DCase10_5


title: peripheral blood-T1DCase13_4


title: peripheral blood-T1DCase13_1


title: peripheral blood-T1DCase13_2


title: T1DCase10_2


title: T1DControl9_5


title: peripheral blood-T1DControl12_3


title: T1DCase10_1


title: T1DControl9_2


title: T1DCase10_3


title: T1DCase10_4


title: peripheral blood-T1DControl12_1


title: T1DCase9_6


title: T1DCase9_5


title: peripheral blood-T1DCase12_5


title: peripheral blood-T1DCase12_6


title: peripheral blood-T1DControl12_2


title: T1DCase9_7


title: T1DControl9_1


title: peripheral blood-T1DCase12_2


title: T1DControl9_4


title: peripheral blood-T1DCase12_4


title: peripheral blood-T1DCase12_3


title: T1DControl9_3


title: T1DCase9_4


title: peripheral blood-T1DCase12_1


title: T1DCase9_3


title: T1DCase9_2


title: peripheral blood-T1DControl11_7


title: T1DControl8_8


title: peripheral blood-T1DControl11_5


title: T1DControl8_5


title: T1DControl8_7


title: peripheral blood-T1DControl11_2


title: peripheral blood-T1DControl11_4


title: peripheral blood-T1DCase11_3


title: peripheral blood-T1DCase11_7


title: peripheral blood-T1DCase11_2


title: peripheral blood-T1DCase11_8


title: T1DControl8_3


title: peripheral blood-T1DCase11_5


title: peripheral blood-T1DControl11_6


title: T1DControl8_6


title: T1DControl8_1


title: T1DControl8_2


title: T1DCase8_11


title: T1DCase8_8


title: T1DCase9_1


title: T1DControl8_4


title: peripheral blood-T1DControl11_3


title: peripheral blood-T1DCase11_1


title: peripheral blood-T1DCase11_6


title: peripheral blood-T1DControl10_7


title: peripheral blood-T1DControl11_1


title: T1DCase8_12


title: peripheral blood-T1DCase11_4


title: T1DCase8_9


title: peripheral blood-T1DControl10_8


title: T1DCase8_10


title: peripheral blood-T1DControl10_6


title: T1DCase8_6


title: peripheral blood-T1DControl10_5


title: T1DCase8_7


title: T1DCase8_3


title: peripheral blood-T1DControl10_2


title: peripheral blood-T1DControl10_4


title: T1DCase8_2


title: T1DCase8_1


title: peripheral blood-T1DControl10_3


title: peripheral blood-T1DCase10_4


title: T1DControl7_7


title: T1DCase8_4


title: peripheral blood-T1DCase10_5


title: T1DControl7_6


title: peripheral blood-T1DControl10_1


title: T1DControl7_5


title: T1DControl7_2


title: T1DControl7_4


title: peripheral blood-T1DCase10_3


title: T1DCase7_3


title: peripheral blood-T1DCase10_1


title: T1DControl7_3


title: peripheral blood-T1DControl9_5


title: peripheral blood-T1DCase10_6


title: T1DControl7_1


title: peripheral blood-T1DControl9_6


title: peripheral blood-T1DControl9_3


title: T1DCase7_4


title: peripheral blood-T1DControl9_4


title: T1DCase7_1


title: T1DControl6_3


title: T1DControl6_4


title: peripheral blood-T1DControl9_2


title: peripheral blood-T1DControl9_1


title: T1DControl6_2


title: peripheral blood-T1DCase9_5


title: peripheral blood-T1DCase9_2


title: peripheral blood-T1DCase9_6


title: peripheral blood-T1DCase9_7


title: peripheral blood-T1DCase10_2


title: T1DCase8_5


title: T1DCase6_6


title: T1DControl5B_4


title: peripheral blood-T1DCase9_3


title: peripheral blood-T1DControl8_7


title: T1DCase6_3


title: T1DControl6_1


title: peripheral blood-T1DCase9_4


title: T1DCase6_4


title: T1DCase6_5


title: peripheral blood-T1DCase9_1


title: peripheral blood-T1DControl8_8


title: T1DCase6_1


title: peripheral blood-T1DControl8_5


title: T1DCase6_2


title: peripheral blood-T1DControl8_4


title: T1DControl5B_5


title: peripheral blood-T1DControl8_6


title: T1DControl5B_1


title: peripheral blood-T1DControl8_3


title: peripheral blood-T1DControl8_2


title: T1DControl5B_3


title: T1DControl5B_2


title: peripheral blood-T1DControl8_1


title: T1DControl5A_6


title: T1DControl5A_1


title: T1DCase5_8


title: peripheral blood-T1DCase8_12


title: peripheral blood-T1DCase8_5


title: T1DControl5A_5


title: T1DControl5A_7


title: peripheral blood-T1DCase8_11


title: peripheral blood-T1DCase8_10


title: T1DControl5A_2


title: T1DCase5_7


title: T1DControl5A_3


title: peripheral blood-T1DCase8_9


title: T1DControl5A_4


title: peripheral blood-T1DCase8_4


title: peripheral blood-T1DCase8_7


title: peripheral blood-T1DCase8_3


title: peripheral blood-T1DCase8_8


title: peripheral blood-T1DCase8_2


title: T1DCase7_2


title: T1DCase5_4


title: peripheral blood-T1DCase8_6


title: T1DCase5_2


title: T1DCase5_3


title: T1DCase5_6


title: peripheral blood-T1DCase8_1


title: peripheral blood-T1DControl7_7


title: T1DCase5_1


title: peripheral blood-T1DControl7_5


title: peripheral blood-T1DControl7_6


title: T1DCase5_5


title: peripheral blood-T1DControl7_2


title: peripheral blood-T1DControl7_3


title: T1DControl4_6


title: peripheral blood-T1DCase7_4


title: T1DControl4_5


title: peripheral blood-T1DControl7_1


title: T1DControl4_7


title: peripheral blood-T1DCase7_3


title: peripheral blood-T1DCase7_2


title: peripheral blood-T1DCase7_1


title: T1DControl4_4


title: T1DControl4_2


title: peripheral blood-T1DControl6_3


title: Microvesicle 4

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

country: USA

institute: OHSU

description:
Released exosome 4 under normoxia
MVNO4

hyb_protocol: 130ng labeled RNA was hybridized for 18 hr at 48C on GeneChip miRNA 3.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Partek Genomcis Suite(v.6.6) using the RMA normalization method

source_name: Exosome Normoxia Pair 2

label_protocol: 130ng RNA was labeled using the Affymetrix HSR miRNA Flash Tag Biotin kit

growth_protocol: Cells were cultured in RPMI + 1X Pen/Strep, 10% exosome-free FBS (prepared through ultracentrifugation of FBS - 100,000xg for 6h).

extract_protocol: RNA was extracted using the Qiagen miRNEasy kit

treatment_protocol: Cells were incubated in BioSpherix hypoxia chamber under hypoxic conditions (1% O2) or in a Thermo Scientific cell culture incubator under “normoxic” conditions (20% O2), in all cases at 37C and 5% CO2.

tag: cell line

tag: oxygen condition

value: normoxia

tag: sample group

value: Released exosome

tag: sample pair id

value: pair 2


title: Cell 4

description:
Parental cell 4 under normoxia
CellNO4

source_name: Cell Normoxia Pair 2

value: Parental cells


title: peripheral blood-T1DCase6_4


title: peripheral blood-T1DCase6_6


title: T1DControl4_1


title: T1DControl4_3


title: Microvesicle Hypoxia 1

description:
Released exosome 1 under hypoxia
MVHO

source_name: Exosome Hypoxia Pair 4

value: hypoxia

value: pair 4


title: peripheral blood-T1DCase6_3


title: peripheral blood-T1DControl6_2


title: Microvesicle 5

description:
Released exosome 5 under normoxia
MVNO5

source_name: Exosome Normoxia Pair 3

value: pair 3


title: T1DCase4_6


title: Cell 5

description:
Parental cell 5 under normoxia
CellNO5

source_name: Cell Normoxia Pair 3


title: peripheral blood-T1DControl6_1

value: no T1D diagnosis


title: peripheral blood-T1DCase6_5


title: peripheral blood-T1DCase6_2


title: peripheral blood-T1DCase6_1


title: T1DCase4_5


title: T1DCase4_4


title: T1DCase4_7


title: peripheral blood-T1DControl5B_3

value: no seroconversion


title: Microvesicle 1

description:
Released exosome 1 under normoxia
MVNO

source_name: Exosome Normoxia Pair 1

value: pair 1


title: Cell Hypoxia 1

description:
Parental cell 1 under hypoxia
CellHO

source_name: Cell Hypoxia Pair 4


title: peripheral blood-T1DControl5B_1


title: peripheral blood-T1DControl5B_2


title: Cell 1

description:
Parental cell 1 under normoxia
CellNO

source_name: Cell Normoxia Pair 1


title: peripheral blood-T1DControl5B_4


title: T1DControl3B_4

value: no diagnosis

value: female


title: T1DCase4_3

value: peripheral blood


title: peripheral blood-T1DControl5A_2


title: peripheral blood-T1DControl5A_4


title: peripheral blood-T1DControl5A_3


title: T1DCase4_2


title: T1DCase4_1


title: Rad51 binding after nitrogen depletion, altered Cdc45 levels rep 2

type: genomic

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

country: France

institute: Institute of Biochemistry and Cellular Genetics

description: Comparison IP to Input

hyb_protocol: Labeled input and IP samples were added to hybridization buffer: 750 ng herring sperm DNA, 40 μg tRNA, 10 μg human Cot1 DNA (Invitrogen), 50 mM Na-MES buffer (pH 6.9), 500 mM NaCl, 6 mM EDTA, 0.5% N-Lauroylsarcosine, 30% formamide, and 30 μg blocking oligo (5′-TT TTT TTT TTT TTT CAC GCG TCT CCC-3′). Samples were hybridized at 42ºC for 18 hours, and washes were performed for 5 minutes at room temperature (wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine, wash 2: 0.06x SSPE).

scan_protocol: Sildes were scanned using an Agilent G2565BA scanner.

data_processing: Agilent Feature Extraction Software was used to obtain data from scanned slides.

label: Alexa 555

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Input DNA from pat1-114 diploid cells with altered Cdc45 levels, -N

label_protocol: ChIP material was amplified using T7 RNA polymerase as in van Bakel et al., NAR (2008) and labeled using Alexa 555 or Alexa 647 dyes.

growth_protocol: Cells were grown in either continuous nitrogen-rich conditions or depleted of nitrogen, followed by induction of synchronous meiosis using the pat1-114 mutation (shift to 34ºC).

extract_protocol: Cells were fixed with 1% formaldehyde for 20 min followed by quenching with 0.125M glycine for 5 min. Cells were lysed using glass beads, and chromatin was sheared using a Bioruptor. The lysate was then centrifuged to remove cell debris. Chromatin was incubated overnight with 7.5µl Rad51 antibody (H-92, Santa Cruz) at 4ºC. This was followed by incubation with protein G sepharose beads (50 µl) for 4h at 4ºC, and protein-DNA complexes were collected by centrifugation, washed, and eluted from the beads at 65ºC for 20 minutes. DNA was recovered after proteinase K digestion, phenol/chloroform extraction, and ethanol precipitation. Input DNA was recovered in the same manner.

treatment_protocol: For Rad51 binding, ChIP-on-chip samples were taken 1h after S phase completion in all conditions, at which time the level of Rad51 binding across the genome reaches its peak (after pat1-114 inactivation, 4h (-N), 2h (+N), and 5h (-N/ Cdc45)

tag: strain

value: pat1-114 with altered Cdc45 levels

tag: antibody

tag: nitrogen

value: depletion

label: Alexa 647

source_name: ChIP DNA from pat1-114 diploid cells with altered Cdc45 levels, -N

tag: antibody catalog/vendor#

value: H-92, Santa Cruz


title: T1DControl3B_3

tag: case/control pair


title: peripheral blood-T1DCase5_7

tag: t1dcase/t1dcontrol pair

tag: age at sample (months)

value: male


title: peripheral blood-T1DControl5A_1

tag: time from seroconversion (months)

tag: time from t1d diagnosis (months)


title: peripheral blood-T1DControl5B_5

tag: gender


title: peripheral blood-T1DControl5A_6

tag: hla-dqb1 genotype


title: peripheral blood-T1DControl5A_7


title: Rad51 binding after nitrogen depletion in a rec12 deletion mutant rep 12

description: Comparison IP to Input

source_name: Input DNA from pat1-114 rec12 diploid cells, -N

tag: cell type

value: pat1-114 rec12 diploid cells

source_name: ChIP DNA from pat1-114 rec12 diploid cells, -N


title: Rad51 binding in conditionuous nitrogen rich conditions in a rec12 deletion mutant rep 12

description: Comparison IP to Input

source_name: Input DNA from pat1-114 rec12 diploid cells, +N

value: rich

source_name: ChIP DNA from pat1-114 rec12 diploid cells, +N


title: peripheral blood-T1DCase5_6

source_name: peripheral blood


title: T1DControl3B_2

tag: tissue


title: T1DControl3B_1


title: Rad51 binding in conditionuous nitrogen rich conditions rep 2

description: Comparison IP to Input

source_name: Input DNA from pat1-114 diploid cells, +N

source_name: ChIP DNA from pat1-114 diploid cells, +N


title: Rad51 binding after nitrogen depletion, altered Cdc45 levels rep 1

description: Comparison IP to Input


title: T1DControl3A_7


title: peripheral blood-T1DCase5_2


title: peripheral blood-T1DCase5_4


title: peripheral blood-T1DCase5_5


title: peripheral blood-T1DControl5A_5


title: peripheral blood-T1DCase5_3


title: Rad51 binding in conditionuous nitrogen rich conditions rep 1

description: Comparison IP to Input


title: T1DControl3A_6


title: T1DControl3A_5


title: Rad51 binding after nitrogen depletion rep 2

description: Comparison IP to Input

source_name: Input DNA from pat1-114 diploid cells, -N

source_name: ChIP DNA from pat1-114 diploid cells, -N


title: peripheral blood-T1DControl4_7


title: Rad51 binding after nitrogen depletion rep 1

description: Comparison IP to Input


title: Origin mapping diploid meiosis -N, altered Cdc45, replicate 2, dye-swap 2

description: Ratio of S phase to G0 arrest

hyb_protocol: Labeled samples from before and after S phase entry were added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18 hours, and washes were performed for 5 min at room temperature (wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine, wash 2: 0.06x SSPE).

source_name: nitrogen starvation,meiosis, G0

label_protocol: Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) with either Alexa 555 or Alexa 647 dyes.

growth_protocol: cdc25-22: haploid cdc25-22 cells were grown in EMM4S to exponential phase at 25ºC, shifted to 36.5ºC for 4 h to arrest cells in G2, then returned to 25ºC for synchronous mitotic cycles. WT or pat1-114, -N: cells were grown in EMM4S at 25ºC, starved of nitrogen for 16 hours, then returned to nitrogen-rich conditions at 34ºC. pat1-114, +N: cells were grown in EMM4S at 25ºC, treated with M-factor for 4.5 h to arrest in G1, then washed and grown in EMM4S at 34ºC.

extract_protocol: Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987.

treatment_protocol: Cells were treated with 12 mM hydroxyurea (HU) at the time of release from restrictive temperature for cdc25-22 or at the return to nitrogen-rich conditions for wild-type -N samples. HU was added at the time of shift to 34ºC for pat1-114 cells. Cells were harvested at the time of HU addition as well as during S phase: cdc25-22, 90 minutes after return to permissive temperature; wild-type and pat1-114 -N, 4 h after addition of nitrogen; pat1-114 +N, 2h after release from M-factor arrest; pat1-114 -N/Cdc45, 5 hours after addition of nitrogen.

value: pat1-114 diploid altered Cdc45

tag: phase

value: G0 arrest

value: starvation

source_name: nitrogen starvation,meiosis, G0 - S phase

value: G0 arrest - S phase


title: Origin mapping diploid meiosis -N, altered Cdc45, replicate 2, dye-swap 1

description: Ratio of S phase to G0 arrest


title: T1DControl3A_3


title: peripheral blood-T1DControl6_4


title: peripheral blood-T1DCase5_1


title: peripheral blood-T1DControl4_5


title: peripheral blood-T1DControl4_4


title: peripheral blood-T1DControl4_3


title: T1DControl3A_2


title: peripheral blood-T1DControl4_6


title: T1DControl3A_1


title: T1DControl3A_4


title: Origin mapping diploid meiosis -N, altered Cdc45, replicate 1, dye-swap 1

description: Ratio of S phase to G0 arrest


title: Origin mapping diploid meiosis +N, replicate 2, dye-swap 2

description: Ratio of S phase to G1 block

source_name: nitrogen-rich, meiosis, G1

value: pat1-114 diploid

source_name: nitrogen-rich, meiosis, G1 - S phase

value: G1 block - S phase


title: Origin mapping diploid meiosis -N, altered Cdc45, replicate 1, dye-swap 2

description: Ratio of S phase to G0 arrest


title: peripheral blood-T1DControl4_1

value: no seroconversion

value: no T1D diagnosis


title: peripheral blood-T1DControl4_2


title: peripheral blood-T1DCase4_7


title: T1DCase3_12


title: Origin mapping diploid meiosis +N, replicate 2, dye-swap 1

description: Ratio of S phase to G1 block


title: Origin mapping diploid meiosis +N, replicate 1, dye-swap 2

description: Ratio of S phase to G1 block


title: T1DCase3_11


title: Origin mapping diploid meiosis +N, replicate 1, dye-swap 1

description: Ratio of S phase to G1 block


title: T1DCase3_10


title: T1DCase3_8


title: T1DCase3_7


title: peripheral blood-T1DCase4_4


title: V79 8x Exp G

city: Barcelona

first: Elisabet

last: Mateu Huertas

state: Barcelona

address: Dr. Aiguader, 88

department: Bioinformatics and Genomics

country: Spain

institute: Center for Genomic Regulation

description:
SH-SY5Y cells were transfects with a  pCAGIG overexpressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_G.V80x2_1_4

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K arrays (G4851A-028004)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Neuroblastoma cell line SH-SY5Y_V79 8x

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the LowInputQuick Amp Labeling kit (Agilent 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA extraction was carreid out using miRNeasy (Qiagen) following manufacturer’s instructions.

tag: cell line

value: Neuroblastoma cell line SH-SY5Y

tag: transfection


title: T1DCase3_6

value: female


title: Origin mapping diploid meiosis -N, replicate 2, dye-swap 2

description: Ratio of S phase to G0 arrest

source_name: nitrogen starvation, meiosis, G0

source_name: nitrogen starvation, meiosis, G0 - S phase


title: Origin mapping diploid meiosis -N, replicate 2, dye-swap 1

description: Ratio of S phase to G0 arrest


title: peripheral blood-T1DCase4_6


title: peripheral blood-T1DCase4_5


title: V79 8x Exp F

description:
SH-SY5Y cells were transfects with a  pCAGIG overexpressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_F.V80x2_1_3


title: V79 8x Exp E

description:
SH-SY5Y cells were transfects with a  pCAGIG overexpressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_E.V80x2_2_3


title: Origin mapping diploid meiosis -N, replicate 1, dye-swap 2

description: Ratio of S phase to G0 arrest


title: T1DCase3_4

value: peripheral blood


title: V79 8x Exp D

description:
SH-SY5Y cells were transfects with a  pCAGIG overexpressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_D.V80x2_1_1


title: Origin mapping diploid -N, replicate 1, dye-swap 2

description: Ratio of S phase to G0 arrest

source_name: nitrogen starvation, G0

value: wild type diploid

source_name: nitrogen starvation, G0 - S phase


title: peripheral blood-T1DCase5_8


title: peripheral blood-T1DCase4_1


title: peripheral blood-T1DControl3B_4


title: Origin mapping diploid -N, replicate 1, dye-swap 1

description: Ratio of S phase to G0 arrest


title: V79 8x Exp C

description:
SH-SY5Y cells were transfects with a  pCAGIG overexpressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_C.V80x2_2_4


title: T1DCase3_5


title: V79 8x Exp B

description:
SH-SY5Y cells were transfects with a  pCAGIG overexpressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_B.V80x2_2_2


title: V79 Exp E

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_E.V80_2_4

source_name: Neuroblastoma cell line SH-SY5Y_V79


title: peripheral blood-T1DCase4_3


title: T1DCase3_2


title: peripheral blood-T1DCase4_2


title: Origin mapping -N, replicate 2, dye-swap 2

description: Ratio of S phase to G0 arrest

value: wild type


title: Origin mapping diploid meiosis -N, replicate 1, dye-swap 1

description: Ratio of S phase to G0 arrest


title: T1DCase3_1


title: V79 Exp D

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_D.V80_1_2


title: Origin mapping -N, replicate 2, dye-swap 1

description: Ratio of S phase to G0 arrest


title: peripheral blood-T1DControl3B_3


title: T1DCase3_3


title: V79 Exp C

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_C.V80_2_2


title: V79 Exp B

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_B.V80_2_1


title: peripheral blood-T1DControl3B_2


title: peripheral blood-T1DCase3_10


title: V79 Exp G

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_G.V80_1_4


title: V21 Exp B

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the wt 5'UTR of the FMR1 gene (21 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_B.V21_1_1

source_name: Neuroblastoma cell line SH-SY5Y_V21


title: peripheral blood-T1DControl3B_1


title: peripheral blood-T1DCase3_12


title: Origin mapping WT, replicate 2, dye-swap 2

description: Ratio of S phase to G2 block

source_name: G2 block

value: G2 block

source_name: G2 block - S phase

value: G2 block - S phase


title: T1DControl2_2

value: no diagnosis

value: male


title: V21 Exp C

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the wt 5'UTR of the FMR1 gene (21 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_C.V21_2_1


title: Origin mapping -N, replicate 1, dye-swap 1

description: Ratio of S phase to G0 arrest


title: V79 Exp F

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_F.V80_1_3


title: T1DCase2_5


title: T1DCase3_9


title: Origin mapping WT, replicate 2, dye-swap 1

description: Ratio of S phase to G2 block


title: T1DControl2_1


title: T1DCase2_6


title: peripheral blood-T1DCase3_9

source_name: peripheral blood


title: Origin mapping WT, replicate 1, dye-swap 2

description: Ratio of S phase to G2 block


title: V21 Exp G

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the wt 5'UTR of the FMR1 gene (21 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_G.V21_1_4


title: peripheral blood-T1DCase3_7


title: Origin mapping WT, replicate 1, dye-swap 1

description: Ratio of S phase to G2 block


title: Origin mapping -N, replicate 1, dye-swap 2

description: Ratio of S phase to G0 arrest


title: peripheral blood-T1DCase3_11


title: peripheral blood-T1DCase3_8


title: Histone H3K4Me3 during pre-meiotic S phase, continuous nitrogen-rich conditions rep 1

description: Comparison IP to Input

hyb_protocol: Equal amounts of labeled input and IP samples were added to hybridization buffer: 750 ng herring sperm DNA, 40 μg tRNA, 10 μg human Cot1 DNA (Invitrogen), 50 mM Na-MES buffer (pH 6.9), 500 mM NaCl, 6 mM EDTA, 0.5% N-Lauroylsarcosine, 30% formamide, and 30 μg blocking oligo (5′-TT TTT TTT TTT TTT CAC GCG TCT CCC-3′). Samples were hybridized at 42ºC for 18 hours, and washes were performed for 5 minutes at room temperature (wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine, wash 2: 0.06x SSPE).

source_name: Input DNA from pat1-114 diploid cells, +N

growth_protocol: Cells were grown in either nitrogen-rich conditions or depleted of nitrogen, followed by induction of synchronous meiosis using the pat1-114 mutation (shift to 34ºC).

extract_protocol: Cells were fixed with 1% formaldehyde for 20 min followed by quenching with 0.125M glycine for 5 min. Cells were lysed using glass beads, and chromatin was sheared using a Bioruptor. The lysate was then centrifuged to remove cell debris. Chromatin was incubated overnight with 2 µl of H3 antibody (ab1791, Abcam) or H3K4Me3 antibody (ab8580, Abcam) at 4ºC. This was followed by incubation with protein G sepharose beads (50 µl) for 4h at 4ºC, and protein-DNA complexes were collected by centrifugation, washed, and eluted from the beads at 65ºC for 20 minutes. DNA was recovered after proteinase K digestion, phenol/chloroform extraction, and ethanol precipitation. Input DNA was recovered in the same manner.

treatment_protocol: ChIP-on-chip samples were taken at the start of pre-meiotic S phase in all conditions (after pat1-114 inactivation, 2h (-N) and 30min (+N)).

source_name: ChIP DNA from pat1-114 diploid cells, +N

tag: antibody vendor

value: ab8580, Abcam


title: Histone H3K4Me3 during pre-meiotic S phase, continuous nitrogen-rich conditions rep 2

description: Comparison IP to Input

tag: strain


title: T1DCase2_4


title: Mock Exp G

description:
SH-SY5Y cells were transfects with a empty pCAGIG vector. Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_G.buit_2_3

source_name: Neuroblastoma cell line SH-SY5Y_Mock

value: empty pCAGIG vector


title: T1DCase2_1


title: peripheral blood-T1DCase3_4


title: peripheral blood-T1DCase3_5


title: peripheral blood-T1DCase3_6


title: T1DControl1_4


title: V21 Exp E

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the wt 5'UTR of the FMR1 gene (21 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_E.V21_2_3


title: V21 Exp D

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the wt 5'UTR of the FMR1 gene (21 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_D.V21_2_1


title: peripheral blood-T1DCase3_3


title: T1DControl1_5


title: Histone H3K4Me3 during pre-meiotic S phase after nitrogen depletion rep 2

description: Comparison IP to Input

source_name: Input DNA from pat1-114 diploid cells, -N

tag: antibody

source_name: ChIP DNA from pat1-114 diploid cells, -N


title: V21 Exp F

description:
SH-SY5Y cells were transfects with a  pCAGIG expressing the wt 5'UTR of the FMR1 gene (21 CGG repeats). Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_F.V21_1_2


title: T1DCase2_2


title: peripheral blood-T1DCase3_2


title: Mock Exp E

description:
SH-SY5Y cells were transfects with a empty pCAGIG vector. Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_E.buit_2_4


title: Mock Exp F

description:
SH-SY5Y cells were transfects with a empty pCAGIG vector. Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_F.buit_2_2


title: T1DControl1_2


title: Histone H3K4Me3 during pre-meiotic S phase after nitrogen depletion rep 1

description: Comparison IP to Input

tag: nitrogen


title: Histone H3 during pre-meiotic S phase, continuous nitrogen-rich conditions rep 1

description: Comparison IP to Input

value: ab1791, Abcam


title: T1DControl1_3


title: Histone H3 during pre-meiotic S phase after nitrogen depletion rep 1

description: Comparison IP to Input


title: peripheral blood-T1DCase3_1


title: Histone H3 during pre-meiotic S phase after nitrogen depletion rep 2

description: Comparison IP to Input


title: Mock Exp D

description:
SH-SY5Y cells were transfects with a empty pCAGIG vector. Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_D.buit_1_3


title: Histone H3 during pre-meiotic S phase, continuous nitrogen-rich conditions rep 2

description: Comparison IP to Input


title: Mock Exp C

description:
SH-SY5Y cells were transfects with a empty pCAGIG vector. Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_C.buit_1_2


title: T1DControl1_1


title: T1DControl2_3


title: peripheral blood-T1DControl2_3


title: T1DCase1_7


title: peripheral blood-T1DControl2_1


title: peripheral blood-T1DControl2_2


title: T1DCase2_3


title: Mock Exp B

description:
SH-SY5Y cells were transfects with a empty pCAGIG vector. Total RNA was isolated 24 h after transfection using  miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_B.buit_1_1


title: peripheral blood-T1DCase2_4


title: T1DCase1_4


title: T1DCase1_2


title: peripheral blood-T1DCase2_6


title: T1DCase1_5


title: CD630_WT1-cy3_SpoIIID1-cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Biological replicate 1 of 2.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: strain C630E grown 15h in MS (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E was grown for 15 hours in MS medium.

extract_protocol: Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.

tag: strain/background

value: C630E Mullany

tag: genotype

value: wild-type

source_name: spoIIID mutant grown 15h in MS

value: spoIIID mutant


title: peripheral blood-T1DCase2_2

tag: t1dcase/t1dcontrol pair


title: peripheral blood-T1DCase2_5

tag: age at sample (months)


title: T1DCase1_3

tag: case/control pair

tag: time from seroconversion (months)


title: peripheral blood-T1DCase2_3

tag: time from t1d diagnosis (months)

tag: gender


title: T1DCase1_6

tag: hla-dqb1 genotype


title: CD630_WT2-cy5_spoIIID2-cy3

description: Biological replicate 2 of 2.


title: CD630_WT2-Cy3_sigK2-Cy5

description: Biological replicate 2 of 4.

source_name: strain C630E grown 24h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 24 hours in MS medium.

tag: genotype/variation

tag: growth condition

value: MS medium

source_name: sigK mutant grown 24h in MS

value: sigK mutation


title: CD630_WT4-Cy5_sigK4-Cy3

description: Biological replicate 4 of 4.


title: CD630_WT1-Cy3_sigK1-Cy5

description: Biological replicate 1 of 4.


title: T1DCase1_1

tag: tissue


title: patient 39, ccRCC tissue

city: Suita

first: Kentaro

last: Jingushi

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

description: miRNA expression data from ccRCC tissue

hyb_protocol: After creating the hybridization cocktail, biotinylated cDNA were hybridized with GeneChip Human Exon 1.0 ST Array (Affymetrix) for 17 hours.

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: Scanned data were processed using the Agilent GeneSpring GX software.

source_name: ccRCC tissue

label_protocol: Total RNA 100 ng were subjected to cDNA synthesis by Ambion WT Expression Kit (Life technologies). Obtained 5.5 μg cDNA were biotinylated and then fragmented by GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Following excision, the tissue samples were immediately immersed in RNAlater, (QIAGEN) and stored at −20°C until RNA extraction. miRNAs were purified using the miRNeasy mini kit (QIAGEN).

value: Male


title: MCC_Poor Prognosis_Patient WB1464

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description:
Gene expression data from Poor Prognosis MCC
WB1464_Poor

hyb_protocol: Target preparation for Affymetrix Human Exon 1.0 ST Arrays was performed using 5μg of amplified cDNA and the Encore Biotin Module following the manufacturer’s recommendations. Hybridization, washing and staining performed with the Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite (version 6.6beta, build 6.11.1115) and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.

source_name: MCC_Poor prognosis_tumor cells

label_protocol: RNA was amplified and labeled using the WT-Ovation™ FFPE System V2, WT-Ovation™ Exon Module, and the Encore™ Biotin Module (NuGEN), which enables amplification and target preparation of the low quality RNA from FFPE, LCM samples.

extract_protocol: RNA was isolated from the LCM tissues using the PureLink™ FFPE RNA Isolation Kit (Invitrogen) according to manufacturer's protocols.

tag: patient prognosis

value: Poor prognosis

tag: disease state

value: Merkel cell carcinoma

tag: cell type

value: tumor cells


title: patient 44, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: patient 38, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: peripheral blood-T1DCase2_1


title: patient 26, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: CD630_WT4-Cy5_sigG4-Cy3

description: Biological replicate 4 of 4.

source_name: strain C630E grown 19h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 19 hours in MS medium.

source_name: sigG mutant grown 19h in MS

value: sigG mutation


title: MCC_Poor Prognosis_Patient RR1596

description:
Gene expression data from Poor Prognosis MCC
RR1596_Poor


title: patient 36, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: CD630_WT3-Cy5_sigK3-Cy3

description: Biological replicate 3 of 4.


title: patient 23, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: peripheral blood-T1DControl1_5

value: no seroconversion

value: no T1D diagnosis


title: patient 21, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: MCC_Poor Prognosis_Patient MW1324

description:
Gene expression data from Poor Prognosis MCC
MW1324_Poor


title: CD630_WT3-Cy3_sigG3-Cy5

description: Biological replicate 3 of 4.


title: peripheral blood-T1DControl1_4


title: patient 42, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: CD630_WT2-Cy5_sigG2-Cy3

description: Biological replicate 2 of 4.


title: CD630_WT4-Cy3_sigF4-Cy5

description: Biological replicate 4 of 4.

source_name: strain C630E grown 14h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 14 hours in MS medium.

source_name: sigF mutant grown 14h in MS

value: sigF mutation


title: patient 43, normal kidney tissue

description: miRNA expression data from normal kidney tissue

source_name: normal kidney tissue


title: patient 43, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: peripheral blood-T1DControl1_3

source_name: peripheral blood

value: male


title: MCC_Poor Prognosis_Patient JM1464

description:
Gene expression data from Poor Prognosis MCC
JM1464_Poor


title: MCC_Poor Prognosis_Patient RD1332

description:
Gene expression data from Poor Prognosis MCC
RD1332_Poor


title: CD630_WT2-Cy5_sigF2-Cy3

description: Biological replicate 2 of 4.


title: CD630_WT3-Cy3_sigF3-Cy5

description: Biological replicate 3 of 4.


title: peripheral blood-T1DControl1_2


title: CD630_WT1-Cy5_sigF1-Cy3

description: Biological replicate 1 of 4.


title: MCC_Moderate Prognosis_Patient SS1421

description:
Gene expression data from Moderate Prognosis MCC
SS1421_Moderate

source_name: MCC_Moderate prognosis_tumor cells

value: Moderate prognosis


title: peripheral blood-T1DControl1_1


title: peripheral blood-T1DCase1_6


title: CD630_WT1-Cy3_sigG1-Cy5

description: Biological replicate 1 of 4.


title: patient 34, ccRCC tissue

description: miRNA expression data from ccRCC tissue

value: Female


title: MCC_Poor Prognosis_Patient ED1329

description:
Gene expression data from Poor Prognosis MCC
ED1329_Poor


title: patient 34, normal kidney tissue


title: CD630_WT4-Cy3_sigE4-Cy5

description: Biological replicate 4 of 4.

source_name: sigE mutant grown 14h in MS

value: sigE mutation


title: MCC_Poor Prognosis_Patient RH1418

description:
Gene expression data from Poor Prognosis MCC
RH1418_Poor


title: CD630_WT2-Cy5_sigE2-Cy3

description: Biological replicate 2 of 4.

value: C630E Mullany


title: MCC_Good Prognosis_Patient PB1325

description:
Gene expression data from Good Prognosis MCC
PB1325_Good

source_name: MCC_Good prognosis_tumor cells

value: Good prognosis


title: MCC_Good Prognosis_Patient PK1419

description:
Gene expression data from Good Prognosis MCC
PK1419_Good


title: peripheral blood-T1DCase1_7


title: MCC_Moderate Prognosis_Patient MR1420

description:
Gene expression data from Moderate Prognosis MCC
MR1420_Moderate


title: peripheral blood-T1DCase1_4


title: patient 33, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: patient 33, normal kidney tissue


title: patient 31, normal kidney tissue


title: CD630_WT1-Cy5_sigE1-Cy3

description: Biological replicate 1 of 4.

value: wild-type


title: CD630_WT3-Cy3_sigE3-Cy5

description: Biological replicate 3 of 4.

value: MS medium


title: MCC_Moderate Prognosis_Patient LR1338

description:
Gene expression data from Moderate Prognosis MCC
LR1338_Moderate


title: patient 42, normal kidney tissue


title: MCC_Good Prognosis_Patient SC1466

description:
Gene expression data from Good Prognosis MCC
SC1466_Good


title: peripheral blood-T1DCase1_5


title: patient 31, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: peripheral blood-T1DCase1_2


title: peripheral blood-T1DCase1_3


title: patient 29, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: MCC_Good Prognosis_Patient ES1327

description:
Gene expression data from Good Prognosis MCC
ES1327_Good


title: MCC_Good Prognosis_Patient JF1330

description:
Gene expression data from Good Prognosis MCC
JF1330_Good


title: peripheral blood-T1DCase1_1


title: peripheral blood-Control10_6

value: female


title: patient 24, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: patient 29, normal kidney tissue

value: Male


title: peripheral blood-Control10_5


title: peripheral blood-Control10_4


title: patient 22, normal kidney tissue


title: peripheral blood-Control10_1


title: peripheral blood-Control10_6

hyb_protocol: 1.5 ug each sample was hybridized to Illumina Sentrix Human-6 V2 Expression Bead Chips at 58 °C overnight (18 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridizations were detected with 1 ug/ml Cyanine3-streptavidine (GE Healthcare Biosciences cat. no PA43001).

scan_protocol: Chips were scanned with Illumina Bead Array Reader. Numerical results were extracted with Bead Studio v3.3without any normalization or background subtraction.

source_name: peripheral blood-Control10

label_protocol: 100 ng of total RNA was amplified and reverse transcribed with Ovation RNA amplification system v2 (NuGEN, cat. no 3100-60), including Ovation whole blood reagent (cat. no 1300-60). 5 ug cDNA was labeled according to NuGEN’s Illumina solution protocol, application note #2. cDNA concentration and quality was controlled with Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).

value: peripheral blood


title: peripheral blood-Case10_3


title: peripheral blood-Case10_2


title: peripheral blood-Control10_5


title: patient 22, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: peripheral blood-Control10_3


title: patient 19, ccRCC tissue

description: miRNA expression data from ccRCC tissue


title: patient 24, normal kidney tissue


title: patient 19, normal kidney tissue


title: peripheral blood-Case10_4

source_name: peripheral blood-Case10


title: peripheral blood-Control10_1


title: peripheral blood-Case10_4


title: peripheral blood-Control10_2


title: peripheral blood-Case10_1


title: peripheral blood-Control9_9


title: peripheral blood-Case10_3


title: peripheral blood-Control10_2


title: peripheral blood-Control10_3


title: peripheral blood-Case10_2


title: peripheral blood-Control10_4


title: peripheral blood-Control9_7


title: fXPC 4

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K microarray (amadid id: 28004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

source_name: Peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: 2,5ml of peripheral blood was extracted from patients. PAXgene Blood RNA Kit was used to isolte total RNA according to the manufacturer's instructions

tag: age of punction

tag: age of onset

tag: clinical signs

tag: adiological signs


title: peripheral blood-Control9_6


title: peripheral blood-Case10_1


title: peripheral blood-Control9_7

source_name: peripheral blood-Control9


title: peripheral blood-Control9_8


title: peripheral blood-Control9_9


title: peripheral blood-Control9_5


title: peripheral blood-Control9_6


title: peripheral blood-Control9_8


title: peripheral blood-Control9_4


title: peripheral blood-Control9_3


title: fXPC 8


title: peripheral blood-Control9_2


title: fXPC 7

value: 1 major

value: 2 major


title: fXPC 1

value: 2minor + 1major

value: 1 minor


title: fXPC 9

value: 1 major + 2 minor


title: DGAT1_Study4_Vehicle_4

city: Boston

first: eric

last: muise

state: MA

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

description: Gene expression data from dorsal skin taken after 14 days of treatment with DGAT1 inhibitor.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

organism: Mus musculus

source_name: Skin

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cDNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: treatment

value: vehicle

value: dorsal skin

tag: genotype

tag: age

value: 8 weeks


title: fXPC 2


title: peripheral blood-Control9_5

tag: case/control pair

tag: age at sample (months)

tag: time from seroconversion (months)

value: no seroconversion

value: no T1D diagnosis

value: male


title: fXPC 3

tag: gender

value: 1major + 1minor


title: DGAT1_Study4_Vehicle_2


title: peripheral blood-Control9_1

tag: time from t1d diagnosis (months)

tag: hla-dqb1 genotype


title: peripheral blood-Control9_2

tag: tissue


title: peripheral blood-Control9_4


title: DGAT1_Study4_Vehicle_3


title: peripheral blood-Case9_10


title: DGAT1_Study4_Vehicle_1


title: peripheral blood-Case9_10

source_name: peripheral blood-Case9


title: fXPC 5

value: 1 major + 1minor


title: DGAT1_Study4_Cmpd6_4

value: DGAT1 inhibitor compound 6


title: fXPC 6


title: peripheral blood-Case9_9


title: peripheral blood-Case9_8


title: peripheral blood-Control9_3


title: peripheral blood-Control9_1


title: peripheral blood-Case9_7


title: Control 3,  biological replicate


title: DGAT1_Study4_Cmpd6_2


title: DGAT1_Study4_Cmpd18_3

value: DGAT1 inhibitor compound 18


title: Control 3

value: Male


title: peripheral blood-Case9_2


title: peripheral blood-Case9_6

value: peripheral blood


title: Control 2


title: DGAT1_Study4_Cmpd18_1


title: peripheral blood-Case9_4


title: DGAT1_Study4_Cmpd18_2


title: Control 5


title: DGAT1_Study4_Cmpd6_3


title: Control 4


title: peripheral blood-Case9_4


title: peripheral blood-Case9_8


title: peripheral blood-Case9_3


title: peripheral blood-Case9_3


title: Control 1


title: peripheral blood-Case9_1


title: peripheral blood-Case9_5


title: peripheral blood-Case9_7


title: peripheral blood-Case9_2


title: peripheral blood-Case9_6


title: DGAT1_Study4_Cmpd18_4


title: peripheral blood-Case9_9


title: DGAT1_Study2_Vehicle_4


title: peripheral blood-Control8_7

source_name: peripheral blood-Control8


title: DGAT1_Study2_Vehicle_3


title: peripheral blood-Control8_7


title: peripheral blood-Case9_1


title: peripheral blood-Control8_5


title: 20 pg Amplification- Prog/LN ratio - Replicate 6

city: Gainesville

first: Oleg

last: Suslov

state: FL

address: 1149 S. Newell Drive

department: Neuroscience

institute: University of Florida

description: SWAP-Technical replicate 6 of 6

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

source_name: LN229, primary glioma cells

label_protocol: Ten micrograms of RNA for the samples before and after amplification (20 pg, 1 ng, 20 ng of RNA input) were taken for Cy5/Cy3 labeling. The RNA was combined with 220 ng of random primer (Invitrogen) and 60 uM of NV-oligodT primer (Sigma-Genosis), incubated at 650C for 5 min and then tubes were kept at 450C. The RT mixture [8uL 5×first-strand buffer; 2 uL of 0.1 M DTT, 0.2 uL of 100 mM dATP, dGTP, and dCTP, 0.12 uL of 100 mM dTTP, and 0.16 uL of 50 mM aminoallyl dUTP] was then added to the tube containing RNA and primers. The tubes were incubated at 420C for 1 min, 350C for 5 min, 300C for 10 min, 250C for 15 min, then 1.9 ul of Superscript III (Invitrogen) was added and tubes were incubated at 250C for 30 min, 420C for 2 hours, 40 min; 700C for 15 min. The final reaction volume was 40 ul. RNA was hydrolyzed with 17.2 ul of 1 M NaOH at 65°C for 10 min. The solution was neutralized with 17.2 ul of 1 M HCl. The resulting cDNA was purified by ethanol precipitation with 10 ug of LPA as a carrier. The pellet was dissolved in 7 ul of a coupling buffer (71.43 M  sodium bicarbonate, pH 9.3), followed by 3 ul dye solution [25 nmol of NHS-ester Cy3 or Cy5 (Enzo),  in DMSO]. The resulting solution was mixed by pipetting every 15 min during the 90 min incubation time at room temperature. The labeling reaction was stopped with 4.5 ul of 4 M hydroxylamine hydrochloride (Sigma). The contents of the tubes were mixed, and incubated for 15 min at room temperature in the dark. The reactions were purified by ethanol precipitation.

growth_protocol: LN229 cells were maintained inDMEM supplemented with 5 % v/v FBS, 2 mM Lglutamine and 100 U/ml Penicillin/Streptomycin

extract_protocol: Total RNA extracted using the RNeasy Mini Kit (Qiagen) following manufacturer's instructions

tag: cell line

tag: source

value: plated glioma cells, 70% confluent

tag: rna prep

value: 20 pg of total RNA for amplification

source_name: pooled embryonic stem/progenitor cells

value: embryonic stem/progenitor cells

tag: developmental stage

value: embryo


title: 20 pg Amplification- Prog/LN ratio - Replicate 5

description: SWAP-Technical replicate 5 of 6

tag: cell type


title: peripheral blood-Control8_5


title: 20 pg Amplification- Prog/LN ratio - Replicate 3

description: Technical replicate 3 of 6


title: peripheral blood-Control8_6


title: peripheral blood-Control8_3


title: peripheral blood-Control8_4


title: peripheral blood-Control8_6


title: 20 pg Amplification- Prog/LN ratio - Replicate 4

description: Technical replicate 4 of 6


title: 1 ng Amplification- Prog/LN ratio - Replicate 5

description: SWAP-Technical replicate 5 of 5

value: 1 ng of total RNA for amplification


title: peripheral blood-Control8_2


title: DGAT1_Study2_Vehicle_2

value: vehicle


title: DGAT1_Study4_Cmpd6_1

value: dorsal skin


title: peripheral blood-Control8_4


title: peripheral blood-Control8_3


title: 1 ng Amplification- Prog/LN ratio - Replicate 4

description: Technical replicate 4 of 5


title: DGAT1_Study2_Vehicle_1

value: 8 weeks


title: peripheral blood-Control8_2

value: no seroconversion


title: 20 pg Amplification- Prog/LN ratio - Replicate 1

description: Technical replicate 1 of 6


title: 20 pg Amplification- Prog/LN ratio - Replicate 2

description: Technical replicate 2 of 6


title: DGAT1_Study2_Cmpd6_4


title: peripheral blood-Control8_1

value: no T1D diagnosis


title: peripheral blood-Case9_5

value: male


title: DGAT1_Study2_Cmpd6_3


title: 1 ng Amplification- Prog/LN ratio - Replicate 3

description: Technical replicate 3 of 5


title: DGAT1_Study2_Cmpd6_1


title: DGAT1_Study2_Cmpd2_4

value: DGAT1 inhibitor compound 2


title: peripheral blood-Control8_1


title: 1 ng Amplification- Prog/LN ratio - Replicate 2

description: Technical replicate 2 of 5


title: peripheral blood-Case8_5


title: 1 ng Amplification- Prog/LN ratio - Replicate 1

description: Technical replicate 1 of 5


title: peripheral blood-Case8_5

source_name: peripheral blood-Case8


title: peripheral blood-Case8_3


title: peripheral blood-Case8_6


title: DGAT1_Study2_Cmpd6_2


title: DGAT1_Study2_Cmpd2_2


title: peripheral blood-Case8_4


title: DGAT1_Study2_Cmpd2_3


title: 20 ng Amplification- Prog/LN ratio - Replicate 5

description: SWAP-Technical replicate 5 of 5

value: 20 ng of total RNA for amplification


title: peripheral blood-Case8_4


title: DGAT1_Study1_Vehicle_8


title: 20 ng Amplification- Prog/LN ratio - Replicate 3

description: Technical replicate 3 of 5


title: DGAT1_Study2_Cmpd2_1


title: peripheral blood-Case8_1


title: 20 ng Amplification- Prog/LN ratio - Replicate 4

description: Technical replicate 4 of 5


title: peripheral blood-Case8_2


title: peripheral blood-Case8_3


title: DGAT1_Study1_Vehicle_7


title: peripheral blood-Control7_7_T1DControl3A_7

tag: t1dcase/t1dcontrol pair

value: female


title: DGAT1_Study1_Vehicle_6


title: 20 ng Amplification- Prog/LN ratio - Replicate 2

description: Technical replicate 2 of 5


title: Control- Prog/LN ratio - Replicate 5

description: SWAP-Technical replicate 5 of 5

value: Total RNA


title: 20 ng Amplification- Prog/LN ratio - Replicate 1

description: Technical replicate 1 of 5


title: peripheral blood-Control7_6_T1DControl3A_6


title: peripheral blood-Case8_1


title: DGAT1_Study1_Vehicle_5


title: peripheral blood-Case8_2


title: peripheral blood-Control7_5_T1DControl3A_5


title: peripheral blood-Control7_7

source_name: peripheral blood-Control7


title: peripheral blood-Control7_6


title: DGAT1_Study1_Vehicle_4


title: peripheral blood-Control7_4_T1DControl3A_4


title: DGAT1_Study1_Vehicle_3


title: Control- Prog/LN ratio - Replicate 4

description: Technical replicate 4 of 5


title: Control- Prog/LN ratio - Replicate 3

description: Technical replicate 3 of 5


title: Control- Prog/LN ratio - Replicate 1

description: Technical replicate 1 of 5


title: DGAT1_Study1_Vehicle_2


title: peripheral blood-Control7_1_T1DControl3A_1


title: peripheral blood-Control7_3_T1DControl3A_3


title: Control- Prog/LN ratio - Replicate 2

description: Technical replicate 2 of 5


title: peripheral blood-Control7_5


title: peripheral blood-Control7_4


title: peripheral blood-Control7_2_T1DControl3A_2


title: DGAT1_Study1_Vehicle_1


title: DGAT1_Study1_Cmpd2_8


title: peripheral blood-Control7_2


title: peripheral blood-Control7_3


title: J82_M3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Gene expression from J82 cells grown on Matrigel RMA extracted, Log2

hyb_protocol: Fragmented and labeled DNA (540 ng) was hybridized following the manufacturer’s directions for 17h at 45C and rotating at 60rpm. Arrays were processed using Genechip Fluidics Station 450 according to recommended protocols (FS450_007) of double-staining and post-hybridization washes using GeneChip hybridization, wash and stain kit (Affymetrix #900720).

scan_protocol: Fluorescent images were captured using gene Array scanner 3000 and GCOS 1.2 software (Affymetrix).

data_processing: Raw microarray data were processed using Affymetrix Expression Console version 1.1 (http://www.affymetrix.com/browse/level_seven_software_products_only.jsp?productId=131414&categoryId=35623#) to extract gene level intensities using the RMA method. The subsequent analysis was performed using the R statistical environment (http://www.R-project.org) and BioConductor packages. Quality control of the data included a comparison of boxplots of gene expression level among the conditions, and hierarchical clustering of condition-specific gene expression profiles to identify potential outliers.  All data conform with the Minimal Information About a Microarray Experiment (MIAME) guidelines. Matrix-specific combined gene/protein expression profiles were compared using the limma (Smyth 2004) package. The Benjamini-Hochberg false discovery rate (FDR) correction for multiple testing was applied, along with 2-fold change cutoff. Gene set enrichment analysis (GSEA) method was used to analyze differentially expressed genes ranked by their fold change. Briefly, GSEA walks down the list of pre-ranked genes and calculates enrichment of gene groups in a given functional category. Functional categories containing genes consistently up- or downregulated are further assessed by a permutation method. GSEA assesses enriched categories in either phenotype by starting from either up- or downregulated genes. In this study, we considered enrichment of the genes in KEGG canonical pathways and all gene ontology categories. Further investigation of functional significance of differentially expressed genes/proteins was carried out by Ingenuity Pathway Analysis (IPA; Ingenuity Systems, Redwood City, CA).

source_name: J82 bladder cancer cell line cultured on Matrigel

label_protocol: Isolated total RNA was used with GeneChip WT Expression kit (Applied Biosystems) to produce fragmented single-stranded DNA, which was labeled using terminal labeling kit (Affymetrix) to generate biotin-labeled sense targeted DNA probes.

growth_protocol: Growth of cells on ECM. Gel matrices were made by layering either 0.8 ml of ice cold Matrigel (Becton-Dickinson, Bedford, MA),  SISgel,  or Type I collagen (BD Biosciences, San Jose, CA)  onto polyethylene terephthalate membranes of 6-well cell culture inserts (Falcon, Becton-Dickinson Labware, Franklin Lakes, NJ), which were then allowed to gel at 37°C. SISgel was prepared either by solubilized small intestine submucosa provided to us by Cook Biotech (Lafayette, IN) or by material we prepared ourselves from decellularized small intestine submucosa using Cooks protocol (17).  Briefly, ground SIS was partially digested with pepsin at pH 2.8 at 4°C for 5 days. This represents an optimization; too little digestion and the material forms clots instead of gelling, and excessive digestion produces material that will not gel. The pepsin was inactivated by raising the pH to 10 and incubating the gel at 4°C for 2 hours, followed by lowering the pH to 4 with 6 N HCl. The product was dialyzed against 10 mM HCl and sterilized with CHCl3, which was then dialyzed out against 10 mM HCl. To form a gel, the material was mixed with 1/10th volume of 10X phosphate-buffered saline and a small amount of Phenol Red to assist with pH adjustment. The pH was adjusted to 7.4 with sterile 1 M NaOH using a visual color standard that was checked against a pH meter. Collagen gels were prepared by mixing rat tail collagen, Type I with 1/10th volume of 10X PBS,  adjusting the pH to 7.4 ± 0.1, and then layering 0.8 ml onto transwell inserts as described above. Cells were layered onto either Matrigel, SISgel or collagen at a concentration of  5 ×105 cells/200 µl media, and 2 ml of Dulbecco’s Modified Eagle Medium (DMEM, Life Technologies, Carlsbad, CA) containing 1% penicillin, streptomycin and 10% fetal calf serum were layered beneath the transwell supports in 6-well plates as described (14).   Cultures were grown for 6 days with media changes every two days. Cultures were removed from the transwells, fixed in 1% formalin after overlaying with agarose or SISgel to prevent loss of cells on cutting of sections. Sections (5 µm) were stained with hematoxylin and eosin.  The role of Integrin Linked Kinase (ILK) signaling was confirmed by adding the ILK inhibitor, QLT0267, (provided by S. Dedhar) to the culture medium of cells grown on Matrigel and SISgel at a concentration of 10 µM and determining the phenotype from stained sections.     Cultured cells grown for 3 days were isolated from the matrices as follows. Cells grown on Matrigel were gently washed with Hank’s Balanced Salts Solution, HBSS, (Life Technologies, Carlsbad, CA), then coarsely minced gels were incubated with 1ml of dispsase (BD Biosciences, San Jose, CA) at 37°C until the gel dissolved. Cells were harvested from SISgel or collagen by washing with HBSS then incubating coarsely minced gels with 1ml of Collagenase IV, 450U/ml, (Life Technologies, Carlsbad, CA) at 37°C until the gel dissolved.  Liberated cells were centrifuged to a pellet, washed twice with HBSS, then resuspended with DMEM.  Cells grown on plastic were trypsinized and resuspended in DMEM.     Growth of Cells Flank Xenograft Model. Cells resuspended in 100µl DMEM/flank were mixed with an equal volume of cold SISgel, Matrigel or collagen, type I.  The mixture of gel and cells prepared as described in the previous section was immediately injected subcutaneously into either the right or left flank of  a 5-week old nude mouse, nu/nu-nuBR, (Charles River Laboratories, Wilmington, MA).  This protocol was reviewed by the Institutional Animal Care and Use Committee to ensure compliance with all standards of animal experimentation. Caliper measurements of tumor size were taken every week for the length of the study as were fluorescent images. Labeled cells were visualized with the Lightool’s LT-9900 system with the EGFP filter set of 470nm excitation filter and 515nm viewing filter and captured with a cooled CCD camera (Lightools, Encinitas, CA).  The area and intensity of the tumor was measured using Adobe Photoshop by first selecting the tumor area, then counting pixels above a threshold selected to eliminate background, non-tumor areas. The integrated intensity was calculated by multiplying the average intensity of detected pixels by the number of pixels detected.

extract_protocol: Total RNA was isolated from J82 and JBV cells grown on Matrigel and SISgel and liberated as described above. Triplicate samples, each from a different six-well transwell, were prepared to use as biological replicates. The RNA was isolated using a filter method with the QuickGene-Mini80 device and reagents (FujiFilm Life Sciences marketed by AutoGen, Holliston, MA).  http://www.autogen.com/assets/pdf/White%20Paper%20-%20QuickGene.pdf. RNA integrity was assessed using the Agilent (Agilent Technologies, Santa Clara, CA) microelectrophoresis system. The RIN was >9.0 for all the RNA preparations. The RNAs were converted to sense cDNA and hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Inc., according to the manufacturer's instructions. This array has 764,885 total 23-mer probes, which correspond to 28,869 annotated gene level probe sets and covers 99% of the sequences present in the RefSeq database.

treatment_protocol: Treatment in the current study implies the use of different matrixes for cell culture.

tag: matrix

value: Matrigel


title: peripheral blood-Case7_8


title: peripheral blood-Case7_6


title: peripheral blood-Case7_9

source_name: peripheral blood-Case7

value: peripheral blood


title: DGAT1_Study1_Cmpd2_7

tag: treatment


title: peripheral blood-Case7_7

source_name: peripheral blood


title: DGAT1_Study1_Cmpd2_4

tag: genotype


title: J82_S3

description: Gene expression from J82 cells grown on SISgel RMA extracted, Log2

source_name: J82 bladder cancer cell line cultured on SISgel

value: SISgel


title: peripheral blood-Case7_5


title: DGAT1_Study1_Cmpd2_6

tag: age


title: peripheral blood-Case7_9

tag: case/control pair


title: DGAT1_Study1_Cmpd2_5


title: peripheral blood-Case7_6

tag: age at sample (months)


title: peripheral blood-Case7_8

tag: time from seroconversion (months)


title: DGAT1_Study1_Cmpd2_3


title: J82_M2


title: DGAT1_Study1_Cmpd2_1


title: J82_M1


title: J82_P2

description: Gene expression from J82 cells grown on Plastic, RMA extracted, Log2

source_name: J82 bladder cancer cell line cultured on Plastic

value: Plastic


title: peripheral blood-Case7_4

tag: gender


title: peripheral blood-Case7_2

tag: time from t1d diagnosis (months)


title: peripheral blood-Case7_5

tag: hla-dqb1 genotype


title: J82_S2


title: DGAT1_Study1_Cmpd2_2

tag: tissue


title: J82_S1

tag: cell line


title: J82_P3


title: peripheral blood-Control7_1


title: peripheral blood-Case7_3


title: DGAT1_Study1_Cmpd1_8

value: DGAT1 inhibitor compound 1


title: peripheral blood-Case7_3


title: peripheral blood-Case7_4


title: DGAT1_Study1_Cmpd1_7


title: peripheral blood-Case8_6


title: DGAT1_Study1_Cmpd1_6


title: peripheral blood-Case7_7


title: peripheral blood-Case7_1


title: DGAT1_Study1_Cmpd1_5


title: J82_P1


title: peripheral blood-Control6_6


title: JBV_M2

description: Gene expression from JBV cells grown on Matrigel RMA extracted, Log2

source_name: JBV bladder cancer cell line cultured on Matrigel

value: JBV


title: JBV_M3


title: peripheral blood-Case7_1


title: DGAT1_Study1_Cmpd1_4


title: peripheral blood-Control6_6

hyb_protocol: 1.5 ug each sample was hybridized to Illumina Sentrix Human-6 V2 Expression Bead Chips at 58 °C overnight (18 h) according to Illumina 11225598_WGGEX_IntelliHyb_Seal_SystemManual_RevA.pdf. Hybridizations were detected with 1 ug/ml Cyanine3-streptavidine (Amersham Biosciences cat. no 146065)

scan_protocol: Chips were scanned with Illumina Bead Array Reader. Numerical results were extracted with Bead Studio v2.3.41 without any normalization or background subtraction.

source_name: peripheral blood-Control6

label_protocol: 500 ng total RNA was amplified and reverse transcribed with RiboAmp OA 1 round RNA amplification kit (Arcturus, cat. no KIT0209). cRNA was biotinylated during the overnight (14 h) IVT reaction with Illumina Total Prep RNA Amplification Kit (Ambion, cat. no L1791). cRNA was purified with RiboAmp OA 1 Round RNA Amplification Kit.


title: peripheral blood-Case7_2


title: JBV_S3

description: Gene expression from JBV cells grown on SISgel RMA extracted, Log2

source_name: JBV bladder cancer cell line cultured on SISgel


title: peripheral blood-Control6_2


title: peripheral blood-Control6_4

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (cat. no 901530).


title: peripheral blood-Control6_4


title: JBV_S1


title: peripheral blood-Control6_2


title: peripheral blood-Control6_5


title: JBV_M1


title: peripheral blood-Control6_1


title: peripheral blood-Control6_3


title: JBV_S2


title: peripheral blood-Control6_5


title: JBV_P3

description: Gene expression from JBV cells grown on Plastic, RMA extracted, Log2

source_name: JBV bladder cancer cell line cultured on Plastic


title: DGAT1_Study1_Cmpd1_3


title: peripheral blood-Control6_3


title: DGAT1_Study1_Cmpd1_1


title: JBV_P2


title: peripheral blood-Case6_6

source_name: peripheral blood-Case6


title: peripheral blood-Case6_4


title: JBV_P1


title: peripheral blood-Case6_3


title: peripheral blood-Case6_4


title: peripheral blood-Case6_5


title: peripheral blood-Case6_2


title: peripheral blood-Case6_3


title: peripheral blood-Case6_6


title: peripheral blood-Control6_1


title: peripheral blood-Case6_5


title: Young4_Mouse430

city: Durham

first: Brigid

last: Hogan

state: North Carolina

address: 388 Nanaline Duke Bldg PO Box 3709

department: Cell Biology

institute: Duke University Medical Center

hyb_protocol: Affymetrix ENZO labeling kit

scan_protocol: Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions

data_processing: Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions. Data analysis was performed using Genomics Suite 6.5 (Partek) software and robust multichip analysis normalization was performed on each dataset. Two-way ANOVA and fold-change analyses were performed to select genes that were differentially expressed between 2 month and 14 month old C57Bl/6 datasets. Top differentially expressed genes were selected with a p-value cutoff of <0.05 based on ANOVA test and a fold-change cutoff of >±2.0.

label: Biotin

source_name: distal trachea and carina region of 2 month old mice

label_protocol: Total RNA was processed using Ambion MessageAmpTM Premier by the Duke Microarray Facility.

extract_protocol: Total RNA was extracted from the distal tracheas and carinas using QIAshredder and RNeasy Micro Kits (QIAGEN).

treatment_protocol: Distal tracheas and carinas of four young (2 month) and four older (14 month) C57Bl/6 female mice were dissected out.

tag: background strain

value: 2 month

value: distal trachea and carina region


title: Young7_Mouse430


title: Young3_Mouse430


title: Old6_Mouse430

source_name: distal trachea and carina region of 14 month old mice

value: 14 month


title: peripheral blood-Case6_1

label_protocol: 50 ng of total RNA was processed to cDNA with Nugen Ovation RNA Amplification System V2 (cat. no 3100-60) and subsequently biotin-labelled and fragmented with Nugen Encore Biotin Module (cat. no 4200-A01) according to manufacture’s protocol.


title: peripheral blood-Case6_2


title: DGAT1_Study1_Cmpd1_2

source_name: Skin

value: dorsal skin

value: 8 weeks


title: Latent TB (Untreated) Mouse 2

city: Baltimore

first: Noton

middle: K

last: Dutta

state: MD

address: 1550 Orleans Street, Room 110

department: Medicine

institute: Johns Hopkins University

description: Immunized C3HeB/FeJ mice #2challenged with H37Rv without treatment

hyb_protocol: Hybridized to Illumina Mouse WG-6 v2.0 BeadArrays according to manufacturer protocols

scan_protocol: Standard Illumina scanning protocol for iScan

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse lung

label_protocol: Biotin-labeled cRNA samples were prepared using Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Six weeks after aerosol-immunization with recombinant M. bovis BCG overexpressing the 30-kilodalton antigen, C3HeB/FeJ mice were aerosol-infected with M. tuberculosis H37Rv. Six weeks later, mice were treated with TNF-neutralizing antibody (TNF-treated/ Active TB/Reactivation) or without treatment (untreated control/LTBI)

extract_protocol: Total RNA was extracted from mouse frozen lungs using the RiboPureTM Kit plus DNA-free reagents (Ambion)

treatment_protocol: TNF neutralizing agent MP6-XT22 (rat IgG1) was injected 0.5 mg intraperitoneally twice weekly per mouse for 4 weeks.

value: Infected

tag: Sex

tag: strain

value: lung


title: Old5_Mouse430


title: peripheral blood-Case6_1


title: miR-181d Knockin #2

city: Dallas

first: Nicolai S.C.

last: van Oers

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using the iScan SQ scanner

data_processing:
The data was processed without normalization using GenomeStudio (version GSGX 1.9.0).
Briefly, two-step normalization procedure was applied. The first step involved the determination of the parameters of the array background. Only the genes expressed above the background were processed for the second step, which further adjusted normalized profiles to each other.
All data analyses were detailed in (1,2,3).
1. Dozmorov, I., and I. Lefkovits. 2009. Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res. 37: 6323–6339.
2. Dozmorov, I. M., J. Jarvis, R. Saban, D. M. Benbrook, E. Wakeland, I. Aksentijevich, J. Ryan, N. Chiorazzi, J. M. Guthridge, E. Drewe, P. J. Tighe, M. Centola, and I. Lefkovits. 2011. Internal standard-based analysis of microarray data2--analysis of functional associations between HVE-genes. Nucleic Acids Res 39: 7881-7899.
3. de la Morena, M. T., J. L. Eitson, I. M. Dozmorov, S. Belkaya, A. R. Hoover, E. Anguiano, M. V. Pascual, and N. S. van Oers. 2013. Signature MicroRNA expression patterns identified in humans with 22q11.2 deletion/DiGeorge syndrome. Clin Immunol 147: 11-22.

source_name: Thymus

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

growth_protocol: Thymus tissues were isolated from the miR-181d transgenic and miR-181d knockin mice.

extract_protocol: RNA was extracted using the Qiagen miRNeasy kit according to the manufacturer's instructions, followed by and DNase treatment. Quality control was performed with Agilent Bioanalyzer.

value: Whole thymus

tag: genotype/variation

value: miR-181d knockin


title: Old2_Mouse430

value: female


title: peripheral blood-T1DControl15_4

scan_protocol: GeneTitan MC Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control GeneTitan hybridization process and in summarizing probe cell intensity data (.CEL file generation).

extract_protocol: Total whole-blood RNA was extracted from the samples using PAX gene RNA Blood RNA kit (Qiagen, Germany) according to manufacturer's instructions. RNA quality and quantity was determined using Nano Drop ND-1000 (Nano Drop Technologies, USA) and Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).

tag: t1dcase/t1dcontrol pair

value: no seroconversion

value: no T1D diagnosis


title: Active TB (TNF-treated) Mouse 1

description: Immunized C3HeB/FeJ mice#1 challenged with H37Rv after 4 weeks of TNF treatment

value: Infected and TNF-treated


title: Latent TB (Untreated) Mouse 1

description: Immunized C3HeB/FeJ mice#1 challenged with H37Rv without treatment


title: miR-181d Knockin #1


title: peripheral blood-Control5_1-T1DControl15_3


title: Young8_Mouse430


title: peripheral blood-Control5_4

source_name: peripheral blood-Control5

value: peripheral blood


title: peripheral blood-Control5_1-T1DControl15_2


title: miR-181d Transgenic #2

value: miR-181d transgenic


title: peripheral blood-Control5_1-T1DControl15_4


title: Tamoxifen-treated, 1 week following surgery male young mouse 2

city: Lexington

first: Christopher

last: Fry

state: KY

address: 900 South Limestone

institute: University of Kentucky

description: Gene expression data from plantaris muscle without satellite cells, 1 week post- surgery

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CHP data were generated using Affymetrix Command Console software and the data analysis was performed using Partek Genomics Suite.

source_name: Tamoxifen-treated 1 week post-surgery plantaris muscle

label_protocol: Biotinylated cDNA were prepared according to the standard Ambion and Affymetrix protocol from 1 µg total RNA (Ambion WT Expression kit and Affymetrix WT Terminal Labeling kit).

growth_protocol: Male and female Pax7-DTA mice (parental strains Pax7-CreER; Rosa26-DTA), 4 months of age were housed in a temperature- and humidity-controlled facility on a 14:10 h light:dark cycle with access to food and water ad libitum

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Skeletal muscle

tag: parental strains

value: Pax7-CreER; Rosa26-DTA

value: 4 months


title: peripheral blood-Control5_1-T1DControl15_1


title: Tamoxifen-treated, 1 week following surgery male young mouse 1


title: peripheral blood-Control5_1


title: Old1_Mouse430

value: distal trachea and carina region


title: miR-181d Transgenic #1


title: peripheral blood-Control5_3


title: Active TB (TNF-treated) Mouse 2

description: Immunized C3HeB/FeJ mice#2 challenged with H37Rv after 4 weeks of TNF treatment

tag: treatment


title: peripheral blood-Casel5_4

source_name: peripheral blood-Case5


title: peripheral blood-Control5_4


title: Tamoxifen-treated, 1 week following surgery female young mouse

tag: genotype


title: Vehicle-treated, 1 week following surgery male young mouse

description: Gene expression data from plantaris muscle with satellite cells, 1 week post- surgery

source_name: Vehicle-treated 1 week post-surgery plantaris muscle

tag: age


title: peripheral blood-Control5_3

source_name: peripheral blood

tag: case/control pair


title: peripheral blood-Control5_2

tag: age at sample (months)


title: Vehicle-treated, 1 week following surgery female young mouse


title: mouse_liver_Wfs1_ko_VPA_replicate_8

city: Tartu

first: Anton

last: Terasmaa

address: Ravila 19

department: Faculty of Medicine, Institute of Bio- and Translational Medicine

country: Estonia

institute: University of Tartu

hyb_protocol: Samples were hybridized on Affymetrix Mouse Gene 1.0 st arrays

scan_protocol: standard Affymetrix protocol

data_processing: Images were processed and cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (Affymetrix). Cel files were  processed using Expression Console v.1.1.2800.28061 to yield RMA summarized Log2 transformed expression values for probesets (CHP files). Normalized expression data (chp files) were further analysed using ANOVA in R (genotype x treatment) using R package Bioconductor.

source_name: Wfs1_KO_mouse_liver_VPA_12 wks_ip

label_protocol: 300 nanograms of total RNA were processed to produce fragmented biotin-labeled cRNA using the Ambion WT expression kit according to manufacturer's instructions.

growth_protocol: Mice were housed under standard laboratory conditions on a 12-h light/dark cycle (lights on at 07:00 AM) with free access to regular chow diet (R70 Lantmännen, Sweden) and water.  Male wild type and Wfs1 mutant mice were used throughout this study, they were 4 to 6 weeks old at the beginning of the experiment.  Mice were treated for three months with valproic acid (VPA, Sigma Aldrich, 300 mg/kg i.p. daily) or vehicle (0.9% saline 10 mL/kg i.p.). A glucose tolerance test (2 g/kg i.p.) was performed 24 hours after the last VPA injection and mice were killed 24 hours after the glucose tolerance test.  Mice were 16 to 18 weeks old when killed. Each experimental group consisted of 8 animals.

extract_protocol: Total liver RNA was extracted using Trizol reagent. Integrity of total RNA was evaluated using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and was within RNA integrity number (RIN) 7 to 9.

treatment_protocol: mice were killed, the liver was dissected out, snap frozen in liquid nitrogen and stored at -80°C until further analysis.

value: male

value: 16-18 weeks

tag: treated with

value: valproic acid (300 mg/kg/day i.p.) for 12 weeks

value: liver


title: mouse_liver_Wfs1_ko_VPA_replicate_5

tag: gender


title: peripheral blood-Control5_1

data_processing: Sample T1DControl7_4 was excluded from the final analysis as an outlier.  The CEL file and a readme for T1DControl7_4 containing the Metadata are provided as supplementary files on the Series record. The intensities were RMA normalized and log2-transformed using R/Bioconductor.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70C until analyzed.

tag: time from seroconversion (months)

tag: time from t1d diagnosis (months)


title: mouse_liver_Wfs1_ko_VPA_replicate_4

tag: tissue


title: peripheral blood-Casel5_3

data_processing: The intensities were quantile normalized and log2-transformed using R/Bioconductor.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70 °C until analyzed.

tag: hla-dqb1 genotype


title: peripheral blood-Casel5_1


title: peripheral blood-Casel5_2


title: mouse_liver_Wfs1_ko_VPA_replicate_6


title: peripheral blood-Control4_3


title: peripheral blood-Control5_2


title: mouse_liver_Wfs1_ko_VPA_replicate_2


title: peripheral blood-Control4_2


title: mouse_liver_Wfs1_ko_VPA_replicate_7


title: mouse_liver_Wfs1_hz_VPA_replicate_7

source_name: Wfs1_HZ_mouse_liver_VPA_12 wks_ip


title: mouse_liver_Wfs1_hz_VPA_replicate_5


title: mouse_liver_Wfs1_hz_VPA_replicate_6


title: peripheral blood_Case4_5


title: mouse_liver_Wfs1_ko_VPA_replicate_3


title: peripheral blood-Control4_2

source_name: peripheral blood-Control4


title: mouse_liver_Wfs1_hz_VPA_replicate_8


title: peripheral blood-Control4_1


title: mouse_liver_Wfs1_ko_VPA_replicate_1


title: peripheral blood_Case4_2


title: peripheral blood-Control4_1


title: PTR4

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: MeDIP of genomic DNA from PTR4 brain sample, technical replicate 1 and 2

hyb_protocol: Samples were hybridized to microarrays for 16 h at 42°C using default instrument settings.

scan_protocol: Microarrays were scanned with a MS200 scanner (Illumina); image gridding and intensity read-out was performed with Nimblescan version 2.6.

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages Starr and IRanges; MeDIP and input sample pairs were within-sample loess normalized followed by calculation of log2 (MeDIP/input) signal ratios and between-sample quantiles normalization; technical replicates were summarized and smoothed by application of a 400 bp sliding window along the genomically ordered data using the function „computeRunningMedians“ implemented in the „Starr“ package; data were then weighted by the number of CpGs with a maximum distance of 400 bp away from each probe position using an adaption of the „MEDIPS“ CpG density normalization [PMID: 24227674] to microarray data.

organism: Pan troglodytes

label_protocol: MeDIP and input DNAs were amplified with the GenomePlex Complete Whole Genome Amplification 2 kit (Sigma-Aldrich) and purified using the QIAquick PCR Purification kit (Qiagen); 1 µg of amplified DNA was denatured and labelled via primer extension with Cy dyes attached to 9-mer primers using the two color protocol (NimbleGen Roche).

extract_protocol: Genomic DNA was extracted using the Precellys Tissue DNA kit (PEQLAB) following the manufacturer's instructions and sheared with a Bioruptor (Diagenode) to fragment sizes from 100 bp to 600 bp; MeDIP samples were generated by overnight incubation of ca. 1.5 µg sheared DNA with monoclonal anti-5-methylcytosine antibody (Diagenode) at 4°C and subsequent magnetic bead-based enrichment of antibody-bound DNA; input samples consisted of untreated sheared DNA.

treatment_protocol: MeDIP

value: brain, frontal cortex tissue area A10

source_name: Input of genomic DNA from PTR4 brain sample

treatment_protocol: input


title: Vehicle-treated, sham operated male young mouse

description: Gene expression data from plantaris muscle with satellite cells, sham surgery

source_name: Vehicle-treated sham plantaris muscle


title: peripheral blood_Case4_1

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

institute: University of Turku


title: HSA6

description: MeDIP of genomic DNA from HSA6 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from HSA6 brain sample


title: peripheral blood-Control4_3


title: peripheral blood_Case4_3


title: peripheral blood_Case4_5


title: PTR3

description: MeDIP of genomic DNA from PTR3 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from PTR3 brain sample


title: peripheral blood_Case4_4


title: Tamoxifen-treated, sham operated male young mouse

description: Gene expression data from plantaris muscle without satellite cells, sham surgery

source_name: Tamoxifen-treated sham plantaris muscle


title: peripheral blood_Case4_4


title: PTR1

description: MeDIP of genomic DNA from PTR1 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from PTR1 brain sample


title: peripheral blood_Case4_2


title: peripheral blood_Case4_3


title: mouse_liver_Wfs1_hz_VPA_replicate_4


title: peripheral blood_Case4_1


title: peripheral blood-Control3_4


title: PTR5

description: MeDIP of genomic DNA from PTR5 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from PTR5 brain sample


title: HSA5

description: MeDIP of genomic DNA from HSA5 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from HSA5 brain sample


title: mouse_liver_Wfs1_hz_VPA_replicate_2


title: PTR2

description: MeDIP of genomic DNA from PTR2 brain sample, technical replicate 1, 2, and 3

source_name: Input of genomic DNA from PTR2 brain sample


title: peripheral blood-Control3_3


title: mouse_liver_Wfs1_hz_VPA_replicate_3


title: peripheral blood-Control3_3

source_name: peripheral blood-Control3


title: mouse_liver_Wfs1_hz_VPA_replicate_1


title: mouse_liver_Wfs1_wt_VPA_replicate_8

source_name: Wfs1_WT_mouse_liver_VPA_12 wks_ip


title: peripheral blood-Control3_2


title: HSA4

description: MeDIP of genomic DNA from HSA4 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from HSA4 brain sample


title: mouse_liver_Wfs1_wt_VPA_replicate_7


title: peripheral blood-Control3_1


title: peripheral blood-Control3_1


title: mouse_liver_Wfs1_wt_VPA_replicate_6


title: peripheral blood-Control3_4


title: peripheral blood-Control3_2


title: peripheral blood-Case3_7


title: HSA3

description: MeDIP of genomic DNA from HSA3 brain sample, technical replicate 1 and 2

source_name: Input of genomic DNA from HSA3 brain sample


title: peripheral blood-Case3_6

source_name: peripheral blood


title: mouse_liver_Wfs1_wt_VPA_replicate_5


title: peripheral blood-Case3_6

source_name: peripheral blood-Case3


title: peripheral blood-Case3_5


title: peripheral blood-Case3_7