title: pooled B6 sera (B6 IgG Profile)

status: Public on Feb 28 2015

type: other

city: Birmingham

first: Jennie

last: Hamilton

state: AL

address: 1825 University Blvd.

department: Department of Medicine, Division of Clinical Immunology and Rheumatology

country: USA

institute: University of Alabama Birmingham

description: pooled B6 sera (3 mice)

hyb_protocol: Peptide arrays were first blocked 60 min in Blocking Buffer for Near Infra Red Fluorescent Western blotting (Rockland Immunochemicals, Inc., Gilbertsville, PA).  The microarray was washed twice in PBS, pH 7.4 with 0.05% Tween 20 (PBS-T), and incubated for an additional 30 min in washing buffer.  The array was then incubated overnight at 4°C with mouse sera diluted 1:200 for anti-mouse IgG-specific analysis or 1:1000 for anti-mouse IgM-specific analysis (secondary Abs from Rockland Immunochemicals, Inc., Gilbertsville, PA).  After multiple washes in washing buffer, the microarrays were incubated for 30 min with the secondary antibody in PBS-T at room temperature.  After two additional washes in washing buffer, the microarrays were rinsed with ultrapure water and dried in a stream of air.

scan_protocol: Green/red fluorescence intensities were acquired on an LI-COR Odyssey Imager (Lincoln, NE) at scanning intensities of 7/7 in both channels (700 nm/800 nm), 1.0 mm offset, at a spatial resolution of 21 µm.  Staining of the Flag and HA control peptides that frame the arrays gave rise to high and homogeneous spot intensities with a coefficient of variation of <2%.

data_processing: Quantification of spot intensities and peptide annotation were based on the 16-bit grey scale tiff file that exhibits a higher dynamic range than the 24-bit colorized tiff file. PepSlide® Analyzer software was used to analyze the data. This program breaks down the fluorescence intensities of each spot into raw, foreground, and background signals, and calculates the standard deviation of the foreground median intensities.

molecule: other

organism: Mus musculus

source_name: B6 Mice Sera

label_protocol: The secondary antibodies used for all arrays were from Rockland Immunochemicals, Gilbertsville, PA.  They were conjugated to the DyLight dyes (DyLight680 or DyLight800) by the company.

extract_protocol: Sera were obtained from B6 mice by retro-orbital eye bleeding.  After separation from blood, sera were stored at -80°C.

tag: strain

tag: age

value: 6-9 months

tag: sample type

value: serum


title: pooled B6 sera (B6 IgM Profile)

description: pooled B6 sera (3 mice)


title: pooled BXD2 sera (BXD2 IgM Profile)

description: pooled BXD2 sera (3 mice)

scan_protocol: Green/red fluorescence intensities were acquired on an LI-COR Odyssey Imager (Lincoln, NE) at scanning intensities of 7/7 in both channels (700 nm/800 nm), 0.8 - 1.0 mm offset, at a spatial resolution of 21 µm.  Staining of the Flag and HA control peptides that frame the arrays gave rise to high and homogeneous spot intensities with a coefficient of variation of <2%.

source_name: BXD2 Mice Sera

extract_protocol: Sera were obtained from BXD2 mice by retro-orbital eye bleeding.  After separation from blood, sera were stored at -80°C.

tag: disease model

value: Lupus

value: 6-9 month


title: pooled sera from six 8-10 month old BXD2 mice

description: Sample name: BXD2 Av. Foreground Median

hyb_protocol: Peptide arrays were first blocked 60 min in Blocking Buffer for Near Infra Red Fluorescent Western blotting (Rockland Immunochemicals, Inc., Gilbertsville, PA).  The microarray was washed twice in PBS, pH 7.4 with 0.05% Tween 20 (PBS-T), and incubated for an additional 30 min in washing buffer.  The array was then incubated overnight at 4°C with mouse sera diluted 1:1000 for anti-mouse IgG (H+L) analysis (Rockland Immunochemicals, Inc., Gilbertsville, PA).  After multiple washes in washing buffer, the microarrays were incubated for 30 min with the secondary antibody in PBS-T at room temperature.  After two additional washes in washing buffer, the microarrays were rinsed with ultrapure water and dried in a stream of air.

scan_protocol: Fluorescence intensities were acquired on an LI-COR Odyssey Imager (Lincoln, NE) at scanning intensity of 7, 0.8 - 1.0 mm offset, at a spatial resolution of 21 µm.

data_processing: Quantification of spot intensities and peptide annotation were based on the 16-bit grey scale tiff file that exhibits a higher dynamic range than the 24-bit colorized tiff file. PepSlide® Analyzer software was used to analyze the data.  A software algorithm breaks down fluorescence intensities of each spot into raw, foreground and background signal, and calculates the standard deviation of foreground median foreground intensities.

label: Red DyLight680


title: Brown adipocytes differentiation day 7

type: RNA

city: Ann Arbor

first: xuyun

last: zhao

state: Michigan

address: 210 washtenaw ave

institute: Life Sciences Institute

description: Gene expression data from brown adipocytes during differentiation day 7

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

source_name: Brown adipocytes during differentiation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

treatment_protocol:
Mice were injected intraperitoneally daily with saline or CL316,243 (1 mg/kg) for 7 days. Brown adipocytes were differentiated for 7 days.
BAT and WAT lysate were harvested after treatment. Brown adipocytes lysate were harvested during differentiation.

tag: cell type

value: brown adipocyte

tag: genotype

value: wild type

tag: feeding


title: Brown adipocytes differentiation day 3

description: Gene expression data from brown adipocytes during differentiation day 3


title: Brown adipose tissue from saline injected mice, biological rep2

description: Gene expression data from saline injected brown adipose tissue, sample 2

tag: tissue

value: brown adipose tissue

value: chow


title: White adipose tissue from saline injected mice, biological rep2

description: Gene expression data from saline injected white adipose tissue, sample 2

value: white adipose tissue


title: White adipose tissue from CL injected mice, biological rep1

description: Gene expression data from CL injected white adipose tissue, sample 1


title: pooled BXD2 sera (BXD2 IgG Profile)

description: pooled BXD2 sera (3 mice)


title: Brown adipocytes differentiation day 5

description: Gene expression data from brown adipocytes during differentiation day 5


title: White adipose tissue from saline injected mice, biological rep1

description: Gene expression data from saline injected white adipose tissue, sample 1


title: White adipose tissue from CL injected mice, biological rep2

description: Gene expression data from CL injected white adipose tissue, sample 2


title: Brown adipocytes differentiation day 0

description: Gene expression data from brown adipocytes during differentiation day 0


title: Brown adipose tissue from saline injected mice, biological rep1

description: Gene expression data from saline injected brown adipose tissue, sample 1


title: 2382.1

type: genomic

city: Exeter

first: Rebecca

middle: Georgina

last: Smith

state: Devon

address: RILD, RD and E

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Illumina Infinium protocol

scan_protocol: Illumina Infinium protocol scanned using Illumina HiScan System

data_processing:
Data loaded into R using methylumi
Beta, methylated and unmethylated signal and wateRmelon normalised betas are available on the series record.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Illumina Infinium protocol

extract_protocol: Phenol chloroform DNA extraction

value: Whole blood

tag: Sex

value: Male


title: 2382.2


title: 8464.1


title: 7810920113_R03C01


title: 47626.2


title: 24632.2


title: 80182.2

value: Female


title: 69595.2


title: 91507.1


title: 8464.2


title: 39487.2


title: 47626.1


title: 26171.2


title: 40507.1


title: 26171.1


title: 40910.1


title: 33284.1


title: 7810920113_R04C01


title: 24632.1


title: 40507.2


title: 80182.1


title: 69595.1


title: 91507.2


title: 60033.2


title: 39487.1


title: 92308.2


title: 40910.2


title: 92308.1


title: 33284.2


title: 54343.2


title: 63904.1


title: 54343.1


title: 13648.2


title: 47229.1


title: 60033.1


title: 7471147076_R05C01


title: 63904.2


title: 84163.2


title: 7951.2


title: 69827.1


title: 73576.1


title: 73576.2


title: 32093.2


title: 7471147076_R06C01


title: 69827.2


title: 32093.1


title: 47229.2


title: 50190.2


title: 13648.1


title: 7471147076_R02C01


title: 7951.1


title: 95032.1


title: 71133.2


title: 71133.1


title: 7471147076_R01C01


title: 95032.2


title: HCC997T, tumor tissue

city: Guangzhou

first: Guo-liang

last: Huang

address: 651 Dongfeng East Road

department: Cancer Center

country: China

institute: Sun Yat-Sen University

hyb_protocol: Hybridization was done with 1 X hybridization solution (5 X Denhart's solution, 0.5% SDS,5 X SSC,20μL of ssDNA/1000 microarray spots) in a Hybridization Chamber (Corning) at 56℃ for 2.5-4h. Chambers were emerged in iced water for 30 sec before opening. The slide was washed at 56℃ with 1 X SSC and 0.1% SDS for 10min,twice with 0.5 X SSC for 30sec, and twice with 0.2 X SSC for 30 sec.

scan_protocol: The microarray was scanned by a LuxScanTM-10K Scanner (CapitalBio Inc., Beijing,China).

data_processing: Genotype call for each SNP was determined by a computer program called AccuTyping2b (Nucleic Acids Res 2006;34: e116)  based on two color signal intensities. If the log ratio of the two color (Cy5 and Cy3) intensities for a SNP was between -3.3 and 3.3, the SNP genotype was considered as heterozygous (C/T). If the log ratio was greater than 3.3 or less than -3.3, the genotype was assigned as homozygous, C/C and T/T, respectively.

label: Cy5 [Cy5-ddGTP/Cy5-ddCTP]

source_name: tumor tissue, hepatocellular carcinoma

label_protocol: Labeling probes (NOT labeling DNA, detail infromation can be found in Genome Res. 2005 Feb;15(2):276-83.) by single-base extension. The 3'ends of the oligonucleotide probes hybridizing to the ssDNA were immediately next to the polymorphic sites. Using ssDNA as a template,each probe was extended by a single dideoxynucleoside triphosphate (ddNTP) conjugated to a fluorescent chromophore (Cy3 or Cy5). In this way, probes hybridizing to different allelic sequences were labeled with different fluorescent colors. Theoretically, when hybridizing ssDNA contains a homozygous SNP, a probe should predominantly incorporate one color (signal color that is specific) over the other (background color),while a probe hybridizing to ssDNA containing a heterozygous SNP should incorporate both colors equally. After normalization and background subtraction, the genotypes were determined based on the logratios between the two normalized color intensities by using empirical linear values as cutoffs, which divided SNPs into three groups, two homozygous and one heterozygous. The cutoff values were validated by comparing the microarray results with those obtained by using independent genotyping methods. The following is the detail for labeling experiment. Probes were labeled in 25μL of labeling solution containing 1/7 volume of Sequenase buffer (supplied by the vendor),0.5 units/μL Sequenase (Amersham Pharmacia Biosciences), Cy3-ddATP and Cy5-ddGTP (PE Biosystems) for AG probes,and Cy3-ddUTP and Cy5-ddCTP for CT probes (750 nM each). The reaction was incubated at 70℃ for 10 min.

growth_protocol: The fresh tissues were immediately immersed in RNAlater (Ambion, Inc., USA) after surgical resection, stored at 4℃ overnight to allow thorough penetration of the RNase inhibitor, and then frozen at -80℃ until use.

extract_protocol: After total RNA extraction using TRIzol reagent (Invitrogen, USA), DNA in the interphase and phenol phase from the initial homogenate was isolated according to the manufacturer's instructions.

tag: gender

label: Cy3 [Cy3-ddATP/Cy3-ddUTP]


title: 7471147063_R01C01


title: 50190.1


title: HCC997N, non-tumor tissue

source_name: adjacent non-tumor tissue, hepatocellular carcinoma


title: HCC998T, tumor tissue


title: HCC995N, non-tumor tissue


title: HCC994N, non-tumor tissue


title: HCC994T, tumor tissue


title: HCC995T, tumor tissue


title: HCC992N, non-tumor tissue


title: HCC991T, tumor tissue


title: HCC990T, tumor tissue


title: 7471147063_R02C01


title: HCC677N, non-tumor tissue


title: HCC678N, non-tumor tissue


title: HCC677T, tumor tissue


title: HCC998N, non-tumor tissue


title: HCC678T, tumor tissue


title: HCC990N, non-tumor tissue


title: HCC996N, non-tumor tissue


title: HCC992T, tumor tissue


title: HCC674T, tumor tissue


title: HCC674N, non-tumor tissue


title: 10918.1


title: 73979.2


title: 10918.2


title: HCC668N, non-tumor tissue


title: 94524.2


title: 17122.2


title: HCC669T, tumor tissue


title: HCC669N, non-tumor tissue


title: HCC668T, tumor tissue


title: HCC663T, tumor tissue


title: HCC663N, non-tumor tissue


title: 17122.1


title: 73979.1


title: 95947.2


title: 96973.1


title: 96973.2


title: HCC991N, non-tumor tissue


title: HCC657N, non-tumor tissue


title: HCC646T, tumor tissue


title: HCC652T, tumor tissue


title: HCC648T, tumor tissue


title: HCC648N, non-tumor tissue


title: HCC646N, non-tumor tissue


title: HCC654N, non-tumor tissue


title: HCC636T, tumor tissue


title: HCC641N, non-tumor tissue


title: HCC652N, non-tumor tissue


title: HCC641T, tumor tissue


title: 95947.1


title: HCC635T, tumor tissue


title: HCC612T, tumor tissue


title: HCC636N, non-tumor tissue


title: HCC625T, tumor tissue


title: HCC654T, tumor tissue


title: HCC996T, tumor tissue


title: HCC625N, non-tumor tissue


title: HCC605T, tumor tissue


title: HCC607N, non-tumor tissue


title: HCC611T, tumor tissue


title: HCC612N, non-tumor tissue


title: HCC635N, non-tumor tissue


title: HCC611N, non-tumor tissue


title: HCC607T, tumor tissue


title: HCC593N, non-tumor tissue


title: HCC590T, tumor tissue


title: HCC591T, tumor tissue


title: HCC591N, non-tumor tissue


title: HCC657T, tumor tissue


title: HCC590N, non-tumor tissue


title: HCC586T, tumor tissue


title: HCC594N, non-tumor tissue


title: HCC597N, non-tumor tissue


title: HCC593T, tumor tissue


title: HCC597T, tumor tissue


title: HCC594T, tumor tissue


title: HCC602N, non-tumor tissue


title: HCC605N, non-tumor tissue


title: HCC602T, tumor tissue


title: HCC581T, tumor tissue


title: HCC586N, non-tumor tissue


title: HCC583T, tumor tissue


title: HCC582N, non-tumor tissue


title: HCC582T, tumor tissue


title: HCC583N, non-tumor tissue


title: HCC581N, non-tumor tissue


title: HCC571T, tumor tissue


title: HCC569T, tumor tissue


title: HCC560T, tumor tissue


title: HCC560N, non-tumor tissue


title: HCC563T, tumor tissue


title: HCC571N, non-tumor tissue


title: HCC563N, non-tumor tissue


title: HCC569N, non-tumor tissue


title: HCC559T, tumor tissue


title: HCC556T, tumor tissue


title: HCC556N, non-tumor tissue


title: HCC551N, non-tumor tissue


title: HCC550T, tumor tissue


title: HCC555N, non-tumor tissue


title: HCC551T, tumor tissue


title: HCC554N, non-tumor tissue


title: HCC554T, tumor tissue


title: HCC550N, non-tumor tissue


title: HCC546N, non-tumor tissue


title: HCC542T, tumor tissue


title: HCC546T, tumor tissue


title: HCC542N, non-tumor tissue


title: HCC555T, tumor tissue


title: HCC548N, non-tumor tissue


title: HCC559N, non-tumor tissue


title: HCC545N, non-tumor tissue


title: HCC548T, tumor tissue


title: HCC541T, tumor tissue


title: HCC541N, non-tumor tissue


title: HCC545T, tumor tissue


title: HCC536N, non-tumor tissue


title: HCC534T, tumor tissue


title: HCC534N, non-tumor tissue


title: HCC533T, tumor tissue


title: HCC533N, non-tumor tissue


title: HCC532T, tumor tissue


title: HCC536T, tumor tissue


title: HCC531T, tumor tissue


title: HCC531N, non-tumor tissue


title: HCC526T, tumor tissue


title: HCC526N, non-tumor tissue


title: HCC525T, tumor tissue


title: HCC525N, non-tumor tissue


title: HCC523T, tumor tissue


title: HCC523N, non-tumor tissue


title: HCC520T, tumor tissue


title: HCC520N, non-tumor tissue


title: HCC510T, tumor tissue


title: HCC532N, non-tumor tissue


title: HCC510N, non-tumor tissue


title: HCC506T, tumor tissue


title: CN1646-2 As (V) 50µm, biological replicate 2

city: Lucknow

first: Debasis

last: Chakarbarty

state: U.P, India

address: Rana Pratap Marg

country: India

institute: National Botanical Research Institute

description: 10 days old seedlings after germination, treated with  As (V) 50µm for24 hr.

hyb_protocol: According to affymatrix gene chip instruction manual using Fluidisc station 450.

scan_protocol: GeneChips were scanned using Affymatrix gene chip scanner.

data_processing: Arrays Images were captured and then raw .cel files were analyzed using affylmGUI biocondcutor R package for RMA algorithm (Irizarry et al., 2003).

label: biotin

organism: Oryza sativa Indica Group

source_name: 10 days grown rice seedlings of CN1646-2 in hydroponic solution, followed by 24 hr. treatment of  As (V) 50µm

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

growth_protocol: Seed sterilization and plant growth conditions were followed as reported earlier (a.rai et.al 2010). All seeds were grown in hydroponic medium in the culture room.  Rice plants were grown under controlled environmental conditions (26±1ºC, 16-h light (110—130 lE m 2 s 1)/8-h dark photoperiod).

extract_protocol: Total RNA was isolated from rice rootss using Sigma Spectrum® Plant total RNA  kit (STRN 50)

treatment_protocol: After sterilization rice seeds transferred to Petri-dishes (3–4 d) kept in culture room at 26±1ºC in dark. The plants were grown in hydroponic medium for 10 d before treatment of As (V) 0µm and 50µm

tag: line

value: Oryza sativa indica (Breeding Line, Parentage :Pusa Basmati 1 x IR 64)

value: root


title: CN1646-2 As (V) 50µm, biological replicate 1

source_name: 10 days grown rice seedlings of CN1646-2 in hydroponic solution, followed by 24 hr.  treatment of As (V) 50µm


title: HCC506N, non-tumor tissue


title: CN1646-2 As (V) 0µm (Control), biological replicate 2

description: 10 days old seedlings after germination, control

source_name: 10 days grown rice seedlings of CN1646-2 in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: HCC505T, tumor tissue


title: CN1646-2 As (V) 50µm, biological replicate 3


title: NAYANMONI As (V) 50µm, biological replicate 2

source_name: 10 days grown rice seedlings of NAYANMONI in hydroponic solution followed by of 24 hr treatment of As (V) 50µm

value: Oryza sativa aus


title: CN1646-2 As (V) 0µm (Control), biological replicate 3


title: HCC503T, tumor tissue


title: HCC503N, non-tumor tissue


title: HCC502N, non-tumor tissue


title: HCC502T, tumor tissue


title: HCC505N, non-tumor tissue


title: CN1646-5 As (V) 50µm, biological replicate 3

source_name: 10 days grown rice seedlings of CN1646-5 in hydroponic solution, followed by 24 hr.  treatment of As (V) 50µm


title: NAYANMONI As (V) 50µm, biological replicate 1

source_name: 10 days grown rice seedlings of NAYANMONI  in hydroponic solution followed by of 24 hr treatment of As (V) 50µm


title: NAYANMONI As (V) 0µm (Control), biological replicate 1

source_name: 10 days grown rice seedlings of NAYANMONI  in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: HCC501T, tumor tissue


title: CN1646-2 As (V) 0µm (Control), biological replicate 1

source_name: 10 days grown rice seedlings of CN1646-2  in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: CN1646-5 As (V) 0µm (Control), biological replicate 3

source_name: 10 days grown rice seedlings of CN1646-5 in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: HCC501N, non-tumor tissue


title: NAYANMONI As (V) 0µm (Control), biological replicate  2

source_name: 10 days grown rice seedlings of NAYANMONI in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: BRG-20 As (V) 50µm, biological replicate 3

source_name: 10 days grown rice seedlings of BRG-20 in hydroponic solution, followed by 24 hr.  treatment of As (V) 50µm


title: CN1646-5 As (V) 50µm, biological replicate 2


title: CN1646-5 As (V) 50µm, biological replicate 1

source_name: 10 days grown rice seedlings of CN1646-5 in hydroponic solution, followed by 24 hr. treatment of  As (V) 50µm


title: HCC496T, tumor tissue


title: HCC499T, tumor tissue


title: CN1646-5 As (V) 0µm (Control), biological replicate 1

source_name: 10 days grown rice seedlings of CN1646-5  in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: HCC496N, non-tumor tissue


title: CN1646-5 As (V) 0µm (Control), biological replicate 2


title: HCC491N, non-tumor tissue


title: HCC499N, non-tumor tissue


title: BRG-20 As (V) 0µm (Control), biological replicate 3

source_name: 10 days grown rice seedlings of BRG-20 in hydroponic solution followed by of 24 hr treatment of As (V) 0µm

value: Oryza sativa indica


title: BRG-20 As (V) 0µm (Control), biological replicate 2


title: BRG-15 As (V) 50µm, biological replicate 1

source_name: 10 days grown rice seedlings of BRG-15  in hydroponic solution followed by of 24 hr treatment of As (V) 50µm


title: HCC488T, tumor tissue

source_name: tumor tissue, hepatocellular carcinoma


title: BRG-15 As (V) 50µm, biological replicate 2

source_name: 10 days grown rice seedlings of BRG-15 in hydroponic solution followed by of 24 hr treatment of As (V) 50µm


title: HCC493N, non-tumor tissue

source_name: adjacent non-tumor tissue, hepatocellular carcinoma


title: Sample 3_C25

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

country: Germany

institute: Hannover Medical School

description: Sample 3

hyb_protocol: According to manufacturer's instructions (Agilent)

scan_protocol: Microarray slides were scanned immediately after washing using an Agilent microarray scanner G2505B at a resolution of 2 µm

data_processing:
Feature extraction and Genomic Workbench (Agilent)
Genome: hg19
Aberration Algorithm: ADM-2
Threshold: 7.0
Fuzzy Zero: ON
GC Correction: ON
Window Size: 2Kb
Centralization (legacy): OFF
Diploid Peak Centralization: ON
Manually Reassign Peaks: OFF
Combine Replicates (Intra Array): ON
Combine Replicates (Inter Array): OFF
Array Level Filter: NONE
Aberration Filter:  ( Minimum Number of Probes for Amplification >= 3
AND Minimum Size (Kb) of Region for Amplification >= 0.0
AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.0 )
OR ( Minimum Number of Probes for Deletion >= 3
AND Minimum Size (Kb) of Region for Deletion >= 0.0
AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.0 )
Feature Level Filter: gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true OR LogRatio = 0
Design Level Filter: Homology = 0 OR IsPseudoautosomal = 1
Genomic Boundary: OFF
Show Flat Intervals: OFF

source_name: blood mononuclear cells

extract_protocol: Qiagen

value: human DNA reference pool XY

value: blood mononuclear cells

source_name: X-CGD iPSC clone

tag: cell line/clone id

value: clone 25

value: iPSC from sample 1


title: HCC491T, tumor tissue


title: BRG-15 As (V) 0µm (Control), biological replicate 1

source_name: 10 days grown rice seedlings of BRG-15  in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: BRG-20 As (V) 50µm, biological replicate 1

source_name: 10 days grown rice seedlings of BRG-20 in hydroponic solution, followed by 24 hr. treatment of  As (V) 50µm


title: HCC488N, non-tumor tissue


title: BRG-20 As (V) 50µm, biological replicate 2


title: Sample 5_TC25.28

description: Sample 5

label_protocol: According to manufacturer's instructions (Agilent)

source_name: iPSC gene corrected

value: clone 25 Talen 28

value: iPSC gene corrected from sample 3


title: Sample 4_ZC7.23

description: Sample 4

value: clone 7 ZNF23

value: iPSC gene corrected from sample 2


title: BRG-15 As (V) 0µm (Control), biological replicate  2

source_name: 10 days grown rice seedlings of BRG-15 in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: HCC487T, tumor tissue


title: BRG-12 As (V) 50µm, biological replicate 3

source_name: 10 days grown rice seedlings of BRG-12 in hydroponic solution, followed by 24 hr.  treatment of As (V) 50µm


title: BRG-20 As (V) 0µm (Control), biological replicate 1

source_name: 10 days grown rice seedlings of BRG-20  in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: Sample 2_C7

description: Sample 2

value: clone 7


title: HCC487N, non-tumor tissue


title: Sample 1_CD34+

description: Sample 1

source_name: X-CGD patient-derived CD34+ cells

value: CD34+ parental line

value: hematopoietic stem cells


title: BRG-12 As (V) 50µm, biological replicate 2

source_name: 10 days grown rice seedlings of BRG-12 in hydroponic solution, followed by 24 hr. treatment of As (V) 50µm


title: HCC484T, tumor tissue

value: Male


title: HCC482T, tumor tissue


title: HCC484N, non-tumor tissue


title: BRG-12 As (V) 50µm, biological replicate 1


title: HCC482N, non-tumor tissue


title: HCC480T, tumor tissue

value: Female


title: BRG-12 As (V) 0µm (Control), biological replicate 1

source_name: 10 days grown rice seedlings of BRG-12  in hydroponic solution followed by of 24 hr treatment of As (V) 0µm


title: Evolved Clone_4N_gen500_431

city: Boston

first: Anna

last: Selmecki

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Evolved Clone vs WT DNA

hyb_protocol: The microarray was hybridized at 65°C for 17 hours

scan_protocol: Default scan settings were used: Scan Area (61 x 21.6 mm), Scan resolution (5 um), Red & Green Dye channel, Green and Red PMT (100%)

data_processing: Agilent Feature Extraction (FE) analysis was performed

organism: Saccharomyces cerevisiae

source_name: Evolved Clone_4N

label_protocol: Labeling was done as described previously (Selmecki et al 2005 Molecular Microbiology, and M. Dunham online protocols, http://dunham.gs.washington.edu/protocols.shtml). Briefly, 2.0 ug of HaeIII-digested (New England Biolabs) genomic DNA was labeled with 2.1 ul of Cy3 or Cy5 (CyDyeTm-Cy3-dUTP or CyDyeTm-Cy5-dUTP, Amersham GE Healthcare).  300 ng of Cy3-labeled DNA (all experimental strains) was mixed with 300 ng of Cy5-labeled DNA (reference control DNA) and the volume was brought to 44 ul with nuclease free water.  Blocking Buffer and Hybridization Buffer 2x HiRPM (Agilent Technologies) were added, and 100 ul was applied to each sub-array; the microarray was hybridized at 65°C for 17 hours and then washed and scanned, according to the manufacturer’s instructions.

growth_protocol: The evolution experiment was performed in 1mL SC+2% Raffinose cultures in 96-well format at 30C with shaking.

extract_protocol: Standard, phenol-chloroform genomic DNA preps were performed

treatment_protocol: The reference and progenitor strains were cultured in 5mL YPD overnight at 30C for genomic isolation.  Single colony clones were isolated from the evolution experiment on SC+2% raffinose agar plates and grown up in 5mL SC+2% raffinose overnight at 30C for genomic isolation.

value: Evolved Clone

source_name: Reference Control_PY3295

value: Reference Control


title: Evolved Clone_4N_gen500_406

description: Evolved Clone vs WT DNA


title: HCC467N, non-tumor tissue


title: Evolved Clone_4N_gen500_418

description: Evolved Clone vs WT DNA


title: HCC469T, tumor tissue


title: HCC463T, tumor tissue


title: HCC480N, non-tumor tissue


title: HCC479T, tumor tissue


title: Evolved Clone_4N_gen500_428

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_gen500_402

description: Evolved Clone vs WT DNA


title: HCC479N, non-tumor tissue


title: BRG-12 As (V) 0µm (Control), biological replicate 2

source_name: 10 days grown rice seedlings of BRG-12 in hydroponic solution followed by of 24 hr treatment of As (V) 0µm

value: root


title: HCC463N, non-tumor tissue


title: Evolved Clone_4N_gen500_407

description: Evolved Clone vs WT DNA


title: HCC466T, tumor tissue

source_name: tumor tissue, hepatocellular carcinoma


title: Evolved Clone_4N_gen500_420

description: Evolved Clone vs WT DNA


title: HCC467T, tumor tissue


title: HCC469N, non-tumor tissue


title: Evolved Clone_4N_gen500_401

description: Evolved Clone vs WT DNA


title: 4N+ChrXII aneuploid_clone 1A_AMSY2180

description: 4N+ChrXII aneuploid_clone 1A vs WT DNA

source_name: 4N+ChrXII aneuploid

value: 4N+ChrXII aneuploid_clone 1A


title: Evolved Clone_4N_gen55_508

description: Evolved Clone vs WT DNA


title: HCC462T, tumor tissue


title: 4N+ChrXIII aneuploid_clone 3A_AMSY2186

description: 4N+ChrXIII aneuploid_clone 3A vs WT DNA

source_name: 4N+ChrXIII aneuploid

value: 4N+ChrXIII aneuploid_clone 3A


title: HCC466N, non-tumor tissue

source_name: adjacent non-tumor tissue, hepatocellular carcinoma


title: 4N+ChrXIII aneuploid_clone 9A_AMSY2195

description: 4N+ChrXIII aneuploid_clone 9A vs WT DNA

value: 4N+ChrXIII aneuploid_clone 9A


title: 2N+ChrXIII aneuploid_RLY4888

description: 2N+ChrXIII aneuploid vs WT DNA

source_name: 2N+ChrXIII aneuploid

value: 2N+ChrXIII aneuploid


title: Evolved Clone_4N_gen55_506

description: Evolved Clone vs WT DNA


title: HCC493T, tumor tissue


title: Evolved Clone_4N_gen55_505

description: Evolved Clone vs WT DNA


title: HCC462N, non-tumor tissue


title: HCC459T, tumor tissue


title: HCC459N, non-tumor tissue


title: HCC456N, non-tumor tissue


title: Evolved Clone_4N_gen55_507

description: Evolved Clone vs WT DNA


title: HCC456T, tumor tissue


title: HCC453T, tumor tissue


title: HCC453N, non-tumor tissue


title: HCC450N, non-tumor tissue


title: HCC450T, tumor tissue


title: Evolved Clone_4N_gen55_502

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_gen35_501

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_gen55_504

description: Evolved Clone vs WT DNA


title: HCC449T, tumor tissue


title: Evolved Clone_4N_gen35_503

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_305

description: Evolved Clone vs WT DNA


title: HCC449N, non-tumor tissue


title: Evolved Clone_4N_316

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_317

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_321

description: Evolved Clone vs WT DNA


title: HCC448T, tumor tissue


title: HCC448N, non-tumor tissue


title: Evolved Clone_4N_304

description: Evolved Clone vs WT DNA


title: DS11_rep1

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

description: Strain DS11 harvested at 50% substrate conversion

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 6.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus DSM 1313

growth_protocol: Cells were grown in anaerobic serum bottle at 60°C with shaking at 150 rpm. Cells were harvested at the time points required to achieve 50% Avicel conversion.

extract_protocol: Cells were harvested by centrifugation and resuspended in Trizol reagent (Life Technologies, CA).  The suspension was transferred to a 2.0 mL screw top tube containing 800 mg of ashed glass beads.  Trizol was added to make up any remaining volume in the tube and then each tube was disrupted for three 20 second bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France).  Chloroform was added and mixed with the sample, and then separated by centrifugation.  The aqueous layer was collected in fresh tubes and a 1:1 volume of 75% ethanol was added.  After mixing, the sample was applied to an RNeasy column (Qiagen, CA) and processed following the manufacturer’s instructions including an on column DNA digestion.  Total cellular RNA was quantified with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE) and RNA quality was assessed with Agilent Bioanalyzer (Agilent, CA).  The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: Strains of C. thermocellum with various genes encoding scaffoldin proteins were deleted. These strains were grown on Avicel until 50% conversion of the substrate was achieved before harvesting the cells for extraction of RNA.

tag: substrate conversion


title: Evolved Clone_4N_315

description: Evolved Clone vs WT DNA


title: DS11_rep2

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

source_name: Strain DS11 harvested at 50% substrate conversion


title: Evolved Clone_4N_319

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_320

description: Evolved Clone vs WT DNA


title: DS3_rep2

description: Strain DS3 harvested at 50% substrate conversion

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: DS3_rep1

source_name: Strain DS3 harvested at 50% substrate conversion


title: HCC446T, tumor tissue


title: CTN7_techrep1

description: Strain CTN7 harvested at 50% substrate conversion


title: DS3_techrep1


title: HCC446N, non-tumor tissue


title: HCC443N, non-tumor tissue


title: HCC443T, tumor tissue


title: CTN4_techrep2

description: Strain CTN4 harvested at 50% substrate conversion


title: Evolved Clone_4N_330

description: Evolved Clone vs WT DNA


title: CTN7_rep1

source_name: Strain CTN7 harvested at 50% substrate conversion


title: CTN7_rep2


title: Oral cancer patient, Female 9

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

description: 9 vs. N(F)

hyb_protocol: Hybridization was done by Agilent’s In situ Hybridzation kit 5188-5220 as per manufacture's instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software was used to extract raw data from scanned images and data analysis is done using DNA Analytics software form Agilent Technologies using ADM2 algorithm. minAvgAbsLogRatio = 0.45, threshold=6.0, fuzzy zero=on

source_name: Freshly operated oral cancer tissue of a female

label_protocol: DNA was lebelled by Agilent Genomic DNA Labeling Kit PLUS as per manufacture's instructions.

growth_protocol: Not applicable

extract_protocol: Total genomic DNA was isolated from 5-10ml blood or from fresh operated tissue samples by QIAGEN blood DNA isolation kit or by the conventional phenol-chloroform method followed by ethanol precepitation (Sambrook, 1989), respectively.

treatment_protocol: Not applicable

tag: disease state

value: oral cancer

value: Freshly operated oral cancer tissue

tag: Stage

tag: tobacco habit

value: Yes

tag: node metastasis

value: Negative

tag: histology

value: WDSCC

tag: sample collection date

source_name: Blood of normal female

value: normal control

value: blood

value: female


title: Evolved Clone_4N_313

description: Evolved Clone vs WT DNA

tag: strain

tag: sample type


title: Evolved Clone_4N_336

description: Evolved Clone vs WT DNA


title: HCC440N, non-tumor tissue


title: HCC440T, tumor tissue


title: Oral cancer patient, Female 4

description: 4 vs. N(F)

tag: age

value: No

value: Positive


title: Evolved Clone_4N_329

description: Evolved Clone vs WT DNA

value: Evolved Clone


title: CTN5_rep1

description: Strain CTN5 harvested at 50% substrate conversion


title: CTN4_rep2

source_name: Strain CTN4 harvested at 50% substrate conversion


title: CTN5_rep2

source_name: Strain CTN5 harvested at 50% substrate conversion


title: Evolved Clone_4N_310

description: Evolved Clone vs WT DNA

value: Reference Control


title: CTN4_rep1


title: Evolved Clone_4N_337

description: Evolved Clone vs WT DNA


title: HCC439N, non-tumor tissue

value: Male


title: Oral cancer patient, Male 12

description: 12 vs. N(M)

source_name: Freshly operated oral cancer tissue of a male

value: MDSCC

source_name: Blood of normal male

value: male


title: Evolved Clone_4N_334

description: Evolved Clone vs WT DNA

source_name: Evolved Clone_4N


title: Evolved Clone_4N_302

description: Evolved Clone vs WT DNA

source_name: Reference Control_PY3295


title: HCC437T, tumor tissue


title: Oral cancer patient, Male 11

description: 11 vs. N(M)


title: Evolved Clone_4N_318

description: Evolved Clone vs WT DNA


title: HCC437N, non-tumor tissue


title: Oral cancer patient, Male 10

description: 10 vs. N(M)


title: HCC431T, tumor tissue


title: HCC431N, non-tumor tissue


title: Evolved Clone_4N_338

description: Evolved Clone vs WT DNA


title: Evolved Clone_4N_335

description: Evolved Clone vs WT DNA


title: HCC428T, tumor tissue


title: Oral cancer patient, Male 7

description: 7 vs. N(M)


title: Evolved Clone_4N_301

description: Evolved Clone vs WT DNA


title: Oral cancer patient, Male 8

description: 8 vs. N(M)


title: Tfh from TONS 5

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

country: France

institute: INSERM UMR1236

description: Gene expression from TONS Tfh

hyb_protocol: Following fragmentation, cARN were hybridized for 16h at 45°C and 60rpm on GeneChip Human U133Plus2 arrays

scan_protocol: not provided

data_processing: The data were normalized by the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO).

source_name: Ex-vivo Tfh

label_protocol: Biotinylated cRNA were amplified according to the small sample labelling protocol

extract_protocol: RNA was extracted using ARN/ADN kit (Qiagen, Valencia, CA)

tag: pathology

value: Tonsillectomy (non-malignant)

value: tonsils

tag: treatment

value: Untreated

tag: cell type

value: T follicular helper cells (Tfh)


title: Tfh from TONS 7

description: Gene expression from TONS Tfh

tag: tissue


title: Evolved Clone_2N_212

description: Evolved Clone vs WT DNA

source_name: Evolved Clone_2N


title: HCC424T, tumor tissue

source_name: tumor tissue, hepatocellular carcinoma

tag: gender


title: HCC428N, non-tumor tissue


title: Tfh from TONS 4

description: Gene expression from TONS Tfh


title: Tfh from TONS 6

description: Gene expression from TONS Tfh


title: Tfh from TONS 3

description: Gene expression from TONS Tfh


title: Tfh from TONS 2

description: Gene expression from TONS Tfh


title: Oral cancer patient, Male 6

description: 6 vs. N(M)

value: oral cancer

value: Freshly operated oral cancer tissue

value: Yes

value: PDSCC


title: Tfh from TONS 1

description: Gene expression from TONS Tfh


title: Oral cancer patient, Male 2

description: 2 vs. N(M)

value: Not known

value: Not Known

value: ASCC

value: normal control

value: blood


title: Evolved Clone_2N_218

description: Evolved Clone vs WT DNA

value: Evolved Clone

value: Reference Control


title: Oral cancer patient, Male 1

description: 1 vs. N(M)

value: Negative

value: WDSCC

value: Male


title: HCC424N, non-tumor tissue


title: Evolved Clone_2N_233

description: Evolved Clone vs WT DNA


title: Tfh from FL 7

description: Gene expression from FL Tfh

value: Follicular Lymphoma patient

value: lymph nodes


title: metastatic 30

city: Columbus

first: Amanda

middle: Ewart

last: Toland

state: OH

address: 460 W. 12th Ave

department: MVIMG

institute: The Ohio State University

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Hybridization reactions were performed with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies) following the manufacturer’s instructions

scan_protocol: For each assay, a high density scan (600 fields of view) was performed.

data_processing: We identified approximately 225 miRNAs expressed in these samples and performed statistical analysis for the top 100 expressed miRNAs.  Expression data for each sample was normalized to the entire miRNA dataset using the global sum through the nSolver software tool.  Paired T-tests compared non-metastatic primary tumors to primary tumors or metastases. A heatmap of the top 100 expressed miRNAs was generated using Cluster 3.0 was able to cluster the majority of metastatic related tumors from non-metastatic cSCCs and normal tissues

source_name: metastatic 30

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies). Preparation of small RNA samples involves the ligation of a specific DNA tag onto the 3’ end of each mature miRNA. These tags are designed to normalize the Tm’s of the miRNAs as well as to provide a unique identification for each miRNA species in the sample. Following the ligation reaction, excess tags and bridges were removed,

extract_protocol: Ambion RecoverAll

value: normal skin


title: HCC422T, tumor tissue


title: Oral cancer patient, Male 5

description: 5 vs. N(M)

value: oral cancer

value: Positive

value: WDMDYS

value: male


title: metastatic 29

source_name: metastatic 29


title: Oral cancer patient, Male 3

description: 3 vs. N(M)

value: Freshly operated oral cancer tissue

value: Yes

value: MDSCC


title: HCC422N, non-tumor tissue

source_name: adjacent non-tumor tissue, hepatocellular carcinoma


title: HCC439T, tumor tissue


title: Tfh from FL 6

description: Gene expression from FL Tfh

value: Untreated

value: T follicular helper cells (Tfh)


title: Evolved Clone_2N_228

description: Evolved Clone vs WT DNA

value: Evolved Clone


title: HCC1031T, tumor tissue


title: HCC1032N, non-tumor tissue


title: HCC1029T, tumor tissue


title: HCC1031N, non-tumor tissue


title: HCC1032T, tumor tissue


title: HCC1029N, non-tumor tissue


title: Evolved Clone_2N_230

description: Evolved Clone vs WT DNA

value: Reference Control


title: metastatic 23

source_name: metastatic 23


title: metastatic 24

source_name: metastatic 24

value: primary tumor


title: metastatic 26

source_name: metastatic 26


title: metastatic 25

source_name: metastatic 25

value: metastatic tumor


title: metastatic 27

source_name: metastatic 27


title: metastatic 28

source_name: metastatic 28


title: Evolved Clone_2N_201

description: Evolved Clone vs WT DNA


title: Evolved Clone_2N_232

description: Evolved Clone vs WT DNA


title: Tfh from FL 4

description: Gene expression from FL Tfh


title: CTN5_techrep1

source_name: Strain CTN5 harvested at 50% substrate conversion


title: HCC1027T, tumor tissue

value: Male


title: HCC1027N, non-tumor tissue


title: HCC1024T, tumor tissue


title: Tfh from FL 5

description: Gene expression from FL Tfh

value: Follicular Lymphoma patient


title: Evolved Clone_1N_114

description: Evolved Clone vs WT DNA

source_name: Evolved Clone_1N


title: Evolved Clone_1N_123

description: Evolved Clone vs WT DNA


title: Tfh from FL 1

description: Gene expression from FL Tfh

value: lymph nodes


title: metastatic 21

source_name: metastatic 21


title: metastatic 20

source_name: metastatic 20

value: normal skin


title: non-metastatic 18

source_name: non-metastatic 18


title: metastatic 22

source_name: metastatic 22


title: Evolved Clone_2N_217

description: Evolved Clone vs WT DNA

source_name: Evolved Clone_2N

source_name: Reference Control_PY3295


title: non-metastatic 17

source_name: non-metastatic 17


title: Evolved Clone_1N_113

description: Evolved Clone vs WT DNA


title: Evolved Clone_1N_131

description: Evolved Clone vs WT DNA


title: Tfh from FL 3

description: Gene expression from FL Tfh

source_name: Ex-vivo Tfh


title: non-metastatic 16

source_name: non-metastatic 16


title: Evolved Clone_1N_110

description: Evolved Clone vs WT DNA


title: metastatic 19

source_name: metastatic 19


title: Muse_99_VALIDATION_Myocardial Infarction

city: La Jolla

first: Eri

last: Kramer

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: The amplified cDNA targets were hybridized to Affymetrix human U133 Plus 2.0 array following protocols as suggested by the supplier (Affymetrix, Santa Clara, CA).

scan_protocol: Following hybridization, arrays were washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner from which data was extracted using the Affymetrix Expression Console

data_processing: Data were processessed using the RMA normalization method, including background and quantile normalization.

source_name: CD146+ Circulating Endothelial Cells

label_protocol: Purified cDNA underwent a two-step fragmentation and labeling process using the Encore Biotin Module (NuGEN).

growth_protocol: Arterial blood was collected from AMI patients into both EDTA containing (Becton Dickinson, Franklin Lakes, NJ, USA) and CellSave (Veridex, Raritan, NJ, USA) tubes in the cardiac catheterization laboratory following the placement of an arterial sheath prior to the introduction of any guide wires or coronary catheters.  The samples were maintained at room temperature and processed within 36 hours of collection.

extract_protocol: Enriched CEC‑derived RNA was isolated using Trizol Reagent (Life Technologies, Carlsbad, CA) according to the manufacturer's instructions

treatment_protocol: The CellTracks®AutoPrep® system was used in conjunction with the CellSearch®CEC kit and the CellSearch®profile kit (Veridex) to immunomagnetically enrich and enumerate CD146+ CECs as previously described 12. The enriched CEC samples were analyzed with the CellTracks®Analyzer II and the number of CECs in the sample determined. For CEC microarray profiling, the AutoPrep tube with the sample from the CellTracks®AutoPrep® system was removed and placed into the MagCellect Magnet for 10-min incubation. With the tube still in the MagCellect Magnet, the supernatant liquid was aspirated without disrupting the ferrofluid bound cells from which RNA was subsequently isolated.  For whole blood samples in EDTA tubes leukocytes and cellular debris was obtained for RNA isolation following RBC lysis with Erythrocyte Lysis Buffer (Qiagen, Valencia, CA).

value: Myocardial Infarction

tag: cohort

value: VALIDATION

value: CD146+ Circulating Endothelial Cells


title: Muse_95_VALIDATION_Myocardial Infarction


title: Muse_97_VALIDATION_Myocardial Infarction


title: non-metastatic 15

source_name: non-metastatic 15


title: Muse_93_VALIDATION_Myocardial Infarction


title: HCC1024N, non-tumor tissue

source_name: adjacent non-tumor tissue, hepatocellular carcinoma


title: Evolved Clone_1N_104

description: Evolved Clone vs WT DNA


title: Ancestor_PY6045

description: Ancestor vs WT DNA

value: Ancestor


title: Evolved Clone_1N_107

description: Evolved Clone vs WT DNA


title: Tfh from FL 2

description: Gene expression from FL Tfh


title: Evolved Clone_1N_132

description: Evolved Clone vs WT DNA


title: HCC1023T, tumor tissue

source_name: tumor tissue, hepatocellular carcinoma


title: HCC1021T, tumor tissue

value: Female


title: HCC1023N, non-tumor tissue


title: Muse_96_VALIDATION_Myocardial Infarction


title: Ancestor_PY6032

description: Ancestor vs WT DNA


title: Ancestor_PY6031

description: Ancestor vs WT DNA


title: HCC1021N, non-tumor tissue


title: Muse_94_VALIDATION_Myocardial Infarction


title: Muse_98_VALIDATION_Myocardial Infarction


title: Muse_91_VALIDATION_Myocardial Infarction


title: metastatic 17

source_name: metastatic 17


title: Ancestor_PY6022

description: Ancestor vs WT DNA


title: non-metastatic 13

source_name: non-metastatic 13


title: HCC1020N, non-tumor tissue


title: Ancestor_PY6040

description: Ancestor vs WT DNA


title: Muse_92_VALIDATION_Myocardial Infarction


title: HCC1020T, tumor tissue


title: metastatic 16

source_name: metastatic 16


title: Muse_90_VALIDATION_Myocardial Infarction


title: metastatic 18

source_name: metastatic 18


title: non-metastatic 14

source_name: non-metastatic 14


title: HCC1019N, non-tumor tissue


title: HCC1019T, tumor tissue


title: Ancestor_PY6014

description: Ancestor vs WT DNA


title: Ancestor_PY5999

description: Ancestor vs WT DNA


title: Muse_87_VALIDATION_Myocardial Infarction


title: HCC1016T, tumor tissue


title: Ancestor_PY6008

description: Ancestor vs WT DNA


title: Muse_89_VALIDATION_Myocardial Infarction


title: Muse_88_VALIDATION_Myocardial Infarction


title: Muse_86_VALIDATION_Control

value: Control


title: Reference Control_PY3295

description: WT DNA vs WT DNA


title: Ancestor_PY5998

description: Ancestor vs WT DNA


title: Ancestor_PY6006

description: Ancestor vs WT DNA


title: Muse_85_VALIDATION_Control


title: Muse_84_VALIDATION_Control


title: non-metastatic 12

source_name: non-metastatic 12


title: HCC1016N, non-tumor tissue


title: metastatic 15

source_name: metastatic 15


title: non-metastatic 11

source_name: non-metastatic 11


title: HCC1014T, tumor tissue


title: metastatic 14

source_name: metastatic 14


title: HCC1014N, non-tumor tissue


title: metastatic 13

source_name: metastatic 13


title: HCC1007N, non-tumor tissue


title: non-metastatic 10

source_name: non-metastatic 10


title: HCC1007T, tumor tissue


title: metastatic 12

source_name: metastatic 12


title: non-metastatic 09

source_name: non-metastatic 09


title: Muse_83_VALIDATION_Control

source_name: CD146+ Circulating Endothelial Cells


title: HCC1004T, tumor tissue


title: HCC1004N, non-tumor tissue


title: HCC1003T, tumor tissue


title: metastatic 11

source_name: metastatic 11


title: Muse_82_VALIDATION_Control


title: line #4

city: Matsuyama

first: Masamichi

last: Nishiguchi

address: 3-5-7 Tarumi

country: Japan

institute: Ehime University

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: the Agilent G2505C DNA microarray scanner.

data_processing: Signal intensities were extracted by Feature Extraction software version 10.5.1.1

organism: Oryza sativa

source_name: leaf

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3- or Cy5-label

growth_protocol: Rice seedlings were transferred to small plastic boxes containing commercial soil for rice cultivation (Iseki, Matsuyama, Japan) and placed in growth chambers (temperature ranged between 23 and 26 ºC under 16 h daylight and 8 h dark)

extract_protocol: Total RNA extracted using Sepazol following manufacturer's instructions

tag: cultivar

value: Nipponbare

tag: developmental stage

value: 4 leaf stage

value: leaf

tag: genotype

value: OsHAP2E overexpression


title: Snai1 knockout organoid 24 hr replicate 3

city: Parkville

first: Gary

last: Hime

state: Victoria

address: Grattan Street

department: Anatomy and Neuroscience

country: Australia

institute: University of Melbourne

description: replicate 3

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard illumina scanning protocol

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

source_name: Mouse small intestinal organoid

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyser.

treatment_protocol: Organoids were treated with 0.5µM Tamoxifen for 24 hours prior to harvesting

value: Villin-Cre, Snai1fl/fl


title: Muse_80_VALIDATION_Control


title: Snai1 knockout organoid 24 hr replicate 1

description: replicate 1


title: metastatic 10

source_name: metastatic 10


title: HCC1003N, non-tumor tissue

source_name: adjacent non-tumor tissue, hepatocellular carcinoma


title: Snai1 knockout organoid 24 hr replicate 2

description: replicate 2


title: Muse_78_VALIDATION_Control


title: Muse_81_VALIDATION_Control


title: Muse_79_VALIDATION_Control


title: Control organoid 24hr replicate 3

description: replicate 3

value: Villin-Cre


title: Muse_77_VALIDATION_Control


title: metastatic 09

source_name: metastatic 09

value: primary tumor


title: non-metastatic 07

source_name: non-metastatic 07


title: non-metastatic 08

source_name: non-metastatic 08


title: non-metastatic 06

source_name: non-metastatic 06


title: HCC1000N, non-tumor tissue

value: Male


title: HCC1000T, tumor tissue

source_name: tumor tissue, hepatocellular carcinoma


title: Muse_76_VALIDATION_Control


title: jej Ex4 5h rep4

city: Toronto

first: Daniel

middle: J

last: Drucker

state: Ont

address: 600 University Ave TCP

department: LTRI

country: Canada

institute: Mount Sinai Hospital

hyb_protocol: The BeadChips were hybridized with Illumina standard protocol at 58°C, with rotation speed 5 for 18 hours.

scan_protocol: The BeadChips were washed and stained as per Illumina protocol and scanned on the iScan (Illumina)

data_processing: Data was normalized in GeneSpring v. 12.6.1 using quantile normalization and log2 transformation.

source_name: jejunum

label_protocol: RNA was labelled using Illumina TotalPrep-96 RNA Amplification kit with 1500 ng of cRNA generated from each.

growth_protocol: C57BL/6 male mice from The Jackson Laboratory (Bar Harbor, ME), were maintained on a standard diet and a 12h light – 12h dark cycle for 2 weeks at the Toronto Centre for Phenogenomics animal facility prior to use.

extract_protocol: RNA was extracted from mucosal scrapings taken from a 2 cm piece of jejunum using Trizol reagent according to the manufacturer's instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: non-fasted C57BL/6 mice (11-12 weeks-old) were injected with a single dose of Ex-4 (10 nmol/kg, ip) or KGF (1 mg/kg) and sacrificed 1, 5 or 20 h later by CO2 inhalation.

tag: agent

value: Ex-4 (10 nmol/kg, ip)

tag: time point

value: male


title: Control organoid 24hr replicate 2

description: replicate 2


title: Blnc1 shRNA expressing brown adipocytes, biological rep2

description:
Gene expression data from Blnc1 shRNA expressing brown adipocyte, sample 2
Scramble and Blnc1 shRNA expressing brown adipocytes were differentiated for 6 days.

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on MG-430 PM Strip Arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Strip Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.15.1. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Blnc1 shRNA expressing brown adipocytes

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3' IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

treatment_protocol: Brown adipocytes lysate were harvested after differentiation.

value: brown adipocyte

tag: shRNA


title: line#18


title: Muse_75_VALIDATION_Control


title: jej PBS 5h rep4

value: PBS


title: Muse_73_VALIDATION_Myocardial Infarction

value: Myocardial Infarction

value: VALIDATION


title: Blnc1 shRNA expressing brown adipocytes, biological rep1

description:
Gene expression data from Blnc1 shRNA expressing brown adipocyte, sample 1
Scramble and Blnc1 shRNA expressing brown adipocytes were differentiated for 6 days.


title: metastatic 07

source_name: metastatic 07

value: metastatic tumor


title: jej Fgf7 1h rep3

value: KGF/Fgf7 (1 mg/kg, ip)


title: Muse_71_VALIDATION_Myocardial Infarction

value: CD146+ Circulating Endothelial Cells


title: Muse_69_VALIDATION_Myocardial Infarction


title: jej Fgf7 20h rep3


title: Control organoid 24hr replicate 1

description: replicate 1


title: metastatic 06

source_name: metastatic 06


title: Scramble expressing brown adipocytes, biological rep1

description:
Gene expression data from scramble expressing brown adipocyte, sample 1
Scramble and Blnc1 shRNA expressing brown adipocytes were differentiated for 6 days.

source_name: Scramble expressing brown adipocytes

value: Scramble


title: Scramble expressing brown adipocytes, biological rep2

description:
Gene expression data from scramble expressing brown adipocyte, sample 2
Scramble and Blnc1 shRNA expressing brown adipocytes were differentiated for 6 days.


title: Muse_72_VALIDATION_Myocardial Infarction


title: jej Ex4 20h rep3


title: metastatic 05

source_name: metastatic 05


title: Muse_70_VALIDATION_Myocardial Infarction

source_name: CD146+ Circulating Endothelial Cells


title: metastatic 04

source_name: metastatic 04

value: normal skin


title: Muse_74_VALIDATION_Control

value: Control


title: jej PBS 20h rep3


title: non-metastatic 05

source_name: non-metastatic 05


title: Blnc1 expressing brown adipocytes, biological rep2

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

description: Gene expression data from Blnc1 expressing brown adipocyte, sample 2

source_name: Blnc1 expressing brown adipocytes

treatment_protocol: Brown adipocytes differentiated from preadipocytes expressing vector or Blnc1

value: wild type

tag: expression


title: Muse_68_VALIDATION_Myocardial Infarction


title: jej Fgf7 5h rep4


title: jej Fgf7 5h rep3


title: Muse_66_VALIDATION_Myocardial Infarction


title: jej Ex4 5h rep3


title: metastatic 03

source_name: metastatic 03


title: ZF overexpression, biological rep2

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

description: Gene expression data from ZF(AT4G29190)-overexpressing plants at 22°C

hyb_protocol: Hybridization and washing were carried out according to the Gene Chip manufacturer's protocol (Affymetrix)

scan_protocol: Scan protocols were carried out according to the Gene Chip manufacturer's protocol (Affymetrix)

data_processing: The data were analyzed with LIMMA package of Bioconductor using GCRMA normalization procedure.

organism: Arabidopsis thaliana

label_protocol: RNA was amplified and biotinylated using a MessageAmp kit (Ambion) according to the manufacturer's protocol

growth_protocol: Plants were grown at 22°C under sterile conditions on solid agar medium which contained Gamborg's B5 medium (Caisson Laboratories) without sucrose and 0.8 % Phytoblend for 12 days at ~100 µmol m–2 s–1 constant light.

extract_protocol: RNA was extracted using the RNeasy plant mini kit (Qiagen)

treatment_protocol: For cold treatment, plants were treated at 4°C under continuous light at ~30 µmol m–2 s–1 for 24-h

value: entire aerial part


title: metastatic 02

source_name: metastatic 02


title: Blnc1 expressing brown adipocytes, biological rep1

description: Gene expression data from Blnc1 expressing brown adipocyte, sample 1


title: jej PBS 5h rep3


title: Muse_67_VALIDATION_Myocardial Infarction


title: Muse_64_VALIDATION_Myocardial Infarction


title: non-metastatic 04

source_name: non-metastatic 04


title: Muse_62_VALIDATION_Myocardial Infarction


title: Muse_63_VALIDATION_Myocardial Infarction


title: Muse_65_VALIDATION_Myocardial Infarction


title: ZF overexpression, biological rep1

source_name: ZF(AT4G29190)-overexpressing plants at 22°C


title: jej Ex4 5h rep2


title: metastatic 01

source_name: metastatic 01


title: jej Fgf7 1h rep2


title: Vector expressing brown adipocytes, biological rep1

description: Gene expression data from vector expressing brown adipocyte, sample 1

source_name: Vector expressing brown adipocytes

value: vector


title: jej Ex4 1h rep3


title: ZAT10 overexpression, biological rep2

description: Gene expression data from ZAT10 (AT1G27730)-overexpressing plants at 22°C


title: non-metastatic 02

source_name: non-metastatic 02

value: primary tumor


title: non-metastatic 03

source_name: non-metastatic 03


title: RAV1 overexpression, biological rep2

description: Gene expression data from RAV1 (AT1G13260)-overexpressing plants at 22°C


title: non-metastatic 01

source_name: non-metastatic 01


title: jej Fgf7 1h rep1

source_name: jejunum


title: RAV1 overexpression, biological rep1

source_name: RAV1 (AT1G13260)-overexpressing plants at 22°C


title: Vector expressing brown adipocytes, biological rep2

description: Gene expression data from vector expressing brown adipocyte, sample 2


title: Muse_60_VALIDATION_Myocardial Infarction


title: MYB7 overexpression, biological rep2

description: Gene expression data from MYB73 (AT4G37260)-overexpressing plants at 22°C


title: jej PBS 1h rep3


title: Muse_58_VALIDATION_Control


title: U118 Adar E/A vs Adar Rep.3

city: Roma

first: Carlo

last: Presutti

state: Italia

address: Via dei Sardi 70

department: Biology and Biotechnology

country: Italy

institute: University Sapienza

description: Biological replicate 3 of 3

hyb_protocol: Labeled RNA was added to arrays and hybridized in Agilent SureHyb-enabled hybridization chambers

scan_protocol: Scanned on a Perkin Elmer ScanArray  GX plus.

data_processing:
Images were quantified using Axon GenePix Software
Single spots have been selected, on the base of intensity and appereance. Spikes values have been subtracted and resulting values were normalized for internal controls, mostly on U6 values. In this way the initial number of miRNAs examinated was reduced to the miRNAs described in the study.  The data matrix is available on the series record and contains normalized log2 ratio (Cy5/Cy3) representing inactive vs active Adar2.

source_name: U118 Glioblastoma Cells

label_protocol: 2 µg of total RNA were labeled according to Exiqon Protocol

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

tag: cell line

tag: adar2 status

value: inactive

value: active


title: U118 Adar E/A vs Adar Rep.2

description: Biological replicate 2 of 3


title: U118 Adar E/A vs Adar Rep.1

description: Biological replicate 1 of 3


title: Muse_56_VALIDATION_Control


title: jej Ex4 20h rep2

value: Ex-4 (10 nmol/kg, ip)

tag: strain

value: male


title: HSFC overexpression, biological rep2

description: Gene expression data from HSFC1 (AT3G24520)-overexpressing plants at 22°C


title: jej PBS 1h rep2

value: PBS


title: Muse_59_VALIDATION_Myocardial Infarction

value: Myocardial Infarction


title: ZAT10 overexpression, biological rep1

source_name: ZAT10 (AT1G27730)-overexpressing plants at 22°C


title: Muse_61_VALIDATION_Myocardial Infarction

source_name: CD146+ Circulating Endothelial Cells

value: VALIDATION


title: jej Fgf7 5h rep2


title: Muse_57_VALIDATION_Control


title: metastatic 08

source_name: metastatic 08


title: jej PBS 20h rep2


title: MYB4 overexpression, biological rep1

description: Gene expression data from MYB44 (AT5G67300)-overexpressing plants at 22°C


title: jej PBS 5h rep2


title: MYB7 overexpression, biological rep1

source_name: MYB73 (AT4G37260)-overexpressing plants at 22°C


title: jej Fgf7 5h rep1


title: ERF5 overexpression, biological rep2

description: Gene expression data from ERF5 (AT5G47230)-overexpressing plants at 22°C


title: HSFC overexpression, biological rep1

source_name: HSFC1 (AT3G24520)-overexpressing plants at 22°C


title: Muse_55_VALIDATION_Control


title: MYB4 overexpression, biological rep2

source_name: MYB44 (AT5G67300)-overexpressing plants at 22°C


title: ERF5 overexpression, biological rep1

source_name: ERF5 (AT5G47230)-overexpressing plants at 22°C


title: Muse_53_VALIDATION_Control


title: Muse_54_VALIDATION_Control


title: Muse_52_VALIDATION_Control


title: jej Ex4 5h rep1


title: Muse_51_VALIDATION_Control


title: jej PBS 5h rep1


title: DEAR overexpression, biological rep2

description: Gene expression data from DEAR1 (AT3G50260)-overexpressing plants at 22°C


title: Muse_50_VALIDATION_Control


title: jej Ex4 1h rep1


title: jej Ex4 1h rep2


title: Wt1_siRNA_Rep3_Mouse430_2_Signal

first: Jordan

last: Kreidberg

address: 300 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

description: Gene expression data from LB-22 cells transfected with Wt1 siRNA

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: Data were normalized using Microarray Suite version 5.0 (MAS 5.0) with default analysis settings.

label: Biotin

source_name: LB-22 cells

label_protocol: RNA was processed for Affymetrix 430.2 arrays as per manufacturer's instructions.

growth_protocol: Cells were expanded at 33 °C in DMEM-F12 50/50 media supplemented with L-Glutamine, with 10 percent fetal bovine serum, 25 ng / ml prostaglandin E1, 2 ng/ml heparan-stabilized basic FGF, 100 nM Hydrocortisone, 2 nM triiodothyronine, 5 µg/ml insulin, 5 µg/ml transferrin, and 10 U/ml Interferon gamma. Upon transfection cells were transferred to 37°C and grown in the absence of Interferon.

extract_protocol: Trizol followed by QIAGEN RNeasy column purification according to manufacturer's protocols.

treatment_protocol: Cells were transfected with 25 pmol WT1 or control siRNA in 25µl Lipofectamine 2000, respectively, for 6 hours and grown for 48 hours.

tag: sirna


title: Wt1_siRNA_Rep2_Mouse430_2_Signal


title: jej PBS 1h rep1


title: Control_siRNA_Rep4_Mouse430_2_Signal

description: Gene expression data from LB-22 cells transfected with control siRNA

value: scramble Control


title: DEAR overexpression, biological rep1

source_name: DEAR1 (AT3G50260)-overexpressing plants at 22°C


title: Wt1_siRNA_Rep4_Mouse430_2_Signal


title: jej Fgf7 20h rep2

value: KGF/Fgf7 (1 mg/kg, ip)


title: Wt1_siRNA_Rep1_Mouse430_2_Signal


title: CZF1 overexpression, biological rep2

description: Gene expression data from CZF1 (AT2G40140)-overexpressing plants at 22°C


title: jej Fgf7 20h rep1


title: Muse_48_VALIDATION_Control

value: CD146+ Circulating Endothelial Cells


title: jej Ex4 20h rep1


title: Muse_49_VALIDATION_Control


title: jej PBS 20h rep1


title: Control_siRNA_Rep2_Mouse430_2_Signal


title: Control_siRNA_Rep3_Mouse430_2_Signal


title: Muse_47_VALIDATION_Control


title: Muse_46_VALIDATION_Control


title: Control_siRNA_Rep1_Mouse430_2_Signal


title: CRF3 overexpression, biological rep2

description: Gene expression data from CRF3 (AT5G53290)-overexpressing plants at 22°C


title: CRF3 overexpression, biological rep1

source_name: CRF3 (AT5G53290)-overexpressing plants at 22°C


title: CRF2 overexpression, biological rep2

description: Gene expression data from CRF2 (AT4G23750)-overexpressing plants at 22°C


title: CRF2 overexpression, biological rep1

source_name: CRF2 (AT4G23750)-overexpressing plants at 22°C


title: Embryonic_ventral_midbrain-Lmx1a_negative-rep2

city: Melbourne

first: Christopher

last: Bye

address: University of Melbourne

institute: The Florey Institute of Neuroscience and Mental Health

description:
Sample name: Lmx1a-GFP_Neg_2
Gene expression data from reference non-dopaminergic progenitor population

hyb_protocol: Affymetrix Mouse Genome 430 2.0 Arrays were hybridized overnight and washed/stained using an Affymetrix Fluidics according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip scanner 3000 according to the manufacture's instructions.

data_processing: The data was normalized using the MAS5 algorithm (Affymetrix® Microarray Suite version 5.0) and statistical  analysis carried out with the limma package using the R (version 2.14.2) statistical computing environment.

source_name: FACS sorted Lmx1a-GFP negative E12.5 ventral mesencephalon

label_protocol: High Yield RNA Transcript Labeling Kit (Qiagen). Biotinylated cRNA was prepared following the manufacturers instructions.

growth_protocol: Animals were housed under a 12h light/dark cycle with ad libitum access to food and water

extract_protocol: RNeasy Micro Kit (Qiagen). Total RNA was extracted following the manufacturer’s instructions, including DNase digestion.

treatment_protocol: FACS was used to isolate GFP positive or negative cell fractions from the ventral mesencephalon of transgenic reporter mice at embyonic day 12.5

value: ventral mesencephalon

tag: age

tag: genotype/variation

value: non-dopaminergic progenitor population


title: Muse_45_VALIDATION_Control

value: Control

tag: cell type


title: Muse_43_DISCOVERY_Control

value: DISCOVERY


title: Embryonic_ventral_midbrain-Ngn2_positive-rep2

description:
Sample name: Ngn2-GFP_Pos_2
Gene expression data from midbrain dopaminergic progenitors

source_name: FACS sorted Ngn2-GFP positive E12.5 ventral mesencephalon

tag: tissue

value: midbrain dopaminergic progenitors


title: Embryonic_ventral_midbrain-Lmx1a_negative-rep3

description:
Sample name: Lmx1a-GFP_Neg_3
Gene expression data from reference non-dopaminergic progenitor population


title: Embryonic_ventral_midbrain-Lmx1a_negative-rep1

description:
Sample name: Lmx1a-GFP_Neg_1
Gene expression data from reference non-dopaminergic progenitor population


title: Col-0 WT, biological rep2

description: Gene expression data from Arabidopsis thaliana Col-0 WT at 22°C, which was used as control for transgenic plants

value: entire aerial part


title: Embryonic_ventral_midbrain-Ngn2_positive-rep3

description:
Sample name: Ngn2-GFP_Pos_3
Gene expression data from midbrain dopaminergic progenitors


title: Muse_41_DISCOVERY_Control


title: Muse_42_DISCOVERY_Control


title: C2C12_shPIP4K_KKTAF3_ETOP_2

city: Southampton

first: nullin

last: divecha

address: Highfield Campus

department: Biological Sciences

institute: University of southampton

description: C2C12 cells depleted of endogenous TAF3, rescued with  murine KK-TAF3 and then depleted of PIP4K2B and treated with etoposide for 7 hours

hyb_protocol: Fragmented and labeled cDNA was hybridised to Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (MoGene-1_0-st-v1) according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual. Hybridized arrays were washed using the Affymetrix GeneChip Fluidics Station 450 using protocol FS450_0007

scan_protocol: Arrays were scanned using the Affymetrix GeneChip scanner 3000 with AGCC software.

data_processing: processed using the Affymetrix Expression Console software (RMA-Sketch)

source_name: C2C12 myoblast cells treated with etoposide for 7 hours

label_protocol: 100 ng of RNA was amplified using the Ambion WT Expression Kit For Affymetrix GeneChip Whole Transcript (WT) Expression Arrays, and fragmented and labelled using the GeneChip WT Terminal Labeling and Hybridization Kit. Affymetrix PolyA controls were included at the same concentration as the sample.

growth_protocol: C2C12 cells modified as indicated were grown to 80% confluency in Hams F12 medium containing 10%FCS

extract_protocol: RNA was extracted using the RNAeasy Kit

treatment_protocol: Cells were either differentiated by switching into Hams F12 medium with 2%horse serum or treated with etoposide (10uM) for seven hours.

tag: treatment

value: etoposide for 7 hours


title: CZF1 overexpression, biological rep1

source_name: CZF1 (AT2G40140)-overexpressing plants at 22°C


title: Muse_39_DISCOVERY_Control

tag: cohort


title: Muse_40_DISCOVERY_Control


title: C2C12_shPIP4K_WTTAF3_ETOP_1

description: C2C12 cells depleted of endogenous TAF3, rescued with WT murine TAF3 and then depleted of PIP4K2B and treated with etoposide for 7 hours


title: C2C12_shPIP4K_KKTAF3_ETOP_3

value: depleted of endogenous TAF3, rescued with murine KK-TAF3 and then depleted of PIP4K2B


title: Col-0 WT 24h cold, biological rep1

description: Gene expression data from Arabidopsis thaliana Col-0 WT at 4°C for 24 hrs

source_name: Col-0 WT at 4°C for 24 hrs


title: C2C12_shPIP4K_KKTAF3_ETOP_1


title: Muse_38_DISCOVERY_Control


title: Col-0 WT warm, biological rep2

description: Gene expression data from Arabidopsis thaliana Col-0 WT at 22°C

source_name: Col-0 WT at 22°C


title: C2C12_shPIP4K_WTTAF3_ETOP_2

value: depleted of endogenous TAF3, rescued with WT murine TAF3 and then depleted of PIP4K2B


title: Muse_44_VALIDATION_Control


title: Col-0 WT 24h cold, biological rep2


title: Col-0 WT warm, biological rep1


title: C2C12_WTTAF3_ETOP_2

description: C2C12 cells depleted of endogenous TAF3, rescued with  murine wild type-TAF3 and treated with etoposide for 7 hours


title: Muse_37_DISCOVERY_Control


title: Wildtype 24h cold, biological rep4

description: Arabidopsis WT WS-2 grown at 22⁰C on agar plates under continuous light for 11 d followed by 24 h at 4⁰C

data_processing: The data were analyzed with LIMMA package of Bioconductor using GC-RMA normalization procedure.

source_name: Arabidopsis WS-2 grown at 22⁰C followed by 24h at 4⁰C

growth_protocol: Plants were grown on Gamborg's B-5 medium solidified with agar at 22⁰C under constant light at ~100 μmol m-2 sec-1 for 11 d

treatment_protocol: Cold treatment was for 24 h at 4⁰C under constant light of ~35 µmol m-2 sec-1


title: Wildtype 24h cold, biological rep2


title: Wildtype 24h cold, biological rep3


title: Muse_36_DISCOVERY_Control

source_name: CD146+ Circulating Endothelial Cells


title: Col-0 WT, biological rep1

source_name: Col-0 WT at 22°C, which was used as control for transgenic plants


title: C2C12_WTTAF3_diff2days_3

description: C2C12 cells depleted of endogenous TAF3, rescued with  murine wild type-TAF3 and differentiated for  2days

source_name: C2C12 myoblast cells differentiated for 2 days


title: C2C12_WTTAF3_ETOP_3

value: depleted of endogenous TAF3, rescued with murine wild type-TAF3


title: Embryonic_ventral_midbrain-Ngn2_positive-rep1

description:
Sample name: Ngn2-GFP_Pos_1
Gene expression data from midbrain dopaminergic progenitors


title: Wildtype 24h cold, biological rep1


title: C2C12_WTTAF3_ETOP_1


title: Muse_35_DISCOVERY_Control


title: Wildtype warm, biological rep3

description: Arabidopsis WT WS-2 grown at 22⁰C on agar plates under continuous light for 11 d

source_name: Arabidopsis WS-2 grown at 22⁰C


title: Wildtype warm, biological rep1


title: Muse_31_DISCOVERY_Myocardial Infarction


title: Muse_33_DISCOVERY_Myocardial Infarction


title: Wildtype warm, biological rep2


title: Muse_29_DISCOVERY_Myocardial Infarction


title: C2C12_shPIP4K_WTTAF3_ETOP_3


title: Wildtype warm, biological rep4


title: C2C12_WTTAF3_diff2days_2

value: depleted of endogenous TAF3, rescued with murine wild type-TAF3 and differentiated for 2days


title: Muse_34_DISCOVERY_Myocardial Infarction


title: Muse_32_DISCOVERY_Myocardial Infarction


title: C2C12_shPIP4K_KKTAF3_diff2days_3

description: C2C12 cells depleted of endogenous TAF3, rescued with  murine KK-TAF3 and then depleted of PIP4K2B and differentiated for  2days


title: Muse_28_DISCOVERY_Myocardial Infarction


title: C2C12_shPIP4K_KKTAF3_diff2days_2

value: depleted of endogenous TAF3, rescued with murine KK-TAF3 and then depleted of PIP4K2B and differentiated for 2days


title: Individual mouse sera  (B12, IgG Intensity)

city: Birmingham

first: Jennie

last: Hamilton

address: 1825 University Blvd.

institute: University of Alabama Birmingham

hyb_protocol: Peptide arrays were first blocked 60 min in Blocking Buffer for Near Infra Red Fluorescent Western blotting (Rockland Immunochemicals, Inc., Gilbertsville, PA).  The microarray was washed twice in PBS, pH 7.4 with 0.05% Tween 20 (PBS-T), and incubated for an additional 30 min in washing buffer.  The array was then incubated overnight at 4°C with mouse sera diluted 1:200 for anti-mouse IgG-specific analysis or 1:1000 for anti-mouse IgM-specific analysis (secondary Abs from Rockland Immunochemicals, Inc., Gilbertsville, PA).  After multiple washes in washing buffer, the microarrays were incubated for 30 min with the secondary antibody in PBS-T at room temperature.  After two additional washes in washing buffer, the microarrays were rinsed with ultrapure water and dried in a stream of air.

scan_protocol: LI-COR Odyssey Imaging System; scanning offset 1 mm, resolution 21 µm, scanning intensities of 5, 7  and 9 (main assays) and 5/7 (red/green, control assay)

data_processing: A software algorithm breaks down fluorescence intensities of each spot into raw, foreground and background signal, and calculates the standard deviation of foreground median intensities.

source_name: Individual mouse sera

label_protocol: The secondary antibodies used for all arrays were from Rockland Immunochemicals, Gilbertsville, PA.  They were conjugated to the DyLight dyes (DyLight680 or DyLight800) by the company.

extract_protocol: Sera were obtained from B6 and BXD2 mice by retro-orbital eye bleeding.  After separation from blood, sera were stored at -80°C.

value: 9 mo

tag: sample type

value: serum


title: C2C12_shPIP4K_KKTAF3_diff2days_1


title: Muse_30_DISCOVERY_Myocardial Infarction

value: Myocardial Infarction


title: Individual mouse sera  (B12, IgM Intensity)


title: Individual mouse sera  (B11, IgG Intensity)


title: C2C12_WTTAF3_diff2days_1


title: CBF2DN, 24h cold, biological rep3

description: CBF2Δc overexpressing line DN96 grown at 22⁰C on agar plates under continuous light for 11 d followed by 24h at 4⁰C

source_name: CBF2DN grown at 22⁰C followed by 24h at 4⁰C


title: Muse_26_DISCOVERY_Myocardial Infarction


title: CBF2DN, 24h cold, biological rep2

description: CBF2Δc overexpressing line DN89 grown at 22⁰C on agar plates under continuous light for 11 d followed by 24h at 4⁰C


title: CBF2DN, 24h cold, biological rep4


title: ovary_patient10_control

city: Tampere

first: Kristina

last: Veskimäe

address: PO Box 2000

department: Department of Obstetrics and Gynecology

country: Finland

institute: Tampere University Hospital

description: Has not been tested for BRCA1/2 mutation but have no personal or family history of ovarian or breast cancer therefore classified as mutation-negative.

hyb_protocol: A total of 5.5 µg of sscDNA was fragmented and hybridized to the GeneChip array (Affymetrix Human Gene 1.0 ST Array; Affymetrix, Santa Clara, CA, USA) in cartridge format during 17-hour incubation at 45 °C. Immediately following hybridization, the array was washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner (Affymetrix Human Gene 1.0 ST Array; Affymetrix, Santa Clara, CA, USA).

data_processing: All ovarian and fallopian tube samples were patient matched. GeneChip® signal intensity data were processed with robust multiarray analysis using re-mapped gene annotations from the Brainarray Custom CDF files (HuGene10stv1_Hs_ENSG, v.14.1.0) (Gentleman et al. 2004).  Additional gene information was extracted from EnsEMBL using BioMart and matching  was done via EnsEMBL gene names. Analysis was implemented in R using the simpleaffy, limma, BioMart and qvalue packages of the Bioconductor project (Durinck et al. 2005; Gentleman et al. 2004; Smyth 2004; Storey, Tibshirani 2003; Wilson, Miller 2005). The significance of differential expression was assessed using the empirical Bayes moderated paired t-statistics followed by p-value adjustment with FDR (false discovery rate) approach (Smyth 2004).  Arrays were quality weighted before statistical testing (Ritchie et al. 2006). Genes with FDR corrected p-values ≤ 0.05 were considered as differentially expressed. Quality of the data was assessed by checking quality values.

source_name: ovary

label_protocol: One hundred ng of total RNA was used in analyses of gene expression. The Ambion WT Expression Kit was used to generate purified sense-strand cDNA (with incorporated 2´-Deoxyuridine, 5´-Triphosphate, dUTP). Fifteen ug of cRNA was used for single-stranded cDNA-synthesis (sscDNA). DNA was labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Approximately 30 mg of unprocessed tissue (i.e. containing both epithelium and underlying stromal tissue) was homogenized (TissueRupter, Qiagen, Venlo, The Netherlands) and total RNA was then automatically extracted using the QIAcube instrument with RNeasy Fibrous Tissue Mini Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions.

treatment_protocol: Approximately 0.5 x 0.5 x 0.5cm sized tissue samples of distal fallopian tube and ovarian surface were collected from the surgery specimens and were immediately snap-frozen with liquid nitrogen and stored in -70°C .

tag: patient number

value: ovary

tag: history of breast cancer

value: No

tag: age at surgery


title: Individual mouse sera  (B11, IgM Intensity)


title: fallopian_tube_patient9_brca2

source_name: fallopian tube

value: fallopian tube

tag: brca2 mutation

value: Yes


title: CBF2DN, warm, biological rep4

description: CBF2Δc overexpressing line DN96 grown at 22⁰C on agar plates under continuous light for 11 d

source_name: CBF2DN grown at 22⁰C


title: CBF2DN, 24h cold, biological rep1


title: Individual mouse sera  (B10, IgG Intensity)

value: 5 mo


title: Muse_24_DISCOVERY_Myocardial Infarction

value: DISCOVERY

value: CD146+ Circulating Endothelial Cells


title: C2C12_shPIP4K_WTTAF3_diff2days_3

description: C2C12 cells depleted of endogenous TAF3, rescued with WT murine TAF3 and then depleted of PIP4K2B and differentiated for  2days


title: Muse_25_DISCOVERY_Myocardial Infarction


title: C2C12_shPIP4K_WTTAF3_diff2days_2

value: depleted of endogenous TAF3, rescued with WT murine TAF3 and then depleted of PIP4K2B and differentiated for 2days


title: Muse_23_DISCOVERY_Myocardial Infarction


title: Individual mouse sera  (B10, IgM Intensity)


title: Individual mouse sera  (B9, IgG Intensity)


title: Individual mouse sera  (B9, IgM Intensity)


title: ovary_patient8_brca1

tag: brca1 mutation


title: Individual mouse sera  (B8, IgG Intensity)

value: 2 mo


title: C2C12_shPIP4K_WTTAF3_diff2days_1


title: CBF3OX, biological rep4

description: CBF3 overexpressing line A30 grown at 22⁰C on agar plates under continuous light for 11 d

source_name: CBF3OX grown at 22⁰C

value: entire aerial part


title: fallopian_tube_patient8_brca1


title: fallopian_tube_patient7_brca1


title: Muse_22_DISCOVERY_Myocardial Infarction


title: CBF3OX, biological rep3


title: Individual mouse sera  (B8, IgM Intensity)


title: CBF2DN, warm, biological rep1

description: CBF2Δc overexpressing line DN89 grown at 22⁰C on agar plates under continuous light for 11 d


title: ovary_patient9_brca2


title: fallopian_tube_patient5_brca2


title: ovary_patient6_brca1


title: CBF2DN, warm, biological rep2


title: fallopian_tube_patient6_brca1


title: Muse_21_DISCOVERY_Myocardial Infarction


title: Muse_19_DISCOVERY_Myocardial Infarction


title: CBF3OX, biological rep1

description: CBF3 overexpressing line A28 grown at 22⁰C on agar plates under continuous light for 11 d


title: CBF3OX, biological rep2


title: CBF2DN, warm, biological rep3


title: Individual mouse sera  (B7, IgM Intensity)


title: Individual mouse sera  (B6, IgG Intensity)


title: CBF2OX, biological rep4

description: CBF2 overexpressing line E24 grown at 22⁰C on agar plates under continuous light for 11 d

source_name: CBF2OX grown at 22⁰C


title: ovary_patient5_brca2


title: Muse_17_DISCOVERY_Myocardial Infarction


title: Individual mouse sera  (B6, IgM Intensity)


title: CBF2OX, biological rep3


title: Muse_18_DISCOVERY_Myocardial Infarction


title: Individual mouse sera  (B7, IgG Intensity)


title: ovary_patient4_brca2

description: Has undergone prophylactic mastectomy.


title: Muse_20_DISCOVERY_Myocardial Infarction


title: CBF2OX, biological rep2

description: CBF2 overexpressing line E2 grown at 22⁰C on agar plates under continuous light for 11 d


title: fallopian_tube_patient3_brca1


title: Muse_14_DISCOVERY_Myocardial Infarction


title: Muse_16_DISCOVERY_Myocardial Infarction


title: Individual mouse sera  (B5, IgG Intensity)


title: CBF2OX, biological rep1


title: ovary_patient3_brca1


title: CBF1OX, biological rep4

description: CBF1 overexpressing line G39 grown at 22⁰C on agar plates under continuous light for 11 d

source_name: CBF1OX grown at 22⁰C


title: Muse_15_DISCOVERY_Myocardial Infarction


title: Muse_12_DISCOVERY_Control

value: Control


title: fallopian_tube_patient2_brca2

description: Daughter of patient number 2


title: Individual mouse sera  (B5, IgM Intensity)


title: Muse_13_DISCOVERY_Control


title: Individual mouse sera  (B4, IgM Intensity)


title: Individual mouse sera  (B4, IgG Intensity)


title: fallopian_tube_patient4_brca2

description: Has undergone prophylactic mastectomy.


title: Individual mouse sera  (B3, IgM Intensity)


title: CBF1OX, biological rep3


title: Individual mouse sera  (B2, IgG Intensity)


title: Individual mouse sera  (B3, IgG Intensity)


title: CBF1OX, biological rep1

description: CBF1 overexpressing line G5 grown at 22⁰C on agar plates under continuous light for 11 d


title: CBF1OX, biological rep2


title: Individual mouse sera  (B2, IgM Intensity)


title: ovary_patient2_brca2

description: Daughter of patient number 1


title: ovary_patient1_brca2

description: Mother of patient number 2


title: ovary_patient12_control


title: fallopian_tube_patient12_control


title: fallopian_tube_patient14_control


title: fallopian_tube_patient13_control


title: Muse_10_DISCOVERY_Control


title: Muse_6_DISCOVERY_Control


title: Muse_7_DISCOVERY_Control


title: Individual mouse sera  (B1, IgG Intensity)


title: Individual mouse sera  (B1, IgM Intensity)


title: Muse_5_DISCOVERY_Control


title: Muse_9_DISCOVERY_Control


title: Muse_11_DISCOVERY_Control


title: Muse_8_DISCOVERY_Control


title: Hansenula 0.5mM hydrogen peroxide 30 min rep4

city: daejeon

first: eun hye

last: kim

address: gwahangno 111

country: South Korea

institute: kribb

description: Transcriptome profiling of H. polymorpha in response to hydrgen perxoide exposure : 30min, dye swap

hyb_protocol: aminoallyl post DNA labeling kits (GeneChem Inc.) according to the manufacturer's instructions

scan_protocol: The hybridized slides were scanned with GenePix 4000B scanner (axon instruments)

data_processing: using GnenPixTM Pro 4.0(Axon) software, spot intensity was quantified for each channel and transferred to Microsoft Excel spreadsheet

organism: Ogataea angusta

source_name: Hansenula reference

label_protocol: The labeling target cDNAs was performed using aminoallyl post DNA labeling kits(GeneChem Inc.)

extract_protocol: Isolation of RNA, cDNA syntehsis were carried out as described in Oh et al., 2004. Oh,.K.S.,Kwon O.,Oh,Y.W.,Sohn,M.J.,Jung,S.,Kim Y.K,Kim M.-G., Rhee,S.K.,Gellissen,G.,and Kang,H.A(2004)

treatment_protocol: without treatment of hydrogen peroxide

value: Hansenula polymorpha Dl1-L

value: untreated

source_name: Hansenula expoure to 0.5mM hydrogen peroxide for 30min

growth_protocol: The cells were cultivated at 37 dgrees with shaking at 200rpm until reach the early exponential phase(OD600 equal to 0.6) at which 0.5mM hydrogen peroxid was added to culture flask and incubated for an extra period of 30min


title: Hansenula 0.5mM hydrogen peroxide 30 min rep3

growth_protocol: The cells were cultivated at 37 dgrees with shaking at 200rpm

treatment_protocol: Hansenula expoure to 0.5mM hydrogen peroxide for 30min


title: Hansenula 0.5mM hydrogen peroxide 30 min rep2

label_protocol: he labeling target cDNAs was performed using aminoallyl post DNA labeling kits(GeneChem Inc.)


title: ovary_patient11_control


title: Muse_1_DISCOVERY_Control


title: Muse_2_DISCOVERY_Control


title: Muse_3_DISCOVERY_Control


title: Muse_4_DISCOVERY_Control


title: Hansenula 0.5mM hydrogen peroxide 30 min rep1


title: Sample 6_TC25.37

city: Hannover

first: Doris

last: Steinemann

institute: Hannover Medical School

description: Sample 6

hyb_protocol: According to manufacturer's instructions (Agilent)

scan_protocol: Microarray slides were scanned immediately after washing using an Agilent microarray scanner G2505B at a resolution of 2 µm

data_processing:
Feature extraction and Genomic Workbench (Agilent)
Genome: hg19
Aberration Algorithm: ADM-2
Threshold: 7.0
Fuzzy Zero: ON
GC Correction: ON
Window Size: 2Kb
Centralization (legacy): OFF
Diploid Peak Centralization: ON
Manually Reassign Peaks: OFF
Combine Replicates (Intra Array): ON
Combine Replicates (Inter Array): OFF
Array Level Filter: NONE
Aberration Filter:  ( Minimum Number of Probes for Amplification >= 3
AND Minimum Size (Kb) of Region for Amplification >= 0.0
AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.0 )
OR ( Minimum Number of Probes for Deletion >= 3
AND Minimum Size (Kb) of Region for Deletion >= 0.0
AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.0 )
Feature Level Filter: gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true OR LogRatio = 0
Design Level Filter: Homology = 0 OR IsPseudoautosomal = 1
Genomic Boundary: OFF
Show Flat Intervals: OFF

source_name: blood mononuclear cells

extract_protocol: Qiagen

value: human DNA reference pool XY

value: blood mononuclear cells

source_name: iPSC gene corrected

tag: cell line/clone id

value: clone25 Talen 37

value: iPSC gene corrected from sample 3


title: 30C_DNA_methylation_3

status: Public on Feb 27 2015

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

description: 30 days withdrawal + extinction test

hyb_protocol: All the steps of hybridization, washing, scanning and feature extraction were performed following the Agilent protocols for chip-on-chip analysis (MeDIP).

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: The extracted intensities were then analyzed using the R software environment for statistical computing (R Development Core Team, 2007). Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray and then microarrays were normalized to one another using quantile-normalization (Bolstad et al., 2003) under the assumption that all samples have identical overall methylation levels. Methylation levels were estimated from normalized probe intensities by applying a Bayesian deconvolution algorithm (Down et al., 2008). Promoter methylation levels were obtained taking the median estimated methylation level across each promoter.

organism: Rattus norvegicus

source_name: 30 days withdrawal + extinction test_IP genomic DNA

label_protocol: After the sonication step, methylated DNA was immunoprecipitated with 10 μg of anti-5methylCytosine antibody (Calbiochem) that is specific to DNA methylation, does not recognize hydroxymethylated DNA, and reveals changes in 5-methylcytoine exclusively. Prior to sonication, two control plasmids were added to the DNA (6pg each), an unmethylated GFP plasmid and an in vitro methylated Luciferase plasmid. The DNA-antibody complex was immuno-precipitated with 5 mg protein A and the methylated DNA was eluted with 150μl of TE at 1.5% SDS. The input and bound fraction were then amplified using the Whole Genome Amplification kit (Sigma). The amplified input and bound fractions were labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer), respectively, using the CGH labeling kit (Invitrogen) following the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (Harlan, Israel) weighing 250-350g were  maintained on a 12-hr light/12-hr dark reversed cycle, with food and water available ad libitum. Rats were housed 2 per cage with a metal divider between them. Experiments were conducted during the dark cycle. Rats were anesthetized with xylazine and ketamine (10mg/kg and 100mg/kg, respectively). Jugular vein catheterization: Immediately after cannula implantation, rats were implanted with intravenous silastic catheters (ID 0.55 mm, OD 0.94 mm, Dow Corning, MI) into the right jugular vein. The catheter was secured to the vein with silk sutures and was passed subcutaneously to the top of the skull, where it exited into a connector (a modified 22-gauge cannula; Plastics One, VA, USA) mounted to the skull with MX-80 screws (Small Parts, Inc., FL, USA) and dental cement (Yates and Bird, IL, USA). Cocaine self-administration: Rats were trained to self-administer cocaine for 6 hrs per day, over 10 days. The self-administration chambers (Med-Associates, Inc.; St Albans, VT, USA) had two levers, one active and one inactive. An active lever press generated a cocaine infusion (0.75 mg/kg, 0.13 ml, 5 sec/infusion; cocaine obtained from the National Institutes on Drug Abuse, MD, USA) through the i.v. catheter, and also activated a light located above the lever, which was lit for 40 sec. Active lever presses during the last 35 sec of the light cue did not result in additional cocaine infusions. Presses on the inactive lever did not activate the infusion pump and light. Control rats were subjected to saline self-administration under the same conditions. The number of active lever responses, infusions, and inactive lever responses were recorded for both treatment and control groups. Rats were returned to their home cages at the end of the daily sessions. Cocaine withdrawal (forced abstinence): After the 10-day period of self-administration training sessions, rats were subjected to either a 1-day period of withdrawal (for cocaine-trained and saline-trained rats) or 30-day period of withdrawal (cocaine-trained rats). During the withdrawal periods, rats were left in their home cages and handled 3 times a week. Extinction test : Rats were placed in the self-administration chambers, and only the contingent light cue appeared during active lever presses, without cocaine reinforcement. Cocaine-seeking behavior was assessed for 60 min. For examining DNA methylation alterations, brains were removed one hour after completion of the session, and the NAc was isolated for further epigenetic analysis.

extract_protocol: Briefly, 3 pools of NAc DNA, each including the DNA of 2 to 3 rats, were used per condition (total 8 rats per condition). Each pool was made up of 2 μg DNA (2 X 1μg for pools of 2 rats, 3 x 700ng for pools of 3 rats) that were sonicated.the dark cycle.

tag: gender

value: males

tag: weight

value: Nucleus Accumbens

value: Sprague-Dawley

tag: chip antibody

value: anti-5 methylcytosine antibody (Calbiochem, Cat. #NA81, Lot:D00048001)

source_name: 30 days withdrawal + extinction test_Input genomic DNA