title: Pooled total RNAs isolated from 4 Dot1lAC mice

city: Houston

first: Wenzheng

last: Zhang

state: TX

address: 6431 Fannin

department: Internal Medicine

institute: University of Texas Medical School at Houston

description: Array 3 Dot1lAC vs. Dot1lf/f on a normal Na+ diet

scan_protocol: The arrays were washed and scanned with Agilent’s dual-laser based scanner.

data_processing:
Feature Extraction software GE2-v5_95 was used to link a feature to a design file and determine the relative fluorescence intensity between the two samples. Genelists were created using pValue information from the internal replicates within the microarray
Genelists (on Series) were created using pValue information from the internal replicates within the microarray

source_name: pooled whole  kidneys of 4 Dot1lAC mice

label_protocol: 200 ng of total RNA from each sample was used and labeled with either Cy3- or Cy5-CTP

growth_protocol: Mice were given free access to water and normal Na+ diet

tag: age

value: 6-8 weeks

value: kidney

tag: strain

source_name: pooled whole  kidneys of 4 Dot1lf/f mice

value: whole kidney


title: BMM_mutLm_3hr_rep2

status: Public on Aug 14 2013

type: RNA

city: Ithaca

first: Helene

last: Marquis

state: NY

address: Vet Medical Center, Room C5-169

department: Microbiology & Immunology

country: USA

institute: Cornell University

description:
3B2
Gene expression after 3 hr infection with mutant L. monocytogenes

hyb_protocol: A total of 825 ng per sample of Cy3-labelled cRNA was fragmented, blocked, hybridized to Agilent Whole Mouse Genome Microarray 4x44K (G4122F), and washed according to manufacturer’s instructions.

scan_protocol: The slides were then scanned using the one-color scan setting for 4x44 array slides (scan area 61 x 21.6 mm, scan resolution 5um, dye channel set to red and green, and PMT 100%) using the Agilent DNA Microarray Scanner (G2505B).  Feature Extraction Software 9.1 (Agilent) analyzed the scanned images for background, subtracted and spatially detrended processed signal intensities, and excluded non-uniform outliers flagged in feature extraction (protocol GE1-105_DEC8 and Grid: 012391_D_20060331).

data_processing: Data was analyzed using GeneSpring11.5 (Agilent Technologies), threshold to raw signal was set 1.0, shifted to 75.0 percentile, and baseline set to median of all samples.  Experimental groupings were created by dividing the samples into conditions (a) wild-type infected (triplicate),(b) plcB∆pro mutant (triplicate), and (c) uninfected (duplicate).  Interpretations were created using the average replicates in condition, non-numeric, continuous parameters, and including detected, not detected, and compromised flags.  Statistical analysis was then performed between conditions (a)/(c) & (b)/(c), unpaired T-test, no correction, p-value <0.05.  We then performed functional annotation using our significant gene lists through the Database for Annotation, Visualization and Integrated Discovery (DAVID 6.7, National Institute of Allergy and Infectious Diseases – National Institutes of Health) to find pathways significantly affected by up- or down-regulated genes

molecule: total RNA

organism: Mus musculus

source_name: BMMs_mutant Listeria monocytogenes_3hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng - 1 ug total RNA using the Low Input Quick Amp Labeling 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.

growth_protocol: Bone marrow cells were collected from BALB/C mice and macrophages were differentiated in medium containing 50% DMEM, 30% Fetal Bovine Serum (FBS), 20% L-cell conditioned medium, 1% 100 U/ml Penicillin G,100 μg/ml Streptomycin, 1mM Sodium pyruvate, and 2mM L-glutamine.  Differentiated macrophages were seeded at a concentration of 3.6 x 106 cells in 100 mm petri dishes containing four 12 mm glass cover slips, and incubated overnight at 37°C, 5% CO2.  Bacteria were grown overnight in BHI at 30°C, passaged 1/10 or 1/100 in BHI and incubated at 30°C, 200 rpm until reaching an OD600 of 0.6-0.8.

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Kit (Qiagen) per manufacturer’s instructions.  RNA sample purity was assessed using Agilent 2100 Bioanalyzer RNA 6000 Nano LabChip (Agilent Technologies).  All samples were >9.1 RIN (RNA Integrity Number).

treatment_protocol: Macrophages were infected with either wild-type L. monocytogenes or L. monocytogenes plcB∆pro at an MOI of 1.  Cells were washed in PBS at 30 min post infection and tissue culture medium was added to dishes.  At one hour post-infection, gentamicin was added at a final concentration of 50 μg/ml.  At three hours post-infection, the medium was replaced with antibiotic-free medium to prevent intracellular bacterial killing as the mutant affects membrane permeability.   Samples were collected at 3, 6, and 9 hr p.i. for RNA purification.  Cover slips were collected at the same time points to determine bacteria counts.

tag: strain background

value: BALB/C

tag: cell type

value: bone marrow derived macrophages (BMMs)

tag: infected with

value: L. monocytogenes plcB∆pro mutant strain

tag: timepoint

value: 3 hours

tag: replicate


title: Germinating wheat seed at P0_biological rep1

city: Beijing

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

country: China

institute: College of Life Science, Capital Normal University

description:
Wheat seed_P0-1
Gene expression data from Wheat seed_before imbibition (0 hour)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Triticum aestivum

source_name: Wheat seed_before imbibition (0 hour)

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

growth_protocol: The collection of germinating seed which germinated naturally according to the different germinating phases (P0-P4).

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

treatment_protocol: Sterile wheat seeds were completely steeped in sterile pure water for 12 hours first, then homogeneously put them into the sterile petri dish which contain moderate sterile pure water for the following germination. The collected seeds of different phases were placed in -80℃ condition for the subsequent experiments.

tag: cultivar

value: Jimai 20

tag: tissue

value: germinating seeds


title: BMM_wtLm_3hr_rep2

description:
3A2
Gene expression after 3 hr infection with wild type L. monocytogenes

source_name: BMMs_wild type Listeria monocytogenes_3hr

value: L. monocytogenes wild-type strain


title: BMM_mutLm_3hr_rep3

description:
3B3
Gene expression after 3 hr infection with mutant L. monocytogenes


title: plasma samples from UA individual 13

status: Public on Aug 13 2013

first: Hong

last: Chen

state: China

address: Xizhimen South Street 11, Xicheng District, Beijing

department: Dept. of Cardiology

institute: Peking University People’s Hospital

description: SAMPLE 26

data_processing:
SDS software (Applied Biosystems) was used to collect data.
Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using DataAssist (Applied Biosystems).
For the normalization it uses Mamm U6 as housekeeping gene.
Raw miRNA expression CT values were normalized to the endogenous housekeeping gene MammU6; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_Mamm U6)

label: FAM

organism: Homo sapiens

source_name: plasma samples from UA individual 13

label_protocol:
Five ul total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards (2 per sample). Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNAs
For each of two cards per sample (A and B), nine ul of pre-amplified, diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.

extract_protocol: Total RNA was isolated from plasma or tissues using miRNeasy Mini Kit (Qiagen, Valencia, CA). 250 µl of EDTA-plasma were mixed with 700 µl Qiazol, incubated for 5 min at room temperature and subsequently mixed with 140 µl chloroform. The organic and aqueous phase was separated by centrifugation at 12,000 g for 15 min. The upper aqueous phase was collected and the RNA was precipitated by adding 100% ethanol. The mixture was applied to a miRNeasy Mini spin column. After washed several times, the RNA was eluted in 25 µl RNase-free water.

tag: gender

value: Male

value: 56 years

tag: disease state

value: unstable angina (disease)

value: plasma


title: plasma samples from UA individual 8

description: SAMPLE 21

source_name: plasma samples from UA individual 8

value: 68 years


title: plasma samples from UA individual 9

description: SAMPLE 22

source_name: plasma samples from UA individual 9

value: 53 years


title: plasma samples from UA individual 12

description: SAMPLE 25

source_name: plasma samples from UA individual 12

value: 62 years


title: plasma samples from UA individual 11

description: SAMPLE 24

source_name: plasma samples from UA individual 11

value: Female

value: 57 years


title: plasma samples from UA individual 6

description: SAMPLE 19

source_name: plasma samples from UA individual 6


title: plasma samples from UA individual 5

description: SAMPLE 18

source_name: plasma samples from UA individual 5

value: 74 years


title: plasma samples from UA individual 4

description: SAMPLE 17

source_name: plasma samples from UA individual 4

value: 59 years


title: plasma samples from UA individual 3

description: SAMPLE 16

source_name: plasma samples from UA individual 3

value: 55 years


title: Comr I

type: genomic

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

hyb_protocol: The labeled  DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containin\herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using ArrayStar software (http://www.dnastar.com/). Each array was RMA background corrected and quantile normalized.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Dam-Comr in drosophila male germ line cells

label_protocol: 1 µg  DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 200 biological samples (testes) were dissected in PBS and homogenized. 10ul of 100mg/ml Dispase II were added to each sample and kept at 56C for 6h. DNA was extracted using standard phoenol-chloroform-isopropanol protocol. DamID samples preparation was performed as described previously (Greil et al., 2006)

treatment_protocol: Dissection in PBS

tag: cell origin

value: testes

source_name: Dam alone in drosophila male germ line cells


title: plasma samples from UA individual 2

description: SAMPLE 15

source_name: plasma samples from UA individual 2


title: plasma samples from normal individual 13

description: SAMPLE 13

value: 60 years

value: non-cardiac chest pain (control)


title: plasma samples from UA individual 1

description: SAMPLE 14

source_name: plasma samples from UA individual 1

value: 49 years


title: plasma samples from normal individual 12

description: SAMPLE 12

value: 43 years


title: plasma samples from normal individual 11

description: SAMPLE 11

value: 63 years


title: plasma samples from UA individual 7

description: SAMPLE 20

source_name: plasma samples from UA individual 7


title: plasma samples from normal individual 10

description: SAMPLE 10

value: 58 years


title: Primary glioblastoma sample 1

city: SAN FRANCISCO

first: RAMAN

middle: PAUL

last: NAGARAJAN

state: CA

address: 1450 3RD ST, ROOM HD200

department: NEUROSURGERY

institute: UCSF

description: frozen surgical resection

hyb_protocol: GeneChip Expression Analysis Technical Manual 702232 Rev 3

data_processing:
AGCC 3.2.2
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: primary glioblastoma

label_protocol: NuGEN Applause Amp Plus ST System and Encore Biotin Module

extract_protocol: Small pieces of snap-frozen samples were homogenized in Trizol following manufacturer's instructions. Samples were then treated with DNase and further purified on Rneasy columns. RNA integrity was verified by Agilent Bioanalyzer.

value: male

tag: age (y)

tag: tumor grade

value: IV


title: Primary glioblastoma sample 5

description: frozen surgical resection


title: plasma samples from normal individual 9

description: SAMPLE 9

source_name: plasma samples from normal individual 9

value: Male

value: 51 years

value: plasma


title: plasma samples from normal individual 8

description: SAMPLE 8

source_name: plasma samples from normal individual 8

value: 40 years


title: Normal brain sample

description: frozen autopsy specimen

source_name: normal brain

value: Not applicable


title: Primary glioblastoma sample 4

description: frozen surgical resection

value: female


title: Primary glioblastoma sample 3

description: frozen surgical resection


title: Primary glioblastoma sample 2

description: frozen surgical resection


title: plasma samples from normal individual 7

description: SAMPLE 7

source_name: plasma samples from normal individual 7

value: Female

value: 59 years


title: plasma samples from normal individual 5

description: SAMPLE 5

source_name: plasma samples from normal individual 5

value: 68 years


title: plasma samples from normal individual 4

description: SAMPLE 4

source_name: plasma samples from normal individual 4

value: 54 years


title: plasma samples from normal individual 3

description: SAMPLE 3

source_name: plasma samples from normal individual 3

value: 60 years

value: non-cardiac chest pain (control)


title: plasma samples from normal individual 6

description: SAMPLE 6

source_name: plasma samples from normal individual 6

value: 67 years


title: Comr II

value: testes


title: plasma samples from normal individual 2

description: SAMPLE 2

source_name: plasma samples from normal individual 2

value: 56 years


title: plasma samples from normal individual 1

description: SAMPLE 1

source_name: plasma samples from normal individual 1

value: 46 years


title: YF21

type: other

city: Chicago

first: Samantha

last: Gadd

state: IL

address: 2430 N Halsted St

department: Pathology

institute: Children's Memorial Research Center

hyb_protocol: The BeadChip was hybridized overnight in the Illumina Hybridization Oven, with a temperature ramp from 60°C to 45°C.

scan_protocol: The chips were scanned on the Illumina iScan.

data_processing: Illumina BeadStudio software (Illumina, Inc., San Diego) was used to translate the scanned images into expression data, which were further log-transformed and normalized by the quantile normalization procedure using the Bioconductor package: Affymetrix. Significance analysis of microarrays (SAM) was used to identify differentially expressed miRNAs for a two-group comparison.  Standardized fold changes were calculated as mean expression differences divided by pooled standard deviation in the log scale. Pearson correlation coefficients were calculated for all miRNA pairs. Ingenuity Pathway Analysis (IPA, www.ingenuity.com) was used to identify enriched pathways or biological functions among differentially expressed miRNAs.

molecule: other

source_name: Blood sample

label_protocol: The amount of microRNA in each sample was evaluated by the small RNA chip using the 2100 Agilent Bioanalyzer. Total RNA (200 ng) was polyadenylated with a PAP enzyme (Poly-A Polymerase). Polyadenylated RNA was converted to cDNA using a biotinylated oligo-dT primer with a universal 5’-end PCR sequence and cDNA templates were hybridized with the set of MSOs corresponding to all the targeted microRNAs. A polymerase was added for MSO extension.

extract_protocol: Whole blood (5ml) from each participant was drawn into two PAXgene tubes and was incubated at room temperature for three hours before being frozen at -70oC. MiRNA was extracted from the second PAXgene blood tube using TRIZOL (Invitrogen) as per the manufacturer’s protocol.

tag: group

value: OLD

tag: race

value: Asian


title: YF6

value: YOUNG


title: YF18

value: White


title: YF22


title: YF16

value: Hispanic


title: YF14


title: YF7


title: YF12


title: YF17


title: YF15


title: YF20


title: YF10


title: YF13


title: YF9


title: YF5


title: YF4


title: RAG1KO FAIRE

first: Eugene

middle: M

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

description: Chip-chip Rag1KO DN cells -FAIRE

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: FAIRE DNA from Rag1-/- DN cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 5 million cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 400 bp using a BiorupterTM sonicator (Diagenode). 5 µg of antibody was incubated with Dynabeads ProteinA beads (Invitrogen at 4C for 2-4 hours . The chromatin (from 5 million cells) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and added to the anitbody conugated to the Dynabeads overnight at 4C. After incubation, the immune complexes were collected by centrifugation and washed with the following buffers each for 3 min at 4C;low salt (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and TE (10 mM Tris pH8.0, 1 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 100 mM NaHCO3) at 65C overnight followed by the addition of proteinaseK to 500 µg/ml and incubaton at 56C for 1 hour. Genomic DNA was isolated using QIAquick PCR purification column and subject to whole genome amplication (Sigma).

treatment_protocol: Rag1KO DN cells were obtained from thymus of 3-4 week old mice.

tag: genotype

value: DN cells

tag: chip antibody

value: FAIRE

source_name: Input (non-cross-linked) DNA from Rag1KO DN cells

value: none, input DNA


title: YF19

tag: age


title: YF8


title: RAG1KO H3K27ac

description: Chip-chip Rag1KO DN cells -H3K27ac

source_name: H3K27ac (abcam-ab4729) ChIP DNA from Rag1-/- DN cells

tag: strain

tag: antibody vendor/catalog

source_name: Input DNA from Rag1KO DN cells


title: Cy5: S16; Cy3: 2hrS16

city: Grand Rapids

first: Sok Kean

last: Khoo

state: MI

address: 333 Bostwick NE

institute: Van Andel Institute

description: S16 at 0 and 2 hr after treatment

hyb_protocol: Cy3- and Cy5-labeled cDNAs were mixed with 2x hybridization solution (50% formamide/10X SSC/0.2% SDS) and hybridized onto prewarmed (42 °C) slides for 20 hr 42 °C.  After hybridization, slides were washed in 1x SSC/0.1% SDS 42 °C 5 min, 0.2x SSC/0.1% SDS room temp 5 min, 0.2x SSC RT 5 min (twice) and 0.1% SSC RT 5 min.

scan_protocol: 532- and 635-nm wavelengths with Scan Arrray Lite by GSI Lumonics (Billerica, CA)

data_processing: Images and software by GENEPIX Pro.  Spots with no signal/obvious defects were excluded.  Local background subtracted from remaining spots and the ratios of net fluorescence from Cy5 to Cy3 were calculated for each spot.  Ratios were in log2 and normalized so that the average log ration equaled zero.

label_protocol: 50 µg of total RNA were 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: Cells cultured in DMEM supplemented with 10% FBS

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

treatment_protocol: After 24 hr of culture, cells were treated with cisplatin at a final concentration of 8.67 µM for 0, 2, or 8 hr.

tag: cell type

value: cisplatin-sensitive cell clones from CNE2

source_name: S16 2 hr


title: RA1KO P300

description: Chip-chip Rag1KO DN cells -P300

source_name: P300 (Santacruz- SC C-20X) ChIP DNA from Rag1-/- DN cells

value: Santa Cruz- SC C-20X


title: YF1


title: YF2


title: YF3


title: High4, HP4

city: Baltimore

first: Supriya

last: Munshaw

address: 855 N. Wolfe St, Suite 530

department: Medicine

institute: Johns Hopkins University

hyb_protocol: The samples were ice quenched and combined with the hybridization cocktail (5 ul oligonucleotide B2 control, 15 ul 20X eukaryotic hybridization controls, 150 ul 2X hybridization buffer, 30 ul 100% DMSO and 70 ul water). After 10 minutes of pre-hybridizing Human U133 Plus 2.0 Genome array at 45ºC, 60 rpm, 200 ul of cocktail was loaded onto each array and the arrays were hybridized for 16 hours at 45ºC, 60 rpm. The cocktail was removed and the arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_001 fluidics script.

scan_protocol: All arrays were scanned in the Affymetrix GeneChip Scanner 3000 and the raw analysis was performed with Affymetrix GeneChip Operating System (GCOS) 1.4.

data_processing: Results from microarray hybridization were analyzed using the Bioconductor package in R. Data were normalized with the “rma” procedure using a custom HGU133Plus2 annotation, to avoid known problems associated with the affymetrix annotation -. The normalized data was then analyzed using the “affy” -and “limma” -packages in Bioconductor.

source_name: Liver Hepatic Parenchyma

label_protocol: One ug total RNA was combined with 2 ul T7 oligo(dT) primer and 2 ul Poly-A controls and brought to a volume of 12 ul. The samples were incubated at 70ºC for 10 minutes. A master mix of 4 ul first strand buffer, 2 ul DTT and 1 ul 10 mM dNTPs was added to the samples, followed by a two minute incubation at 42ºC. One ul Superscript II (Invitrogen, Carlsbad, CA) was added to each sample and the samples were incubated at 42ºC for one hour for first strand cDNA synthesis. A master mix of 91 ul water, 30 ul 5X second strand buffer, 3 ul 10 mM dNTPs, 4 ul DNA polymerase I, 1 ul E.coli DNA ligase, and 1 ul RNase H was added to each sample and the samples were incubated for two hours at 16ºC for second strand cDNA synthesis. Two ul of T4 DNA polymerase was added followed by a five minute incubation at 16ºC. Ten ul, 0.5 M EDTA was added to stop the reaction. cDNA clean-up was performed with the Affymetrix GeneChip Sample Clean-up Module, as per manufacturer’s instructions. The cDNA was eluted in 14 ul elution buffer. The final elution volume (~12ul) was combined with 28 ul of IVT mix master mix (4 ul 10X IVT labeling buffer, 12 ul Labeling NTP mix, 4 ul labeling enzyme mix, and 8 ul RNAse-free water) for the in vitro transcription cRNA synthesis reaction. The samples were incubated overnight for 16 hours at 37ºC followed by a hold at 4ºC. Clean-up was performed as per the manufacturer’s protocol using the Affymetrix GeneChip Sample Clean-up Module. The final elution volume was ~19ul. Concentration was checked via a nanodrop spectrophotometer. Six ul 5X fragmentation buffer was then combined with 15 ug cRNA and incubated at 95ºC for 35 minutes to fragment the cRN

growth_protocol: Tissues were divided into two at the time of biopsy. One piece was immediately placed in OCT and snap-frozen in liquid nitrogen.

extract_protocol: RNA was extracted and isolated from each sample separately using the Agencourt® RNAdvance Cell v2 system (Beckman Coulter Genomics, Danvers, MA); this extraction platform relies on paramagnetic bead purification of nucleic acids.  It was linearly amplified using the NuGEN Ovation Pico WTA (linear amplification) System® (NuGEN Technologies, Inc., San Carlos, CA)

treatment_protocol: H&E and trichrome stained sections were then graded and staged (Ishak fibrosis and Metavir) by a hepatopathologist who was blinded to all clinical information.

tag: ishak fibrosis

value: Male

value: Black


title: High4, PT2

source_name: Liver Portal Tract


title: High4, HP6


title: Cy5: 8hrS16; Cy3: S16

description: S16 at 0 and 8 hr after treatment

source_name: S16 8 hr


title: Cy5: CNE2; Cy3: 8hrCNE2

description: CNE2 at 0 and 8 hr after treatment

value: An epithelial cell line derived from poorly differentiated nasopharyngeal carcinoma (Ref:Sizhong Z et al Int. J. Cancer 1983; 216:480-485)

source_name: CNE2 8 hr


title: Cy5: 8hrCNE2; Cy3: 8hrS16

description: NPCs at 8 hr after treatment


title: Cy5: 2hrCNE2; Cy3: CNE2

description: CNE2 at 0 and 2 hr after treatment

source_name: CNE2 2 hr


title: Cy5: CNE2; Cy3: 2hrCNE2

description: CNE2 at 0 and 2 hr after treatment


title: Cy5: 2hrS16; Cy3: S16

description: S16 at 0 and 2 hr after treatment


title: High4, PT1


title: Low5, HP6


title: Low5, HP5


title: High4, HP5


title: Low4, HP5


title: High4, HP3


title: Cy5: 2hrS16; Cy3: 2hrCNE2

description: NPCs at 2 hr after treatment


title: Cy5: 8hrCNE2; Cy3: CNE2

description: CNE2 at 0 and 8 hr after treatment


title: Low5, HP4


title: Cy5: S16; Cy3: 8hrS16

description: S16 at 0 and 8 hr after treatment


title: Cy5: 2hrCNE2; Cy3: 2hrS16

description: NPCs at 2 hr after treatment


title: Low4, HP4


title: Low5, PT1


title: Low5, PT2


title: Low5, HP3


title: Low4, HP6


title: YF11


title: Low4, HP2


title: Low4, HP3


title: Low4, PT1


title: Cy5: S16; Cy3: CNE2

description: Control NPCs (0 hr), untreated.


title: High3, HP6


title: High3, HP5


title: High3, PT2


title: Cy5: 8hrS16; Cy3: 8hrCNE2

description: NPCs at 8 hr after treatment


title: Low4, HP1


title: Cy5: CNE2; Cy3: S16

description: Control NPCs (0 hr), untreated.


title: High3, PT1


title: High2, HP6

value: Female


title: High3, HP2


title: High2, HP5


title: High3, HP1


title: High3, HP3


title: High2, HP2


title: High2, PT1


title: High3, HP4


title: High2, HP3


title: plasma samples from UA individual 10

description: SAMPLE 23

source_name: plasma samples from UA individual 10

value: 76 years

value: unstable angina (disease)

value: plasma


title: High2, HP1


title: High2, PT2


title: Low3, PT2


title: Low3, HP5


title: Low3, PT1


title: High2, HP4


title: Low3, HP6


title: Low2, HP5


title: Low3, HP4


title: Low2, HP6


title: Low2, HP4


title: Low2, PT2


title: Low3, HP3


title: Low2, HP2


title: Low2, HP3


title: Low1, PT1


title: Low2, HP1


title: Low1, HP3


title: Low1, HP4


title: Low1, HP5


title: Low1, HP6


title: Low2, PT1


title: High1, HP5


title: High1, HP6


title: Low4, PT2


title: High1, PT2


title: (Biological replicate 3) E18.5 fetal cells sorted on CD31-CD45-Ter119-EpCAM++CD49f+

city: Vancouver

first: Maisam

last: Makarem

state: BC

country: Canada

institute: BC Cancer Research Center

description:
E18.5_3
Gene expression from freshly isolated sorted cells

hyb_protocol: 1.65ug of Cy3 labeled cRNA is hybridized to the microarray at 65°C for 17 hours

scan_protocol: Preliminary fluorescence data is extracted from each microarray by the Agilent DNA Microarray Scanner

data_processing:
The resulting data are processed by the Agilent Feature Extraction software (v.11.0.1.1). A QC report is generated for each microarray with a series of control panels evaluates the quality of the hybridization.
Green processed signal was quantile normalized with Agilent GeneSpring 12.0.

label_protocol: Fluorescent cRNA (complimentary RNA) was generated from 25 - 200 ng of RNA using Agilent's Low Input Quick Amp Labeling Kit. Prior to labeling, the integrity of the total RNA is checked with the Agilent 2100 Bioanalyzer (RNA), quantified with the NanoDrop ND-1000 UV-VIS spectrophotometer to measure A260/280 and A260/230 ratios or RiboGreen assay.Total RNA is initially converted into cDNA using a T7 polymerase primed reverse transcriptase reaction to synthesize first and second strand of cDNA. This cDNA then served as a template for cRNA synthesis by T7 RNA polymerase in the presence of cyanine 3-labeled CTP (Cy3).

growth_protocol: CD31-CD45-Ter119-BP-1-EpCAM+CD49f+ adult basal cells and CD31-CD45-Ter119-EpCAM++CD49f+ E18.5 fetal cellswere isolated by FACS

extract_protocol: RNA was isolated using the Absolutely RNA Nanoprep kit (Agilent) following the manufacturer's instructions

value: female

tag: developmental stage

value: Embryonic day 18.5

value: mammary gland


title: High1, HP2


title: High1, HP3


title: High1, HP1


title: High1, HP4


title: Low1, PT2


title: (Biological replicate 2) E18.5 fetal cells sorted on CD31-CD45-Ter119-EpCAM++CD49f+

description:
E18.5_2
Gene expression from freshly isolated sorted cells


title: High1, PT1


title: (Biological replicate 1) E18.5 fetal cells sorted on CD31-CD45-Ter119-EpCAM++CD49f+

description:
E18.5_1
Gene expression from freshly isolated sorted cells


title: High4, HP2


title: (Biological replicate 2) Basal cells sorted on CD31-CD45-Ter119-BP-1-EpCAM+CD49f+

description:
Basal_2
Gene expression from freshly isolated sorted cells

source_name: Adult basal cells sorted on CD31-CD45-Ter119-BP-1-EpCAM+CD49f+

value: 8-12 week adult


title: Low5, HP1


title: Low3, HP2


title: (Biological replicate 3) Basal cells sorted on CD31-CD45-Ter119-BP-1-EpCAM+CD49f+

description:
Basal_3
Gene expression from freshly isolated sorted cells

value: Adult basal cells sorted on CD31-CD45-Ter119-BP-1-EpCAM+CD49f+


title: High4, HP1


title: Low5, HP2


title: Low3, HP1


title: (Biological replicate 1) Basal cells sorted on CD31-CD45-Ter119-BP-1-EpCAM+CD49f+

description:
Basal_1
Gene expression from freshly isolated sorted cells


title: Low1, HP2


title: Low1, HP1


title: S8_3yrs_F_naive

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description: This is naive MIRA-chip sample from subject 8

hyb_protocol: Samples were hybridized onto a NimbleGen 2.1M Deluxe Human Promoter Array following NimbleGen’s protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565BA DNA Microarray Scanner.  Images were processed using the NimbleScan software.

data_processing:
The log2(Cy5) values were normalized using Lowess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. These signal values were further quantile normalized to adjust for between sample variations.
The GC Lowess method referred in this fields utilizes both 'log2(Cy3)' and 'log2(Cy5)' values as following:
Classify probes into bins according to CG content (proportion of number of C and G nucleotides in probe sequence)
For each CG content bin (k), we fit lowess regression to predict log2(Cy5)_k value using log2(Cy3)_k value
Compute normalized value  = sigma_bar *(observed log2(Cy5)_k - predicted log2(Cy5)_k)/sigma_k, where sigma_k is mean absolute deviation of (observed log2(Cy5)_k - predicted log2(Cy5)_k) and sigma_bar is geometric mean of all sigma_k's.
This normalization corrects for both dye bias and CG bias simultaneously.

source_name: MIRA-enriched DNA

label_protocol: Amplified input and methylated CpG DNA fragments labeled with Cy3 and Cy5 random nonomers (Trilink Biotechnologies) following NimbleGen’s protocol.

growth_protocol: isolated ex vivo from tonsil

extract_protocol: Genomic DNA was purified using Allprep DNA/RNA/protein columns (Qiagen).  Purified genomic DNA was sonicated using a Bioruptor (Diagenode) to generate 200-500 bp fragments.  Methylated CpG DNA fragments were enriched from 200 ng of sonicated DNA using the MethylCollector Ultra Kit (Actif Motif) following the manufacturer’s protocol.  20 ng of input and enriched DNA fractions were amplified twice with WGA2 (Sigma).

treatment_protocol: FACS purified

tag: sample type

value: methylated DNA fraction

tag: subject

value: F

value: tonsils

value: naive

source_name: Input DNA

value: input DNA


title: S7_2yrs_M_naive

description: This is naive MIRA-chip sample from subject 7

tag: gender

value: M


title: SM2

city: wuhan

first: Xia

last: Fang

state: hubei

address: Shizishan Street

institute: Huazhong Agricultural University

description: This sample is of Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the second of four mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed using NimbleGen Hybridization Kit.

scan_protocol: Slides were scanned by Axon Instruments Gene Pix 4000B.

data_processing: The raw data (.pair file) was subjected to RMA(Irizarry, et al. 2003), quantile normalization, and background correction as implemented in the NimbleScan software package. The sample data table contains gene-level normalized data and the *norm_RMA.pair files contain probe-level normalized data.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

label_protocol: cDNA samples were labeled by the one-color DNA Labeling Kit.

growth_protocol:
Campylobacter jejuni NCTC11168 (S) was grown to mid-log phase (O.D.600nm 0.8) microaerobic conditions (85% N2, 10% CO2, 5% O2) at 42°C in MH media
Campylobacter jejuni NCTC11168 delta-Cj0440c (SM) was grown to mid-log phase (O.D.600nm 0.8) microaerobic conditions (85% N2, 10% CO2, 5% O2) at 42°C in MH media

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

value: Deletion Cj0440c mutant delta-Cj0440c

tag: phenotype

value: broken flagellar

tag: accession


title: SM3

description: This sample is of Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the third of four mutant strain biological replicates used in this experiment, each from separate cultures.


title: S8_3yrs_F_GC

description: This is GC MIRA-chip sample from subject 8

value: GC


title: SM4

description: This sample is of Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the forth of four mutant strain biological replicates used in this experiment, each from separate cultures.


title: S7_2yrs_M_memory

description: This is memory MIRA-chip sample from subject 7

value: memory


title: S4

description: This sample is of wild-type Campylobacter jejuni NCTC11168. It is the forth of four wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Campylobacter jejuni NCTC11168 wild-strain

value: Wild-type

value: normal


title: S3-2

description: This sample is of wild-type Campylobacter jejuni NCTC11168. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures.


title: S7_2yrs_M_GC

description: This is GC MIRA-chip sample from subject 7


title: S4_5yrs_F_naive

description: This is naive MIRA-chip sample from subject 4


title: S3-1

description: This sample is of wild-type Campylobacter jejuni NCTC11168. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures.


title: S7_2yrs_M_PC

description: This is PC MIRA-chip sample from subject 7

value: PC


title: S6_2yrs_M_PC

description: This is PC MIRA-chip sample from subject 6


title: SM1

description: This sample is of Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the first of four mutant strain biological replicates used in this experiment, each from separate cultures.


title: S8_3yrs_F_PC

description: This is PC MIRA-chip sample from subject 8


title: S8_3yrs_F_memory

description: This is memory MIRA-chip sample from subject 8


title: S6_2yrs_M_naive

description: This is naive MIRA-chip sample from subject 6


title: RM3

description: This sample is of erythrocin-resistant Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the third of four mutant strain biological replicates used in this experiment, each from separate cultures.

growth_protocol:
Erythrocin-resistant Campylobacter jejuni NCTC11168(R) was grown to mid-log phase (O.D.600nm 0.8) microaerobic conditions (85% N2, 10% CO2, 5% O2) at 42°C in MH media
Erythrocin-resistant Campylobacter jejuni NCTC11168 delta-Cj0440c (RM) was grown to mid-log phase (O.D.600nm 0.8) microaerobic conditions (85% N2, 10% CO2, 5% O2) at 42°C in MH media

value: aflagellar


title: RM1

description: This sample is of erythrocin-resistant Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the first of four mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: Erythrocin-resistant Campylobacter jejuni NCTC11168 delta-Cj0440c


title: S5_4yrs_F_naive

description: This is naive MIRA-chip sample from subject 5


title: RM2

description: This sample is of erythrocin-resistant Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the second of four mutant strain biological replicates used in this experiment, each from separate cultures.


title: S5_4yrs_F_PC

description: This is PC MIRA-chip sample from subject 5


title: R4

description: This sample is of resistant-type Campylobacter jejuni NCTC11168. It is the forth of four resistant-type biological replicates used in this experiment, each from separate cultures.

source_name: Erythrocin-resistant Campylobacter jejuni NCTC11168

value: Erythrocin-resistant


title: S6_2yrs_M_GC

description: This is GC MIRA-chip sample from subject 6


title: S6_2yrs_M_memory

description: This is memory MIRA-chip sample from subject 6


title: S5_4yrs_F_memory

description: This is memory MIRA-chip sample from subject 5


title: R1

description: This sample is of resistant-type Campylobacter jejuni NCTC11168. It is the first of four resistant-type biological replicates used in this experiment, each from separate cultures.


title: S4_5yrs_F_PC

description: This is PC MIRA-chip sample from subject 4


title: RM4

description: This sample is of erythrocin-resistant Campylobacter jejuni NCTC11168 delta-Cj0440c. It is the forth of four mutant strain biological replicates used in this experiment, each from separate cultures.


title: Cy5: 2hrS16; Cy3: 2hrCNE2

description: NPCs at 2 hr after treatment

value: cisplatin-sensitive cell clones from CNE2

value: An epithelial cell line derived from poorly differentiated nasopharyngeal carcinoma (Ref:Sizhong Z et al Int. J. Cancer 1983; 216:480-485)


title: S4_5yrs_F_memory

description: This is memory MIRA-chip sample from subject 4

value: methylated DNA fraction


title: S2

description: This sample is of wild-type Campylobacter jejuni NCTC11168. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: R2

description: This sample is of resistant-type Campylobacter jejuni NCTC11168. It is the second of four resistant-type biological replicates used in this experiment, each from separate cultures.


title: Cy5: 2hrCNE2; Cy3: CNE2

description: CNE2 at 0 and 2 hr after treatment


title: Replicate 3

city: Pittsburgh

first: James

last: Bina

state: PA

address: 450 Technology Dr

department: Microbiology and Molecular Genetics

institute: University of Pittsburgh

hyb_protocol: PFGRC Microbial Hybridization of Labeled Probes Protocol (http://pfgrc.jcvi.org/index.php/microarray/protocols.html)

scan_protocol: Scanned using an Axon scanner.

data_processing: Analyzed using the TM4 microarray suite

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: AKI + cFP

label_protocol: PFGRC Microbial Genomic DNA Aminoallyl Labeling Protocol (http://pfgrc.jcvi.org/index.php/microarray/protocols.html)

growth_protocol: Bacteria was grown under AKI conditions for 2.5 or 3 hours when total RNA was extracted.

extract_protocol: Trizol followed by Rneasy cleanup according to the manufacturer's directions.

treatment_protocol: Plus or minus 1 mM cFP

tag: condition

value: AKI + cFP

source_name: AKI

value: AKI


title: S8_3yrs_F_PC_B2

description: This is PC gene expression sample from subject 8

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction (Ding et al. Nucleic Acids Research, 36 (10) e58).as implemented in the Biocondutor/R software packages. The hybridization batch corrected using Empirical Bayes Location-Scale Method (Johnson and Li, Biostatistics 8(1):118).

source_name: S8, 3yrs, F, PC, B2

label_protocol: Amplified cDNA samples were labeled with Cy3 random nonomers (Trilink Biotechnologies) following NimbleGen’s protocol.

growth_protocol: Cells were isolated ex-vivo from tonsil samples

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA/protein columns (Qiagen).  cDNA was sythesized and amplifed using WTA2 (Sigma).

treatment_protocol: Cell populations were FACS purified

value: 3 yrs

value: F

tag: tissue

value: tonsils

tag: batch


title: Cy5: CNE2; Cy3: 2hrCNE2

description: CNE2 at 0 and 2 hr after treatment


title: Cy5: S16; Cy3: 8hrS16

description: S16 at 0 and 8 hr after treatment


title: S5_4yrs_F_GC

description: This is GC MIRA-chip sample from subject 5

value: input DNA


title: Cy5: 2hrCNE2; Cy3: 2hrS16

description: NPCs at 2 hr after treatment

source_name: S16 2 hr


title: Cy5: 8hrCNE2; Cy3: CNE2

description: CNE2 at 0 and 8 hr after treatment


title: S3_1yrs_M_naive

description: This is naive MIRA-chip sample from subject 3

value: M

value: naive


title: S8_3yrs_F_naive_B2

description: This is naive gene expression sample from subject 8

source_name: S8, 3yrs, F, naive, B2


title: Mutant DG, biological rep6

city: Toyoake

first: Juzoh

last: Umemori

address: 1-98 Kutsukakecho, Dengakugakubo

country: Japan

institute: Fujita Health University

description:
Shn2_12_DG
Gene expression data from the DG of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000).

data_processing: The data were analyzed with Affymetrix Expression Console (version 1.1). The normalization used in RMA is quantile normalization.

source_name: DG of adult Shn-2 mutant mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

extract_protocol: Trizol extraction of total RNA and cleanup by the RNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

tag: strain/background

value: (BALB/c x C57BL/6J) F1

value: Shn-2 mutant

value: dentate gyrus


title: S8_3yrs_F_memory_B2

description: This is memory gene expression sample from subject 8

source_name: S8, 3yrs, F, memory, B2

value: memory


title: R3

description: This sample is of resistant-type Campylobacter jejuni NCTC11168. It is the third of four resistant-type biological replicates used in this experiment, each from separate cultures.

tag: genotype

value: normal


title: Control DG, biological rep6

description:
Shn2_11_DG
Gene expression data from the DG of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

source_name: DG of adult control mouse

value: wild-type


title: S8_3yrs_F_GC_B2

description: This is GC gene expression sample from subject 8

source_name: S8, 3yrs, F, GC, B2

value: GC


title: S7_2yrs_M_naive_B3

description: This is technical replicate of S7_naive_B2 sample

source_name: S7, 2yrs, M, naive, B3

value: 2 yrs


title: Cy5: S16; Cy3: CNE2

description: Control NPCs (0 hr), untreated.

value: cisplatin-sensitive cell clones from CNE2

value: An epithelial cell line derived from poorly differentiated nasopharyngeal carcinoma (Ref:Sizhong Z et al Int. J. Cancer 1983; 216:480-485)


title: S7_2yrs_M_naive_B2

description: This is naive gene expression sample from subject 7

source_name: S7, 2yrs, M, naive, B2


title: Replicate 1

value: AKI + cFP

value: AKI


title: Control DG, biological rep5

description:
Shn2_10_DG
Gene expression data from the DG of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: S3_1yrs_M_PC

description: This is PC MIRA-chip sample from subject 3

data_processing: The log2(Cy5) values were normalized using Lowess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:1

value: methylated DNA fraction

value: PC


title: Cy5: 2hrS16; Cy3: S16

description: S16 at 0 and 2 hr after treatment


title: Cy5: S16; Cy3: 2hrS16

description: S16 at 0 and 2 hr after treatment


title: Cy5: 8hrS16; Cy3: S16

description: S16 at 0 and 8 hr after treatment

source_name: S16 8 hr


title: Mutant DG, biological rep5

description:
Shn2_09_DG
Gene expression data from the DG of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: Mutant DG, biological rep4

description:
Shn2_08_DG
Gene expression data from the DG of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: S7_2yrs_M_PC_B2

description: This is PC gene expression sample from subject 7

source_name: S7, 2yrs, M, PC, B2

value: tonsils


title: YF22

hyb_protocol: A normalized amount of labeled cRNA was hybridized to Human Ref-8 beadchips (Illumina, San Diego) for 18 hours at 55 ºC.

scan_protocol: After washing and staining with Cy3, the chips were scanned on the Illumina iScan.

data_processing: Illumina BeadStudio software (Illumina, Inc., San Diego) was used to translate the scanned images into expression data, which were further log-transformed and normalized by the quantile normalization procedure using the Bioconductor package: Affymetrix.  Standardized fold changes were calculated as mean expression differences divided by pooled standard deviation in the log scale. Pearson correlation coefficients were calculated for all mRNA pairs. Ingenuity Pathway Analysis (IPA, www.ingenuity.com) was used to identify enriched pathways or biological functions among differentially expressed miRNAs.

source_name: Blood sample

label_protocol: The concentration and the quality of the extracted total RNA were accessed by NanoDrop (ThermoFisher Scientific Inc., Waltham, MA) and Bioanalzyer 2100 (Agilent technologies Inc., Santa Clara, CA), respectively.  Total RNA preparations with a 260/280 ratio between 1.98-2.22 and a RIN number > 7.4 with sufficient quantity were used for the mRNA expression analysis.  Globin reduction was performed using the Ambion GLOBINclear kit (Ambion Inc., Austin, TX).  The quality of the globin-reduced RNA samples was assessed by the Bioanalyzer 2100.  High quality samples were used to make first and second strand DNA followed by an IVT reaction.  The size distribution of the resulting biotin-labeled cRNA and the yield was checked by Agilent 2100 and NanoDrop, respectively.

extract_protocol: Whole blood (5ml) from each participant was drawn into two PAXgene tubes and was incubated at room temperature for three hours before being frozen at -70oC. Total RNA was extracted from the first PAXgene blood tubes tube using the PAXgene blood RNA extraction kit according to the manufacturer’s protocol.

tag: group

value: OLD

tag: race

value: White


title: Control DG, biological rep4

description:
Shn2_07_DG
Gene expression data from the DG of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: (BALB/c x C57BL/6J) F1

tag: age


title: YF21

value: Asian


title: S7_2yrs_M_GC_B2

description: This is GC gene expression sample from subject 7

source_name: S7, 2yrs, M, GC, B2

value: M


title: S4_5yrs_F_GC

description: This is GC MIRA-chip sample from subject 4

source_name: MIRA-enriched DNA

value: F

source_name: Input DNA

value: input DNA


title: S6_2yrs_M_naive_B3

description: This is technical replicate of S6_naive_B2 sample

source_name: S6, 2yrs, M, naive, B3

value: naive


title: Cy5: 8hrCNE2; Cy3: 8hrS16

description: NPCs at 8 hr after treatment

source_name: CNE2 8 hr


title: S2_6yrs_F_naive

description: This is naive MIRA-chip sample from subject 2

data_processing:
The log2(Cy5) values were normalized using Lowess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. These signal values were further quantile normalized to adjust for between sample variations.
DETAILS: The GC Lowess method utilizes both 'log2(Cy3)' and 'log2(Cy5)' values as following:
* Classify probes into bins according to CG content (proportion of number of C and G nucleotides in probe sequence)
* For each CG content bin (k), we fit lowess regression to predict log2(Cy5)_k value using log2(Cy3)_k value
* Compute normalized value  = sigma_bar *(observed log2(Cy5)_k - predicted log2(Cy5)_k)/sigma_k, where sigma_k is mean absolute deviation of (observed log2(Cy5)_k - predicted log2(Cy5)_k) and sigma_bar is geometric mean of all sigma_k's.
This normalization corrects for both dye bias and CG bias simultaneously.


title: Cy5: CNE2; Cy3: 8hrCNE2

description: CNE2 at 0 and 8 hr after treatment


title: S2_6yrs_F_PC

description: This is PC MIRA-chip sample from subject 2


title: Cy5: 8hrS16; Cy3: 8hrCNE2

description: NPCs at 8 hr after treatment


title: YF20

value: YOUNG


title: S6_2yrs_M_naive_B2

description: This is naive gene expression sample from subject 6

source_name: S6, 2yrs, M, naive, B2

value: 2 yrs


title: S3_1yrs_M_memory

description: This is memory MIRA-chip sample from subject 3

value: memory


title: Control DG, biological rep3

description:
Shn2_05_DG
Gene expression data from the DG of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: wild-type

value: dentate gyrus


title: Mutant DG, biological rep3

description:
Shn2_06_DG
Gene expression data from the DG of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: Shn-2 mutant


title: S7_2yrs_M_memory_B2

description: This is memory gene expression sample from subject 7

source_name: S7, 2yrs, M, memory, B2


title: S6_2yrs_M_memory_B2

description: This is memory gene expression sample from subject 6

source_name: S6, 2yrs, M, memory, B2


title: YF19


title: Replicate 2

source_name: AKI + cFP

value: AKI + cFP

source_name: AKI

value: AKI


title: S6_2yrs_M_PC_B2

description: This is PC gene expression sample from subject 6

source_name: S6, 2yrs, M, PC, B2

value: tonsils

value: PC


title: S1_2yrs_F_memory

description: This is memory MIRA-chip sample from subject 1

value: methylated DNA fraction


title: Mutant DG, biological rep1

description:
Shn2_02_DG
Gene expression data from the DG of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

source_name: DG of adult Shn-2 mutant mouse

value: (BALB/c x C57BL/6J) F1


title: YF17

value: OLD

value: White


title: S2_6yrs_F_memory

description: This is memory MIRA-chip sample from subject 2

value: F


title: Control DG, biological rep2

description:
Shn2_03_DG
Gene expression data from the DG of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

source_name: DG of adult control mouse


title: YF18


title: YF16

value: Hispanic


title: S2_6yrs_F_GC

description: This is GC MIRA-chip sample from subject 2

value: GC

value: input DNA


title: S5_4yrs_F_naive_B1

description: This is naive gene expression sample from subject 5

source_name: S5, 4yrs, F, naive, B1

value: 4 yrs

value: naive


title: HSC-3-5 tongue tumor

city: Tainan

first: Yi-Ting

address: No. 1 University Road

department: Department of Medical Laboratory Science and Biotecnology

country: Taiwan

institute: National Cheng Kung University

description: Gene expression of HSC-3-5 tumor after 1 week inoculated

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE 8×60K microarray (Agilent Technologies, USA) at 65°C for 17 hours.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: HSC-3-5 tumor, tongue tumor, 1 weeks

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Sub-populations from HSC-3 cells were base on their differential invasiveness to be isolated via using Transwell matrigel coated plates. Briefly, transwell matrigel invasion assay were performed to sub-lines selection of HSC-3 cells. After incubation for 72 hours, we harvested the cells that migrated through the upper chambers with matrigel coated or attached to the lower chambers. Then we amplified the cells that we harvested for second-round selection. We named the sub-line of the first-round selection cells as HSC-3-1. Following that other sub-lines from 2, 3, 4, and 5 rounds of selection were named as HSC-3-2, -3, -4, and -5, respectively. Both HSC-3 and HSC-3-5 cells were maintained in Eagle's minimal essential medium with 10% calf serum supplemented.

treatment_protocol: HSC-3 and HSC-3-5 oral cancer cells (2.5 × 105/ 20 μL) were respectively mixed with 20 μL matrigel and presently injected into the tongue of mice. After 1 week, total RNA was extracted from the tumor tissues on tongue.

value: tumor of HSC-3-5

value: 1 week of tumor on SCID mice tongue


title: Control DG, biological rep1

description:
Shn2_01_DG
Gene expression data from the DG of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: wild-type

value: dentate gyrus


title: HSC-3-5 subcutaneous tumor

description: Gene expression of HSC-3-5 tumor after 6 weeks inoculated

source_name: HSC-3-5 tumor, subcutaneous tumor, 6 weeks

treatment_protocol: HSC-3 and HSC-3-5 oral cancer cells (2.5 × 105/ 50 μL) were respectively mixed with 50 μL matrigel and subcutaneously injected into SCID mice. After 6 weeks, total RNA was extracted from the tumor tissue on SCID flank.

value: 6 weeks of tumor on SCID mice flank


title: S5_4yrs_F_naive_B3

description: This is technical replicate of S5_naive_B1 sample

source_name: S5, 4yrs, F, naive, B3

value: tonsils


title: Mutant DG, biological rep2

description:
Shn2_04_DG
Gene expression data from the DG of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: Shn-2 mutant


title: YF15

source_name: Blood sample

value: YOUNG


title: Cy5: CNE2; Cy3: S16

description: Control NPCs (0 hr), untreated.

value: An epithelial cell line derived from poorly differentiated nasopharyngeal carcinoma (Ref:Sizhong Z et al Int. J. Cancer 1983; 216:480-485)

value: cisplatin-sensitive cell clones from CNE2


title: Mutant PFC, biological rep6

description:
Shn-2_12_PFC
Gene expression data from the PFC of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

source_name: PFC of adult Shn-2 mutant mouse

value: (BALB/c x C57BL/6J) F1

value: medial prefrontal cortex


title: Replicate 4

value: AKI + cFP

value: AKI


title: S5_4yrs_F_memory_B1

description: This is memory gene expression sample from subject 5

source_name: S5, 4yrs, F, memory, B1

value: F

value: memory


title: HSC-3 cells (control) vs. HSC-3-5 cells (high invasive)

description: 1 X 10^7cells of total RNA was extracted after 24hours subculture

hyb_protocol: 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Agilent Feature Extraction Software (v10.5.1), an image analysis and normalization software,  is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: Control HSC-3-0 cells

label_protocol: RNA from HSC-3 cells was labeled by Cy3 and RNA from HSC-3-5 cells was labeled by Cy5. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: HSC-3 cells which metastasized to the lymph nodes were maintained in Eagle's minimal essential medium with 10% calf serum supplemented.

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

treatment_protocol: Sub-populations from HSC-3 cells were base on their differential invasiveness to be isolated via using Transwell matrigel coated plates. Briefly, transwell matrigel invasion assay were performed to sub-lines selection of HSC-3 cells. After incubation for 72 hours, we harvested the cells that migrated through the upper chambers with matrigel coated or attached to the lower chambers. Then we amplified the cells that we harvested for second-round selection. We named the sub-line of the first-round selection cells as HSC-3-1. Following that other sub-lines from 2, 3, 4, and 5 rounds of selection were named as HSC-3-2, -3, -4, and -5, respectively.

tag: cell line

value: tongue

source_name: HSC-3-5 cells

value: drived from the parental HSC-3 (JCRB0623)


title: HSC-3 tongue tumor

description: Gene expression of HSC-3 tumor after 1 week inoculated

source_name: HSC-3 tumor, tongue tumor, 1 weeks

value: tumor of HSC-3

value: 1 week of tumor on SCID mice tongue


title: S1_2yrs_F_GC

description: This is GC MIRA-chip sample from subject 1

source_name: MIRA-enriched DNA

value: methylated DNA fraction

tag: cell type

value: GC

source_name: Input DNA

value: input DNA


title: YF14

value: OLD

value: White


title: Control PFC, biological rep6

description:
Shn-2_11_PFC
Gene expression data from the PFC of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

source_name: PFC of adult control mouse

value: wild-type


title: S5_4yrs_F_PC_B1

description: This is PC gene expression sample from subject 5

source_name: S5, 4yrs, F, PC, B1

value: 4 yrs

value: tonsils

value: PC


title: Control PFC, biological rep5

description:
Shn-2_10_PFC
Gene expression data from the PFC of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: (BALB/c x C57BL/6J) F1

value: medial prefrontal cortex


title: YF13

value: Asian


title: Mutant PFC, biological rep5

description:
Shn-2_09_PFC
Gene expression data from the PFC of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: Shn-2 mutant


title: S1_2yrs_F_PC

description: This is PC MIRA-chip sample from subject 1

value: F


title: S3_1yrs_M_GC

description: This is GC MIRA-chip sample from subject 3

value: M


title: S2R+cells_M1BPRNAi_rep4

city: University Park

first: David

middle: Scott

last: Gilmour

state: Pennsylvania

address: 465 North Frear

department: Biochemistry and Molecular Biology

institute: Penn State University

description: M1BP-depleted sample

hyb_protocol: Hybridzation was performed by the Penn State Genomics Core facility, following nimbleGen Standard scanning protocol (see www.nimblegen.com).

scan_protocol: Scanning was performed by the Penn State Genomics Core facility, following nimbleGen Standard scanning protocol (see www.nimblegen.com).

data_processing: Data processing with ArrayStar 3.0 software package: background correction method: RMA background correction; normalization method: quantile; summarization method: median polish.

source_name: S2R+ cells

label_protocol: Labeling was performed by the Penn State Genomics Core facility, following NimbleGen standard operating protocol (see www.nimblegen.com).

growth_protocol: Cells were grown in Schneider's media with 10% FBS at 24 degrees C

extract_protocol: Total RNA was isolated using Qiagen's RNeasy Mini Kit

treatment_protocol: RNAi experiments were done as previously described (Clemens et al., 2000), with the following modifications.  30 ug of dsRNA was applied to 1 million cells in 1.5 ml of FBS-free Schneider's media.  The cells were indubated for 1 hr at 24 degrees C followed by addition of 1.5 ml of Schnedier's media containing 20% FBS.  The cells were incubated for an additional 5 days at 24 degrees C before expression analysis.

tag: RNAi


title: YF12

value: YOUNG


title: S5_4yrs_F_GC_B1

description: This is GC gene expression sample from subject 5

source_name: S5, 4yrs, F, GC, B1


title: S2R+cells_LacZRNAi_rep4

description: Control sample

value: LacZ


title: YF11


title: S4_5yrs_F_naive_B3

description: This is technical replicate of S4_naive_B1 sample

source_name: S4, 5yrs, F, naive, B3

value: 5 yrs

value: naive


title: S1_2yrs_F_naive

description: This is naive MIRA-chip sample from subject 1

value: methylated DNA fraction

value: input DNA


title: S2R+cells_M1BPRNAi_rep3

description: M1BP-depleted sample


title: S2R+cells_LacZRNAi_rep3

description: Control sample


title: YF10

value: OLD

value: White


title: S6_2yrs_M_GC_B2

description: This is GC gene expression sample from subject 6

source_name: S6, 2yrs, M, GC, B2

value: 2 yrs

value: GC


title: Mutant PFC, biological rep4

description:
Shn-2_08_PFC
Gene expression data from the PFC of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: Control PFC, biological rep4

description:
Shn-2_07_PFC
Gene expression data from the PFC of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: wild-type


title: YF9


title: Mutant PFC, biological rep3

description:
Shn-2_06_PFC
Gene expression data from the PFC of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: (BALB/c x C57BL/6J) F1


title: S4_5yrs_F_memory_B1

description: This is memory gene expression sample from subject 4

source_name: S4, 5yrs, F, memory, B1

value: tonsils

value: memory


title: S4_5yrs_F_naive_B1

description: This is naive gene expression sample from subject 4

source_name: S4, 5yrs, F, naive, B1


title: S4_5yrs_F_PC_B1

description: This is PC gene expression sample from subject 4

source_name: S4, 5yrs, F, PC, B1

value: PC


title: YF8

source_name: Blood sample


title: S2R+cells_M1BPRNAi_rep2

description: M1BP-depleted sample


title: S2R+cells_LacZRNAi_rep1

description: Control sample


title: YF6

value: Asian


title: YF7


title: S2R+cells_M1BPRNAi_rep1

description: M1BP-depleted sample


title: Control PFC, biological rep3

description:
Shn-2_05_PFC
Gene expression data from the PFC of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

value: medial prefrontal cortex


title: Control PFC, biological rep2

description:
Shn-2_03_PFC
Gene expression data from the PFC of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: S4_5yrs_F_GC_B1

description: This is GC gene expression sample from subject 4

source_name: S4, 5yrs, F, GC, B1

value: F


title: Mutant PFC, biological rep2

description:
Shn-2_04_PFC
Gene expression data from the PFC of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.

source_name: PFC of adult Shn-2 mutant mouse

value: Shn-2 mutant


title: YF5

value: YOUNG


title: S3_1yrs_M_naive_B1

description: This is naive gene expression sample from subject 3

source_name: S3, 1yrs, M, naive, B1

value: 1 yrs

value: M

value: naive


title: YF4


title: Control PFC, biological rep1

description:
Shn-2_01_PFC
Gene expression data from the PFC of a control mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: S3_1yrs_M_memory_B1

description: This is memory gene expression sample from subject 3

source_name: S3, 1yrs, M, memory, B1


title: Mutant PFC, biological rep1

description:
Shn-2_02_PFC
Gene expression data from the PFC of a Shn-2 mutant mouse.
(BALB/c x C57BL/6J) F1: obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background.


title: S3_1yrs_M_PC_B1

description: This is PC gene expression sample from subject 3

source_name: S3, 1yrs, M, PC, B1


title: YF2

value: OLD


title: S2R+cells_LacZRNAi_rep2

description: Control sample

value: LacZ


title: YF1


title: Shn2_Wildtype_3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

data_processing: The data were analyzed with Affymetrix Expression Cosole (v.1.1). The normalization used in RMA is quantile normalization.

source_name: Shn2_wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

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

tag: strain background

value: (BALB/c x C57BL/6J) F1 obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background

tag: genotype/variation

value: wild type

value: adult

value: male

value: hippocampus


title: S2_6yrs_F_naive_B3

description: This is naive gene expression sample from subject 2

source_name: S2, 6yrs, F, naive, B3

tag: subject

value: 6 yrs

value: tonsils


title: YF3

value: White


title: S3_1yrs_M_GC_B1

description: This is GC gene expression sample from subject 3

source_name: S3, 1yrs, M, GC, B1

tag: gender

value: GC


title: Shn2_Wildtype_4


title: Shn2_Wildtype_2


title: HSC-3 subcutaneous tumor

description: Gene expression of HSC-3 tumor after 6 weeks inoculated

source_name: HSC-3 tumor, subcutaneous tumor, 6 weeks

value: tumor of HSC-3

value: 6 weeks of tumor on SCID mice flank


title: S2_6yrs_F_PC_B3

description: This is PC gene expression sample from subject 2

source_name: S2, 6yrs, F, PC, B3

value: F

value: PC


title: S2_6yrs_F_memory_B3

description: This is memory gene expression sample from subject 2

source_name: S2, 6yrs, F, memory, B3

value: memory


title: Shn2_Wildtype_1


title: Shn2_Mutant_4

value: Shn2 deficient


title: Shn2_Mutant_3


title: S1_2yrs_F_naive_B3

description: This is naive gene expression sample from subject 1

source_name: S1, 2yrs, F, naive, B3

value: 2 yrs

value: naive


title: Shn2_Mutant_2

value: (BALB/c x C57BL/6J) F1 obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background


title: S1_2yrs_F_memory_B3

description: This is memory gene expression sample from subject 1

source_name: S1, 2yrs, F, memory, B3


title: MCF10A_CSE_21weeks

status: Public on Aug 12 2013

first: Francescopaolo

last: Di Cello

state: MD

address: 1650 Orleans Street

institute: The Johns Hopkin University School of Medicine

description:
non-tumorigenic breast epithelial cells
CSE

hyb_protocol: Bisulphite converted (EZ DNA methylation kit) DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.3

label: Cy5 and Cy3

source_name: MCF10A mammary epithelial cells CSE-treated for 21weeks

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was purified by phenol-chloroform extraction, and bisulfite-treated using EZ DNA methylation kit (Zymo Research).

tag: organ

value: mammary gland; breast

tag: disease

value: fibrocystic disease

value: epithelial

tag: growth properties

value: adherent

tag: source

value: ATCC

tag: treatment

value: cigarette smoke extract (CSE)


title: S2_6yrs_F_GC_B3

description: This is GC gene expression sample from subject 2

source_name: S2, 6yrs, F, GC, B3

value: 6 yrs

tag: tissue

value: tonsils

tag: batch


title: S1_2yrs_F_GC_B3

description: This is GC gene expression sample from subject 1

source_name: S1, 2yrs, F, GC, B3

value: GC


title: Primary glioblastoma sample 5

description: Cy3=primary glioblastoma, Cy5=pooled genomic DNA

hyb_protocol: Labelled tumor and normal DNA were combined together and with hybridization buffer (Agilent Oligo aCGH Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner

data_processing: CN data was mapped to the human genome sequence hg19 freeze and log2 intensity ratios were segmented using circular binary segmentation (CBS) to translate noisy intensity measurements into regions of equal CN

source_name: primary glioblastoma

label_protocol: 500 ng of tumor genomic DNA were labeled with Cy-3 and 500 ng normal reference DNA labelled with Cy-5 along with 5X Buffer, 10X dNTP and Exo-Klenow enzyme, incubated at 37C for 2 hr and 65C for 10 min. All reagents from the Agilent Genomic DNA Labeling Kit PLUS

extract_protocol: Small pieces of snap-frozen samples were homogenized in Tris-SDS-Proteinase K lysis buffer overnight, then extracted with phenol/chloroform/isoamyl alcohol, precipitated with sodium acetate and ethanol, and resuspended in TE buffer.

value: male

tag: age (y)

tag: tumor grade

value: IV

source_name: Pooled genomic DNA from healthy anonymous donors


title: Primary glioblastoma sample 4

value: female


title: Primary glioblastoma sample 2


title: S1_2yrs_F_PC_B3

description: This is PC gene expression sample from subject 1

source_name: S1, 2yrs, F, PC, B3

tag: age

value: F

value: PC


title: Shn2_Mutant_1

value: Shn2 deficient

value: adult

value: hippocampus


title: MCF10A_Mock_21weeks

description:
non-tumorigenic breast epithelial cells
Mock

source_name: MCF10A mammary epithelial cells mock-treated for 21weeks

value: mammary gland; breast

value: control


title: Primary glioblastoma sample 3


title: Primary glioblastoma sample 1


title: tx303

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: This Sample represents up to 3 replicates.

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the arrays according to the array manufacturer protocol (42°C, 16-20hrs).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the GenePix4000B Scanner (Axon/Molecular Devices) or MS2000 Scanner (Nimblegen) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files for 2.1M and 1.4M platforms that were exported from NimbleScan were imported into the Bioconductor statistical environment (Gentleman et al., 2004). 2.1M platform pair files were subset to the 1.4M platform probes to facilitate combined analysis. For each genotype, designated as HapMap2 ‘HM’ lines (excluding B73), microarray data channels were assigned the following factors: B73, HM_line, B73 input, or HM_line input depending on sample derivation. For samples in which three replicates were not available, individual replicates were duplicated to maintain normalization methods across all samples. Non-maize probes and vendor-supplied process control probes were configured to have analytical weights of zero. Variance-stabilizing normalization was used to account for array-specific effects. Factor-specific hybridization coefficients were estimated by fitting fixed linear model accounting for dye and sample effects to the data using the limma package (Smyth 2004). To compute biologically relevant information about each HM line’s DNA methylation, the following contrasts were then computed: B73 IP vs B73 input (B73 methylation); HM_line input vs B73 input (CGH and differential hybridization efficiency); HM_line IP vs [HM_line input vs B73 input] (HM_line methylation corrected for differential hybridization efficiency); B73 IP vs HM_line IP vs [HM_line input vs B73 input]] (differential DNA methylation corrected for differential hybridization efficiency). Moderated t-statistics and the log-odds score for differential MeDIP enrichment were computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05 (Smyth 2004).

organism: Zea mays

source_name: tx303 input

label_protocol: Amplified input and methylated DNA samples were labeled (3 x 1ug per reaction), hybridized to the array and washed according to the array manufacturers protocol.  Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5.

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation.  15-30ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps).  Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

treatment_protocol: genomic DNAs were sonicated, amplified, and fluorophore-labeled

tag: genotype

value: seedling leaf (L3)

tag: dna

value: input control

source_name: tx303 IP

treatment_protocol: genomic DNAs were sonicated, methylated DNAs were isolated, amplified, and fluorophore-labeled

tag: antibody

value: anti-5-methylcytosine monoclonal antibody (Zymo, Cat # D5101)

value: methylated DNA


title: oh43

source_name: oh43 input

source_name: oh43 IP


title: m37w

source_name: m37w input

source_name: m37w IP


title: mo17

source_name: mo17 input

source_name: mo17 IP


title: ki11

source_name: ki11 input

source_name: ki11 IP


title: p39

source_name: p39 input

source_name: p39 IP


title: ms71

source_name: ms71 input

source_name: ms71 IP


title: w22

source_name: w22 input

source_name: w22 IP


title: mo18w

source_name: mo18w input

source_name: mo18w IP


title: m162w

source_name: m162w input

source_name: m162w IP


title: Healthy control 18

city: Jaen

first: Octavio

last: Caba

state: Jaen

address: Paraje de las Lagunillas

department: Health Sciences

country: Spain

institute: University of Jaen

description: Gene expression data from peripheral blood of control 18

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST v2 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner

data_processing: Raw data was preprocessed using the RMA method. For transcript probe set definition the custom CDF package from the brainarray group (hugene10stv1enstcdf version 13, defining probe sets for transcripts from Ensembl core database version 58) was used

source_name: Peripheral blood of control 18

label_protocol: RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station

extract_protocol: Total RNA was extracted from peripheral blood samples using the PAXgene Blood RNA Kit (PreAnalytix). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 7.

value: Male

tag: disease state

tag: pathological staging

tag: cell type

value: PBMC


title: ki3

source_name: ki3 input

source_name: ki3 IP


title: nc358

source_name: nc358 input

source_name: nc358 IP


title: oh7b

source_name: oh7b input

source_name: oh7b IP


title: cml333

source_name: cml333 input

source_name: cml333 IP


title: b73

source_name: b73 input

source_name: b73 IP


title: Healthy control 15

description: Gene expression data from peripheral blood of control 15

source_name: Peripheral blood of control 15

tag: gender


title: Healthy control 17

description: Gene expression data from peripheral blood of control 17

source_name: Peripheral blood of control 17

value: Female


title: Healthy control 16

description: Gene expression data from peripheral blood of control 16

source_name: Peripheral blood of control 16


title: il14h

source_name: il14h input

source_name: il14h IP


title: ky21

source_name: ky21 input

source_name: ky21 IP


title: W64A

source_name: w64a input

source_name: w64a IP


title: b97

source_name: b97 input

source_name: b97 IP


title: cml322

source_name: cml322 input

source_name: cml322 IP


title: Healthy control 14

description: Gene expression data from peripheral blood of control 14

source_name: Peripheral blood of control 14


title: hp301

source_name: hp301 input

source_name: hp301 IP


title: Healthy control 12

description: Gene expression data from peripheral blood of control 12

source_name: Peripheral blood of control 12


title: Healthy control 13

description: Gene expression data from peripheral blood of control 13

source_name: Peripheral blood of control 13


title: TIL11

source_name: til11 input

source_name: til11 IP


title: cml277

source_name: cml277 input

source_name: cml277 IP


title: cml103

source_name: cml103 input

source_name: cml103 IP


title: Healthy control 11

description: Gene expression data from peripheral blood of control 11

source_name: Peripheral blood of control 11


title: MCF10A_CSE_21weeks_clone 1

description:
non-tumorigenic breast epithelial cells
SC1

hyb_protocol: Samples were amplified and labeled using Quick Amp Labeling Kit (Cat# 5190-0447, Agilent Technologies), Full Spectrum Primers (Cat# RA300A-2, System Bioscience), Cynine-3-CTP and Cynine-5-CTP (Perkin Elmer), and hybridized using Gene Expression Hybridization Kit by following manufacturer's protocol (G4140-90050, Agilent Technologies)

scan_protocol: Microarrays were scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for gene expression microarrays with 100% PMT and 5 micrometer resolutions. Data were extracted using Feature Extraction Software v9.5.3.1 (Agilent Technologies) and protocol for gene expression microarrays.

data_processing: Raw median foreground and background signals were taken for both channels. Followed by background substraction, LOESS normalization for within-array normalization, and AQUANTILE normalization for between-array normalization.

source_name: MCF10A mammary epithelial cells Mock-treated for 21 weeks

label_protocol: Agilent low RNA input linear amplification kit

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

tag: organ

value: fibrocystic disease

value: epithelial

value: adherent

value: ATCC

source_name: MCF10A mammary epithelial cells CSE-treated for 21 weeks

value: cigarette smoke extract (CSE)


title: MCF10A_CSE_21weeks_clone 2

description:
non-tumorigenic breast epithelial cells
SC2

tag: disease


title: Healthy control 10

description: Gene expression data from peripheral blood of control 10

source_name: Peripheral blood of control 10


title: TIL14

source_name: til14 input

source_name: til14 IP


title: Healthy control 9

description: Gene expression data from peripheral blood of control 9

source_name: Peripheral blood of control 9


title: TIL16

source_name: til16 input

source_name: til16 IP


title: cml228

source_name: cml228 input

source_name: cml228 IP


title: Healthy control 7

description: Gene expression data from peripheral blood of control 7

source_name: Peripheral blood of control 7


title: Healthy control 8

description: Gene expression data from peripheral blood of control 8

source_name: Peripheral blood of control 8


title: cml52

source_name: cml52 input

source_name: cml52 IP


title: TIL09

source_name: til09 input

source_name: til09 IP


title: Healthy control 2

description: Gene expression data from peripheral blood of control 2

source_name: Peripheral blood of control 2


title: Healthy control 3

description: Gene expression data from peripheral blood of control 3

source_name: Peripheral blood of control 3


title: Healthy control 1

description: Gene expression data from peripheral blood of control 1

source_name: Peripheral blood of control 1


title: TIL15

description: This Sample represents up to 3 replicates.

source_name: til15 input

source_name: til15 IP


title: Healthy control 5

description: Gene expression data from peripheral blood of control 5

source_name: Peripheral blood of control 5


title: Healthy control 6

description: Gene expression data from peripheral blood of control 6

source_name: Peripheral blood of control 6


title: Healthy control 4

description: Gene expression data from peripheral blood of control 4

source_name: Peripheral blood of control 4


title: TIL06

source_name: til06 input

source_name: til06 IP


title: 2012-T7-MRT_N

city: Tokyo

first: Riki

last: Nishimura

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

label: Biotin

source_name: unclassified RMS tumor specimen

label_protocol: Affymetrix standard protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from resected fresh tumor blocks or freeze tumor blocks.

value: RMS

tag: histology subtype

value: unclassified


title: TIL01

source_name: til01 input

source_name: til01 IP


title: 96-T63-SJRH4-RMS-cl_N

description: Hybridized to 50K_Hind

source_name: RMS cell line


title: TIL07

source_name: til07 input

source_name: til07 IP


title: RMS35_N

description: Hybridized to 250K_Nsp

source_name: RMS tumor specimen (unknown histological type)

value: unknown histological type


title: mr22

source_name: mr22 input

source_name: mr22 IP


title: RMS30_N

description: Hybridized to 250K_Nsp


title: mr25

source_name: mr25 input

source_name: mr25 IP


title: mr20

source_name: mr20 input

source_name: mr20 IP


title: RMS10_N

description: Hybridized to 250K_Nsp

source_name: ERMS tumor specimen

value: ERMS


title: RMS905_N

description: Hybridized to 250K_Nsp


title: mr19

source_name: mr19 input

source_name: mr19 IP


title: 93-ERMS-hamamed_N

description: Hybridized to 250K_Nsp


title: 2007-T3-RMS_N

description: Hybridized to 250K_Nsp


title: mr01

source_name: mr01 input

source_name: mr01 IP


title: mr02

source_name: mr02 input

source_name: mr02 IP


title: RMS7_N

description: Hybridized to 250K_Nsp


title: mr10

source_name: mr10 input

source_name: mr10 IP


title: G217B Y/M expression, sample 1

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

hyb_protocol: Cy5-labeled samples were competitively hybridized against the Cy3-labeled samples on custom glass slide 70-mer oligomer microarrays.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments/Molecular Devices).

data_processing:
Arrays were gridded using GenePix Pro, version 6.0 (Molecular Devices)
and median normalized using NOMAD 2.0 (http://nomad2.ucsf.edu/).  To
eliminate elements with low signal, we analyzed only elements for
which the sum of the medians for the 635 nm and 532 nm channels was >=
150 intensity units.  Median normalized ratios for elements passing this
threshold are given in the VALUE column.

organism: Histoplasma capsulatum

source_name: G217B yeast

label_protocol:
Fluorescently labeled cDNA was synthesized by
incorporating amino-allyl dUTP during reverse transcription with
Superscript II (Life Technologies) of 15 ug total RNA with
oligonucleotide-dT and random hexamers used as primers. Cy3 or Cy5 dyes (GE
Life Sciences) were coupled to the amino-allyl group as described
previously (Science 278: 680-686).

extract_protocol:
For the microarray time-course study, G217B yeast cells were grown at 37C
in HMM medium and subjected to passage at 1:25 dilution into HMM medium.
After 1 day of growth to early log phase, a portion of cells were harvested
for the t = 0 timepoints and the remaining cells were washed in PBS and
then resuspended with no dilution into 200 mL HMM (glucose) and HMM/100 mM
GlcNAc media for t =1 h, 4 h, and 24 h timepoints or resuspended with a
1:10 dilution into 200 mL HMM (glucose) and HMM/100 mM GlcNAc media for t =
4 d and 7 d timepoints. Cultures for all timepoints were allowed to
continue to grow at 37C under 5% CO2 for yeast-phase growth or transferred
to RT for filamentous-phase growth. For the endpoint microarray experiment,
G217B yeast cells were grown for 2 days at 37C in HMM glucose medium and
filamentous cells were grown for 4-6 weeks with passaging 3 times (1:5
dilution) into fresh HMM glucose medium at RT before reaching a sufficient
density of cells for harvesting. At each indicated timepoint,
cells were harvested by centrifugation or filtration and total RNA was
isolated using a guanidine thiocyanate lysis protocol as previously
described (Mol Biol Cell 14: 2314-2326).

tag: strain

value: Histoplasma capsulatum G217B

tag: sample type

value: yeast

source_name: G217B mycelia

value: mycelia


title: mr14

source_name: mr14 input

tag: tissue

value: seedling leaf (L3)

value: input control

source_name: mr14 IP

value: anti-5-methylcytosine monoclonal antibody (Zymo, Cat # D5101)


title: mr18

source_name: mr18 input

source_name: mr18 IP

value: methylated DNA


title: RMS902_N

description: Hybridized to 250K_Nsp


title: RT Glucose 24hours expression, sample 1

source_name: RT Glucose 24hours

tag: treatment

value: room temperature

tag: medium

value: Glucose

tag: time

source_name: pooled reference

value: pooled reference


title: TZI8 Rep 1

hyb_protocol: 20ug (30ug if possible) of labeled DNAs (30ug input DNA + 30ug IP DNA) were hybridized to the 12x270K arrays according to the array manufacturer protocol (42°C, 72hrs). Arrays were then washed according to the array manufacturers protocol.  (NimbleGen Arrays User’s Guide: CGH and CGH/LOH Arrays v9.1 chap. 4,5).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the MS 200 Microarray Scanner and the MS 200 Data Collection Software was used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files exported from Nimblescan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Samples were frist normalized within arrays to minimize dye-bias,  and then normalized across arrays to achieve consistency between arrays. The normalized log2 (IP/input) ratio was used for downstream analyses.

source_name: TZI8 Rep 1 input

label_protocol: Amplified input and methylated DNA samples were labeled (.666 ug per subarray sample), hybridized to the 12x270K  feature array. Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5. (NimbleGen Arrays User’s Guide: CGH and CGH/LOH Arrays v9.1 chap. 3).

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation.  2ug of genomic DNA were sheared using a Covaris S220 Focused-ultrasonicator. Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of corresponding sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-50RXN).

tag: replication

source_name: TZI8 Rep 1 IP


title: RMS904_N

description: Hybridized to 250K_Nsp

source_name: ERMS tumor specimen


title: Stage_I_Aggregates_dark_grown

type: SAGE

anchor: DpnII

city: Utrecht

last: Wösten

address: Padualaan 8

country: Netherlands

institute: Utrecht University

description: Anchoring enzyme: DpnII

data_processing: Tags of 16 bp were identified using custom scripts. Note that the restriction site of DpnII (GATC) is not included in these 16 bp.

organism: Schizophyllum commune

source_name: Stage I Aggregates - Dark grown

growth_protocol: A 7-day-old dikaryotic colony grown on solid mnimal medium at 30 degrees C in the dark was homogenized in 200 ml Minimal Medium using a Waring blender for 1 min at low speed. 2 ml of the homogenized mycelium was spread out over a polycarbonate membrane that was placed on top of solidified minimal medium. The dikaryon was grown for 4 days in the dark at 25 degrees C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified over a column (Qiagen RNeasy Mini). PolyA RNA was isolated using oligo-dT beads.

tag: developmental stage

value: stage I aggregates

value: Dikaryon, resulting from a cross of the monokaryotic co-isogenic strains 4-40 (CBS 340.81) and 4-39 (CBS 341.81)


title: mr09

source_name: mr09 input

tag: genotype

tag: dna

source_name: mr09 IP


title: RT Glucose 4hour expression, sample 1

source_name: RT Glucose 4hour


title: TIL17 Rep 1

source_name: TIL17 Rep 1 input

source_name: TIL17 Rep 1 IP


title: cml330

source_name: cml330 input

source_name: cml330 IP

tag: antibody


title: mr11

source_name: mr11 input

source_name: mr11 IP


title: RMS41_N

description: Hybridized to 250K_Nsp


title: cml505

source_name: cml505 input

source_name: cml505 IP


title: 37C Glucose 24hours expression, sample 1

source_name: 37C Glucose 24hours


title: deltaSC3_deltaSC4_dikaryon

description: Anchoring enzyme: DpnII

source_name: Dikaryon of deltaSC3 deltaSC4 strain

growth_protocol: A 7-day-old dikaryotic colony grown on solid mnimal medium at 30 degrees C in the dark was homogenized in 200 ml Minimal Medium using a Waring blender for 1 min at low speed. 2 ml of the homogenized mycelium was spread out over a polycarbonate membrane that was placed on top of solidified minimal medium. The dikaryon was grown for 4 days in the light at 25 degrees C.

value: vegetative mycelium with few aerial hyphae

value: Dikaryon, resulting from a cross of the monokaryotic co-isogenic strains 4-40 (CBS 340.81) and 4-39 (CBS 341.81). In both strains, the sc3 and sc4 genes have been deleted, as described in Van Wetter et al (2000), Mol Microbiol 36(1):201-211


title: cml504

source_name: cml504 input

source_name: cml504 IP


title: Monokaryon_dark_grown

description: Anchoring enzyme: DpnII

source_name: Monokaryon, vegetative mycelium, dark grown

growth_protocol: A 7-day-old colony grown on solid mnimal medium at 30 degrees C in the dark was homogenized in 200 ml Minimal Medium using a Waring blender for 1 min at low speed. 2 ml of the homogenized mycelium was spread out over a polycarbonate membrane that was placed on top of solidified minimal medium. Vegetative monokaryotic mycelium was grown for 4 days in the dark at 25 degrees C.

value: vegetative mycelium

value: Monokaryon, strain 4-40 (CBS 340.81)


title: TIL07 Rep 1

source_name: TIL07 Rep 1 input

source_name: TIL07 Rep 1 IP


title: RT GlcNAc 24hours expression, sample 1

source_name: RT GlcNAc 24hours

value: GlcNAc

source_name: pooled reference


title: CML85 Rep 1

source_name: CML85 Rep 1 input

source_name: CML85 Rep 1 IP


title: RMS32_N

description: Hybridized to 250K_Nsp

source_name: ERMS tumor specimen

value: RMS

value: ERMS


title: 37C Glucose 4hour expression, sample 1

source_name: 37C Glucose 4hour

value: Histoplasma capsulatum G217B


title: RT GlcNAc 4hour expression, sample 1

source_name: RT GlcNAc 4hour


title: CML418 Rep 1

source_name: CML418 Rep 1 input

value: seedling leaf (L3)

source_name: CML418 Rep 1 IP


title: NC350 Rep 1

source_name: NC350 Rep 1 input

source_name: NC350 Rep 1 IP


title: cml206

source_name: cml206 input

value: input control

source_name: cml206 IP


title: CML96 Rep 1

source_name: CML96 Rep 1 input

source_name: CML96 Rep 1 IP


title: cml202

source_name: cml202 input

source_name: cml202 IP

value: anti-5-methylcytosine monoclonal antibody (Zymo, Cat # D5101)


title: CML99 Rep 1

source_name: CML99 Rep 1 input

source_name: CML99 Rep 1 IP


title: RT GlcNAc 1hour expression, sample 1

source_name: RT GlcNAc 1hour

source_name: pooled reference


title: CML69 Rep 1

source_name: CML69 Rep 1 input

source_name: CML69 Rep 1 IP


title: 37C Glucose 1hour expression, sample 1

source_name: 37C Glucose 1hour


title: CML511 Rep 1

source_name: CML511 Rep 1 input

source_name: CML511 Rep 1 IP


title: CML479 Rep 1

source_name: CML479 Rep 1 input

source_name: CML479 Rep 1 IP


title: CML411 Rep 1

source_name: CML411 Rep 1 input

source_name: CML411 Rep 1 IP


title: IBM0379 Rep 1

source_name: IBM0379 Rep 1 input

source_name: IBM0379 Rep 1 IP


title: RMS28_N

description: Hybridized to 250K_Nsp

source_name: ERMS tumor specimen


title: RMS31_N

description: Hybridized to 250K_Nsp


title: IBM0325 Rep 1

source_name: IBM0325 Rep 1 input

source_name: IBM0325 Rep 1 IP


title: 37C GlcNAc 24hours expression, sample 1

source_name: 37C GlcNAc 24hours


title: cml192

source_name: cml192 input

source_name: cml192 IP

value: methylated DNA


title: IBM0062 Rep 1

source_name: IBM0062 Rep 1 input

source_name: IBM0062 Rep 1 IP


title: RT Glucose 1hour expression, sample 1

source_name: RT Glucose 1hour

value: room temperature

source_name: pooled reference


title: RMS25_N

description: Hybridized to 250K_Nsp


title: 37C GlcNAc 4hour expression, sample 1

source_name: 37C GlcNAc 4hour


title: RMS27_N

description: Hybridized to 250K_Nsp


title: 37C GlcNAc 1hour expression, sample 1

source_name: 37C GlcNAc 1hour


title: IBM0048 Rep 1

source_name: IBM0048 Rep 1 input

source_name: IBM0048 Rep 1 IP


title: IBM0012 Rep 1

source_name: IBM0012 Rep 1 input

source_name: IBM0012 Rep 1 IP


title: IBM0311 Rep 1

source_name: IBM0311 Rep 1 input

source_name: IBM0311 Rep 1 IP


title: RMS14_N

description: Hybridized to 250K_Nsp

source_name: ERMS tumor specimen


title: t=0, 37C Glucose Early Time Course expression, sample 1

source_name: t=0, 37C Glucose Early Time Course

value: Glucose


title: IBM0352 Rep 1

source_name: IBM0352 Rep 1 input

source_name: IBM0352 Rep 1 IP