title: MR siRNA rep2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: primary endometrial stromal cells transfected with siRNA oligos against MR followed by decidualization.

hyb_protocol: Standard Affymentrix hybridization protocols.

scan_protocol: Affymetrix GeneChip 7G Scanner according to standard protocol.

data_processing: Microarray analysis on total RNA samples was performed by University College London Genomics using Bioconductor v 2.0 and R version 2.9.0. The Robust Multi-Array Analysis (RMA) algorithm was used to obtain normalised data and gene signals.

source_name: endometrial stromal cells

label_protocol: NuGen Encore Biotin Module as per manufacturer's protocol on cDNA prepared using Ovation Pico SL Kit according to manufacturer's protocol.

growth_protocol: Endometrial samples were obtained from premenopausal women without uterine pathology and human endometrial stromal cells were isolated, cultured and maintained. The tissues were washed twice in a 1:1 mixture of DMEM and Ham's F12 (DMEM/F12) (Sigma, Poole, UK), finely minced, and enzymatically digested with collagenase (134 U/ml) and deoxyribonuclease type I (156 U/ml) (Sigma, Poole, UK) for 1 h at 37°C. After centrifugation at 400 xg for 4 min the pellet was resuspended in maintenance medium of DMEM/F12 containing 10% dextran coated charcoal treated fetal bovine serum (DCC-FBS), 1% L-glutamine and 1% antibiotic-antimycotic solution. Proliferating endometrial stromal cells were cultured in maintenance medium until confluence.

extract_protocol: Total RNA was extracted using STAT-60 reagent (AMS Biotechnology, Abingdon, UK). RNA quality was analyzed on an Agilent 2100 bioanalyzer (Agilent Technologies, Waldbronn, Germany).  All samples had RIN >9.6.

treatment_protocol: Primary human endometrial stromal cells were transfected using the ProFection mammalian transfection kit (Promega, Madison, WI), with 100 nM per well of the following siRNA reagents (Dharmacon, Lafayette, CO): siCONTROL non-targeting (NT) siRNA pool (Group A), GR siGENOME SMARTpool siRNA (Group B), or MR siGENOME SMARTpool siRNA (Group C). In decidualization experiments, confluent monolayers were maintained in DMEM/F12 now containing 2% DCC-FBS and treated with 0.5mM 8-bromoadenosine cAMP (8-bromo-cAMP; Sigma, St Louis, MO), 1μM progesterone (P4; Sigma), and 0.1μM cortisone (E; Sigma) for four days.

value: 32 years

tag: patient #

value: patient 2

value: female

tag: cell type

value: endometrial stromal cells

value: mineralocorticoid receptor siRNA


title: MR siRNA rep3

status: Public on Nov 28 2012

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: age

value: 37 years

value: patient 3

tag: gender

tag: treatment


title: MR siRNA rep4

value: 39 years

value: patient 4


title: Lymph node patient 44

city: Darlinghurst

first: David

last: Ma

state: NSW

address: L8 Lowy Packer Building, 405 Liverpool St

department: Haematology research

country: Australia

institute: St Vincent's Hospital

hyb_protocol: Tagged probes in hybridisation buffer (3DNA 900MPX kit) were hybridised to a microarray overnight in a humidified slide chamber box After hybridization, slides were washed sequentially and hybridisation repeated using tagged Cy3 or Cy5 3DNA capture reagents

scan_protocol: Scanned on a GenePix 4000A scanner; fluorescent signals were quantified using GenePix Pro 3.0

data_processing: Data from GenePix result files were pre-processed by within-array print-tip Lowess normalisation using R.

source_name: Lymph node patient 44

label_protocol: Probe (with capture sequences) synthesis was carried out on 2ug of patient (Cy5) and reference (Cy3) total RNA using the 3DNA 900MPX kit (Genisphere) following manufacturer's instructions.

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

value: Female

tag: age at diagnosis

tag: hospital

value: St Vincent's Hospital

tag: array batch

tag: diagnosis

value: DLBCL

tag: subtype/fl grade

value: GCB (BCL6 +)

tag: nhl or chl

value: NHL

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects

tag: tissue

value: PBMSC


title: 996-P-ck-1

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road, Furong District

country: China

institute: Hunan Agricultural University

description:
Gene expression of rice spikelets of developmental stage7-9,0min after 40 degree centigrade
rice spikelets of developmental stage7-9 at the middle of main panicle

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rice Genome Oligo Microarrays (015241) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, respectively), and the scan data with 100% and 10% PMT were merged automatically.

data_processing: The above hybridization signal data files in text format from the Feature Extraction Software were imported into GeneSpring GX (Agilent Technologies). The data were marked with specific flag such as P, A, M (representing detected, not detected and compromised, respectively) using the default parameter and algorithm, and then normalized by Quantile algorithm followed by the process of baseline to median of all samples. The normalized data from two replicates of each sample were log2 transformed, and the correlation coefficient of replicates was determined through hierarchical clustering using complete linkage algorithm as implemented TIGR MeV version 4.0.

organism: Oryza sativa

source_name: rice spikelets of developmental stage7-9,0min after 40 degree centigrade,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by QIAGEN RNeasy Mini Kit (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Heat-tolerant rice cultivar 996 was cultivated in the field until phase 7-9 of panicle development with half length of mature spikelets.

extract_protocol: Young spikelets with the phase 7-9 at the middle of main panicles were collected at the time point of 0min (as control), 20min, 1hr, 2hr, 4hr, and 8hr, respectively, after heat treatment, and frozen in liquid nitrogen immediately, and stored at -80°C for microarray hybridization.

treatment_protocol: The proper rice plants transplanted into pots were moved in a growth chamber (Binder, Tuttlingen, Germany) under the condition of 32°C with 80% humidity at day, and 28°C with 80% relative humidity at night for one day, and then at 40°C with 80% relative humidity and 600 μmol m-2 s-1 of photosynthetically active radiation for 8hr.

tag: cultivar

value: Heat-tolerant rice cultivar 996

tag: developmental stage

tag: stress

value: control

tag: time


title: Lymph node patient 35

source_name: Lymph node patient 35

value: Male

value: Small lymphocytic lymphoma


title: Lymph node patient 45

source_name: Lymph node patient 45

value: FL

value: Grade 2


title: Lymph node patient 43

source_name: Lymph node patient 43


title: Lymph node patient 31

source_name: Lymph node patient 31

value: Grade 3


title: Lymph node patient 33

source_name: Lymph node patient 33

value: cHL

value: Nodular sclerosing


title: non-targeting siRNA rep4

description: primary endometrial stromal cells transfected with control non-targeting siRNA followed by decidualization.

value: 39 years

value: female

value: endometrial stromal cells

value: non-targeting siRNA


title: Lymph node patient 25

source_name: Lymph node patient 25

value: St Vincent's Hospital

value: DLBCL

value: Non-GCB (NUM-1 +)


title: GR siRNA rep2

description: primary endometrial stromal cells transfected with siRNA oligos against GR followed by decidualization.

value: 32 years

value: patient 2

value: glucocorticoid receptor siRNA


title: non-targeting siRNA rep3

value: 37 years

value: patient 3


title: Lymph node patient 46

source_name: Lymph node patient 46

value: Male

value: FL

value: NHL

value: PBMSC


title: GR siRNA rep3


title: GR siRNA rep1

value: 28 years

value: patient 1


title: GR siRNA rep4

value: 39 years

value: patient 4

value: female


title: Lymph node patient 26

source_name: Lymph node patient 26

value: Female

value: St Vincent's Hospital

value: Grade 3


title: Lymph node patient 48

source_name: Lymph node patient 48

value: Grade 2


title: Lymph node patient 29

source_name: Lymph node patient 29

value: Reactive


title: MR siRNA rep1

value: endometrial stromal cells

value: mineralocorticoid receptor siRNA


title: Lymph node patient 30

source_name: Lymph node patient 30


title: non-targeting siRNA rep1

value: non-targeting siRNA


title: Lymph node patient 24

source_name: Lymph node patient 24

value: Male

value: Grade 1


title: non-targeting siRNA rep2

value: 32 years

value: patient 2


title: Lymph node patient 12

source_name: Lymph node patient 12

value: cHL

value: Mixed cellularity

value: PBMSC


title: Lymph node patient 21

source_name: Lymph node patient 21

value: FL

value: NHL


title: Lymph node patient 11

source_name: Lymph node patient 11

value: Female

value: Small lymphocytic lymphoma


title: Lymph node patient 14

source_name: Lymph node patient 14

value: St Vincent's Hospital

value: Grade 3

source_name: Total RNA pooled from the mobilised peripheral blood stem cells (PBSMC) of 10 healthy subjects


title: Lymph node patient 22

source_name: Lymph node patient 22


title: Lymph node patient 20

source_name: Lymph node patient 20

value: Grade 2


title: Lymph node patient 6

source_name: Lymph node patient 6

value: Reactive


title: Lymph node patient 15

source_name: Lymph node patient 15


title: Lymph node patient 10

source_name: Lymph node patient 10


title: macrophage uninfected control biological rep2

city: Buenos Aires

first: Marcelo

middle: Abel

last: Soria

address: Ave. San Martin 4453

country: Argentina

institute: University of Buenos Aires. College of Agronomy

description: Gene expression data 4 hours after mock infection

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: Array scanning was performed according to the standard Affymetrix protocol using an Affymetrix GeneChip Scanner 3000

data_processing: The array data were analysed with R/Bioconductor (http://www.r-project.org; http://www.bioconductor.org) using Robust Multichip Analysis (RMA) as implemented in the Affy package.

organism: Bos taurus

source_name: Bovine macrophage cells in culture were incubated for 7 days, uninfected control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Blood from healthy animals was taken in sterile conditions and peripheral blood mononuclear cells (PBMCs) were separated from heparinized blood by centrifugation over histopaque 1077 (Sigma, USA) following manufacturer’s protocol. Cells (2 X 10e8) were incubated in T75 flasks at 37 ˚C for one week in RPMI 1640 complete medium supplemented whit 10% of autologous plasma and washed periodically. Only adherent cells were maintained in culture.

extract_protocol: Four hours post infection, the cells were scraped and lysed with 1 ml of chilled Trizol (Invitrogen, Carlsbad, USA). Trizol was removed from the flasks and the lysate homogenized. Cells RNAs extractions were then performed according manufacter´s instruction for Trizol reagent (Invitrogen).

treatment_protocol: M. bovis strains 04-303 and 534 were grown in either Middlebrook 7H9 medium supplemented with 0.05 % Tween 80 or Middlebrook 7H11 medium, both supplemented with albumin/dextrose/catalase and 0.4% pyruvate. Bacterial cultures were harvested, resuspended in RPMI medium, vortexed, sonicated for 1 min in an ultrasonic cleaner and passed through a syringe needle (25 gauge) to disaggregate clumps. The infection was performed at a multiplicity of infection (m.o.i.) of 5 bacteria/cell. Infected cells were incubated for 4 h, and then washed three times with fresh RPMI medium.

value: macrophages (peripheral blood mononuclear cells)

tag: infectious agent

value: mock RPMI

tag: breed

value: Holstein


title: vasa_Rep2

city: Worcester

first: Jie

last: Wang

state: MA

address: 364 Plantation St.

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

hyb_protocol: Recommended Affymetrix protocol

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G according to manufacturer's instructions.

data_processing:
Since transposons account for more than 10% of the probes on the tiling array, a special normalization workflow has been taken to avoid over-normalization of signals. Coordinates and raw signal values for Drosophila tiling 2.0R array probes were extracted from Affymetrix Tiling Array Software. Then probes mapped to transposon regions were identified. The remaining non-transposon probes were quantile-normalized across wild type and mutant replicates based on the assumption that the overall signal distribution of these probes should remain the same across the different strains. Then the signals for transposon probes were calculated by looking up the normalized values of non-transposon probes at same raw signal level. To summarize the signal for each transposon element, probes mapped to any copy of the element were grouped together and Hodges-Lehmann estimator (ref1) was used to calculate the pseudomedian of their normalized signals. We used pseudomedian as it is less sensitive to the large number of outlier probes (probes with value of 1) in the tiling array experiments. Differentially expressed transposon elements were identified by contrasting their pseudomeidan values in three mutant replicates against three wild type replicates. To correct for multiple testing, False Discovery Rates (FDRs) were calculated from t-test P-values. FDR<0.05 were used to call significantly changed transposons. Expression values of mRNAs were summarized by calculating the pseudomedian of probes mapped to each of the RefSeq mRNA transcripts. Differentially expressed transcripts were identified using FDR<0.05 cutoff.
The first column is the transposon ids from flybase or transcript ids from RefSeq. The second column is the the summarized/normalized expression value.

organism: Drosophila melanogaster

label_protocol: GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix)

growth_protocol: The flies were raised at 25 deg C, on standard cornmeal media, and the adults were fed wet yeast paste.

extract_protocol: The RNA was purified using Qiagen RNAeasy® kit following the manufacturer's protocol (Qiagen)

treatment_protocol: The ovaries were dissected in 1X Robb's medium, follwed by RNA extraction.

value: ovaries


title: Adapted-BY-2-11days-Rep3

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Gene expression data from salt adapted BY-2 cells derived from Nicotiana tabacum cv. Bright Yellow 2

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Nicotiana tabacum

source_name: Adapted-BY-2 cells 11days

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

growth_protocol: BY-2 cells (derived from Nicotiana tabacum cv. Bright Yellow 2) were routinely propagated in Murashige & Skoog medium, modified by increasing the concentrations of KH2PO4  and thiamine hydrochloride to 200 and 1 mg L-1 respectively and supplemented with 3% (w/v) sucrose,  0,2 mg L-1  of 2,4-dichlorophenoxyacetic acid and  100 mg L-1 of inositol. The medium was adjusted to pH 5.8 and sterilized by autoclaving at 121 ºC for 15 min prior to use. The cells were sub-cultured to fresh culture medium at weekly intervals and were incubated on a rotary shaker at 130 rpm at 26 ºC in darkness.

extract_protocol: 100 mg of fresh tobacco cell growing at exponential phase was grinded thoroughly in liquid nitrogen with a mortar and pestle. Total RNA was extracted with the RNeasy Plant Mini Kit from Qiagen according to the supplier’s instruction.

treatment_protocol: Tobacco BY-2 cells were adapted to 1.5% salt by initial transfer to media containing 0.5% NaCl for 1 month, 1% NaCl for several weeks and then to 1.5% NaCl-yielding adapted lines cultured for at least 6 months.

value: Salt adapted BY-2 cells


title: Lymph node patient 16

source_name: Lymph node patient 16

value: Male

value: Grade 1


title: vasa_Rep3

description: The first column is the transposon ids from flybase or transcript ids from RefSeq. The second column is the the summarized/normalized expression value.


title: Control-By-2-4days-Rep4

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: Gene expression data from control BY-2 cells derived from Nicotiana tabacum cv. Bright Yellow 2

source_name: Control-BY-2 cells 4 days

value: Control BY-2 cells


title: Adapted-BY-2-11days-Rep4


title: WT mice, Saline

city: Kyoto

first: MEGUMI

last: AIZAWA-ABE

address: Shokogin Kawahara-cho

department: Translational Research Center

country: Japan

institute: Kyoto University Hospital

description: Gene expression data from WT mice with saline administration intraperitonealy

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

organism: Mus musculus

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

value: male

value: 20 weeks-old

tag: genetic background

value: liver

tag: genotype

value: WT

value: saline


title: Adapted-BY-2-11days-Rep1


title: macrophage uninfected control biological rep1

tag: cell type


title: Lepob/Lepob mice, Leptin

description: Gene expression data from Lepob/Lepob mice with leptin administration intraperitonealy

tag: gender

tag: age

value: Lepob/Lepob

tag: treatment

value: leptin


title: Lymph node patient 23

source_name: Lymph node patient 23

tag: age at diagnosis

tag: hospital

value: St Vincent's Hospital

tag: array batch

value: DLBCL

value: Non-GCB (NUM-1 +)

value: NHL

value: PBMSC


title: macrophage infected with strain 534 biological rep4

description: Gene expression data 4 hours post-infection

source_name: Bovine macrophage cells in culture were incubated for 7 days, and then infected with M. bovis strain 534

value: macrophages (peripheral blood mononuclear cells)

value: Mycobacterium bovis strain 534 (atenuatted)

value: Holstein


title: Lymph node patient 49

source_name: Lymph node patient 49

value: Male

tag: diagnosis

value: FL

tag: subtype/fl grade

value: Grade 2

tag: nhl or chl


title: macrophage infected with strain 534 biological rep2


title: macrophage infected with strain 534 biological rep3


title: Control-By-2-4days-Rep1

tag: tissue

value: Control BY-2 cells


title: Control-By-2-4days-Rep3


title: Adapted-BY-2-11days-Rep2

value: Salt adapted BY-2 cells


title: Control-By-2-4days-Rep2


title: vasa_Rep1

value: ovaries


title: Lepob/Lepob mice, Saline

description: Gene expression data from Lepob/Lepob mice with saline administration intraperitonealy

value: male

value: 20 weeks-old

value: liver

value: saline


title: uap56_Rep3


title: uap56_Rep1


title: uap56_Rep2


title: macrophage infected with strain 04-303 biological rep3

source_name: Bovine macrophage cells in culture were incubated for 7 days, and then infected with M. bovis strain 04-303

value: Mycobacterium bovis strain 04-303 (virulent)


title: macrophage infected with strain 04-303 biological rep2


title: macrophage infected with strain 04-303 biological rep1


title: macrophage infected with strain 534 biological rep1


title: macrophage infected with strain 04-303 biological rep4


title: Trachea_GSM463940

status: Public on Nov 27 2012

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

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

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

data_processing:
The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.
The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).

source_name: pooled Human trachea total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).

extract_protocol: Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

value: trachea

tag: ethnicity

value: caucasian


title: Pancreas_GSM463929

source_name: pooled Human pancreas total RNA

value: pancreas


title: Uterus_GSM463941

source_name: pooled Human uterus total RNA

value: uterus


title: Thyroid_GSM463939

source_name: pooled Human thyroid total RNA

value: thyroid


title: Stomach_GSM463936

source_name: pooled Human stomach total RNA

value: stomach


title: SpinalCord_GSM463934

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: SmallIntestine_GSM463933

source_name: pooled Human small intestine total RNA

value: small intestine


title: Kidney_GSM463926

source_name: pooled Human kidney total RNA

value: kidney


title: Thymus_GSM463938

source_name: pooled Human thymus total RNA

value: thymus


title: Prostate_GSM463930

source_name: pooled Human prostate total RNA

value: prostate


title: SalivaryGland_GSM463931

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Lung_GSM463928

source_name: pooled Human lung total RNA

value: lung


title: SkeletalMuscle_GSM463932

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Liver_GSM463927

source_name: pooled Human liver total RNA

value: liver


title: Cortex_GSM463923

source_name: pooled Human cortex total RNA

value: cortex


title: Testes_GSM463937

source_name: pooled Human testes total RNA

value: testes


title: Spleen_GSM463935

source_name: pooled Human spleen total RNA

value: spleen


title: Heart_GSM463925

source_name: pooled Human heart total RNA

value: heart

value: caucasian


title: FetalBrain_GSM463924

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Hepatocytes from human 57YM

source_name: Hepatocytes from human 57YM

growth_protocol: uPA/SCID mice were transplanted with human hepatocytes derived from a Caucasian 9-month-old male infant and an African American 6-year-old girl. Around 60 days after transplantation the mouse livers were replated with human hepatocytes.

extract_protocol: Total RNA was extracted from cells or liver tissues with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

treatment_protocol: No treatment

tag: donor of hepatocytes

value: male

tag: weeks post-tarnsplantation

tag: human albumin level in mouse blood (mg/ml)


title: Hepatocytes from chimeric mouse 5 #17

source_name: Hepatocytes from chimeric mouse 5

value: African American 6-years-old-female


title: Hepatocytes from human 61YF

source_name: Hepatocytes from human 61YF

value: female


title: Colon_GSM463922

source_name: pooled Human colon total RNA

value: colon


title: Hepatocytes from human 28YM

source_name: Hepatocytes from human 28YM


title: Hepatocytes from chimeric mouse 2 #14

source_name: Hepatocytes from chimeric mouse 2

value: Caucasian 9-month-old male infant


title: Hepatocytes from chimeric mouse 4 #16

source_name: Hepatocytes from chimeric mouse 4


title: BoneMarrow_GSM463920

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: Hepatocytes from chimeric mouse 6 #18

source_name: Hepatocytes from chimeric mouse 6


title: Hepatocytes from chimeric mouse 1 #13

source_name: Hepatocytes from chimeric mouse 1


title: 454310A03_preB

type: genomic

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 3770

hyb_protocol: See Roche NimbleGen website for the detailed manufacturers protocol.

scan_protocol: Scanning was performed using NimbleGen MS 200 scanner

data_processing: Raw data (.pair) files generated using NimbleScan software. Signal intensities at each HpaII amplifiable fragment were calculated as a robust (20% trimmed) mean of their component probe-level signal intensities (as described in Khulan et al. Genome Research 2006). Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were considered as “failed” probes and marked as NA values. After QC processing for each array, a median normalization was performed on each array by subtracting the median log-ratio (HpaII/MspI) of that array (resulting in median log-ratio of 0 for each array).

molecule: genomic DNA

source_name: preB, MspI representation of genomic DNA

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat #  06370381001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: pathology

value: normal preB cells

tag: cytogenetics

tag: immunophenotype

value: Pre-B

tag: site (pb

value: peripheral blood; BM:bone marrow):BM

tag: white blood count (wbc, 10^9/l)

tag: %blasts

tag: imatinib

tag: overall_survival (days)

tag: code_os (dead_1)

tag: hyperdiploid

source_name: preB, HpaII representation of genomic DNA


title: Hepatocytes from chimeric mouse 3 #15

source_name: Hepatocytes from chimeric mouse 3

tag: gender

tag: age


title: Cerebellum_GSM463921

source_name: pooled Human cerebellum total RNA

tag: tissue

value: cerebellum


title: 452076A01_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 4021


title: 453554A01_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 4011


title: 453553A01_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 4012


title: 453554A02_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 3772


title: 453554A03_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 3780


title: 454310A02_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 3807


title: 402198_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: Donor_B


title: 453553A03_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 4042


title: 454310A01_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 3782


title: 453553A02_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: 4027


title: 402197_preB

description:
HELP DNA methylation array for normal preB cells from healthy bone marrows
Sample name: Donor_A


title: DC_unstimulated_1_rep1_exon

city: Lisbon

first: Raquel

middle: Ferreira

last: Rodrigues

address: Av. Prof. Egas Moniz, Edifício Egas Moniz - Sala P3-A-16

country: Portugal

institute: Molecular Medicine Institute

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) using Affymetrix hybridization kit materials

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Microarray data pre-processing and summarization was performed using AltAnalyze application, which includes several rigorous statistical methods for data filtering, summarization and determination of differential splicing. Briefly, low quality probesets were removed according to detection above background (DABG) p-value and absolute expression values. Next, probesets were summarized with RMA algorithm and using the AltAnalyze annotations, derived from Ensembl and UCSC databases. Gene expression levels were determined using only probesets targeting constitutive exons.
Determination of overall gene level variation was assessed using linear models and empirical Bayes methods as implemented in ‘limma’ package. The B-statistics gives the log odds of differential expression and it requires an ‘a priori’ value for the estimated proportion of differentially expressed genes. To determine this value, we visually inspected the volcano plot, which compares biological significance (represented by fold-changes) with statistical significance (B-values), finding the value which enabled genes to be distinguished from the majority (logFC≤~1.585). Additionally, we verified the P-values corresponding to moderated F-statistics. Using the Benjamini and Hochberg method, all genes selected as differentially expressed had adjusted P-values<0.05.  Detection of alternative splicing variations were determined using splicing-index and FIRMA approache, calculating MiDAS and normalized intensity p-values (p-value <0.05).

label: Biotin

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Elutriated human monocytes (Advanced Biotechnology Inc., Columbia, MD) were grown in RPMI with 10% fetal bovine serum (Life Technologies, Paisley, UK) supplemented with 1000 U/ml GM-CSF (R&D Systems, Minneapolis, MN) and 1000 U/ml IL-4 (R&D Systems Minneapolis, MN) for 7 days in 24 well plates (106 cells in 1 ml medium/well), and fed every 2 days after plating

extract_protocol: At each timepoint control and stimulated DCs were harvested and lysed using TRIzol® (Molecular Research Center Inc., Cincinnati, OH).

treatment_protocol: On day 7, DCs were harvested and aliquoted into 100mm plates at 107 cells/plate/timepoint and incubated at 37°C for 60 min. E.coli SD54 (ATCC, Middlesex, UK) [multiplicity of infection (MOI) 5:1] was then added to the DCs and cultured for 4 hours (timepoint 1 – T1), 8 hours (timepoint 2 – T2) and 18 hours (timepoint 3 – T3). Control DCs (non-stimulated cells) were collected at equivalent timepoints.

tag: cell type

value: Dendritic cells

tag: treatment

value: not stimulated


title: 347559

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18667

source_name: ALL, MspI representation of genomic DNA

value: ALL

value: Early-Pre-B

value: neg

source_name: ALL, HpaII representation of genomic DNA


title: 256540

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18866

value: BCR/ABL

value: Pos


title: 349169

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18583

value: Pre-B-ALL


title: 256734

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18432

value: peripheral blood; BM:bone marrow):PB

value: male


title: 27479702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18764

value: Neg

value: Pro-B

value: female


title: 349261

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18507


title: 347604

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18671


title: 347592

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18594


title: 27225002

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18630


title: 256539

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18530


title: 349250

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18696


title: 27217702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18552


title: 27221902

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18546


title: 267189

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18433


title: 267487

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18417


title: 27450602

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18236


title: 349229

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18415

value: Transitional-Pre-B


title: 349270

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18292


title: 347594

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18228


title: DC_stimulated_8h_exon

value: stimulated with E.coli


title: DC_stimulated_4h_exon


title: 347631

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18224

value: peripheral blood; BM:bone marrow):BM


title: DC_stimulated_18h_exon


title: DC_unstimulated_3_rep3_exon


title: DC_unstimulated_2_rep2_exon


title: 27498702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18173


title: 267492

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18076


title: 266021

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18040


title: 347589

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17647


title: 349206

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18062

value: Mature-B-ALL


title: EC109_NC_rep1

city: Nanjing

first: Ran

last: Liu

address: 87 Dingjiaqiao Street

institute: Southeast University

description: This sample is of scrambled negative control-treated EC109 cells. It is the first of two negative control biological duplicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by CapitalBio Corporation (Beijing,China) following their standard operating protocol.

scan_protocol: Scanning was performed by CapitalBio Corporation (Beijing,China), following their standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249).

source_name: scrambled negative control transfected EC109 cells

label_protocol: Labeling was performed by CapitalBio Corporation (Beijing,China), following their standard operating protocol.

growth_protocol: EC109 cells were cultured in RPMI1640 medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 1% penicillin/streptomycin (Sigma-Aldrich). Cells were incubated in a humidified incubator at 37°C and 5% CO2 and passaged every three days.

extract_protocol: Total RNA samples were isolated with the RNeasy Mini Kit (Qiagen) with on-column DNA digestion. RNA quality and concentration was determined by analysis at CapitalBio Corporation (Beijing,China).

treatment_protocol: Cells were transfected with either a miR-139-5p mimic or a scrambled negative control (Guangzhou RiboBio Co., Ltd.) using the LipofectamineTM RNAiMAX transfection reagent (Invitrogen) and incubated at 37°C and 5% CO2 for 48 hours.

value: esophageal cancer

tag: cell line

value: esophageal cancer cell line EC109

tag: transfection

value: control


title: 267069

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17913

tag: pathology

value: ALL

value: Early-Pre-B


title: Hepatocytes from human 25YF

source_name: Hepatocytes from human 25YF

tag: donor of hepatocytes

tag: weeks post-tarnsplantation

tag: human albumin level in mouse blood (mg/ml)


title: EC109_MiR-139-5p_rep1

description: This sample is of miR-139-5p mimic-treated EC109 cells. It is the first of two miR-139-5p treated biological duplicates used in this experiment, each from separate cultures.

source_name: miR-139-5p mimic transfected EC109 cells

value: miR-139-5p mimic


title: EC109_NC_rep2

description: This sample is of scrambled negative control-treated EC109 cells. It is the second of two negative control biological duplicates used in this experiment, each from separate cultures.


title: 349249

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18046

tag: cytogenetics

tag: immunophenotype

tag: site (pb

tag: white blood count (wbc, 10^9/l)

value: neg


title: 267558

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17634

value: BCR/ABL

tag: %blasts

tag: imatinib

value: Pos

tag: overall_survival (days)

tag: code_os (dead_1)


title: 267490

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17661

tag: age

tag: gender

value: male

tag: hyperdiploid


title: JP1 strain T6h [T6h- 4]

city: Recife

first: Marcos

middle: Antonio

last: Morais

state: Pernambuco

address: Av. Moraes Rego, 1235

department: Department of Genetics

country: Brazil

institute: Federal University of Pernambuco

hyb_protocol: RNA from lab strain BY4741 was labelled with Cy3 and mixed with Cy5-labelled RNA from industrial strains. Target and reference cRNA samples were mixed and the hybridizations were performed on yeast gene expression 8x15K spots slides (cat. nr. G4813A-016322, Agilent, USA) at 65 ºC for 17 hours at 10 r.pm. in the Microarray Hybridization Oven (cat. nr. G2545A, Agilent, USA).

scan_protocol: The slides were placed into the High-Resolution Microarray Scanner (cat. nr. G2505-60502, Agilent, USA). The fluorescence data were extracted (.txt files) for each spot  by using Scan Control 8.5.1 software (Agilent, USA)

data_processing: Data were then analyzed using specific packages from the R statistical language [20] with the specific LIMMA and MArray  packages. Background correction was done with normexp method. Robust spline and quantile methods were used for normalization within and between arrays, respectively. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests [20]. Groups of genes with statistical significance (Adj.p<0.05) were utilized.

organism: Saccharomyces cerevisiae

source_name: JP1 strain T6h

label_protocol: Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling. For comparison among industrial strains, dye-swap procedure was used for labelling the same sample with Cy3 or Cy5 CTP.

extract_protocol: total RNA in the lysates was purified by using RNAspin Mini RNA Isolation Kit (cat. nr. 25-0500-71, GE HealthCare, USA) following manufacturer´s instructions and suspended in 25 μl nuclease-free water.

treatment_protocol: Yeast cells were cultivated in YPD medium (20 g/l glucose, 20 g/l yeast extract and 10 g/l peptone) at 33ºC and 130 rpm in a rotatory shaker in batches of 24 h. After this period, yeast cells were recovered and suspended in fresh medium for a new batch. This procedure was repeated until reaching enough biomass for the fermentations assays.

tag: strain

value: diploid homothallic yeast  isolated from Japungu Agroindustrial (Santa Rita, PB)

tag: developmental stage

value: T6h fermetaion stage

source_name: Lab strain BY4741

value: Lab strain BY4741 (EUROSCARF collection)

value: T0h fermetaion stage


title: BY strain T6h [T6h- 3]

source_name: BY strain T6h


title: CAT-1 strain T6h [T6h- 5]

source_name: Cat strain T6h

value: diploid heterothallic yeast isolated from Usina Catanduva (Catanduva, SP)


title: 27221802

description:
HELP DNA methylation array for ALL primary sample
Sample name: 18047

tag: pathology

value: Neg

value: peripheral blood; BM:bone marrow):BM


title: 267001

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17682

value: female


title: 401987

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17521

value: peripheral blood; BM:bone marrow):PB


title: CAT-1 strain T6h [T6h- 2]

source_name: Cat1 strain T6h


title: JP1 strain T6h [T6h- 1]


title: CAT-1 strain T0h [T0h- 3]

source_name: Cat strain T0h


title: JP1 strain T0h [T0h- 2]

source_name: JP1 strain T0h


title: 266407

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17490


title: 347588

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17522


title: 256562

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17510


title: 27214702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17463


title: 264461

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17383

value: pos


title: 27248502

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17329

value: ALL

value: Pro-B


title: 256732

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17433

value: Early-Pre-B


title: EC109_MiR-139-5p_rep2

description: This sample is of miR-139-5p mimic-treated EC109 cells. It is thesecond of two miR-139-5p treated biological duplicates used in this experiment, each from separate cultures.

tag: tissue

value: esophageal cancer

tag: cell line

value: esophageal cancer cell line EC109

tag: transfection

value: miR-139-5p mimic


title: 411405

data_processing: RMA normalization using the RMA algorithm in NimbleScan 2.5 software (Roche NimbleGen, Inc).

source_name: normal preB, total RNA

label_protocol: Random priming with 7-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat #  06370381001)

extract_protocol: Total RNA extracted with Qiagen's RNeasy Plus Mini kit from Qiagen (Valencia, CA), per manufacturer's instructions.

value: normal preB cells

tag: cytogenetics

tag: Sex


title: 256731

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17299

value: BCR/ABL

tag: immunophenotype

tag: site (pb

value: neg

value: Pos


title: 347602

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17213

tag: white blood count (wbc, 10^9/l)

tag: %blasts


title: 411406

tag: imatinib


title: 347476

source_name: ALL, total RNA

value: F

tag: code_os (dead_1)


title: 347526

tag: age


title: 349193

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17310

tag: gender

tag: overall_survival (days)


title: 402091

tag: hyperdiploid


title: 38224602


title: 347439

value: Pre-B-ALL


title: 38220602


title: PE-2 strain T0h [T0h- 1]

source_name: Pe strain T0h

tag: strain

value: diploid heterothallic yeast isolated from Usina da Pedra (Serrana, SP)

tag: developmental stage

value: T0h fermetaion stage

value: Lab strain BY4741 (EUROSCARF collection)


title: 347554

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17040

tag: pathology

value: Neg

value: peripheral blood; BM:bone marrow):PB

value: male


title: 347606

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17031

value: ALL


title: 267486

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16930

value: Early-Pre-B

value: female


title: 348957

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16832

value: peripheral blood; BM:bone marrow):BM


title: 347451


title: 27225702

value: M


title: 349221

description:
HELP DNA methylation array for ALL primary sample
Sample name: 17293

value: pos


title: 27237302

value: BCR/ABL


title: 349245

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16816

value: Pro-B

value: neg


title: 349155

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16781


title: 27248302

value: F

value: Pos


title: 267073

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16789


title: 27707702


title: 347786

value: Pre-B-ALL


title: 347208


title: 349226

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16774


title: 347659

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16750


title: 267070

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16773


title: 349238

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16730


title: 349205

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16729


title: 347527


title: 27636302


title: 349204

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16642


title: 38262702


title: 38224202


title: 347542

value: Mature-B-ALL


title: 27217002

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16615

value: peripheral blood; BM:bone marrow):BM+PB


title: 256729

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16510


title: 27240302

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16531

value: Neg


title: 256728

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16500

value: peripheral blood; BM:bone marrow):PB


title: 27645202


title: 27702902


title: 27219702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16557

value: male


title: 349259

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16411

value: ALL


title: 347485


title: 27239702

value: Early-Pre-B


title: 347437


title: 347450


title: 349265

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16378


title: 349197

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16289

value: female


title: 347522

value: Transitional-Pre-B


title: 27217602

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16270

value: peripheral blood; BM:bone marrow):BM


title: 27245502

value: M


title: 27688602

value: BCR/ABL


title: 347436


title: 27217802

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16193


title: 27247902


title: 27219602

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16225


title: 349271

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16212


title: 267535

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16136


title: 256730

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16245


title: 27983802

value: pos


title: 27216902

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16192

value: neg


title: 349272

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16191

value: Pro-B


title: 349199

description:
HELP DNA methylation array for ALL primary sample
Sample name: 16010


title: 27240002


title: 27239802

value: Pos


title: 347487

value: F


title: 347282


title: 347644


title: 27689002


title: 27215002

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15739


title: 346537

value: Pre-B-ALL


title: 347475


title: 27217902

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15901


title: 27230402


title: 27219502

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15762


title: 27678802


title: 347537


title: 266996

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15808


title: 349262

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15508


title: 266093

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15402


title: 27696102


title: 349156

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14998


title: 347447


title: 347568

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14695


title: 347593

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15184


title: 264460

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15524


title: 27674602


title: 347580

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15090


title: 347541


title: 349185

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15129


title: 347448


title: 347494


title: 349161

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15080


title: 401985

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14717


title: 27698302

value: peripheral blood; BM:bone marrow):BM+PB


title: 266092

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15177


title: 347490

value: Neg


title: 27233302

value: peripheral blood; BM:bone marrow):PB


title: 347534


title: 347449


title: 27685202


title: 27217502

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14663


title: 264459

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15047


title: 27459702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14681

value: male


title: 27233402

value: ALL


title: 349184

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15006

value: Early-Pre-B


title: 349163


title: 347472


title: 27226202


title: 27701202


title: 349220

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14609

value: female


title: 27697202


title: 347429


title: 27217102

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14155


title: 267557

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14572


title: 347550


title: 27636402


title: 27216802

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14570


title: 27218002

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14399

value: Mature-B-ALL


title: 347728

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14419

value: peripheral blood; BM:bone marrow):BM


title: 347615

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13938


title: 349269

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14283


title: 27480402

value: M


title: 27498502

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14151


title: 347248


title: 38225502

value: BCR/ABL


title: 349201

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14237


title: 349267

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14070


title: 349266

description:
HELP DNA methylation array for ALL primary sample
Sample name: 14272


title: 38262902


title: 347587

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13792


title: 347431


title: 27459102

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15156


title: 38265802


title: 38262502

value: Transitional-Pre-B


title: 256561

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13784

value: neg


title: 266108

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13757

value: pos


title: 266098

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13732

value: Pos


title: 27640502


title: 347433

value: F


title: 349186

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13677


title: 347440


title: 27678302


title: 38226002


title: 349157

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13582

value: Pre-B-ALL


title: 347492


title: 27484102

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13361


title: 27467302

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13360


title: 267554

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13532


title: 347477

value: Pro-B


title: 267534

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13662


title: 347627

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13418

value: Neg


title: 266061

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13457

value: BCR/ABL, MLL/AF4

value: peripheral blood; BM:bone marrow):PB


title: 267533

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13291

value: ALL


title: 347539


title: 347482


title: 267532

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13290

value: Early-Pre-B

value: male


title: 264466

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13177

value: female


title: 27239902


title: 347636


title: 349227

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13495

value: peripheral blood; BM:bone marrow):BM


title: 347667

value: M


title: 38224802

value: BCR/ABL


title: 27645102


title: 347648

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13151


title: 27467502

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13149

value: Transitional-Pre-B


title: 347432

value: neg


title: 27240402


title: 264456

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12947


title: 27479502

description:
HELP DNA methylation array for ALL primary sample
Sample name: 15255


title: 266048

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12916


title: 342480


title: 27654602

value: Mature-B-ALL


title: 256727

description:
HELP DNA methylation array for ALL primary sample
Sample name: 13008

value: Pos


title: 27660502

value: F


title: 347520


title: 38221502


title: 27634002


title: 347488


title: 27232302


title: 347452


title: 347601

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12832


title: 38293402

value: pos


title: 27458602

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12889


title: 349237

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12873

value: Pro-B


title: 347504

value: Neg


title: 27222902

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12830


title: 264465

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12820


title: 27225202

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12886


title: 27250802

value: Pre-B-ALL


title: 256724

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12623


title: 347535


title: 347483

value: peripheral blood; BM:bone marrow):PB


title: 264463

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12577

value: ALL


title: 349194

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12656


title: 349207

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12415


title: 266400

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12659


title: 349159

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12475


title: 27217402

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12383


title: 299926

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12551

value: Early-Pre-B


title: 347495


title: 27240802


title: 347596

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12388

value: male


title: 349236

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12390

value: E2A/PBX1, TEL_AML


title: 27467802

value: peripheral blood; BM:bone marrow):BM


title: 256725

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12322


title: 256559

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12321

value: female


title: 349254

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12047


title: 27679502

value: BCR/ABL, MLL/AF4

value: M


title: 27459202

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12163

value: neg


title: 256544

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12200

value: BCR/ABL


title: 347491


title: 347443


title: 27638702


title: 27230302

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12267


title: Central starchy endosperm vs Aleurone layers replicate 2

city: Tsukuba

first: Tsutomu

last: Ishimaru

state: Ibaraki

address: 1-1 Ohwashi

institute: JIRCAS

description:
E1vsA_rep2_color swap
Biological replicate 2 of 3. Central starchy endosperm-Cy3. Aleurone-Cy5

hyb_protocol: A rice 44K oligo-microarray (Agilent Technologies), in which probes were synthesized based on the nucleotide sequences and full-length cDNA data of archived by the Rice Annotation Progect Project (RAP-DB, http://rapdb.dna.affrc.go.jp/), was hybridized with with 825 ng of amplified RNA (aRNA). The microarray hybridization comprised consisted of a dye-swap experimental design using totally six arrays (three biological replications by two-color dye swaps).

scan_protocol: Arrays were scanned with an Agilent Microarray Scanner (Agilent Technologies).

data_processing: Imaging analysis and data extraction processes for each spot were performed with the Feature Extraction software (Agilent Technologies) according to the manufacturer’s instructions (Agilent Technologies).

source_name: Central starchy endosperm

label_protocol: Microarray analysis was conducted based on the method of Suwabe et al. (2008). 2.5 ng of Total RNA (2.5 ng) were used, and mRNA was labeled with fluorescent probes (Cy3 or Cy5), by amplifying with the oligo-dT T7 strand-specific method (Agilent Technologies).

growth_protocol: Oryza sativa cv. Koshihikari (a japonica rice variety) was used. One month-aged -old seedlings were transplanted into 0.02 m2 pots.

extract_protocol: Aleurone cells at the dorsal side and starchy endosperm at in the center were microdissected with an AS Laser MicroDissection system (Leica Microsystems, Wetzlar, Germany). Total RNA was extracted with a Picopure RNA isolation kit (Molecular Devices, Sunnyvale, CA) using DNase I.

treatment_protocol: At the booting stage, plants were transferred into a naturally-illuminated temperature-controlled chamber. Day (13h) and night (11h) air temperatures were maintained at 26 oC and 20 oC, respectively until maturity.

value: seven days after flowering

tag: cultivar

value: Koshihikari

tag: tissue

value: developing endosperm

tag: tissue region

value: Central starchy endosperm

tag: tissue region enriched for

value: starch

source_name: Aleurone layers

value: Aleurone layers

value: lipid


title: 27634402

value: ALL

tag: cytogenetics

value: Neg

tag: immunophenotype

tag: Sex


title: 349172

description:
HELP DNA methylation array for ALL primary sample
Sample name: 12011

source_name: ALL, MspI representation of genomic DNA

value: Early-Pre-B

tag: site (pb

value: peripheral blood; BM:bone marrow):PB

value: male

tag: white blood count (wbc, 10^9/l)

tag: %blasts


title: 27488002

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11860

value: Pre-B-ALL

value: peripheral blood; BM:bone marrow):BM

tag: age

value: female

tag: imatinib

tag: code_os (dead_1)

source_name: ALL, HpaII representation of genomic DNA


title: 264457

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11753

tag: gender

value: neg

tag: overall_survival (days)

tag: hyperdiploid

value: pos


title: Aleurone layers vs Central starchy endosperm replicate 1

description:
AvsE1_rep1
Biological replicate 1 of 3. Aleurone-Cy3. Central starch endosperm-Cy5

tag: developmental stage

value: seven days after flowering


title: 347591

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11759

tag: pathology

value: Pro-B


title: Aleurone layers vs Central starchy endosperm replicate 3

description:
AvsE1_rep3
Biological replicate 3 of 3. Aleurone-Cy3. Central starch endosperm-Cy5

tag: cultivar

value: Koshihikari

tag: tissue

value: developing endosperm


title: 27258802

value: BCR/ABL

value: F


title: 38266702


title: 27240602

value: M


title: 349183

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11471

value: ALL


title: Aleurone layers vs Central starchy endosperm replicate 2

description:
AvsE1_rep2
Biological replicate 2 of 3. Aleurone-Cy3. Central starch endosperm-Cy5

tag: tissue region

value: Aleurone layers

tag: tissue region enriched for

value: lipid

value: Central starchy endosperm

value: starch


title: Central starchy endosperm vs Aleurone layers replicate 1

description:
E1vsA_rep1_color swap
Biological replicate 1 of 3. Central starchy endosperm-Cy3. Aleurone-Cy5


title: Central starchy endosperm vs Aleurone layers replicate 3

description:
E1vsA_rep3_color swap
Biological replicate 3 of 3. Central starchy endosperm-Cy3. Aleurone-Cy5


title: 347532

tag: cytogenetics

value: Neg

tag: immunophenotype

value: Early-Pre-B


title: 267531

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11433

tag: site (pb

value: peripheral blood; BM:bone marrow):PB

value: female

value: Pos


title: 27250302

tag: Sex

tag: white blood count (wbc, 10^9/l)

value: neg


title: 27679002

tag: age

tag: %blasts


title: 267561

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11392

value: male

tag: imatinib

tag: code_os (dead_1)


title: 264462

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11427

value: Pre-B-ALL

tag: gender

tag: overall_survival (days)


title: 349222

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11412

tag: hyperdiploid


title: Whole_Blood_73

city: Kodaira

first: Daimei

last: Sasayama

address: 4-1-1 Ogawahigashi-machi

institute: National Center of Neurology and Psychiatry

hyb_protocol: Cy3-labeled cRNA was hybridized to Agilent Human Genome 4 x 44 K arrays (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Arrays were scanned by a DNA Microarray Scanner (Agilent G2505C). Microarray images were analyzed with Agilent Feature Extraction software.

data_processing:
Microarray images were analyzed with Agilent Feature Extraction software.
Raw signal data for each of the 3 independent samples were analyzed separately by the GeneSpring GX software (Agilent Technologies). Data were filtered according to the expression level for quality control to eliminate genes that were below the 20th percentile threshold. The expression value of each gene was normalized to the median expression value of all genes in each chip. A total of 30,465 probes were included in the analysis.

source_name: Peripheral blood

label_protocol: After cDNA synthesis from total RNA, cyanine-3 (Cy3) labeled cRNA was prepared using transcribed using T7 RNA polymerase.

extract_protocol: Venous blood was collected between 1100 and 1200 h in PAXgene tubes (Qiagen, Valencia) from each subject and was incubated at room temperature for 24 h for RNA stabilization. RNA was extracted from whole blood according to the manufacturer's guidelines by using the PAXgene Blood RNA System Kit (PreAnalytix GmbH, Hombrechtikon, Switzerland). The extracted RNA was quantified by optical density readings at A260nm by using the NanoDrop ND-1000 (Thermo Scientific, Rockford) and agrose gel electrophoresis.

value: whole blood

tag: physical status

value: healthy


title: 27648802

tag: pathology

value: peripheral blood; BM:bone marrow):BM


title: 349189

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11370


title: Whole_Blood_76

tag: tissue


title: 267538

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11283

value: BCR/ABL


title: 38220302

value: ALL

value: Transitional-Pre-B

value: M


title: Whole_Blood_75


title: 38261002

value: F


title: Whole_Blood_71


title: Whole_Blood_74


title: 27654702


title: Whole_Blood_72


title: Whole_Blood_67


title: 347486


title: Whole_Blood_70


title: Whole_Blood_68


title: 347446

value: Pro-B


title: Whole_Blood_69


title: 267553

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11134


title: 27458402

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11153

value: Neg


title: 38224702

value: Early-Pre-B


title: 266095

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11102

value: peripheral blood; BM:bone marrow):PB


title: 266096

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11227


title: 349234

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11039

value: Mature-B-ALL


title: Whole_Blood_66

value: female


title: 38224102

value: neg

value: pos


title: 264454

description:
HELP DNA methylation array for ALL primary sample
Sample name: 11034

value: male

value: Pos


title: Whole_Blood_65

value: whole blood

value: healthy


title: 347489


title: Whole_Blood_64


title: 267559

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10940

value: BCR/ABL

value: peripheral blood; BM:bone marrow):BM


title: 38220902

value: ALL


title: 38220802

value: M


title: 267552

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10902


title: Whole_Blood_63


title: DNA_Physically Healthy_75

description: Sample name: S0500

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
GenomeStudio software was used for data processing.
Matrix_signal_intensities.txt (linked as supplementary file on Series record): X Raw and Y Raw columns represent raw intensities of A allele and B allele, respectively. X and Y columns represent normalized intensities of A allele and B allele, respectively.
Genotyping was performed by Riken Genesis (Yokohama, Japan) using the Illumina HumanOmni1-Quad BeadChip (Illumina, Inc., San Diego). A total of 713,495 autosomal SNPs were assessed for quality using the PLINK v1.07 software. All SNPs with a call rate below 95%, a deviation from Hardy-Weinberg equilibrium at an error level of P < 0.001, or a minor allele frequency of less than 10% were excluded. The remaining 534,404 SNPs were used for further analysis.

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: The buffy coat was collected from venous blood collected in tubes containing EDTA. DNA was extracted using Maxwell 16 Tissue DNA Purification Kit (Promega, Madison, WI) according to manufacturer's instructions.

value: Peripheral blood


title: 38221102

value: F


title: 349257

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10774

value: Neg


title: DNA_Physically Healthy_76

description: Sample name: S1076


title: Whole_Blood_62


title: DNA_Physically Healthy_74

description: Sample name: S0929


title: 27467702

value: Early-Pre-B


title: 349256

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10652

value: peripheral blood; BM:bone marrow):PB


title: 347498

value: Pro-B


title: Whole_Blood_61


title: Whole_Blood_60


title: 266018

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10735


title: 347543


title: 349253

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10651

value: female


title: DNA_Physically Healthy_72

description: Sample name: S0003


title: DNA_Physically Healthy_71

description: Sample name: S1078


title: 347670

value: E2A/PBX1, TEL_AML

value: Pre-B-ALL

value: neg


title: Whole_Blood_59


title: 267500

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10623

value: Pos


title: DNA_Physically Healthy_73

description: Sample name: S0765


title: 38266202

value: pos


title: Whole_Blood_57

value: whole blood

value: male

value: healthy


title: DNA_Physically Healthy_68

description: Sample name: M0068


title: DNA_Physically Healthy_66

description: Sample name: S0775


title: DNA_Physically Healthy_64

description: Sample name: S1234


title: 267536

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10557

value: ALL

value: BCR/ABL


title: 256541

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10500


title: 27637602

value: peripheral blood; BM:bone marrow):BM


title: Whole_Blood_58


title: 256542

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10608


title: 27237202

value: M


title: Whole_Blood_56


title: Whole_Blood_55


title: DNA_Physically Healthy_70

description: Sample name: M0012

value: Peripheral blood


title: DNA_Physically Healthy_67

description: Sample name: S0931


title: DNA_Physically Healthy_69

description: Sample name: S0734


title: 27226102

value: Early-Pre-B

value: F


title: 255892

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10468

value: peripheral blood; BM:bone marrow):PB


title: Whole_Blood_54


title: 349209

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10467

value: Pro-B

value: female


title: 27459002

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10449

value: Neg


title: 266036

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10439

value: neg


title: Whole_Blood_53


title: DNA_Physically Healthy_59

description: Sample name: S0900


title: 347502

value: Pre-B-ALL


title: DNA_Physically Healthy_61

description: Sample name: S1124


title: 27631702


title: 347438


title: DNA_Physically Healthy_62

description: Sample name: S1005


title: Whole_Blood_51


title: 38267202

value: pos


title: DNA_Physically Healthy_63

description: Sample name: S0716


title: DNA_Physically Healthy_60

description: Sample name: M0008


title: Whole_Blood_52

value: whole blood


title: DNA_Physically Healthy_65

description: Sample name: M0022

value: male


title: Whole_Blood_50

value: healthy


title: Whole_Blood_49


title: 27467602

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10394

value: ALL


title: 349263

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10357


title: 27240702

value: BCR/ABL


title: DNA_Physically Healthy_58

description: Sample name: M0057


title: Whole_Blood_48


title: 347651

value: peripheral blood; BM:bone marrow):BM


title: DNA_Physically Healthy_57

description: Sample name: M0033


title: 27225802


title: DNA_Physically Healthy_56

description: Sample name: M0030


title: Whole_Blood_47


title: 266094

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10380

value: Pos


title: 347444

value: M


title: DNA_Physically Healthy_53

description: Sample name: S0732

value: Peripheral blood


title: Whole_Blood_46


title: 347585

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10311

value: Early-Pre-B


title: 27516602

value: peripheral blood; BM:bone marrow):PB


title: Whole_Blood_45


title: 27217302

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10268


title: 27479402

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10176


title: Whole_Blood_44


title: 347642


title: DNA_Physically Healthy_51

description: Sample name: S1209


title: DNA_Physically Healthy_55

description: Sample name: M0193


title: Whole_Blood_43


title: DNA_Physically Healthy_54

description: Sample name: S0724


title: 27679402


title: 27458702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10161

value: Pro-B


title: 266017

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10163

value: female


title: Whole_Blood_42


title: 27248602


title: 349258

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10115


title: Whole_Blood_41


title: 38220702

value: Neg


title: 349228

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10233

value: neg


title: 349210

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10157


title: 27688302


title: DNA_Physically Healthy_50

description: Sample name: M0006


title: DNA_Physically Healthy_49

description: Sample name: S1279


title: 38261802

value: F


title: 264476

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10086


title: 347546

value: Mature-B-ALL


title: Whole_Blood_40

value: whole blood


title: Whole_Blood_38


title: Whole_Blood_37

value: male


title: 349268

description:
HELP DNA methylation array for ALL primary sample
Sample name: 10054


title: Whole_Blood_39

value: healthy


title: DNA_Physically Healthy_52

description: Sample name: S1098


title: 266129

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9926

value: ALL


title: 27240502

value: BCR/ABL


title: 347625

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9890

value: peripheral blood; BM:bone marrow):BM


title: 27248002


title: 27248202

value: pos


title: DNA_Physically Healthy_43

description: Sample name: S1108


title: DNA_Physically Healthy_48

description: Sample name: M0098


title: 38221402

value: M


title: Whole_Blood_36


title: 264474

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9830

value: Pos


title: Whole_Blood_35


title: Whole_Blood_34


title: DNA_Physically Healthy_47

description: Sample name: S1157

value: Peripheral blood


title: DNA_Physically Healthy_41

description: Sample name: M0053


title: DNA_Physically Healthy_46

description: Sample name: S1132


title: 264473

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9806

value: Early-Pre-B


title: 27216702

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9871

value: Pro-B


title: Whole_Blood_33


title: 347435


title: DNA_Physically Healthy_40

description: Sample name: S1151


title: DNA_Physically Healthy_42

description: Sample name: S1164

value: female


title: DNA_Physically Healthy_44

description: Sample name: S0668


title: 27225102

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9770

value: Neg


title: 27227502

value: neg


title: 347598

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9767

value: peripheral blood; BM:bone marrow):PB


title: Whole_Blood_32


title: 27225902


title: DNA_Physically Healthy_45

description: Sample name: S0993


title: 264472

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9696


title: Whole_Blood_31


title: 349196

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9603

value: Pre-B-ALL


title: Whole_Blood_30

value: whole blood


title: Whole_Blood_29

value: male


title: Whole_Blood_28

value: healthy


title: 400979

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9670

value: ALL


title: DNA_Physically Healthy_38

description: Sample name: S1150


title: 27545402

value: BCR/ABL

value: F


title: 347503


title: 349187

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9503

value: peripheral blood; BM:bone marrow):BM


title: Whole_Blood_26


title: 347555


title: 27487902


title: 349211

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9487


title: 38292702

value: M


title: 27232402


title: Whole_Blood_27


title: 348469

description:
HELP DNA methylation array for ALL primary sample
Sample name: 9467

value: Pos


title: DNA_Physically Healthy_37

description: Sample name: S1213

value: Peripheral blood


title: DNA_Physically Healthy_36

description: Sample name: S0722


title: DNA_Physically Healthy_34

description: Sample name: M0227


title: 27647302

value: Early-Pre-B


title: 27286802

description:
HELP DNA methylation array for ALL primary sample
Sample name: 8672


title: 401981

description:
HELP DNA methylation array for ALL primary sample
Sample name: 8807


title: Whole_Blood_24


title: DNA_Physically Healthy_33

description: Sample name: S1163


title: Whole_Blood_23


title: 38267002


title: DNA_Physically Healthy_35

description: Sample name: S0992


title: Whole_Blood_25


title: Whole_Blood_22


title: 349233

description:
HELP DNA methylation array for ALL primary sample
Sample name: 8475

value: Pro-B


title: 27678402


title: DNA_Physically Healthy_31

description: Sample name: S1256

value: female


title: 347616


title: DNA_Physically Healthy_39

description: Sample name: S1193


title: DNA_Physically Healthy_30

description: Sample name: S1227


title: 264453

description:
HELP DNA methylation array for ALL primary sample
Sample name: 7933


title: DNA_Physically Healthy_29

description: Sample name: M0277


title: Whole_Blood_20


title: 27633902

value: Neg


title: 349252

description:
HELP DNA methylation array for ALL primary sample
Sample name: 7787

value: neg


title: Whole_Blood_18


title: 347209


title: DNA_Physically Healthy_27

description: Sample name: S0769


title: Whole_Blood_19


title: DNA_Physically Healthy_26

description: Sample name: S1195


title: DNA_Physically Healthy_28

description: Sample name: M0264


title: 349235

description:
HELP DNA methylation array for ALL primary sample
Sample name: 6589

value: peripheral blood; BM:bone marrow):PB


title: DNA_Physically Healthy_32

description: Sample name: S1184


title: 347521


title: 401289

description:
HELP DNA methylation array for ALL primary sample
Sample name: 6076

value: Mature-B-ALL

value: peripheral blood; BM:bone marrow):BM+PB


title: Whole_Blood_17

value: whole blood

value: male


title: 27226302

description:
HELP DNA methylation array for ALL primary sample
Sample name: 8104

value: ALL

value: Transitional-Pre-B

value: peripheral blood; BM:bone marrow):NA


title: 38261102

value: BCR/ABL


title: 27745002

value: F


title: DNA_Physically Healthy_23

description: Sample name: S0964

value: healthy


title: Whole_Blood_21


title: Whole_Blood_15


title: 349264

description:
HELP DNA methylation array for ALL primary sample
Sample name: 5702


title: DNA_Physically Healthy_25

description: Sample name: M0228

value: Peripheral blood


title: Whole_Blood_16


title: Whole_Blood_14


title: DNA_Physically Healthy_21

description: Sample name: M0181


title: 38294302

value: Early-Pre-B

value: peripheral blood; BM:bone marrow):BM


title: Whole_Blood_13


title: 347509

value: Pro-B

value: M


title: 347442

value: neg


title: DNA_Physically Healthy_24

description: Sample name: S1009

value: female


title: DNA_Physically Healthy_22

description: Sample name: M0159


title: Whole_Blood_12


title: 27679102


title: 38261702

value: Neg


title: Whole_Blood_10


title: Whole_Blood_9


title: 27689102


title: 38266902


title: DNA_Physically Healthy_18

description: Sample name: S0981


title: Whole_Blood_11


title: Whole_Blood_8


title: Whole_Blood_7


title: 347441

value: peripheral blood; BM:bone marrow):PB


title: Whole_Blood_6

value: whole blood


title: 27688802


title: Whole_Blood_5

value: male


title: 347586

value: ALL


title: Whole_Blood_4


title: 347409

value: Pre-B-ALL


title: PR9692 expressing anti-HOPX shRNA, biological rep1

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

description: Gene expression data from sarcoma derived PR9692 cell line stably transfected with anti-HOPX shRNA

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite (version 6.4) using Affymetrix default annotation and GC-RMA as normalization method.

organism: Gallus gallus

source_name: PR9692 cells stably transfected with anti-HOPX shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the PR9692 derived cell lines were grown in Iscove´s modified Dulbecco´s minimal essential medium supplemented with 8% fetal calf serum, 2% chicken serum, and antibiotics. The cells were cultured at 40°C in a humidified atmosphere with 5% CO2.

extract_protocol: Approximately 10 millions cultured cells were dissolved in 2 ml of RNAzol (Sigma-aldrich) and total RNA was extracted according to manufacturer's protocol.

tag: cell line

tag: tranfection

value: anti-HOPX shRNA

tag: strain


title: 347389

tag: cytogenetics

tag: immunophenotype


title: PR9692 expressing control shRNA, biological rep1

description: Gene expression data from sarcoma derived PR9692 cell line stably transfected with control shRNA

source_name: PR9692 cells stably transfected with control shRNA

value: control shRNA


title: Whole_Blood_2


title: Whole_Blood_1


title: Whole_Blood_3


title: 27679602

value: BCR/ABL

tag: site (pb

tag: Sex

value: F


title: PR9692 expressing anti-HOPX shRNA, biological rep2


title: DNA_Physically Healthy_16

description: Sample name: S0963

value: Peripheral blood

tag: age

value: healthy


title: DNA_Physically Healthy_15

description: Sample name: S0950


title: 38224502

value: Early-Pre-B

tag: white blood count (wbc, 10^9/l)

tag: %blasts


title: PR9692 expressing control shRNA, biological rep2


title: DNA_Physically Healthy_20

description: Sample name: S0896


title: DNA_Physically Healthy_13

description: Sample name: S1129


title: DNA_Physically Healthy_19

description: Sample name: M0185


title: VAL-11B

city: Valencia

last: Montaner

address: C/ Eduardo Primo Yufera, 3

department: Bioinformatics

country: Spain

institute: CIPF

hyb_protocol: 3 μg of labelled cRNA was hybridised with the Whole Human Genome Oligo Microarray Kit (Agilent p/n G2519F-014850) containing 41,000+ unique human genes and transcripts

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA).

data_processing: Data were extracted using Agilent Feature Extraction Software 9.5.3 following the Agilent protocol GE1-v5_95_Feb07 and the QC Metric Set GE1_QCMT_Jan08

label_protocol: 480 ng of total RNA was used to produce Cyanine 3-CTP-labeled cRNA using the One-Color Quick Amp Labelling Kit (Agilent p/n 5190-0442) according to the manufacturer’s instructions

growth_protocol: All hESC lines were cultured and maintained on irradiated human foreskin fibroblasts in multiwell cell culture plates  in 80% Knockout DMEM, 20% Knockout SR , 1 mM glutamine, 0.1 mM β-Mercaptoethanol, 1% non-essential amino acids stock, containing  10 ng/ml of bFGF . The colonies were incubated at 37° C with 5% CO2, and the medium was changed every 48 h.  The colonies were mechanically dissected into clumps every 4 to 5 days and transferred to dishes containing new inactivated human foreskin feeder cells. The colonies were mechanically dissected into clumps every 4 to 5 days and transferred to dishes containing new inactivated human foreskin feeder cells.   All hESC lines were cultured and maintained on irradiated human foreskin fibroblasts (ATTC) in multiwell cell culture plates (Becton, Dickinson, and Company, Erembodegem, Belgium) in 80% Knockout DMEM (Gibco/BRL, Paisley, Scotland, UK), 20% Knockout SR (Gibco/BRL), 1 mM glutamine (Sigma, St. Louis, MO), 0.1 mM β-Mercaptoethanol (Sigma), 1% non-essential amino acids stock (Gibco/BRL), containing  10 ng/ml of bFGF (Invitrogen, Life Technologies, Carlsbad, CA). The colonies were incubated at 37° C with 5% CO2, and the medium was changed every 48 h.

extract_protocol: The RNA from hESCs was isolated using Zymo Research’s Mini RNA Isolation Kit™ following the manufacturer´s recommendations. A total of 100,000 cells per VAL line were used for the RNA extraction destined for microarray analyses.

tag: cell type

value: hESC derived from single blastomere

tag: class


title: DNA_Physically Healthy_14

description: Sample name: M0192

tag: gender


title: DNA_Physically Healthy_11

description: Sample name: M0194


title: VAL-8

value: hESC derived from ICM


title: VAL-7


title: MYC ChIP-chip in mutu3 cells, replicate 2

description: MYC ChIP-chip in mutu3 cells - replicate 2 of 2.

hyb_protocol: Described in www.nimblegen.com

scan_protocol: Described in www.nimblegen.com

data_processing: Take all the probes in the promoter region and perform log2 transformation of IP/INPUT (Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter. The detailed analysis method (script) was published in Ci et al. Blood. 2009 May 28;113(22):5536-48 (PMID 19307668).

source_name: mutu3 cells, input

label_protocol: Described in www.nimblegen.com

extract_protocol: Sonicated genomic DNA, and then purified by Qiagen column. The detailed method was published in Polo et al. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3207-12 (PMID 17360630).

value: Burkitt lymphoma cells

tag: genotype

value: Ph+

tag: chip antibody

source_name: mutu3 cells, MYC ChIP

extract_protocol: Chromatin immunoprecipitation to isolate genomic regions bound by MYC, and then purified by Qiagen column. The detailed method was published in Polo et al. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3207-12 (PMID 17360630).

value: rabbit anti-c-MYC (N-262) polyclonal

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number


title: MYC ChIP-chip in mutu3 cells, replicate 1

description: MYC ChIP-chip in mutu3 cells - replicate 1 or 2.

tag: cell line


title: 347669

tag: pathology

value: Pro-B

value: peripheral blood; BM:bone marrow):PB

tag: imatinib

value: neg

tag: code_os (dead_1)

tag: hyperdiploid


title: DNA_Physically Healthy_12

description: Sample name: S0909

tag: tissue

value: female

tag: physical status


title: 38219402

value: ALL

tag: cytogenetics

tag: immunophenotype

tag: site (pb

value: peripheral blood; BM:bone marrow):BM

tag: age

tag: Sex

value: M


title: MYC ChIP-chip in ramos cells, replicate 2

description: MYC ChIP-chip in ramos cells - replicate 2 of 2.

source_name: ramos cells, input

value: ramos

tag: cell type

source_name: ramos cells, MYC ChIP


title: 38266402

value: Neg

value: Transitional-Pre-B

value: peripheral blood; BM:bone marrow):NA

tag: white blood count (wbc, 10^9/l)

tag: %blasts


title: 27634202

value: Early-Pre-B

value: F


title: VAL-5

value: hESC derived from ICM

tag: class


title: VAL-5.2


title: 347434


title: DNA_Physically Healthy_9

description: Sample name: S0849

value: Peripheral blood

tag: gender

value: healthy


title: VAL-10B

value: hESC derived from single blastomere


title: 347608

value: Mature-B-ALL

value: peripheral blood; BM:bone marrow):BM+PB


title: MYC ChIP-chip in ramos cells, replicate 1

description: MYC ChIP-chip in ramos cells - replicate 1 of 2.

tag: cell line

value: Burkitt lymphoma cells

tag: genotype

value: Ph+

tag: chip antibody

value: rabbit anti-c-MYC (N-262) polyclonal

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number


title: FOXP3 ChIP stim 2

status: Public on Nov 26 2012

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

description:
FOXP3-bound promoter regions in PMA / ionomycin activated J-FOXP3 T cells defined by the comparison of ChIP-on-Chip data from FOXP3-specific IP vs. isotype control IP
FOXP3 bound stim 2
test CEL file: HZI2043_Hs_PromPR_v02.CEL
ctrl CEL file: HZI2042_Hs_PromPR_v02.CEL

hyb_protocol: Following fragmentation 7.5 µg of ChIP-DNA were hybridized for 16 h at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000

data_processing:
Basic tiling array data analysis was performed with TAS software (Version 1.1.02, Affymetrix). FOXP3-bound ChIP-enriched genomic regions were identified by comparing FOXP3 IP to a matched isotype control IP from the same cell material. Only continuous genomic regions exhibiting a p-value higher than the 95th percentile of all p-values were included in subsequent analyses. Calculated ChIP intervals were visualized with IGB software. The web-based Galaxy analysis tool was used to compare repetitive ChIP-on-chip experiments. Positional intersecting ChIP regions between two replicate experiments were calculated. Moreover, the range of intersection was calculated, and only the corresponding genomic coordinates of intersecting areas were considered for further analysis.
RESULTS files:
The bar and bed files are all TAS generated.
Results file "FOXP3 ChIP regions.xls" description: Combined list of identified FOXP3 ChIP regions in resting and PMA/ionomycin-stimulated FOXP3-over-expressing Jurkat T cells including chromosomal coordinates (based on HG18 reference assembly).  Linked as supplementary file on Series record.

source_name: FOXP3 ChIP-DNA

label_protocol: Amplified ChIP-DNA was labelled and prepared for hybridization with the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix)

growth_protocol: Jurkat T cells were cultivated in IMDM medium supplemented with 10% FCS (PAA Laboratories) and 100 U/ml penicillin/streptomycin.

extract_protocol: Protein crosslinking was ensured by the addition of formaldehyde (1% v/v) and by incubation on a shaker for 10 min at room temperature. Formaldehyde was quenched for 5 min by the addition of glycine (125 mM final concentration). After centrifugation, the culture supernatant was removed, and cells were washed once with ice-cold PBS. Cells were lysed in IP cell-lysis Buffer (10 mM Tris HCL [pH 7.5], 10 mM NaCl, 3 mM MgCl2, 1 mM phenylmethanesulfonyl fluoride [PMSF], 0.5% v/v IGEPAL CA-630) and incubated on ice for 10 min. Lysed cells were centrifuged at 2500 rpm for 5 min at 4°C, and the supernatant was discarded. The chromatin material was obtained by lysing the cell nuclei with IP nuclei-lysis buffer (50 mM Tris HCL [pH 8.0], 10 mM EDTA, 1% [v/v] sodium dodecyl sulfate [SDS], complete protease inhibitors) and incubating them on ice for 10 min. Chromatin was diluted in IP dilution buffer (20 mM Tris HCl [pH 8], 2 mM EDTA, 1% v/v Triton X-100, 150 mM NaCl, 1 mM PMSF) and stored at -80°C.

treatment_protocol: Prior usage dead cells were removed from Jurkat cell cultures by ficoll gradient centrifugation. If stated, cells were stimulated with PMA (10 ng/ml, Sigma-Aldrich) and ionomycin (1 µg/ml, Sigma-Aldrich) for 4 h.

value: Jurkat T cells

tag: foxp3 expression

value: yes

tag: activation status

value: stimulated

tag: ip antibody

tag: ip antibody description

value: Purified anti-human FOXP3 Antibody; Clone 206D

tag: ip antibody vendor

value: BioLegend

tag: ip antibody lot#

tag: ip antibody catalog#

source_name: Isotype control ChIP-DNA

value: isotype

value: Purified Mouse IgG1, kappa Isotype Ctrl Antibody; Clone MOPC-21


title: FOXP3 ChIP resting 2

description:
FOXP3-bound promoter regions in resting J-FOXP3 T cells defined by the comparison of ChIP-on-Chip data from FOXP3-specific IP vs. isotype control IP
FOXP3 bound resting 2
test CEL file: HZI2814_Hs_PromPR_v02.CEL
ctrl CEL file: HZI2813_Hs_PromPR_v02.CEL

value: resting


title: FOXP3 ChIP resting 1

description:
FOXP3-bound promoter regions in resting J-FOXP3 T cells defined by the comparison of ChIP-on-Chip data from FOXP3-specific IP vs. isotype control IP
FOXP3 bound resting 1
test CEL file: HZI2812_Hs_PromPR_v02.CEL
ctrl CEL file: HZI2811_Hs_PromPR_v02.CEL


title: FOXP3 ChIP stim 1

description:
FOXP3-bound promoter regions in PMA / ionomycin activated J-FOXP3 T cells defined by the comparison of ChIP-on-Chip data from FOXP3-specific IP vs. isotype control IP
FOXP3 bound stim 1
test CEL file: HZI2552_Hs_PromPR_v02.CEL
ctrl CEL file: HZI2551_Hs_PromPR_v02.CEL


title: DNA_Physically Healthy_17

description: Sample name: S0927

tag: tissue

value: Peripheral blood

value: male

tag: age

tag: physical status


title: 347620

tag: pathology

value: ALL

tag: cytogenetics

tag: immunophenotype

value: Pro-B

tag: site (pb

value: peripheral blood; BM:bone marrow):PB

tag: Sex

value: M

tag: white blood count (wbc, 10^9/l)

tag: %blasts

tag: imatinib

value: neg

tag: code_os (dead_1)

tag: hyperdiploid


title: MDA-MB-231-Control

first: Jonathan

last: Chou

address: 513 Parnassus Ave, Box 0452, HSW1301

department: Anatomy

institute: Univ of California, San Francisco

description: Control

data_processing:
SABioscience normalization software was used.
Data are normalized to the following house-keeping RNAs: SNORD48, SNORD47, SNORD44, RNU6-2
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: Sybr Green

label_protocol: PCR assays were performed using the Human Cancer miRNA PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1 microgram total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (ABI) with 45 cycles at 94 degrees C for 15 seconds and 60 degrees C for 60 seconds.

growth_protocol: DMEM-H21 high glucose + 10% FBS + Pen/Strep in normal 2D tissue culture plates

extract_protocol: Qiagen miRNeasy Kit for Total RNA

tag: cell line

tag: disease state

value: breast cancer

tag: overexpression


title: DNA_Physically Healthy_7

description: Sample name: S0705

tag: gender

value: healthy