title: SF Bay RNA, fluorescence (low)

description:
SF Bay seawater; samples were from a mixed natural community which includes hundreds of different species.
fluorescently labeled RNA
Fluorescence signals representing ribosomal RNA abundance for treatment low

hyb_protocol: 1X Nimblegen hub buffer, 18 hours, 42 degrees We used a slide chamber that divides the array into 4, and each quarter had a different sample.

data_processing:
Fluorescence data were averaged (not background corrected)
The NDF file includes thousands of probes that were not analyzed with the mass spectrometer; these probes are not represented in the edited .pair file linked below. The original .pair file is linked to the Series record.

label: alexafluor 532

source_name: SF Bay RNA, fluorescent (low isotopic)


title: genomic DNA from breast tumor tissue [39_127af]

status: Public on Mar 26 2014

type: genomic

city: Oslo

first: Ann Rita

last: Halvorsen

address: Montebello

country: Norway

institute: OUS- The Norwegian Radium Hospital

description: breast tumor biopsy

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2 [data processing]

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor and normal samples using Maxwell 16 DNA Purification Kit according to standard instructions

tag: gender

value: Female

tag: irradiation status

value: Irradiated

tag: disease state

value: breast cancer


title: genomic DNA from breast tumor tissue [35_124af]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [37_125af]

description: breast tumor biopsy


title: Blood male Sarasota, FL SAR 2005_118

type: RNA

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

description: Gene expression wild dolphin blood

hyb_protocol: 500ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custom Tursiops truncatus Microarray (Agilent) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately with a wash in acetonitrile (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software A8.5.3 (Agilent) using default parameters (protocol GE1) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Tursiops truncatus

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Amplification  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA from blood samples from wild dolphins was extracted using the RNAeasy Kit according to the manufacturer (Qiagen, Valencia, CA). RNA was quantified using a NanoDrop ND-1000 (Wilmington, DE), qualified on an Agilent 2100 Bioanalyzer (Foster City, CA) and stored at −80°C until needed for gene expression profiling.

treatment_protocol: Blood samples were collected from wild dolphins in PAXgene™ Blood tubes (Qiagen, Valencia, CA, USA), mixed immediately to stabilize the RNA, and stored according to the manufacturer’s instructions.

tag: tissue

value: whole blood

value: male

tag: location

value: Sarasota, FL


title: genomic DNA from healty normal breast controls [48_rp73]

description: normal breast biopsy

source_name: norma breast tissue

value: Non-irradiated

value: normal


title: genomic DNA from breast tumor tissue [31_121af]

description: breast tumor biopsy


title: SF Bay RNA, fluorescence (medium and high)

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

country: USA

institute: Lawrence Livermore National Laboratory

description:
SF Bay seawater; samples were from a mixed natural community which includes hundreds of different species.
fluorescently labeled RNA
Fluorescence signals representing ribosomal RNA abundance for treatments high and medium

scan_protocol: Genescan 4000B, PMT = 650 for fluorescence data; NanoSIMS 50 for isotopic data

organism: marine metagenome

source_name: SF Bay RNA, fluorescent (medium and high isotopic)

label_protocol: Alexafluor 532 Ulysis labeling

growth_protocol: seawater collected at Berkeley pier and incubated in glass bottles in the dark with added 15N labeled mixed amino acids for 12 hours

extract_protocol: the cells are collected and the  RNA is extracted with Qiagen RNEasy kit from the total community

treatment_protocol: amino acids were added at 3 different concentrations (50 nM, 500 nM, 5 uM)

tag: treatment

value: 15N labeled mixed amino acids, medium and high concentration


title: genomic DNA from breast tumor tissue [29_120af]

description: breast tumor biopsy


title: Blood female Sarasota, FL SAR 2005_75

description: Gene expression wild dolphin blood

value: female


title: Blood female Brunswick, GA GEO 2009_Z25

description: Gene expression wild dolphin blood

value: Brunswick, GA


title: genomic DNA from breast tumor tissue [18_109af]

description: breast tumor biopsy


title: Blood male Brunswick, GA GEO 2009_Z26

description: Gene expression wild dolphin blood


title: Blood female Brunswick, GA GEO 2009_Z23

description: Gene expression wild dolphin blood


title: Ncl-KD ES cells siRNA #1 96hr, rep2

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

hyb_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

data_processing: Raw signal values were normalized using RMAExpress

label: biotin

organism: Mus musculus

source_name: Ncl-KD ES cells siRNA #1 96hr

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen)

tag: cell line

value: E14Tg2a Embryonic Stem Cells

tag: genotype/variation

value: Ncl siRNA #1


title: Blood male Brunswick, GA GEO 2009_Z22

description: Gene expression wild dolphin blood


title: Control ES cells 96hr, rep1

source_name: Control ES cells 96hr

value: control siRNA


title: Blood female Brunswick, GA GEO 2009_Z29

description: Gene expression wild dolphin blood


title: genomic DNA from breast tumor tissue [20_112af]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [26_117af]

description: breast tumor biopsy


title: Ncl-KD ES cells siRNA #2 96hr, rep1

source_name: Ncl-KD ES cells siRNA #2 96hr

value: Ncl siRNA #2


title: genomic DNA from breast tumor tissue [14_107af]

description: breast tumor biopsy


title: Blood male Brunswick, GA GEO 2009_Z24

description: Gene expression wild dolphin blood


title: Blood female Brunswick, GA GEO 2009_Z21

description: Gene expression wild dolphin blood


title: genomic DNA from breast tumor tissue [22_113af]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [16_108af]

description: breast tumor biopsy


title: Ncl-KD ES cells siRNA #2 96hr, rep2


title: genomic DNA from breast tumor tissue [24_114af]

description: breast tumor biopsy


title: Ncl-KD ES cells siRNA #1 96hr, rep1


title: Control ES cells 96hr, rep2


title: Blood female Brunswick, GA GEO 2009_Z19

description: Gene expression wild dolphin blood


title: Blood male Brunswick, GA GEO 2009_Z20

description: Gene expression wild dolphin blood


title: Mouse_hippo_PAMAM

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

description: Gene expression in mouse hippocampus. PAMAM exposed

hyb_protocol: Samples were then hybridized to the G4852A SurePrint G3 Mouse GE 8x60K Microarray slides (60000 probes, Agilent Technologies).

scan_protocol: The scanned images were analyzed using the standard procedures described in Agilent Feature Extraction software 10.7.3.1 (Agilent Technologies).

data_processing: Data analysis was performed with GeneSpring GX12.1 (Agilent Technologies).

source_name: mouse brain hippocampus, PAMAM

label_protocol: RNA was amplified into cRNA and labeled with Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies).

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

treatment_protocol: A single dose of PAMAM dendrimers or saline (control) was intranasally administered to 8-week old male BALB/c mice. Then, olfactory bulb, hippocampus, and cerebral cortex tissues were isolated at 24 hours after thePAMAM exposure.

value: brain hippocampus

tag: age

tag: strain

value: BALB/c

tag: agent

value: PAMAM dendrimers


title: genomic DNA from breast tumor tissue [8_104af]

description: breast tumor biopsy

value: Female

value: Irradiated


title: genomic DNA from breast tumor tissue [10_105af]

description: breast tumor biopsy

value: breast cancer


title: genomic DNA from breast tumor tissue [12_106af]

description: breast tumor biopsy


title: Mouse_cortex_Control

description: Gene expression in mouse cortex. Saline exposed

source_name: mouse brain cortex, control

value: brain cortex

value: male

value: saline (control)


title: Mouse_cortex_PAMAM

description: Gene expression in mouse cortex. PAMAM exposed

source_name: mouse brain cortex, PAMAM


title: Blood male Brunswick, GA GEO 2009_Z18

description: Gene expression wild dolphin blood

value: whole blood


title: Blood male Brunswick, GA GEO 2009_Z16

description: Gene expression wild dolphin blood


title: Blood male Brunswick, GA GEO 2009_Z14

description: Gene expression wild dolphin blood


title: Mouse_ob_PAMAM

description: Gene expression in mouse olfactory bulb. PAMAM exposed

source_name: mouse brain, olfactory bulb, PAMAM

value: brain olfactory bulb


title: liver_old_fish oil_sample3

city: ARMILLA

first: PATRICIA

last: PEREZ

state: GRANADA

address: AVDA DEL CONOCIMIENTO S/N

department: INYTA

country: Spain

institute: CIBM

description: Gene expression data from liver from old rat fed on fish oil

hyb_protocol: Following fragmentation, 0,05μg/μl of cRNA were hybridized for 16 hr at 45C on GeneChip RAT GENOME 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 Targeted Genotyping System

data_processing: The data were analyzed with dChip using Affymetrix default analysis settings and global scaling as normalization method.The intensity values of each probe in the microarray are processed and standardized by the method RMA (Robust Multichip Average) to obtain a single intensity value for each probe set, using the analysis program v7.3.1 Partek Genomics Suite.

organism: Rattus norvegicus

source_name: liver from old rats fed on fish oil

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 µg total RNA using the GeneChip® IVT Labelling Kit.

growth_protocol: Eighteen male Wistar rats (Ratus norvegicus) initially weighing 80-90 g were were randomly assigned into three experimental groups and match-fed from weaning until 24 months of age on a semi-synthetic and isoenergetic diet according to the AIN93 criteria, but modified in relation to the dietary fat source. We replaced this oil by virgin olive oil (virgin olive oil fed group), sunflower oil (sunflower oil fed group) or fish oil (fish oil fed group,) to formulate the experimental diets and groups. Modified AIN-93G diet was administered to rats from weaning to 2 months of age and AIN-93M was administered for the rest of the experiment. Diets were prepared weekly and stored in darkness at 4ºC to avoid lipid peroxidation. Animals were placed in a climate-controlled room (20ºC, 12 h dark/12h light cycle) for two years in collective cages, in groups of three animals per cage, with free access to water. Diet was delivered ad libitum for the first two months and then at 25 grams/rat/day for the rest of the experiment (in order to avoid overweight). Food intake was indirectly monitored through the weekly body weight control and daily spillage monitoring. At 6 and 24 months the rats were killed by cervical dislocation followed by decapitation and the liver were removed.

extract_protocol: The hepatic tissue was pulverized in a homogenizer in the presence of liquid nitrogen. Total RNA was extracted with RNeasy Mini kit (Qiagen, Düsseldorf, Germany) following manufacturer recommendations.

treatment_protocol: About 50 mg of liver tissue was introduced in RNA later during 24 hours, and stored at -80°C for gene expression analyses.

value: Wistar

value: liver

value: old (24 months)

tag: dietary fat source

value: fish oil


title: genomic DNA from breast tumor tissue [4_102af]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [6_103af]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [2_101af]

description: breast tumor biopsy


title: Blood female Sapelo Island, GA GEO 2009_Z13

description: Gene expression wild dolphin blood

value: female

value: Sapelo Island, GA


title: Mouse_ob_Control

description: Gene expression in mouse olfactory bulb. Saline

source_name: mouse brain, olfactory bulb, control


title: liver_old_sunflower oil_sample3

description: Gene expression data from liver from old rat fed on sunflower oil

source_name: liver from old rats fed on sunflower oil

value: sunflower oil


title: liver_old_virgin olive oil_sample3

description: Gene expression data from liver from old rat fed on virgin olive oil

source_name: liver from old rats fed on virgin olive oil

value: virgin olive oil


title: Mouse_hippo_Control

description: Gene expression in mouse hippocampus. Saline exposed

source_name: mouse brain hippocampus, control

value: brain hippocampus

value: BALB/c


title: liver_old_virgin olive oil_sample2


title: liver_old_fish oil_sample2


title: Dex Replicate 4

city: Durham

first: Arpit

last: Tandon

address: 2605, Meridian Parkway

institute: SRA International

description: Gene expression after 6 hours of 100nM dexamethasone

hyb_protocol: 1.65ug Cy3 labeled cRNA was fragmented and hybridized to Aglient Rat Whole Genome 4x44 multiplex format oligo arrays for 17 hours in rotating hybridization oven.

scan_protocol: Slides were washed and scanned with an Agilent Scanncer using one color scan setting for 4x44k array slides

data_processing: Feature extractor processed signal was log2-transformed and quantile normalized

source_name: 6 hr after 100nM dex, Replicate 4

label_protocol: Agilent 1-color microarry based gene expression analysis protocol; 500 ng of total RNA was Cy3 labeled according to manufacturer's protocol.

growth_protocol: Primary thymocytes were isolated from adrenalectomized male Sprague-Dawley rats ~1-2 after surgery. Following decapitation, the thymi of 3 rats were pooled in RPMI 1640 medium containing 10% heat inactivated FBS, 4mM glutamine, 75 units/mL streptomycin, and 100 units/mL penicllin. Thymi were sheared and filtered through 200 micron mesh twice and centrifuged at 3,000xg for 5 min at room temperature. The cell pellet was then resuspended in fresh RPMI media and filtered into a sterile conical tube. Cells were cultured at a final concetration of 2x10^6 cells/mL and incubated at 37C, 5% C02 atmosphere.

extract_protocol: Ambion miRvana total RNA isolation protocol (Austin, Texas)

treatment_protocol: Rat primary thymocyes were isolated and cultured in the presence of absence of 100nM dexamethasone for 6 hours at 37C, 5% C02 atmosphere.

value: Dex

tag: replicate


title: Blood male Sapelo Island, GA GEO 2009_Z12

description: Gene expression wild dolphin blood


title: liver_old_sunflower oil_sample2


title: Dex Replicate 3

source_name: 6 hr after 100nM dex, Replicate 3


title: genomic DNA from breast tumor tissue [38_127be]

description: breast tumor biopsy

source_name: tumor tissue

value: Female

value: Non-irradiated

value: breast cancer


title: genomic DNA from breast tumor tissue [34_124be]

description: breast tumor biopsy


title: Blood female Sapelo Island, GA GEO 2009_Z11

description: Gene expression wild dolphin blood

source_name: Peripheral Blood


title: genomic DNA from breast tumor tissue [36_125be]

description: breast tumor biopsy


title: Dex Replicate 2

source_name: 6 hr after 100nM dex, Replicate 2


title: Dex Replicate 1

source_name: 6 hr after 100nM dex, Replicate 1


title: genomic DNA from breast tumor tissue [32_123be]

description: breast tumor biopsy


title: Blood male Sapelo Island, GA GEO 2009_Z08

description: Gene expression wild dolphin blood

value: male


title: Control Replicate 4

description: Gene expression of untreated rat

source_name: Control, Replicate 4

value: Control


title: Blood male Sapelo Island, GA GEO 2009_Z10

description: Gene expression wild dolphin blood

value: whole blood


title: Blood female Sapelo Island, GA GEO 2009_Z07

description: Gene expression wild dolphin blood


title: genomic DNA from breast tumor tissue [28_120be]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [30_121be]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [27_118be]

description: breast tumor biopsy


title: Control Replicate 2

description: Gene expression of untreated rat

source_name: Control, Replicate 2


title: liver_old_sunflower oil_sample1

value: Wistar


title: Control Replicate 1

description: Gene expression of untreated rat

source_name: Control, Replicate 1


title: Control Replicate 3

description: Gene expression of untreated rat

source_name: Control, Replicate 3


title: liver_old_fish oil_sample1

value: liver


title: liver_old_virgin olive oil_sample1

value: old (24 months)


title: Blood male Sapelo Island, GA GEO 2009_Z06

description: Gene expression wild dolphin blood


title: Blood female Sapelo Island, GA GEO 2009_Z09

description: Gene expression wild dolphin blood


title: Blood female Sapelo Island, GA GEO 2009_Z03

description: Gene expression wild dolphin blood


title: liver_young_virgin olive oil_sample3

description: Gene expression data from liver from young rat fed on virgin olive oil

source_name: liver from young rats fed on virgin olive oil

value: young (6 months)


title: Blood female Sapelo Island, GA GEO 2009_Z01

description: Gene expression wild dolphin blood

value: female


title: genomic DNA from breast tumor tissue [23_114be]

description: breast tumor biopsy


title: Blood male Sapelo Island, GA GEO 2009_Z00

description: Gene expression wild dolphin blood

value: Sapelo Island, GA


title: liver_young_fish oil_sample3

description: Gene expression data from liver from young rat fed on fish oil

source_name: liver from young rats fed on fish oil

value: fish oil


title: Blood male Sapelo Island, GA GEO 2009_Z04

description: Gene expression wild dolphin blood


title: liver_young_sunflower oil_sample1

description: Gene expression data from liver from young rat fed on sunflower oil

source_name: liver from young rats fed on sunflower oil

value: sunflower oil


title: genomic DNA from breast tumor tissue [21_113be]

description: breast tumor biopsy


title: liver_young_sunflower oil_sample3


title: liver_young_fish oil_sample1


title: Blood female Beaufort, NC BEA 2006_467

description: Gene expression wild dolphin blood

value: Beaufort, NC


title: liver_young_virgin olive oil_sample2

value: virgin olive oil


title: genomic DNA from breast tumor tissue [17_109be]

description: breast tumor biopsy


title: liver_young_sunflower oil_sample2


title: liver_young_virgin olive oil_sample1


title: Blood male Sapelo Island, GA GEO 2009_Z02

description: Gene expression wild dolphin blood


title: genomic DNA from breast tumor tissue [25_117be]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [13_107be]

description: breast tumor biopsy


title: Blood female Beaufort, NC BEA 2006_465

description: Gene expression wild dolphin blood


title: liver_young_fish oil_sample2


title: Blood male Beaufort, NC BEA 2006_464

description: Gene expression wild dolphin blood


title: genomic DNA from breast tumor tissue [19_112be]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [15_108be]

description: breast tumor biopsy


title: genomic DNA from sample 305

status: Public on Mar 25 2014

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

country: China

institute: Fudan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing:
minfi, R. The *signal_matrix.txt contains raw data.
Quantile normalized methylation beta values and then adjusted for estimated cell proportions and sex (processed_methylation_matrix.txt)

label: cy3, cy5

source_name: Whole blood

extract_protocol: genomic DNA was extracted and purified from whole blood using Qiagen DNeasy Kit according to standard instructions

value: Normal

tag: race

value: CEU

value: Whole blood


title: Blood male Beaufort, NC BEA 2006_460

description: Gene expression wild dolphin blood


title: genomic DNA from sample 303


title: genomic DNA from sample 300


title: genomic DNA from sample 304


title: Blood female Beaufort, NC BEA 2006_461

description: Gene expression wild dolphin blood


title: KO TH2 cells

city: St. Louis

first: Chih-Chung

last: Lin

state: MO

address: 660 S. Euclid Ave. Box 8118

department: Pathology and Immunology

description: Gene expression data from KO TH2 cells

hyb_protocol: Hybridization was performed by standard methods at the GTAC at Washington University School of Medicine.

scan_protocol: GeneChips were scanned at the GTAC at Washington University School of Medicine.

data_processing: Array data were imported into Arraystar 5 software (DNAstar) and then normalized using the robust multi-array analysis method with quantile normalization.

source_name: KO TH2 cells

label_protocol: RNA was amplified (Ovation Pico SL WTA System V2, Nugen), labeled (Encore Biotin Module, Nugen), and fragmented.

growth_protocol: Purified naïve CD4+B220-CD25-CD44loCD62Lhi cells were cultured in TH0, TH1, TH2, or TH17 conditions for 4 days.

extract_protocol: Total RNA was isolated by the E.Z.N.A. MicroElute Total RNA Kit, Omega Bio-Tek.

treatment_protocol: Cells were stimulated with PMA and ionomycin for 4 hours prior to collection of total RNA.

value: Bhlhe40 KO

tag: cell type

value: purified splenic CD4 T cells

tag: cell culture conditions

value: TH2 conditions for 4 days


title: genomic DNA from sample 297


title: genomic DNA from sample 296


title: genomic DNA from sample 298


title: KO TH1 cells

institute: Washington University School of Medicine

description: Gene expression data from KO TH1 cells

source_name: KO TH1 cells

value: TH1 conditions for 4 days

value: stimulated with PMA and ionomycin for 4 hours prior to collection of total RNA


title: genomic DNA from sample 299


title: genomic DNA from breast tumor tissue [7_104be]

description: breast tumor biopsy

value: Female

value: Non-irradiated

value: breast cancer


title: genomic DNA from breast tumor tissue [9_105be]

description: breast tumor biopsy


title: genomic DNA from breast tumor tissue [11_106be]

description: breast tumor biopsy


title: Blood female Beaufort, NC BEA 2006_457

description: Gene expression wild dolphin blood

value: whole blood

value: female


title: KO TH17 cells

description: Gene expression data from KO TH17 cells

source_name: KO TH17 cells

value: TH17 conditions for 4 days


title: WT TH1 cells

description: Gene expression data from WT TH1 cells

source_name: WT TH1 cells

value: WT


title: genomic DNA from breast tumor tissue [3_102be]

description: breast tumor biopsy


title: genomic DNA from sample 301


title: genomic DNA from breast tumor tissue [5_103be]

description: breast tumor biopsy


title: WT TH2 cells

description: Gene expression data from WT TH2 cells

source_name: WT TH2 cells


title: Blood female Beaufort, NC BEA 2006_449

description: Gene expression wild dolphin blood

value: Beaufort, NC


title: WT TH17 cells

description: Gene expression data from WT TH17 cells

source_name: WT TH17 cells


title: genomic DNA from breast tumor tissue [1_101be]

description: breast tumor biopsy

source_name: tumor tissue


title: genomic DNA from sample 294


title: genomic DNA from sample 291


title: genomic DNA from sample 283

value: male


title: genomic DNA from sample 285

value: Normal


title: genomic DNA from sample 282

value: CEU


title: genomic DNA from sample 279

value: Whole blood


title: genomic DNA from sample 289


title: genomic DNA from sample 292


title: genomic DNA from sample 284


title: genomic DNA from sample 290


title: genomic DNA from sample 286


title: genomic DNA from sample 277


title: genomic DNA from sample 293


title: genomic DNA from sample 281


title: genomic DNA from sample 278


title: genomic DNA from sample 280


title: genomic DNA from sample 275


title: genomic DNA from sample 295


title: genomic DNA from sample 274


title: genomic DNA from sample 273


title: genomic DNA from sample 272


title: genomic DNA from sample 270


title: genomic DNA from sample 269


title: genomic DNA from sample 268


title: genomic DNA from sample 288


title: genomic DNA from sample 287


title: genomic DNA from sample 267


title: genomic DNA from sample 266


title: genomic DNA from sample 263


title: genomic DNA from sample 262


title: genomic DNA from sample 265


title: genomic DNA from sample 264


title: genomic DNA from sample 259


title: genomic DNA from sample 261


title: genomic DNA from sample 257


title: genomic DNA from sample 258


title: genomic DNA from sample 253


title: genomic DNA from sample 252


title: genomic DNA from sample 255


title: genomic DNA from sample 254


title: genomic DNA from sample 276


title: genomic DNA from sample 250


title: genomic DNA from sample 249


title: genomic DNA from sample 251


title: genomic DNA from sample 271


title: genomic DNA from sample 245


title: genomic DNA from sample 246


title: genomic DNA from sample 248


title: genomic DNA from sample 247


title: genomic DNA from sample 244


title: genomic DNA from sample 243


title: genomic DNA from sample 242


title: genomic DNA from sample 240


title: genomic DNA from sample 256


title: genomic DNA from sample 260


title: genomic DNA from sample 241


title: genomic DNA from sample 237


title: genomic DNA from sample 236


title: genomic DNA from sample 233


title: genomic DNA from sample 235


title: genomic DNA from sample 234


title: genomic DNA from sample 230


title: genomic DNA from sample 228


title: genomic DNA from sample 226


title: genomic DNA from sample 229


title: genomic DNA from sample 227


title: genomic DNA from sample 224


title: genomic DNA from sample 225


title: genomic DNA from sample 222


title: genomic DNA from sample 221


title: genomic DNA from sample 220


title: genomic DNA from sample 219


title: genomic DNA from sample 217


title: genomic DNA from sample 218


title: genomic DNA from sample 239


title: genomic DNA from sample 238


title: genomic DNA from sample 215


title: genomic DNA from sample 216


title: genomic DNA from sample 232


title: genomic DNA from sample 211


title: genomic DNA from sample 210


title: genomic DNA from sample 209


title: genomic DNA from sample 207


title: genomic DNA from sample 214


title: genomic DNA from sample 231


title: genomic DNA from sample 213


title: genomic DNA from sample 204


title: genomic DNA from sample 203


title: genomic DNA from sample 212


title: genomic DNA from sample 201


title: genomic DNA from sample 208


title: genomic DNA from sample 206


title: genomic DNA from sample 223


title: genomic DNA from sample 200


title: genomic DNA from sample 198


title: genomic DNA from sample 194


title: genomic DNA from sample 195


title: genomic DNA from sample 192


title: genomic DNA from sample 193


title: genomic DNA from sample 197


title: genomic DNA from sample 196


title: genomic DNA from sample 190


title: genomic DNA from sample 191


title: genomic DNA from sample 189


title: genomic DNA from sample 186


title: genomic DNA from sample 188


title: genomic DNA from sample 205


title: genomic DNA from sample 184


title: genomic DNA from sample 185


title: genomic DNA from sample 183


title: genomic DNA from sample 181


title: genomic DNA from sample 202


title: genomic DNA from sample 182


title: genomic DNA from sample 199


title: genomic DNA from sample 176


title: genomic DNA from sample 177


title: genomic DNA from sample 174


title: genomic DNA from sample 179


title: genomic DNA from sample 178


title: genomic DNA from sample 180


title: genomic DNA from sample 173


title: genomic DNA from sample 172


title: genomic DNA from sample 175


title: genomic DNA from sample 187


title: genomic DNA from sample 171


title: genomic DNA from sample 170


title: genomic DNA from sample 169


title: genomic DNA from sample 166


title: genomic DNA from sample 167


title: genomic DNA from sample 168


title: genomic DNA from sample 164


title: genomic DNA from sample 163


title: genomic DNA from sample 165


title: genomic DNA from sample 162


title: genomic DNA from sample 161


title: genomic DNA from sample 157


title: genomic DNA from sample 160


title: genomic DNA from sample 156


title: genomic DNA from sample 159


title: genomic DNA from sample 155


title: genomic DNA from sample 302


title: genomic DNA from sample 154


title: genomic DNA from sample 153


title: genomic DNA from sample 152


title: genomic DNA from sample 149


title: genomic DNA from sample 147


title: genomic DNA from sample 148


title: genomic DNA from sample 146


title: genomic DNA from sample 150


title: genomic DNA from sample 144


title: genomic DNA from sample 145


title: genomic DNA from sample 143


title: genomic DNA from sample 138


title: genomic DNA from sample 139


title: genomic DNA from sample 140


title: genomic DNA from sample 141


title: genomic DNA from sample 137


title: genomic DNA from sample 134


title: genomic DNA from sample 136


title: genomic DNA from sample 132


title: genomic DNA from sample 135


title: genomic DNA from sample 158


title: genomic DNA from sample 131


title: genomic DNA from sample 133


title: genomic DNA from sample 130


title: genomic DNA from sample 126


title: genomic DNA from sample 125


title: genomic DNA from sample 129


title: genomic DNA from sample 151


title: genomic DNA from sample 124


title: genomic DNA from sample 127


title: genomic DNA from sample 142


title: genomic DNA from sample 120


title: genomic DNA from sample 122


title: genomic DNA from sample 123


title: genomic DNA from sample 117


title: genomic DNA from sample 119


title: genomic DNA from sample 118


title: genomic DNA from sample 116


title: genomic DNA from sample 115


title: genomic DNA from sample 121


title: genomic DNA from sample 114


title: genomic DNA from sample 109


title: genomic DNA from sample 112


title: genomic DNA from sample 128


title: genomic DNA from sample 111


title: genomic DNA from sample 108


title: genomic DNA from sample 110


title: genomic DNA from sample 105


title: genomic DNA from sample 107


title: genomic DNA from sample 113


title: genomic DNA from sample 104


title: genomic DNA from sample 102


title: genomic DNA from sample 100


title: genomic DNA from sample 101


title: genomic DNA from sample 98


title: genomic DNA from sample 99


title: genomic DNA from sample 97


title: genomic DNA from sample 103


title: genomic DNA from sample 95


title: genomic DNA from sample 96


title: genomic DNA from sample 93


title: genomic DNA from sample 94


title: genomic DNA from sample 90


title: genomic DNA from sample 92


title: genomic DNA from sample 91


title: genomic DNA from sample 89


title: genomic DNA from sample 88


title: genomic DNA from sample 86


title: genomic DNA from sample 106


title: genomic DNA from sample 85


title: genomic DNA from sample 82


title: genomic DNA from sample 84


title: genomic DNA from sample 83


title: genomic DNA from sample 80


title: genomic DNA from sample 81


title: genomic DNA from sample 77


title: genomic DNA from sample 78


title: genomic DNA from sample 76


title: genomic DNA from sample 79


title: genomic DNA from sample 75


title: genomic DNA from sample 74


title: genomic DNA from sample 87


title: genomic DNA from sample 72


title: genomic DNA from sample 73


title: genomic DNA from sample 70


title: genomic DNA from sample 71


title: genomic DNA from sample 69


title: genomic DNA from sample 68


title: genomic DNA from sample 65


title: genomic DNA from sample 66


title: genomic DNA from sample 67


title: genomic DNA from sample 63


title: genomic DNA from sample 62


title: genomic DNA from sample 64


title: genomic DNA from sample 61


title: genomic DNA from sample 59


title: genomic DNA from sample 60


title: genomic DNA from sample 58


title: genomic DNA from sample 57


title: genomic DNA from sample 56


title: genomic DNA from sample 55


title: genomic DNA from sample 54


title: genomic DNA from sample 51


title: genomic DNA from sample 50


title: genomic DNA from sample 49


title: genomic DNA from sample 52


title: genomic DNA from sample 48


title: genomic DNA from sample 47


title: genomic DNA from sample 53


title: genomic DNA from sample 43


title: genomic DNA from sample 44


title: genomic DNA from sample 40


title: genomic DNA from sample 45


title: genomic DNA from sample 42


title: genomic DNA from sample 41


title: genomic DNA from sample 39


title: genomic DNA from sample 37


title: genomic DNA from sample 34


title: genomic DNA from sample 36


title: genomic DNA from sample 35


title: genomic DNA from sample 31


title: genomic DNA from sample 32


title: genomic DNA from sample 30


title: genomic DNA from sample 29


title: genomic DNA from sample 27


title: genomic DNA from sample 22


title: genomic DNA from sample 24


title: genomic DNA from sample 46


title: genomic DNA from sample 21


title: genomic DNA from sample 25


title: genomic DNA from sample 20


title: genomic DNA from sample 16


title: genomic DNA from sample 15


title: genomic DNA from sample 28


title: genomic DNA from sample 38


title: genomic DNA from sample 14


title: genomic DNA from sample 13


title: genomic DNA from sample 12


title: genomic DNA from sample 26


title: genomic DNA from sample 33


title: genomic DNA from sample 23


title: genomic DNA from sample 11


title: genomic DNA from sample 10


title: genomic DNA from sample 8


title: genomic DNA from sample 18


title: genomic DNA from sample 9


title: genomic DNA from sample 19


title: genomic DNA from sample 7


title: A00423_Q2

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

hyb_protocol: Hybridization to arrays was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

scan_protocol: Slides were scanned as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

data_processing:
Data analysis was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)
Values are expression of M, i.e. a log2 ratio of treated sample at a particular time in a particular strain to the pre-treatment sample from the same strain, e.g Mtb treated with diamide at 60 min relative to Mtb prior to diamide treatment

organism: Mycobacterium tuberculosis CDC1551

source_name: Mycobacterium tuberculosis CDC1551 complement of D-Rv2745c knockout mutant , t=0, diamide

label_protocol: cDNA labeling was performed as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

growth_protocol: Mtb strains were cultured as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

extract_protocol: RNA was extracted as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

treatment_protocol: Bacterial cultures were treated with Diamide as described earlier (Mehra and Kaushal, PMCID: PMC2698404)

value: complement of D-Rv2745c knockout mutant

value: control

tag: time

source_name: Mycobacterium tuberculosis CDC1551 complement of D-Rv2745c knockout mutant , t=90, diamide

value: diamide


title: A00423_Q1


title: A00304_Q3

source_name: Mycobacterium tuberculosis CDC1551 complement of D-Rv2745c knockout mutant , t=30, diamide


title: A00304_Q1


title: A00433_Q2

source_name: Mycobacterium tuberculosis CDC1551 complement of D-Rv2745c knockout mutant , t=60, diamide


title: A00433_Q3


title: A00433_Q1


title: A00423_Q3


title: A00466_Q3

source_name: Mycobacterium tuberculosis CDC1551 D-Rv2745c knockout mutant, t=0, diamide

value: D-Rv2745c knockout mutant

source_name: Mycobacterium tuberculosis CDC1551 D-Rv2745c knockout mutant, t=60, diamide


title: genomic DNA from sample 4

tag: gender


title: A00306_Q2

source_name: Mycobacterium tuberculosis CDC1551 D-Rv2745c knockout mutant, t=90, diamide


title: A00466_Q2


title: A00306_Q1


title: A00306_Q3


title: genomic DNA from sample 3


title: genomic DNA from sample 2


title: genomic DNA from sample 1


title: A00466_Q1


title: A00304_Q2


title: A00023_Q3

source_name: Mycobacterium tuberculosis CDC1551 D-Rv2745c knockout mutant, t=30, diamide


title: genomic DNA from sample 6


title: genomic DNA from sample 5


title: A00023_Q1


title: A00023_Q2


title: A00436_Q1

source_name: Mycobacterium tuberculosis CDC1551, t=0, diamide

value: wild-type Mtb

source_name: Mycobacterium tuberculosis CDC1551, t=90, diamide


title: A00436_Q2


title: A00437_Q3

source_name: Mycobacterium tuberculosis CDC1551, t=60, diamide


title: A00436_Q3


title: A00437_Q2


title: A00437_Q1


title: A00470_Q2

source_name: Mycobacterium tuberculosis CDC1551, t=30, diamide


title: A00470_Q3


title: A00470_Q1


title: NY451

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: Raw data were extracted by using GenomeStudio software v.3 (Illumina), and normalized by using cubic spline algorithm implemented in Illumina normalizer module of GenePattern Genomic analysis tool kit (www.broadinstitute.org/genepattern).

extract_protocol: RNA was isolated from fresh frozen tissues with RNeasy kit (Qiagen) according to manufacturer’s protocol.

tag: tissue type

value: cirrhosis

tag: location in tumor nodule


title: NY450

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: NY430

label_protocol: Refer to the Illumina beadarray Assay System Manual

value: hepatocellular carcinoma

value: tumor central


title: NY453


title: NY452

value: tumor peripherial


title: GER-2E3

city: Houston

first: Stephen

middle: Mack

last: Christopher

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

description:
Bisulphite Treated (Zymo)
6026818094_R04C01

hyb_protocol: Hybridization protocol was performed according to Illumina manufacturers protocol.

scan_protocol: Scanning protocol was performed according to Illumina manufacturers protocol.

data_processing:
Samples were background corrected using Illumina Genome Studio, where Average Beta Values were then exported
matrix signal intensities: SIGNAL A IS UNMETHYLATED AND SIGNAL B IS METHYLATED

label_protocol: Labeling protocol was performed according to Illumina manufacturers protocol.

extract_protocol: DNA was extracted according to (Witt et al., Cancer Cell 2011) and bisulfite treated with the zymo kit

treatment_protocol: Fresh frozen samples

tag: tissue

value: Ependymoma

tag: tumor type

value: PF tumour


title: BT2010182

description:
Bisulphite Treated (Zymo)
6026818094_R05C02


title: NY428


title: GER-2E27

description:
Bisulphite Treated (Zymo)
6026818091_R05C02


title: GER-1E29

description:
Bisulphite Treated (Zymo)
6026818094_R03C02


title: GER2E4

description:
Bisulphite Treated (Zymo)
6026818094_R04C02


title: GER-2e6

description:
Bisulphite Treated (Zymo)
6026818091_R04C02


title: GER-1E36

description:
Bisulphite Treated (Zymo)
6026818091_R02C02


title: BT2010207

description:
Bisulphite Treated (Zymo)
6026818094_R06C02


title: NY427


title: GER-1E38

description:
Bisulphite Treated (Zymo)
6026818091_R03C02


title: genomic DNA from sample 17

source_name: Whole blood

tag: disease state

value: female


title: GER-1E7

description:
Bisulphite Treated (Zymo)
6026818091_R01C02


title: GER-3E18

description:
Bisulphite Treated (Zymo)
6026818094_R02C01


title: GER-2E17

description:
Bisulphite Treated (Zymo)
6026818091_R05C01


title: GER-3E25

description:
Bisulphite Treated (Zymo)
6026818094_R05C01


title: GER-2E36

description:
Bisulphite Treated (Zymo)
6026818094_R01C01


title: GER-1E31

description:
Bisulphite Treated (Zymo)
6026818091_R04C01


title: GER-3E48

description:
Bisulphite Treated (Zymo)
6026818094_R06C01


title: GER-3E49

description:
Bisulphite Treated (Zymo)
6026818094_R03C01


title: GER-1E23

description:
Bisulphite Treated (Zymo)
6026818094_R01C02


title: GER-1E3

description:
Bisulphite Treated (Zymo)
6026818091_R06C01


title: GER-2E31

description:
Bisulphite Treated (Zymo)
6026818091_R06C02


title: NY422


title: NY429


title: NY421


title: GER-1E15

description:
Bisulphite Treated (Zymo)
6026818091_R03C01


title: GER-3E29

description:
Bisulphite Treated (Zymo)
6026818091_R02C01


title: NY410_replicate


title: NY420


title: GER-2E22

description:
Bisulphite Treated (Zymo)
6026818094_R02C02


title: NY416


title: NY417


title: NY413


title: NY414


title: NY412


title: GER-1E25

description:
Bisulphite Treated (Zymo)
6026818110_R06C02


title: NY419


title: GER-1E37

description:
Bisulphite Treated (Zymo)
6026818110_R05C02


title: NY415


title: NY411


title: GER-1E11

description:
Bisulphite Treated (Zymo)
6026818091_R01C01


title: NY409


title: NY410


title: NY403_replicate


title: NY408


title: NY418


title: GER-3E15

description:
Bisulphite Treated (Zymo)
6026818110_R03C02


title: NY407


title: NY404


title: UHS47

description:
Bisulphite Treated (Zymo)
6026818110_R01C02


title: NY402


title: NY403


title: GER-1E16

description:
Bisulphite Treated (Zymo)
6026818110_R04C02


title: NY405


title: NY406


title: UHS30

description:
Bisulphite Treated (Zymo)
6026818110_R05C01


title: UHS50

description:
Bisulphite Treated (Zymo)
6026818110_R02C02


title: UHS16

description:
Bisulphite Treated (Zymo)
6026818110_R04C01


title: MDT-EP19

description:
Bisulphite Treated (Zymo)
6026818101_R06C02


title: UHS39

description:
Bisulphite Treated (Zymo)
6026818110_R02C01


title: UHS36

description:
Bisulphite Treated (Zymo)
6026818110_R03C01


title: Primary calvarial osteoblast,Transfected with SC,RNA extracted 48 hours post-transfection,rep1

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed by the Genome Sciences Laboratory in the Center for Public Health Genomics at the University of Virginia.

data_processing: Illumina GenomeStudio generated raw intensity values. The expression values were transformed using the Variance Stabilizing Transformation (VST), and quantile normalized using the LumiR R package.

label: Biotin

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).

growth_protocol: Primary calvarial osteoblasts were isolated from 3-9 day old neonates using sequential Collagenase P digestions.  Cells were plated into 6 well plates at 300,000 cells/2ml sterile plating media (DMEM, 10% heat-inactivated FBS, 100 U/ml penicillin, 100 μg/ml streptomycin) per well.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini Kit.

treatment_protocol: siRNA transfection experiments cells were handled as outlined above except they were plated at 150,000 cells/well, transfected ~24h after plating using Lipofectamine 2000 Reagent (Invitrogen) according to manufacturer’s directions

value: Mixed Gender

value: primary calvarial osteoblasts


title: Primary calvarial osteoblast,Transfected with BICC1_2,RNA extracted 48 hours post-transfection,rep1


title: NY398


title: UHS3

description:
Bisulphite Treated (Zymo)
6026818101_R05C02


title: Primary calvarial osteoblast,Transfected with BICC1_3,RNA extracted 48 hours post-transfection,rep2


title: Primary calvarial osteoblast,Transfected with BICC1_1,RNA extracted 48 hours post-transfection,rep1


title: Primary calvarial osteoblast,Transfected with BICC1_3,RNA extracted 48 hours post-transfection,rep1


title: NY400


title: UHS37

description:
Bisulphite Treated (Zymo)
6026818101_R04C02


title: NY387_replicate


title: NY397


title: UHS42

description:
Bisulphite Treated (Zymo)
6026818101_R04C01


title: EPT259

description:
Bisulphite Treated (Zymo)
6026818101_R06C01


title: UHS51

description:
Bisulphite Treated (Zymo)
6026818101_R03C01


title: NY401


title: EPT279

description:
Bisulphite Treated (Zymo)
6026818110_R01C01


title: EPT274

description:
Bisulphite Treated (Zymo)
6026818101_R01C02


title: EPT272

description:
Bisulphite Treated (Zymo)
6026818101_R03C02


title: NY399


title: Primary calvarial osteoblast,Transfected with BICC1_3,RNA extracted 48 hours post-transfection,rep4


title: EPT297

description:
Bisulphite Treated (Zymo)
6026818101_R02C02


title: UHS63

description:
Bisulphite Treated (Zymo)
6026818101_R02C01


title: Primary calvarial osteoblast,Transfected with BICC1_2,RNA extracted 48 hours post-transfection,rep2


title: Primary calvarial osteoblast,Transfected with SC,RNA extracted 48 hours post-transfection,rep3


title: NY391


title: Primary calvarial osteoblast,Transfected with BICC1_1,RNA extracted 48 hours post-transfection,rep3


title: NY383_replicate


title: Primary calvarial osteoblast,Transfected with BICC1_2,RNA extracted 48 hours post-transfection,rep3


title: EPT298

description:
Bisulphite Treated (Zymo)
6026818101_R05C01


title: NY393


title: Primary calvarial osteoblast,Transfected with BICC1_3,RNA extracted 48 hours post-transfection,rep3


title: Primary calvarial osteoblast,Transfected with SC,RNA extracted 48 hours post-transfection,rep2


title: UHS52

description:
Bisulphite Treated (Zymo)
6026818101_R01C01


title: NY386


title: NY384


title: NY385


title: NY387


title: Primary calvarial osteoblast,Transfected with BICC1_2,RNA extracted 48 hours post-transfection,rep4


title: 71_Active

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX10software

source_name: Human whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions, and subsequently subjected to DNAse treatment using RNAse free DNAse Set. RNA integrity was assessed by 1% agarose gel electrophoresis and samples of poor quality were excluded from analysis.

value: whole blood

tag: phenotype

value: TB patient

tag: condition

value: Active


title: NY358_replicate


title: 70_Control

value: Control


title: Primary calvarial osteoblast,Transfected with SC,RNA extracted 48 hours post-transfection,rep4


title: Primary calvarial osteoblast,Transfected with BICC1_1,RNA extracted 48 hours post-transfection,rep4


title: NY381


title: NY382


title: 68_Active


title: 69_Recover

value: Recover


title: 64_Control


title: NY371


title: 61_Recover


title: 63_Recover


title: NY380


title: NY374


title: 67_Control


title: 65_Treatment

value: Treatment


title: 60_Active


title: NY369


title: NY383


title: 66_Recover


title: NY373


title: NY392


title: NY367


title: NY368


title: NY372


title: 62_Treatment


title: UHS40

description:
Bisulphite Treated (Zymo)
6026818110_R06C01


title: 59_Recover


title: 58_Treatment


title: NY366


title: NY360


title: 57_Active


title: 56_Control


title: 53_Control


title: NY350


title: NY357


title: NY351


title: NY359


title: 49_Control


title: 50_Active


title: 51_Treatment


title: NY358


title: 48_Recover


title: NY396


title: 52_Recover


title: 54_Treatment


title: 47_Treatment


title: NY349


title: NY348


title: 55_Recover


title: CLF1 cells,biological rep3

city: Taipei

first: Wan-Jiun

last: Chen

address: No.1 Jen Ai Road section 1

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CLF1 cells,biological rep3.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: cancer associated fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37°C under a humidified atmosphere consisting of 20% O2 and 5% CO2.

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

treatment_protocol: CLS1 sphere after  CLS1/CAF co-culture and compared this profile with that obtained for CLS1 cells cultured without feeder cells through different passages (CLS1 p3, p6, and p14) and CLF1

tag: cell line

value: CLF1 cells


title: Primary calvarial osteoblast,Transfected with BICC1_1,RNA extracted 48 hours post-transfection,rep2

tag: strain


title: CLF1 cells,biological rep2

description: Gene expression data from CLF1 cells,biological rep2.


description: Gene expression data from CLS1 cells cultured without feeder cells through 14 passages.

source_name: Lung cancer cell

value: CLS1 cells

tag: culture condition


description: Gene expression data from CLS1 cells cultured without feeder cells through 8 passages.


title: CLS1 cells cultured without feeder cells through 6 passages,biological rep1

description: Gene expression data from CLS1 cells cultured without feeder cells through 6 passages.


title: 46_Active


title: 42_Treatment


description: Gene expression data from CLS1 cells cultured without feeder cells through 3 passages.


description: Gene expression data from CLS1 sphere generated by co-culture with CAF then pick up CLS1 sphere,biological rep1

value: CLS1 sphere

value: co-culture with CAF


title: CLF1 cells,biological rep1

description: Gene expression data from CLF1 cells,biological rep1.


title: 38_Control


title: 40_Control


title: 41_Active


title: 44_Control


title: 37_Recover


title: 34_Control


title: 35_Active


title: Paucigranulocytic Asthma 4310479166_E

city: New Lambton Heights

first: Katie

last: Baines

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

hyb_protocol: 750ng reverse-transcribed cRNA was hybridized to the Illumina Sentrix HumanRef-8 Version 2 Expression BeadChip, which measured the expression of 20590 genes.

scan_protocol: BeadChips were scanned using the Illumina Bead Station and data was captured using VeadScan 3.5.11.

data_processing: Sample and gene profiling results were included in the analysis if the sample was of suitable purity (OD 260/280 ratio between 1.7-2.1) and was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (correlation coefficients and principle component analysis plots)

source_name: induced sputum

label_protocol: 500ng extracted RNA was reverse-transcribed into cRNA and labeled with biotin-uridine-5'-triphosphate by using the Illumina TotalPrep RNA Amplication Kit.

extract_protocol: RNA was extracted from induced sputum using the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quatitation was performed using the Quanti-iT RiboGreen RNA Quantitation Assay Kit (Molecular Probes Inc, Invitrogen, Eugene, OR, USA).

tag: asthma phenotype

value: Paucigranulocytic Asthma

value: Female

tag: smoking pack years

tag: age

tag: sample type

value: sputum

value: asthma


title: 39_Recover


title: CLS1 cells cultured without feeder cells through 6 passages,biological rep2


title: 33_Recover


title: 32_Treatment


title: 43_Recover


title: CLS1 cells cultured without feeder cells through 6 passages,biological rep3


description: Gene expression data from CLS1 sphere generated by co-culture with CAF then pick up CLS1 sphere,biological rep3


title: 36_Treatment


description: Gene expression data from CLS1 sphere generated by co-culture with CAF then pick up CLS1 sphere,biological rep2


title: Paucigranulocytic Asthma 4310479168_H


title: NY394

value: hepatocellular carcinoma

value: tumor central


title: 31_Active


title: 27_Treatment


title: Paucigranulocytic Asthma 4310479166_A


title: 20_Recover


title: 26_Active


title: 18_Control


title: 24_Recover


title: 23_Treatment


title: 22_Active


title: 21_Control


title: 30_Active


title: 25_Control


title: 28_Recover


title: 29_Control


title: Paucigranulocytic Asthma 4310479156_G

value: Male


title: Paucigranulocytic Asthma 4135447178_A


title: Paucigranulocytic Asthma 4310479156_E


title: 16_Active

value: whole blood


title: 17_Recover

value: TB patient


title: Paucigranulocytic Asthma 4310479163_B


title: 15_Control


title: Paucigranulocytic Asthma 4135447179_B


title: HUES8_S0.2

city: Boston

first: Sinisa

last: Hrvatin

state: MA

address: 220 Longwood ave, GB405

department: Neurobiology

institute: Harvard Medical School

hyb_protocol: 750 ng cRNA per sample was then hybridized to Human HT-12 Expression BeadChips (Illumina) using the Whole- Genome Expression Direct Hybridization kit (Illumina)

scan_protocol: Illumina Beadstation 500

data_processing: GenomeStudio (Illumina, V2011.1). Raw data were adjusted by background subtraction and rank-invariant normalization. Before calculating fold change, an offset of 20 was added to all probe set means to eliminate negative signals. The p- values for differences between mean signals were calculated in GenomeStudio by t-test and corrected for multiple hypotheses testing by the Benjamini-Hochberg method in combination with the Illumina custom false discovery rate (FDR) model.

source_name: HUES8 human embryonic stem cells

label_protocol: Using the Illumina TotalPrep RNA Amplification kit (Ambion), double-stranded cDNA was generated following reverse transcription from 100 ng of total RNA. In vitro transcription overnight with biotin-labeled nucleotides created amplified mRNA (cRNA), which was concentrated by vacuum centrifugation at 30°

growth_protocol: Human embryonic stem cells were grown on matrigel using mTeSR media

extract_protocol: RNA was isolated using MARIS. Detailed protocol is described in the manuscript: MARIS: Method for Analyzing RNA following Intracellular Sorting

treatment_protocol: Detailed methods are available in the manuscript: Differentiated human stem cells resemble fetal, not adult, β cells

tag: cell type

value: human pluripotent stem cells


title: Paucigranulocytic Asthma 4135447179_H


title: 19_Active

value: Active


title: 14_Recover

value: Recover


title: 10_Recover


title: 12_Active


title: H1_S0.2

source_name: H1 human embryonic stem cells


title: Paucigranulocytic Asthma 4135447194_G


title: 9_Treatment

value: Treatment


title: 13_Treatment


title: Paucigranulocytic Asthma 4147931008_C


title: HUES8_S0.1


title: Paucigranulocytic Asthma 4135447179_D


title: 11_Control

value: Control


title: Paucigranulocytic Asthma 4147931008_B


title: iPS_S0.2

source_name: human induced pluripotent stem cells

value: human iPS-17b


title: 7_Recover


title: iPS_S0.1


title: Paucigranulocytic Asthma 4147931029_D


title: Adult.3

source_name: isolated human adult pancreatic islets

value: isolated human adult pancreatic islets

value: human adult pancreatic islets


title: Paucigranulocytic Asthma 4147931029_C

value: Paucigranulocytic Asthma


title: 5_Active


title: 8_Control


title: Paucigranulocytic Asthma 4135447160_H

value: Female


title: H1_S0.1


title: 4_Control


title: 45_Active


title: 3_Recover


title: 6_Treatment


title: Paucigranulocytic Asthma 4147931029_A

value: sputum


title: Adult.1


title: 1_Active


title: Neutrophilic Asthma 4310479166_G

value: Neutrophilic Asthma

value: asthma


title: Adult.2


title: AzaRCA3

city: Atlanta

first: Jessilyn

last: Dunn

state: GA

address: 1760 Haygood Drive HSRB E197

department: Biomedical Engineering

institute: Georgia Tech & Emory University

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse right carotid artery, unligated contralateral control, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), replicate #2

scan_protocol: BeadChips were scanned using Illumina HiScan.

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.3

source_name: right carotid artery, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), unligated contralateral control

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

growth_protocol: C57Bl6 mice were fed normal chow diet for 9 weeks.

extract_protocol: Mice were perfused with saline and carotid arteries were extracted and flushed with 150 ul of Qiazol. The Qiagen miReasy Kit was used to extract and purify total RNA. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were treated with either saline control or 5-Aza-2'deoxycytidine (0.2mg/kg/day) by daily I.P. injection for 3 weeks. After 2 weeks of treament, 3 out of the 4 caudal branches of the left carotid artery (LCA) of mice were ligated while the right carotid artery (RCA) was left untouched as the contralateral internal control. After 1 week of ligation, mice were sacrificed by CO2 inhalation.

tag: treatment

value: 5-Aza-2'deoxycytidine treatment, unligated contralateral control

value: 9 weeks

value: carotid artery intima


title: AzaRCA1

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse right carotid artery, unligated contralateral control, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), replicate #1


title: Neutrophilic Asthma 4310479156_F

tag: gender

value: Male


title: 2_Treatment

value: whole blood

value: TB patient


title: Neutrophilic Asthma 4310479173_E


title: Adult_ins.3

source_name: insulin-expressing cells sorted from human adult pancreatic islets


title: NY395

tag: tissue type

value: cirrhosis


title: E11.5 mouse esophagus

city: Tsukuba

first: Mari

last: Sekine

address: 1-1-1 Tennoudai

department: Graduate School of Life and Environmental Sciences

institute: The University of Tsukuba

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 18 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile, then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10. 5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.

source_name: mouse esophagus E11.5

label_protocol: RNA was labeled using the ‘Agilent Low Input Quick Amp Kit’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.

growth_protocol: ICR mouse were harbored following the guidelines of the National Institute of Advanced Industrial Science and Technology Animal Experiment Committee.

extract_protocol: The primordium stomach was dissected from mouse embryo at E11.5. Total RNA was isolated from stomach using the ‘RNeasy micro kit’ (Quiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Male and female mice were mated and the day of identification of a vaginal plug was E0.5. After 11days, mouse embryos were collected as E11.5.

value: esophagus

tag: stain

value: ICR


title: AzaLCA4

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse left carotid artery, 7 days ligated, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), replicate #3

source_name: left carotid artery, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), 7 days ligated

value: 5-Aza-2'deoxycytidine treatment, 7 days ligated

tag: tissue


title: Adult_ins.2

value: insulin-expressing cells sorted from human adult pancreatic islets


title: Fetal_ins.3

source_name: insulin-expressing cells sorted from human week 16 fetal pancreata

value: human week 16 fetal pancreas


title: Paucigranulocytic Asthma 4135447160_A

value: Paucigranulocytic Asthma


title: AzaLCA2

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse left carotid artery, 7 days ligated, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), replicate #2


title: Neutrophilic Asthma 4310479166_D

value: Female


title: AzaLCA1

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse left carotid artery, 7 days ligated, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), replicate #1


title: E11.5 mouse gustric

source_name: mouse gustric E11.5

value: gustric


title: E11.5 mouse intestine

source_name: mouse intestine E11.5

value: intestine


title: AzaRCA4

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse right carotid artery, unligated contralateral control, 21 days of 5-Aza-2'deoxycytidine treatment (0.2mg/kg/day by I.P. injection), replicate #3


title: Neutrophilic Asthma 4135447178_D

value: Neutrophilic Asthma

value: sputum

value: asthma


title: cells after transduction with shHIF-1a

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

institute: San Raffaele Scientific Institute

description: Gene expression data from adult mouse BM-derived mesenchymal progenitors

hyb_protocol: cRNA was hybridized on the Affimetrix GeneChip HT_MG_430_PM. GeneChip was washed and scanned according to the manufacturer’s recommendations on a GeneChip HT Array Plate Scanner.

data_processing: The data were analyzed with expressionFileCreator, from the GenePattern Suite of the Broad Institute. Data were normalized with RMA.

source_name: Mesenchyma progenitors PaS+

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 7 days culture in low oxygen concentration (1% oxygen)

extract_protocol: Total RNA was extracted using RNeasy Mini Kits (QIAGEN)

treatment_protocol: cells were maintained in MesenCult complete medium for the enitre culture process. Transduction with lentiviral vectors cointaning shRNAs has been performed overnight.

value: adult BM-derived cells

value: 8 weeks


title: Fetal_ins.2

value: insulin-expressing cells sorted from human week 16 fetal pancreata


title: Neutrophilic Asthma 4135447194_H


title: Fetal_ins.1


title: cells after transduction with shCTR

scan_protocol: GeneChip was washed and scanned according to the manufacturer’s recommendations on a GeneChip HT Array Plate Scanner.


title: RCA4

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse right carotid artery, unligated contralateral control, saline-treated control, replicate #3

source_name: right carotid artery, saline-treated control, unligated contralateral control

value: 9 weeks

value: carotid artery intima


title: Neutrophilic Asthma 4147931034_D

value: Male


title: RCA2

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse right carotid artery, unligated contralateral control, saline-treated control, replicate #2

value: saline-treated control, unligated contralateral control


title: Fetal.2

source_name: whole dissected human week 16 fetal pancreas


title: cells after transduction with shHIF-2a


title: Neutrophilic Asthma 4135447179_A


title: LCA4

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse left carotid artery, 7 days ligated, saline-treated control, replicate #3

source_name: left carotid artery, saline-treated control, 7 days ligated

value: saline-treated control, 7 days ligated


title: iPS_ins.2

source_name: insulin-expressing cells sorted from hiPS cells differentiated to stage 6

value: insulin-expressing cells sorted from human pluripotent stem cells differentiated to stage 6

value: human iPS-17b


title: iPS_ins.1


title: RCA1

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse right carotid artery, unligated contralateral control, saline-treated control, replicate #1


title: E11.5 mouse lung

source_name: mouse lung E11.5

value: lung

value: ICR


title: Fetal.1

value: whole dissected human week 16 fetal pancreas

value: human week 16 fetal pancreas


title: LCA2

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse left carotid artery, 7 days ligated, saline-treated control, replicate #2


title: Neutrophilic Asthma 4147931029_B

source_name: induced sputum

value: Neutrophilic Asthma

value: Female


title: LCA1

description:
endothelial-enriched RNA from carotid artery of C57Bl6 male 9 weeks of age
endothelial-enriched RNA (3 pooled arteries),mouse left carotid artery, 7 days ligated, saline-treated control, replicate #1


title: Neutrophilic Asthma 4147931029_H

value: sputum

value: asthma


title: H1_ins.2

source_name: insulin-expressing cells sorted from H1 cells differentiated to stage 6


title: Neutrophilic Asthma 4147931008_E


title: HUES8_ins.2

source_name: insulin-expressing cells sorted from HUES8 cells differentiated to stage 6


title: C10-HDAC7 cells treated with β-estradiol for 72h, biological rep1

city: Barcelona

first: Maribel

last: Parra

state: Barcelona

address: Avda. Gran Via 199-203, L'Hospitalet de Llobregat

department: Cancer Epigenetics and Biology Programme (PEBC)

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Gene expression data from C10-HDAC7 cells induced with b-estradiol for 72h

hyb_protocol: PCR amplified biotinylated cDNA were hybridized against Affymetrix HT MG-430 PM Array Plate (Mouse Genome 430 PM strip).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Affymatrix CEL files were background corrected and normalized using Bioconductor package “affy”. Particularly we used Affy 'expresso' algorithm. Since the Affymetrix chip version used in this study contains only perfect match (pm) probes, for normalization and acquiring raw probe intensities to expression values we used following parameters: background correction method rma; normalization method constant;  pm correct method pmonly; and  summary method avgdiff. Normalized absolute values were conveter to Log2 intensities using R program.

source_name: C10 cells transduced with a vector for HDAC7 expression, induced with b-estradiol for 72 hours

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

growth_protocol: C10-MSCV and C10-HDAC7 cells were cultured at 37ºC in RPMI 1640 without phenol red supplemented with 10% of charcoal treated fetal bovine serum, 2 mM glutamine, and 50 U/ml streptomycin/penicillin. For the generation of C10-MSCV and C10-HDAC7 cells, C10 cells were spin infected and 48 hours after were selected in the presence of 3ug/ml of puromycin. For transdifferentiation induction, cells were treated with 100nM β-estradiol in the presence of 10nM of IL-3 and 10nM of mCsf1 for the indicated periods of time.

extract_protocol: RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)

treatment_protocol: Biological duplicates of C10-MSCV and C10-HDAC7 cells were treated with 100nM β-estradiol in the presence of 10nM of IL-3 and CSF-1 and harvested for RNA extraction at various times thereafter. Uninduced C10-MSCV and C10-HDAC7 were maintained for 24h in 0.1% ethanol.

value: pre-B cells


title: H1_ins.1


title: HUES8_ins.1


title: C10-HDAC7 cells treated with β-estradiol for 48h, biological rep2

description: Gene expression data from C10-HDAC7 cells induced with b-estradiol for 48h

source_name: C10 cells transduced with a vector for HDAC7 expression, induced with b-estradiol for 48 hours


title: Eosinophilic Asthma 4310479168_D

value: Eosinophilic Asthma


title: Eosinophilic Asthma 4310479167_D


title: H1_S6.2

source_name: H1 cells differentiated to stage 6 containing insulin-expressing cells

value: human pluripotent stem cells differentiated to stage 6 containing insulin-expressing cells


title: C10-HDAC7 cells treated with β-estradiol for 72h, biological rep2


title: Eosinophilic Asthma 4310479173_F


title: C10-HDAC7 cells untreated, biological rep1

description: Gene expression data from uninduced C10-HDAC7 cells

source_name: C10 cells transduced with a vector for HDAC7 expression, control


title: Eosinophilic Asthma 4310479173_C


title: C10-HDAC7 cells treated with β-estradiol for 48h, biological rep1


title: iPS_S6.1

source_name: hiPSC cells differentiated to stage 6 containing insulin-expressing cells


title: Eosinophilic Asthma 4310479173_D


title: C10-MSCV cells treated with β-estradiol for 72h, biological rep2

description: Gene expression data from C10-MSCV cells induced with b-estradiol for 72h

source_name: C10 cells transduced with empty vector, induced with b-estradiol for 72 hours


title: infection(3)

city: jilin

first: liu

last: qianhong

state: jilin

address: No.77, Hanlin Road, Economic Development Districe

department: College of Animal Science and Veterinary Medicine

institute: Jilin Agricultural Science and Technology University

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained . In the current research, P <0.01, FDR <0.001, and the absolute value of the log2Ratio >2 was used as the threshold to assess the significance of the difference in gene expression.

label: not applicable

source_name: mononuclear macrophage cells

label_protocol: not applicable

growth_protocol: Brucella melitensis 16M was grown on tryptic soy agar (TSA) plates at 37 °C. This was used to inoculate tryptic soy broth (TSB). Twenty-four-hour bacterial cultures were used to infect cells.

extract_protocol: The total RNA were extracted from the cells at 0, 4 and 24 h post infection according to the manufacturer's protocol (Promega). Sequence tag preparation was performed using a Digital Gene Expression Tag Profile Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: The mouse macrophage cell line RAW264.7 (our lab) was maintained in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum. The cells were passaged every 3 to 5 days and discarded after the 15th passage. Macrophage RAW264.7 at low passage was used to seed the wells of a 24-well plate at 2.5 x 105 per well in 0.5 ml DMEM.

value: mouse mononuclear macrophage cells

tag: passages

tag: post infection

value: 4 h


title: Eosinophilic Asthma 4310479168_A

value: Male

tag: disease state


title: C10-HDAC7 cells untreated, biological rep2


title: H1_S6.1


title: C10-MSCV cells treated with β-estradiol for 48h, biological rep2

description: Gene expression data from C10-MSCV cells induced with b-estradiol for 48h

source_name: C10 cells transduced with empty vector, induced with b-estradiol for 48 hours


title: Transcription profile at 30 and 5 % DSW Replicate 2 (dye-swap)

city: Bayreuth

first: Alfons

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

hyb_protocol: Labeled cRNA was quantified spectroscopically and equal amounts of cRNA (825 ng each) were used for hybridizations. Hybridization was carried out using Agilent's 'Gene Expression Hybridization Kit' (no. 5188-5242) as recommended by Agilent; after hybridization, microarrays were washed using Agilent's 'Gene Expression Wash Buffer 1 and 2' (nos. 5188-5325 and 5188-5326) and ozone-induced degradation of cyanine dyes was prevented by treatment of the microarray slides with Agilent's 'Stabilization and Drying Solution' (no. 5185-5979).

scan_protocol: Scanned on an Agilent G2565AA scanner. The scanned images were analyzed with Agilent's Feature Extraction Software Version 9.5.3.1 (Agilent) using default parameters (protocol GE2-v5_95_Feb07 and Grid: 040802_D_F_20120509).

data_processing: The raw data files were uploaded to Babelomics microarray analysis suite (ver. 4.3; http://babelomics.bioinfo.cipf.es/) and normalized using the Agilent two-channel script based on the LIMMA package (background correction: normexp; within arrays normalization: loess; between arrays normalization: quantiles).

organism: Aspergillus ruber

source_name: Eurotium rubrum liquid culture

label_protocol: RNA was labeled using Agilent's 'Low Input Quick Amp Labeling' kit (no. 5190-2306); 200 ng total RNA were used in each labeling reaction. Labeled cRNA was purified using Qiagen's 'RNeasy Mini Spin Columns' (no. 74804).

growth_protocol:
Water taken from the Dead Sea (Israel) was dilluted as indicated and used to prepare growth media.
One milliliter of spore suspension was used to inoculate a 'starter culture' in GY medium (1% glucose, 0.1% yeast extract) prepared with 30% Dead Sea Water; the culture was grown in a rotary shaker (150 rpm) at 27°C for 3 days.
Three milliliter of the starter culture were used to inoculate GY media prepared with 5%, 30%, and 50% Dead Sea Water, respectively; the cultures were grown in a rotary shaker (150 rpm) at 27°C for 7 days. Replicate samples were prepared from separate cultures.

extract_protocol: Fungal cells were harvested by filtration and immediately frozen in liquid nitrogen. Samples were extracted using Qiagen's RNeasy Plant Mini Kit (No. 974904).

tag: salt  condition

value: grown at 30% DSW

value: grown at 5% DSW


title: infection(4)


title: C10-MSCV cells treated with β-estradiol for 72h, biological rep1


title: Transcription profile at 30 and 50 % DSW Replicate 2 (dye-swap)

value: grown at 50% DSW


title: C10-MSCV cells treated with β-estradiol for 48h, biological rep1


title: hsp33_rep3

city: Lisboa

first: Leonor

last: Miller-Fleming

state: select a state

address: Avenida Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

hyb_protocol: We followed the instructions of the manufacturer's - Agilent

scan_protocol: GenePix 4200A 01  [99709], FocusPosition=0; Temperature=24.63; LinesAveraged=1, PMTGain=400; ScanPower=50; LaserPower=2.54; Filters=Standard Green-; ScanRegion=0,0,4400,14300

data_processing: normalization was performed in ArrayTrackTM using mean, median scaling without background subtraction

organism: Saccharomyces cerevisiae

source_name: strain deleted for hsp33, diauxic-shift

label_protocol: Low input Quick Amp Labelling, following the instructions of the manufacturer - Agilent

growth_protocol: Cultures were grown in synthetic complete media until reached diauxic shift. At this time cultures were collected.

extract_protocol: RNA Qiagen kits

tag: genotype/variation


title: control (0)

tag: strain


title: HUES8_S6.2

source_name: HUES8 cell differentiated to stage 6 containing insulin-expressing cells

tag: cell line


title: HUES8_S6.1


title: Eosinophilic Asthma 4147931034_C

tag: asthma phenotype


title: hsp31 ko_rep2

source_name: strain deleted for hsp31, diauxic-shift

value: hsp31 ko


title: hsp31 ko_rep1


title: hsp32 ko_rep1

source_name: strain deleted for hsp32, diauxic-shift

value: hsp32 ko


title: Eosinophilic Asthma 4135447178_F

tag: smoking pack years


title: C10-MSCV cells untreated, biological rep1

description: Gene expression data from uninduced C10-MSCV cells

source_name: C10 cells transduced with empty vector, control


title: Transcription profile at 50 and 30 % DSW Replicate 1


title: Eosinophilic Asthma 4135447194_D

source_name: induced sputum

tag: age


title: wt_rep1

source_name: wild-type strain, diauxic-shift

value: wt


title: wt_rep3

source_name: Wild-type strain, diauxic-shift


title: Transcription profile at 5 and 30 % DSW Replicate 1


title: hsp32 ko_rep2


title: Eosinophilic Asthma 4147931034_E

tag: sample type


title: Adult_ins.1

source_name: insulin-expressing cells sorted from human adult pancreatic islets

tag: cell type

value: human adult pancreatic islets


title: Eosinophilic Asthma 4135447179_C


title: Eosinophilic Asthma 4147931034_G


title: C10-MSCV cells untreated, biological rep2


title: Eosinophilic Asthma 4147931034_A


title: Neutrophilic Asthma 4310479163_E

value: Neutrophilic Asthma


title: Eosinophilic Asthma 4135447179_E

value: Female


title: hsp33 ko_rep2

value: hsp33 ko


title: hsp32 ko_rep3


title: hsp31 ko_rep3


title: wt_rep2

source_name: wild-type, diauxic-shift


title: hsp33 ko_rep1


title: Eosinophilic Asthma 4135447160_F

value: sputum

value: asthma


title: Eosinophilic Asthma 4147931008_H

value: Eosinophilic Asthma


title: Eosinophilic Asthma 4147931008_A


title: Human germinal center B-cell sub-populations from tonsils B

status: Public on Mar 24 2014

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Tonsil samples were first fine-minced in normal culture medium (RPMI1640, 10% FBS, Life Technologies, Paisley, UK) and passed through a cell strainer (BD) with a 70 µm grid to obtain single cell suspensions. Total B-cells were first enriched by using EasySep human B-cell enrichment kit, negative selection (Stem cell Technology, Vancouver, Canada) using RoboSep instrument (Stemcell Technology). Tonsil B-cells were first stained with the following antibodies: FITC-polyclonal anti-IgD (Dako, Glostrup, Denmark), APC anti-CD19 mAb (BD), PE-polyclonal anti-IgM (Dako), Pe-Cy5 (Beckman Coulter, Brea, CA, USA) or PE-CF594 (BD) anti-CD27 mAb, PE-Cy7 anti-CD38 mAb (BD). Gating CD19+ B-cells were further purified by FACS sorting based on the expression of IgD versus CD38. In particular, the following non abutting gates were drawn to separate naïve B-cells (N) (IgD bright CD38 - CD27 - ); marginal zone (MZ)-like B-cells (IgD low IgM bright  CD38 ? ); germinal center (GC) B cells (IgD - CD38 + ) and switched memory (SM) B cells (IgD - IgM - CD38 - )

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The raw intensity expression values were processed by Robust Multi-array Average (RMA) complete procedure with the re-mapped Chip Definition Files (CDF) from BrainArray libraries version 15.0.0 available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.asp.

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

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

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: vh status = igvh mutational status (fais et al. j clin invest, 1998)


title: Human marginal zone B-cell sub-populations from tonsils D


title: Human naive B-cell sub-populations from tonsils B


title: Human germinal center B-cell sub-populations from tonsils G


title: Human germinal center B-cell sub-populations from tonsils C


title: Human memory B-cell sub-populations from tonsils C


title: constitutively active PKA

city: Daejeon

first: Jongkyun

last: Kang

address: 335 Gwahangro, Yuseong-gu

country: South Korea

institute: KAIST

description: Gene expression data from the Drosophila adult head to identify the genes showing altered expression levels in responses to the high or low PKA activity.

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

scan_protocol: GeneChips were scanned using theAffymetrix GeneChip Scanner 3000 7G

data_processing: he data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed target intensity of each array was arbitrarily set to 90.

organism: Drosophila melanogaster

source_name: Drosophila adult head

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

growth_protocol: All transgenic flies were rasied on standard cornmeal food at 18oC and 40-50% relative humidity until three-day-old adults. Then to transiently induce PKA transgenes flies were moved to 32oC for 12-16hrs by repressing the temperature-sensitive Gal80.

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

treatment_protocol: All flies were collected and frozen immediately in liquid nitrogen. Head were removed from bodies by vortex-mixing and separated in a chilled sieve.

value: adult total head

tag: genotype

value: 4-6 days old after hatching


title: Human B-cell from peripheral blood BC3

description: Total B-cells were first enriched by using EasySep human B-cell enrichment kit, negative selection (Stem cell Technology, Vancouver, Canada) using RoboSep instrument (Stemcell Technology). B-cells from buffy coats were further purified by FACS sorting (FACS Aria II, BD, San Jose, CA, USA) using anti-CD19 APC (BD) to obtain purified CD19+ B-cells.

source_name: Human B-cell from peripheral blood BC3


title: Human germinal center B-cell sub-populations from tonsils F


title: Human B-cell from peripheral blood BC7

source_name: Human B-cell from peripheral blood BC7


title: Human memory B-cell sub-populations from tonsils B


title: Human B-cell from peripheral blood BC6

source_name: Human B-cell from peripheral blood BC6


title: Human naive B-cell sub-populations from tonsils C


title: Human marginal zone B-cell sub-populations from tonsils E


title: Human naive B-cell sub-populations from tonsils A


title: control


title: Human chronic lymphocytic leukemia patient WB0269

description: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

value: unmut


title: Human B-cell from peripheral blood BC1

source_name: Human B-cell from peripheral blood BC1


title: Human memory B-cell sub-populations from tonsils A


title: Human B-cell from peripheral blood BC2

source_name: Human B-cell from peripheral blood BC2


title: Human chronic lymphocytic leukemia patient VG0442


title: Human chronic lymphocytic leukemia patient VS0140

value: mut


title: Human chronic lymphocytic leukemia patient VD0026


title: Human B-cell from peripheral blood BC4

source_name: Human B-cell from peripheral blood BC4


title: Human chronic lymphocytic leukemia patient VD0354


title: dominant-negative PKA


title: Human chronic lymphocytic leukemia patient VP0089


title: Human chronic lymphocytic leukemia patient VC0315


title: Human chronic lymphocytic leukemia patient TM0259


title: Human chronic lymphocytic leukemia patient TL0397


title: Human chronic lymphocytic leukemia patient VS0016


title: Human chronic lymphocytic leukemia patient TG0263


title: Human chronic lymphocytic leukemia patient VB0013


title: Human chronic lymphocytic leukemia patient TG0139


title: Human chronic lymphocytic leukemia patient UL0266


title: Human chronic lymphocytic leukemia patient SV0046


title: Human chronic lymphocytic leukemia patient SF0098


title: Human chronic lymphocytic leukemia patient SS0299


title: Human chronic lymphocytic leukemia patient SA0205


title: Human chronic lymphocytic leukemia patient SA0021


title: Human chronic lymphocytic leukemia patient VC0142


title: Human chronic lymphocytic leukemia patient SA0219


title: Human chronic lymphocytic leukemia patient SA0093


title: Human chronic lymphocytic leukemia patient SS0275


title: Human chronic lymphocytic leukemia patient SG0168


title: Human chronic lymphocytic leukemia patient RM0400


title: Human chronic lymphocytic leukemia patient SG0114


title: Human chronic lymphocytic leukemia patient SL0083


title: Human chronic lymphocytic leukemia patient RD0296


title: Human chronic lymphocytic leukemia patient RB0087


title: Human chronic lymphocytic leukemia patient RS0325


title: Human chronic lymphocytic leukemia patient RR0157


title: Human chronic lymphocytic leukemia patient RG0443


title: Human chronic lymphocytic leukemia patient RB0040


title: Human chronic lymphocytic leukemia patient RA0023


title: Human chronic lymphocytic leukemia patient PV0322


title: Human chronic lymphocytic leukemia patient PS0212


title: Human chronic lymphocytic leukemia patient PP0195


title: Human chronic lymphocytic leukemia patient RG0077


title: Human chronic lymphocytic leukemia patient PG0276


title: Human chronic lymphocytic leukemia patient RA0211


title: Human chronic lymphocytic leukemia patient RG0045


title: Human chronic lymphocytic leukemia patient PI0172


title: Human chronic lymphocytic leukemia patient PR0084


title: Human chronic lymphocytic leukemia patient PZ0305


title: Human chronic lymphocytic leukemia patient PG0028


title: Human chronic lymphocytic leukemia patient RA0288


title: Human chronic lymphocytic leukemia patient PM0340


title: Human chronic lymphocytic leukemia patient PV0286


title: Human chronic lymphocytic leukemia patient PS0044


title: Human chronic lymphocytic leukemia patient PG0216

value: nd


title: Human chronic lymphocytic leukemia patient PF0024


title: Human chronic lymphocytic leukemia patient PD0164


title: Human chronic lymphocytic leukemia patient PA0351


title: Human chronic lymphocytic leukemia patient PF0177


title: Human chronic lymphocytic leukemia patient PA0271


title: Human chronic lymphocytic leukemia patient PM0117


title: Human chronic lymphocytic leukemia patient PA0234


title: Human chronic lymphocytic leukemia patient PC0304


title: Human chronic lymphocytic leukemia patient NS0060


title: Human chronic lymphocytic leukemia patient PA0145


title: Human chronic lymphocytic leukemia patient NG0068


title: Human chronic lymphocytic leukemia patient NM0156


title: Human chronic lymphocytic leukemia patient OM0201


title: Human chronic lymphocytic leukemia patient OV0127


title: Human chronic lymphocytic leukemia patient MS0357


title: Human chronic lymphocytic leukemia patient PA0146


title: Human chronic lymphocytic leukemia patient MO0174


title: Human chronic lymphocytic leukemia patient MM0097


title: Human chronic lymphocytic leukemia patient MS0321


title: Human chronic lymphocytic leukemia patient MV0334


title: Human chronic lymphocytic leukemia patient MS0189


title: Human chronic lymphocytic leukemia patient MS0115


title: Human chronic lymphocytic leukemia patient MM0330


title: Human chronic lymphocytic leukemia patient MN0167


title: Human chronic lymphocytic leukemia patient MP0137


title: Human chronic lymphocytic leukemia patient NB0333


title: Human chronic lymphocytic leukemia patient ML0298


title: Human chronic lymphocytic leukemia patient OI0282


title: Human chronic lymphocytic leukemia patient MO0323


title: Human chronic lymphocytic leukemia patient MG0248


title: Human chronic lymphocytic leukemia patient MG0449


title: Human chronic lymphocytic leukemia patient MS0273


title: Human chronic lymphocytic leukemia patient MG0170


title: Human chronic lymphocytic leukemia patient MC0134


title: Human chronic lymphocytic leukemia patient MF0274


title: Human chronic lymphocytic leukemia patient MA0151


title: Human chronic lymphocytic leukemia patient MF0048


title: Human chronic lymphocytic leukemia patient MA0209


title: Human chronic lymphocytic leukemia patient MG0110


title: Human chronic lymphocytic leukemia patient LI0133


title: Human chronic lymphocytic leukemia patient LL0130


title: Human chronic lymphocytic leukemia patient LM0150


title: Human chronic lymphocytic leukemia patient MA0088


title: Human chronic lymphocytic leukemia patient MF0379


title: Human chronic lymphocytic leukemia patient MC0105


title: Human chronic lymphocytic leukemia patient IA0025


title: Human chronic lymphocytic leukemia patient MC0055


title: Human chronic lymphocytic leukemia patient MB0065


title: Human chronic lymphocytic leukemia patient LG0337


title: Human chronic lymphocytic leukemia patient IL0066


title: Human chronic lymphocytic leukemia patient HG0135


title: Human chronic lymphocytic leukemia patient GS0343


title: Human chronic lymphocytic leukemia patient LP0364


title: Human chronic lymphocytic leukemia patient LG0224


title: Human chronic lymphocytic leukemia patient LR0247


title: Human chronic lymphocytic leukemia patient LP0076


title: Human chronic lymphocytic leukemia patient LG0038


title: Human chronic lymphocytic leukemia patient LV0118


title: Human chronic lymphocytic leukemia patient GR0092


title: Human chronic lymphocytic leukemia patient GR0033


title: Human chronic lymphocytic leukemia patient GR0169


title: Human chronic lymphocytic leukemia patient GP0348


title: Human chronic lymphocytic leukemia patient GM0252


title: Human chronic lymphocytic leukemia patient GP0329


title: Human chronic lymphocytic leukemia patient GN0095


title: Human chronic lymphocytic leukemia patient GG0301


title: Human chronic lymphocytic leukemia patient GP0171


title: Human chronic lymphocytic leukemia patient GB0293


title: Human chronic lymphocytic leukemia patient GC0147


title: Human chronic lymphocytic leukemia patient GD0262


title: Human chronic lymphocytic leukemia patient GC0015


title: Human chronic lymphocytic leukemia patient GL0368


title: Human chronic lymphocytic leukemia patient GE0125


title: Human chronic lymphocytic leukemia patient GA0398


title: Human chronic lymphocytic leukemia patient GG0027


title: Human chronic lymphocytic leukemia patient GD0051


title: Human chronic lymphocytic leukemia patient GF0281


title: Human chronic lymphocytic leukemia patient GC0328


title: Human chronic lymphocytic leukemia patient GM0041


title: Human chronic lymphocytic leukemia patient GB0267


title: Human chronic lymphocytic leukemia patient LF0102


title: Human chronic lymphocytic leukemia patient GD0158


title: Human chronic lymphocytic leukemia patient GA0141


title: Human chronic lymphocytic leukemia patient GC0096


title: Human chronic lymphocytic leukemia patient FS0155


title: Human chronic lymphocytic leukemia patient FR0283


title: Human chronic lymphocytic leukemia patient FM0309


title: Human chronic lymphocytic leukemia patient FS0257


title: Human chronic lymphocytic leukemia patient FI0152


title: Human chronic lymphocytic leukemia patient FP0153


title: Human chronic lymphocytic leukemia patient GA0091


title: Human chronic lymphocytic leukemia patient FO0291


title: Human chronic lymphocytic leukemia patient FC0075


title: Human chronic lymphocytic leukemia patient FA0429


title: Human chronic lymphocytic leukemia patient FB0332


title: Human chronic lymphocytic leukemia patient FA0347


title: Human chronic lymphocytic leukemia patient EB0042


title: Human chronic lymphocytic leukemia patient DT0300


title: Human chronic lymphocytic leukemia patient ET0128


title: Human chronic lymphocytic leukemia patient EG0341


title: Human chronic lymphocytic leukemia patient DA0094


title: Human chronic lymphocytic leukemia patient DC0371


title: Human chronic lymphocytic leukemia patient DE0085


title: Human chronic lymphocytic leukemia patient FA0294