title: m1

description:
human neuroblastoma cell line
cellular gDNA

source_name: mock

tag: treatment

value: only cellular gDNA 500ng


title: CP-19

status: Public on Jun 01 2015

type: genomic

city: Pittsburgh

first: Svetlana

middle: A

last: Yatsenko

state: PA

address: 300 Halket St

country: USA

institute: University of Pittsburgh

description: copy number and homozygosity mapping

hyb_protocol: According to Agilent protocol

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Cytogenomics Software (2.5.8.1).

data_processing: Copy number variants (CNVs), including gains and losses, were identified using the Aberration Detection Method 2 (ADM-2) algorithm, with modifications that support the determination of the clonal fraction of genomic imbalances in cancer cells. A minimum of five consecutive probes per region, with absolute average log2 ratio of 0.3 for any given region or a minimum region of 1 Mb in size, with a minimum absolute average log2 ratio of 0.08 (Agilent mosaic protocol).  Loss of homozygosity (LOH) regions were detected according to the Agilent protocol.

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

label_protocol: According to Agilent protocol

growth_protocol: uncultured

extract_protocol: DNA extracted using Puregene Kit following manufacturer's instructions

tag: tissue

value: Bone marrow

tag: gender

value: Female

tag: disease

value: B-ALL

source_name: commercially-available DNA used as reference

tag: reference dna gender

tag: reference dna cell line


title: Cpa3Cre/+ LFD, 2

type: RNA

city: Heidelberg

first: Dario

middle: Alejandro

last: Gutierrez

state: BW

address: Im Neuenheimer Feld 280

department: Cellular Immunology

country: Germany

institute: German Cancer Research center

description:
Group 4
SAMPLE 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalized using the Chipster 3.1.1 software (Genome studio) by the quatile method

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse epididymal AT

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was isolated using Quiagen RNA minikit

treatment_protocol:
Mice were fed a HFD (60% kcal from fat) or chow diet (6% fat) for 12 weeks
eAT was isolated after a 5h morning fast

tag: diet

value: LFD

tag: background

value: WBB6F1 (WB X C57Bl/6)

tag: genotype/variation


title: CP-15

description: copy number and homozygosity mapping

value: CML


title: tomato-WT-transgenic SlDREB2-salinity-48h replicat 1

city: Louvain-La-Neuve

first: IMENE

last: HICHRI

address: 5 (Bte 7.07.13) Place Croix du Sud

country: Belgium

institute: UCL

description: biological replicate 1 of 2

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus) and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B, Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Solanum lycopersicum

label_protocol: First strand cDNA was synthetized from 10 micrograms RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).

growth_protocol: 6 weeks-old tomato plants were grown in hydroponics (half-strength Hoagland nutrient solution)  in a growth chamber 24°C/22°C under a 16h day/8h night photoperiod as described in Hichri et al. (2014)

extract_protocol: Total RNA were extracted as described in Hichri et al. (2010)

treatment_protocol: Salt (125 mM NaCl) was added to the culture tank (52L) and plants exposed to salinity treatement for 48h.

tag: age

value: 6 weeks-old plants

tag: cultivar

value: Ailsa Craig

value: treatment with NaCl (125 mM) during 48h

value: WT

label: Alexa Fluor 647

source_name: tomato - transgenic SlDREB2-salinity-48h


title: CP-14

description: copy number and homozygosity mapping

source_name: peripheral blood

value: peripheral blood


title: CP-3

description: copy number and homozygosity mapping

value: AML


title: CP-17

description: copy number and homozygosity mapping


title: CLL Patient Sample JB2009052217

city: Boston

first: Jennifer

middle: R.

last: Brown

state: MA

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from CLL patients

hyb_protocol: Samples were hybridized to a microarray chip overnight at 45 degree in a solution containg several biotinylated control oligonucleotides.

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

data_processing: Normalization and batch correction were performed using the Partek Genomics Suite tool (Partek Inc).  Class prediction was performed with the Prediction Analysis of Microarrays (PAM) method using the R Bioconductor package.

source_name: CLL Cells

label_protocol: Samples were enzymatically fragmented and end-labled with a biotinylated nucleotide analog.

extract_protocol: Total RNA was isolated using RNEasy kits (Qiagen), performed according to the manufacturer's instructions.

treatment_protocol: CLL cells were isolated via density gradient centrifugation using Ficoll-Paque Plus and enrichment for B-cell fractions was performed using Rosette Sep (Stemcell Technologies).

value: Peripheral Blood

tag: genotype

value: IGHV unknown MYD88 wt

value: Adult


title: CP-6

description: copy number and homozygosity mapping


title: CLL Patient Sample JB2009091022

description: Gene expression data from CLL patients

value: IGHV unmutated MYD88 wt


title: CP-11

description: copy number and homozygosity mapping

value: Male

value: MDS


title: CLL Patient Sample JB2009071037

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009091001

description: Gene expression data from CLL patients


title: CP-1

description: copy number and homozygosity mapping

value: Bone marrow


title: CLL Patient Sample JB2009091003

description: Gene expression data from CLL patients


title: tomato-transgenic SlDREB2-WT-salinity-48h replicat 2

description: biological replicate 2 of 2, dye swap


title: CLL Patient Sample 49_CW210

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071041

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071049

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009091005

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2009081158

description: Gene expression data from CLL patients


title: CLL Patient Sample 82_CW258

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031036

description: Gene expression data from CLL patients


title: 56248702_532

city: Madison

first: Gregory

middle: M

last: Gauthier

state: WI

address: 1550 Linden Drive

department: Medicine

institute: University of Wisconsin - Madison

description: B. dermatitidis SREBΔ incubated for 6-hrs at 22oC. It is the 3rd biological replicate for this time point, each from separate cultures.

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction (NimbleScan software package, version 2.4.27 - Roche NimbleGen, Inc.).

organism: Blastomyces dermatitidis

source_name: Blastomyces dermatitidis SREBΔ

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.

growth_protocol: 3 biological replicates of SREBΔ and the isogenic wild-type control (ATCC 26199) were grown 37oC and for 6, 24, and 48-hrs at 22oC. All cultures were grown in liquid HMM (Histoplasma macrophage media) containing 10 uM FeSO4.  All glassware was pre-treated with 2N HCl and extensively washed with ddH2O.

extract_protocol: For all samples, total RNA was extracted using the phenol-guanidinium thiocyanate-1-bromo-3-chloropropane method [Sambrook J and Russell DW. Molecular cloning: a laboratory manual, 3rd Ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2001. pp. 7.4 – 7.8.].  B. dermatitidis cells were washed with PBS (pre-warmed to 37oC or 22oC), frozen in liquid nitrogen, lysed by grinding in a mortar and pestle, and treated with TRI Reagent followed by 1-bromo-3-chloropropane (Molecular Research Center Inc., Cincinnati, OH).  Total RNA was precipitated using a 1:1 concentration of isopropanol and high salt solution (Molecular Research Center, Inc., Cincinnati, OH), and washed with 75% ethanol.  Following resuspension in water pre-treated with diethyl pyrocarbonate (DEPC; Calbiochem, San Diego, CA), total RNA was treated with turboDNAase (Applied Biosystems/Ambion, Austin Texas), and purified using an RNeasy kit (Qiagen, Valencia, CA).  To optimally remove guanidine salts, an extra wash of RPE buffer was performed during RNAeasy purification.  RNA quality was assessed using an Agilent bioanalyzer (Agilent Technoligies, Santa Clara, CA).  Double-stranded cDNA was synthesized and purified at the Gene Expression Center at the University of Wisconsin – Madison.  Roche NimbleGen performed Cy3 labeling, hybridization, scanning, and RMA (Robust Multi-Array analysis) normalization for all 24 microarrays at their facility in Reykjavík, Iceland.

tag: strain

value: SREBΔ

tag: time point

value: 6-hrs 22oC

tag: replicate

value: C


title: CP-16

description: copy number and homozygosity mapping

value: Female

value: polycythemia vera


title: CLL Patient Sample JB2009071040

description: Gene expression data from CLL patients


title: EBs_d8_Hopx-Null vs Hopx-Het_rep2

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

description: Replicate 2 of 3. Null vs hererozygous EBs

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed in Agilent GE wash buffers 1-3.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: d8 mouse embryoid bodies

label_protocol: cDNA labeled at 40°C for 2 hours with 25 µM dCTP or 25 µM Cy3-label in the prescence of T7 RNA Polymerase (Agilent)

growth_protocol: Embryonic stem cells were derived from Hop+/- and Hopx-/- blastocysts using standard protocols. Briefly, blastocysts were collected at E3.5 and cultured on STO feeder cells in standard ESC media +LIF + 50µM MEK1 inhibitor (Cell Signaling) for 7 days until the blastocyst hatches and forms colony. Individual colonies were subcultured for approximately 1 week when MEK1 inhibitor is removed and cells passaged as a normal ESC line.

extract_protocol: 200ng of total RNA were primed with 7 µl of 100 µM T7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1.2ul of Affinity Script BlockMix (Agilent) and 100 µM each dATP, dTTP, dGTP

treatment_protocol: Cardiac differentiation was adapted from published protocols. Briefly, ESCs were cultured and maintained on a feeder layer of mitotically inactivated MEFs in DMEM with 15% FBS (Fisher Scientific) and ESGRO leukemia inhibitory factor. Differentiation through hanging droplets method was initiated following ESC dissociation and suspension at 5 x 104 cells/ml in DMEM with 10% FBS (Atlanta Biologicals) without LIF in 20µl drops. Two days after droplets formation, EBs were transferred in suspension onto poly-HEMA coated dishes. After another two days, EBs were plated on gelatin coated dishes in cardiac differentiation media [StemPro-34 SF medium (Invitrogen) supplemented with 5 ng/ml VEGF (R&D systems), 10 ng/ml bFGF (R&D systems), 12.5 ng/ml FGF10 (R&D systems), 1mM Ascorbic Acid (Sigma) and 2mM Glutamax (Invitrogen)]. RNA was isolated from day 8 cultures using Trizol (Life Techonologies) according to manufacturer's instructions.

value: d8 mouse embryoid bodies

value: Hopx-/- EBs

value: Hopx+/- EBs


title: CLL Patient Sample JB2009071006

description: Gene expression data from CLL patients


title: EBs_d8_Hopx-Null vs Hopx-Het_rep3

description: Replicate 3 of 3. Null vs hererozygous EBs


title: WT in the dark+DBMIB+Rif at 60min (3rd)

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

country: Japan

institute: Waseda University

description: Gene expression data from Synechococcus elongatus PCC 7942

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 using Affymetrix default analysis settings to obtain raw data.

label: biotin

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Synechococcus wild type cells incubated for 60 min in the dark with DBMIB and rifampicin after the start point (hour 12 under continuous light after the two LD cycles)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30C under the light (40 micromol/m^2/sec)

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use

tag: protocol


title: EBs_d8_Hopx-Null vs Hopx-Het_rep1

description: Replicate 1 of 3. Null vs hererozygous EBs


title: CLL Patient Sample JB2009071003

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2009091602

description: Gene expression data from CLL patients


title: WT in the light at 0min (4th)

source_name: Synechococcus wild type cells collected at hour 12 (start point) under continuous light after the two LD cycles


title: EBs_d8_Hopx-Null + Wnt_Inhibitor vs Hopx-Het_rep2

description: Replicate 2 of 3. Null + Wnt Inibitor vs hererozygous EBs

treatment_protocol: Cardiac differentiation was adapted from published protocols. Briefly, ESCs were cultured and maintained on a feeder layer of mitotically inactivated MEFs in DMEM with 15% FBS (Fisher Scientific) and ESGRO leukemia inhibitory factor. Differentiation through hanging droplets method was initiated following ESC dissociation and suspension at 5 x 104 cells/ml in DMEM with 10% FBS (Atlanta Biologicals) without LIF in 20µl drops. Two days after droplets formation, EBs were transferred in suspension onto poly-HEMA coated dishes. After another two days, EBs were plated on gelatin coated dishes in cardiac differentiation media [StemPro-34 SF medium (Invitrogen) supplemented with 5 ng/ml VEGF (R&D systems), 10 ng/ml bFGF (R&D systems), 12.5 ng/ml FGF10 (R&D systems), 1mM Ascorbic Acid (Sigma), 2mM Glutamax (Invitrogen)], and XAV939 as indicated. RNA was isolated from day 8 cultures using Trizol (Life Techonologies) according to manufacturer's instructions.

value: Hopx-/- + Wnt Inibitor EBs


title: EBs_d8_Hopx-Null + Wnt_Inhibitor vs Hopx-Het_rep3

description: Replicate 3 of 3. Null + Wnt Inibitor vs hererozygous EBs


title: WT in the light at 0min (3rd)


title: WT in the dark+DBMIB at 30min (2nd)

source_name: Synechococcus wild type cells incubated for 30 min in the dark with DBMIB after the start point (hour 12 under continuous light after the two LD cycles)


title: WT in the dark+DBMIB+Rif at 60min (4th)


title: CLL Patient Sample JB2009071018

description: Gene expression data from CLL patients


title: WT in the dark+DBMIB at 60min (2nd)

source_name: Synechococcus wild type cells incubated for 60 min in the dark with DBMIB after the start point (hour 12 under continuous light after the two LD cycles)


title: CLL Patient Sample JB2009052243

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009021973

description: Gene expression data from CLL patients


title: EBs_d8_Hopx-Null + Wnt_Inhibitor vs Hopx-Het_rep1

description: Replicate 1 of 3. Null + Wnt Inibitor vs hererozygous EBs


title: CLL Patient Sample JB2009052225

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009052201

description: Gene expression data from CLL patients


title: WT in the dark+DBMIB+Rif at 30min (3rd)

source_name: Synechococcus wild type cells incubated for 30 min in the dark with DBMIB and rifampicin after the start point (hour 12 under continuous light after the two LD cycles)


title: WT in the dark+DBMIB+Rif at 30min (4th)


title: CLL Patient Sample CW2011052737

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009021965

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009052237

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009021967

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009052239

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011090866

description: Gene expression data from CLL patients


title: WT in the light+DBMIB at 60min (2nd)

source_name: Synechococcus wild type cells incubated for 60 min in the light with DBMIB after the start point (hour 12 under continuous light after the two LD cycles)


title: Vir1_0.5

first: Nigel

last: Fraser

address: 3101 Walnut St

department: Dept. of Microbiology

institute: Upenn

description:
human neuroblastoma cell line and Herpes Simplex Virus 1
cellular gDNA mixed with 0.5ng purified virion DNA

hyb_protocol: CGH protocols were used for hybridization and washing (Oligo aCGH/CHiP Hybridization Kit and Wash Buffer Kit, Agilent #5188-5220 and #5188-5226, no Cot-1 DNA).  The following protocol modifications were used for hybridization: hybridization buffer contained 30% de-ionized formamide, hybridization was carried out at 60oC, and the final wash solution was heated to 60oC.  All other steps were carried out according to the manufacturer’s instructions.

scan_protocol: Microarray images were acquired using an Agilent Technologies High Resolution-C Scanner.  Data extraction was carried out using Agilent Feature Extraction software, version 9.5.3.  Scanning and data extraction were conducted according to the manufacturer’s instructions to produce a raw signal for each probe that incorporates background pixel correction and averaging of duplicate features.

data_processing: The raw signal was first processed by “backgroundCorrect” and “normalizeBetweenArrays” functions in the limma package in R/Biocoductor.  The normalized signal was then log2 transformed.

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: Virion 1- 0.5ng

label_protocol: 500ng of 150bp DNA were labeled with Cy3 dye (SureTag Complete DNA Labeling Kit, direct labeling option, Agilent #5190-4240)

growth_protocol: Two 175 cm2 flasks of SY5Y cells (human neuroblastoma cell line) at 100% confluence in RPMI 1640 medium supplemented with 10% fetal calf serum and penicillin (150u/ml) and streptomycin antibiotics (150u/ml)  were infected with HSV-1 F strain at a moi of 5 PFU per cell.

extract_protocol: For Mnase digestion, peleted nuclei were digested with Nuclease S7 Micrococcal nuclease (MNase) at 5U/ul of sample for complete digestion, added 12mM EDTA to stop reaction on ice, and treated with 100ug/ml of proteinase K for overnight at 37’C. DNA was purified by a Wizard DNA clean-up kit (Promega) according to the manufacturer’s instructions.  MNase digested DNA were checked by running on 1.5% low melting point (LMP) agarose gel and 150bp bands were extracted by a QIAEX II gel extraction kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were harvested by scraping, re-suspended in 10ml RSB (10mM Tris, pH 7.5, 10mM 5M NaCl, and 3mM MgCl2), and incubated for 5min on ice. Following addition of 10ml 1%NP40 (in RSB), the cells were mixed, incubated for 2 min on ice, overlaid with 10ml of 0.33M sucrose (in RSB), and centrifuged at 1700rpm for 10min at 4’C.  The pelleted nuclei were re-suspended in 1ml of MNase buffer (20mM 1M Pipes, pH7, 1mM MgCl2, 10mM NaCl, 1mM CaCl2, 5mM 2-mercaptoethanol, 0.25M sucrose, and 0.1mM PMSF).

value: mixed with cellular gDNA 500ng

tag: cell line

tag: virus strain

value: F strain


title: WT in the light+DCMU at 30min (2nd)

source_name: Synechococcus wild type cells incubated for 30 min in the light with DCMU after the start point (hour 12 under continuous light after the two LD cycles)


title: WT in the light+DCMU at 60min (2nd)

source_name: Synechococcus wild type cells incubated for 60 min in the light with DCMU after the start point (hour 12 under continuous light after the two LD cycles)


title: WT in the light+DBMIB at 30min (2nd)

source_name: Synechococcus wild type cells incubated for 30 min in the light wirh DBMIB after the start point (hour 12 under continuous light after the two LD cycles)


title: CLL Patient Sample CW2011052731

description: Gene expression data from CLL patients

tag: tissue

value: Peripheral Blood


title: WT in the light at 60min (2nd)

source_name: Synechococcus wild type cells incubated for 60 min in the light after the start point (hour 12 under continuous light after the two LD cycles)


title: WT in the dark at 30min (2nd)

source_name: Synechococcus wild type cells incubated for 30 min in the dark after the start point (hour 12 under continuous light after the two LD cycles)


title: CLL Patient Sample CW2011052732

description: Gene expression data from CLL patients

value: Adult


title: CLL Patient Sample CW2011052729

description: Gene expression data from CLL patients

value: IGHV unmutated MYD88 wt


title: WT in the dark at 60min (2nd)

source_name: Synechococcus wild type cells incubated for 60 min in the dark after the start point (hour 12 under continuous light after the two LD cycles)


title: WT in the dark+DBMIB at 60min (1st)


title: WT in the dark+DBMIB at 30min (1st)


title: WT in the light+DBMIB at 30min (1st)


title: WT in the light+DCMU at 60min (1st)


title: CLL Patient Sample CW2011052728

description: Gene expression data from CLL patients


title: WT in the light+DBMIB at 60min (1st)


title: WT in the light at 0min (2nd)


title: CLL Patient Sample CW2011032238

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031037

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011052720

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031023

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031028

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031033

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031035

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031027

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031022

description: Gene expression data from CLL patients


title: Patient 9_before therapy_d0

city: Bergisch-Gladbach

first: Yvonne

last: Diener

address: Friedrich-Ebert-Str. 68

institute: Miltenyi Biotec GmbH

hyb_protocol: Hybridization samples were prepared using the Human microRNA Microarray Kit (Agilent Technologies, Rel16.0) following to the manufacturer’s instruction and hybridization was performed for 20 hours at 55°C in a rotating Agilent hybridization oven.

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505C (Agilent Technologies) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed using Agilent feature extraction software (v10.7.3.1) using default parameters (protocol miRNA_107_Sep09 and Grid: 031181_D_F_20111226) to obtain background subtracted and outlier rejected signal intensities. These raw Total Gene Signal intensities (SI, gTotalGeneSignal column) were normalized to the array median as follows: SI were filtered for not detected miRNAs (SI = 0.1) and these values were replaced by empty cells. Another filter was set on miRNAs which were detected in all patient samples before and after chemotherapy (= 18 samples), resulting in 66 miRNAs (including Agilent positive controls: dmr, hur). The median over these 66 miRNAs was calculated for each sample and then each miRNA's value was normalized to the second highest median value (because the highest median value presumably results from an outlier).

source_name: serum

label_protocol: Total RNA was labeled with Cyanine 3 (Cy3) using the Human microRNA Microarray Kit (Agilent Technologies, Rel16.0) according to the manufacturer’s protocol.

extract_protocol: Frozen serum samples were thawed at RT and total RNA was extracted from serum using TRIzol LS Reagent (ambion) and the miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Serum was taken from patients before chemotherapy and HSCT or after therapy (during aplasia). Serum from healthy donors was used as controls.

tag: treatment

value: before chemotherapy

tag: sample type

value: serum

tag: time

tag: sample group

value: before therapy

tag: serum volume [µl]


title: Patient 8_after therapy_d8

value: after chemotherapy

value: after therapy


title: WT in the light at 30min (2nd)

source_name: Synechococcus wild type cells incubated for 30 min in the light after the start point (hour 12 under continuous light after the two LD cycles)


title: Patient 8_before therapy_d0


title: Patient 7_after therapy_d8


title: WT in the light+DCMU at 30min (1st)


title: Patient 9_after therapy_d7


title: Patient 6_after therapy_d8


title: WT in the dark at 60min (1st)


title: Patient 7_before therapy_d0


title: WT in the dark at 30min (1st)


title: Patient 6_before therapy_d0


title: Patient 4_before therapy_d0


title: Patient 4_after therapy_d8


title: WT in the light at 30min (1st)


title: WT in the light at 60min (1st)


title: Patient 3_after therapy_d8


title: Patient 5_after therapy_d8


title: WT in the light at 0min (1st)


title: CLL Patient Sample CW2011031015

description: Gene expression data from CLL patients

source_name: CLL Cells


title: Patient 5_before therapy_d0


title: CLL Patient Sample CW2011031016

description: Gene expression data from CLL patients


title: Patient 1_after therapy_d14


title: CLL Patient Sample CW2009081157

description: Gene expression data from CLL patients


title: Patient 2_before therapy_d0


title: Patient 3_before therapy_d0


city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from Human germinal center B-cell sub-populations from tonsils F

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55°C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 10.7.3.1 software (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as “absent” (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37°C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

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

treatment_protocol: 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 - )

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


title: Patient 2_after therapy_d7


title: CLL Patient Sample CW2011031018

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031013

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011052727

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human germinal center B-cell sub-populations from tonsils G


title: Patient 1_before therapy_d0


description: MicroRNA profiling data from Human germinal center B-cell sub-populations from tonsils C


title: CLL Patient Sample 79_CW248

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071028

description: Gene expression data from CLL patients


title: Healthy donor 7

tag: treatement

value: control

value: healthy


description: MicroRNA profiling data from Human germinal center B-cell sub-populations from tonsils B


title: Healthy donor 6


title: Healthy donor 5


title: CLL Patient Sample CW2011052734

description: Gene expression data from CLL patients

tag: age


title: Healthy donor 3


description: MicroRNA profiling data from Human memory B-cell sub-populations from tonsils C


title: CLL Patient Sample 78_CW247

description: Gene expression data from CLL patients


title: Healthy donor 2


title: Healthy donor 1


description: MicroRNA profiling data from Human memory B-cell sub-populations from tonsils B


description: MicroRNA profiling data from Human memory B-cell sub-populations from tonsils A


title: CLL Patient Sample 71_CW236

description: Gene expression data from CLL patients


title: CLL Patient Sample 65_CW230

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human marginal zone B-cell sub-populations from tonsils E


description: MicroRNA profiling data from Human marginal zone B-cell sub-populations from tonsils D


title: Healthy donor 4


description: MicroRNA profiling data from Human marginal zone B-cell sub-populations from tonsils A


description: MicroRNA profiling data from Human naive B-cell sub-populations from tonsils C


description: MicroRNA profiling data from Human naive B-cell sub-populations from tonsils B


description: MicroRNA profiling data from Human naive B-cell sub-populations from tonsils A


title: CLL Patient Sample 60_CW224

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient WB0269

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).

value: unmut


title: CLL Patient Sample 59_CW222

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VS0016

value: mut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VR0031


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VS0140


title: CLL Patient Sample 52_CW213

description: Gene expression data from CLL patients


title: CLL Patient Sample 53_CW215

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VP0089


title: CLL Patient Sample 42_CW166

description: Gene expression data from CLL patients


title: CLL Patient Sample 41_CW139

description: Gene expression data from CLL patients


title: CLL Patient Sample 47_CW207

description: Gene expression data from CLL patients


title: CLL Patient Sample 37_CW106

description: Gene expression data from CLL patients


title: CLL Patient Sample 40_CW135

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VD0354


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VD0026


title: CLL Patient Sample 33_CW049

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009091025

description: Gene expression data from CLL patients

value: IGHV mutated MYD88 wt


title: CLL Patient Sample 56_CW218

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009091024

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VC0315


title: CLL Patient Sample 50_CW211

description: Gene expression data from CLL patients


title: M-19-2cy5+M-25-1cy3

city: Beijing

first: Chu

last: Bizhu

address: Haidian District, Beijing Tsinghua University

country: China

institute: Tsinghua Univercity

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by quantile normalization.

source_name: breast cancer cell

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

growth_protocol: Cells were cultured in Leibovitz's L-15 Medium (Gibco) supplemented with 10% FBS (Gibco), and plated in 60mm culture dishes (Corning).

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After 12 hr, one copy of cells were treated with 10 μM 5a  for 24 hours as experimental study. The other copy of cells from the same subject were left untreated as paired control.

value: cells cultured in vitro

tag: gender

value: female

value: 48 years

value: Gene expression after 24hr treatment with 10 μM 5a

value: Gene expression without treatment


title: Human in vivo,high arsenic exposure, female 5

city: Tuxedo

first: Alexandra

middle: Brooke

last: Munoz

state: New York

address: 57 Old Forge Road

department: Environmental Medicine

institute: NYU Medical Center

hyb_protocol: The fragmented and labeled DNA underwent hybridization with Affymetrix GeneChip Human Gene 1.0 ST Array at the NYU Cancer Insitute Genomics Facility.

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

data_processing:
Gene expression analyses were performed using R. Gene expression data were imported and normalized using a single-sample method, single channel array normalization (Piccolo et al. 2012) in R 2.15.0 GUI 1.53 64-bit.  SCAN normalization performs probe summarization as part of normalization procedure and utilizes the custom CDF provided by Brainarray to do so. Data was further processed to expression sets using the Affymetrix package version 1.30.0. in R 2.15.1 GUI 1.42 Leopard build 64-bit.
HuGene10stv1_Hs_ENTREZG_15.1.0 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.asp
HuGene10stv1_Hs_ENTREZG_15.1.0 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.asp

source_name: Human PBMC, occupational exposure nickel

label_protocol: Sense strand cDNA probes were synthesized (amplified) using Ambion Whole Transcript Expression Kit. Amplified single stranded c.DNA was fragmented and labeled  using  GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Blood and urine collection, sample handling, and PBMC isolation for this study were performed as previously described (Chervona et al., 2012). Briefly, blood samples were obtained by venipuncture, and collected into EDTA-containing vacutainer tubes, which were then placed in IsoRack/IsoPack cool packs (Brinkmann Instruments). Samples were transported in hand-carried coolers to the local laboratory at the field clinic in Araihazar, within four hours of collection. Samples were centrifuged for 10 minutes at 3,000 × g at 4°C, and the plasma fraction was stored at −80°C. PBS was added to the remaining cells followed by a ficoll-hypaque gradient extraction of PBMCs using standard techniques. PBMCs were stored at −80°C

extract_protocol: Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)

treatment_protocol: At the time of enrollment, study participants had been exposed to water arsenic (wAs) between 50 and 1000 µg/L and were given a water filtration system for removal of As

tag: cell type

value: PBMC

tag: exposure

value: High Arsenic Drinking Water

tag: batch


title: M-4-2cy5+M-4-1cy3


title: M-25-2cy5+M-25-1cy3


title: Human in vivo,high arsenic exposure, female 6


title: CLL Patient Sample JB2009091021

description: Gene expression data from CLL patients

value: Peripheral Blood

tag: genotype

value: Adult


title: CLL Patient Sample JB2009091014

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VC0142


title: Human in vivo,high arsenic exposure, female 3


title: Human in vivo,high arsenic exposure, female 1


title: Human in vivo, low arsenic exposure, female 6

value: Low Arsenic Drinking Water


title: Human in vivo,high arsenic exposure, female 2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient TM0259


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient UL0266


title: Human in vivo,high arsenic exposure, female 4


title: Human in vivo, low arsenic exposure, female 5


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient TL0397


title: Human in vivo, low arsenic exposure, female 4


title: CLL Patient Sample JB2009091007

description: Gene expression data from CLL patients


title: Human in vivo, low arsenic exposure, female 2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient TG0263


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient VB0013


title: Human in vivo, low arsenic exposure, female 3


title: CLL Patient Sample JB2009091009

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009091011

description: Gene expression data from CLL patients


title: Human in vivo, low arsenic exposure, female 1


title: Human in vivo, high arsenic exposure, male 7

value: male


title: CLL Patient Sample JB2009071038

description: Gene expression data from CLL patients


title: Human in vivo, high arsenic exposure, male 4


title: Human in vivo, high arsenic exposure, male 5


title: Human in vivo, high arsenic exposure, male 6


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient TE0069


title: Human in vivo, high arsenic exposure, male 3


title: Human in vivo, high arsenic exposure, male 2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient TG0139


title: CLL Patient Sample JB2009091010

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009091019

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071033

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071047

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SS0275


title: Human in vivo, high arsenic exposure, male 1

source_name: Human PMBC Environmental


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SV0046


title: Human in vivo, low arsenic exposure, male 8


title: Human in vivo, low arsenic exposure, male 4


title: Human in vivo, low arsenic exposure, male 5


title: Human in vivo, low arsenic exposure, male 6


title: Human in vivo, low arsenic exposure, male 7


title: Human in vivo, low arsenic exposure, male 3


title: Human in vivo, low arsenic exposure, male 9


title: CLL Patient Sample JB2009071025

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SS0299


title: CLL Patient Sample JB2009071016

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071010

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071012

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071009

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SR0112


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SM0303


title: Human in vivo, low arsenic exposure, male 1


title: Human in vivo, low arsenic exposure, male 2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SG0168


title: control shRNA #3

city: Marburg

first: Peter

middle: Harry

last: Störchel

address: Karl-von-Frisch-Str. 1

department: Institut für Physiologische Chemie

institute: Philipps-Universität Marburg

hyb_protocol: Standard Affymetrix protocol. According to standard procedure of the Genecore Facility at EMBL Heidelberg.

data_processing: Expression Console (Affymetrix) and GeneSpring (Agilent).

organism: Rattus norvegicus

source_name: Neurons expressing control shRNA from 3rd experiment

growth_protocol: Hippocampi of E18 rats were dissected and cultured in the presence of 10 µM of 5-fluorodeoxyuridine (FUDR).

extract_protocol: Total RNA was isolated after 14 div using Mirvana-Kit and subjected to this microarray analysis.

treatment_protocol: After 4 days in vitro the neurons were infected with 1.8*10^6 IFU/ml adeno-associated virus (AAV) expressing either control shRNA (samples 1, 3, 5) or Ncoa3 shRNA (samples 2, 4, 6).

value: neuron


title: Ncoa3 shRNA #3

scan_protocol: Standard Affymetrix protocol. According to standard procedure of the Genecore Facility at EMBL Heidelberg.

source_name: Neurons expressing Ncoa3 shRNA from 3rd experiment

value: Ncoa3 shRNA


title: CLL Patient Sample JB2009071002

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071004

description: Gene expression data from CLL patients


title: Ncoa3 shRNA #2

source_name: Neurons expressing Ncoa3 shRNA from 2nd experiment

label_protocol: Standard Affymetrix protocol. According to standard procedure of the Genecore Facility at EMBL Heidelberg.


title: CLL Patient Sample JB2009052244

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SG0114


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SL0083


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SF0098


title: Ncoa3 shRNA #1

source_name: Neurons expressing Ncoa3 shRNA from 1st experiment


title: Human in vivo,high arsenic exposure, female 7


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SA0205


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SA0219


title: control shRNA #1

source_name: Neurons expressing control shRNA from 1st experiment

value: control


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SA0093

value: unmut


title: CP-25

description: copy number mapping

data_processing: Copy number variants (CNVs), including gains and losses, were identified using the Aberration Detection Method 2 (ADM-2) algorithm, with modifications that support the determination of the clonal fraction of genomic imbalances in cancer cells. A minimum of five consecutive probes per region, with absolute average log2 ratio of 0.3 for any given region or a minimum region of 1 Mb in size, with a minimum absolute average log2 ratio of 0.08 (Agilent mosaic protocol).

source_name: Bone marrow

value: Bone marrow

value: Female

tag: disease

value: plasma cell myeloma

source_name: commercially-available DNA used as reference

tag: reference dna gender

tag: reference dna cell line


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SA0080


title: CLL Patient Sample JB2009052241

description: Gene expression data from CLL patients

tag: tissue

value: IGHV mutated MYD88 wt


title: CLL Patient Sample JB2009052240

description: Gene expression data from CLL patients


title: K-3

description: copy number mapping

source_name: myeloblast cell line

value: myeloblast cell line

value: Male

value: AML


title: K-1

description: copy number mapping


title: CP-22

description: copy number mapping

source_name: peripheral blood

value: peripheral blood

value: CLL


title: CLL Patient Sample JB2009052223

description: Gene expression data from CLL patients

value: Peripheral Blood


title: CLL Patient Sample JB2009052220

description: Gene expression data from CLL patients

value: Adult


title: CLL Patient Sample JB2009052222

description: Gene expression data from CLL patients


title: control shRNA #2

source_name: Neurons expressing control shRNA from 2nd experiment

tag: treatment


title: CLL Patient Sample JB2009052242

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RS0325


title: CP-24

description: copy number mapping


title: CLL Patient Sample JB2009052219

description: Gene expression data from CLL patients


title: CP-21

description: copy number mapping


title: CP-13

description: copy number mapping

value: MDS


title: CP-20

description: copy number mapping

value: B-ALL


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient SA0021

value: mut


title: CP-8

description: copy number mapping


title: CP-18

description: copy number mapping


title: CP-7

description: copy number mapping


title: CP-12

description: copy number mapping


title: CLL Patient Sample JB2009052218

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RG0045


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RR0157


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RD0296


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RG0077


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RC0116


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RM0400


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RB0087


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RB0040


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RA0288


title: CP-10

description: copy number mapping


title: CLL Patient Sample JB2009052206

description: Gene expression data from CLL patients


title: CP-5

description: copy number mapping


title: CLL Patient Sample JB2009021962

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009052205

description: Gene expression data from CLL patients


title: CP-4

description: copy number mapping


title: CP-9

description: copy number mapping


title: CLL Patient Sample JB2009021966

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009021969

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009052208

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009021971

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009021963

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RA0211


title: CP-2

description: copy number mapping


title: CLL Patient Sample JB2009052202

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RA0023


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PZ0305


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient RS0260


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PV0322


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PV0286


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PS0212


title: CD46-3 CD4+ T cells_3

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

description: replicate 3

hyb_protocol: Illumina HT12.v4 arrays were hybridized using standard Illumina protocols at 48 C

scan_protocol: Standard Illumina scanning

data_processing: data was quantile normalized within Illumina Genome Studio

source_name: T cells

label_protocol: cDNA was labelled  usin NuGen Encore Biotin IL kits

extract_protocol: Genomic DNA and RNA was isolated using Qiagen Allprep. 5pg total RNA was amplified using  NuGen Ovation Pico WTA System V2

treatment_protocol: Cells were treated with anti-CD3 and anti-CD46 for 2 h

value: T cells

tag: cell markers

tag: disease status

value: aHUS, CVID


title: CLL Patient Sample CW2011052723

description: Gene expression data from CLL patients


title: CD46-3 CD4+ T cells_1

description: replicate 1


title: CLL Patient Sample CW2011052722

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PS0044


title: Healthy Donor CD4+ T Cells_3

description: replicate 3

value: healthy


title: CLL Patient Sample CW2011052726

description: Gene expression data from CLL patients


title: Healthy Donor CD4+ T Cells_2

description: replicate 2


title: CLL Patient Sample CW2011052725

description: Gene expression data from CLL patients


title: dLMP1-MAVS-CD4 Tcell rep3

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

data_processing: The data was preprocessed on GeneSpring GX 13.0 from Agilent. Raw data was quantile normalized and log2 transformed

source_name: Primary CD4 T cell

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

growth_protocol: Cultured in completed media

extract_protocol: Qiagen Rneasy mini kit

treatment_protocol: CD4 T cells were incubated for 24 hours with supernatant from 293T cells transfected with pdLMP1-MAVS and cultured for 36 hours

value: Primary CD4 T cell

tag: transfection

value: pdLMP1-MAVS plasmid


title: Healthy Donor CD4+ T Cells_1

description: replicate 1


title: CLL Patient Sample CW2011052716

description: Gene expression data from CLL patients


title: dLMP1-MAVS-CD4 Tcell rep2


title: CD46-3 CD4+ T cells_2

description: replicate 2


title: CLL Patient Sample CW2011052712

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PR0084


title: pcDNA-CD4 Tcell rep3

treatment_protocol: CD4 T cells were incubated for 24 hours with supernatant from 293T cells transfected with pcDNA3.1 and cultured for 36 hours

value: pcDNA3.1 plasmid


title: dLMP1-MAVS-CD4 Tcell rep1


title: CLL Patient Sample CW2011031032

description: Gene expression data from CLL patients

value: IGHV mutated MYD88 wt


title: pcDNA-CD4 Tcell rep2


title: dLMP1-MAVS-293T rep2

source_name: 293T cell line

treatment_protocol: 293T cells were transfected with pdLMP1-MAVS plasmid using Genjet plus transfection reagent and cultured for 36 hours in DMEM media plus 10% fetal bovine serum

tag: cell line


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PP0195

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

value: unmut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PM0340


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PM0117


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PI0172


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PG0327


title: CLL Patient Sample CW2011031034

description: Gene expression data from CLL patients

source_name: CLL Cells


title: dLMP1-MAVS-293T rep1


title: CLL Patient Sample CW2011031029

description: Gene expression data from CLL patients


title: pcDNA-293T rep3

treatment_protocol: 293T cells were transfected with pcDNA3.1 plasmid using Genjet plus transfection reagent and cultured for 36 hours in DMEM media plus 10% fetal bovine serum


title: pcDNA-293T rep2


title: pcDNA-CD4 Tcell rep1


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PG0276


title: pcDNA-293T rep1


title: CLL Patient Sample CW2011031030

description: Gene expression data from CLL patients


title: TS patient 3

city: Washington

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

description:
SAMPLE 11
Brain epilepsy surgical isolate from patient with Tuberous Sclerosis (TS)

data_processing: The data were normalised using Quantile  normalisation in Partek

source_name: TS patient_brain

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX)

extract_protocol: RNA was extracted with Trizol reagent,  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: subject condition

value: patient with Tuberous Sclerosis (TS)

value: brain


title: FCD patient 5

description:
SAMPLE 10
Brain epilepsy surgical isolate from patient with Focal Cortical Dysplasia (FCD)

source_name: FCD patient_brain tissue


title: TS patient 2

description:
SAMPLE 8
Brain epilepsy surgical isolate from patient with Tuberous Sclerosis (TS)


title: dLMP1-MAVS-293T rep3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PG0216

value: nd


title: FCD patient 3

description:
SAMPLE 7
Brain epilepsy surgical isolate from patient with Focal Cortical Dysplasia (FCD)


title: CLL Patient Sample CW2011031021

description: Gene expression data from CLL patients

tag: age


title: FCD patient 4

description:
SAMPLE 9
Brain epilepsy surgical isolate from patient with Focal Cortical Dysplasia (FCD)


title: CLL Patient Sample CW2011031025

description: Gene expression data from CLL patients


title: TS patient 1

description:
SAMPLE 6
Brain epilepsy surgical isolate from patient with Tuberous Sclerosis (TS)


title: CLL Patient Sample CW2009091601

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031024

description: Gene expression data from CLL patients


title: CLL Patient Sample CW2011031017

description: Gene expression data from CLL patients


title: FCD patient 2

description:
SAMPLE 4
Brain epilepsy surgical isolate from patient with Focal Cortical Dysplasia (FCD)


title: control 2

description:
SAMPLE 3
Brain surgical isolate from normal tissue

source_name: normal brain tissue control

value: control


title: control 1

description:
SAMPLE 2
Brain surgical isolate from normal tissue


title: control 3

description:
SAMPLE 5
Brain surgical isolate from normal tissue


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PG0028


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PG0065


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PF0177


title: FCD patient 1

description:
SAMPLE 1
Brain epilepsy surgical isolate from patient with Focal Cortical Dysplasia (FCD)


title: CLL Patient Sample 84_CW260

description: Gene expression data from CLL patients

value: Peripheral Blood


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PF0024


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PD0164


title: CLL Patient Sample JB2009052211

description: Gene expression data from CLL patients

value: Adult


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PC0304


title: V411

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description: CRC cell line

hyb_protocol: Hybridization of cRNAs (750 ng) was carried out using Illumina Human 48k gene chips (Human HT-12 V4 BeadChip)

scan_protocol: Hybridized Beadchips were scanned with the Illumina  BeadArray Reader

data_processing:
Non-normalized data were generated by the Illumina GenomeStudio software version V2011.1 . Data were Loess normalized with the Lumi R package
Signal values and detection p-values as provided by the Illumina Genome Studio software. Normalized signal values as provided by the Lumi R package.

source_name: V411 CRC cell line, standard culture conditions

label_protocol: Synthesis of cDNA and biotinylated cRNA was performed using the IlluminaTotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol using 500ng of total RNA

growth_protocol: Standard culture conditions for each cell line

extract_protocol: total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol, without the separation step between mRNAs and microRNAs

treatment_protocol: No treatment


title: CLL Patient Sample 83_CW259

description: Gene expression data from CLL patients

treatment_protocol: CLL cells were isolated via density gradient centrifugation using Ficoll-Paque Plus and enrichment for B-cell fractions was performed using Rosette Sep (Stemcell Technologies).


title: CLL Patient Sample 81_CW251

description: Gene expression data from CLL patients


title: CLL Patient Sample 80_CW250

description: Gene expression data from CLL patients


title: VACO6

description: CRC cell line

source_name: VACO6 CRC cell line, standard culture conditions


title: SW948

description: CRC cell line

source_name: SW948 CRC cell line, standard culture conditions


title: NCIH684

description: CRC cell line

source_name: NCIH684 CRC cell line, standard culture conditions


title: CLL Patient Sample 74_CW239

description: Gene expression data from CLL patients


title: CLL Patient Sample 77_CW245

description: Gene expression data from CLL patients


title: SNU977

description: CRC cell line

source_name: SNU977 CRC cell line, standard culture conditions


title: SNU175

description: CRC cell line

source_name: SNU175 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PA0271


title: NCIH498

description: CRC cell line

source_name: NCIH498 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PA0351


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PA0234


title: CLL Patient Sample 72_CW237

description: Gene expression data from CLL patients


title: SNU1181

description: CRC cell line

source_name: SNU1181 CRC cell line, standard culture conditions


title: SNU407

description: CRC cell line

source_name: SNU407 CRC cell line, standard culture conditions


title: SW620

description: CRC cell line

source_name: SW620 CRC cell line, standard culture conditions


title: SNU70

description: CRC cell line

source_name: SNU70 CRC cell line, standard culture conditions


title: CLL Patient Sample 70_CW235

description: Gene expression data from CLL patients


title: CLL Patient Sample 73_CW238

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PA0146


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PA0145


title: SNU503

description: CRC cell line

source_name: SNU503 CRC cell line, standard culture conditions


title: SNU254

description: CRC cell line

source_name: SNU254 CRC cell line, standard culture conditions


title: CLL Patient Sample 69_CW234

description: Gene expression data from CLL patients

source_name: CLL Cells


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient PA0058


title: SNU479

description: CRC cell line

source_name: SNU479 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient OV0127


title: SNU1684

description: CRC cell line

source_name: SNU1684 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient OM0201


title: CLL Patient Sample 67_CW232

description: Gene expression data from CLL patients


title: C80

description: CRC cell line

source_name: C80 CRC cell line, standard culture conditions


title: CLL Patient Sample 64_CW229

description: Gene expression data from CLL patients


title: CLL Patient Sample 66_CW231

description: Gene expression data from CLL patients


title: SNU1746

description: CRC cell line

source_name: SNU1746 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient OI0282


title: C146

description: CRC cell line

source_name: C146 CRC cell line, standard culture conditions


title: C99

description: CRC cell line

source_name: C99 CRC cell line, standard culture conditions


title: C70

description: CRC cell line

source_name: C70 CRC cell line, standard culture conditions


title: CLL Patient Sample 58_CW220

description: Gene expression data from CLL patients


title: SW403

description: CRC cell line

source_name: SW403 CRC cell line, standard culture conditions


title: SKCO1

description: CRC cell line

source_name: SKCO1 CRC cell line, standard culture conditions


title: C10

description: CRC cell line

source_name: C10 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient NS0060


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient NF0056


title: CLL Patient Sample 57_CW219

description: Gene expression data from CLL patients


title: C84

description: CRC cell line

source_name: C84 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient NM0156


title: C106

description: CRC cell line

source_name: C106 CRC cell line, standard culture conditions


title: SW837

description: CRC cell line

source_name: SW837 CRC cell line, standard culture conditions


title: CLL Patient Sample 62_CW226

description: Gene expression data from CLL patients


title: SNU1544

description: CRC cell line

source_name: SNU1544 CRC cell line, standard culture conditions


title: C75

description: CRC cell line

source_name: C75 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient NG0068


title: CLL Patient Sample 48_CW209

description: Gene expression data from CLL patients


title: KM12SM

description: CRC cell line

source_name: KM12SM CRC cell line, standard culture conditions


title: SNU769B

description: CRC cell line

source_name: SNU769B CRC cell line, standard culture conditions


title: SNU1406

description: CRC cell line

source_name: SNU1406 CRC cell line, standard culture conditions


title: SNU1235

description: CRC cell line

source_name: SNU1235 CRC cell line, standard culture conditions


title: KM12L4

description: CRC cell line

source_name: KM12L4 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient NB0333


title: C32

description: CRC cell line

source_name: C32 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MS0357


title: CLL Patient Sample 46_CW206

description: Gene expression data from CLL patients

source_name: CLL Cells


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MV0334


title: KM12C

description: CRC cell line

source_name: KM12C CRC cell line, standard culture conditions


title: CLL Patient Sample 45_CW201

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MS0321


title: HUTU80

description: CRC cell line

source_name: HUTU80 CRC cell line, standard culture conditions


title: CLL Patient Sample 38_CW132

description: Gene expression data from CLL patients


title: HDC114

description: CRC cell line

source_name: HDC114 CRC cell line, standard culture conditions


title: FHS

description: CRC cell line

source_name: FHS CRC cell line, standard culture conditions

value: FHS


title: COLO320HSR

description: CRC cell line

source_name: COLO320HSR CRC cell line, standard culture conditions


title: C125PM

description: CRC cell line

source_name: C125PM CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MS0273


title: CLL Patient Sample 39_CW134

description: Gene expression data from CLL patients


title: CLL Patient Sample 55_CW217

description: Gene expression data from CLL patients


title: HCA46

description: CRC cell line

source_name: HCA46 CRC cell line, standard culture conditions


title: CLL Patient Sample 36_CW080

description: Gene expression data from CLL patients


title: CLL Patient Sample JB2009071030

description: Gene expression data from CLL patients

value: IGHV mutated MYD88 L265P


title: HCT15

description: CRC cell line

source_name: HCT15 CRC cell line, standard culture conditions


title: HDC143

description: CRC cell line

source_name: HDC143 CRC cell line, standard culture conditions


title: HT29

description: CRC cell line

source_name: HT29 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MS0115


title: COLO678

description: CRC cell line

source_name: COLO678 CRC cell line, standard culture conditions


title: GEO

description: CRC cell line

source_name: GEO CRC cell line, standard culture conditions

value: GEO


title: DIFI

description: CRC cell line

source_name: DIFI CRC cell line, standard culture conditions

value: DIFI


title: CLL Patient Sample JB2009071014

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MO0323

value: mut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MS0189


title: COLO320DM

description: CRC cell line

source_name: COLO320DM CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MO0174


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MP0137


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MM0330


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MM0097


title: CLL Patient Sample JB2009071026

description: Gene expression data from CLL patients


title: SW480

description: CRC cell line

source_name: SW480 CRC cell line, standard culture conditions


title: COLO205

description: CRC cell line

source_name: COLO205 CRC cell line, standard culture conditions


title: CLL Patient Sample JB2009052238

description: Gene expression data from CLL patients

source_name: CLL Cells


title: LIM2550

description: CRC cell line

source_name: LIM2550 CRC cell line, standard culture conditions


title: LS174T

description: CRC cell line

source_name: LS174T CRC cell line, standard culture conditions


title: CLL Patient Sample JB2009052203

description: Gene expression data from CLL patients


title: HCT8

description: CRC cell line

source_name: HCT8 CRC cell line, standard culture conditions


title: HCC2998

description: CRC cell line

source_name: HCC2998 CRC cell line, standard culture conditions


title: CLL Patient Sample 68_CW233

description: Gene expression data from CLL patients


title: COCM1

description: CRC cell line

source_name: COCM1 CRC cell line, standard culture conditions


title: CLL Patient Sample 54_CW216

description: Gene expression data from CLL patients


title: CL14

description: CRC cell line

source_name: CL14 CRC cell line, standard culture conditions


title: DLD1

description: CRC cell line

source_name: DLD1 CRC cell line, standard culture conditions


title: SW48

description: CRC cell line

source_name: SW48 CRC cell line, standard culture conditions


title: CACO2

description: CRC cell line

source_name: CACO2 CRC cell line, standard culture conditions


title: LOVO

description: CRC cell line

source_name: LOVO CRC cell line, standard culture conditions

value: LOVO


title: CLL Patient Sample 51_CW212

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient ML0298


title: CLL Patient Sample CW2011031019

description: Gene expression data from CLL patients


title: CAR1

description: CRC cell line

source_name: CAR1 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MG0248


title: SNU81

description: CRC cell line

source_name: SNU81 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MG0170


title: CLL Patient Sample JB2009052210

description: Gene expression data from CLL patients


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MG0110


title: FET

description: CRC cell line

source_name: FET CRC cell line, standard culture conditions

value: FET


title: Hep3B infected with AdHNF4α for 48 hours

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

description: After Hep3B was infected by AdHNF4α  for 48 hours, the cells were collected for cDNA Microarray analysis.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

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: Hep3B cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA

growth_protocol: Hep3B cell line

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Hep3B infected with AdHNF4α and AdGFP for 72 hours

tag: construct


title: SNU1040

description: CRC cell line

source_name: SNU1040 CRC cell line, standard culture conditions


title: SNU1411

description: CRC cell line

source_name: SNU1411 CRC cell line, standard culture conditions


title: RW7213

description: CRC cell line

source_name: RW7213 CRC cell line, standard culture conditions


title: Hep3B infected with AdHNF4α for 72 hours

description: After Hep3B was infected by AdHNF4α  for 72 hours, the cells were collected for cDNA Microarray analysis.


title: COLO320

description: CRC cell line

source_name: COLO320 CRC cell line, standard culture conditions


title: FHC

description: CRC cell line

source_name: FHC CRC cell line, standard culture conditions

value: FHC


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MF0379


title: SNU1460

description: CRC cell line

source_name: SNU1460 CRC cell line, standard culture conditions


title: COLO94H

description: CRC cell line

source_name: COLO94H CRC cell line, standard culture conditions


title: phymatous rosacea (PhR)  [GRDS0027_R III 9_2]

city: Sophia Antipolis

first: Isabelle

last: Carlavan

address: 2400 route des colles

department: Research

country: France

institute: Galderma R&D

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix) with RMA normalization.

source_name: Human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: miRNeasy (Qiagen) RNA extraction was performed according to the manufacturer's instructions.

tag: group

value: phymatous rosacea (PhR)


title: COGA5

description: CRC cell line

source_name: COGA5 CRC cell line, standard culture conditions


title: Hep3B infected with AdGFP for 72 hours

description: After Hep3B was infected by AdGFP for 72 hours, the cells were collected for cDNA Microarray analysis.

value: AdGFP


title: CL11

description: CRC cell line

source_name: CL11 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MF0274


title: COGA5L

description: CRC cell line

source_name: COGA5L CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MB0065

value: unmut


title: phymatous rosacea (PhR)  [GRDS0027_R III 9_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MA0209


title: phymatous rosacea (PhR)  [GRDS0027_R III 7_2]


title: phymatous rosacea (PhR)  [GRDS0027_R III 8_2]


title: NCIH630

description: CRC cell line

source_name: NCIH630 CRC cell line, standard culture conditions


title: phymatous rosacea (PhR)  [GRDS0027_R III 8_1]


title: phymatous rosacea (PhR)  [GRDS0027_R III 7_1]


title: LS411N

description: CRC cell line

source_name: LS411N CRC cell line, standard culture conditions


title: LS180

description: CRC cell line

source_name: LS180 CRC cell line, standard culture conditions


title: LS123

description: CRC cell line

source_name: LS123 CRC cell line, standard culture conditions


title: phymatous rosacea (PhR)  [GRDS0027_R III 5_1]


title: OXCO1

description: CRC cell line

source_name: OXCO1 CRC cell line, standard culture conditions


title: LIM1899

description: CRC cell line

source_name: LIM1899 CRC cell line, standard culture conditions


title: phymatous rosacea (PhR)  [GRDS0027_R III 5_2]


title: LIM2099

description: CRC cell line

source_name: LIM2099 CRC cell line, standard culture conditions


title: LIM2537

description: CRC cell line

source_name: LIM2537 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MN0167


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MA0151


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MA0088


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MA0002


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LR0247


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MF0048


title: phymatous rosacea (PhR)  [GRDS0027_R III 4_2]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MC0134


title: phymatous rosacea (PhR)  [GRDS0027_R III 4_1]


title: NCIH747

description: CRC cell line

source_name: NCIH747 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LV0118


title: COLO741

description: CRC cell line

source_name: COLO741 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LP0076


title: SNUC4

description: CRC cell line

source_name: SNUC4 CRC cell line, standard culture conditions


title: SNUC5

description: CRC cell line

source_name: SNUC5 CRC cell line, standard culture conditions


title: HDC142

description: CRC cell line

source_name: HDC142 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 9_2]

source_name: Human skin

value: papulopustular rosacea (PPR)


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MC0105


title: RKO

description: CRC cell line

source_name: RKO CRC cell line, standard culture conditions

value: RKO


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LM0150


title: OXCO2

description: CRC cell line

source_name: OXCO2 CRC cell line, standard culture conditions


title: HCA7

description: CRC cell line

source_name: HCA7 CRC cell line, standard culture conditions


title: phymatous rosacea (PhR)  [GRDS0027_R III 3_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LL0130


title: HDC54

description: CRC cell line

source_name: HDC54 CRC cell line, standard culture conditions


title: LS513

description: CRC cell line

source_name: LS513 CRC cell line, standard culture conditions


title: LIM2405

description: CRC cell line

source_name: LIM2405 CRC cell line, standard culture conditions


title: SNU283

description: CRC cell line

source_name: SNU283 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 5_2]


title: VACO5

description: CRC cell line

source_name: VACO5 CRC cell line, standard culture conditions


title: HDC82

description: CRC cell line

source_name: HDC82 CRC cell line, standard culture conditions


title: phymatous rosacea (PhR)  [GRDS0027_R III 3_2]


title: NCIH716

description: CRC cell line

source_name: NCIH716 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 9_1]


title: CL34

description: CRC cell line

source_name: CL34 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LG0337


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LI0133


title: HRA16

description: CRC cell line

source_name: HRA16 CRC cell line, standard culture conditions


title: VACO432

description: CRC cell line

source_name: VACO432 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 5_1]


title: MDST8

description: CRC cell line

source_name: MDST8 CRC cell line, standard culture conditions


title: CX1

description: CRC cell line

source_name: CX1 CRC cell line, standard culture conditions


title: LIM1215

description: CRC cell line

source_name: LIM1215 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 13_2]

source_name: Human skin


title: papulopustular rosacea (PPR) [GRDS0027_R II 13_1]


title: SW1463

description: CRC cell line

source_name: SW1463 CRC cell line, standard culture conditions


title: MIP101

description: CRC cell line

source_name: MIP101 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient MC0055


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LG0038


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LG0224


title: LS1034

description: CRC cell line

source_name: LS1034 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LF0102


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient LA0070


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient IL0066


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient IF0044


title: CL40

description: CRC cell line

source_name: CL40 CRC cell line, standard culture conditions


title: Hep3B infected with AdGFP for 48 hours

description: After Hep3B was infected by AdGFP for 48 hours, the cells were collected for cDNA Microarray analysis.

source_name: Hep3B cells


title: papulopustular rosacea (PPR) [GRDS0027_R II 12_1]


title: papulopustular rosacea (PPR) [GRDS0027_R II 11_2]


title: papulopustular rosacea (PPR) [GRDS0027_R II 12_2]


title: HT115

description: CRC cell line

source_name: HT115 CRC cell line, standard culture conditions


title: C170

description: CRC cell line

source_name: C170 CRC cell line, standard culture conditions


title: GP2D

description: CRC cell line

source_name: GP2D CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 11_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient IA0025


title: HCA24

description: CRC cell line

source_name: HCA24 CRC cell line, standard culture conditions


title: HDC8

description: CRC cell line

source_name: HDC8 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 10_2]


title: OXCO3

description: CRC cell line

source_name: OXCO3 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient HG0135


title: V481

description: CRC cell line

source_name: V481 CRC cell line, standard culture conditions


title: COGA12

description: CRC cell line

source_name: COGA12 CRC cell line, standard culture conditions


title: COGA8

description: CRC cell line

source_name: COGA8 CRC cell line, standard culture conditions


title: COGA2

description: CRC cell line

source_name: COGA2 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 9_2]

value: erythematotelangiectatic rosacea (ETR)


title: V703

description: CRC cell line

source_name: V703 CRC cell line, standard culture conditions


title: Gp5D

description: CRC cell line

source_name: Gp5D CRC cell line, standard culture conditions


title: COGA3

description: CRC cell line

source_name: COGA3 CRC cell line, standard culture conditions


title: papulopustular rosacea (PPR) [GRDS0027_R II 10_1]

source_name: Human skin


title: COGA1

description: CRC cell line

source_name: COGA1 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GS0343


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 8_2]


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 9_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GR0169


title: CCK81

description: CRC cell line

source_name: CCK81 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GR0033


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 7_2]


title: RCM1

description: CRC cell line

source_name: RCM1 CRC cell line, standard culture conditions


title: HCT116

description: CRC cell line

source_name: HCT116 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 8_1]


title: HROC18

description: CRC cell line

source_name: HROC18 CRC cell line, standard culture conditions


title: SNUC2A

description: CRC cell line

source_name: SNUC2A CRC cell line, standard culture conditions


title: T84

description: CRC cell line

source_name: T84 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GP0329


title: HROC80

description: CRC cell line

source_name: HROC80 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GR0092


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 6_2]


title: WIDR

description: CRC cell line

source_name: WIDR CRC cell line, standard culture conditions

value: WIDR


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 6_1]


title: SW1417

description: CRC cell line

source_name: SW1417 CRC cell line, standard culture conditions


title: SW1222

description: CRC cell line

source_name: SW1222 CRC cell line, standard culture conditions


title: COLO60H

description: CRC cell line

source_name: COLO60H CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GP0278


title: SNUC2B

description: CRC cell line

source_name: SNUC2B CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GP0171


title: SNU1047

description: CRC cell line

source_name: SNU1047 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 7_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GN0095


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GM0252


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GM0041


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GL0368


title: HROC46

description: CRC cell line

source_name: HROC46 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 11_1]


title: HT55

description: CRC cell line

source_name: HT55 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 11_2]

source_name: Human skin


title: OUMS23

description: CRC cell line

source_name: OUMS23 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 2_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GP0348


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 10_1]


title: HROC39

description: CRC cell line

source_name: HROC39 CRC cell line, standard culture conditions


title: SNU61

description: CRC cell line

source_name: SNU61 CRC cell line, standard culture conditions


title: HROC69

description: CRC cell line

source_name: HROC69 CRC cell line, standard culture conditions


title: KM20

description: CRC cell line

source_name: KM20 CRC cell line, standard culture conditions


title: SNU1033

description: CRC cell line

source_name: SNU1033 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GG0027


title: LIM2412

description: CRC cell line

source_name: LIM2412 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 10_2]


title: LIM2551

description: CRC cell line

source_name: LIM2551 CRC cell line, standard culture conditions


title: V457

description: CRC cell line

source_name: V457 CRC cell line, standard culture conditions


title: SW1116

description: CRC cell line

source_name: SW1116 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GG0301


title: KM12

description: CRC cell line

source_name: KM12 CRC cell line, standard culture conditions


title: SNUC1

description: CRC cell line

source_name: SNUC1 CRC cell line, standard culture conditions


title: erythematotelangiectatic rosacea (ETR)  [GRDS0027_R I 2_2]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GD0262


title: Healthy volunteer [GRDS0027_HV6_1]

value: Healthy volunteer


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GD0158


title: Healthy volunteer [GRDS0027_HV31_2]


title: COLO201

description: CRC cell line

source_name: COLO201 CRC cell line, standard culture conditions


title: HDC9

description: CRC cell line

source_name: HDC9 CRC cell line, standard culture conditions


title: HROC87

description: CRC cell line

source_name: HROC87 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GF0281


title: Healthy volunteer [GRDS0027_HV6_2]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GE0125


title: HDC135

description: CRC cell line

source_name: HDC135 CRC cell line, standard culture conditions


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GC0328


title: CO115

description: CRC cell line

source_name: CO115 CRC cell line, standard culture conditions


title: Healthy volunteer [GRDS0027_HV30_2]

source_name: Human skin


title: Healthy volunteer [GRDS0027_HV30_1]


title: BJ_0h_REP2

city: Houston

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description: replicate 2

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted and quantile-normalized using the lumi package within R

growth_protocol: Cells were maintained in either TeSR2 (Stem Cell Technologies, Vancouver, BC) or Nutristem medium (Stemgent, Cambridge, MA, ) on Matrigel-coated 6-well plates in the absence of feeder cells.

extract_protocol: RNA was extracted and prepared using Aurum Total RNA kit (Bio-Rad) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Cells were plated in 6-well plates and treated with 100 nM T3 for 0 or 6 h.

value: BJ

value: T3 0 h


title: Healthy volunteer [GRDS0027_HV3_2]


title: BJ_6h_REP1

description: replicate 1

value: T3 6 h


title: BJ_0h_REP1

description: replicate 1


title: zz4_6h_REP3

description: replicate 3


title: BJ_6h_REP3

description: replicate 3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GC0147


title: zz4_6h_REP2

description: replicate 2


title: NCIH508

description: CRC cell line

source_name: NCIH508 CRC cell line, standard culture conditions


title: BJ_6h_REP2

description: replicate 2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GC0096


title: Healthy volunteer [GRDS0027_HV31_1]


title: Healthy volunteer [GRDS0027_HV3_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GC0015


title: Healthy volunteer [GRDS0027_HV29_1]


title: Healthy volunteer [GRDS0027_HV29_2]


title: Healthy volunteer [GRDS0027_HV28_2]


title: z34_0h_REP3

description: replicate 3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GB0293


title: zz4_0h_REP2

description: replicate 2


title: Healthy volunteer [GRDS0027_HV27_2]


title: zz4_0h_REP1

description: replicate 1


title: z34_6h_REP2

description: replicate 2


title: zz4_0h_REP3

description: replicate 3


title: Healthy volunteer [GRDS0027_HV28_1]


title: Myoblasts_old-AZA-treated-3, biological rep6

first: Svetlana

description: mRNA gene expression data from Human myoblasts

data_processing: The data were normalised (quantile normalisation),  and background was subtructed in Illumina Genome Studio program

source_name: Human old myoblasts, treated with AZA

label_protocol: Biotinylated cRNA were prepared with Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: The myoblasts were expanded in proliferative medium: DMEM supplemented with 20% FBS and then differentiated  in DMEM for 3 days.

extract_protocol: Cell pellete (myoblasts) were subjected to total RNA isolation procedure using  mirVana™ miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX). Concentration of each RNA sample was determined by NanoDrop® spectrophotometer ND-1000 (NanoDrop Technologies, Wilmington, DE). The quality of RNA samples was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

treatment_protocol: no treatment

tag: lab id

tag: Sex

value: female


title: z34_6h_REP1

description: replicate 1


title: zz4_6h_REP1

description: replicate 1


title: z34_6h_REP3

description: replicate 3


title: z34_0h_REP1

description: replicate 1


title: z34_0h_REP2

description: replicate 2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GA0141


title: HROC24

description: CRC cell line

source_name: HROC24 CRC cell line, standard culture conditions


title: BJ_0h_REP3

description: replicate 3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GB0267


title: Myoblasts_old-AZA-treated-1, biological rep4


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GA0398


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GA0091


title: Healthy volunteer [GRDS0027_HV27_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FS0257


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient GD0051


title: Healthy volunteer [GRDS0027_HV26_2]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FS0155


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FR0283


title: Myoblasts_old-AZA-untreated-2, biological rep2

source_name: Human old myoblasts, AZA untreated


title: Myoblasts_old-AZA-untreated-3, biological rep3


title: Myoblasts_old-AZA-treated-2, biological rep5


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FP0153


title: Healthy volunteer [GRDS0027_HV2_1]


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FO0291