title: RT_0_15d_110_Lung_ACO2_RSTSRP805

description: RT_0_15d_110_Lung_ACO2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Air Control, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

value: ul

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Air Control

value: 15, Units of Duration:days


title: RT_03_5d_118_Lung_CLPR03_RSTSRP805

status: Public on Oct 12 2012

type: RNA

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

country: USA

institute: CIIT Centers for Health Research

description: RT_03_5d_118_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing:
RMAExpress
Written by B. M. Bolstad <bmb@bmbolstad.com>
Version: 1.0.5 Release
http://rmaexpress.bmbolstad.com

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lung tissue

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0.3, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

value: good

value: RNAlater

value: adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Weeks at start of exposure

value: Lung

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: GD0158_GEP

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

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

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

data_processing: Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 31 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions were summarized as median value for each sample.

organism: Homo sapiens

source_name: Human multiple myeloma patient GD0158

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

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

tag: vh status

value: mut

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: GD0051_GEP

source_name: Human multiple myeloma patient GD0051


title: GL0368_GEP

source_name: Human multiple myeloma patient GL0368


title: DG0193_GEP

source_name: Human multiple myeloma patient DG0193

value: unmut


title: RT_03_5d_121r_Lung_CLPR03_RSTSRP805

description: RT_03_5d_121r_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

value: ul

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.


title: GA0091_GEP

source_name: Human multiple myeloma patient GA0091

tag: vh status

tag: disease state


title: FA0429_GEP

source_name: Human multiple myeloma patient FA0429

tag: sample type

tag: patient


title: GC0015_GEP

source_name: Human multiple myeloma patient GC0015


title: EB0042_GEP

source_name: Human multiple myeloma patient EB0042


title: DN0063_GEP

source_name: Human multiple myeloma patient DN0063


title: GC0147_GEP

source_name: Human multiple myeloma patient GC0147


title: FS0155_GEP

source_name: Human multiple myeloma patient FS0155


title: ET0128_GEP

source_name: Human multiple myeloma patient ET0128


title: GA0141_GEP

source_name: Human multiple myeloma patient GA0141


title: GE0125_GEP

source_name: Human multiple myeloma patient GE0125


title: RT_03_5d_119_Lung_CLPR-03_RSTSRP805

description: RT_03_5d_119_Lung_CLPR-03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

value: RNAlater

value: adult

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: FC0075_GEP

source_name: Human multiple myeloma patient FC0075

tag: vh status

tag: disease state


title: FP0153_GEP

source_name: Human multiple myeloma patient FP0153

tag: sample type

tag: patient


title: DG0186_GEP

source_name: Human multiple myeloma patient DG0186


title: FI0152_GEP

source_name: Human multiple myeloma patient FI0152


title: RT_03_5d_120_Lung_CLPR-03_RSTSRP805

description: RT_03_5d_120_Lung_CLPR-03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

source_name: Lung tissue

tag: array type

tag: amount to core

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

tag: tissue harvest methods


title: GG0027_GEP

source_name: Human multiple myeloma patient GG0027

tag: vh status

tag: disease state


title: Primary Plasma Cell Leukemia PCL-037 Copy number

type: genomic

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-037

hyb_protocol: Following fragmentation, 90 micrograms of biotin-labeled DNA were hybridized for 16 hr at 49°C on GeneChip Human Mapping 250K NspI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 250K NspI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Images were acquired using Affymetrix GeneChip® Operating System (GCOS 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS), (Olshen et al., Biostatistics 2004) and the median of the estimated probes was scaled back to a nominal multiplicity of two. After scaling, a k-means clustering algorithm was used on the cumulative profile of all the data to determine the thresholds for inferring discrete CN values. Inferred CN higher than 2.2, 2.5 and 3.4 corresponded to 3, 4 and 5 or more copies whereas CN below 1.7 and 1.3 to loss and biallelic deletion, respectively.

molecule: genomic DNA

source_name: Primary Plasma Cell Leukemia PCL-037

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol starting from 250 nanograms of genomic DNA.

extract_protocol: Genomic DNA extraction was performed using Wizard® Genomic DNA Purification kit according to the manufacturer's instructions (Promega).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: cell type

value: plasma cell

value: plasma cell leukemia

tag: genome variation

value: translocation t(11;14)


title: Primary Plasma Cell Leukemia PCL-036 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-036

source_name: Primary Plasma Cell Leukemia PCL-036


title: DE0279_GEP

source_name: Human multiple myeloma patient DE0279

tag: sample type

tag: patient


title: Primary Plasma Cell Leukemia PCL-032 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-032

source_name: Primary Plasma Cell Leukemia PCL-032

value: translocation t(4;14)


title: Primary Plasma Cell Leukemia PCL-035 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-035

source_name: Primary Plasma Cell Leukemia PCL-035


title: CI0005_GEP

source_name: Human multiple myeloma patient CI0005


title: DE0085_GEP

source_name: Human multiple myeloma patient DE0085


title: DA0029_GEP

source_name: Human multiple myeloma patient DA0029


title: DC0371_GEP

source_name: Human multiple myeloma patient DC0371


title: Primary Plasma Cell Leukemia PCL-030 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-030

source_name: Primary Plasma Cell Leukemia PCL-030

value: translocation t(14,20)


title: CG0166_GEP

source_name: Human multiple myeloma patient CG0166


title: CA0345_GEP

source_name: Human multiple myeloma patient CA0345


title: CR0159_GEP

source_name: Human multiple myeloma patient CR0159


title: CS0030_GEP

source_name: Human multiple myeloma patient CS0030


title: CE0399_GEP

source_name: Human multiple myeloma patient CE0399


title: CR0203_GEP

source_name: Human multiple myeloma patient CR0203


title: CP0104_GEP

source_name: Human multiple myeloma patient CP0104


title: DA0094_GEP

source_name: Human multiple myeloma patient DA0094


title: CP0109_GEP

source_name: Human multiple myeloma patient CP0109


title: CE0078_GEP

source_name: Human multiple myeloma patient CE0078


title: CA0160_GEP

source_name: Human multiple myeloma patient CA0160


title: CM0057_GEP

source_name: Human multiple myeloma patient CM0057


title: CA0101_GEP

source_name: Human multiple myeloma patient CA0101


title: Primary Plasma Cell Leukemia PCL-026 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-026

source_name: Primary Plasma Cell Leukemia PCL-026

value: translocation t(14,16)


title: Primary Plasma Cell Leukemia PCL-019 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-019

source_name: Primary Plasma Cell Leukemia PCL-019


title: Primary Plasma Cell Leukemia PCL-028 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-028

source_name: Primary Plasma Cell Leukemia PCL-028


title: CA0058_GEP

source_name: Human multiple myeloma patient CA0058


title: Primary Plasma Cell Leukemia PCL-029 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-029

source_name: Primary Plasma Cell Leukemia PCL-029


title: Primary Plasma Cell Leukemia PCL-023 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-023

source_name: Primary Plasma Cell Leukemia PCL-023


title: BG0163_GEP

source_name: Human multiple myeloma patient BG0163

value: mut


title: AR0242_GEP

source_name: Human multiple myeloma patient AR0242

value: B-cell chronic lymphocytic leukemia


title: BC0047_GEP

source_name: Human multiple myeloma patient BC0047

value: peripheral blood mononuclear cells


title: Primary Plasma Cell Leukemia PCL-020 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-020

source_name: Primary Plasma Cell Leukemia PCL-020

value: translocation none


title: BV0176_GEP

source_name: Human multiple myeloma patient BV0176


title: AS0012_GEP

source_name: Human multiple myeloma patient AS0012


title: Primary Plasma Cell Leukemia PCL-021 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-021

source_name: Primary Plasma Cell Leukemia PCL-021


title: AM0106_GEP

source_name: Human multiple myeloma patient AM0106


title: AS0407_GEP

source_name: Human multiple myeloma patient AS0407


title: BE0192_GEP

source_name: Human multiple myeloma patient BE0192

value: unmut


title: AM0220_GEP

source_name: Human multiple myeloma patient AM0220


title: AR0131_GEP

source_name: Human multiple myeloma patient AR0131


title: AM0067_GEP

source_name: Human multiple myeloma patient AM0067


title: Primary Plasma Cell Leukemia PCL-027 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-027

source_name: Primary Plasma Cell Leukemia PCL-027


title: AM0034_GEP

description: legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

source_name: Human multiple myeloma patient AM0034


title: Primary Plasma Cell Leukemia PCL-018 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-018

source_name: Primary Plasma Cell Leukemia PCL-018


title: BL0162_GEP

source_name: Human multiple myeloma patient BL0162


title: AG0403_GEP

source_name: Human multiple myeloma patient AG0403


title: TF0001_GWP

data_processing: Images were acquired using Affymetrix GeneChip® Operating System (GCOS 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS), (Olshen et al., Biostatistics 2004) and the median of the estimated pro?les was scaled back to a nominal multiplicity of two. After scaling, a k-means clustering algorithm was used on the cumulative profile of all the data to determine the thresholds for inferring discrete CN values. Inferred CN higher than 2.1 and 2.6 corresponded to gain and amplification whereas CN below 1.9 and 1.29 to loss and biallelic deletion, respectively.

source_name: Human B-cell chronic lymphocytic leukemia patient TF0001


title: VM0107_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient VM0107


title: AB0350_GEP

source_name: Human multiple myeloma patient AB0350


title: Primary Plasma Cell Leukemia PCL-015 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-015

source_name: Primary Plasma Cell Leukemia PCL-015


title: Primary Plasma Cell Leukemia PCL-016 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-016

source_name: Primary Plasma Cell Leukemia PCL-016


title: Primary Plasma Cell Leukemia PCL-017 Copy number

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Genome-wide profiling data from Primary Plasma Cell Leukemia PCL-017

source_name: Primary Plasma Cell Leukemia PCL-017


title: PG0028_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient PG0028


title: 3T3F442A-shGFP-rep1

city: Boston

first: Li

last: Ye

state: MA

address: 450 brookline ave. CLSB11118

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C on Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: The label, hyb and scan were performed by the Dana-Farber Cancer institute Core facility using affymetrix Gene Chip Mouse Genome 430 2.0 arrays according to established methods.

data_processing: The data were normalized using the DNA-chip Analyzer (dChip) software.

source_name: full differentiated 3T3F422A adipocyte

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

growth_protocol: 3T3-F442A adipocytes with stable expression of shGFP or shTRPV4 were cultured in DMEM with 10%FBS.  Adipocyte differentiation was induced s by treating confluent cells with 850 nM insulin for 8 days. Rosiglitozone was used for the first two days to faciliate differentiation.

extract_protocol: Total RNA was isolated by TRIzol extraction and purification using QIAGEN Rneasy mini columns according to the manufacturer's instructions.

treatment_protocol: To generate stable knockdown adipocytes, 3T3-F442A pre-adipocytes were infected with shRNA-expressing retrovirus for overnight, followed by a puromycin selection (2ug/ml) for 2 days.

tag: genotype/variation

value: control


title: 3T3F442A-shTRPV4-rep2

value: TRPV4 knockdown


title: NM0156_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient NM0156


title: SNAPC1_unstimulated_rep3

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description:
SNAPC1_0_rep3
unstimulated_rep3

hyb_protocol: Biotin labeled aRNA at 750ng was hybridized  to  Illumina HumanHT-12V4 expression Beadchip with Illumina  HumanHT-12 v4 Expression BeadChip Kit(cat# BD-103-0204 )         Subsequent steps include washing, blocking, and streptavadin-Cy3 staining of the beadchip.

scan_protocol: Fluorescence emission by Cy3 is quantitatively detected with Illumina BeadArray Reader( scan software : Illumina BeadSacn) and GenomeStudio  software provides results in standard file format

data_processing: Intensity raw data were log2 transformed and normalized by quantile normalization using BeadArray package on R

source_name: Hela

label_protocol: samples were biotin-labeled using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)

growth_protocol: Hela cells were transfected with sh vectors and selected in puromycin, medium was DMEM + 10% FBS

extract_protocol: cells were harvested and lysed in RLT buffer (Qiagen), total RNA was extracted with Rneasy mini kit

treatment_protocol: cells were starved in 1% serum overnight, then treated with 100 ng/microl of recombinant EGF

tag: cell line

value: Hela

tag: treatment

value: unstimulated


title: 3T3F442A-shTRPV4-rep1


title: SNAPC1_EGF_rep3

description:
SNAPC1_30_rep3
EGF_30min_rep3

value: EGF


title: 3T3F442A-shGFP-rep2


title: SCR_unstimulated_rep3

description:
SCR 0_rep3
unstimulated_rep3


title: SCR_EGF_rep3

description:
SCR 30_rep3
EGF_30min_rep3


title: SCR_EGF_rep2

description:
SCR 30_rep2
EGF_30min_rep2


title: SNAPC1_unstimulated_rep2

description:
SNAPC1_0_rep2
unstimulated_rep2


title: MB0065_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient MB0065


title: SNAPC1_EGF_rep2

description:
SNAPC1_30_rep2
EGF_30min_rep2


title: SNAPC1_EGF_rep1

description:
SNAPC1_30_rep1
EGF_30min_rep1


title: SCR_unstimulated_rep2

description:
SCR 0_rep2
unstimulated_rep2


title: FA0347_GEP

source_name: Human multiple myeloma patient FA0347


title: SNAPC1_unstimulated_rep1

description:
SNAPC1_0_rep1
unstimulated_rep1


title: GP0171_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient GP0171


title: SCR_unstimulated_rep1

description:
SCR 0_rep1
unstimulated_rep1


title: SCR_EGF_rep1

description:
SCR 30_rep1
EGF_30min_rep1


title: DA0094_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient DA0094


title: CP0104_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient CP0104


title: CA0058_GWP

source_name: Human B-cell chronic lymphocytic leukemia patient CA0058


title: CG0037_GWP_2

source_name: Human B-cell chronic lymphocytic leukemia patient CS12


title: AG0136_GEP

source_name: Human multiple myeloma patient AG0136


title: Chronic lymphocytic leukemia 352 unpaired

status: Public on Oct 11 2012

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: Hybridized to GenomeWide SNP 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix® fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL-files were generated using Affymetrix Command console software
CHP-files were generated using Affymetrix Genotyping console (BRLMM2)

label: Biotin

source_name: peripherel blood

label_protocol: As per manufacturer (Affymetrix®)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood (CD19 positive and negative fraction after immunomagnetic tumor cell enrichment by Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia

tag: pair

value: 352 unpaired


title: Chronic lymphocytic leukemia 349 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 349 unpaired


title: Chronic lymphocytic leukemia 350 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 350 unpaired


title: Chronic lymphocytic leukemia 348 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 348 unpaired


title: Chronic lymphocytic leukemia 145 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 145 unpaired


title: Chronic lymphocytic leukemia 336 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 336 unpaired


title: Chronic lymphocytic leukemia 344 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 344 unpaired


title: Chronic lymphocytic leukemia 330 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 330 unpaired


title: Chronic lymphocytic leukemia 353 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 353 unpaired


title: Chronic lymphocytic leukemia 332 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 332 unpaired


title: Chronic lymphocytic leukemia 327 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 327 unpaired


title: Chronic lymphocytic leukemia 345 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 345 unpaired


title: Chronic lymphocytic leukemia 341 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 341 unpaired


title: Chronic lymphocytic leukemia 342 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 342 unpaired


title: Chronic lymphocytic leukemia 329 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 329 unpaired


title: Chronic lymphocytic leukemia 337 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 337 unpaired


title: Chronic lymphocytic leukemia 335 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 335 unpaired


title: Chronic lymphocytic leukemia 339 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 339 unpaired


title: Chronic lymphocytic leukemia 333 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 333 unpaired


title: Chronic lymphocytic leukemia 340 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 340 unpaired


title: Chronic lymphocytic leukemia 346 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 346 unpaired


title: Chronic lymphocytic leukemia 338 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 338 unpaired


title: Chronic lymphocytic leukemia 331 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 331 unpaired


title: Chronic lymphocytic leukemia 347 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 347 unpaired


title: Chronic lymphocytic leukemia 351 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 351 unpaired


title: Chronic lymphocytic leukemia 328 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 328 unpaired


title: Chronic lymphocytic leukemia 334 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 334 unpaired


title: Chronic lymphocytic leukemia 325 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 325 unpaired


title: Chronic lymphocytic leukemia 343 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 343 unpaired


title: Chronic lymphocytic leukemia 326 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 326 unpaired


title: Chronic lymphocytic leukemia 323 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 323 unpaired


title: Chronic lymphocytic leukemia 324 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 324 unpaired


title: Chronic lymphocytic leukemia 322 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 322 unpaired


title: Chronic lymphocytic leukemia 321 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 321 unpaired


title: Chronic lymphocytic leukemia 316 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 316 unpaired


title: Chronic lymphocytic leukemia 312 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 312 unpaired


title: Chronic lymphocytic leukemia 315 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 315 unpaired


title: Chronic lymphocytic leukemia 314 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 314 unpaired


title: Chronic lymphocytic leukemia 309 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 309 unpaired


title: Chronic lymphocytic leukemia 311 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 311 unpaired


title: Chronic lymphocytic leukemia 297 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 297 unpaired


title: Chronic lymphocytic leukemia 317 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 317 unpaired


title: Chronic lymphocytic leukemia 304 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 304 unpaired


title: Chronic lymphocytic leukemia 303 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 303 unpaired


title: Chronic lymphocytic leukemia 308

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 305 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 305 unpaired


title: Chronic lymphocytic leukemia 319 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 319 unpaired


title: Chronic lymphocytic leukemia 307 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 307 unpaired


title: Chronic lymphocytic leukemia 313 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 313 unpaired


title: Chronic lymphocytic leukemia 318 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 318 unpaired


title: Chronic lymphocytic leukemia 306 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 306 unpaired


title: Chronic lymphocytic leukemia 302 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 302 unpaired


title: Chronic lymphocytic leukemia 298 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 298 unpaired


title: Chronic lymphocytic leukemia 299 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 299 unpaired


title: Chronic lymphocytic leukemia 320 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 320 unpaired


title: Chronic lymphocytic leukemia 296 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 296 unpaired


title: Chronic lymphocytic leukemia 310 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 310 unpaired


title: Chronic lymphocytic leukemia 301 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 301 unpaired


title: Chronic lymphocytic leukemia 295 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 295 unpaired


title: Chronic lymphocytic leukemia 293 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 293 unpaired


title: Chronic lymphocytic leukemia 294 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 294 unpaired


title: Chronic lymphocytic leukemia 291 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 291 unpaired


title: Chronic lymphocytic leukemia 308 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: Chronic lymphocytic leukemia 285 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 285 unpaired


title: Chronic lymphocytic leukemia 287 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 287 unpaired


title: Chronic lymphocytic leukemia 280

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 292 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 292 unpaired


title: Chronic lymphocytic leukemia 300 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 300 unpaired


title: Chronic lymphocytic leukemia 288 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 288 unpaired


title: Chronic lymphocytic leukemia 277 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 277 unpaired


title: Chronic lymphocytic leukemia 286 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 286 unpaired


title: Chronic lymphocytic leukemia 281 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 281 unpaired


title: Chronic lymphocytic leukemia 280 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 279 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 279 unpaired


title: Chronic lymphocytic leukemia 274 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 274 unpaired


title: Chronic lymphocytic leukemia 290 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 290 unpaired


title: Chronic lymphocytic leukemia 272 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 272 unpaired


title: Chronic lymphocytic leukemia 271 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 271 unpaired


title: Chronic lymphocytic leukemia 282 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 282 unpaired


title: Chronic lymphocytic leukemia 283 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 283 unpaired


title: Chronic lymphocytic leukemia 275 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 275 unpaired


title: Chronic lymphocytic leukemia 284 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 284 unpaired


title: Chronic lymphocytic leukemia 270 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 270 unpaired


title: Chronic lymphocytic leukemia 289 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 289 unpaired


title: Chronic lymphocytic leukemia 268 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 268 unpaired


title: Chronic lymphocytic leukemia 269 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 269 unpaired


title: Chronic lymphocytic leukemia 267 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 267 unpaired


title: Chronic lymphocytic leukemia 265 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 265 unpaired


title: Chronic lymphocytic leukemia 266 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 266 unpaired


title: Chronic lymphocytic leukemia 255 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 255 unpaired


title: Chronic lymphocytic leukemia 263 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 263 unpaired


title: Chronic lymphocytic leukemia 276 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 276 unpaired


title: Chronic lymphocytic leukemia 273 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 273 unpaired


title: Chronic lymphocytic leukemia 257 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 257 unpaired


title: Chronic lymphocytic leukemia 259 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 259 unpaired


title: Chronic lymphocytic leukemia 251 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 251 unpaired


title: Chronic lymphocytic leukemia 261 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 261 unpaired


title: Chronic lymphocytic leukemia 252 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: Chronic lymphocytic leukemia 253 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 253 unpaired


title: Chronic lymphocytic leukemia 258 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 258 unpaired


title: Chronic lymphocytic leukemia 260 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 260 unpaired


title: Chronic lymphocytic leukemia 278 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 278 unpaired


title: Chronic lymphocytic leukemia 264 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 264 unpaired


title: Chronic lymphocytic leukemia 262 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 262 unpaired


title: Chronic lymphocytic leukemia 250 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 250 unpaired


title: Chronic lymphocytic leukemia 252

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 245 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 245 unpaired


title: Chronic lymphocytic leukemia 247 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 247 unpaired


title: Chronic lymphocytic leukemia 248 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 248 unpaired


title: Chronic lymphocytic leukemia 256 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 256 unpaired


title: Chronic lymphocytic leukemia 246 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 246 unpaired


title: Chronic lymphocytic leukemia 244 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 244 unpaired


title: Chronic lymphocytic leukemia 249 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 249 unpaired


title: Chronic lymphocytic leukemia 243 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 243 unpaired


title: Chronic lymphocytic leukemia 242 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 242 unpaired


title: Chronic lymphocytic leukemia 241 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 241 unpaired


title: Chronic lymphocytic leukemia 239 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 239 unpaired


title: Chronic lymphocytic leukemia 240 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 240 unpaired


title: Chronic lymphocytic leukemia 232 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 232 unpaired


title: Chronic lymphocytic leukemia 237 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 237 unpaired


title: Chronic lymphocytic leukemia 254 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 254 unpaired


title: Chronic lymphocytic leukemia 236 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 236 unpaired


title: Chronic lymphocytic leukemia 228 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 228 unpaired


title: Chronic lymphocytic leukemia 231 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 231 unpaired


title: Chronic lymphocytic leukemia 226 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 226 unpaired


title: Chronic lymphocytic leukemia 234 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 234 unpaired


title: Chronic lymphocytic leukemia 233 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 233 unpaired


title: Chronic lymphocytic leukemia 229 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 229 unpaired


title: Chronic lymphocytic leukemia 227 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 227 unpaired


title: Chronic lymphocytic leukemia 235 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 235 unpaired


title: Chronic lymphocytic leukemia 225 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 225 unpaired


title: Chronic lymphocytic leukemia 222 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 222 unpaired


title: Chronic lymphocytic leukemia 230 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 230 unpaired


title: Chronic lymphocytic leukemia 221 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 221 unpaired


title: Chronic lymphocytic leukemia 216 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 216 unpaired


title: Chronic lymphocytic leukemia 224 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 224 unpaired


title: Chronic lymphocytic leukemia 215 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 215 unpaired


title: Chronic lymphocytic leukemia 218 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 218 unpaired


title: Chronic lymphocytic leukemia 219 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 219 unpaired


title: Chronic lymphocytic leukemia 220 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 220 unpaired


title: Chronic lymphocytic leukemia 223 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 223 unpaired


title: Chronic lymphocytic leukemia 217 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 217 unpaired


title: Chronic lymphocytic leukemia 213 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 213 unpaired


title: Chronic lymphocytic leukemia 212 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 212 unpaired


title: Chronic lymphocytic leukemia 214 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 214 unpaired


title: Chronic lymphocytic leukemia 238 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 238 unpaired


title: Chronic lymphocytic leukemia 209 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 209 unpaired


title: Chronic lymphocytic leukemia 202 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 202 unpaired


title: Chronic lymphocytic leukemia 208 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 208 unpaired


title: Chronic lymphocytic leukemia 204 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 204 unpaired


title: Chronic lymphocytic leukemia 207 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 207 unpaired


title: Chronic lymphocytic leukemia 200 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 200 unpaired


title: Chronic lymphocytic leukemia 206 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 206 unpaired


title: Chronic lymphocytic leukemia 201 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 201 unpaired


title: Chronic lymphocytic leukemia 196 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 196 unpaired


title: Chronic lymphocytic leukemia 198 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 198 unpaired


title: Chronic lymphocytic leukemia 210 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 210 unpaired


title: Chronic lymphocytic leukemia 195 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 195 unpaired


title: Chronic lymphocytic leukemia 203 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 203 unpaired


title: Chronic lymphocytic leukemia 205 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 205 unpaired


title: Chronic lymphocytic leukemia 211 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 211 unpaired


title: Chronic lymphocytic leukemia 189 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 189 unpaired


title: Chronic lymphocytic leukemia 190 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 190 unpaired


title: Chronic lymphocytic leukemia 191 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 191 unpaired


title: Chronic lymphocytic leukemia 186 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 186 unpaired


title: Chronic lymphocytic leukemia 194 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 194 unpaired


title: Chronic lymphocytic leukemia 193 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 193 unpaired


title: Chronic lymphocytic leukemia 187 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 187 unpaired


title: Chronic lymphocytic leukemia 184 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 184 unpaired


title: Chronic lymphocytic leukemia 197 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 197 unpaired


title: Chronic lymphocytic leukemia 199 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 199 unpaired


title: Chronic lymphocytic leukemia 185 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 185 unpaired


title: Chronic lymphocytic leukemia 188 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 188 unpaired


title: Chronic lymphocytic leukemia 183 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 183 unpaired


title: Chronic lymphocytic leukemia 182 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 182 unpaired


title: Chronic lymphocytic leukemia 172 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 172 unpaired


title: Chronic lymphocytic leukemia 175 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 175 unpaired


title: Chronic lymphocytic leukemia 192 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 192 unpaired


title: Chronic lymphocytic leukemia 178 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 178 unpaired


title: Chronic lymphocytic leukemia 177 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 177 unpaired


title: Chronic lymphocytic leukemia 171 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 171 unpaired


title: Chronic lymphocytic leukemia 176 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 176 unpaired


title: Chronic lymphocytic leukemia 180 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 180 unpaired


title: Chronic lymphocytic leukemia 166 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 166 unpaired


title: Chronic lymphocytic leukemia 181 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 181 unpaired


title: Chronic lymphocytic leukemia 170 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 170 unpaired


title: Chronic lymphocytic leukemia 169 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 169 unpaired


title: Chronic lymphocytic leukemia 168 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 168 unpaired


title: Chronic lymphocytic leukemia 173 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 173 unpaired


title: Chronic lymphocytic leukemia 174 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 174 unpaired


title: Chronic lymphocytic leukemia 165 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 165 unpaired


title: Chronic lymphocytic leukemia 167 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 167 unpaired


title: Chronic lymphocytic leukemia 163 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 163 unpaired


title: Chronic lymphocytic leukemia 157 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 157 unpaired


title: Chronic lymphocytic leukemia 162 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 162 unpaired


title: Chronic lymphocytic leukemia 179 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 179 unpaired


title: Chronic lymphocytic leukemia 158 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 158 unpaired


title: Chronic lymphocytic leukemia 159 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: 159 unpaired


title: Chronic lymphocytic leukemia 160 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 160 unpaired


title: Chronic lymphocytic leukemia 156 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 156 unpaired


title: Chronic lymphocytic leukemia 161 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia

value: 161 unpaired


title: Chronic lymphocytic leukemia 164 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 164 unpaired


title: Chronic lymphocytic leukemia 155 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 155 unpaired


title: Chronic lymphocytic leukemia 151 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 151 unpaired


title: Chronic lymphocytic leukemia 149 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 149 unpaired


title: Chronic lymphocytic leukemia 152 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 152 unpaired


title: Chronic lymphocytic leukemia 150 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 150 unpaired


title: Chronic lymphocytic leukemia 153 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 153 unpaired


title: Chronic lymphocytic leukemia 148 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 148 unpaired


title: Chronic lymphocytic leukemia 154 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 154 unpaired


title: Chronic lymphocytic leukemia 147 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 147 unpaired


title: Chronic lymphocytic leukemia 144

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 146 unpaired

description: Hybridized to GenomeWide SNP 6.0 array

value: 146 unpaired


title: Chronic lymphocytic leukemia 143 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: Chronic lymphocytic leukemia 144 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 142 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 141

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+


title: Chronic lymphocytic leukemia 140 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 143

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 142

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 140

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 139 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 138 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 139

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 138

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 141 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 137 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 137

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 136 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 136

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 135 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 134

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 133 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 131

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 131 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 133

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 132

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 130

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 128 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 130 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 127 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 134 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 126

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 129 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 132 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 125

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 128

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 124 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 127

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 135

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 122

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 122 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 121

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 123

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 121 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 124

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 129

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 126 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 120 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 125 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 123 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Col-0 vs. triple mutant, replicate 2 dye-swap

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

country: South Korea

institute: KonKuk University

description: Col-0 vs triple 4 vs 3

hyb_protocol: Standard Agilent's Gene Expression Hybridization Kit protocol.

scan_protocol: Images were scanned using Agilent's DNA microarray scanner and quantified using Feature Extraction Software.

data_processing: Agilent's GeneSpring Software was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: shr scl23 scr

label_protocol: Agilent's Low RNA Input Linear Amplification kit PLUS.

growth_protocol: Plants were grown on MS medium under a 16 h light/ 8 h dark cycle at 22°C.

extract_protocol: RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's protocol.

tag: ecotype

value: vegetative part

value: stage 1.04

value: shr-2 scl23-1 scr-5

source_name: wild type

value: WT


title: Col-0 vs. triple mutant, replicate 2

description: Col-0 vs triple 3 vs 4


title: Chronic lymphocytic leukemia 117

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia


title: Col-0 vs. triple mutant, replicate 1

description: Col-0 vs triple 1 vs 2


title: Chronic lymphocytic leukemia 119 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Stromal-cells-125

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the BeadArray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the BeadArray package.

source_name: human mammary tissue, stromal

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

growth_protocol: Discarded tissues from reduction mammoplasties received from Addenbrooke’s hospital. Freshly sorted cells were used for this study.

extract_protocol: Human breast tissue were dissociated in collagenase and hyaluronidase for 14-16 h at 37°C, treated with ammonium chloride, trypsin, dispase, DNase and filtered to obtain a single cell suspension. Mammary cells were stained with fluorochrome-conjugated antibodies and the viability dye DAPI and were then passed through a cell sorter. Total RNA was extracted using a PicoPure RNA extraction kit. Total RNA was quality checked using a Bioanalyser.

tag: gender

value: female

value: breast

value: stromal


title: Col-0 vs. triple mutant, replicate 1 dye-swap

description: Col-0 vs triple 2 vs 1


title: NCL-cells-125

source_name: human mammary tissue, ncl

value: luminal


title: Chronic lymphocytic leukemia 117 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Erbb3-neg-cells-125

source_name: human mammary tissue, erbb3-


title: Chronic lymphocytic leukemia 115 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 113 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 114

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 118 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-125

source_name: human mammary tissue, basal

value: basal


title: Chronic lymphocytic leukemia 120

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 116

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 116 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-pos-cells-125

source_name: human mammary tissue, aldh+


title: ALDH-neg-cells-125

source_name: human mammary tissue, aldh-


title: Chronic lymphocytic leukemia 118

description: Hybridized to GenomeWide SNP 6.0 array


title: NCL-cells-124


title: Chronic lymphocytic leukemia 111 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 112

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-124


title: ALDH-pos-cells-124


title: Chronic lymphocytic leukemia 115

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 113

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 110

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-124


title: Chronic lymphocytic leukemia 109

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 112 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-110


title: NCL-cells-110


title: Chronic lymphocytic leukemia 119

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 111

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 110 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 114 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 109 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 108

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-pos-cells-110


title: NCL-cells-100


title: Chronic lymphocytic leukemia 108 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Stromal-cells-100


title: ALDH-neg-cells-110


title: Chronic lymphocytic leukemia 107 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 107

description: Hybridized to GenomeWide SNP 6.0 array


title: Erbb3-neg-cells-100


title: ALDH-pos-cells-100


title: Stromal-cells-110


title: NCL-cells-075


title: Basal-cells-100


title: NCL-cells-071


title: Chronic lymphocytic leukemia 106

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-100


title: Stromal-cells-071


title: Erbb3-neg-cells-071


title: Chronic lymphocytic leukemia 105

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-071


title: ALDH-pos-cells-071


title: Chronic lymphocytic leukemia 103 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 105 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Erbb3-neg-cells-061


title: Chronic lymphocytic leukemia 102 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-061


title: NCL-cells-061


title: Chronic lymphocytic leukemia 106 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 104

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 101

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-pos-cells-061


title: Chronic lymphocytic leukemia 104 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 102

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 101 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-061


title: Stromal-cells-056


title: Chronic lymphocytic leukemia 99 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: NCL-cells-056


title: Erbb3-neg-cells-056


title: Chronic lymphocytic leukemia 98

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-056


title: Chronic lymphocytic leukemia 98 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-pos-cells-056


title: Chronic lymphocytic leukemia 96 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: NCL-cells-050


title: Stromal-cells-050


title: Chronic lymphocytic leukemia 99

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 97

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 95 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 97 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 100

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 95

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-056


title: Chronic lymphocytic leukemia 94

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-050


title: Chronic lymphocytic leukemia 94 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-050


title: Erbb3-neg-cells-045


title: ALDH-pos-cells-050


title: Erbb3-neg-cells-050


title: Chronic lymphocytic leukemia 92 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 96

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-045


title: ALDH-neg-cells-045


title: ALDH-pos-cells-045


title: Stromal-cells-022


title: Chronic lymphocytic leukemia 93

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 92

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-022


title: Chronic lymphocytic leukemia 93 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 91

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 89 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 88

description: Hybridized to GenomeWide SNP 6.0 array


title: Erbb3-neg-cells-022


title: ALDH-pos-cells-022


title: Chronic lymphocytic leukemia 90

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 100 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: ALDH-neg-cells-022


title: Chronic lymphocytic leukemia 88 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 91 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 103

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 90 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 86

description: Hybridized to GenomeWide SNP 6.0 array


title: Stromal-cells-019


title: Chronic lymphocytic leukemia 84

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 85 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 84 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 86 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: NCL-cells-019


title: Erbb3-neg-cells-019


title: ALDH-pos-cells-019


title: Chronic lymphocytic leukemia 87

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 83

description: Hybridized to GenomeWide SNP 6.0 array


title: Basal-cells-019


title: ALDH-neg-cells-019


title: Stromal-cells-010


title: Basal-cells-010


title: Erbb3-neg-cells-010


title: ALDH-pos-cells-010


title: Chronic lymphocytic leukemia 81 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: NCL-cells-010


title: Stromal-cells-007


title: ALDH-neg-cells-010


title: Chronic lymphocytic leukemia 82

description: Hybridized to GenomeWide SNP 6.0 array


title: NCL-cells-022


title: Chronic lymphocytic leukemia 82 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Erbb3-neg-cells-007


title: NCL-cells-007


title: ALDH-neg-cells-007


title: Basal-cells-007


title: ALDH-pos-cells-007


title: Chronic lymphocytic leukemia 80 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN14, replicate d, in utero Ovalbumin-exposed

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were standard background corrected and quantile normalized using the R Bioconductor package lumi.

organism: Rattus norvegicus

source_name: rat whole lung

extract_protocol: RNA from whole lung tissue and primary lung cells was isolated using Trizol reagent (Invitrogen, Burlington, ON, Canada) according to the manufacturer’s instructions. RNA was resuspended in 1x RNASecure (Ambion, Austin, TX, USA) and treated with the Turbo DNase-free kit (Ambion, Austin, TX, USA) to remove any traces of DNA.

tag: strain

value: Lewis

tag: age (postnatal days)

tag: exposure in utero

value: Ovalbumin

value: whole lung

tag: beadchip sentrix barcode

tag: beadchip section

value: B

tag: short label

tag: selected for reproducibility analysis

value: Yes


title: whole lung Fisher rat, age PN1, replicate d, in utero Saline-exposed

value: Fisher

value: Saline

tag: tissue

value: H


title: Chronic lymphocytic leukemia 83 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

tag: cell type

value: mononuclear cells CD19-

tag: disease state

value: normal


title: whole lung Fisher rat, age PN14, replicate d, in utero Ovalbumin-exposed

value: I

value: No


title: Chronic lymphocytic leukemia 79 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 77 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 76 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 80

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 78 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 78

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 77

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 75 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 76

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 79

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 75

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 74 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 81

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN14, replicate d, in utero Ovalbumin-exposed

value: Brown Norway

value: L


title: Chronic lymphocytic leukemia 72 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 73

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN14, replicate c, in utero Ovalbumin-exposed


title: Chronic lymphocytic leukemia 74

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN14, replicate c, in utero Ovalbumin-exposed

value: C


title: whole lung Brown Norway rat, age PN14, replicate b, in utero Ovalbumin-exposed

value: G


title: Chronic lymphocytic leukemia 87 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN14, replicate a, in utero Ovalbumin-exposed

value: Ovalbumin

value: D


title: Chronic lymphocytic leukemia 89

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN14, replicate b, in utero Ovalbumin-exposed

value: whole lung

value: K


title: whole lung Lewis rat, age PN14, replicate c, in utero Ovalbumin-exposed

value: Lewis

value: F

value: Yes


title: Chronic lymphocytic leukemia 71

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN14, replicate a, in utero Ovalbumin-exposed

value: Fisher

value: H


title: Chronic lymphocytic leukemia 72

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 71 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: whole lung Lewis rat, age PN14, replicate b, in utero Ovalbumin-exposed

value: E

value: No


title: Chronic lymphocytic leukemia 70

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: whole lung Brown Norway rat, age PN14, replicate d, in utero Saline-exposed

value: Brown Norway

value: Saline

value: L


title: whole lung Lewis rat, age PN14, replicate a, in utero Ovalbumin-exposed

value: Ovalbumin

value: A


title: whole lung Brown Norway rat, age PN14, replicate c, in utero Saline-exposed

value: whole lung

value: K


title: whole lung Fisher rat, age PN14, replicate d, in utero Saline-exposed


title: whole lung Brown Norway rat, age PN14, replicate b, in utero Saline-exposed

value: J


title: whole lung Fisher rat, age PN14, replicate c, in utero Saline-exposed

value: G


title: Chronic lymphocytic leukemia 85

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN14, replicate b, in utero Saline-exposed

value: Fisher

value: F

value: Yes


title: whole lung Fisher rat, age PN14, replicate a, in utero Saline-exposed


title: Chronic lymphocytic leukemia 70 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: Chronic lymphocytic leukemia 69

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN14, replicate a, in utero Saline-exposed

value: I

value: No


title: whole lung Lewis rat, age PN14, replicate d, in utero Saline-exposed

value: Lewis

value: D


title: whole lung Lewis rat, age PN14, replicate c, in utero Saline-exposed

value: Saline

value: C


title: whole lung Lewis rat, age PN14, replicate b, in utero Saline-exposed

value: E


title: whole lung Lewis rat, age PN14, replicate a, in utero Saline-exposed


title: Chronic lymphocytic leukemia 68 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN7, replicate d, in utero Ovalbumin-exposed

value: Brown Norway

value: Ovalbumin


title: Chronic lymphocytic leukemia 69 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN7, replicate c, in utero Ovalbumin-exposed

value: whole lung

value: L


title: whole lung Brown Norway rat, age PN7, replicate a, in utero Ovalbumin-exposed

value: A


title: whole lung Brown Norway rat, age PN7, replicate b, in utero Ovalbumin-exposed

value: B


title: Chronic lymphocytic leukemia 65 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 67

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 68

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 67 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: whole lung Fisher rat, age PN7, replicate d, in utero Ovalbumin-exposed

value: Fisher


title: whole lung Fisher rat, age PN7, replicate c, in utero Ovalbumin-exposed


title: Chronic lymphocytic leukemia 66 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: normal


title: whole lung Fisher rat, age PN7, replicate b, in utero Ovalbumin-exposed

value: Yes


title: Chronic lymphocytic leukemia 63

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 64

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 73 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 62 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN7, replicate d, in utero Ovalbumin-exposed

value: Lewis

value: K


title: whole lung Fisher rat, age PN7, replicate a, in utero Ovalbumin-exposed


title: Chronic lymphocytic leukemia 66

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 65

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 64 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN7, replicate c, in utero Ovalbumin-exposed

value: J

value: No


title: Chronic lymphocytic leukemia 63 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 62

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN7, replicate b, in utero Ovalbumin-exposed


title: Chronic lymphocytic leukemia 61 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 60

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 61

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN7, replicate c, in utero Saline-exposed

value: Saline

value: G


title: Chronic lymphocytic leukemia 60 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN7, replicate a, in utero Ovalbumin-exposed

value: Ovalbumin

value: I


title: whole lung Brown Norway rat, age PN7, replicate b, in utero Saline-exposed

value: Brown Norway

value: whole lung

value: F


title: whole lung Brown Norway rat, age PN7, replicate d, in utero Saline-exposed

value: H


title: whole lung Brown Norway rat, age PN7, replicate a, in utero Saline-exposed

value: E


title: whole lung Fisher rat, age PN7, replicate c, in utero Saline-exposed


title: whole lung Fisher rat, age PN7, replicate b, in utero Saline-exposed

value: D


title: Chronic lymphocytic leukemia 59

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 58 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-

value: normal


title: Chronic lymphocytic leukemia 57

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 58

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 56

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 57 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN7, replicate b, in utero Saline-exposed

value: Lewis

value: B

value: Yes


title: Chronic lymphocytic leukemia 59 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN7, replicate c, in utero Saline-exposed

value: Saline

value: No


title: whole lung Lewis rat, age PN7, replicate a, in utero Saline-exposed

value: A


title: whole lung Lewis rat, age PN7, replicate d, in utero Saline-exposed

value: G


title: whole lung Brown Norway rat, age PN1, replicate d, in utero Ovalbumin-exposed

value: Brown Norway

value: Ovalbumin


title: Chronic lymphocytic leukemia 56 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 55

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN1, replicate b, in utero Ovalbumin-exposed

value: whole lung

value: L


title: whole lung Brown Norway rat, age PN1, replicate c, in utero Ovalbumin-exposed


title: whole lung Brown Norway rat, age PN1, replicate a, in utero Ovalbumin-exposed

value: K


title: whole lung Fisher rat, age PN7, replicate a, in utero Saline-exposed

value: Fisher

value: C


title: Chronic lymphocytic leukemia 54 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN1, replicate b, in utero Ovalbumin-exposed

value: J


title: whole lung Fisher rat, age PN1, replicate c, in utero Ovalbumin-exposed


title: Chronic lymphocytic leukemia 52 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: whole lung Fisher rat, age PN1, replicate a, in utero Ovalbumin-exposed

value: I


title: Chronic lymphocytic leukemia 50 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: normal


title: Chronic lymphocytic leukemia 53 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 55 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN1, replicate c, in utero Ovalbumin-exposed

value: Lewis


title: Chronic lymphocytic leukemia 51 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN1, replicate d, in utero Ovalbumin-exposed

value: Yes


title: Chronic lymphocytic leukemia 49 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN1, replicate b, in utero Ovalbumin-exposed

value: H


title: whole lung Lewis rat, age PN1, replicate d, in utero Ovalbumin-exposed


title: Chronic lymphocytic leukemia 54

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 50

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 49

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN1, replicate c, in utero Saline-exposed

value: Saline

value: No


title: Chronic lymphocytic leukemia 53

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN1, replicate d, in utero Saline-exposed

value: Brown Norway


title: Chronic lymphocytic leukemia 48 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN1, replicate b, in utero Saline-exposed

value: whole lung

value: F


title: Chronic lymphocytic leukemia 46 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 52

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Brown Norway rat, age PN1, replicate a, in utero Saline-exposed

value: E


title: Chronic lymphocytic leukemia 48

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Lewis rat, age PN1, replicate a, in utero Ovalbumin-exposed

value: Ovalbumin

value: G


title: Chronic lymphocytic leukemia 51

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 45 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 46

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 45

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 47 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: whole lung Fisher rat, age PN1, replicate a, in utero Saline-exposed

value: Fisher

value: C


title: Chronic lymphocytic leukemia 42 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 44 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: normal


title: whole lung Fisher rat, age PN1, replicate b, in utero Saline-exposed

value: D


title: whole lung Lewis rat, age PN1, replicate c, in utero Saline-exposed

value: Lewis


title: whole lung Lewis rat, age PN1, replicate d, in utero Saline-exposed

value: Yes


title: Chronic lymphocytic leukemia 44

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19+


title: whole lung Lewis rat, age PN1, replicate a, in utero Saline-exposed

value: A


title: whole lung Lewis rat, age PN1, replicate b, in utero Saline-exposed

value: Saline

value: B


title: Chronic lymphocytic leukemia 47

description: Hybridized to GenomeWide SNP 6.0 array

value: Chronic lymphocytic leukemia


title: Chronic lymphocytic leukemia 42

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 43

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 43 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: DCs co-stimulated with CpG and inactivated H9N2 at 12h

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

country: China

institute: nanjing agricultural university

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (WT Expression_kit_manual  Affymetrix).

growth_protocol: All used mice were C57BL/6 and between 6 and 8 wk at the time of study. Briefly, bone marrow cells were prepared from the femurs and tibias of sacrificed mice. Cells were released by crushing the marrow into a 100mm dish with culture medium, and then were passed through a 100mm nylon mesh to remove small pieces of bone and debris. After wash cells twice by centrifuging at 1500 rpm for 5 min, cells were treated with red blood cells lysing buffer for 2–3 min at room temperature. After centrifuged at 1500 rpm for 5 min, cells were collected and seeded in 6-well plates with 2.5ml complete culture medium. Complete medium was RPMI 1640 (Gibco, Carlsbad, CA) containing 10% FBS, 1% penicillin/streptomycin, 50ng/ml GM-CSF and IL-4 (PeproTech, USA). The cultures were nourished every 60h by gently aspirating the spent medium and adding fresh medium. At day 6, the non-adherent, relatively immature DCs were harvested for subsequent in vitro assays.

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

treatment_protocol: The cultured mouse BMDCs were randomly divided into 6 groups (1: control DCs group, 2: CpG stimulated group, 3: H9N2 stimulated group, 4: CpG/H9N2 co-stimulated group, 5: inactivated H9N2 stimulated group, 6: CpG/inactivated H9N2 co-stimulated group).

value: Dendritic cells


title: DCs stimulated with inactivated H9N2 at 12h


title: DCs co-stimulated with CpG and H9N2 at 12h


title: Chronic lymphocytic leukemia 41 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: DCs stimulated with CpG at 12h

source_name: DCs stimulated with CpG at 12h


title: control DCs 12h

source_name: control DCs at 12h


title: DCs stimulated with H9N2 at 12h

source_name: DCs stimulated with H9N2 at 12h


title: HESCs, control siRNA

city: Urbana

first: Wei

last: Wang

state: IL

address: 2001 S Lincoln Ave.

department: comparative biosciences

institute: University of Illinois

description:
HESCs control
HESCs-STAT3-1

hyb_protocol: 10 micrograms of labeled aRNA were hybridized to GeneChip Human Geneme U133 A Plus 2.0 arrays.  Washings and staining were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by the Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics, the Comparative and Functional Genomics Unit generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

source_name: HESCs_control siRNA_in vitro decidualization

label_protocol: The RNA samples were processed by Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign. Total RNA (100 nanograms) was amplified, biotin-labeled, and processed using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: The HESC were provided by Dr. Robert N. Taylor (Emory University Medical School). These cells were isolated from biopsies obtained from the proliferative stage endometria of normal cycling women and cultured in DMEM/F-12 (Invitrogen) containing 5% (v/v) fetal bovine serum (Hyclone), 50 µg/ml penicillin, and 50 µg/ml streptomycin (Invitrogen).The medium was changed every 48 h. To induce in vitro decidualization, the cells were treated with medium, containing 1 µM progesterone (Sigma), 10 nM 17ß-estradiol (Sigma) and 0.5 mM 8-bromo-adenosine-3', 5'-cyclic monophosphate (8-Br-cAMP) (Sigma).

extract_protocol: Total RNA was extracted from siRNA-treated HESC using the Qiagen RNAeasy total RNA isolation kit, according to the manufacturer's instructions.

treatment_protocol: The HESC were transfected with siRNA against C/EBPβ or STAT3 siRNA or  control scrambled siRNA (Silencer select pre-designed, Ambion) following the manufacturer’s protocol. Briefly, SilentFect transfection reagent (Bio-Rad Laboratories) was mixed with 40 nM of siRNA and added to HESC at 80% confluency. After 24h, hormone cocktail (E+P+cAMP) were added in the culture with siRNA present for next 24 h. Then siRNAs were removed and incubation with hormone cocktail continued for another 48 h.

value: human endometrial stromal cells (HESC)

tag: transfected with

value: control scrambled siRNA


title: HESCs, STAT3 siRNA

description:
HESCs STAT3 deficient
HESCs-STAT3-2

source_name: HESCs_STAT3 siRNA_in vitro decidualization

value: siRNA against STAT3


title: whole lung Fisher rat, age PN1, replicate c, in utero Saline-exposed

value: whole lung

value: I


title: HESCs, C/EBP beta siRNA, rep3

description:
HESCs C/EBP beta deficient-3
HESCs-CEBPB6

source_name: HESCs_C/EBPb siRNA_in vitro decidualization

value: siRNA against C/EBPβ


title: Chronic lymphocytic leukemia 39 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 40 paired normal

description: Hybridized to GenomeWide SNP 6.0 array

value: normal


title: Chronic lymphocytic leukemia 37 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: HESCs, Control siRNA, rep2

description:
HESCs control-2
HESCs-CEBPb3


title: HESCs, C/EBP beta siRNA, rep2

description:
HESCs C/EBP beta deficient-2
HESCs-CEBPb4


title: Chronic lymphocytic leukemia 39

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 40

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 38

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 37

description: Hybridized to GenomeWide SNP 6.0 array


title: HESCs, C/EBP beta siRNA, rep1

description:
HESCs C/EBP beta deficient-1
HESCs-CEBPb2


title: HESCs, Control siRNA, rep1

description:
HESCs control-1
HESCs-CEBPb1


title: HESCs, Control siRNA, rep3

description:
HESCs control-3
HESCs-CEBPb5


title: Chronic lymphocytic leukemia 35 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_CA09_12 [20091001_05_Hs_CA09_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: hTEC

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Microarrays were normalized at the gene level using the BrainArray custom CDF (ENST, Version 14) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization [R: 2.15.1 and Bioconductor: 2.11].

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

growth_protocol: Differentiated human airway epithelial (HAE) cultures were obtained from MatTek, Inc. These cultures consist of tracheo-bronchial tissues obtained from healthy donors which are grown in 24-well inserts at the air-liquid interface to generate well-differentiated multi-layers consisting of both ciliated and non-ciliated cells as well as mucous producing goblet cells. The cultures were maintained and subsequent assays were carried out with maintenance media (AIR100 MM, MatTek Corp, Ashland, MA, USA) at 37°C and 5% CO2.

extract_protocol: RNA was extracted from HAE cultures using Trizol (Invitrogen), analyzed for overall quality using an Agilent 2100 Bioanalyzer. mRNA was labeled using the Affymetrix WT Expression kit from Ambion in conjunction with the Affymetrix Gene Chip WT Terminal Labeling kit.. Labeled cRNA was hybridized to an Affymetrix GeneChip Human Exon ST 1.0 Arrays using standard protocols and reagents from Affymetrix. Probe intensities were measured using the Affymetrix GeneChip Scanner 3000 and processed into CEL files using Affymetrix GeneChip Operating Software.

treatment_protocol: HAE and pTEC cultures were rinsed 4 times with normal saline to remove mucous and infected with the respective viruses at an MOI of 0.01 in 140 µl of HBSS at 37°C and 5% CO2. After 1 hour of virus incubation, the inoculum was removed.

value: human trachea epithelial cells

tag: time (hours)

tag: moi


title: hTEC_CA09_12 [20091001_04_Hs_CA09_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: hTEC_Mock_12 [20091001_02_Hs_Mock_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC

value: Mock


title: Chronic lymphocytic leukemia 34 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 38 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 31 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_Mock_12 [20091001_03_Hs_Mock_InVitro__0720_____hTEC_U_SA_PA_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 32 paired normal

description: Hybridized to GenomeWide SNP 6.0 array


title: Chronic lymphocytic leukemia 36

description: Hybridized to GenomeWide SNP 6.0 array


title: hTEC_NC02_24 [20110816_Hs_NC02_InVitro__1440_____hTEC_F_S3_AD_Std_.CEL]

description: hTEC


title: Chronic lymphocytic leukemia 33

description: Hybridized to GenomeWide SNP 6.0 array