title: 2d dark-grown WT(Col-0)/1 hr red light /replicate 1

city: Albany

first: james

middle: m

last: tepperman

address: 800 Buchanan St.

institute: Plant Gene Expression Center/UC Berkeley

description: 2d dark grown WT(Col-0) seedlings/1hr Red light/replicate 1

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: BioConductor software (RMA) to normalize and correct background on all the data

source_name: whole seedling (root, hypocotyl,cotyledon)

label_protocol: standard Affymetrix procedures

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/S) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s).

extract_protocol: Total RNA was extracted from ~400 mg (fw) tissue using the method of Chang et al. (Chang, S., Puryear, J. & Cairney, J. (1993) Plant Mol. Biol. Rep. 11, 113-116) followed by further purification using Qiagen RNeasy columns.

treatment_protocol: Dark 2d 21°C followed by 1 hr Red light (7.5 μmol/m2/s)

tag: genotype

value: WT (Col-0)


title: Aged Unimpaired CA3, biological rep2

status: Public on Nov 01 2009

type: RNA

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

country: USA

institute: Johns Hopkins Univ. School of Medicine

description: Hippocampal RNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data. Sample RHab-HCA-AUCA3_12-1a_2-RAE230_2 (originally loaded in GEO as GSM367861 and since removed) was omitted from the study as a result of quality control procedures.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: RNA from CA3 region of the hippocampus: Aged Unimpaired

label_protocol: RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.

growth_protocol: Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.

extract_protocol: All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.

treatment_protocol: There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).

tag: aged (24-26 months old) cognitively unimpaired male long-evans rats (charles river laboratories, raleigh, nc) were individually housed on a 12

value: 12-hr light/dark cycle with ad libitum access to food and water.


title: sMDS19

city: Palo Alto

first: Kunju

middle: J

last: Sridhar

state: CA

address: 3801 Miranda Ave, bldg 100, Rm E4-230

department: Hematology

institute: Stanford University

description: Bone Marrow Cd34+ from MDS subjects

hyb_protocol: After labeling, 20ug COT1 human DNA (2GIBCO-BRL), 20ug tRNA (GICO-BRL) along with 20X SSC and 10% SDS were added and the probe and the mixture was denatured by heating at 100oC for 2 mins. The entire probe mixture was placed on the array and overlaid with a cover slip. The arrays were then placed in a hybridization chamber (Die tech) and hybridized overnight at 65oC. Hybridized arrays were washed in successive buffers of 2X SSC with 0.1% SDS, 1X SSC and 0.5X SSC with gentle plunging for 2 minutes in each of the wash buffer.

scan_protocol: The arrays were scanned using Axon Genepix 4000 scanner (Axon Instruments, Foster City, CA) using Genepix software (10um scan).

data_processing: Log (base 2) of the ratio of the median of Channel 2  (635 nm) to Channel 1 (532 nm), default computed normalization procedure, see SMD website

organism: Homo sapiens

source_name: RNA from 5 pooled Normal CD34+ cells

label_protocol: 3-6 ug of amplified RNA was labelled with Cy3 and Cy5 conjugated nucleotide using superscript II(Life technologies) and dN6 primers and dNTP's for 2hrs at 42oC, to make the cDNA probe. The probe was purifed using microcon YM-30 columns (Millipore, Bedford MA) with 20ug polyA RNA (Sigma).

extract_protocol: RNA was extracted using RNeasy Kit as per manufacturers instructions

tag: tissue

value: bone marrow

tag: cell type

value: Normal CD34+

source_name: RNA from MDS CD34+ cells with del(5q)

value: MDS CD34+


title: Aged Impaired CA3, biological rep4

description: Hippocampal RNA

source_name: RNA from CA3 region of the hippocampus: Aged Impaired

tag: aged (24-26 months old) cognitively impaired male long-evans rats (charles river laboratories, raleigh, nc) were individually housed on a 12


title: Aged Impaired CA3, biological rep3

description: Hippocampal RNA


title: Aged Impaired CA3, biological rep5

description: Hippocampal RNA


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/replicate 6

department: Plant and Microbial Biology

description: 2d dark grown pifq mutant seedlings/replicate 6

organism: Arabidopsis thaliana

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s). Seeds were then placed in dark (D) at 21°C for 45h (2d-old seedlings).

treatment_protocol: Dark 2d 21°C

value: pif1pif3pif4pif5 (pifq) mutant


title: sMDS20

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS21

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Impaired CA3, biological rep2

description: Hippocampal RNA


title: Young CA1, biological rep8

description: Hippocampal RNA

data_processing: All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.

source_name: RNA from CA1 region of the hippocampus: Young

tag: young (6 months old) male long-evans rats (charles river laboratories, raleigh, nc) were individually housed on a 12


title: sMDS15

description: Bone Marrow Cd34+ from MDS subjects

source_name: RNA from MDS CD34+ cells


title: Young CA1, biological rep6

description: Hippocampal RNA


title: Aged Unimpaired CA1, biological rep8

description: this array/sample was omitted from the study as a result of quality control procedures

source_name: RNA from CA1 region of the hippocampus: Aged Unimpaired


title: Young CA1, biological rep7

description: Hippocampal RNA


title: sMDS14

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS13

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Impaired CA3, biological rep1

description: Hippocampal RNA


title: Young CA1, biological rep5

description: Hippocampal RNA


title: Young CA1, biological rep4

description: Hippocampal RNA


title: sMDS11

description: Bone Marrow Cd34+ from MDS subjects


title: Young CA1, biological rep3

description: Hippocampal RNA


title: Young CA1, biological rep2

description: Hippocampal RNA


title: Aged Unimpaired CA1, biological rep7

description: Hippocampal RNA


title: sMDS10

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS9

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS12

description: Bone Marrow Cd34+ from MDS subjects


title: iPS 4 input, methyl-depleted

type: genomic

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

description: DNA methylation data from iPS cells

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

molecule: genomic DNA

source_name: Input fraction from PD-iPS5

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

growth_protocol: iPS cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 M nonessential amino acids, 100 M 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

treatment_protocol: no treatment

tag: cell line

value: iPS cells derived from PD

source_name: Methyl-depleted fraction from PD-iPS5


title: sMDS6

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS3

description: Bone Marrow Cd34+ from MDS subjects


title: Fibroblast 1 input, methyl-depleted

description: DNA methylation data from fibroblasts

source_name: Input fraction from DMD

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine.

value: GM04981 from Coriell

source_name: Methyl-depleted fraction from DMD


title: Aged Unimpaired CA1, biological rep5

description: Hippocampal RNA


title: Young CA1, biological rep1

description: Hippocampal RNA


title: sMDS8

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS7

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Unimpaired CA1, biological rep4

description: Hippocampal RNA


title: sMDS4

description: Bone Marrow Cd34+ from MDS subjects


title: sMDS2

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Unimpaired CA1, biological rep2

description: Hippocampal RNA


title: sMDS1

description: Bone Marrow Cd34+ from MDS subjects


title: Normal6

description: Bone Marrow Cd34+ from Normal

source_name: RNA from Normal CD34+ cells


title: Young CA1, biological rep9

description: Hippocampal RNA


title: sMDS5

description: Bone Marrow Cd34+ from MDS subjects


title: Aged Unimpaired CA1, biological rep1

description: Hippocampal RNA


title: Aged Unimpaired CA1, biological rep3

description: Hippocampal RNA


title: Normal4

description: Bone Marrow Cd34+ from Normal


title: Normal5

description: Bone Marrow Cd34+ from Normal


title: Aged Impaired CA1, biological rep6

description: Hippocampal RNA

source_name: RNA from CA1 region of the hippocampus: Aged Impaired


title: Aged Impaired CA1, biological rep5

description: Hippocampal RNA


title: Normal1

description: Bone Marrow Cd34+ from Normal


title: Normal2

description: Bone Marrow Cd34+ from Normal


title: Aged Impaired CA1, biological rep2

description: Hippocampal RNA


title: Aged Impaired CA1, biological rep8

description: Hippocampal RNA


title: Aged Impaired CA1, biological rep1

description: Hippocampal RNA


title: Aged Impaired CA1, biological rep3

description: Hippocampal RNA


title: Aged Impaired CA1, biological rep4

description: Hippocampal RNA


title: Normal3

description: Bone Marrow Cd34+ from Normal


title: Aged Impaired CA1, biological rep7

description: Hippocampal RNA


title: Placenta, Term spontaneous delivery, Biological Replicate #3

status: Public on Oct 31 2009

city: Shatin

first: Stephen

middle: S

last: Chim

address: Dept of Obstetrics & Gynaecology, The Chinese University of Hong Kong

department: Obstetrics & Gynaecology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: delivery location: Prince of Wales Hospital, Hong Kong; ethnicity of the pregnant women: Chinese

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The intensity data in .CEL files were analyzed using GeneSpring GX10 and normalized by the RMA method.

source_name: term spontaneous delivery (38-39 weeks)

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

growth_protocol: The placental biopsy was collected and extracted for RNA without culturing.

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

treatment_protocol: Each placental biopsy was collected, rinsed in phosphate buffered saline, and submerged into RNA later (Ambion) as soon as possible after delivery.

tag: delivery location

value: Prince of Wales Hospital, Hong Kong

tag: maternal ethnicity

value: Chinese

value: placenta

tag: developmental stage

value: term spontaneous delivery (38-39 weeks of gestation)


title: Placenta, Term spontaneous delivery, Biological Replicate #5


title: Placenta, Preterm spontaneous delivery, Biological Replicate #2

source_name: preterm spontaneous delivery (<34 weeks)

value: preterm spontaneous delivery (<34 weeks of gestation)


title: Placenta, Term spontaneous delivery, Biological Replicate #1


title: Placenta, Preterm spontaneous delivery, Biological Replicate #5


title: Placenta, Preterm spontaneous delivery, Biological Replicate #3


title: Placenta, Term spontaneous delivery, Biological Replicate #2


title: Placenta, Term spontaneous delivery, Biological Replicate #4


title: Placenta, Preterm spontaneous delivery, Biological Replicate #4


title: Duke CLL 218-02

city: Durham

first: Daphne

middle: R

last: Friedman

state: NC

address: 101 Science Drive, Room 2121, CIEMAS Bldg

institute: Duke University Medical Center

description: gene expression data from CLL lymphocytes

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: MAS5 algorithm using the statistical environment, R.  Scaling value = 500

label_protocol: Affymetrix in vitro transcription Protocol

growth_protocol: CLL lymphocytes were isolated using negative selection and stored in 10 to 15 million cell aliquots at -80C

extract_protocol: QiaShredder and Rneasy Mini Kit from Qiagen


title: Duke CLL 218-01


title: Caco2.sample3

city: Chicago

first: Christopher

middle: John

last: Ott

state: IL

address: 2430 N Halsted St. Rm C357

department: Pediatrics

institute: Northwestern University

description: DNase-chip, Caco2 cells

hyb_protocol: Sample was hybridized by Nimblegen according to their established protocol.

scan_protocol: Sample was scanned by Nimblegen according to their established protocol.

data_processing: Log2-ratio values for each feature is scaled to center at zero by subtracting bi-weight mean for all log2-ratio values from each log2-ratio value.

source_name: DNased DNA from Caco2 cells

label_protocol: Sample was labeled by Nimblegen according to their established protocol.

growth_protocol: Caco2 cells cultured in DMEM w/10% FCS

extract_protocol:
DNase-treated DNA was extracted and amplified.
Details on extract protocol:  Genomic DNA was extracted with SDS lysis buffer w/ proteinase K addition  (100mM NaCl, 10mM Tris-Cl pH8, 25mM EDTA pH8, 0.5% SDS, 0.1mg/mL proteinase  K), overnight at 37deg. Genomic DNA was then purified via phenol:choloroform  extraction and precipitated with EtOH.

treatment_protocol: Cells were lysed and nuclei digested with increasing amounts of DNase I; digested chromatin was embedded in agarose plugs, digested ends blunted and ligated to biotinylated linkers, purified with streptavidin, amplified by LM-PCR and hybridized to arrays

value: Caco2 cells

source_name: Randomly sonicated genomic DNA

treatment_protocol: genomic DNA purified via standard protocol, sonicated, ends are blunted, ligated to biotinylated linkers, purified with streptavidin and amplified via LM-PCR; material is then labelled and hybridized to arrays


title: Placenta, Preterm spontaneous delivery, Biological Replicate #1


title: Duke CLL 207-01


title: Epididymis.sample1

description: DNase-chip, Primary human epididymis cells

source_name: DNased DNA from epididymis cells

growth_protocol: Epididymis cultured in CMRL1066 media w/10% FCS

value: Primary epididymis cells from human male genital duct


title: NHBE.sample1

description: DNase-chip, Primary normal human bronchial/tracheal epithelial cells

source_name: DNased DNA from NHBE cells

growth_protocol: NHBE cells cultured in BEGM media

value: Primary normal human bronchial/tracheal cells

growth_protocol: genomic DNA purified directly from human lung tissue

value: Primary human lung cells


title: Duke CLL 203-01


title: Caco2.sample2

description: DNase-chip, Caco2 cells


title: Duke CLL 200-01


title: pHTE.sample1

description: DNase-chip, Primary human tracheal epithelial cells

source_name: DNased DNA from pHTE cells

growth_protocol: pHTE cells cultured in BEGM media

value: Primary human tracheal epithelial cells


title: Duke CLL 205-01


title: SkinFibro.sample1

description: DNase-chip, Human skin fibroblasts

source_name: DNased DNA from skin fibroblasts

growth_protocol: Skin fibroblasts cultured in MEM w/15% FCS

value: Human skin fibroblasts


title: Duke CLL 175-01


title: SkinFibro.sample2

description: DNase-chip, Human skin fibroblasts


title: NHBE.sample2


title: Duke CLL 172-01


title: Duke CLL 169-01


title: Duke CLL 129-01


title: Duke CLL 220-01


title: HT29.sample2

description: DNase-chip, HT29 cells

source_name: DNased DNA from HT29 cells

growth_protocol: HT29 cells cultured in DMEM w/10% FCS

value: HT29 cells


title: Duke CLL 152-01


title: pHTE.sample2


title: Caco2.sample1

description: DNase-chip, Caco2 cells


title: Duke CLL 132-01


title: Duke CLL 126-02


title: Duke CLL 100-01


title: Duke CLL 102-03


title: Duke CLL 102-01


title: Duke CLL 126-01


title: Duke CLL 109-01


title: Duke CLL 94-01


title: Duke CLL 73-01


title: Duke CLL 99-01


title: Duke CLL 95-01


title: Duke CLL 88-01


title: INO80 Distribution at whole chromosome level

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: INO80 binding profile after 1h in HU.

hyb_protocol: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).

scan_protocol: Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

organism: Saccharomyces cerevisiae

source_name: INO80-3XFLAG was immuno-precipitated from HU arrested Wild Type Cells

label_protocol: DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

extract_protocol: 1.5X10^8 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (Genome wide location analysis web page, MIT). Purified DNA was random primed and amplified by the protocol of Brown’s lab (Stanford). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

tag: strain

tag: antibody


title: Duke CLL 68-02


title: Mayo CLL 107

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label_protocol: Biotinylated cRNA prepared per Affymetrix standard protocol

growth_protocol: CLL lymphocytes were isolated by ficoll-hypaque gradient, and if CLL cells were not >85%, there was further purification using CD19+ magnetic beads

extract_protocol: Trizol reagent


title: Duke CLL 76-01


title: Duke CLL 85-01


title: Mayo CLL 106


title: Mayo CLL 105


title: Duke CLL 64-01


title: Duke CLL 136-01


title: Mayo CLL 104


title: Duke CLL 83-01


title: Duke CLL 56-04


title: HT29.sample1

description: DNase-chip, HT29 cells


title: Duke CLL 233-01


title: Mayo CLL 101


title: Duke CLL 224-01


title: Mayo CLL 102


title: Mayo CLL 67


title: Mayo CLL 64


title: Duke CLL 165-04


title: Duke CLL 56-03


title: Duke CLL 156-03


title: Duke CLL 154-01


title: Duke CLL 160-01


title: Mayo CLL 58


title: Mayo CLL 57


title: Duke CLL 153-02


title: e1368_5

city: St. Louis

first: C

middle: Michael

last: Crowder

state: MO

address: 660 S. Euclid Ave Campus Box 8054

department: Anesthesiology

institute: Washington University in St. Louis

description: m596_5_17.txt: Ch1 is Cy3,Ch2 is Cy5

hyb_protocol: The first hyb was done at 62C overnight (16 hours) and then second hyb was done at 50C for 3 hours. Three washes followed each hyb, the first wash was at the same temperature of the hyb, the remaining washes were done at room temperature.

scan_protocol: Scanning was done on a Perkin Elmer ScanArray 3000.

data_processing: Data were normalized using Lowess.

organism: Caenorhabditis elegans

source_name: L4 staged whole organism

label_protocol: We used Cy3/Cy5 dyes to label cDNA made from the total RNA.

growth_protocol: C. elegans were grown at 20C on standard NGM plates spotted with OP50 bacteria.

extract_protocol: Synchrounously staged L4 animals were lysed with Trizol reagent (Invitrogen) to extract total RNA.

treatment_protocol: C. elegans were washed off plates using M9 buffer into 1.5mL Eppendorf tubes, spun at 1K RPM and washed three more times with excess M9 buffer.

value: whole organism

tag: stage/age


title: Mayo CLL 60


title: e1368_4

description: m596_4_16.txt: Ch1 is Cy3,Ch2 is Cy5


title: e1368_6

description: m596_6_18.txt: Ch1 is Cy3,Ch2 is Cy5


title: Duke CLL 141-04


title: Duke CLL 134-03


title: Mayo CLL 56


title: Mayo CLL 52


title: Mayo CLL 63


title: e1370_6

description: e1368_3_15.txt: Ch1 is Cy3,Ch2 is Cy5


title: e1370_5

description: e1368_2_14.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 51


title: Mayo CLL 54


title: e1370_3

description: m596_3_12.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 50


title: Duke CLL 134-01


title: Duke CLL 133-01


title: Duke CLL 128-01


title: Mayo CLL 48


title: Mayo CLL 49


title: e1370_4

description: e1368_1_13.txt: Ch1 is Cy3,Ch2 is Cy5


title: Duke CLL 125-01


title: Duke CLL 97-01


title: Duke CLL 111-06


title: Duke CLL 106-01


title: e1370_2

description: m596_2_11.txt: Ch1 is Cy3,Ch2 is Cy5


title: e1370_1

description: m596_1_10.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 46


title: m596_6

description: m596_6_9.txt: Ch1 is Cy3,Ch2 is Cy5


title: m596_5

description: m596_5_8.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 45


title: Duke CLL 107-01


title: Duke CLL 96-01


title: Mayo CLL 47


title: e1368_2

description: e1368_2_5.txt: Ch1 is Cy3,Ch2 is Cy5


title: m596_4

description: m596_4_7.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 42


title: Duke CLL 89-04


title: Duke CLL 93-01


title: m596_2

description: m596_2_2.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 43


title: m596_3

description: m596_3_3.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 44


title: e1368_1

description: e1368_1_4.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 39


title: Duke CLL 84-01


title: m596_1

description: m596_1_1.txt: Ch1 is Cy3,Ch2 is Cy5


title: Mayo CLL 36


title: Mayo CLL 40


title: Mayo CLL 32


title: Mayo CLL 38


title: Duke CLL 81-06


title: Duke CLL 87-05


title: Duke CLL 77-01


title: Duke CLL 63-03


title: Duke CLL 52-13


title: Mayo CLL 31


title: Mayo CLL 27


title: Mayo CLL 22


title: Duke CLL 81-03


title: Duke CLL 55-11


title: Mayo CLL 21


title: Mayo CLL 25


title: Duke CLL 44-08


title: Mayo CLL 26


title: Duke CLL 50-01


title: Mayo CLL 30


title: Duke CLL 7-03


title: Mayo CLL 23


title: Duke CLL 44-05


title: Duke CLL 20-06


title: Mayo CLL 18


title: Duke CLL 30-13


title: Duke CLL 11-11


title: miRNA profiling from freshly harvested livers, T240 minutes

status: Public on Oct 30 2009

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

country: Germany

institute: University of Heidelberg

description: Evaluation of the effect of RNA degradation on miRNA expression profiling.

hyb_protocol: Labeling of total RNA for miChip v9.2 July 2009 (Mouse) hybridizations has been described in detail before (Castoldi M et al., Nature Protocol, miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes, 2008. For each sample a microarray chamber with a microarray gasket slide (Agilent technologies, cat. G2534-60005) was prepared and labeled samples are sandwiched between the microarray gasket slide and the printed arrays. The secured holders were placed into the hybridization oven (Agilent technologies, cat. G2545A), and hybridization is carried out for at least 16 h with a rotating speed of four using a hybridization temperature of 54 °C. After hybridization, arrays were washed. Microarray chambers are removed one by one from the hybridization oven. Microarray chambers are opened and the gasket slide-array sandwiches are submerged in washing buffer 1 (W1; 2 x SSC, 0.1%SDS, at room temperature), and separated using forceps. Subsequently, hybridized arrays were stored in W1 (room temperature) until all arrays have been removed from the oven and separated from the microarray gasket slides. Successively, arrays were transferred into fresh W1 (room temperature) and washed on a rocking shaker for 10 min. Then, arrays were washed once in washing buffer 2 (W2, 0.2 x SSC, at room temperature) and washing buffer 3 (W3, 0.1 x SSC, at room temperature), each time for 10 min, and once in W3 for 5 min (all washes are performed at room temperature on a shaker). Finally, arrays are rinsed in double-distilled water (room temperature) and dried by centrifugation at 1500 rpm for 2 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4200AL microarray scanner (Axon instruments). Microarray images are analyzed using Genepix Pro 6.0 software (Axon instruments).

data_processing: Array images were generated by using the Genepix 4200AL laser scanner (Auto Loader, Axon Instruments). For this purpose, miChip arrays are scanned in batches using the Genepix auto PMT (Photo Multiplayer) algorithm, with pixel saturation tolerance set to 1% following the supplier’s protocol. The tiff images generated by the Genepix 4200AL scanner were loaded into Genepix 6 microarray analysis software. Artifact-associated spots were removed by both software- and visual-guided flags. Genepix measures signal intensities according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels. miChip data analysis was performed by one of the following options: (A) using Genespring GX software (Agilent Technologies)for both data normalization and clustering or (B) using Bioconductor running the miCHIP library (v 0.5.3) for data normalization in combination with the TMeV tool for data clustering.

organism: Mus musculus

source_name: Liver from C57Bl/6 mice, T240

label_protocol:
Labeling of total RNA for miChip v9.2 July 2009 (Mouse) hybridizations has been described in detail before (Castoldi M et al., Nature Protocol, miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes, 2008).
1 µg of total RNA was aliquoted in a volume of 10 µl of RNase free water and placed on ice. To minimize variability a labeling master mix was prepared that contains 1 x T4 RNA ligase buffer (Ambion), ATP (1.3 mM, final concentration), RNase inhibitors (20 U, final amount), RNA ligase (10 U, final amount), Cy3 labeled RNA linker (5´-p-rUrUrUrU-Cy3-3´, Biospring; 6.67 lM, final concentration) and PEG (15.5%, final concentration) per reaction. 20 µl of the labeling master mix was added to the 5 µg of total RNA to yield a final volume of 30 µl. The reaction mix was then incubated for 12–16 h at 4°C. T4 RNA ligase and RNase inhibitor were heat denatured for 5 min at 95 °C and the reaction is briefly spun to collect the condensate at the bottom of the tube. Samples were stored on ice until further use. 70 µl of precipitation master mix containing sodium acetate (300 mM, final concentration) and linear acrylamide (2.5 lg, final amount) per reaction was added to each sample. To precipitate the RNA, 300 µl of 100% ethanol were added to each sample and then samples are incubated for at least one hour at -80 °C. Samples are spun for 30 min at 20,000g, 4 °C. The supernatant was discarded and pellets were washed with 1 ml of 75% ethanol and centrifuged for 5 min at 13,000 rpm at room temperature. Pellets are then briefly air-dried at room temperature. Subsequently, pellets were dissolved in 440 µl of hybridization buffer [5 x SSC, 0.1% SDS, 25% formamide and 100 µg/ml of herring sperm DNA (Promega, D181B)], denatured for 5 min at 95 °C, and centrifuged for 5 min at 13,000 rpm at room temperature.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer’s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol:
Snap frozen tissues stored form more then 1 year were removed from the freezer and
Mouse were anesthetized by using sacrificedFresh tissues were harvested from the mouse.
A total of 3 female mice on the C57BL/6J genetic background were used for this experiment. Mice were housed in the EMBL animal facility under a constant light-dark cycle, maintained on a standard mouse diet, and allowed ad libitum access to food and water. Mice were euthanized by CO2 inhalation and duodenums were immediately harvested and In order to obtain RNA of different quality tissues were cut in 5 fragments of similar size, placed into individual eppendorf tubes and stored in ice. At different time points 1 ml of Trizol (Invitrogen) was added to the sample. Tissues were immediately disrupted by using mechanical shearing (Tissuelyzer, Quiagen).

value: liver


title: miRNA profiling from freshly harvested livers, T60 minutes

source_name: Liver from C57Bl/6 mice, T60


title: miRNA profiling from freshly harvested livers, T120 minutes

source_name: Liver from C57Bl/6 mice, T120


title: Mayo CLL 19


title: miRNA profiling from freshly harvested livers, T0b

source_name: Liver from C57Bl/6 mice, T0 replica B


title: miRNA profiling from freshly harvested livers, T30 minutes

source_name: Liver from C57Bl/6 mice, T30


title: miRNA profiling from freshly harvested livers, T0a

source_name: Liver from C57Bl/6 mice, T0 replica A


title: Duke CLL 92-01


title: e1368_3

description: e1368_3_6.txt: Ch1 is Cy3,Ch2 is Cy5


title: miRNA profiling from freshly harvested duodenums, T240 minutes

data_processing: Array images were generated by using the Genepix 4200AL laser scanner (Auto Loader, Axon Instruments). For this purpose, miChip arrays are scanned in batches using the Genepix auto PMT (Photo Multiplayer) algorithm, with pixel saturation tolerance set to 1% following the supplier’s protocol. The tiff images generated by the Genepix 4200AL scanner were loaded into Genepix 6 microarray analysis software. Artifact-associated spots were removed by both software- and visual-guided flags. Genepix measures signal intensities according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels. miChip data analysis was performed by one of the following options: (A) using Genespring GX software (Agilent Technologies)for both data normalization and clustering or (B) using Bioconductor running the miCHIP library (v 0.5.3) for data normalization in combination with the TMeV tool for data clustering

source_name: Duodenum from C57Bl/6 mice, T240 minutes

treatment_protocol: A total of 3 female mice on the C57BL/6J genetic background were used for this experiment. Mice were housed in the EMBL animal facility under a constant light-dark cycle, maintained on a standard mouse diet, and allowed ad libitum access to food and water. Mice were euthanized by CO2 inhalation and duodenums were immediately harvested and In order to obtain RNA of different quality tissues were cut in 5 fragments of similar size, placed into individual eppendorf tubes and stored in ice. At different time points 1 ml of Trizol (Invitrogen) was added to the sample. Tissues were immediately disrupted by using mechanical shearing (Tissuelyzer, Quiagen).

value: duodenum


title: miRNA profiling from freshly harvested duodenums, T30 minutes

source_name: Duodenum from C57Bl/6 mice, T30 minutes


title: miRNA profiling from freshly harvested duodenums, T120 minutes

source_name: Duodenum from C57Bl/6 mice, T120 minutes


title: miRNA profiling from freshly harvested duodenums, T60 minutes

source_name: Duodenum from C57Bl/6 mice, T60 minutes


title: miRNA profiling from freshly harvested duodenums, T0

source_name: Duodenum from C57Bl/6 mice, T0 replica A


title: miRNA profiling from freshly harvested duodenums, T0b

source_name: Duodenum from C57Bl/6 mice, T0 replica B


title: rep 1 at 5% vs rep 3 at 21 %

city: MARSEILLE

first: Charles

last: Chapus

address: Allée du Médecin colonel Eugène Jamot

country: France

institute: IMTSSA

description: exposition time to oxygen conditions: 8h

hyb_protocol: Dye swap hybridization was performed for 17 h at 60°C using the In situ Hybridization Kit Plus (Agilent Technologies) following Agilent’s protocol. All processing steps were performed in an ozone-controlled environment ([O3] < 2 ppb) to avoid ozone-induced degradation of cyanine dyes on microarray slides.

scan_protocol: Slides were scanned at 5 µm resolution with a G2505B DNA microarray scanner (Agilent Technologies),

data_processing: Agilent Feature Extractor Software A.9.1.3 were used for background subtraction and LOWESS normalization

organism: Plasmodium falciparum

source_name: late ring stage

label_protocol: 300 ng of total RNA were labeled with Cy3 and Cy5 using Agilent’s instructions for two-color gene expression.

growth_protocol: The 3D7 P. falciparum strain was obtained from the Malaria Research and Reference Reagent source center (MR4). Parasitized human red blood cells (type A+) were maintained in culture in RPMI 1640 medium (Invitrogen, Paisley, United Kingdom) supplemented with 10% human serum and buffered with 25 mM HEPES (Sigma-Aldrich, St Louis, MI, USA) and 25 mM NaCO3 (Sigma) and in an atmosphere of 5% O2, 5% CO2, and 90% N2. The hematocrit was maintained at 6% and the parasitemia at 3-5%.

extract_protocol: Total RNA from parasitized erythrocytes were extracted with TRIzol reagent (Invitrogen), according to the manufacturer’s instructions. RNA extracts were treated with 1 U of RNase-free DNase I (Applied Biosystems, CA, United States of America) and quantified using a NanoDrop ND-1000 (Nanodrop Technologies, Wilmington, United States of America). The integrity of the RNA was controlled with an RNA nano chip (2100 Bioanalyzer, Agilent Biotechnologies, Wilmington, DE).

treatment_protocol: Tightly synchronized cultures (late ring stage aged between 4-9 hours), were split and submitted to two different atmospheric conditions, either under a normoxic condition (5% O2, 5% CO2, 90% N2 gas mixture), or under a hyperoxic condition (21% O2, 5% CO2, 74% N2 gas mixture) at 37°C. Culture conditions were maintained over 8 hours for transcript analysis (parasites aged between 12-17 hours). For each culture condition, three biological replicates were performed.

tag: replicate number

tag: stress

value: hyperoxia

value: normoxia (control)


title: rep 1 at 5% vs rep 3 at 21 %: dye swaped


title: rep 1 at 5% vs rep 2 at 21 %: dye swaped


title: rep 1 at 5% vs rep 2 at 21 %


title: ASD61A_Exo_2

city: Eggenstein-Leopoldshafen

first: Irina

last: Nazarenko

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genetics

institute: Karlsruhe Insitute of Technology (KIT)

description:
SAMPLE 12
replica2

hyb_protocol: Standard Illumina scanning protocol, performed in the core facility of german cancer research center (DKFZ), Hedelberg, Germany

data_processing: The data were proceeced and analysed by the corer facility of  german cancer research center (DKFZ), Hedelberg, Germany; the Raw data background (non-related probes) (71 +/-5); system noise (non-probe related signals) (12 +/-4)

source_name: Exosomes produced by AS-Tspan8 cells

label_protocol: Standard Illumina hybridization protocol, performed in the core facility of german cancer research center (DKFZ), Hedelberg, Germany

growth_protocol: Tumour cells were cultured in RPMI medium supplemented with 10% FCS and 2mM Gluthamined. For exosomes isolation cells were starved for 36 hours, and exosomes were isolated from serum-free supernatants. Endothelial cells were maintananed in EBM2 (Promocells) or MCDB131 (Invitrogen) cell culture medium supplented with 2-5% FCS and 5ng/ml VEGF.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Prior RNA isolation, endothelial cells were starved overnight, then RPMI medium supplemented with 2% FCS with or without 10 ug/ml exosomes or VEGF was added and incubated for 24 hours.

value: BDX

value: pancreas

tag: cells/exosomes

value: exosomes


title: rep 2 at 5% vs rep 3 at 21 %: dye swaped


title: rep 2 at 5% vs rep 3 at 21 %


title: AS_Exo_2

description:
SAMPLE 10
replica2

scan_protocol: The data were proceeced and analysed by the corer facility of  german cancer research center (DKFZ), Hedelberg, Germany

source_name: Exosomes produced by AS cells


title: ASD61A_Exo_1

description:
SAMPLE 11
replica1


title: AS_Exo_1

description:
SAMPLE 9
replica1


title: ASD61A

description:
SAMPLE 8
single sample

source_name: AS derivative stably expressing tetraspanin 8, Tspan8/D6.1A/CO-029

value: cells


title: MM-253_miRNA

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from multiple myeloma patient MM-253

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

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 9.5 software (Agilent Technologies) was used to obtain the microarray raw data. The human miRNAs included in the platform were annotated according to Sanger miRBase Release 12.0.

data_processing: After discarding non-human miRNAs, the data were normalized using the Aroma Light package for Bioconductor. To overcome scaling biases due to background subtraction, the data were converted to obtain positive values throughout the dataset, at a minimum value of 1.

source_name: Multiple myeloma patient MM-253

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

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

treatment_protocol: 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: disease status

value: multiple myeloma patient

tag: sex

value: F

tag: age at diagnosis (years)

tag: stage (durie-salmon)

value: nd

tag: monoclonal component

value: G

tag: tc classification

tag: related gene expression profiling (gep) data available (geo id)

tag: related genome-wide dna analysis data available (geo id)


title: AS

description:
SAMPLE 7
single sample

source_name: parental rat pancreas carcinoma cell line AS

tag: tissue


title: Breast_tumor_BLC_T15

city: Paris

first: Marc-Henri

last: Stern

address: 26 rue d'Ulm

department: Research Dept

institute: INSERM/Curie Institute

description: Genomic DNA extracted from breast tumors was genotyped using 300K Illumina SNP arrays.

hyb_protocol: Illumina standard protocoles

scan_protocol: Illumina standard protocoles

data_processing: Normalization of cell files was performed on Illumina BeadStudio version 3.1. Genotyping was performed in the Beadstudio framework by Genotyping modul, vesion 3.3.7, using standard HumanHap300v2_A.

label: C-Bio and A-DNP

source_name: Primary tumor

label_protocol: Illumina standard protocoles

extract_protocol: genomic DNA extracted from frozen tissues or cell lines with standard protocol

tag: cell type

value: Primary tumor

tag: gender

value: female

value: breast

tag: disease

value: carcinoma


title: PCL-006_miRNA

description: MicroRNA profiling data from multiple myeloma patient PCL-006

source_name: Multiple myeloma patient PCL-006

value: M

value: PCL

value: Gk

value: no


title: PCL-011_miRNA

description: MicroRNA profiling data from multiple myeloma patient PCL-011

source_name: Multiple myeloma patient PCL-011

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


title: MM-243_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-243

source_name: Multiple myeloma patient MM-243

value: Gl


title: Breast_tumor_BLC_B1_T22


title: Breast_tumor_BLC_T34


title: Breast_tumor_BLC_B1_T14


title: Breast_tumor_BLC_T09


title: Breast_tumor_L_B1_T47


title: Breast_tumor_BLC_T10


title: Breast_tumor_BLC_T31


title: Breast_tumor_BLC_T37


title: Breast_tumor_L_B1_T24B


title: MM-206_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-206

source_name: Multiple myeloma patient MM-206

value: IA


title: MM-229_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-229

source_name: Multiple myeloma patient MM-229

value: IIA


title: MM-212_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-212

source_name: Multiple myeloma patient MM-212

value: IIIA

value: Al


title: MM-179_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-179

source_name: Multiple myeloma patient MM-179

value: multiple myeloma patient

value: Ak


title: Breast_tumor_BLC_T23


title: Breast_tumor_BLC_T07


title: MM-246_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-246

source_name: Multiple myeloma patient MM-246

value: nd


title: MM-154_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-154

source_name: Multiple myeloma patient MM-154

value: F


title: MM-177_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-177

source_name: Multiple myeloma patient MM-177


title: MM-143_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-143

source_name: Multiple myeloma patient MM-143

value: l


title: Breast_tumor_BLC_B1_T20

value: Primary tumor

value: female


title: ECmitAS_Exo_2

description:
SAMPLE 4
replica2

source_name: endothelial cells cultured in the presence of AS exosomes for 24 hours

tag: strain

value: BDX

value: aorta

value: cells


title: Breast_tumor_BLC_B1_T17

value: breast

value: carcinoma


title: MM-131_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-131

source_name: Multiple myeloma patient MM-131

value: M

value: A


title: MM-123_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-123

source_name: Multiple myeloma patient MM-123

value: Gk

value: no


title: ECmitAS_Exo_1

description:
SAMPLE 3
replica1


title: 13688881 - Clv1.12_c vs WS_C

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

description: Clavata1 (Clv1.12) and clavata2 (RPL10) mutants display an increased resistance to the bacteria Ralstonia solanacearum. Transcriptome analysis aims to understand resistance mechanisms.

hyb_protocol: WS_C Cy5 / Clv1.12_c Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media : Murashige & Skoog + Vitamines Temperature : 25°C Light : 8h

tag: genotype

tag: original entry

value: arabidopsis thaliana (wassilewskija)  - age:12day

value: arabidopsis thaliana (wassilewskija)  mutant (clv1-/-) - age:12day


title: Breast_tumor_L_B1_T25A


title: MM-115_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-115

source_name: Multiple myeloma patient MM-115

value: multiple myeloma patient

value: IIIA


title: ECmitASD61A_Exo_2

description:
SAMPLE 6
replica2

source_name: endothelial cells cultured in the presence of AS-Tspan8 exosomes for 24 hours


title: Breast_tumor_BLC_B1_T19

source_name: Primary tumor


title: Breast_cancer_cell_line_MDA_468

source_name: Cell line MDA-MB-468

tag: cell line


title: MM-104_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-104

source_name: Multiple myeloma patient MM-104

value: F

value: Al


title: MM-087_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-087

source_name: Multiple myeloma patient MM-087

value: Gl


title: 13688875 - RLP10_c vs Col0_C

hyb_protocol: Col0_C Cy5 / RLP10_c Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (col-0)  - age:12day

value: arabidopsis thaliana (col-0)  mutant (clv2) - age:12day


title: 13688874 - Col0_C vs RLP10_c

hyb_protocol: RLP10_c Cy5 / Col0_C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Breast_tumor_BLC_B1_T45

description: Genomic DNA extracted from breast tumors was genotyped using 300K Illumina SNP arrays.

value: Primary tumor

value: female


title: 13688873 - RLP10_b vs Col0_B

hyb_protocol: Col0_B Cy5 / RLP10_b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688880 - WS_C vs Clv1.12_c

hyb_protocol: Clv1.12_c Cy5 / WS_C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688879 - Clv1.12_b vs WS_B

hyb_protocol: WS_B Cy5 / Clv1.12_b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: whole plant - Media : Murashige & Skoog + Vitamines Temperature : 25°C Light : 8h:


title: EC_2

description:
SAMPLE 2
replica2

source_name: endothelial cells

value: BDX

value: aorta

tag: cells/exosomes

value: cells


title: 13688876 - WS_A vs Clv1.12_a

hyb_protocol: Clv1.12_a Cy5 / WS_A Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ECmitASD61A_Exo_1

description:
SAMPLE 5
replica1


title: 13688878 - WS_B vs Clv1.12_b

hyb_protocol: Clv1.12_b Cy5 / WS_B Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: EC_1

description:
SAMPLE 1
replica1


title: MM-074_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-074

source_name: Multiple myeloma patient MM-074

tag: disease status

value: M


title: MM-069_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-069

source_name: Multiple myeloma patient MM-069

tag: sex

value: IIA

value: Gk


title: MM-067_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-067

source_name: Multiple myeloma patient MM-067

tag: age at diagnosis (years)

value: no


title: MM-052_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-052

source_name: Multiple myeloma patient MM-052

tag: stage (durie-salmon)

value: IA

value: nd


title: MM-050_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-050

source_name: Multiple myeloma patient MM-050

value: multiple myeloma patient

tag: monoclonal component


title: MM-049_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-049

source_name: Multiple myeloma patient MM-049

value: IIIB

tag: tc classification


title: 13688872 - Col0_B vs RLP10_b

hyb_protocol: RLP10_b Cy5 / Col0_B Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MM-043_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-043

source_name: Multiple myeloma patient MM-043

value: F

value: k

tag: related gene expression profiling (gep) data available (geo id)


title: MM-042_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-042

source_name: Multiple myeloma patient MM-042

value: IIIA

value: Gk + Gl

tag: related genome-wide dna analysis data available (geo id)


title: MM-040_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-040

source_name: Multiple myeloma patient MM-040

value: Gl


title: 13688870 - Col0_A vs RLP10_a

hyb_protocol: RLP10_a Cy5 / Col0_A Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (col-0)  mutant (clv2) - age:12day

value: arabidopsis thaliana (col-0)  - age:12day


title: 13688871 - RLP10_a vs Col0_A

hyb_protocol: Col0_A Cy5 / RLP10_a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MM-039_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-039

source_name: Multiple myeloma patient MM-039


title: MM-037_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-037

source_name: Multiple myeloma patient MM-037

value: II A


title: 13756852 - mpk11-2 vs wt-Col0-2

description: Gain insight into the function of mpk genes by characterizing the transcriptional profile of the mpk5, mpk10 and mpk11 KO mutants in comparison with that of the Arabidopsis wt plants.

hyb_protocol: wt-Col0-2 Cy5 / mpk11-2 Cy3 : 30pmol.

molecule: polyA RNA

growth_protocol: plantlet - Medium : MS medium + sucrose 3g/l T°: 25°C Long day

value: arabidopsis thaliana (col-0)  - dev.stage (boyes et al. plant cell 2001):boyes:1.02

value: arabidopsis thaliana (col-0)  mutant (mpk11) - dev.stage (boyes et al. plant cell 2001):boyes:1.02


title: MM-036_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-036

source_name: Multiple myeloma patient MM-036

value: M

value: IIA


title: Breast_tumor_L_B1_T30

source_name: Primary tumor

value: Primary tumor

value: female

tag: tissue

value: breast

value: carcinoma


title: 13756849 - wt-Col0-2 vs mpk11-2

hyb_protocol: mpk11-2 Cy5 / wt-Col0-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756840 - mpk10-2 vs wt-Col0-3

hyb_protocol: wt-Col0-3 Cy5 / mpk10-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (col-0)  mutant (mpk10) - dev.stage (boyes et al. plant cell 2001):boyes:1.02


title: 13756841 - wt-Col0-3 vs mpk10-2

hyb_protocol: mpk10-2 Cy5 / wt-Col0-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756828 - wt-Col0-2 vs mpk10-1

hyb_protocol: mpk10-1 Cy5 / wt-Col0-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756837 - wt-ws-3 vs mpk5-3

hyb_protocol: mpk5-3 Cy5 / wt-ws-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (wassilewskija)  mutant (mpk5) - dev.stage (boyes et al. plant cell 2001):boyes:1.02

value: arabidopsis thaliana (wassilewskija)  - dev.stage (boyes et al. plant cell 2001):boyes:1.02


title: 13756830 - mpk10-1 vs wt-Col0-2

hyb_protocol: wt-Col0-2 Cy5 / mpk10-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MM-035_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-035

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

source_name: Multiple myeloma patient MM-035

value: multiple myeloma patient

value: IA

value: nd

value: no


title: MM-038_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-038

source_name: Multiple myeloma patient MM-038

value: F

value: Gk


title: MM-034_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-034

source_name: Multiple myeloma patient MM-034


title: 13756842 - mpk5-3 vs wt-ws-3

hyb_protocol: wt-ws-3 Cy5 / mpk5-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688877 - Clv1.12_a vs WS_A

description: Clavata1 (Clv1.12) and clavata2 (RPL10) mutants display an increased resistance to the bacteria Ralstonia solanacearum. Transcriptome analysis aims to understand resistance mechanisms.

hyb_protocol: WS_A Cy5 / Clv1.12_a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (wassilewskija)  - age:12day

value: arabidopsis thaliana (wassilewskija)  mutant (clv1-/-) - age:12day


title: MM-032_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-032

source_name: Multiple myeloma patient MM-032

value: M

value: IIIB

value: Gl


title: MM-030_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-030

source_name: Multiple myeloma patient MM-030

value: IIIA

value: k


title: 13756826 - wt-ws-2 vs mpk5-2

hyb_protocol: mpk5-2 Cy5 / wt-ws-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MM-027_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-027

source_name: Multiple myeloma patient MM-027

value: Gl + Al


title: 13756839 - mpk11-3 vs wt-Col0-3

hyb_protocol: wt-Col0-3 Cy5 / mpk11-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (col-0)  - dev.stage (boyes et al. plant cell 2001):boyes:1.02

value: arabidopsis thaliana (col-0)  mutant (mpk11) - dev.stage (boyes et al. plant cell 2001):boyes:1.02


title: 13688399 - mpk11-1 vs wt-Col0-1

hyb_protocol: wt-Col0-1 Cy5 / mpk11-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688395 - wt-Col0-1 vs mpk11-1

hyb_protocol: mpk11-1 Cy5 / wt-Col0-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Breast_cancer_cell_line_MDA_175

description: Genomic DNA extracted from breast tumors was genotyped using 300K Illumina SNP arrays.

hyb_protocol: Illumina standard protocoles

source_name: Cell line MDA-MB-175

value: female

value: breast

value: carcinoma


title: 13756827 - mpk5-2 vs wt-ws-2

hyb_protocol: wt-ws-2 Cy5 / mpk5-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: arabidopsis thaliana (wassilewskija)  - dev.stage (boyes et al. plant cell 2001):boyes:1.02

value: arabidopsis thaliana (wassilewskija)  mutant (mpk5) - dev.stage (boyes et al. plant cell 2001):boyes:1.02


title: Breast_tumor_BLC_T12

tag: cell type

value: Primary tumor


title: 13688131 - mpk5-1 vs wt-ws-1

hyb_protocol: wt-ws-1 Cy5 / mpk5-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697201 - wt-Col0-3 vs mpk11-3

hyb_protocol: mpk11-3 Cy5 / wt-Col0-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MM-026_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-026

source_name: Multiple myeloma patient MM-026

value: multiple myeloma patient

value: F

value: Gk + Ak

value: no


title: MM-016_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-016

source_name: Multiple myeloma patient MM-016

value: M

value: IIIB


title: MM-015_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-015

source_name: Multiple myeloma patient MM-015

value: II A

value: Gk


title: MM-025_miRNA

description: MicroRNA profiling data from multiple myeloma patient MM-025

source_name: Multiple myeloma patient MM-025

value: IA

value: Gl


title: CD138+_T5_miRNA

description: MicroRNA profiling data from normal donor

source_name: Human normal donor CD138+_T5

value: normal donor


title: CD138+_T4_miRNA

source_name: Human normal donor CD138+_T4


title: CD138+_T6_miRNA

source_name: Human normal donor CD138+_T6


title: 13688128 - wt-ws-1 vs mpk5-1

hyb_protocol: mpk5-1 Cy5 / wt-ws-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756838 - BB vs wt-Col0

hyb_protocol: wt-Col0 Cy5 / BB Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: plantlet - 1/2 MS agar medium,22°C, longday

value: arabidopsis thaliana (col-0)  mutant (bak1-4/bkk1) - age:2weekdev.stage (Boyes et al. Plant Cell 2001):boyes:1.03

value: wild type

tag: developmental stage

value: boyes 1.03

tag: age

value: 2 week

source_name: BB

value: bak1-4/bkk1 mutant


title: 13756843 - wt-Col0 vs BB

hyb_protocol: BB Cy5 / wt-Col0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Maxillary prominence, biological rep2

city: Vancouver

first: Joy

last: Richman

state: BC

address: 2350 Health Sciences Mall

department: Oral Health Sciences

country: Canada

institute: University of British Columbia

description: Gene expression data from stage 18 maxillary prominences

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis Technical Manual by the London Regional Genomics Centre, London, Ontario, Canada

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000

data_processing: The data were analyzed with GCOS1.4  using Affymetrix default analysis settings and Scaling within 3 fold of each other as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Gallus gallus

source_name: Stage 18 chicken embryos

label_protocol: Biotinylated cRNA were prepared according to two-cycle Affymetrix protocol from 500 ng total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Embryos were incubated at 38 degrees C until they reached Hamburger Hamilton Stage 18

extract_protocol: Qiagen RNAeasy kit was used.

treatment_protocol: No treatment was done to the embryos. These are normal tissues.

value: Mesenchyme plus epithelium

value: Unknown

value: Hamburger Hamilton stage 18


title: Frontonasal mass prominence, biological rep2

description: Gene expression data from stage 18 frontonasal mass prominences, between the nasal pits


title: Frontonasal mass prominence, biological rep1


title: Mandibular prominence, biological rep3

description: Gene expression data from stage 18 mandibular prominences


title: Maxillary prominence, biological rep3


title: Maxillary prominence, biological rep1