title: 996-L-8hr-2

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road, Furong District

institute: Hunan Agricultural University

description: Gene expression of rice spikelets of developmental stage7-9, 8hr after 40 degree centigrade

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

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

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

organism: Oryza sativa

source_name: rice flag leaf at reproductive stage, 8hr after 40 degree centigrade, replicate 2

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

growth_protocol: Heat-tolerant rice cultivar 996 was cultivated in the field until reproductive stage

extract_protocol: Middle part of rice flag leaves was collected at the time point of 0 min (as control), 20 min, 1 hr, 2 hr, 4 hr, and 8 hr, respectively, after heat treatment, and frozen in liquid nitrogen immediately, and stored at -80°C for microarray hybridization.

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

tag: cultivar

tag: tissue

value: middle part of rice flag leaf at reproductive stage


title: Pt17_before_drug

status: Public on Sep 10 2013

type: RNA

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression sample from Patient 17 before drug

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the Illumina BeadStation 500x manual. Essentially the amplified, biotin-labeled human cRNA samples were resuspended in a solution of Hyb E1 buffer (Illumina) and 25% (v/v) formamide at a final concentration of 25 ng/µL. 1.5 µg of each cRNA were hybridized.

scan_protocol: The arrays were scanned on the Illumina BeadArray Reader.

data_processing: The data were log2 transformed, normalised using robust spline normalisation (rsn) with Bioconductor package lumi in R and adjusted for batch effect using ComBat (http://statistics.byu.edu/johnson/ComBat/Usage.html).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit, Catalog #1L1791 (Ambion, Inc., Austin, TX) according to the manufacturer's directions starting with ~250 ng total RNA. mRNA was converted to cDNA, followed by an amplification/labeling step mediated by T7 DNA polymerase. The cDNA and cRNA filter cartridges (Ambion) were used according to the manufacturer's instructions for RT and IVT cleanup, respectively.

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 2100 Bioanalyzer.

tag: Sex

value: Male

tag: age

value: 33 years

tag: ethnicity

value: White

tag: drug regimen

value: PI

tag: cd4+ t cell count measurement

value: baseline

tag: cd4+ t cell count, cells/ul

tag: batch

tag: reanalysis

value: re-analysis of GSM477711

tag: sdf file

tag: analysis

value: Patient included in analysis

tag: subject

tag: treatment


title: BPA-Series6-1000 nM

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

country: USA

institute: MGH Cancer Center

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 200 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip Human U133 version 2 plu (GPL570) sarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (protocol FS450_0001).

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

data_processing: The data were analyzed with Affymetrix GeneChip Command Console (AGCC).  affymetrix-algorithm-name = rma-gene-default  affymetrix-algorithm-version = 1.0  program-name = Expression Console

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: MCF-7 cells were grown in DMEM supplemented with 5% FCS, 2 mM glutamine, and 1X Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted directly from cell cultures grown on 10 cm dishes using QIAGEN RNeasy kit.

treatment_protocol: Subconfluent MCF-7 cells in 10 cm dishes were exposed to varying concentrations of xenoestrogen chemicals for exactly 48 hours and subjected to immediate isolation of total RNA. Xenoestrogen chemicals tested in this study were Bisphenol A, Diethylstilbestrol, 17alpha-ethynylestradiol, p-nonylphenol, genistein, and daidzein. Transcriptomal effects of physiological estrogen 17beta-estradiol was also examined.

tag: xenoestrogen

value: Bisphenol A

tag: series

tag: molar concentration

tag: cell line


title: Pt18_before_drug

description: Gene expression sample from Patient 18 before drug

value: 24 years

value: American Indian

value: re-analysis of GSM477712


title: BPA-Series6-125 nM


title: BPA-Series6-15.6 nM


title: 996-L-2hr-2

country: China

description: Gene expression of rice spikelets of developmental stage7-9, 2hr after 40 degree centigrade

source_name: rice flag leaf at reproductive stage, 2hr after 40 degree centigrade, replicate 2

tag: cultivar

tag: tissue


title: BPA-Series6-500 nM


title: Pt15_before_drug

description: Gene expression sample from Patient 15 before drug

tag: Sex

tag: age

value: 58 years

value: re-analysis of GSM477709

value: Patient dropped from analysis


title: 996-L-4hr-2

description: Gene expression of rice spikelets of developmental stage7-9, 4hr after 40 degree centigrade

source_name: rice flag leaf at reproductive stage, 4hr after 40 degree centigrade, replicate 2


title: 996-L-8hr-1

source_name: rice flag leaf at reproductive stage, 8hr after 40 degree centigrade, replicate 1


title: BPA-Series6-250 nM


title: 996-L-2hr-1

source_name: rice flag leaf at reproductive stage, 2hr after 40 degree centigrade, replicate 1


title: 996-L-4hr-1

source_name: rice flag leaf at reproductive stage, 4hr after 40 degree centigrade, replicate 1


title: BPA-Series6-control


title: BPA-Series5-4 uM


title: BPA-Series5-2 uM


title: BPA-Series2-62.5 pM


title: Pt11_before_drug

description: Gene expression sample from Patient 11 before drug

value: 28 years

tag: ethnicity

tag: drug regimen

value: NNRTI

value: re-analysis of GSM477705


title: BPA-Series5-62.5 nM


title: Pt14_before_drug

description: Gene expression sample from Patient 14 before drug

value: Male

value: 50 years

tag: cd4+ t cell count measurement

tag: cd4+ t cell count, cells/ul

value: re-analysis of GSM477708


title: BPA-Series5-1000 nM


title: 996-L-1hr-2

description: Gene expression of rice spikelets of developmental stage7-9, 1hr after 40 degree centigrade

source_name: rice flag leaf at reproductive stage, 1hr after 40 degree centigrade, replicate 2

value: middle part of rice flag leaf at reproductive stage


title: Pt10_before_drug

description: Gene expression sample from Patient 10 before drug

value: 33 years

value: Asian

value: baseline

tag: batch

tag: reanalysis

value: re-analysis of GSM477704


title: 996-L-20min-1

description: Gene expression of rice spikelets of developmental stage7-9, 20min after 40 degree centigrade

source_name: rice flag leaf at reproductive stage, 20min after 40 degree centigrade, replicate 1


title: 996-L-20min-2

source_name: rice flag leaf at reproductive stage, 20min after 40 degree centigrade, replicate 2


title: BPA-Series5-125 nM

value: Bisphenol A


title: BPA-Series4-62.5 nM


title: BPA-Series5-500 nM


title: Pt22_before_drug

description: Gene expression sample from Patient 22 before drug

value: 37 years

value: PI

value: re-analysis of GSM477716

tag: sdf file

tag: analysis

value: Patient included in analysis


title: BPA-Series5-250 nM


title: Pt13_before_drug

description: Gene expression sample from Patient 13 before drug

value: 29 years

value: White

value: re-analysis of GSM477707

value: Patient dropped from analysis

tag: subject

tag: treatment


title: BPA-Series5-15.6 nM

tag: xenoestrogen

tag: series


title: BPA-Series5-8 uM

tag: molar concentration

tag: cell line


title: 996-L-1hr-1

source_name: rice flag leaf at reproductive stage, 1hr after 40 degree centigrade, replicate 1

tag: cultivar

tag: tissue


title: Pt12_before_drug

description: Gene expression sample from Patient 12 before drug

tag: Sex

value: Male

tag: age

value: 19 years

value: NNRTI

value: re-analysis of GSM477706


title: Pt9_before_drug

description: Gene expression sample from Patient 9 before drug

value: 28 years

tag: ethnicity

tag: drug regimen

value: re-analysis of GSM477703


title: BPA-Series5-control


title: BPA-Series4-50 uM


title: 996-L-ck-2

description: Gene expression of rice spikelets of developmental stage7-9, 0min after 40 degree centigrade

source_name: rice flag leaf at reproductive stage, 0min after 40 degree centigrade, replicate 2

value: middle part of rice flag leaf at reproductive stage


title: 996-L-ck-1

source_name: rice flag leaf at reproductive stage, 0min after 40 degree centigrade, replicate 1


title: BPA-Series4-250 nM


title: BPA-Series4-15.6 nM


title: BPA-Series4-12.5 uM


title: Pt6_before_drug

description: Gene expression sample from Patient 6 before drug

value: 42 years

tag: cd4+ t cell count measurement

value: baseline

tag: cd4+ t cell count, cells/ul

value: re-analysis of GSM477700


title: BPA-Series4-25 uM

value: Bisphenol A


title: Pt7_before_drug

description: Gene expression sample from Patient 7 before drug

value: 24 years

value: African American

tag: batch

tag: reanalysis

value: re-analysis of GSM477701


title: Pt4_before_drug

description: Gene expression sample from Patient 4 before drug

value: 38 years

value: White

value: re-analysis of GSM477698

tag: sdf file

tag: analysis

value: Patient included in analysis


title: Pt8_before_drug

description: Gene expression sample from Patient 8 before drug

value: Male

value: re-analysis of GSM477702

tag: subject

tag: treatment


title: Pt3_before_drug

description: Gene expression sample from Patient 3 before drug

value: 39 years

value: American Indian

value: NNRTI

value: re-analysis of GSM477697


title: BPA-Series4-100 uM

description: RMA expression value derived from Expression Console software; core-exon analysis

tag: xenoestrogen

tag: series


title: Pt27_before_drug

description: Gene expression sample from Patient 27 before drug

value: 49 years

value: Switchers

value: New analysis


title: Pt2_before_drug

description: Gene expression sample from Patient 2 before drug

value: 36 years

value: baseline

value: re-analysis of GSM477696


title: Pt5_before_drug

description: Gene expression sample from Patient 5 before drug

value: 52 years

value: re-analysis of GSM477699


title: BPA-Series4-control

value: Bisphenol A

tag: molar concentration

tag: cell line


title: BPA-Series4-1000 nM


title: Pt31_before_drug

description: Gene expression sample from Patient 31 before drug

value: 42 years

value: White


title: Saline control 3

city: Little Rock

first: Shmuel

last: Yaccoby

state: AR

address: 4301 W Markham, Slot 776

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciences

description: Microarray data of myeloma-bearing human bone from SCID-mouse treated with saline

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Huamn Genome 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 data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: myeloma-bearing SCID-hu mouse treated with saline

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

growth_protocol: SCID-hu mice were constructed as reported (Yaccoby et al., Blood 1998;1999). The human myeloma cell line, Hg, was engrafted in SCID-hu mice by direct injection of myeloma cells into the implanted human bone in SCID-hu mice.

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

treatment_protocol: Myeloma-bearing SCID-hu mice were treated with saline or intermittent PTH for 4 weeks.

tag: tissue

value: myeloma-bearing human bone from cell line Hg

value: saline


title: Pt1_before_drug

description: Gene expression sample from Patient 1 before drug

tag: Sex

value: Male

value: 31 years

value: re-analysis of GSM477695

value: Patient included in analysis


title: Intermittent PTH 5

description: Microarray data of myeloma-bearing human bone from SCID-mouse treated with intermittent PTH

source_name: myeloma-bearing SCID-hu mouse treated with intermittent PTH

value: PTH


title: Intermittent PTH 2


title: Saline control 4


title: Intermittent PTH 1


title: CD14 Fixed 24hr Donor 2 Rep 2

status: Public on Sep 09 2013

city: Baltimore

first: Lucio

last: Gama

state: MD - EUA

address: 733 N Broadway St - BRB 831

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins School of Medicine

description: CD14+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 2 replicate 2

hyb_protocol: Samples were hybridized according to NanoString Technologies' protocol.

scan_protocol: Samples were scanned according to NanoString Technologies' protocol.

data_processing: Normalization was performed by multiplying each sample by a normalization factor obtained for that sample. The normalization factor was calculated by first summing the positive control counts for each sample in a given run. The average of the positive control sums for a given run was then obtained and this average was divided by the positive control sum of each sample in that run to obtain the normalization factor for that sample. Each count value (including negative control counts) was multiplied by the normalization factor calculated for a given sample. For background subtraction, the highest negative control count value of a given sample was subtracted from the normalized counts of that sample. If a normalized sample count was negative following background subtraction, then it was considered to be zero. Counts per 100 ng of RNA were then obtained using the total RNA loaded for each sample. The data in the sheet labeled Matrix - Normalized Data represent normalized data with background subtraction and values represent counts per 100 ng of RNA. For sorted cells, genes were removed from the analysis if any sample had a zero value for that gene unless 100 ng of RNA were loaded for all samples with a zero value. *Samples were not used in our analysis, but were used in the normalization process since they were included in the same run as other samples used in the analysis.

source_name: CD14+ cells sorted from human PBMCs

label_protocol: The nCounter Human Reference GX Kit Gene Expression CodeSet (NanoString Technologies, Seattle, WA, USA) was used. Samples were labeled according to NanoString Technologies' protocol.

growth_protocol: Cell lines were cultured in RPMI containing 10% FBS, 2 mM L-glutamine, 1 mM HEPES and 2 mg/ml gentamicin. Human PBMCs were isolated from whole blood using a Ficoll-Paque (GE Healthcare, Pittsburgh, PA, USA) gradient following the manufacturer's protocol.

extract_protocol: Total RNA was extracted from unfixed cells using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol. Total RNA was extracted from fixed cells using the RNeasy FFPE Kit (Qiagen) and the RNeasy Plus Mini Kit (Qiagen) according to modified manufacturers' protocols. See publication for details.

treatment_protocol: Two types of experiments were performed. In the first experiment, K562 and CEMx174 cell lines as well as human PBMCs were split into two groups, unfixed and fixed. The unfixed group was kept on ice while the fixed group was treated with BD FACS Lysing Solution (BD Bioscience, San Jose, CA, USA) at 1X concentration for 10 minutes. RNA extraction was performed directly following the fixation process. Three biological replicates were performed for each cell type. In the second experiment, human PBMCs were stained with anti-CD3 (PE; clone SP34; BD Bioscience) and anti-CD14 (FITC; clone M5E2; BD Bioscience) for 20 minutes and then half of the cells were kept on ice while the remaining cells were fixed as previously described. Cells were sorted on a BDFACSAria II cytometer. A group of fixed cells from the same PBMC sample was incubated overnight at 4°C and then sorted as described above. RNA was extracted from sorted cells immediately following the sorting process. This experiment was performed using PBMCs from two donors and two technical replicates were performed for each donor sample.

tag: run number

tag: fixed

value: yes

tag: total rna loaded (ng)

tag: sorted


title: CD3 Fixed 24hr Donor 2 Rep 2

description: CD3+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 2 replicate 2

label: nCounter Human Reference GX Kit Gene Expression CodeSet

source_name: CD3+ cells sorted from human PBMCs


title: Saline control 1


title: CD14 Fixed 24hr Donor 2 Rep 1

description: CD14+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 2 replicate 1


title: Intermittent PTH 3


title: 529591A09 - F_1 vs BF_1

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: A comparative assessment of the Arabidopsis sequencing approach High-throughput sequencing cDNA GAII or HiSeq2000 sequenceur (technology Solexa) and data on CATMA array hybridation (version 6). These different characteristics will be studied through the analysis of control samples but also samples from mutants in genes coding for cytosolic or nuclear PPR proteins

hyb_protocol: BF_1 Cy5 / F_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: flower bud - in soil, greenhouse

extract_protocol: BF_1:15ug. (miRVana_manuel.pdf)

treatment_protocol: no treatment

tag: ecotype

tag: harvest date

value: flower bud

growth_protocol: aerial - in soil, greenhouse

extract_protocol: F_1:20ug. (miRVana_manuel.pdf)

value: leaves


title: Saline control 5


title: 529591A12 - BF_1 vs F_1

hyb_protocol: F_1 Cy5 / BF_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Saline control 2


title: CD14 Fixed Donor 2 Rep 2

description: CD14+ cells sorted from fixed human PBMCs by FACS; donor 2 replicate 2


title: CD14 Unfixed Donor 2 Rep 2

description: CD14+ cells sorted from unfixed human PBMCs by FACS; donor 2 replicate 2

value: no


title: CD3 Fixed Donor 2 Rep 1

description: CD3+ cells sorted from fixed human PBMCs by FACS; donor 2 replicate 1


title: CD14 Unfixed Donor 2 Rep 1

description: CD14+ cells sorted from unfixed human PBMCs by FACS; donor 2 replicate 1


title: 528995A12 - F_3 vs BF_3

hyb_protocol: BF_3 Cy5 / F_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

extract_protocol: BF_3:16ug. (miRVana_manuel.pdf)

extract_protocol: F_3:16ug. (miRVana_manuel.pdf)


title: CD3 Unfixed Donor 2 Rep 1

description: CD3+ cells sorted from unfixed human PBMCs by FACS; donor 2 replicate 1


title: CD3 Fixed Donor 2 Rep 2

description: CD3+ cells sorted from fixed human PBMCs by FACS; donor 2 replicate 2


title: CD14 Fixed Donor 2 Rep 1

description: CD14+ cells sorted from fixed human PBMCs by FACS; donor 2 replicate 1


title: Intermittent PTH 4


title: CD14 Fixed 24hr Donor 1 Rep 2

description: CD14+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 1 replicate 2


title: CD3 Fixed 24hr Donor 1 Rep 1

description: CD3+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 1 replicate 1


title: CD14 Fixed 24hr Donor 1 Rep 1

description: CD14+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 1 replicate 1


title: CD3 Fixed 24hr Donor 1 Rep 2

description: CD3+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 1 replicate 2


title: LNA-antimir-146a + LPS vs LNA-control + LPS

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Biological replicate 1 of 1.  25 nM LNA-antimiR-146a 24 h + 1 ug/mL LPS 24 h vs  25 nM LNA-control 24 h + 1 ug/mL LPS 24 h

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Whole Human Genome 4x44k oligo microarray (Agilent Technologies) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: HUVEC

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies) and labeled with Cy3-CTP or Cy5-CTP (PerkinElmer, Waltham, MA) during the in vitro transcription process. RNA from the experimental groups and control group was labeled by Cy5 and Cy3, respectively. A total of 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies) at 60oC for 30 minutes.

growth_protocol: HUVEC were obtained from the Bioresource Collection and Research Center (BCRC), Taiwan and cultured in 90% Medium 199 with 50 U/ml of penicillin (Invitrogen, San Diego, CA), 50 U/ml of streptomycin (Invitrogen), and 50 /ml endothelial cell growth supplement (ECGS) (Upstate, temecula, CA) adjusted to contain 2.2 g/L sodium bicarbonate and 10% fetal bovine serum (FBS) (Gibio, Grand Island, NY). All the cells were incubated at 37 °C in a humidified atmosphere containing 5% CO2. HUVEC were seeded onto 6-cm or 10-cm dishes for treatment with LPS (Catalog No. L3755, Sigma, St Louis, MO) in subsequent experiments. All groups of experiment were performed in sextuplicate in this study, if not indicated other where. The experiments on the cultured cells and subsequent analysis below were done in a blinded way.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen), and followed by RNeasy Mini Kit (Qiagen, Germantown, MD). Samples of purified RNAs were evaluated for quantity by absorbance at 260 nm using an SSP-3000 Nanodrop spectrophotometer (Infinigen Biotechnology, Inc., City of Industry, CA) and for quality using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). The miR-146a cDNA (10 ng) was obtained using TaqMan miRNA Reverse Transcription Kit (Applied Biosystems, Caralsbad, CA) with miRNA being reverse transcribed to hsa-miR-146a using sequence-specific stem-loop primers for quantitative real-time polymerase chain reaction (qRT-PCR) experiment.

treatment_protocol: Knockdown of miR-146a was performed by adding the locked nucleic acid (LNA)-antimiR-146a (Exiqon, Vedbaek, Denmark) against those with LNA-control (Exiqon). The LNA-antimiR-146a molecules were synthesized as unconjugated and fully phosphorothioated mixed LNA/DNA oligonucleotides specific for knocking down hsa-miR-146a. LNA-control was designed with mismatch oligonucleotides for the seed region of known miRNAs to eliminate the interference factors during silencing. HUVEC in 1×106 cells were seeded in 6-cm plates. The effective concentration of LNA-antimiR-146a and LNA-control was determined within the concentration ranged from 1 to 25 nM for 24 h. A level of miR-146a was measured using the qRT-PCR. In addition, experiment with LNA-antimiR-146a was designed to evaluate the effect of miR-146a knockdown on cell proliferation, migration, and tube formation of HUVEC as well as to find the target genes by using a combined approach involving computational prediction and a whole genome microarray experiment described below.

value: 25 nM LNA-antimiR-146a 24 h + 1 ug/ml LPS 24h

value: 25 nM LNA-control 24 h + 1 ug/ml LPS 24h


title: 528995A11 - BF_3 vs F_3

hyb_protocol: F_3 Cy5 / BF_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: CD14 Unfixed Donor 1 Rep 2

description: CD14+ cells sorted from unfixed human PBMCs by FACS; donor 1 replicate 2


title: CD3 Unfixed Donor 2 Rep 2

description: CD3+ cells sorted from unfixed human PBMCs by FACS; donor 2 replicate 2


title: CD14 Fixed Donor 1 Rep 2

description: CD14+ cells sorted from fixed human PBMCs by FACS; donor 1 replicate 2


title: CD14 Fixed Donor 1 Rep 1

description: CD14+ cells sorted from fixed human PBMCs by FACS; donor 1 replicate 1


title: CD3 Fixed Donor 1 Rep 2

description: CD3+ cells sorted from fixed human PBMCs by FACS; donor 1 replicate 2


title: BPA-Series2-control

description: RMA expression value derived from Expression Console software; core-exon analysis


title: LPS vs control

description: Biological replicate 1 of 1. 1 ug/mL LPS 24 h vs medium treatment only 24 h

value: 1 ug/ml LPS 24 h

value: control (medium treatment only)


title: CD3 Fixed Donor 1 Rep 1

description: CD3+ cells sorted from fixed human PBMCs by FACS; donor 1 replicate 1


title: PBMC Fixed 3

description: PBMCs fixed replicate 3

source_name: PBMCs


title: CD3 Unfixed Donor 1 Rep 2

description: CD3+ cells sorted from unfixed human PBMCs by FACS; donor 1 replicate 2


title: CD14 Unfixed Donor 1 Rep 1

description: CD14+ cells sorted from unfixed human PBMCs by FACS; donor 1 replicate 1


title: PBMC Unfixed 3

description: PBMCs unfixed replicate 3


title: PBMC 4 (Sample not used)*

description: SAMPLE NOT USED


title: PBMC Fixed 1

description: PBMCs fixed replicate 1


title: PBMC 3 (Sample not used)*

description: PBMC sample was not used in our analysis, but was used in normalization process since it was included in the same run as other samples.


title: PBMC Unfixed 2

description: PBMCs unfixed replicate 2


title: PBMC 2 (Sample not used)*


title: K562 Unfixed 3

description: K562 unfixed replicate 3

source_name: K562 cell line


title: K562 Fixed 3


title: CEM Fixed 3

description: CEMx174 fixed replicate 3

source_name: CEMx174 cell line


title: CEM Unfixed 3

description: CEMx174 unfixed replicate 3


title: PBMC Unfixed 1

description: PBMCs unfixed replicate 1


title: CEM Fixed 2

description: CEMx174 fixed replicate 2


title: CD3 Unfixed Donor 1 Rep 1

description: CD3+ cells sorted from unfixed human PBMCs by FACS; donor 1 replicate 1


title: PBMC 1 (Sample not used)*


title: CEM Unfixed 2

description: CEMx174 unfixed replciate 2


title: CEM Unfixed 1

description: CEMx174 unfixed replicate 1


title: CEM Fixed 1

description: CEMx174 fixed replicate 1


title: K562 Fixed 2

description: K562 fixed replciate 2


title: K562 Unfixed 2

description: K562 unfixed replicate 2


title: K562 Fixed 1

description: K562 fixed replicate 1


title: Genes expression in T cells

city: He fei

first: yan

middle: fu

last: Wang

address: 443 huangshan road

institute: University of Science and Technology of China

description: Gene expression in T cells

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 44K Human Whole Genome microarays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel Greenis set to Green)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood T cells

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

extract_protocol: Total RNA was extracted from each sample using Trizol (Qiagen) according to the manufacturer's protocol. RNA was then further purified using RNeasy mini spin columns (Qiagen).

treatment_protocol: CD56+CD3- NK cells from normal decidua,cord blood,and CD56+CD3- NK cells, CD56+T and T cells  from peripheral blood have been sorted by FACS Aria.

value: Peripheral blood

tag: cell type

value: CD56-CD3+ T cells


title: K562 Unfixed 1

description: K562 unfixed replicate 1


title: CH3HgCl_7.5uM_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Gene expression at 24hr after 7.5uM CH3HgCl treatment
US22502532_251506110335_S01_H.tif
US22502532_251506110335_S01_L.tif

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

data_processing: Slides were washed and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Caenorhabditis elegans

source_name: 7.5 uM CH3HgCl

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Forty L4 stage N2 nematodes were placed on K-agar plates and allowed to grow for 4 days at 20°C.  All nematodes were then transferred into a flask containing complete S-medium  with OP50 and were grown in a 200 rpm shaker for 4 days at 20°C.

extract_protocol: Nematodes were then rinsed in 0.1M NaCl and living nematodes were isolated by sucrose floatation, frozen in liquid nitrogen and stored at -80°C.  Nematodes were ground with a liquid nitrogen-cooled mortar and pestle, and total RNA was isolated using the RNeasy Midi Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: Fifty mL aliquots of the mixed-stage C. elegans population were treated to sub- (2 µM HgCl2, 0.75 µM MeHgCl), low- (7.5 µM HgCl2, 2 µM MeHgCl) or high- (20 µM HgCl2, 7.5 µM MeHgCl) toxic mercurial concentrations for 24 hours in a 200 rpm shaker at 20°C.

tag: developmental stage

value: Mixed-stage

tag: exposure level

value: high-toxic

tag: exposure time


title: CH3HgCl_2uM_rep3

description:
Gene expression at 24hr after 2uM CH3HgCl treatment
US22502532_251506110336_S01_H.tif
US22502532_251506110336_S01_L.tif

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

source_name: 2 uM CH3HgCl

value: low-toxic


title: CH3HgCl_2uM_rep1

description:
Gene expression at 24hr after 2uM CH3HgCl treatment
US22502532_251506110333_S01_H.tif
US22502532_251506110333_S01_L.tif


title: CH3HgCl_0.75uM_rep2

description:
Gene expression at 24hr after 0.75uM CH3HgCl treatment
US22502532_251506110334_S01_H.tif
US22502532_251506110334_S01_L.tif

source_name: 0.75 uM CH3HgCl

value: sub-toxic


title: Genes expression in CD56+T cells

description: Gene expression in CD56+T cells

source_name: Peripheral blood CD56+T cells

value: CD56+CD3+ T cells


title: CH3HgCl_7.5uM_rep1

description:
Gene expression at 24hr after 7.5uM CH3HgCl treatment
US22502532_251506110333_S01_H.tif
US22502532_251506110333_S01_L.tif


title: CH3HgCl_2uM_rep2

description:
Gene expression at 24hr after 2uM CH3HgCl treatment
US22502532_251506110334_S01_H.tif
US22502532_251506110334_S01_L.tif


title: CH3HgCl_0.75uM_rep3

description:
Gene expression at 24hr after 0.75uM CH3HgCl treatment
US22502532_251506110336_S01_H.tif
US22502532_251506110336_S01_L.tif


title: CH3HgCl_7.5uM_rep2

description:
Gene expression at 24hr after 7.5uM CH3HgCl treatment
US22502532_251506110334_S01_H.tif
US22502532_251506110334_S01_L.tif


title: CH3HgCl_0.75uM_rep1

description:
Gene expression at 24hr after 0.75uM CH3HgCl treatment
US22502532_251506110333_S01_H.tif
US22502532_251506110333_S01_L.tif


title: CH3HgCl_0_rep2

description:
Gene expression at 24hr after 0uM CH3HgCl treatment
US22502532_251506110334_S01_H.tif
US22502532_251506110334_S01_L.tif

source_name: CH3HgCl untreated

value: untreated


title: CH3HgCl_0_rep3

description:
Gene expression at 24hr after 0uM CH3HgCl treatment
US22502532_251506110336_S01_H.tif
US22502532_251506110336_S01_L.tif


title: HgCl2_20uM_rep2

description:
Gene expression at 24hr after 20uM  HgCl2 treatment
US22502532_251506110175_S01_H.tif
US22502532_251506110175_S01_L.tif

source_name: 20 uM HgCl2


title: HgCl2_20uM_rep3

description:
Gene expression at 24hr after 20uM  HgCl2 treatment
US22502532_251506110270_S01_H.tif
US22502532_251506110270_S01_L.tif


title: CH3HgCl_0_rep1

description:
Gene expression at 24hr after 0uM CH3HgCl treatment
US22502532_251506110333_S01_H.tif
US22502532_251506110333_S01_L.tif


title: HgCl2_7.5uM_rep3

description:
Gene expression at 24hr after 7.5uM  HgCl2 treatment
US22502532_251506110177_S01_H.tif
US22502532_251506110177_S01_L.tif

source_name: 7.5 uM HgCl2


title: HgCl2_20uM_rep1

description:
Gene expression at 24hr after 20uM  HgCl2 treatment
US22502532_251506110173_S01_H.tif
US22502532_251506110173_S01_L.tif


title: HgCl2_2uM_rep3

description:
Gene expression at 24hr after 2uM  HgCl2 treatment
US22502532_251506110176_S01_H.tif
US22502532_251506110176_S01_L.tif

source_name: 2 uM HgCl2


title: HgCl2_7.5uM_rep2

description:
Gene expression at 24hr after 7.5uM  HgCl2 treatment
US22502532_251506110175_S01_H.tif
US22502532_251506110175_S01_L.tif


title: HgCl2_7.5uM_rep1

description:
Gene expression at 24hr after 7.5uM  HgCl2 treatment
US22502532_251506110196_S01_H.tif
US22502532_251506110196_S01_L.tif


title: HgCl2_0_rep3

description:
Gene expression at 24hr after 0uM  HgCl2 treatment
US22502532_251506110176_S01_H.tif
US22502532_251506110176_S01_L.tif

source_name: HgCl2 untreated


title: HgCl2_2uM_rep2

description:
Gene expression at 24hr after 2uM  HgCl2 treatment
US22502532_251506110175_S01_H.tif
US22502532_251506110175_S01_L.tif

source_name: 2uM HgCl2


title: HgCl2_2uM_rep1

description:
Gene expression at 24hr after 2uM  HgCl2 treatment
US22502532_251506110173_S01_H.tif
US22502532_251506110173_S01_L.tif


title: HgCl2_0_rep2

description:
Gene expression at 24hr after 0uM  HgCl2 treatment
US22502532_251506110174_S01_H.tif
US22502532_251506110174_S01_L.tif


title: glial progenitors-control vs. EAE-rep2

city: Marseille

first: Myriam

last: CAYRE

address: Parc Scientifique de Luminy

hyb_protocol: The corresponding Cy3- and Cy5- labeled cDNAs were combined (table 3) and hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 4 x 44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).

organism: Mus musculus

source_name: SVZ glial progenitors from healthy adult mice

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.In general, control samples are labeled with Cy3 and experimental samples are labeled with Cy5.

extract_protocol: Cell samples were lysed using SuperAmp™ Lysis Buffer and stored appropriately by the customer according to the instructions of the SuperAmp Preparation Kit. SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed procedure. Briefly, the amplification is based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: For EAE induction,  C57/Bl6 two month-old micewere immunized  with an emulsion consisting of MOG 35-55 peptide (1 mg/mL) in complete Freund’s adjuvant supplemented with Mycobacterium tuberculosis. Pertusis toxin  (500 ng) was injected on day 1 and day 3 (intraperitoneally).

value: glial progenitors

tag: disease status

value: healthy

source_name: SVZ glial progenitors from adult mice at peak of EAE

value: peak of EAE scores


title: HgCl2_0_rep1

description:
Gene expression at 24hr after 0uM  HgCl2 treatment
US22502532_251506110173_S01_H.tif
US22502532_251506110173_S01_L.tif


title: act_rTreg_rep2

type: genomic

city: Parkville

first: Jovana

last: Maksimovic

state: Victoria

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

description: Sample name: M30_act_rTreg

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Illumina iScan was used to scan the BeadChips with standard settings

data_processing: R 2.15; Bioconductor 2.11; minfi 1.4.0

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Naïve CD4+ T (CD45RA+ CD45RO- CD25-) and rTreg (CD45RA+ CD45RO-CD25+) (rTreg) T cells were Flow-sorted from peripheral blood mononuclear cells of healthy male donors. Cells were cultured in IP5 medium (Iscove’s modified Dulbecco’s medium [Gibco] supplemented with 5% pooled human serum, 2mM glutamine, 0.05mM 2-mercaptoethanol, 100U/ml penicillin, 100μg/ml streptomycin and 100μM non-essential amino acids).

extract_protocol: Genomic DNA was isolated with the DNeasy blood & tissue kit (Qiagen, Doncaster, Victoria, Australia) following the protocol for cultured animal cells and precipitated with ethanol

treatment_protocol: For activation, freshly sorted naïve CD4+ T cells and rTreg were labeled with CellTracer Violet (CTV) dye (Invitrogen) and co-cultured with irradiated (3000 rad) autologous CD4+ T cell-depleted PBMCs at a 1:4 ratio. T cells were activated for 3 days with soluble anti-CD3 (100 ng/ml) (clone OKT3) (Walter and Eliza Hall Institute Monoclonal Lab) and anti-CD28 (200ng/ml)  (clone CD28.2) (BD) antibodies. On day 4, fresh IP5 medium containing recombinant human IL-2 (final of 20 U/ml) was added and cells were cultured for a further 2 days. On day 6, cells that had proliferated and were CD25+ (CTVdim CD25+) were sorted for preparation of genomic DNA

tag: donor id

tag: gender

value: Male

tag: disease state

value: Normal


title: HMLE transduced with Slug_b

city: Cambridge

first: Wai Leong

last: Tam

address: 9 Cambridge Center

institute: Whitehead Institute

description: SAMPLE 14

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using cross-correlation normalisation in Matlab.

label: Biotin

source_name: HMLE cells, Slug overexpression

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: MEGM medium; Lonza

extract_protocol: Trizol followed by Qiagen RNA columns

treatment_protocol: Cells were transduced with Twist, Snail or Slug overexpression vectors. Control cells were wild-type or transduced with vector.

tag: genotype/variation

value: Slug overexpression


title: HMLE transduced with Slug_a

description: SAMPLE 13


title: HMLE transduced with Snail_c

description: SAMPLE 12

source_name: HMLE cells, Snail overexpression

value: Snail overexpression


title: HMLE transduced with Slug_c

description: SAMPLE 15


title: neuronal progenitors-control vs. EAE-rep1

source_name: SVZ neuronal progenitors from healthy adult mice

value: neuronal progenitors

source_name: SVZ neuronal progenitors from adult mice at peak of EAE


title: HMLE transduced with Twist_c

description: SAMPLE 9

source_name: HMLE cells, Twist overexpression

value: Twist overexpression


title: glial progenitors-control vs. EAE-rep1


title: HMLE transduced with Snail_b

description: SAMPLE 11


title: HMLE transduced with Snail_a

description: SAMPLE 10


title: act_naive_rep2

description: Sample name: M29_act_naive


title: act_rTreg_rep1

description: Sample name: M29_act_rTreg


title: act_naive_rep3

description: Sample name: M30_act_naive


title: neuronal progenitors-control vs. EAE-rep2


title: rTreg_rep2

description: Sample name: M30_rTreg

source_name: rTreg

value: rTreg


title: act_naive_rep1

description: Sample name: M28_act_naive


title: naïve_rep3

description: Sample name: M30_naive

source_name: naive

value: naïve


title: naïve_rep2

description: Sample name: M29_naive


title: IMR90-Senescent-5

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: SAMPLE 10

hyb_protocol: Standard Affymetrix hybridization, per manual.

scan_protocol: Standard Affymetrix scanning, per manual.

data_processing: Data were imported into Partek and background-subtracted using GC-RMA. Data were quantile-normalized, median-polished, and subjected to a log2 transform.

source_name: IMR90 fibroblasts_90 population doublings

label_protocol: Standard Affymetrix labeling, per manual.

growth_protocol: IMR90 cells (obtained from Coriell Institute for Medical Research, Camden, NJ) were grown in standard tissue culture medium (DMEM with 10% FBS and 1% penicillin streptomycin) at 3% oxygen.  For senescence studies, cells were replicatively passaged until growth ceased.

extract_protocol: RNA was purified using Trizol extraction.

treatment_protocol: Senescence cells were maintained in dishes for 2 weeks to ensure growth termination.  Senescence was determined by monitoring p16 upregulation, downregulation of cyclin genes, and by SA-beta galactosidase staining.

tag: cell line

value: primary human fibroblasts

value: senescent

tag: population doublings


title: CD3 Fixed 24hr Donor 2 Rep 1

description: CD3+ cells sorted from fixed human PBMCs by FACS; PBMCs were incubated at 4°C for 24 hours prior to sorting; donor 2 replicate 1

source_name: CD3+ cells sorted from human PBMCs

tag: run number

value: yes


title: HMLE transduced with Twist_a

description: SAMPLE 7


title: IMR90-Senescent-4

description: SAMPLE 9


title: HMLE transduced with empty vector_c

description: SAMPLE 6

source_name: HMLE cells, Vector control

value: Vector control


title: IMR90-Senescent-3

description: SAMPLE 8


title: HMLE untreated_b

description: SAMPLE 2

source_name: HMLE cells, Parental

value: Parental


title: PBMC Fixed 2

description: PBMCs fixed replicate 2

source_name: PBMCs

tag: fixed

value: no


title: naïve_rep1

description: Sample name: M28_naive


title: rTreg_rep1

description: Sample name: M28_rTreg


title: HMLE untreated_c

description: SAMPLE 3


title: IMR90-Proliferating-3

description: SAMPLE 3

source_name: IMR90 fibroblasts_28 population doublings

value: proliferating


title: IMR90-Senescent-1

description: SAMPLE 6


title: IMR90-Senescent-2

description: SAMPLE 7


title: pairing unexperienced males (UM) biol.repl.3 vs. pairing-experienced males (EM) biol.repl.3 - tech.repl.4

city: Giessen

first: Silke

last: Leutner

address: Rudolf-Buchheim-Straße 2

country: Germany

institute: Institute for Parasitology

description:
dye swap
UM_3/EM_3_tech.rep.4

hyb_protocol: Samples were combined and hybridized on a custom oligoarray with 4 x 44k elements produced by Agilent Technologies (GPL8606), the hybridization and washing steps were perfomed according to agilent instructions.

scan_protocol: The washed slides were scanned using the equipament GenePix4000B (molecular devices).

data_processing: Data was extracted using Feature Extraction software (v.9.0, Agilent Technologies), the intensities were LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. The log2 ratio data were presented as [pairing unexperienced males]/[pairing-experienced males] (i.e. UM/EM) for all the samples. Agilent software was used.

organism: Schistosoma mansoni

source_name: pairing-experienced males (EM)

label_protocol: All samples were linearly amplified and labeled using Agilent protocol with Low input RNA amplification kit

growth_protocol: Worms were obtained by portal perfusion in 42-days infected hamsters

extract_protocol: RNA from all samples was extract using Trizol reagent (invitrogen)  followed by DNAse treatment using RNeasy kit (QIAGEN) according to manufacturer´s instructions.

treatment_protocol: EM were seperated from females after perfusion and frozen in RNAlater, UM were frozen in RNAlater after perfusion

value: male

tag: pairing phenotype

value: pairing-experienced (EM)

source_name: pairing unexperienced males (UM)

value: pairing-unexperienced (UM)


title: IMR90-Proliferating-4

description: SAMPLE 4


title: Male-Cerebral-Hemisphere-Folic acid-4mg-rep3

city: Staten Island

first: Mohammed

middle: A.

last: Junaid

state: NY

address: 1050 Forest Hill Road

department: Developmental Biochemistry

institute: New York State Institute for Basic Research in Developmental Disabilities

description: Maternal folic acid supplementation at 4mg/kg throughout the gestational period.

hyb_protocol: A total of 600ng of cRNA from sample was fragmented and hybridized to the SurePrint G3 mouse gene expression 8 x 60 k arrays (G4852A) (Agilent Technologies, Santa Clara, CA), at 65°C for 17hr in Agilent Microarray  Hybridization Chambers (Agilent Technologies, Santa Clara, CA).

scan_protocol: Slides were scanned immediately on Agilent G2539A DNA scanner using one-color setting for 8x60k slides at 3 mm resolution using Green channel at 100%.

data_processing: Scanned image was processed using the Feature Extraction Software v10.7.3.1 using default parameters (Protocol: GE1_107_Sep09, Grid: 028005-D-F20120201).

source_name: Cerebral hemisphere

label_protocol: Total RNA was converted to cDNA, followed by conversion to cyanine-3-labelled cRNA using the one-color, low-input QuickAmp labelling kit (Agilent Technologies, Santa Clara, CA) by following manufacturer’s instructions. Purification of the cRNA was done with RNeasy kit (Qiagen) and the incorporation of cyanine-3 was assessed by Nano Drop spectrometer.

extract_protocol: Three pups from different dams of each group were sacrificed at P1. Tissues from cerebral hemisphere of male and female pups were extracted separately and samples from three independent pups of same gender were pooled together. Total RNA was extracted by lysing the cells with Trizol reagent ( Invitrogen Life Technologies, Inc. Carlsbad, CA) and further purification of  RNA was done by Qiagen RNeasy kit( Qiagen, Valencia, CA), according to the manufacturer’s instructions. To remove contaminating DNA in the sample, on-column DNase digestion was performed. RNA quality were assessed by measuring the absorbance ratio at 260/280 nm and the integrity was assessed by formaldehyde-gel electrophoresis.

treatment_protocol: One week prior to mating C57BL/6J female mice were separated into two groups of ten mice and supplemented with a custom AIN-93G amino acid–based diet (Research Diet, Inc. New-Brunswick, NJ). Low-dose group were supplemented  with FA at 0.4 mg/kg, while the high-dose group received FA at 4 mg/kg diet

tag: tissue

value: Whole brain

value: Male

tag: strain

tag: age

value: Post natal day 1

tag: maternal diet

value: high dose FA


title: IMR90-Proliferating-5

description: SAMPLE 5

tag: cell type


title: IMR90-Proliferating-1

description: SAMPLE 1


title: pairing unexperienced males (UM) biol.repl.3 vs. pairing-experienced males (EM) biol.repl.3 - tech.repl.3

source_name: pairing-unexperienced males (UM)


title: HMLE untreated_a

description: SAMPLE 1


title: GGS_124_MidLog

city: Tokyo

first: Shinya

last: Watanabe

address: 1-21-1 Toyama

department: Department of Infectious Diseases

country: Japan

institute: National Center for Global Health and Medicine

description: Gene expression of mid log phase culture (OD=0.6) in BHI

hyb_protocol: 0.6 ug of Cy3-labeled cDNA was used for hybridization. Hybridization and wash processes were carried out using Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Streptococcus dysgalactiae subsp. equisimilis GGS_124

source_name: SDSE GGS_124, Mid log phase culture (OD=0.6) in BHI

label_protocol: 5 ug total RNA was labeled with FairPlay III Microarray Labeling Kit (Agilent).

growth_protocol: SDSE strains were incubated in BHI in a 10% CO2 incubator at 37C.

extract_protocol: To collect GGS cells from mice, the peritoneal cavity was rinsed with 5 ml of BHI broth and the cell suspension was transferred into a tube containing twice volume of RNAprotect Bacteria Reagent (Qiagen). The cell-wall of collected cells was lysed by 3000 units of Mutanolysin (Sigma) in TE buffer at 37oC for 1hr. After cell lysis, RNA was extracted by RNeasy mini kit (Qiagen) and RNase-Free DNase set (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cell number was adjusted at 10^8 CFU/ml and was intraperitoneally inculated in a 6 week age ddY mouse. Cells were collected from the abdominal cavity at 0, 2, 4 and 8 h post infection. GGS_124 cells were also collected from OD600=0.6 culture in brain heart infusion broth as a control.

tag: growth phase

value: mid log

tag: host

value: Mus musculus

tag: genetic background

tag: genotype

value: wild type


title: IMR90-Proliferating-2

description: SAMPLE 2

value: primary human fibroblasts


title: HMLE transduced with empty vector_a

description: SAMPLE 4


title: Male-Cerebral-Hemisphere-Folic acid-4mg-rep2

tag: gender


title: pairing unexperienced males (UM) biol.repl.3 vs. pairing-experienced males (EM) biol.repl.3 - tech.repl.2

description:
dye swap
UM_3/EM_3_tech.rep.2


title: pairing unexperienced males (UM) biol.repl.3 vs. pairing-experienced males (EM) biol.repl.3 - tech.repl.1


title: Male-Cerebral-Hemisphere-Folic acid-0.4mg-rep3

description: Maternal folic acid supplementation at 0.4mg/kg throughout the gestational period.

value: low dose FA


title: Male-Cerebral-Hemisphere-Folic acid-4mg-rep1


title: csrS_8hr

description: Gene expression after 8hr post infection

source_name: SDSE GGS_124 csrS deficient mutant, 8hr post infection

tag: time

value: 8 h post infection

value: csrS deficient mutant


title: csrS_4hr

description: Gene expression after 4hr post infection

source_name: SDSE GGS_124 csrS deficient mutant, 4hr post infection

value: 4 h post infection


title: csrS_2hr

description: Gene expression after 2hr post infection

source_name: SDSE GGS_124 csrS deficient mutant, 2hr post infection

value: 2 h post infection


title: csrS_0hr

description: Gene expression after 0hr post infection

source_name: SDSE GGS_124 csrS deficient mutant, 0hr post infection

value: 0 h post infection


title: pairing unexperienced males (UM) biol.repl.2 vs. pairing-experienced males (EM) biol.repl.2 - tech.repl.3

value: male


title: Male-Cerebral-Hemisphere-Folic acid-0.4mg-rep2


title: pairing unexperienced males (UM) biol.repl.2 vs. pairing-experienced males (EM) biol.repl.2 - tech.repl.4

description:
dye swap
UM_2/EM_2_tech.rep.4

value: pairing-experienced (EM)


title: pairing unexperienced males (UM) biol.repl.1 vs. pairing-experienced males (EM) biol.repl.1 - tech.repl.4

description:
dye swap
UM_1/EM_1_tech.rep.4

value: pairing-unexperienced (UM)


title: Female-Cerebral-Hemisphere-Folic acid-4mg-rep3

value: Whole brain

value: Female


title: GGS_124_4hr

source_name: SDSE GGS_124, 4hr post infection


title: GGS_124_0hr

source_name: SDSE GGS_124, 0hr post infection


title: pairing unexperienced males (UM) biol.repl.2 vs. pairing-experienced males (EM) biol.repl.2 - tech.repl.2

description:
dye swap
UM_2/EM_2_tech.rep.2


title: pairing unexperienced males (UM) biol.repl.1 vs. pairing-experienced males (EM) biol.repl.1 - tech.repl.1


title: GGS_124_8hr

source_name: SDSE GGS_124, 8hr post infection


title: pairing unexperienced males (UM) biol.repl.2 vs. pairing-experienced males (EM) biol.repl.2 - tech.repl.1


title: Female-Cerebral-Hemisphere-Folic acid-4mg-rep2

value: Post natal day 1


title: pairing unexperienced males (UM) biol.repl.1 vs. pairing-experienced males (EM) biol.repl.1 - tech.repl.3


title: Male-Cerebral-Hemisphere-Folic acid-0.4mg-rep1

value: Male


title: Female-Cerebral-Hemisphere-Folic acid-0.4mg-rep1


title: pairing unexperienced males (UM) biol.repl.1 vs. pairing-experienced males (EM) biol.repl.1 - tech.repl.2

description:
dye swap
UM_1/EM_1_tech.rep.2


title: GGS_124_2hr

source_name: SDSE GGS_124, 2hr post infection


title: 0.26 µg/L 4

status: Public on Sep 08 2013

city: Charlottetown

first: Megan

last: Bauer

state: Prince Edward Island

address: 550 University Ave

country: Canada

institute: University of Prince Edward Island

description:
0.26 µg/L Biological Replicate 132
Endosulfan 132

hyb_protocol: The RNA samples were fragmented (Ambion Fragmentation Kit), injected into dual chambers of the Tecan hybridization station and a 16h hybridization protocol was run.

scan_protocol: Slides were scanned using Agilent's high resolution C scanner and Agilent scan control software.

data_processing: Feature information was extracted using Agilent's Feature Extraction version 11. Lowess normalized log2 ratio (test/reference). There was no data obtained for the 416 blank spots and they were removed from the data set.

organism: Homarus americanus

source_name: RNA-0.26 µg/L endosulfan exposed

label_protocol: RNA was labelled using Agilent's Two-color microarray Low Input Quick Amp labeling kit as per the manufacturers protocol.

growth_protocol: Stage I H.americanus were obtained from Coastal Zones Research Institute in Shippagan, New Brunswick Canada.  The larvae were transported to Environment Canada toxicology laboratory in Moncton, New Brunswick Canada and were cultured until the larvae reached stage III.

extract_protocol: Total RNA was extracted using Trizol and following the manufacturers protocol.

treatment_protocol: At stage III, the 14 day chronic enoduslfan exposure was started.  Lobster larvae were housed in individual mason jars and the test solution was renewed 3 times a week. At the termination of the test, surviving animals were preserved in Trizol, homogenized and frozen at -80C.

tag: Stage

value: Stage III

source_name: RNA- pooled reference sample

value: 15 stage III and 15 stage IV


title: 0.26 µg/L 1

description:
0.26 µg/L Biological Replicate 129
Endosulfan 129


title: 0.26 µg/L 2

description:
0.26 µg/L Biological Replicate 130
Endosulfan 130


title: 0.05 µg/L 6

description:
0.05 µg/L Biological Replicate 125
Endosulfan 125

source_name: RNA-0.05 µg/L endosulfan exposed

value: Stage IV


title: 0.26 µg/L 3

description:
0.26 µg/L Biological Replicate 131
Endosulfan 131


title: 0.26 µg/L 5

description:
0.26 µg/L Biological Replicate 133
Endosufan 133


title: Female-Cerebral-Hemisphere-Folic acid-4mg-rep1

value: high dose FA


title: Female-Cerebral-Hemisphere-Folic acid-0.4mg-rep2

value: low dose FA


title: Female-Cerebral-Hemisphere-Folic acid-0.4mg-rep3


title: 0.26 µg/L 6

description:
0.26 µg/L Biological Replicate 134
Endosulfan 135


title: 0.05 µg/L 5

description:
0.05 µg/L Biological Replicate 121
Endosulfan 121


title: 0.05 µg/L 4

description:
0.05 µg/L Biological Replicate 118
Endosulfan 118


title: 0.021 µg/L 6

description:
0.021 µg/L Biological Replicate 104
Endosulfan 104

source_name: RNA-0.021 µg/L endosulfan exposed


title: 0.05 µg/L 1

description:
0.05 µg/L Biological Replicate 107
Endosulfan 107


title: 0.05 µg/L 2

description:
0.05 µg/L Biological Replicate 108
Endosulfan 108


title: HMLE transduced with Twist_b

description: SAMPLE 8

source_name: HMLE cells, Twist overexpression

tag: genotype/variation

value: Twist overexpression


title: 0.021 µg/L 4

description:
0.021 µg/L Biological Replicate 92
Endosulfan 92


title: 0.021 µg/L 2

description:
0.021 µg/L Biological Replicate 88
Endosulfan 88


title: 0.021 µg/L 1

description:
0.021 µg/L Biological Replicate 83
Endosulfan 83


title: 0.008 µg/L 5

description:
0.008 µg/L Biological Replicate 79
Endosulfan 79

source_name: RNA-0.008 µg/L endosulfan exposed


title: 0.005 µg/L 6

description:
0.005 µg/L Biological Replicate 51
Endosulfan 51

source_name: RNA-0.005 µg/L endosulfan exposed


title: 0.008 µg/L 6

description:
0.008 µg/L Biological Replicate 80
Endosulfan 80


title: 0.05 µg/L 3

description:
0.05 µg/L Biological Replicate 117
Endosulfan 117


title: 0.005 µg/L 5

description:
0.005 µg/L Biological Replicate 46
Endosulfan 46


title: 0.021 µg/L 3

description:
0.021 µg/L Biological Replicate 90
Endosulfan 90


title: Control 6

description:
Control Biological Replicate 27
Endosulfan 27

source_name: RNA-control


title: 0.005 µg/L 1

description:
0.005 µg/L Biological Replicate 29
Endosulfan 29


title: Control 4

description:
Control Biological Replicate 24
Endosulfan 24


title: Control 3

description:
Control Biological Replicate 13
Endosulfan 13


title: Control 5

description:
Control Biological Replicate 25
Endosulfan 25


title: 0.005 µg/L 2

description:
0.005 µg/L Biological Replicate 31
Endosulfan 31


title: 0.021 µg/L 5

description:
0.021 µg/L Biological Replicate 100
Endosulfan 100


title: 0.005 µg/L 4

description:
0.005 µg/L Biological Replicate 42
Endosulfan 42


title: 0.005 µg/L 3

description:
0.005 µg/L Biological Replicate 34
Endosulfan 34


title: 0.008 µg/L 2

description:
0.008 µg/L Biological Replicate 57
Endosulfan 57


title: 0.008 µg/L 1

description:
0.008 µg/L Biological Replicate 56
Endosulfan 56


title: 0.008 µg/L 4

description:
0.008 µg/L Biological Replicate 63
Endosulfan 63


title: HMLE transduced with empty vector_b

description: SAMPLE 5

source_name: HMLE cells, Vector control

value: Vector control


title: 0.008 µg/L 3

description:
0.008 µg/L Biological Replicate 61
Endosulfan 61


title: Control 2

description:
Control Biological Replicate 2
Endosulfan 2


title: Case 25 NMPT

city: Yufu-city

first: shunichi

last: yoshioka

address: Hasama-machi Idaigaoka 1-1

department: Depertment of Molecular Pathology

institute: Faculty of Medicine, Oita University

description: Twelve non-neoplastic kidney tissue's mix was used as the source of control DNA

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). Following normalization of the raw data, the log2ratio of Cy3 (tumor) to Cy5 (Control) was calculated. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 7.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0., maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.163 to detect regions showing a change in the averaged copy number equal to or more than 1.12-fold (log2(1.12)=0.163).

source_name: OSCC non-metastatic primary tumor

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: standard proteinase K-digestion method

value: OSCC non-metastatic primary tumor

tag: Sex

tag: site

value: tongue

tag: differentiation

value: well

tag: metastatic neck lymph node

tag: delayed lymph node metastasis

tag: primary tumor thickness

tag: sample type

value: kidney


title: Case 22 NMPT

tag: tissue

tag: age

value: male

source_name: Twelve non-neoplastic kidney tissue's mix


title: Case 8 LNM2

source_name: OSCC neck lymph-node metastasis

value: OSCC neck lymph-node metastasis

value: Twelve non-neoplastic kidney tissue's mix


title: Case 16 NMPT

value: female


title: Case 21 NMPT

value: floor of mouth

value: moderate


title: Case 17 NMPT


title: Case 18 NMPT


title: Case 23 NMPT


title: Case 19 NMPT


title: Case 8 LNM1


title: Case 15 LNM


title: Case 24 NMPT


title: Case 8 LNM


title: Case 1 LNM


title: Case 9 LNM


title: Stationary vs. late exponential phase,  Axenic Experiment

first: Katie Rose

last: Boissonneault

address: 77 Massachusetts Ave., 76-553

department: Biology

web_link: http://to be added

institute: Massachusetts Institute of Technology

description:
RNA samples were extracted from cells in late exponential vs. stationary growth phase. Experiments were dye-swapped to account for differences in dye labeling and detection efficiencies.

Raw data files (.txt):
AX Hybe 1.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
AX Hybe 2.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase
AX Hybe 3.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
AX Hybe 4.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase

hyb_protocol: Ps-n microarrays were processed before hybridization by holding them face-down over a steaming water bath for a few seconds, and then snap-drying them on a 95ºC heat block. The DNA was immobilized onto the slides by UV cross-linking at 65 mJoules. Cross-linked slides were soaked for 15 min in freshly prepared succinic anhydride/sodium borate solution with gentle agitation, soaked for 2 min in boiling nuclease-free, de-ionized water and finally, rinsed in 95% ethanol, and spun dry. Processed microarrays were pre-hybridized at room temperature for 1 h. Pre-hybridization solution was composed of 50% formamide, 5X SSC, 0.1% SDS, and 1% BSA. Hybridization buffer was composed of 50% formamide, 10X SSC, 0.2% SDS, and 0.26% salmon sperm. Labeled cDNA was denatured prior to hybridization by heating for 2 min at 80ºC, while the cassette and microarray were pre-warmed at 42ºC. The cDNA was then loaded onto the array, and arrays were hybridized for 16 h at 42ºC in humidified chambers. Hybridized arrays were washed successively in 1X SSC, 0.03% SDS, 0.1X SSC, 0.01% SDS, and 0.1X SSC, and dried by brief centrifugation. Replicate hybridizations were repeated within each biological experiment and dye-swapped to account for differences in dye labeling and detection efficiencies. Non-axenic experiments 1 and 2 each included six technical replicates, while the axenic experiment included four technical replicates.

scan_protocol: Dual-channel arrays were scanned at 595 nm (Cy3) and 685 nm (Cy5) on ArrayWoRx scanners (Applied Precision, Inc., Issaquah, WA, USA). The scanning system converts signal from fluors to “pixel” values, which allows the data to be saved as tiff files. DigitalGenome software (MolecularWare, Cambridge, MA, USA) was then used to integrate annotated chip information with the tiff files and to visualize, edit and export the data for normalization.

data_processing: A loess algorithm was applied to the spot mean intensity values across replicate arrays within each biological experiment to correct for systematic biases using S+ArrayAnalyzer software (Insightful Corp., Seattle, WA, USA). Normalized spot mean intensity values for each complete dataset were used in further statistical analysis. Data was compiled from two non-axenic and one axenic cultures each with dye-swap replicates, thus providing three biological repeats within a total of sixteen technical repeats. Any negative values, outliers (defined as two standard deviations away from the mean for individual spots), and any spots that did not include data for at least three replicate arrays within each dataset, were removed from further analysis. These parameters resulted in the removal of data for <1.5% of the original 10,772 features printed on array (final datasets: Axenic experiment 1 = 10,723; Axenic experiment 2 = 10,614; Non-axenic experiment = 10,630). Significance analysis of gene expression was performed using a t-test algorithm modified for multiple tests: Significance Analysis of Microarrays (SAM) [http://www-stat.stanford.edu/~tibs/SAM/]. SAM reports a set of significantly differentially expressed genes based on the overall false discovery rate (FDR). We also reported the local false discovery rate (LFDR) in the matrix table (linked as a Supplementary file on the Series record).

organism: Pseudo-nitzschia multiseries

source_name: late exponential growth phase replicate samples extracted from axenic culture experiment

label_protocol: Ten micrograms of Ps-n RNA from each harvest were spiked with mRNA from the SpotReport Alien Array Validation System, incubated for 10 min at 65ºC with oligo-dT and then cooled at 25°C for 5 min. Four microliters of 1 mM Cy3- or Cy5-conjugated dUTPs were added to each RNA sample and the mixtures were incubated at 42ºC for 2 min. A master mix, including 4.5 µL of 0.2 M DTT, 18 µL of 5X 1st strand buffer, 1.8 µL of 25 mM dATP, dGTP and dCTP, 1.8 µL of 10 mM dTTP, and 2 µL of Superscript II reverse transcriptase, was added to each RNA mixture and incubated for 1 h at 42°C. After 1 h, an additional 1 µL of Superscript II was added to each and the reactions were incubated at 42°C for another hour. Starting RNA was degraded by addition of stop solution (3 µL of 0.5 M EDTA, pH 8; 3 µL of 1 N NaOH) and incubated for 30 min at 60ºC. Labeled cDNA was cleaned using RNeasy columns (Qiagen); Cy3-labeled cDNA and the corresponding Cy5-labeled cDNA that were to be compared were combined and loaded onto the same column. The labeled target cDNA pools were then hybridized to the probe cDNAs on the Ps-n cDNA microarrays.

growth_protocol:
sample-specific growth protocol: Biological Replicate Experiment 3 represents: Ps-n cells grown under axenic conditions.
Ps-n strain CL-125 cultures were grown in 0.2 µm-filtered, autoclaved seawater (from Woods Hole, MA) enriched with f/2 nutrients and amended with 10-8 µM Se. These batch cultures were grown in 15 L of f/2 medium in 19 L borosilicate carboys, and incubated at 20ºC. The irradiance was maintained continously at 100 µmol photons m-2 s-1. The cultures were aerated using aquarium pumps with sterile cotton and activated carbon filters and were constantly mixed with magnetic stirrers.

extract_protocol: Eight liters of culture were harvested at an initial time point during the late exponential growth phase and the remaining 7 L were harvested at a final time point during the stationary phase. Cell suspensions were centrifuged in 0.5-L aliquots for 15 min at 1000 g, which resulted in loose pellets that were pooled, split among 2-4, 50-mL conical tubes and spun again briefly to remove any remaining liquid. Ten to 20 mL (depending on cell pellet volume) of TRIzol® (Invitrogen Corporation, Carlsbad, CA, USA) were added to the conical tubes, and the pellets were homogenized (Polytron, Kinematica, Inc, Bohemia, NY) for 60 s, frozen in liquid N, and stored at -80ºC until RNA extraction. Insoluble material was removed by low-speed centrifugation of the samples. RNA was precipitated twice in salt and ethanol, and cleaned with RNeasy columns (Qiagen, Valencia, CA, USA). RNA was run on formaldehyde agarose gels to confirm the quality of the RNA.

treatment_protocol: RNA was compared from cells harvested during: (1) an initial time point from the late exponential (i.e., non-detectable domoic acid producing) phase, and (2) a final time point during the stationary (i.e., active domoic acid producing) phase

tag: strain

tag: axenic or non-axenic

value: axenic

tag: growth state

value: late exponential phase

tag: domoic acid

value: non-detectable domoic acid

source_name: Stationary growth phase replicate samples extracted from axenic culture experiment

value: Stationary Growth Phase

value: 38 ng per mL domoic acid (41 fg per cell)


title: Case 14 LNM


title: Case 12 LNM


title: Case 11 LNM

value: buccal mucosa


title: Case 13 LNM


title: Case 3 LNM


title: Case 10 LNM


title: Case 7 LNM


title: Case 6 LNM

value: gingiva


title: Case 2 LNM


title: Case 20 NMPT

value: OSCC non-metastatic primary tumor


title: Case 5 LNM

value: tongue


title: Case 4 LNM


title: Case 14 MPT

source_name: OSCC metastatic primary tumor

value: OSCC metastatic primary tumor

value: well


title: Stationary vs. late exponential phase,  Non-axenic Experiment 1

description:
RNA samples were extracted from cells in late exponential vs. stationary growth phase. Experiments were dye-swapped to account for differences in dye labeling and detection efficiencies.

Raw data files (.txt):
NonAX 1 Hybe 1.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
NonAX 1 Hybe 2.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase
NonAX 1 Hybe 3.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
NonAX 1 Hybe 4.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase
NonAX 1 Hybe 5.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
NonAX 1 Hybe 6.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase

source_name: late exponential growth phase replicate samples extracted from non-axenic culture experiment 1

growth_protocol:
sample-specific growth protocol: Biological Replicate Experiment 1 represents: Ps-n cells grown under non-axenic conditions.
Ps-n strain CL-125 cultures were grown in 0.2 µm-filtered, autoclaved seawater (from Woods Hole, MA) enriched with f/2 nutrients and amended with 10-8 µM Se. These batch cultures were grown in 15 L of f/2 medium in 19 L borosilicate carboys, and incubated at 20ºC. The irradiance was maintained continously at 100 µmol photons m-2 s-1. The cultures were aerated using aquarium pumps with sterile cotton and activated carbon filters and were constantly mixed with magnetic stirrers.

value: non-axenic

source_name: Stationary growth phase replicate samples extracted from non-axenic culture experiment 1

value: 314 ng per mL domoic acid (888 fg per cell)


title: Sertoli cells 2 [536583A03_SC2]

city: Houston

first: Pawel

last: Stankiewicz

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

description: 4C Sertoli cells 2/control

hyb_protocol: hybridization of 4C DNA libraries was done according NimbleGen Array User’s Guide v8.1 for ChIP-chip arrays.

scan_protocol: The arrays were scanned on Agilent DNA Microarray Scanner, and analyzed using Agilent Scan Control

data_processing:
Arrays were processed using NimbleGen software DEVA v1.1
normalized_ratio.gff: scaled, log2 Normalized (Biweight) Ratio (Cy5/Cy3)
peaks.gff: Peak Results (Cy5/Cy3)

source_name: genomic DNA from Sertoli cells

label_protocol: Labeling of 4C DNA libraries was done according NimbleGen Array User’s Guide v8.1 for ChIP-chip arrays.

extract_protocol: 1x10E7 cells were treated with 1% formaldehyde for 10 min at room temperature, following by quenching of the reaction with 0.1 M glycine. Cells were lysed in hypotonic buffer containing 0.2% Igepal using a Dounce homogenizer. Nuclei were treated overnight with EcoRI at 37°C, followed by DNA ligation at low DNA concentration with T4 ligase for 2 hr at 16°C. DNA was de-cross-linked and purified by proteinase K and RNase digestion, followed by phenol/chloroform extraction. The 3C library was then processed according to the procedure described by Simonis et al. (2007). The ligation junctions were trimmed by DNA digestion with DpnII at 37°C overnight, followed by phenol/chloroform extraction, re-ligation at low DNA concentration with T4 ligase for 4 hr at 16°C, and re-digestion with HindIII at 37°C overnight. The 4C template was created by linear amplification of DNA using Expand Long Template PCR System (Roche Applied Science, Indianapolis, IN). 200 ng of 4C template was amplified per reaction. Primers used for amplification were: 5´-GAAATTCTCCCGGAAGGACATTGA-3´ and 5´-CTGGACTGCTTTGCTGCTGAGATTTA-3´. The primers were designed within the EcoRI- DpnII fragment, containing PolII binding site of the SOX9 promoter. PCR cycling conditions were: 94°C for 30 sec, 55°C for 1 min, and 68°C for 3 min. Sixteen reactions were conducted for each template. Pooled PCR products were purified using Qiagen PCR cleanup kit (Qiagen, Valencia, CA).   To generate reference DNA for hybridization, we used uncross-linked DNA isolated from Sertoli cells or lymphoblasts with Puregene Blood Core Kit A, and digested overnight with EcoRI and DpnII.

treatment_protocol: cross-linked DNA from Sertoli cells digested overnight with EcoRI and DpnII

tag: cell type

value: Sertoli cells

tag: gender

value: male

source_name: reference Sertoli cells

treatment_protocol: uncross-linked DNA isolated from Sertoli cells and digested with EcoRI and DpnII


title: Sertoli cells 1 [536583A01_SC1]

description: 4C Sertoli cells 1/control


title: Case 15 MPT

tag: Stage

value: Twelve non-neoplastic kidney tissue's mix

value: kidney


title: Sertoli cells 1 [536624A03_SC1]

description: 4C Sertoli cells 1/control


title: Case 12 MPT

value: floor of mouth

value: moderate


title: Stationary vs. late exponential phase,  Non-axenic Experiment 2

description:
RNA samples were extracted from cells in late exponential vs. stationary growth phase. Experiments were dye-swapped to account for differences in dye labeling and detection efficiencies.

Raw data files (.txt):
NonAX 2 Hybe 1.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
NonAX 2 Hybe 2.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase
NonAX 2 Hybe 3.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
NonAX 2 Hybe 4.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase
NonAX 2 Hybe 5.txt: Cy3 = Late exponential phase, Cy5 = Stationary phase
NonAX 2 Hybe 6.txt: Cy3 = Stationary phase, Cy5 = Late exponential phase

source_name: late exponential growth phase replicate samples extracted from non-axenic culture experiment 2

growth_protocol:
sample-specific growth protocol: Biological Replicate Experiment 2 represents: Ps-n cells grown under non-axenic conditions.
Ps-n strain CL-125 cultures were grown in 0.2 µm-filtered, autoclaved seawater (from Woods Hole, MA) enriched with f/2 nutrients and amended with 10-8 µM Se. These batch cultures were grown in 15 L of f/2 medium in 19 L borosilicate carboys, and incubated at 20ºC. The irradiance was maintained continously at 100 µmol photons m-2 s-1. The cultures were aerated using aquarium pumps with sterile cotton and activated carbon filters and were constantly mixed with magnetic stirrers.

value: late exponential phase

value: non-detectable domoic acid

source_name: Stationary growth phase replicate samples extracted from non-axenic culture experiment 2

value: 267 ng per mL domoic acid (853 fg per cell)


title: Case 13 MPT

value: female

value: buccal mucosa


title: Lymphoblasts 1 [536624A01_L1]

description: 4C Lymphoblasts 1/control

source_name: genomic DNA from lymphoblasts

treatment_protocol: cross-linked DNA from lymphoblasts digested overnight with EcoRI and DpnII

value: lymphoblasts

source_name: reference EBV -transformed lymphoblasts

treatment_protocol: uncross-linked DNA isolated from lymphoblasts and digested with EcoRI and DpnII

value: EBV -transformed lymphoblasts


title: Case 11 MPT

value: OSCC metastatic primary tumor


title: Lymphoblasts 2 [536624A02_L2]

description: 4C Lymphoblasts 2/control


title: Lymphoblasts 1 [536583A02_L1]

description: 4C Lymphoblasts 1/control


title: Case 9 MPT

value: tongue

value: well


title: Case 7 MPT


title: Case 8 MPT


title: Case 10 MPT


title: Case 6 MPT

value: gingiva


title: Case 1 MPT


title: Case 3 MPT


title: Case 2 MPT


title: Case 5 MPT


title: Case 4 MPT


title: ZF_control_rep2

status: Public on Sep 07 2013

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Normal eye, replicate 2

hyb_protocol: Hybridization was performed at 65°C for 17 hours at 10 rpm in Agilent's hybridization chambers

scan_protocol: Arrays were scanned with an Agilent scanner (G2565CA) at 3 μm resolution

data_processing: Data were extracted by Agilent Feature Extraction software (v.10.5.1.1) using GE1_105_Jan09 protocol; and quantile normalization on background-subtracted signal intensity was performed among the samples

organism: Danio rerio

source_name: Normal eye

label_protocol: 200 ng total RNA was labeled by using an Agilent Low Input Quick Amp labeling kit (part number 5190-2305) and following the one color protocol (v6.5)

growth_protocol: Transgenic zebrafish expressing oncogenic smoa1 developed gross eye tumors and  tumors from 4-month-old fish were dissected

extract_protocol: RNAs were extracted with Trizol and then purified with Qiagen RNeasy MinElute Cleanup Kit

treatment_protocol: No other treatments were applied

value: normal eye

value: 4 months


title: ZF_control_rep3

description: Normal eye, replicate 3


title: ZF_tumor_rep3

description: Eye tumor, replicate 3

source_name: Eye tumor

value: eye tumor


title: ZF_tumor_rep4

description: Eye tumor, replicate 4


title: ZF_tumor_rep2

description: Eye tumor, replicate 2


title: ZF_control_rep4

description: Normal eye, replicate 4


title: ZF_tumor_rep1

description: Eye tumor, replicate 1


title: ZF_control_rep1

description: Normal eye, replicate 1


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 88

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

description: DS2-88 CLL specimen as test DNA and Promega normal DNA as reference

hyb_protocol: Oligoarray hybridization buffer, block (both from Agilent In Situ Hybridization Kit Plus), and Cot-1 DNA (Life Technologies) were added to each sample prior to application to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization for 24 hours, slides were washed sequentially as described by the manufacturer.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B.

data_processing: Data extraction was performed using Feature Extraction Version 10.7.3.1 (Agilent Technologies).

source_name: Human CLL specimen

label_protocol: Genomic DNA samples were labeled using the Agilent Genomic DNA Enzymatic Labeling Kit, according to the manufacturer's protocol, except that 1μg of DNA was used per 25μl labeling reaction mix.

extract_protocol: Extraction of genomic DNA was performed using Qiagen DNeasy Blood and Tissue kit according to the manufacturer's instructions.

tag: disease state

value: chronic lymphocytic leukemia

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).

value: reference

value: healthy


title: Control 1

description:
Control Biological Replicate 1
Endosulfan 1

source_name: RNA-control

value: Stage IV

source_name: RNA- pooled reference sample

value: 15 stage III and 15 stage IV


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 89

description: DS2-89 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 87

description: DS2-87 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 83

description: DS2-83 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 84

description: DS2-84 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 8

description: DS2-8 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 82

description: DS2-82 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 96

description: DS2-96 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 9

description: DS2-9 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 92

description: DS2-92 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 79

description: DS2-79 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 94

description: DS2-94 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 90

description: DS2-90 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 78

description: DS2-78 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 76

description: DS2-76 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 98

description: DS2-98 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 85

description: DS2-85 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 73

description: DS2-73 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 70

description: DS2-70 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 74

description: DS2-74 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 65

description: DS2-65 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 64

description: DS2-64 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 67

description: DS2-67 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 69

description: DS2-69 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 68

description: DS2-68 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 63

description: DS2-63 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 71

description: DS2-71 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 75

description: DS2-75 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 61

description: DS2-61 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 59

description: DS2-59 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 56

description: DS2-56 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 62

description: DS2-62 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 6

description: DS2-6 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 5

description: DS2-5 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 49

description: DS2-49 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 46

description: DS2-46 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 52

description: DS2-52 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 48

description: DS2-48 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 55

description: DS2-55 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 57

description: DS2-57 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 43

description: DS2-43 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 41

description: DS2-41 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 4

description: DS2-4 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 40

description: DS2-40 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 50

description: DS2-50 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 51

description: DS2-51 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 36

description: DS2-36 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 37

description: DS2-37 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 265

description: DS2-265 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 45

description: DS2-45 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 267

description: DS2-267 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 33

description: DS2-33 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 38

description: DS2-38 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 35

description: DS2-35 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 32

description: DS2-32 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 27

description: DS2-27 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 263

description: DS2-263 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 260

description: DS2-260 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 262

description: DS2-262 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 28

description: DS2-28 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 261

description: DS2-261 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 29

description: DS2-29 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 259

description: DS2-259 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 255

description: DS2-255 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 26

description: DS2-26 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 258

description: DS2-258 CLL specimen as test DNA and Promega normal DNA as reference