title: HapMap normal cell line NA18857

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18857


title: Control7

status: Public on Jan 30 2010

type: RNA

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

country: USA

institute: Penn State College of Medicine

description:
4256337010_G
Replicate 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization using BeadStudio software.

molecule: total RNA

organism: Mus musculus

source_name: Un-treated retina

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

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

tag: strain

tag: treatment

value: control


title: Control8

description:
4256337010_H
Replicate 8


title: STZ1

description:
4256337002_A
Replicate 1

source_name: STZ-treated retina

value: Streptozotocin


title: Ins2Akita7

description:
4256337088_G
Replicate 7

source_name: Ins2Akita retina

tag: genotype


title: Control3

description:
4256337010_C
Replicate 3


title: Ins2Akita8

description:
4256337088_H
Replicate 8


title: melanoma cell line 501Mel

status: Public on Feb 01 2010

type: genomic

city: Cambridge

first: Michael

last: Berger

state: MA

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Instititute

description: hybridized to Affy SNP 6.0

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing:
Probe-level intensities were scaled so that the sample-specific median value is 1000.
For further data processing details, please see: The Cancer Genome Atlas Research Network (2008) Nature, 455:1061-1068.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: melanoma cell line 501Mel

label_protocol: Standard Affymetrix protocol.

growth_protocol: melanoma cell lines and short-term cultures were grown as described in Lin et al, Cancer Research (2008), 68:664-673

extract_protocol: DNA was extracted from melanomas as described in Lin et al, Cancer Research (2008), 68:664-673. DNA from HapMap normal samples was obtained from Coriell cell repository

treatment_protocol: cells were grown under standard conditions

tag: disease status

value: melanoma

tag: melanoma type

value: cell line 501Mel


title: Control1

description:
4256337010_A
Replicate 1


title: Control2

description:
4256337010_B
Replicate 2


title: Control4

description:
4256337010_D
Replicate 4


title: Ins2Akita9

description:
4256337002_H
Replicate 9


title: Ins2Akita5

description:
4256337088_E
Replicate 5


title: HapMap normal cell line NA18517

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18517

value: normal


title: Ins2Akita4

description:
4256337088_D
Replicate 4


title: Ins2Akita3

description:
4256337088_C
Replicate 3


title: Ins2Akita6

description:
4256337088_F
Replicate 6


title: Ins2Akita2

description:
4256337088_B
Replicate 2


title: Ins2Akita1

description:
4256337088_A
Replicate 1


title: WT8

description:
4256337042_H
Replicate 8

source_name: WT retina


title: STZ2

description:
4256337002_B
Replicate 2


title: WT6

description:
4256337042_F
Replicate 6


title: WT2

description:
4256337042_B
Replicate 2


title: WT3

description:
4256337042_C
Replicate 3


title: Bmi1 knockout primary cerebellar granule progenitor cells 2

status: Public on Jan 20 2010

city: London

first: Tatiana

last: Subkhankulova

address: 4 Newark Street

department: Neuroscience

country: United Kingdom

institute: Queen Mary University London

description:
2_Bmi1minusCGCs.CEL
mz_141205_mz_2_Bmi1--CGCs.CHP

hyb_protocol: Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing:
Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spike
in controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).

source_name: Cerebellum

label_protocol: The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

growth_protocol:
Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).

Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA).

tag: cell type

value: Primary cerebellar granule precursor cells (GCPs)

tag: tissue

value: cerebellum (brain)

tag: developmental stage

tag: genome/variation

value: Bmi1 knockout


title: Wild type primary cerebellar granule progenitor cells treated with Shh 9

description:
9_Bmi1plusShh.CEL
mz_141205_mz_9_Bmi1++Shh.CHP

label: Biotin

label_protocol: The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100

treatment_protocol: Shh (R&D Systems) was added for 24 hours to give a at final concentration of 3 mg/ml.

value: wild type

tag: treatment group

value: treated with Shh


title: WT7

description:
4256337042_G
Replicate 7


title: WholeBlood_SubjectNo5_8hr_Rep1

status: Public on Jan 08 2010

city: Minato-ku

first: Seiji

last: Nakamura

state: Tokyo

address: 1-15-1, Kaigan, Suzuebaydium 5F

country: Japan

institute: DNA Chip Research Inc.

description: Gene expression in human blood 8hr after the start of exercise

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Peripheral Whole Blood, SubjectNo5, 8hr after the start of exercise, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

treatment_protocol: Healthy, physically active male subjects, who had not been involved in any kind of resistance or endurance exercises, were assigned to a stationary bicycle at 80% of their predicted  maximum workload in a room where temperature and humidity were kept at 25 ± 1°C and 50 ± 10%, respectively. They refrained from eating food and drinking alcohol, coffee, or tea for 12hr before the exercise, and were asked to report to the laboratory at 8:30am. The subjects were seated for 30min, blood (2.5ml) was collected in PAXgene Blood RNA Tube (QIAGEN, Valencia, CA) by venous puncture for the time zero sample, and then they started exercise on an electrically braked cycle ergometer with rest at every 1hr. After 4hrs of exercise, they were asked to take some food and rest for 4hrs. They were asked to report to the laboratory at 24hr after start of the exercise. Blood (2.5ml) was collected by venous puncture at 4, 8 and 24 hr after the start of exercise.

value: peripheral whole blood

tag: gender

value: male


title: WholeBlood_SubjectNo5_0hr_Rep1

description: Gene expression in human blood before exercise

source_name: Peripheral Whole Blood, SubjectNo5, before exercise, replicate1


title: WT4

description:
4256337042_D
Replicate 4


title: Bmi-1- knockout primary cerebellar granule progenitor cells 6

description:
6_Bmi1minusCGCs.CEL
mz_141205_mz_6_Bmi1--CGCs.CHP

growth_protocol:
Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 Bmi-1 knockout mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).

Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.


title: Wild type primary cerebellar granule progenitor cells 5

description:
5_Bmi1plusCGCs.CEL
mz_141205_mz_5_Bmi1++CGCs.CHP


title: WholeBlood_SubjectNo4_24hr_Rep1

description: Gene expression in human blood 24hr after the start of exercise

source_name: Peripheral Whole Blood, SubjectNo4, 24hr after the start of exercise, replicate1


title: Wild type primary cerebellar granule progenitor cells 3

description:
3_Bmi1plusCGCs.CEL
mz_141205_mz_3_Bmi1++CGCs.CHP

source_name: Cerebellar granule progenitor cells

growth_protocol:
Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 96-, 24- or 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).

Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.

treatment_protocol: Shh (R&D Systems)i f applicable was added for 24 hours to give a at final concentration of 3 mg/ml.


title: WT5

description:
4256337042_E
Replicate 5


title: WholeBlood_SubjectNo5_4hr_Rep1

description: Gene expression in human blood immediately after 4hrs of exercise

source_name: Peripheral Whole Blood, SubjectNo5, 4hr after the start of exercise (immediately after 4hrs of exercise), replicate1


title: Bmi-1-knockout primary cerebellar granule progenitor cells treated with Shh 10

description:
10_Bmi1minusShh.CEL
mz_141205_mz_10_Bmi1--Shh.CHP


title: WholeBlood_SubjectNo4_8hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo4, 8hr after the start of exercise, replicate1


title: Wild type primary cerebellar granule progenitor cells treated with Shh 7

description:
7_Bmi1plusShh.CEL
mz_141205_mz_7_Bmi1++Shh.CHP

hyb_protocol: Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target


title: Bmi-1 knockout primary cerebellar granule progenitor cells treated with Shh 8

description:
8_Bmi1minusShh.CEL
mz_141205_mz_8_Bmi1--Shh.CHP


title: WholeBlood_SubjectNo4_4hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo4, 4hr after the start of exercise (immediately after 4hrs of exercise), replicate1


title: Wild type primary cerebellar granule progenitor cells 1

description:
1_Bmi1plusCGCs.CEL
mz_141205_mz_1_Bmi1++CGCs.CHP

data_processing: Raw data processing was performed using the Affymetrix GCOS 1.2 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes

source_name: Mouse cerebellar granule cells primary culture

label_protocol: Total RNA samples (1.5 μg) were reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

growth_protocol:
Primary cerebellar granule cell precursors (GCPs) cultures were prepared as described before using a modification of the procedure described by {Messer, 1977 #810}. Briefly, cerebella were isolated from P5–7 mice, the meninges and the blood vessels were removed, and tissue was dissociated in HIB solution, supplemented with 0.1% glucose, 1% trypsin, 0.1% DNase (Worthington, Lakewood,NJ) at 37 °C for 12 min. Cells were collected by quick centrifugation until 3300 rpm are reached, resuspended in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin, and triturated using 20 ml syringe with a 2 inch 18 gauge needle to obtain a single cell suspension. The cell suspension was passed through a cell strainer (BD Biosciences), centrifuged for 12 min at 1000 rpm (300 g), resuspended in the same media and plated into 96-, 24- or 6-well plates coated with 10 mg/ml poly-L-lysine (PLL).

Cells were grown in Dulbecco MEM high Glucose without Glutamine medium (Invitrogen, # 31053-028), supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed.


title: WT1

description:
4256337042_A
Replicate 1


title: WholeBlood_SubjectNo5_24hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo5, 24hr after the start of exercise, replicate1


title: Bmi1 knockout primary cerebellar granule progenitor cells 4

description:
4_Bmi1minusCGCs.CEL
mz_141205_mz_4_Bmi1--CGCs.CHP


title: WholeBlood_SubjectNo4_0hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo4, before exercise, replicate1


title: WholeBlood_SubjectNo3_24hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo3, 24hr after the start of exercise, replicate1


title: WholeBlood_SubjectNo2_24hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo2, 24hr after the start of exercise, replicate1


title: WholeBlood_SubjectNo3_8hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo3, 8hr after the start of exercise, replicate1


title: WholeBlood_SubjectNo2_8hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo2, 8hr after the start of exercise, replicate1


title: WholeBlood_SubjectNo1_4hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo1, 4hr after the start of exercise (immediately after 4hrs of exercise), replicate1


title: WholeBlood_SubjectNo3_0hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo3, before exercise, replicate1


title: WholeBlood_SubjectNo3_4hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo3, 4hr after the start of exercise (immediately after 4hrs of exercise), replicate1


title: WholeBlood_SubjectNo1_8hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo1, 8hr after the start of exercise, replicate1


title: WholeBlood_SubjectNo2_4hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo2, 4hr after the start of exercise (immediately after 4hrs of exercise), replicate1


title: WholeBlood_SubjectNo2_0hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo2, before exercise, replicate1


title: WholeBlood_SubjectNo1_0hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo1, before exercise, replicate1


title: U251 cells IP H3acetyl

status: Public on Jan 05 2010

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

hyb_protocol: Labeled DNAs were hybridized with custom microarrays for 40 hrs at 65°C.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Intensity data was extracted using Feature Extraction software v.10.5 (Agilent) and normalized using linear method. Data table was assembled in DNA Analytics 4.0.76 software (Agilent).

source_name: U251 chromatin immunoprecipitated against H3acetyl

label_protocol: The amplified IP DNA and WCE DNA samples (1 µg) were labeled with Cy5-dUTP and Cy3-dUTP, respectively, using Genomic DNA Enzymatic Labeling Kit (Agilent).

growth_protocol: Human glioblastoma U251 and breast carcinoma MCF-7 cells (60-80% confluent) grown in DMEM supplemented with 10% fetal bovine serum (DMEM/FBS) were used in our experiments.

extract_protocol: Chromatin samples (100 μg each) were diluted in 500 μl ChIP buffer (50 mM HEPES, pH 7.5, containing 150 mM NaCl, 0.5% Triton X100, 1 mM EDTA, 0.1% sodium deoxycholate, 0.1% SDS, and the Complete Proteinase Inhibitor Cocktail). The samples were pre-cleared by incubating for 1 h at 4ºC with 50 μl Protein G-coated magnetic Dynabeads suspension (Invitrogen). The H3ac, H3K4me2, H3K4me2 or H3K27me3 antibodies (10 μg each) and 50 μl Protein G-coated magnetic Dynabeads suspension were then added to the pre-cleared samples. Non-immune rabbit IgG was used as a control. To reduce non-specific binding, the beads were pre-treated for 1 h with the sonicated salmon sperm DNA (10 mg/ml). The final volume of the samples was made 600 μl using the ChIP buffer. ChIP samples were prepared in triplicate. The samples which did not contain the antibody were used as a control. The samples were then incubated at 4ºC for 12 h on a rotating platform. The beads were captured using a magnetic rack (Qiagen), washed 4 times in the ChIP buffer and twice in the ChIP buffer containing 0.5 M NaCl. The bound material was eluted from the beads at 37ºC for 30 min in 100 μl 0.1% NaHCO3-1% SDS. The soluble fraction was separated from the beads by centrifugation (10,000xg, 5 min). The soluble material was incubated 68ºC for 4 h in the presence of 0.5 M NaCl. RNA and proteins were digested using 10 μg/ml RNAse A (37ºC; 15 min) and 0.25 mg/ml Proteinase K (50ºC; 15 min), respectively. DNA was purified using the DNA GenElute PCR Clean-up System. DNA concentration was measured at 260 nM. The immunoprecipitated DNA samples (10 ng each) were amplified using the WGA2 whole genome amplification system. Amplification products were purified using the DNA GenElute PCR Clean-up System. DNA concentration was measured at 260 nM. The quality of the amplified DNA samples was confirmed using 2% agarose gel-electrophoresis.

treatment_protocol: Cells were treated for 10 min with 1% p-formaldehyde and then with sodium glycine (100 mM) to inactivate p-formaldehyde. Cells were next washed twice with ice-cold PBS, detached and collected by centrifugation. The pellet was re-suspended in 20 mM Tris-HCl, pH 7.5, containing 150 mM NaCl, 3 mM CaCl2, 0.2% Triton X-100 and the Complete Proteinase Inhibitor Cocktail (Roche). Chromatin DNA was digested at 37ºC for 10 min using micrococcal nuclease (Roche) to generate approximately 80% mono-nucleosomal and 20% di-nucleosomal DNA fragments. The reactions were stopped using 5 mM EDTA. Digested chromatin was solubilized for 15 min on ice using 0.2% SDS. The pellet was removed by centrifugation (10,000xg, 20 min).   For each chromatin sample a corresponding control fraction of the input DNA was prepared as follows. Genomic DNA samples (50 μg each) were incubated for 16 h at 65ºC with 0.5 NaCl. RNA and proteins were digested using 10 μg/ml RNAse A (37ºC; 15 min) and 1 mg/ml Proteinase K (50ºC; 1 h), respectively. DNA was purified using the DNA GenElute PCR Clean-up System. DNA fragmentation was confirmed using 2% agarose gel-electrophoresis. DNA concentration was measured at 260 nm.

tag: cell description

value: migratory cells

value: U251 glioma cells

tag: antibody

source_name: U251 genomic DNA (WCE)


title: U251 cells IP H3K27me3

source_name: U251 chromatin immunoprecipitated against H3K27me3


title: MCF7 cells IP POL2

source_name: MCF7 chromatin immunoprecipitated against POL2

value: non-migratory cells

value: MCF7 breast carcinoma

source_name: MCF7 genomic DNA (WCE)


title: MCF7 cells IP H3K4me2

source_name: MCF7 chromatin immunoprecipitated against H3K4me2


title: MCF7 cells IP H3acetyl

source_name: MCF7 chromatin immunoprecipitated against H3acetyl


title: U251 cells IP H3K4me2

source_name: U251 chromatin immunoprecipitated against H3K4me2


title: MCF-7 miRNA profile rep 2

description: Biological replicate 2 of 2

hyb_protocol: The labeled samples were then hybridized for 20 h at 55ºC with Agilent Human miRNA Microarray Version 2 designed using Sanger Database version 10.1 (http://microrna.sanger.ac.uk).

scan_protocol: scanned using a DNA microarray scanner G2565CA (Agilent)

data_processing: The raw data was processed using Feature Extraction software version 10.5 and normalized using DNA Analytics and GeneSpring 10 software (Agilent). Differentially expressed miRNAs with the signal intensities higher than two-fold than the background standard deviation were filtered by t-test with p<0.05.

label_protocol: Total RNA (100 ng) was labeled with a cyanine 3-pCp reagent using the miRNA Complete Labeling and Hybridization HybKit (Agilent).

extract_protocol: Total RNA was purified from cells using the miRNA Mini system (Qiagen).


title: MCF7 cells IP H3K27me3

source_name: MCF7 chromatin immunoprecipitated against H3K27me3


title: U251 cells IP POL2

source_name: U251 chromatin immunoprecipitated against POL2


title: WholeBlood_SubjectNo1_24hr_Rep1

source_name: Peripheral Whole Blood, SubjectNo1, 24hr after the start of exercise, replicate1


title: MCF-7 miRNA profile rep 1

description: Biological replicate 1 of 2


title: U251 miRNA profile rep 2

description: Biological replicate 2 of 2


title: U251 miRNA profile rep 1

description: Biological replicate 1 of 2


title: heat 37degC 0min

status: Public on Jan 01 2010

city: Potsdam-Golm

first: Dirk

last: Walther

address: Am Mühlenberg 1

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Molecular Plant Physiology

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ GeneChip Expression Analysis Technical Manual. The final concentration of cRNA is 60 ng/µl. Spike-in controls: pre-labelled cRNAs (Affymetrix, Cat. No. 900454) are spiked in at defined concentrations: - bioB: 1.5 pM; - bioC: 5 pM; - bioD: 25 pM; - cre: 100 pM. Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix) controlled by Affymetrix´ software GeneChip Operating System (GCOS). Primary data analysis was performed with Affymetrix´ software GeneChip Operating System (GCOS).

data_processing: probeset quantile normalization (Bioconductor, cerevisiae probes), RMA (RMAExpress, pombe probes)

organism: Saccharomyces cerevisiae

source_name: yeast culture in liquid medium

label_protocol: Control and cold samples: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II Kit (Cat. No. 1751). Heat Samples: cDNA synthesis and in vitro-transcription was done with Roche´s Microarray Target Amplification Kit (Cat No 3310191), in combination with Standard-in vitro-transcription with the Message Amp II Kit (#1751) from Ambion.

growth_protocol: Yeast cells of the strain S288C were grown in SD-Medium under optimal conditions of 28°C until they reached a OD600 of 1, afterwards cultures were shifted to ambient temperatures of 37°C, 10°C as well as kept at 28°C; a time series of 8 time points in a range of 24 hours was collected.

extract_protocol: For extraction of total RNA the MasterPure™ Yeast RNA Purification Kit (Epicentre Biotechnologies, Madison, Wisconsin, USA) was used. Subsequent RNA clean-up was performed using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: Samples were kept at -80°C until RNA extraction.

tag: temperature

tag: time


title: heat 37degC 15min


title: control 28degC 24h


title: control 28degC 8h


title: heat 37degC 2h


title: heat 37degC 24h


title: heat 37degC 1h


title: U251 Replica

description: Replica 2 of 2

hyb_protocol: according to manufacturers protocol

scan_protocol: according to manufacturers protocol

data_processing: Data were collected and the initial analysis was performed using GeneSpring software (Agilent). Only the statistically significant data (p<0.05) were analyzed further.

label_protocol: according to manufacturers protocol

extract_protocol: Total RNA was extracted from cultured cells (107) using TRIzol reagent (Invitrogen) and dissolved in DEPC-treated H2O to a final concentration 500 ng/µl.


title: MCF-7 Replica

description: Replica 2 of 2

value: MCF-7 breast carcinoma


title: DpDf siblings in family segregating for T5-6b DpDf plants; Meristem tissue; Biological replicate 3

city: Saint Paul

first: Irina

last: Makarevitch

state: MN

address: 1536 Hewitt Ave

department: Biology

institute: Hamline University

description: Gene expression in meristem tissues of DpDf seedlings segregating for T5-6b

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: The GCOS software package v1.2 (Affymetrix) was used for signal acquisition and initial analysis.  GeneSpring (Agilent Technologies, Palo Alto CA) software was used for GC-RMA (GC-content robust multi-array) processing of the .cel files that involved normalization between the arrays and a subsequent per gene normalization of the resulting values.

organism: Zea mays

source_name: Zea mays 14-day seedling meristem tissue; DpDf siblings in family segregating for T5-6b DpDf plants

label_protocol: Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).

growth_protocol: Maize stocks carrying a T5-6b translocation, backcrossed into the B73 genetic background for over 10 generations, were obtained from the University of Minnesota collection.  The interchange T5-6b carries a break at 5S.1 (ca. 350 cM on IBM2 2008 Neighbors genetic map; in contig 238, according to maizesequence.org) and between the middle and distal chromomere satellites of 6S (break occurs prior to 70 cM on IBM2 2008 Neighbors genetic map; in contig 257, according to maizesequence.org) (Phillips, 1969; Phillips and Suresh, 1997).  Duplicate-Deficient (DpDf) heterozygous plants were identified among progeny derived from crossing a female B73/T5-6b translocation heterozygote by a male B73 plant.  The DpDf plants contain one normal chromosome 6 and one 65 chromosome that is lacking the terminal chromomere of the chromosome 6 satellite and contains ~90% of the short arm of chromosome 5 (Makarevitch et al., 2008).  Thus, the DpDf plants are trisomic for the majority of the short arm of chromosome 5 and monosomic for a small region of chromosome 6.  For microarray experiments, three biological replicates were grown using standard greenhouse conditions (1:1 mix of autoclaved field soil and MetroMix; 16 hours light and 8 hours dark; daytime temperature of 300C and night temperature of 220C) and sampled for gene expression on the 14th day after planting between 9:00 and 10:00 am.  For each biological replicate, sibling seeds produced by self pollination of a DpDf plant that segregate for wild-type and DpDf plants were planted individually and thirty plants were collected and genotyped using an SSR marker (bnlg161) that is tightly linked to the translocation breakpoint on chromosome 5, as described in (Makarevitch et al., 2008).  A pool of eight wild-type plants and a separate pool of eight DpDf plants were generated for each of the biological replicates.  For each plant, a shoot apical meristem-enriched tissue (approximately 1cm of tissue from the shoot apical meristems containing leaf primordium) was collected for RNA isolation.  The sampled tissues were flash frozen in liquid nitrogen and stored at -800C prior to RNA isolation.

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

value: meristem

value: B73; segregating for T5-6b; DpDf

value: 14 day-old seedlings


title: control 28degC 4h


title: heat 37degC 4h


title: heat 37degC 30min


title: heat 37degC 8h


title: Wild type siblings in family segregating for T5-6b DpDf plants; Meristem tissue; Biological replicate 1

description: Gene expression in meristem tissues of wild type seedlings segregating for T5-6b

source_name: Zea mays 14-day seedling meristem tissue; wild type siblings in family segregating for T5-6b DpDf plants

treatment_protocol: A pool of eight wild-type plants and a separate pool of eight DpDf plants were generated for each of the biological replicates.  For each plant, a shoot apical meristem-enriched tissue (approximately 1cm of tissue from the shoot apical meristems containing leaf primordium) was collected for RNA isolation.  The sampled tissues were flash frozen in liquid nitrogen and stored at -800C prior to RNA isolation.

value: B73; segregating for T5-6b; wild type


title: control 28degC 15min


title: DpDf siblings in family segregating for T5-6b DpDf plants; Meristem tissue; Biological replicate 2


title: control 28degC 30min


title: control 28degC 2h


title: Wild type siblings in family segregating for T5-6b DpDf plants; Meristem tissue; Biological replicate 3


title: control 28degC 1h


title: MCF-7

description: Replica 1 of 2


title: cold 10degC 24h


title: DpDf siblings in family segregating for T5-6b DpDf plants; Meristem tissue; Biological replicate 1


title: U251

description: Replica 1 of 2


title: control 28degC 0min


title: cold 10degC 8h


title: Wild type siblings in family segregating for T5-6b DpDf plants; Meristem tissue; Biological replicate 2


title: cold 10degC 1h


title: cold 10degC 4h


title: cold 10degC 2h


title: cold 10degC 30min


title: cold 10degC 15min


title: cold 10degC 0min


title: Fe+ 4hr replicate 2

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

description: gene expression data from iron replete growth conditions

hyb_protocol: Arrays were hybridized using streptavidin phycoerythrin according to Affymetrix protocol ProkGE-WS2v3_450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Data was processed using Genechip Operating Software (GCOS) version 1.4 (Affymetix, Inc.)  GCOS data was then imported into GeneSpring GX 7.3.1 (Agilent Technologies) and normalized per chip by dividing each measurement by the 50th percentile of all the measurements in that sample and per gene by dividing each gene by the median of its measurements across all samples.  The cross-gene error model was operating based on replicates.  The normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering.

organism: Neisseria gonorrhoeae FA 1090

source_name: 4hr time point

label_protocol: Biotinylated cRNA was prepared according to Affymetrix Genechip® Expression Analysis Technical Manual prokaryotic protocol from 10ug of total RNA

growth_protocol: Cells were inoculated to an absorbance reading of 0.100  @600nm in CDM-0 and iron starved @ 37C on a shaker (225rpm) for 1-1.5 hours to an absorbance of 0.200.  The culture was then split into two flasks and iron (10uM final conc) added to one flask. Time points were collected from this point forward.  For a detailed description see: Ducey, T. F., M. B. Carson, J. Orvis, A. P. Stintzi, and D. W. Dyer. 2005.  Identification of the iron-responsive genes of Neisseria gonorrhoeae in microarray analysis in defined medium. J. Bacteriol 187, 4865-4874.

extract_protocol: RNA was isolated by a hot phenol method according to: Ducey, T. F., M. B. Carson, J. Orvis, A. P. Stintzi, and D. W. Dyer. 2005. J.  Identification of the iron-responsive genes of Neisseria gonorrhoeae in microarray analysis in defined medium. J. Bacteriol 187, 4865-4874. Cells were collected for RNA isolation at 1, 2, 3, and 4 hr.  RNA samples were then DNA digested on column (Qiagen RNeasy kit) with Qiagen RNase Free DNase  prior to quantifying. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: Ferric chloride was added to a final concentration of 10uM.

tag: time point

value: 4 hr

tag: growth condition

value: iron replete


title: Fe+ 4hr replicate 3


title: Fe+ 4hr replicate 1


title: Fe+ 2hr replicate 3

source_name: 2hr time point

value: 2 hr


title: Fe- 3hr replicate 1

description: gene expression data iron from deplete growth conditions

source_name: 3hr time point

value: 3 hr

value: iron deplete


title: Fe- 2hr replicate 2

description: gene expression data from iron deplete growth conditions


title: Fe- 4hr replicate 1


title: Fe- 4hr replicate 3


title: Fe+ 3hr replicate 3


title: Fe- 4hr replicate 2


title: Fe+ 2hr replicate 2


title: Fe+ 2hr replicate 1


title: Fe- 3hr replicate 3


title: Fe+ 3hr replicate 1


title: Fe+ 3hr replicate 2


title: Fe- 3hr replicate 2


title: Fe- 2hr replicate 3


title: Fe+ 1hr replicate 3

source_name: 1hr time point

value: 1 hr


title: Fe- 2hr replicate 1


title: Fe- 1hr replicate 3


title: Fe- 1hr replicate 1


title: Fe- 1hr replicate 2


title: Fe+ 1hr replicate 1


title: Fe+ 1hr replicate 2


title: RC-K8-R cells, untreated

city: Miami

first: Kristopher

middle: A

last: Sarosiek

state: FL

address: 1580 NW 10th Ave

institute: University of Miami

hyb_protocol: Labeled cDNA was hybridized to Agilent Oligo microarrays for 17 hours at 60oC according to manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the GenePix 4000A. The data were analyzed with GenePix Pro 5.1.

data_processing: Data extracted from the images were transferred to the software package Acuity 4.0 (Molecular Devices) for normalization and statistical analysis. Each array was normalized for signal intensities across the whole array and locally, using Lowess normalization. Features for further analysis were selected according to the following quality criteria: (1) at least 90% of the pixels in the spot had intensity higher than background plus two standard deviations; (2), there were less than 2% saturated pixels in the spot; (3) signal to noise ratio (defined as ratio of the background subtracted mean pixel intensity to standard deviation of background) was 3 or above for each channel; (4) the spot diameter was between 110 and 150 micron; (5) the regression coefficient of ratios of pixel intensity was 0.6 or above.  cDNA array results were filtered for absolute fold change of  = 2 and genes that were modulated similarly by IL-21 across similarly-responding cell lines were identified.

source_name: RC-K8-R cells, untreated

label_protocol: cDNA was resuspended in the carbonate buffer (pH 9.0 – 9.3) and mixed with the Cy3- and Cy5-NHS ethers (Amersham Biosciences, Piscataway NJ). After 1 hour incubation in the dark 20 mMol of hydroxylamine was added to quench the reaction, and labeled cDNA was purified using QIAquick PCR purification Kit (Qiagen).

growth_protocol: RC-K8 and RC-K8-R cells were grown in RPMI media supplemented with 10% FBS, Penicillin/Streptomycin, and L-Glutamine.  6mL of cells were seeded in a 6-well plate at 100K cells per mL.  Interleukin-21 was added at 100ng/mL for 6 hours.

tag: cell line

source_name: Human Reference Total RNA

tag: sample type

value: reference RNA


title: RC-K8 cells, treated with Interleukin-21


title: RC-K8-R cells, treated with Interleukin-21

source_name: RC-K8-R cells, treated with Interleukin=21


title: RC-K8 cells, untreated

source_name: RC-K8 cells, untreated


title: 16h_PolyRNA_serie3

status: Public on Dec 31 2009

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

country: France

institute: CIML - CNRS - INSERM

description: For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)

hyb_protocol: Standard Affymetrix hybridization procedure

scan_protocol: Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure

data_processing: The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix). The data were normalized using the GC-RMA algorithm and bioinformatic analysis was performed using the GeneSpring GX 7.0 software (Agilent)

molecule: polyA RNA

source_name: monocyte-derived dendritic cells

label_protocol: Standard Affymetrix labelling procedure

growth_protocol: Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.

extract_protocol: Polysomal RNA (Poly) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: 16h LPS

tag: Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 15th of December 2006. RNA extracted out of day5 MoDCs on the 9th of January 2007. (MoDC Poly # 10)


title: 4h_TotRNA_serie4

treatment_protocol: 4h LPS

tag: Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 12th of October 2006. RNA extracted out of day5 MoDCs on the 20th of October 2006. (MoDC Poly # 7)


title: 4h_TotRNA_serie2

tag: Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23rd of November 2006. RNA extracted out of day5 MoDCs on the 4th of December 2006. (MoDC Poly # 9)


title: 4h_PolyRNA_serie1

tag: Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.


title: 0h_TotRNA_serie3

treatment_protocol: NO LPS


title: 0h_PolyRNA_serie3


title: 16h_TotRNA_serie1


title: 4h_PolyRNA_serie2


title: 16h_TotRNA_serie3


title: 16h_TotRNA_serie2


title: 0h_TotRNA_serie2


title: 16h_PolyRNA_serie1


title: 4h_TotRNA_serie3


title: 0h_TotRNA_serie4


title: 0h_PolyRNA_serie1

treatment_protocol: Oh, NO LPS


title: 16h_PolyRNA_serie4


title: 0h_PolyRNA_serie4


title: 16h_TotRNA_serie4


title: 4h_PolyRNA_serie3


title: 4h_TotRNA_serie1


title: 0h_PolyRNA_serie2

tag: Monocyte isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 23h of November 2006. RNA extracted out of day5 MoDCs on the 4th of december 2006 (MoDC poly #9, serie 2)


title: 4h_PolyRNA_serie4


title: 0h_TotRNA_serie1

extract_protocol: Polysomal RNA (P = other) was enriched by sucrose gradient fractionation following the protocol originally developed by Garcia-Sanz and collaborators (Müllner, Immunology Methods Manual, 1997). Total RNA (T) was directly extracted out of DCs without fractionation. Total and Polysomal RNA were purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).

tag: Monocytes isolated from human peripheral blood mononuclear cells (PBMC). PBMC isolated on the 24th of July 2008. RNA extracted out of day5 MoDCs on the 28th of July 2006.


title: Pf0-1(pCAR1)_CustomExpress IncP-7 plasmid pCAR1 Tiling Array

status: Public on Dec 25 2009

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: RNA mapping on pCAR1 carried by Pf0-1

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 130 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using pCAR1_8b520435FF-3.bpmap for the forward strand and pCAR1_8b520435FR-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas fluorescens Pf0-1

source_name: cDNA prepared from succinate culture of Pf0-1(pCAR1)

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: 100 ml of NMM-4 (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 1.0 mg ml-1 sodium succinate or carbazole was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

tag: strain

tag: plasmid

tag: carbon source

value: succinate

tag: growth phase

value: exponential


title: KT2440(pCAR1)_CustomExpress IncP-7 plasmid pCAR1 Tiling Array

description: RNA mapping on pCAR1 carried by KT2440

organism: Pseudomonas putida KT2440

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)


title: KT2440(pCAR1)_Pseudomonas putida KT2440 chromosome Array

description: RNA mapping on KT2440(pCAR1) chromosome

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 50˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of ‘the Post Hyb Wash #2” to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using KT2440b520511FF-3.bpmap for the forward strand and KT2440b520511FR-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.


title: human age 347 months

city: Oslo

first: Kristin

last: Jensen

address: Kirkeveien 166

department: Department of Clinical Chemistry

country: Norway

institute: Ullevål University Hospital

description: Gene expression data from whole bone marrow stabilized on PAXgene medium

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Robust Multichip Average (RMA) was used to convert the intensity values to normalized expression values. Signal values were scaled by global methods to a target value of 100.

source_name: Human composite bone marrow, 347 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

tag: Female


title: KT2440_Pseudomonas putida KT2440 chromosome Array

description: RNA mapping on KT2440 chromosome

source_name: cDNA prepared from succinate culture of KT2440


title: human age 352 months

source_name: Human composite bone marrow, 352 months

tag: Male


title: human age 197 months

source_name: Human composite bone marrow, 197 months


title: PAO1(pCAR1)_CustomExpress IncP-7 plasmid pCAR1 Tiling Array

description: RNA mapping on pCAR1 carried by PAO1

organism: Pseudomonas aeruginosa PAO1

source_name: cDNA prepared from succinate culture of PAO1(pCAR1)


title: PAO1(pCAR1)_Pseudomonas aeruginosa PAO1 chromosome array

description: RNA mapping on PAO1(pCAR1) chromosome

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using PAO1b520519FF-3.bpmap for the forward strand and PAO1b520519FR-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.


title: human age 348 months

source_name: Human composite bone marrow, 348 months


title: human age 126 months

source_name: Human composite bone marrow, 126 months


title: human age 144 months

source_name: Human composite bone marrow, 144 months


title: human age 313 months

source_name: Human composite bone marrow, 313 months


title: human age 112 months

source_name: Human composite bone marrow, 112 months


title: human age 168 months

source_name: Human composite bone marrow, 168 months


title: human age 59 months

source_name: Human composite bone marrow, 59 months


title: human age 78 months

source_name: Human composite bone marrow, 78 months


title: human age 338 months

source_name: Human composite bone marrow, 338 months


title: human age 129 months

source_name: Human composite bone marrow, 129 months


title: human age 57 months

source_name: Human composite bone marrow, 57 months


title: human age 119 months

source_name: Human composite bone marrow, 119 months


title: human age 88 months

source_name: Human composite bone marrow, 88 months


title: human age 74 months

source_name: Human composite bone marrow, 74 months


title: human age 65 months

source_name: Human composite bone marrow, 65 months


title: PAO1_Pseudomonas aeruginosa PAO1 chromosome array

description: RNA mapping on PAO1 chromosome

source_name: cDNA prepared from succinate culture of PAO1


title: Pf0-1_Pseudomonas fluorescens Pf0-1 chromosome array

description: RNA mapping on Pf0-1 chromosome

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using PFO1b520543F-3-FWD.bpmap for the forward strand and PFO1b520543F-3-REV.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

source_name: cDNA prepared from succinate culture of Pf0-1


title: Growth of Salmonella in Maillard Reaction Product-3, Rep 2A

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

description: Genes analyzed using these programs were further sorted and grouped based on their function using our in-house software Salmonella Gene Sorter (SAGS).

hyb_protocol: The labeled cDNA was purified (Qiagen PCR purification kit) and hybridized with Salmonella Typhimurium/Typhi version 5  genome microarrays obtained from Pathogen Functional Genomics Resource Center (National Institute of Allergy and Infectious Diseases).  Briefly, the slides were prehybridized in a buffer containing 5X SSC, 0.1% SDS and 0.1% BSA, and then washed and blown to dry. The two differentially labelled cDNA samples were dried and the resuspended in hybridization solution [40% deionized formamide, 5X SSC, 0.1% SDS, 0.6 µg/µl sheared Salmon sperm DNA (Ambion)]. The labelled cDNA samples were hybridized with the slides at 42 °C for 18-20 h. After hybridization, the slides were washed in low stringency buffer (2X SSC, 0.1% SDS) for 2 min, then in medium stringency (0.1x SSC, 0.1% SDS) buffer for 5 min and finally high stringency buffer (0.1x SSC) for 10 min.

scan_protocol: Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 6.0 software and scans were saved as TIFF image.

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html software using one class mode.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella Typhimurium

label_protocol: cDNA was generated by using random hexamers (Invitrogen) as primers for reverse transcription. The primers were annealed (70°C for 10 min, followed by snap-freezing in ice for 1 min) to total RNA (2 μg) and were extended with SuperScript II reverse transcriptase (Invitrogen) with 0.1 M dithiothreitol 12.5 mM dNTP/ aa-UTP (Ambion, Austin, TX) mix at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then labeled with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacturer’s instruction.

growth_protocol: Overnight grown and washed S. Typhimurium LT2 cells (10 5 CFU mL-1) were used to inoculate 5 ml defined media containing glucose. The cells were collected by centrifugation (10 min at 3 800 rpm) in the mid-logarithmic phases

extract_protocol: Total bacterial RNA was extracted from 3 ml of culture which was mixed with 6 ml of bacterial RNA protect solution (Qiagen, Valencia, CA) and the mixture was centrifuged at 3000 rpm for 20 min in swinging-bucket rotor centrifuge to collect the cells. Pellets were resuspended in 1 ml of Trizol (Invitrogen, Grand Island, NY) and the cells were broken using the FastPrep system (Qbiogene, Irvine, CA) at a speed of 6.0 for 40 seconds. From the broken cell lysate RNA was extracted as per the manufacturer’s instructions. Extracted RNA was purified using the RNeasy mini kit (Qiagen). DNase treated and purified mRNA was used for microarray analysis.

tag: media

value: glucose

growth_protocol:
Overnight grown and washed S. Typhimurium LT2 cells (10 5 CFU mL-1) were used to inoculate 5 ml defined media containing only glu-lys3 (3 mg mL-1)
mixtures as a carbon source. The cells were collected by centrifugation (10 min at 3 800 rpm) in the mid-logarithmic phase.


title: Growth of Salmonella in Maillard Reaction Product-3, Rep 2B


title: Growth of Salmonella in Maillard Reaction Product-3, Rep 3A


title: Growth of Salmonella in Maillard Reaction Product-3, Rep 3B


title: Growth of Salmonella in Maillard Reaction Product-3, Rep 1A


title: Growth of Salmonella in Maillard Reaction Product-2, Rep 2A

growth_protocol:
Overnight grown and washed S. Typhimurium LT2 cells (10 5 CFU mL-1) were used to inoculate 5 ml defined media containing only glu-lys2 (0.6 mg mL-1)
mixtures as a carbon source. The cells were collected by centrifugation (10 min at 3 800 rpm) in the mid-logarithmic phase.


title: Growth of Salmonella in Maillard Reaction Product-2, Rep 1A


title: Growth of Salmonella in Maillard Reaction Product-1, Rep 3B

growth_protocol:
Overnight grown and washed S. Typhimurium LT2 cells (10 5 CFU mL-1) were used to inoculate 5 ml defined media containing only glu-lys1 (0.6 mg mL-1)
mixtures as a carbon source. The cells were collected by centrifugation (10 min at 3 800 rpm) in the mid-logarithmic phase.


title: Growth of Salmonella in Maillard Reaction Product-2, Rep 2B


title: Growth of Salmonella in Maillard Reaction Product-2, Rep 1B


title: Growth of Salmonella in Maillard Reaction Product-3, Rep 1B


title: Growth of Salmonella in Maillard Reaction Product-1, Rep 1B


title: Growth of Salmonella in Maillard Reaction Product-1, Rep 2A


title: Growth of Salmonella in Maillard Reaction Product-1, Rep 2B


title: Growth of Salmonella in Maillard Reaction Product-1, Rep 3A


title: Growth of Salmonella in Maillard Reaction Product-2, Rep 3A


title: Growth of Salmonella in Maillard Reaction Product-2, Rep 3B


title: Growth of Salmonella in Maillard Reaction Product-1, Rep 1A


title: HTM - miR control scramble- replica 2

status: Public on Dec 20 2009

city: Durham

first: Coralia

last: Luna

state: NC

address: 2351 Erwin Road

department: Ophthalmology

institute: Duke University

description: Human trabecular meshwork cells

hyb_protocol: Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U133A 2.0 microarray

scan_protocol: The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

data_processing: Technology: Affymetrix.GeneChip.HG-U133A_2.  Algorithm: RMA.  Normalization: quantile.  Baseline transformation: median of all samples   Summarization Algorithm: RMA    Technology: Affymetrix.GeneChip.HG-U133A_2   Normalization: Quantile   Baseline Transformation: Median of all samples   This experiment is created from experiment New Experiment   Summarization Algorithm: RMA    Technology: Affymetrix.GeneChip.HG-U133A_2   Normalization: Quantile   Baseline Transformation: Median of all samples

source_name: HTM - miR control scramble- replica 2

growth_protocol: HTM cells were growth in DMEM media with 10% FBS and antibiotics, 37OC 5% CO2.

extract_protocol: total RNA was extracted with RNAeasy mini kit and  DNAse treatment (Qiagen) .

treatment_protocol: HTM cells were transfected using  Amaxa technology (Lonza) and nucleofactor reagents for endothelial cells ( Lonza). Program T023

value: HTM


title: HTM-  miR 29b mimic- replica 2

description: Human trabecular meshwork cells

source_name: HTM-  miR 29b mimic- replica 2

label_protocol: Biotinylated cRNA, produced through in vitro transcription


title: HTM - miR control scramble- replica 3

description: Human trabecular meshwork cells

source_name: HTM - miR control scramble- replica 3


title: HTM-  miR 29b mimic- replica 1

description: Human trabecular meshwork cells

source_name: HTM-  miR 29b mimic- replica 1


title: HTM-  miR 29b mimic- replica 3

description: Human trabecular meshwork cells

source_name: HTM-  miR 29b mimic- replica 3


title: Pf0-1(pCAR1)_Pseudomonas fluorescens Pf0-1 chromosome array

description: RNA mapping on Pf0-1(pCAR1) chromosome

source_name: cDNA prepared from succinate culture of Pf0-1(pCAR1)


title: MRC5 fibroblasts_ young (PDL28) vs senescent (PDL63)_repOP2014

status: Public on Dec 15 2009

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description: A total of six arrays, including biological and technical replicates were hybridized. OP2014 is the reverse hybridization of OP2013

hyb_protocol: Complex probes containing Cy3-labeled cDNA and Cy5-labeled cDNA were denatured, hybridized to glass slides were denatured, hybridized to glass slides overnight at 42°C in a water bath. The slides were washed successively in 1XSSC–0.1% SDS, 1X SSC, and 0.2X SSC for 2 min each, then rinsed in 0.5X SSC and spin-dried.

scan_protocol: Hybridized arrays were scanned with a GenePix 4000A scanner (Axon Instruments, Foster City, CA) with variable voltages to achieve saturated signal intensities for about 1% of the total spot number. Acquired images were processed with GenePix Pro 3.0 software (Axon Instruments).

data_processing:
Raw data were uploaded to the NCI MicroArray Database (madb, http://nciarray.nci.nih.gov/) for median normalization, data extraction, and further analysis. Data were extracted based on these parameters:
Include Spots not flagged BAD or Not Found
AND Both Chan A and Chan B Signal/Background Ratios >= 1.000
AND Both Chan A and Chan B Signal >= 250
Override other Chan A & B criteria and Include if Chan A Signal >= 5000 OR Chan B Signal >= 5000
Exclude genes present in less than 50% arrays
Select genes with average ratio >= 2 or <= 0.5

source_name: MRC5 fibroblasts_young (PDL28)

label_protocol: Fluorescently labeled cDNA probes were generated from 40 µg total RNA by a single round of reverse transcription in the presence of aminoallyl-dUTP (Sigma, St. Louis, MO), followed by a coupling reaction to Cy5 monofunctional N-hydroxysuccinimide ester (Amersham Pharmacia, Piscataway, NJ).

extract_protocol: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturer’s instructions. RNA integrity was assessed by spectrophotometry with A260/A280 ratios > 1.7.

tag: cell type

value: MRC5 fibroblasts_young (PDL28)

source_name: MRC5 fibroblasts_senescent (PDL63)

label_protocol: Fluorescently labeled cDNA probes were generated from 40 µg total RNA by a single round of reverse transcription in the presence of aminoallyl-dUTP (Sigma, St. Louis, MO), followed by a coupling reaction to Cy3 monofunctional N-hydroxysuccinimide ester (Amersham Pharmacia, Piscataway, NJ).

value: MRC5 fibroblasts_senescent (PDL63)


title: Feather-10mg-R4

status: Public on Dec 10 2009

city: Hattiesburg

first: Arun

last: Rawat

state: MS

address: 118 College Drive # 5018

department: Biological Sciences

institute: University of Southern Mississippi

hyb_protocol: We followed the Agilent One-Color hybridization protocal for all aspects of the hybridization

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (MDS Analytical Technologies Inc., Toronto, Canada) was used to scan microarrays at 5 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies).  Background subtracted adjusted median signal intensities were normalized on a per-chip basis that transforms the signal intensity by dividing signal intensity for each gene, with the mean intensity in each array.

organism: Colinus virginianus

label_protocol: Agilent One-Color hybridization kits and protocol were used.  One microgram of RNA was used / biological replicate as starting material.

extract_protocol: RNA was fixed in RNA Later.  RNA was extracted using Qiagen, Mini-prep extraction columns.  RNA quality was assessed by NanoDrop analysis followed by Agilent, Bioanalyzer, NanoChip electrophoresis.

tag: dose

value: 10 mg 2,6 DNT

tag: tissue

value: Feather pulp


title: MRC5 fibroblasts_senescent (PDL63) vs young (PDL28)_repOP2011

description: A total of six arrays, including biological and technical replicates were hybridized

value: MRC5 fibroblasts_senescence (PDL63)


title: Liver-60mg-R2

value: 60 mg 2,6 DNT

value: Liver


title: Feather-60mg-R1


title: Liver-60mg-R4


title: Feather-10mg-R2


title: Liver-60mg-R3


title: Feather-60mg-R3


title: Feather-60mg-R4


title: Feather-0mg-R4

value: 0 mg 2,6 DNT


title: Feather-10mg-R3


title: Feather-60mg-R2


title: Feather-0mg-R2


title: MRC5 fibroblasts_senescent (PDL63) vs young (PDL28)_repOP2013

description: A total of six arrays, including biological and technical replicates were hybridized.


title: Feather-0mg-R3


title: MRC5 fibroblasts_senescent (PDL63) vs young (PDL28)_repOP515


title: Feather-0mg-R1


title: Feather-10mg-R1


title: 16h_PolyRNA_serie2

source_name: monocyte-derived dendritic cells


title: MRC5 fibroblasts_ young (PDL28) vs senescent (PDL63)_repOP2012

description: A total of six arrays, including biological and technical replicates were hybridized. OP2012 is the reverse hybridization of OP2011


title: MRC5 fibroblasts_ young (PDL28) vs senescent (PDL63)_repOP518

description: A total of six arrays, including biological and technical replicates were hybridized. OP518 is the reverse hybridization of OP515


title: Liver-10mg-R4


title: Liver-60mg-R1


title: Liver-10mg-R3


title: HTM - miR control scramble- replica 1

description: Human trabecular meshwork cells

source_name: HTM - miR control scramble- replica 1

tag: cell line


title: 7 NCEP 042408 7-8-08

city: Augusta

first: Lesleyann

last: Hawthorn

state: GA

department: Molecular Oncology

institute: Medical College of Georgia Cancer Center

description: Comparion data--colon tumor and normal were available at (http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx).

hyb_protocol: The hybridization cocktail was loaded on the Human Exon 1.0 ST GeneChip and hybridized for 16 hours at 45oC and 60 rpm

scan_protocol: The stained array was scanned at 532 nm using an Affymetrix GeneChip Scanner 3000, generating CEL files for each array.

data_processing: PARTEK background correction, quantile normalization and probe summarization was performed using RMA

source_name: colon

extract_protocol: Using a random hexamer incorporating a T7 promoter, double-stranded cDNA was synthesized from 500 ng total RNA from which the majority of the ribosomal RNA had been removed using a RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA). cRNA was generated from the double-stranded cDNA template though an in-vitro transcription reaction and purified using the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The RNA was hydrolyzed with RNase H and the cDNA purified. The cDNA was then fragmented by incubation with a mixture of UDG and APE 1 restriction endonucleases; and end-labeled via a terminal transferase reaction incorporating a biotinylated dideoxynucleotide. 5.5 ug of the fragmented, biotinylated cDNA was added to a hybridization cocktail,

tag: gender

value: female


title: 8 NCEP 050108 7-8-08

label_protocol: The cDNA was then fragmented by incubation with a mixture of UDG and APE 1 restriction endonucleases; and end-labeled via a terminal transferase reaction incorporating a biotinylated dideoxynucleotide. 5.5 ug of the fragmented, biotinylated cDNA was added to a hybridization cocktail,


title: 5 NCEP 030608 7-8-08

value: male


title: 9 NCEP 050808 7-8-08


title: 10 NCEP EPNC4 2-20-08


title: 3 NCEP 011408 2-20-08


title: 4a CEP 011808 2-12-08


title: 4 NCEP 011808 2-5-08


title: 6 NCEP 032608 7-8-08


title: 1a NCEP 010308 2-5-08


title: Liver-10mg-R1


title: 2 NCEP 010708 2-20-08


title: Liver-10mg-R2


title: Liver-0mg-R4


title: Liver-0mg-R1


title: Liver-0mg-R2


title: Liver-0mg-R3


title: 1 NCEP 010308 2-5-08


title: 3D7-2

status: Public on Dec 01 2009

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

description: total genomic DNA, fragmented and end-labeled

hyb_protocol: Affymetrix protocol FS450_0001

scan_protocol: Standard Affymetrix scan procedures

data_processing: Raw Affymetrix probe intensity data was used to generate 150bp running mean of the Log2 ratio of ChIP data divided by the average of two hybridizations of 3D7 gDNA.  Custom Matlab scripts available upon request from Elizabeth Winzeler.  Normalized data files for each chromosome are available on the Series record.

label: streptavidin-phycoerythrin (SAPE)

organism: Plasmodium falciparum

label_protocol: Fragmentation of amplified ChIP DNA, and end-labeling with Biotin-N6 ddATP.

extract_protocol: Formaldehyde cross-linking, sonication, immnunoprecipitation with Ab, isolation with beads, DNA purification with phenol/chloroform.

tag: antibody ip

tag: developmental stage

value: Mixed


title: 3D7-1


title: H3K9ac_troph

description: Cross-linked, sonicated gDNA immunoprecipitated with a histone H4 Ab, amplified and end-labeled

source_name: PTDP08022201 H3K9ac troph sonic

value: Trophozoite


title: H4_troph

source_name: PTDP08020601 H4 troph sonic


title: H4_schizont

source_name: PTDP08022205 H4 schizont sonic

value: Schizont


title: Mouse_+il-3 replicate 3 p53-/- time 0

status: Public on Dec 07 2009

city: Parkville

first: Anissa

last: Jabbour

state: Victoria

address: 1G Royal Parade

department: Cell Signalling and Cell Death

country: Australia

institute: Walter and Eliza Hall Institute

description: IL-3  study.

hyb_protocol: A total of 1.5ug of labelled cRNA was then prepared for hybridisation to the MouseWG-6_V1_1_R3 by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip).  A total hybridisation volume of 30ul is prepared for each sample and 30ul loaded into a single array on the MouseWG-6_V1_1_R3.  A total of 6 different labelled samples can be loaded into 6 individual arrays per beadchip.  The chip is hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip is washed using the appropriate protocols as outlined in the illumina manual.

scan_protocol: Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.  The scanner operating software, BeadStudio, converts the signal on the array into a TXT file for analysis.

data_processing: The Bioconductor/R package lumi was used to perform variance stabilizing transformation and quantile normalization

source_name: FDM, +il-3

label_protocol: A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. – IL1791).  The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

extract_protocol: Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

value: myeloid progenitor cells


title: Mouse_+il-3 replicate 1 p53-/- time 0

description: IL-3  study.


title: Mouse_+il-3 replicate 2 p53-/- time 0

description: IL-3  study.


title: H4_ring

source_name: PTDP08022204 H4 ring sonic

value: Ring


title: Mouse_-il-3 replicate 1 p53-/- time 6hrs

description: IL-3  study.

source_name: FDM, -il-3


title: Mouse_-il-3 replicate 3 time 18hrs

description: IL-3  study.

value: WT


title: Mouse_-il-3 replicate 2 p53-/- time 6hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 2 p53-/- time 18hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 1 p53-/- time 18hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 2 time 18hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 3 p53-/- time 6hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 2 time 6hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 1 time 18hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 1 time 6hrs

description: IL-3  study.


title: Mouse_-il-3 replicate 3 p53-/- time 18hrs

description: IL-3  study.


title: Mouse_+il-3 replicate 2 time 0

description: IL-3  study.


title: Mouse_+il-3 replicate 3 time 0

description: IL-3  study.


title: Mouse_+il-3 replicate 1 time 0

description: IL-3  study.


title: Mouse_-il-3 replicate 3 time 6hrs

description: IL-3  study.


title: Caruncular_Non-Pregnant_9786

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

hyb_protocol: 825ng of both Cy3 and Cy5 labelled aRNA was used for microarray hybridisation using the Agilent Gene Expression Hybridisation Kit (60-mer oligo microarray protocol version 4.0) (Agilent Technologies, Bioresearch Solutions Unit, 3500 Deer Creek Road, Palo Alto, CA 94034, USA).  Dye-labelled, fragmented aRNA was then added to each Agilent 44k 60-mer oligonucleotide microarray, hybridised over night (17 hours), washed and allowed to air dry.

scan_protocol: Arrays were then scanned using the Agilent DNA microarray scanner.

data_processing: Agilent feature extraction software version 7.1 was used to analyse the scanned Agilent microarray. The 44 scanned microarray image files were uploaded to the feature extraction software. Using the design file (015354) the feature extraction software locates features and converts the extracted data from each feature into a quantitative log ratio. The software removes pixel outliers, does statistics on the non outlier pixels, subtracts background from features and flags any outlier features. The software was then used to perform a LOWESS (locally weighted linear regression analysis) dye normalisation and to calculate a p-value for each feature.   Data analysis was performed with Genespring GX 7.3.1. (Agilent, Palo Alto, CA, USA). Microarray data were imported into Genespring using Agilent’s two-colour ‘Enhanced FE’ import scenario which included ‘Per Spot: Divide by control channel’ and ‘Per Chip: Normalize to 50th percentile’ normalisation steps. Filters applied to the data to improve the quality of the normalised dataset include; Firstly, filtering ‘on flags’ such that any probes that were not deemed ‘present or marginal’ (according to feature extraction spot quality guidelines) in at least 22 of the 44 arrays were omitted from analysis. Second, probes that did not have a minimum threshold of 300 raw intensity units in at least 22 of 44 arrays were also omitted from analysis. The raw intensity cut off value of 300 was determined based on the calculation of base over proportional (C=a/b) calculation, which is calculated by plotting the standard deviation of normalised values against the control values. The point at which the curve flattens out is where the data measurement becomes reliable or where C (control strength) = a/b (where a = base and b = the proportional coefficient).

organism: Bos taurus

label_protocol: One ug of RNA was amplified using the amino Allyl MessageAmp ™ aRNA Kit (Ambion, 2130 Woodward St, Austin TX, 78744) to generate amino allyl modified aRNA for use in microarray hybridisation.  aRNA quantity was measured by spectrophotometry using a ND-1000 (Nanodrop Technologies, Wilmington, DE).  Five ug of aRNA was then vacuum dried and labelled with Cy3 and Cy5 NHS ester dyes (Amersham Cy3 and Cy5 Mono-Reactive Dye Packs, GE Healthcare UK Ltd., Little Chalfont, Buckinghamshire). Labelled aRNA was then purified on column, quantified and dye coupling efficiency measured using the Nanodrop (Nanodrop Technologies, Wilmington, DE) instrument.

extract_protocol: Endometrial tissue was homogenised in Qiagen buffer RLT (QIAGEN GmbH, QIAGEN, Hilden, Germany) using FastPrep Lysing Matrix D tubes in a FastPrep instrument (MP Biomedicals, Solon, OH).   Total RNA was extracted using a Qiagen RNeasy kit (QIAGEN). All samples were DNase treated using the Ambion DNA-free kit (Ambion, Austin, TX) according to the manufacturer’s instructions. RNA quantity was determined by spectrophotometry in a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA integrity was checked using the Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).

treatment_protocol: All Animals had estrous cycles syncronised with 12 animals receiving grade 1 embryo transfers at day 7 of the reproductive cycle, animals were then slaughtered at day 17 of the reproductive cycle and endometrial tissue samples obtained.

tag: tissue type

value: caruncular endometrium

tag: reproductive state

value: non-pregnant (cycling)

source_name: Pooled endometrial tissue

value: intercaruncular and caruncular endometrium

value: pregnant and non-pregnant (cycling)


title: Caruncular_Non-Pregnant_9778 (repeat)


title: Caruncular_Non-Pregnant_9813 (repeat)


title: Caruncular_Non-Pregnant_9960 (repeat)


title: Caruncular_Non-Pregnant_1940


title: Caruncular_Non-Pregnant_1950


title: Intercaruncular_Non-Pregnant_9813

value: intercaruncular endometrium


title: Caruncular_Non-Pregnant_9778


title: Caruncular_Non-Pregnant_9813


title: Caruncular_Non-Pregnant_3811


title: Intercaruncular_Non-Pregnant_9786


title: Caruncular_Non-Pregnant_2952


title: Caruncular_Non-Pregnant_3972


title: Intercaruncular_Non-Pregnant_2970


title: Caruncular_Non-Pregnant_2970


title: Intercaruncular_Non-Pregnant_9778


title: Intercaruncular_Non-pregnant_2952


title: Intercaruncular_Non-Pregnant_9960


title: Intercaruncular_Non-Pregnant_1940


title: Intercaruncular_Non-Pregnant_1950


title: Intercaruncular_Non-Pregnant_3972


title: Intercaruncular_Non-Pregnant_3811


title: Before vs after surgery experiment: Pt.3.01408.081.QbM63.n.AC

city: Philadelphia

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

description:
CPT purified PBMC
Before vs after surgery experiment

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
Expression levels and normalization. Samples were processed as mixed batches (total of 12 batches) of patients and controls and hybridized to the Illumina WG-6v2 human whole genome bead arrays.  Raw data was processed by Bead Studio v. 3.0 software. Expression levels were exported for signal and negative control probes. The set of negative control probes was used to calculate average background level for further filtering and background subtraction steps. Average values of the signal probe expression data for the 137 patient (NSCLC) and 91 control (NHC) sample arrays were used as a base for normalization and all the arrays, including 18 PRE/18 POST samples and NYU samples, were quantile normalized against this base.
Array quality control. After each hybridization batch, we computed gene-wise global correlation as a median Spearman correlation across all pairs of microarrays from all batches using expression levels of all signal probes (>48K). Median absolute deviation of the global correlation was also calculated. Then for each microarray a median spearman correlation against all other arrays was computed. The arrays whose median correlation differs from global correlation more than 8 absolute deviations (threshold was picked empirically) were marked as outliers and were not used for further analysis.

source_name: PBMC

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: Class

value: POST

tag: Smoking

value: Q

tag: Race

value: b

tag: Gender

value: M

tag: Age

tag: COPD

value: n

tag: Dx

value: AC

tag: Stage


title: Caruncular_Non-Pregnant_9960


title: Before vs after surgery experiment: Pt.8.01433.082.QwM64.y.AC

value: w

value: y


title: Before vs after surgery experiment: Pt.3.01297.085.QwF69.y.LSCC

value: F

value: LSCC


title: Before vs after surgery experiment: Pt.4.01220.084.QwM62.n.LSCC


title: Before vs after surgery experiment: Pt.3.01246.079.QwF47.n.AC


title: Before vs after surgery experiment: Pt.4.01391.061.QwM69.y.NSCLC

value: NSCLC


title: Before vs after surgery experiment: Pt.8.01485.083.QwM68.n.AC


title: Before vs after surgery experiment: Pt.4.01240.077.QwF55.y.AC


title: Before vs after surgery experiment: Pt.3.01407.087.QwF87.n.LSCC


title: Before vs after surgery experiment: Pt.8.01252.078.QwF65.n.AC


title: Before vs after surgery experiment: Pt.3.01345.086.QwM72.y.LSCC


title: Before vs after surgery experiment: Pt.8.01498.089.NwF78.n.AC

value: N


title: Before vs after surgery experiment: Pt.4.01610.064.SwM68.n.NSCLC

value: S


title: Before vs after surgery experiment: P.3.01297.098.QwF69.y.LSCC

value: PRE


title: Before vs after surgery experiment: Pt.3.01394.062.QwF75.n.LSCC


title: Before vs after surgery experiment: P.4.01391.055.QwM69.y.NSCLC


title: Before vs after surgery experiment: P.3.01433.095.QwM64.y.AC


title: Before vs after surgery experiment: Pt.4.01319.060.QwF67.y.AC


title: Before vs after surgery experiment: Pt.3.01374.080.NwM83.n.AC


title: Before vs after surgery experiment: Pt.3.01278.059.QwM68.y.BAC

value: BAC


title: Before vs after surgery experiment: P.4.01220.097.QwM62.n.LSCC


title: Before vs after surgery experiment: P.3.01485.096.QwM68.n.AC


title: Before vs after surgery experiment: Pt.4.01417.088.QwM57.n.LSCC


title: Before vs after surgery experiment: P.3.01408.094.QbM63.n.AC


title: Before vs after surgery experiment: P.3.01246.092.QwF47.n.AC


title: Before vs after surgery experiment: P.3.01407.100.QwF87.n.LSCC


title: Before vs after surgery experiment: P.3.01394.056.QwF75.n.LSCC


title: Before vs after surgery experiment: P.4.01240.090.QwF55.y.AC


title: Before vs after surgery experiment: P.4.01417.101.QwM57.n.LSCC


title: Before vs after surgery experiment: P.3.01498.102.NwF78.n.AC


title: Before vs after surgery experiment: P.3.01252.091.QwF65.n.AC


title: Before vs after surgery experiment: P.4.01610.058.SwM68.n.NSCLC


title: Before vs after surgery experiment: P.8.01278.053.QwM68.y.BAC


title: Before vs after surgery experiment: P.3.01374.093.NwM83.n.AC


title: validation experiment: NYU_2_4_GGO

description:
CPT purified PBMC
validation experiment

value: NHC

value: GGO

tag: Stage:


title: validation experiment: NYU_2_18_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_13_N

description:
CPT purified PBMC
validation experiment


title: Before vs after surgery experiment: P.3.01345.099.QwM72.y.LSCC


title: validation experiment: NYU_2_11_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_7_GGO

description:
CPT purified PBMC
validation experiment


title: Before vs after surgery experiment: P.4.01319.054.QwF67.y.AC


title: validation experiment: NYU_2_17_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_12_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_15_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_5_GGO

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_1_1002R_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_8_GGO

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_14_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_2_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_16_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_3_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_6_GGO

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_9_GGO

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_10_N

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_1_975R_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_2_1_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_1_1111R_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_1_970R_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_1_1000R_AC

description:
CPT purified PBMC
validation experiment


title: Case/control experiment: P.5.01709.075.QwF76.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1709


title: validation experiment: NYU_1_1208R_AC

description:
CPT purified PBMC
validation experiment


title: validation experiment: NYU_1_1016R_AC

description:
CPT purified PBMC
validation experiment


title: Case/control experiment: P.2.01656.069.QwF80.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1656


title: Case/control experiment: P.5.01681.073.SwM52.n.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1681


title: validation experiment: NYU_1_971R_AC

description:
CPT purified PBMC
validation experiment


title: Case/control experiment: P.2.01674.071.QwM46.u.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1674

value: u


title: Case/control experiment: P.2.01713.076.QwM50.u.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1713

value: Q


title: validation experiment: NYU_1_964R_AC

description:
CPT purified PBMC
validation experiment


title: Case/control experiment: P.5.01647.068.QwM69.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1647


title: Case/control experiment: P.3.01622.030.QwF69.n.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1622


title: Case/control experiment: Pm.3.01630.032.QwM58.n.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1630


title: Case/control experiment: P.3.01631.033.QwF76.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1631


title: Case/control experiment: P.3.01600.026.QwM81.y.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1600


title: Case/control experiment: P.3.01614.029.QwM82.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1614


title: Case/control experiment: P.3.01602.027.QwM75.u.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1602


title: Case/control experiment: P.3.01604.028.QwF72.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1604


title: Case/control experiment: P.4.01598.009.SwF68.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1598


title: Case/control experiment: P.2.01632.066.SbM54.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1632

value: b


title: Case/control experiment: P.2.01643.067.QwM67.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1643

value: M


title: Case/control experiment: P.4.01592.023.QwM50.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1592


title: Case/control experiment: P.4.01595.024.QwF70.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1595

value: n


title: Case/control experiment: P.5.01591.022.QwF75.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1591

value: AC


title: Case/control experiment: P.4.01586.020.SwM70.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1586

value: w


title: Case/control experiment: P.4.01589.021.SwF57.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1589

value: y


title: Case/control experiment: P.4.01573.016.QwM43.u.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1573


title: Case/control experiment: P.4.01566.013.SwM69.u.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1566


title: Case/control experiment: P.4.01584.019.QwM78.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1584


title: Case/control experiment: P.3.01597.025.QwM45.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1597


title: Case/control experiment: P.4.01569.014.QwM74.n.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1569


title: Case/control experiment: P.5.01572.015.QbF77.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1572

value: F


title: Case/control experiment: P.5.01582.017.QwM61.u.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1582


title: Case/control experiment: P.8.01559.142.QwF72.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1559


title: Case/control experiment: P.4.01561.012.QwM60.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1561

value: LSCC


title: Case/control experiment: P.4.01550.008.NwM53.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1550

value: NSCLC


title: Case/control experiment: P.4.01548.007.QwM84.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1548


title: Case/control experiment: P.9.01519.144.QbM57.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1519


title: Case/control experiment: P.6.01489.250.QbF62.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1489


title: Case/control experiment: P.4.01557.010.QwM76.y.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1557


title: Case/control experiment: P.4.01560.011.NwF48.n.ACx

description:
CPT purified PBMC
Case/control experiment
NSCLC.1560

value: N


title: Case/control experiment: P.6.01542.225.QbF59.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1542


title: Case/control experiment: P.6.01491.246.QwF66.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1491


title: Case/control experiment: P.4.01590.057.QwM71.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1590


title: Case/control experiment: P.4.01583.018.NaF57.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1583

value: a


title: Case/control experiment: P.9.01484.138.QwF73.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1484


title: Case/control experiment: P.8.01475.273.SwF73.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1475

value: S


title: Case/control experiment: P.8.01482.281.QwM73.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1482


title: Case/control experiment: P.6.01473.247.QwM56.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1473


title: Case/control experiment: P.9.01468.284.SwF73.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1468


title: Case/control experiment: P.8.01455.269.QwM73.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1455


title: Case/control experiment: P.9.01466.285.SwM73.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1466


title: Case/control experiment: P.4.01471.006.SwM67.y.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1471


title: Case/control experiment: P.9.01463.286.QwF73.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1463


title: Case/control experiment: P.9.01451.289.NwF52.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1451


title: Case/control experiment: P.9.01454.147.NwM73.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1454


title: Case/control experiment: P.8.01449.274.QwF73.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1449


title: Case/control experiment: P.6.01430.257.QwF61.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1430


title: Case/control experiment: P.6.01469.241.QwF65.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1469


title: Case/control experiment: P.6.01436.253.QbM53.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1436


title: Case/control experiment: P.8.01429.275.QwF77.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1429


title: Case/control experiment: P.10.01435.320.NwM65.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1435


title: Case/control experiment: P.6.01445.228.QwF56.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1445