title: LIVER EXP2 Liver3 GluMspI


title: 110spc4 micro PSY 3

status: Public on Aug 24 2012

type: RNA

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum 110spc4 strain grown microaerobically

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com).

label: biotin

molecule: total RNA

organism: Bradyrhizobium japonicum

source_name: B. japonicum strain 110spc4 grown microaerobically

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase which corresponded to an OD600 of 0.4 to 0.5 in microoxic cultures (PSY-arabinose medium)

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

treatment_protocol: Where indicated cultures were treated with 2 mM H2O2 for 10 min immediately prior to cell harvest

tag: strain

value: 110spc4 (wild type)

tag: growth condition

value: microaerobiosis

tag: medium

value: PSY


title: 0202 micro PSY 3

description: B. japonicum strain 0202 grown microaerobically


title: 0202 micro 2mM H2O2 10min PSY 3

description: B. japonicum strain 0202 grown microaerobically treated with 2 mM H2O2 for 10 min

source_name: B. japonicum strain 0202 grown microaerobically stressed with 2 mM H2O2 for 10 min

tag: treatment

value: 2 mM H2O2, 10 min


title: LIVER EXP2 Liver9 GluMspI

type: genomic

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: Post mortem liver samples from databanks: Curline & Cambridge Biosci.

hyb_protocol: Approximately 9 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. All array sets were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

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

data_processing:
We distinguished between three types of probes on the tiling microarray: “target probes”, which contain the restriction site CCGG, “flanking probes”, which do not contain the recognition sequence but could lie up to 200 bp upstream or downstream of a target probe (sheared DNA fragments were of average 200 bp), and “non-target probes” that neither contain a target sequence nor are within 200 bp (on either side) of the target sequence. After comparing different array preprocessing algorithms, we chose to use a sequence-based algorithm after Potter et al (Supplementary Note). The model (Supplementary Note, equation 1) was applied to non-target probes matched proportionally to target probes by GC content.  Normalized intensities were obtained by subtracting the fitted value from raw probe intensities, resulting in a normal distribution of probe-level intensities.  Each chip was independently normalized.  All downstream analyses were carried out at the single-probe level (i.e. without windowing or peak-calling) and solely on target probes. Probes overlapping repeats were excluded. Probes were required to have a ‘CCGG’ in both the Affymetrix probe sequence and the chromosomal sequence downloaded from UCSC; probes that did not meet this criterion were excluded.
EXP2_Human_BrainLiver_sample_metadata.xls, HumanBrain_sample_metadata.xls
BED files of normalized intensities for target probes. Unless otherwise specified, probes overlapping repeats are excluded. Unless otherwise specified, target probes that did not contain a CCGG in the UCSC genome sequence were also excluded.

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

label_protocol: 9 ug of PCR amplified DNA products were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Human and mouse untreated tissues were analyzed in this study

extract_protocol: Genomic DNA was extracted applying standard phenol chloroform and isopropanol precipitation method. Genomic DNA was then sheared to 200bp fragment length on Covaris S2 sonifier (Covaris, USA); blunt ended and ligated to adaptors before subjecting for glucosylation and restriction enzyme digestion. Glucosylation reaction was performed in presence of 200 µM uridine-5’-diphospho-α -D-glucose (UDP-Glc, Sigma) and 80ng BGT (Lariviere, Kurzeck et al. 2002) in 100mM Tris-HCl (pH 8.0) and 25mM MgCl2 for 3 h at 37ºC.

treatment_protocol: No treatment for human and mouse tissues. Only one human cell line underwent SAHA treatment protocol; stated in the sample description.

tag: age (y)

tag: Sex

value: F

tag: post-mortem interval

tag: tissue

value: Liver

tag: enzymatic digestion

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: 110spc4 micro PSY 2


title: LIVER EXP2 Liver7 GluMspI


title: 110spc4 micro 2mM H2O2 10min PSY 2

description: B. japonicum strain 110spc4 grown microaerobically treated with 2 mM H2O2 for 10 min

source_name: B. japonicum strain 110spc4 grown microaerobically stressed with 2 mM H2O2 for 10 min


title: LIVER EXP2 Liver6 GluMspI

value: M


title: LIVER EXP2 Liver5 GluMspI


title: 110spc4 micro PSY 1


title: LIVER EXP2 Liver1 GluMspI


title: LIVER EXP2 Liver12 GluMspI


title: LIVER EXP2 Liver6 HpaII

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: LIVER EXP2 Liver11 GluMspI


title: LIVER EXP2 Liver7 HpaII


title: LIVER EXP2 Liver8 HpaII


title: LIVER EXP2 Liver5 HpaII


title: LIVER EXP2 Liver2 HpaII


title: LIVER EXP2 Liver3 HpaII


title: LIVER EXP2 Liver4 HpaII


title: LIVER EXP2 Liver9 HpaII


title: LIVER EXP2 Liver13 HpaII


title: LIVER EXP2 Liver12 HpaII


title: LIVER EXP2 Liver11 HpaII


title: LIVER EXP2 Liver10 HpaII


title: LIVER EXP2 Liver1 HpaII


title: LIVER EXP2 Liver5 MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: LIVER EXP2 Liver7 MspI


title: LIVER EXP2 Liver9 MspI


title: LIVER EXP2 Liver8 MspI


title: LIVER EXP2 Liver3 MspI


title: LIVER EXP2 Liver2 MspI


title: LIVER EXP2 Liver13 MspI


title: LIVER EXP2 Liver4 MspI


title: LIVER EXP2 Liver6 MspI


title: LIVER EXP2 Liver10 GluMspI


title: LIVER EXP2 Liver11 MspI


title: LIVER EXP2 Liver12 MspI


title: LIVER EXP2 Liver10 MspI


title: BA10 EXP2 86 GluMspI

description: Post-mortem brain samples (BA10) of individuals with no diagnosis of major psychosis. Databanks: Stanley & Maclean

source_name: Frontal cortex of the brain (BA10)

value: Frontal cortex of the brain (BA10)


title: BA10 EXP2 80 GluMspI


title: BA10 EXP2 90 GluMspI


title: BA10 EXP2 38 GluMspI


title: BA10 EXP2 53 GluMspI


title: BA10 EXP2 1049 GluMspI


title: BA10 EXP2 1107 GluMspI


title: BA10 EXP2 1087 GluMspI


title: BA10 EXP2 24 GluMspI


title: BA10 EXP2 90 HpaII


title: BA10 EXP2 1003 GluMspI


title: BA10 EXP2 86 HpaII


title: BA10 EXP2 1029 GluMspI


title: BA10 EXP2 80 HpaII


title: BA10 EXP2 1049 HpaII


title: BA10 EXP2 38 HpaII


title: BA10 EXP2 1087 HpaII


title: LIVER EXP2 Liver1 MspI


title: BA10 EXP2 24 HpaII


title: BA10 EXP2 1029 HpaII


title: BA10 EXP2 1003 HpaII


title: BA10 EXP2 90 MspI


title: BA10 EXP2 80 MspI


title: BA10 EXP2 86 MspI


title: BA10 EXP2 56 MspI


title: BA10 EXP2 53 MspI


title: BA10 EXP2 56 GluMspI


title: BA10 EXP2 38 MspI


title: BA10 EXP2 1107 MspI


title: BA10 EXP2 24 MspI


title: BA10 EXP2 1049 MspI


title: BA10 EXP2 56 HpaII


title: BA10 EXP2 53 HpaII


title: BA10 EXP2 1107 HpaII


title: BA10 EXP2 1029 MspI


title: BA10 EXP2 1003 MspI


title: BA10 MBD UNBOUND sample9 GluMspI

extract_protocol:
Enrichment of methylated genomic DNA (5-mC) was performed with Methyl Miner kit (Invitrogen) according to the manufacturer's protocol. Each fraction (MBD-bound and -unbound) was then processed using the standard protocol of this study (genomic DNA glucosylation followed by restriction enzyme digestion).
Genomic DNA was extracted applying standard phenol chloroform and isopropanol precipitation method. Genomic DNA was then sheared to 200bp fragment length on Covaris S2 sonifier (Covaris, USA); blunt ended and ligated to adaptors before subjecting for glucosylation and restriction enzyme digestion. Glucosylation reaction was performed in presence of 200 µM uridine-5’-diphospho-α -D-glucose (UDP-Glc, Sigma) and 80ng BGT (Lariviere, Kurzeck et al. 2002) in 100mM Tris-HCl (pH 8.0) and 25mM MgCl2 for 3 h at 37ºC.

tag: sample type

value: MBD unbound


title: BA10 MBD UNBOUND sample79 GluMspI

description: Enrichment of methylated genomic DNA (5-mC) was performed with Methyl Miner kit (Invitrogen) according to the manufacturer's protocol. Each fraction (MBD-bound and -unbound) was then processed using the standard protocol of this study (genomic DNA glucosylation followed by restriction enzyme digestion).


title: BA10 MBD UNBOUND sample57 HpaII


title: BA10 MBD BOUND sample9 GluMspI

value: MBD bound


title: BA10 MBD UNBOUND sample70 HpaII


title: BA10 MBD BOUND sample79 GluMspI


title: BA10 MBD BOUND sample86 GluMspI


title: BA10 MBD UNBOUND sample105 HpaII


title: BA10 MBD UNBOUND sample86 HpaII


title: BA10 MBD UNBOUND sample9 HpaII


title: BA10 MBD UNBOUND sample79 HpaII


title: BA10 MBD UNBOUND sample70 GluMspI


title: BA10 MBD BOUND sample70 GluMspI


title: BA10 MBD BOUND sample105 GluMspI


title: BA10 MBD UNBOUND sample57 GluMspI


title: BA10 MBD UNBOUND sample105 GluMspI


title: BA10 MBD BOUND sample86 HpaII


title: BA10 MBD BOUND sample57 GluMspI


title: BA10 EXP2 1087 MspI


title: BA10 MBD BOUND sample79 HpaII


title: BA10 MBD BOUND sample9 HpaII


title: BA10 MBD BOUND sample105 HpaII


title: BA10 PSYCHOSIS 98 GluMspI

description: Post-mortem brain samples (BA10) of individuals with diagnosis of major psychosis (SCZ or BP). Databanks: Stanley & Maclean

tag: disease state

value: psychosis


title: BA10 PSYCHOSIS 74 GluMspI


title: BA10 MBD UNBOUND sample86 GluMspI


title: BA10 PSYCHOSIS 89 GluMspI


title: BA10 PSYCHOSIS 72 GluMspI


title: BA10 PSYCHOSIS 69 GluMspI


title: BA10 PSYCHOSIS 64 GluMspI


title: BA10 PSYCHOSIS 63 GluMspI


title: BA10 PSYCHOSIS 58 GluMspI


title: BA10 PSYCHOSIS 46 GluMspI


title: BA10 PSYCHOSIS 42 GluMspI


title: BA10 PSYCHOSIS 48 GluMspI


title: BA10 PSYCHOSIS 18 GluMspI


title: BA10 PSYCHOSIS 32 GluMspI


title: BA10 MBD BOUND sample70 HpaII


title: BA10 PSYCHOSIS 13 GluMspI


title: BA10 PSYCHOSIS 21 GluMspI


title: BA10 MBD BOUND sample57 HpaII


title: BA10 PSYCHOSIS 102 GluMspI


title: BA10 PSYCHOSIS 1119 GluMspI


title: BA10 PSYCHOSIS 05 GluMspI


title: BA10 PSYCHOSIS 1012 GluMspI


title: BA10 PSYCHOSIS 08 GluMspI


title: BA10 PSYCHOSIS 04 GluMspI


title: BA10 PSYCHOSIS 93 GluMspI


title: BA10 PSYCHOSIS 97 GluMspI


title: BA10 PSYCHOSIS 82 GluMspI


title: BA10 PSYCHOSIS 88 GluMspI


title: BA10 PSYCHOSIS 85 GluMspI


title: BA10 PSYCHOSIS 87 GluMspI


title: BA10 PSYCHOSIS 81 GluMspI


title: BA10 PSYCHOSIS 75 GluMspI


title: BA10 PSYCHOSIS 78 GluMspI


title: BA10 PSYCHOSIS 66 GluMspI


title: BA10 PSYCHOSIS 28 GluMspI


title: BA10 PSYCHOSIS 14 GluMspI


title: BA10 PSYCHOSIS 44 GluMspI


title: BA10 PSYCHOSIS 55 GluMspI


title: BA10 PSYCHOSIS 45 GluMspI


title: BA10 PSYCHOSIS 31 GluMspI


title: BA10 PSYCHOSIS 41 GluMspI


title: BA10 PSYCHOSIS 47 GluMspI


title: BA10 PSYCHOSIS 17 GluMspI


title: BA10 PSYCHOSIS 11 GluMspI


title: BA10 PSYCHOSIS 1113 GluMspI


title: BA10 PSYCHOSIS 20 GluMspI


title: BA10 PSYCHOSIS 26 GluMspI


title: BA10 PSYCHOSIS 1102 GluMspI


title: BA10 PSYCHOSIS 09 GluMspI


title: BA10 PSYCHOSIS 100 GluMspI


title: BA10 PSYCHOSIS 1098 GluMspI


title: BA10 PSYCHOSIS 1060 GluMspI


title: BA10 PSYCHOSIS 1126 GluMspI


title: BA10 PSYCHOSIS 03 GluMspI


title: BA10 PSYCHOSIS 98 HpaII


title: BA10 PSYCHOSIS 1009 GluMspI


title: BA10 PSYCHOSIS 74 HpaII


title: BA10 PSYCHOSIS 89 HpaII


title: BA10 PSYCHOSIS 73 GluMspI


title: BA10 PSYCHOSIS 72 HpaII


title: BA10 PSYCHOSIS 64 HpaII


title: BA10 PSYCHOSIS 69 HpaII


title: BA10 PSYCHOSIS 63 HpaII


title: BA10 PSYCHOSIS 48 HpaII


title: BA10 PSYCHOSIS 58 HpaII


title: BA10 PSYCHOSIS 42 HpaII


title: BA10 PSYCHOSIS 32 HpaII


title: BA10 PSYCHOSIS 46 HpaII


title: BA10 PSYCHOSIS 21 HpaII


title: BA10 PSYCHOSIS 20 HpaII


title: BA10 PSYCHOSIS 1089 GluMspI


title: BA10 PSYCHOSIS 18 HpaII


title: BA10 PSYCHOSIS 13 HpaII


title: BA10 PSYCHOSIS 14 HpaII


title: BA10 CTRL F 15 MspI

value: control


title: BA10 CTRL F 1141 MspI


title: BA10 CTRL F 1123 MspI


title: BA10 PSYCHOSIS 102 HpaII


title: BA10 PSYCHOSIS 1119 HpaII


title: BA10 PSYCHOSIS 05 HpaII


title: BA10 PSYCHOSIS 1012 HpaII


title: BA10 CTRL F 1087 MspI


title: BA10 CTRL F 1107 MspI


title: BA10 PSYCHOSIS 04 HpaII


title: BA10 CTRL F 1049 MspI


title: BA10 CTRL F 105 MspI


title: BA10 PSYCHOSIS 97 HpaII


title: BA10 CTRL F 1029 MspI


title: BA10 CTRL F 1003 MspI


title: BA10 PSYCHOSIS 93 HpaII


title: BA10 PSYCHOSIS 88 HpaII


title: BA10 PSYCHOSIS 28 HpaII


title: BA10 PSYCHOSIS 87 HpaII


title: BA10 PSYCHOSIS 85 HpaII


title: BA10 CTRL F 99 GluMspI


title: BA10 CTRL F 96 GluMspI


title: BA10 CTRL F 90 GluMspI


title: BA10 PSYCHOSIS 82 HpaII


title: BA10 CTRL F 86 GluMspI


title: BA10 PSYCHOSIS 81 HpaII


title: BA10 CTRL F 80 GluMspI


title: BA10 PSYCHOSIS 78 HpaII


title: BA10 CTRL F 83 GluMspI


title: BA10 PSYCHOSIS 08 HpaII


title: BA10 PSYCHOSIS 75 HpaII


title: BA10 PSYCHOSIS 55 HpaII


title: BA10 PSYCHOSIS 66 HpaII


title: BA10 CTRL F 77 GluMspI


title: BA10 PSYCHOSIS 73 HpaII


title: BA10 CTRL F 70 GluMspI


title: BA10 PSYCHOSIS 45 HpaII


title: BA10 PSYCHOSIS 47 HpaII


title: BA10 CTRL F 79 GluMspI


title: BA10 CTRL F 71 GluMspI


title: BA10 CTRL F 59 GluMspI


title: BA10 PSYCHOSIS 44 HpaII


title: BA10 CTRL F 67 GluMspI


title: BA10 PSYCHOSIS 41 HpaII


title: BA10 CTRL F 53 GluMspI


title: BA10 CTRL F 56 GluMspI


title: BA10 PSYCHOSIS 26 HpaII


title: BA10 CTRL F 49 GluMspI


title: BA10 PSYCHOSIS 31 HpaII


title: BA10 CTRL F 38 GluMspI


title: BA10 CTRL F 33 GluMspI


title: BA10 PSYCHOSIS 17 HpaII


title: BA10 PSYCHOSIS 1126 HpaII


title: BA10 PSYCHOSIS 1113 HpaII


title: BA10 CTRL F 24 GluMspI


title: BA10 CTRL F 19 GluMspI


title: BA10 PSYCHOSIS 1102 HpaII


title: BA10 CTRL F 1141 GluMspI


title: BA10 CTRL F 15 GluMspI


title: BA10 PSYCHOSIS 11 HpaII


title: BA10 PSYCHOSIS 1098 HpaII


title: BA10 CTRL F 1123 GluMspI


title: BA10 PSYCHOSIS 1089 HpaII


title: BA10 PSYCHOSIS 1060 HpaII


title: BA10 CTRL F 1107 GluMspI


title: BA10 PSYCHOSIS 1009 HpaII


title: BA10 CTRL F 1087 GluMspI


title: BA10 PSYCHOSIS 09 HpaII


title: BA10 PSYCHOSIS 100 HpaII


title: BA10 CTRL F 105 GluMspI


title: BA10 CTRL F 1029 GluMspI


title: BA10 CTRL F 1049 GluMspI


title: BA10 PSYCHOSIS 03 HpaII


title: BA10 CTRL F 99 HpaII


title: BA10 PSYCHOSIS 89 MspI


title: BA10 CTRL F 96 HpaII


title: BA10 PSYCHOSIS 74 MspI


title: BA10 CTRL F 90 HpaII


title: BA10 CTRL F 86 HpaII


title: BA10 CTRL F 83 HpaII


title: BA10 PSYCHOSIS 69 MspI


title: BA10 PSYCHOSIS 72 MspI


title: BA10 PSYCHOSIS 63 MspI


title: BA10 CTRL F 80 HpaII


title: BA10 PSYCHOSIS 64 MspI


title: BA10 CTRL F 79 HpaII


title: BA10 PSYCHOSIS 58 MspI


title: BA10 PSYCHOSIS 48 MspI


title: BA10 CTRL F 77 HpaII


title: BA10 PSYCHOSIS 98 MspI


title: BA10 CTRL F 70 HpaII


title: BA10 PSYCHOSIS 32 MspI


title: BA10 CTRL F 59 HpaII


title: BA10 CTRL F 1003 GluMspI


title: BA10 PSYCHOSIS 46 MspI


title: BA10 PSYCHOSIS 21 MspI


title: BA10 PSYCHOSIS 20 MspI


title: BA10 CTRL F 56 HpaII


title: BA10 PSYCHOSIS 28 MspI


title: BA10 CTRL F 49 HpaII


title: BA10 CTRL F 38 HpaII


title: BA10 PSYCHOSIS 18 MspI


title: BA10 CTRL F 71 HpaII


title: BA10 PSYCHOSIS 13 MspI


title: BA10 CTRL F 24 HpaII


title: BA10 PSYCHOSIS 1119 MspI


title: BA10 CTRL F 19 HpaII


title: BA10 CTRL F 15 HpaII


title: BA10 PSYCHOSIS 102 MspI


title: BA10 PSYCHOSIS 42 MspI


title: BA10 CTRL F 1141 HpaII


title: BA10 CTRL F 1123 HpaII


title: BA10 PSYCHOSIS 08 MspI


title: BA10 CTRL F 53 HpaII


title: BA10 CTRL F 67 HpaII


title: BA10 PSYCHOSIS 05 MspI


title: BA10 CTRL F 1107 HpaII


title: BA10 PSYCHOSIS 04 MspI


title: BA10 CTRL F 1087 HpaII


title: BA10 CTRL F 1049 HpaII


title: BA10 PSYCHOSIS 14 MspI


title: BA10 CTRL F 105 HpaII


title: BA10 PSYCHOSIS 93 MspI


title: BA10 PSYCHOSIS 88 MspI


title: BA10 PSYCHOSIS 97 MspI


title: BA10 CTRL F 1029 HpaII


title: BA10 CTRL F 33 HpaII


title: BA10 PSYCHOSIS 87 MspI


title: BA10 PSYCHOSIS 85 MspI


title: BA10 CTRL F 1003 HpaII


title: BA10 CTRL F 99 MspI


title: BA10 CTRL F 96 MspI


title: BA10 PSYCHOSIS 82 MspI


title: BA10 PSYCHOSIS 1012 MspI


title: BA10 PSYCHOSIS 78 MspI


title: BA10 CTRL F 86 MspI


title: BA10 CTRL F 83 MspI


title: BA10 PSYCHOSIS 73 MspI


title: BA10 CTRL F 80 MspI


title: BA10 PSYCHOSIS 66 MspI


title: BA10 PSYCHOSIS 55 MspI


title: BA10 CTRL F 79 MspI


title: BA10 PSYCHOSIS 45 MspI


title: BA10 PSYCHOSIS 47 MspI


title: BA10 PSYCHOSIS 44 MspI


title: BA10 CTRL F 67 MspI


title: BA10 CTRL F 70 MspI


title: BA10 PSYCHOSIS 41 MspI


title: BA10 PSYCHOSIS 31 MspI


title: BA10 CTRL F 56 MspI


title: BA10 PSYCHOSIS 26 MspI


title: BA10 CTRL F 90 MspI


title: BA10 PSYCHOSIS 81 MspI


title: BA10 CTRL F 49 MspI


title: BA10 CTRL F 59 MspI


title: BA10 PSYCHOSIS 17 MspI


title: BA10 CTRL F 33 MspI


title: BA10 CTRL F 38 MspI


title: BA10 PSYCHOSIS 1113 MspI


title: BA10 PSYCHOSIS 1126 MspI


title: BA10 PSYCHOSIS 1102 MspI


title: BA10 PSYCHOSIS 75 MspI


title: BA10 CTRL F 24 MspI


title: BA10 PSYCHOSIS 11 MspI


title: BA10 CTRL F 19 MspI


title: BA10 CTRL F 77 MspI


title: BA10 PSYCHOSIS 1098 MspI


title: BA10 CTRL F 71 MspI


title: BA10 CTRL F 53 MspI


title: BA10 PSYCHOSIS 1089 MspI


title: BA10 PSYCHOSIS 1060 MspI


title: BA10 PSYCHOSIS 100 MspI


title: BA10 PSYCHOSIS 1009 MspI


title: BA10 PSYCHOSIS 09 MspI


title: BA10 PSYCHOSIS 03 MspI


title: BA10 CTRL 90 GluMspI


title: BA10 CTRL 99 GluMspI


title: BA10 CTRL 96 GluMspI


title: Prostate_cancer_vs._benign_UW-01

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

hyb_protocol: Labeled cDNA probes were hybridized in a head-to-head fashion, normal versus neoplastic from the same individual, simultaneously to custom-made microarrays composed of 6,760 clones derived from the Prostate Expression Database, a public sequence repository of expressed sequence tag data derived from human prostate cDNA libraries (32). Microarrays were constructed as described previously with each cDNA represented twice per array (28). Following probe addition, coverslips were applied and microarrays were incubated at 63°C for 16 h in a humid hybridization chamber. Unbound probe was removed through washes with gradients of SSC buffer.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA). The image intensity data were gridded and extracted using GenePix Pro 4.1 software.

data_processing: GenePix Pro 4.1 software was used to grid and extract image intensity data. Spots of poor quality as determined by visual inspection were removed from further analysis. Normalization of the Cy3 and Cy5 fluorescent signal on each array was done using Silicon Genetics GeneSpring 7.3 software (Agilent Technologies). A print tip-specific Lowess curve was fit to the background-subtracted log intensity versus log ratio plot and 20.0% of the data were used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10, then 10 was used instead.

label_protocol: cDNA was separately synthesized from 3 μg of aRNA amplified from benign and neoplastic epithelium in a reaction volume of 30 μL containing 5 μg random hexamers (Invitrogen); 0.5 mmol/L each of dATP, dCTP, and dGTP; 0.3 mmol/L dUTP; 0.2 mmol/L aminoallyl-dUTP (Sigma); and 380 units of SuperScript II reverse transcriptase (Invitrogen). Reactants were incubated at 42°C for 120 min followed by the hydrolysis of RNA in 0.2N NaOH at 65°C for 15 min and neutralized by Tris-Cl (pH 7.4). cDNA was cleaned using a Microcon 30 filter (Millipore) to remove primers and salts followed by coupling to Cy3 and Cy5 fluorescent dyes (Amersham Biosciences). To eliminate potential dye bias, we randomly alternated Cy3 and Cy5 labeling to neoplastic and benign epithelium across 31 samples.

extract_protocol: Total RNA was extracted from laser captured epithelium using a Picopure RNA isolation kit according to the manufacturer's instructions (Molecular Devices). Extracted RNA underwent two rounds of amplification by a linear T7-RNA polymerase method developed by Van Gelder et al. (31) using a MessageAMP aRNA kit (Applied Biosystems/Ambion).

tag: gender

value: male

tag: age

value: prostate needle biopsy tissue frozen in OCT blocks


title: Prostate_cancer_vs._benign_KP-01


title: BA10 CTRL 77 GluMspI


title: BA10 CTRL 80 GluMspI


title: Prostate_cancer_vs._benign_UW-09


title: BA10 CTRL 79 GluMspI


title: BA10 CTRL 71 GluMspI


title: Prostate_cancer_vs._benign_KP-04


title: BA10 CTRL 70 GluMspI


title: Prostate_cancer_vs._benign_6082-03


title: BA10 CTRL 59 GluMspI


title: BA10 CTRL 67 GluMspI


title: Prostate_cancer_vs._benign_KP-05


title: BA10 CTRL 86 GluMspI


title: Prostate_cancer_vs._benign_KP-03


title: BA10 CTRL 83 GluMspI


title: Prostate_cancer_vs._benign_6082-02


title: MOUSE RESTBRAIN B29 GluMspI

description: Mouse brain was partitioned into frontal cortex and the rest of the brain.

organism: Mus musculus

source_name: Whole brain (including cerebellum and brain stem), minus the frontal cortex

value: 8 weeks


title: MOUSE RESTBRAIN B28 GluMspI

value: Whole brain (including cerebellum and brain stem), minus the frontal cortex


title: MOUSE RESTBRAIN B27 GluMspI


title: Prostate_cancer_vs._benign_6082-04


title: Prostate_cancer_vs._benign_6082-36


title: Prostate_cancer_vs._benign_KP-02


title: MOUSE RESTBRAIN B26 GluMspI


title: NiV_2

city: LYON

first: HORVAT

last: Branka

address: 21 avenue Tony Garnier

department: human virology

country: France

institute: INSERM

hyb_protocol: 10 µg of biotin-labeled RNA were fragmented using 5 µl fragmentation buffer in a final volume of 20 µl, then mixed with 240 µl Amersham hybridization solution and injected onto Codelink Uniset Human Whole Genome bioarrays. Arrays were hybridized overnight at 37°C, then washed in stringent TNT buffer at 46°C for 1 h before performing a streptavidin-cy5 detection step. Each array was incubated for 30 min in 3,4 ml streptavidin-cy5 solution, washed four times in 240 ml TNT buffer, rinsed twice in 240 ml water containing 0.2M Triton X-100, and then, dried by centrifugation at 650g.

scan_protocol: Arrays were then scanned at 635nm using an Axon Genepix 4000B Scanner (Axon).

data_processing: Data extraction and raw data normalization were performed using the CodeLink Gene Expression Analysis v4.0 software. Normalization was performed by the global method. The threshold was calculated using the normalized signal intensity of the negative controls supplemented by 3 times the standard deviation. Spots with signal intensity below this threshold were referred to as “absent”.

source_name: NiV-infected HUVEC

label_protocol: Amplified and biotin-labeled RNAs were obtained from 2µg of total RNA, by a round of in vitro transcription (dIVT) using the Message Amp a RNA kit version II (Ambion), following the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer’s protocol

tag: cell line

value: HUVEC

tag: infection

value: NiV (Nipah virus)


title: NiV_1


title: BA10 CTRL 56 GluMspI

value: F


title: MOCK_2

source_name: uninfected HUVEC

value: Mock


title: MOCK_1


title: BA10 CTRL 53 GluMspI

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: BA10 CTRL 49 GluMspI

value: M


title: BA10 CTRL 38 GluMspI


title: MOUSE RESTBRAIN B24 GluMspI


title: MOUSE RESTBRAIN B22 GluMspI


title: MOUSE RESTBRAIN B21 GluMspI


title: BA10 CTRL 33 GluMspI


title: MOUSE RESTBRAIN B20 GluMspI


title: MOUSE RESTBRAIN B18 GluMspI


title: MOUSE RESTBRAIN B17 GluMspI


title: MOUSE RESTBRAIN B16 GluMspI


title: BA10 CTRL 19 GluMspI


title: BA10 CTRL 1123 GluMspI


title: BA10 CTRL 1141 GluMspI


title: BA10 CTRL 15 GluMspI


title: MOUSE RESTBRAIN B25 GluMspI


title: BA10 CTRL 1107 GluMspI


title: BA10 CTRL 1087 GluMspI


title: MOUSE RESTBRAIN B29 HpaII

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: BA10 CTRL 1003 GluMspI


title: MOUSE RESTBRAIN B26 HpaII


title: BA10 CTRL 1049 GluMspI


title: BA10 CTRL 1029 GluMspI


title: MOUSE RESTBRAIN B28 HpaII


title: MOUSE RESTBRAIN B27 HpaII


title: BA10 CTRL 96 HpaII


title: MOUSE RESTBRAIN B24 HpaII


title: MOUSE RESTBRAIN B25 HpaII


title: BA10 CTRL 24 GluMspI


title: BA10 CTRL 99 HpaII


title: MOUSE RESTBRAIN B19 GluMspI


title: BA10 CTRL 90 HpaII


title: BA10 CTRL 86 HpaII


title: MOUSE RESTBRAIN B22 HpaII


title: MOUSE RESTBRAIN B21 HpaII


title: BA10 CTRL 83 HpaII


title: MOUSE RESTBRAIN B20 HpaII


title: MOUSE RESTBRAIN B15 GluMspI


title: MOUSE RESTBRAIN B14 GluMspI


title: MOUSE RESTBRAIN B19 HpaII


title: BA10 CTRL 79 HpaII


title: BA10 CTRL 105 GluMspI


title: BA10 CTRL 80 HpaII


title: MOUSE RESTBRAIN B18 HpaII


title: BA10 CTRL 77 HpaII


title: MOUSE RESTBRAIN B17 HpaII


title: MOUSE RESTBRAIN B16 HpaII


title: BA10 CTRL 71 HpaII


title: MOUSE RESTBRAIN B15 HpaII


title: BA10 CTRL 70 HpaII


title: BA10 CTRL 67 HpaII


title: MOUSE RESTBRAIN B14 HpaII


title: MOUSE RESTBRAIN B29 MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: BA10 CTRL 56 HpaII

value: Frontal cortex of the brain (BA10)


title: BA10 CTRL 53 HpaII


title: BA10 CTRL 59 HpaII


title: MOUSE RESTBRAIN B28 MspI


title: MOUSE RESTBRAIN B26 MspI


title: MOUSE RESTBRAIN B25 MspI


title: MOUSE RESTBRAIN B24 MspI


title: MOUSE RESTBRAIN B22 MspI


title: BA10 CTRL 33 HpaII


title: MOUSE RESTBRAIN B21 MspI


title: MOUSE RESTBRAIN B20 MspI


title: BA10 CTRL 15 HpaII


title: BA10 CTRL 38 HpaII


title: BA10 CTRL 19 HpaII


title: BA10 CTRL 24 HpaII


title: MOUSE RESTBRAIN B18 MspI


title: BA10 CTRL 1141 HpaII


title: BA10 CTRL 1107 HpaII


title: MOUSE RESTBRAIN B17 MspI


title: MOUSE RESTBRAIN B27 MspI


title: MOUSE RESTBRAIN B15 MspI


title: BA10 CTRL 105 HpaII


title: BA10 CTRL 1049 HpaII


title: BA10 CTRL 1029 HpaII


title: BA10 CTRL 1003 HpaII


title: BA10 CTRL 49 HpaII


title: BA10 CTRL 99 MspI


title: MOUSE FRONTALCTX FC29 GluMspI

source_name: Frontal cortex of the brain

value: Frontal cortex of the brain


title: MOUSE RESTBRAIN B14 MspI


title: MOUSE FRONTALCTX FC27 GluMspI


title: MOUSE FRONTALCTX FC26 GluMspI


title: MOUSE FRONTALCTX FC28 GluMspI


title: BA10 CTRL 96 MspI


title: MOUSE FRONTALCTX FC25 GluMspI


title: BA10 CTRL 86 MspI


title: MOUSE FRONTALCTX FC22 GluMspI


title: MOUSE RESTBRAIN B19 MspI


title: MOUSE FRONTALCTX FC21 GluMspI


title: MOUSE FRONTALCTX FC24 GluMspI


title: BA10 CTRL 1123 HpaII


title: BA10 CTRL 79 MspI


title: BA10 CTRL 83 MspI


title: MOUSE FRONTALCTX FC20 GluMspI


title: BA10 CTRL 1087 HpaII


title: MOUSE RESTBRAIN B16 MspI


title: BA10 CTRL 77 MspI


title: MOUSE FRONTALCTX FC19 GluMspI


title: MOUSE FRONTALCTX FC18 GluMspI


title: BA10 CTRL 71 MspI


title: MOUSE FRONTALCTX FC17 GluMspI


title: BA10 CTRL 80 MspI


title: MOUSE FRONTALCTX FC14 GluMspI


title: MOUSE FRONTALCTX FC15 GluMspI


title: BA10 CTRL 59 MspI


title: BA10 CTRL 67 MspI


title: MOUSE FRONTALCTX FC28 HpaII


title: BA10 CTRL 70 MspI


title: MOUSE FRONTALCTX FC16 GluMspI


title: BA10 CTRL 56 MspI


title: BA10 CTRL 53 MspI


title: MOUSE FRONTALCTX FC29 HpaII


title: BA10 CTRL 49 MspI


title: BA10 CTRL 90 MspI


title: MOUSE FRONTALCTX FC27 HpaII


title: BA10 CTRL 24 MspI


title: BA10 CTRL 33 MspI


title: BA10 CTRL 38 MspI


title: MOUSE FRONTALCTX FC26 HpaII


title: MOUSE FRONTALCTX FC25 HpaII


title: MOUSE FRONTALCTX FC24 HpaII


title: BA10 CTRL 19 MspI


title: BA10 CTRL 1141 MspI


title: MOUSE FRONTALCTX FC20 HpaII


title: MOUSE FRONTALCTX FC21 HpaII


title: BA10 CTRL 15 MspI


title: BA10 CTRL 1123 MspI


title: MOUSE FRONTALCTX FC19 HpaII


title: BA10 CTRL 1087 MspI


title: MOUSE FRONTALCTX FC18 HpaII


title: MOUSE FRONTALCTX FC17 HpaII


title: BA10 CTRL 105 MspI


title: MOUSE FRONTALCTX FC16 HpaII


title: BA10 CTRL 1029 MspI


title: MOUSE FRONTALCTX FC14 HpaII


title: BA10 CTRL 1049 MspI


title: MOUSE FRONTALCTX FC15 HpaII


title: BA10 CTRL 1003 MspI


title: MOUSE FRONTALCTX FC28 MspI


title: MOUSE FRONTALCTX FC27 MspI


title: MOUSE FRONTALCTX FC29 MspI


title: MOUSE FRONTALCTX FC25 MspI


title: MOUSE FRONTALCTX FC26 MspI


title: MOUSE FRONTALCTX FC22 HpaII


title: MOUSE FRONTALCTX FC18 MspI


title: MOUSE FRONTALCTX FC24 MspI


title: MOUSE FRONTALCTX FC21 MspI


title: MOUSE FRONTALCTX FC17 MspI


title: MOUSE FRONTALCTX FC20 MspI


title: MOUSE FRONTALCTX FC19 MspI


title: MOUSE FRONTALCTX FC22 MspI


title: MULTIORGAN A 93 Brain GluMspI

description: Organs were harvested from adult male mice.

data_processing:
We distinguished between three types of probes on the tiling microarray: “target probes”, which contain the restriction site CCGG, “flanking probes”, which do not contain the recognition sequence but could lie up to 200 bp upstream or downstream of a target probe (sheared DNA fragments were of average 200 bp), and “non-target probes” that neither contain a target sequence nor are within 200 bp (on either side) of the target sequence. After comparing different array preprocessing algorithms, we chose to use a sequence-based algorithm after Potter et al (Supplementary Note). The model (Supplementary Note, equation 1) was applied to non-target probes matched proportionally to target probes by GC content.  Normalized intensities were obtained by subtracting the fitted value from raw probe intensities, resulting in a normal distribution of probe-level intensities.  Each chip was independently normalized.  All downstream analyses were carried out at the single-probe level (i.e. without windowing or peak-calling) and solely on target probes. These samples contain probes overlapping repeats. They also contain probes that had a CCGG in the probe sequence but not in the UCSC genome sequence for the corresponding coordinates. Such probes will need to be excluded before replicating the exon-intron analysis.
We distinguished between three types of probes on the tiling microarray: “target probes”, which contain the restriction site CCGG, “flanking probes”, which do not contain the recognition sequence but could lie up to 200 bp upstream or downstream of a target probe (sheared DNA fragments were of average 200 bp), and “non-target probes” that neither contain a target sequence nor are within 200 bp (on either side) of the target sequence. After comparing different array preprocessing algorithms, we chose to use a sequence-based algorithm after Potter et al (Supplementary Note). The model (Supplementary Note, equation 1) was applied to non-target probes matched proportionally to target probes by GC content.  Normalized intensities were obtained by subtracting the fitted value from raw probe intensities, resulting in a normal distribution of probe-level intensities.  Each chip was independently normalized.  All downstream analyses were carried out at the single-probe level (i.e. without windowing or peak-calling) and solely on target probes. Probes overlapping repeats were excluded. Probes were required to have a ‘CCGG’ in both the Affymetrix probe sequence and the chromosomal sequence downloaded from UCSC; probes that did not meet this criterion were excluded.
EXP2_Human_BrainLiver_sample_metadata.xls, HumanBrain_sample_metadata.xls
BED files of normalized intensities for target probes. Unless otherwise specified, probes overlapping repeats are excluded. Unless otherwise specified, target probes that did not contain a CCGG in the UCSC genome sequence were also excluded.

source_name: Brain

value: Brain


title: MOUSE FRONTALCTX FC16 MspI


title: MOUSE FRONTALCTX FC15 MspI


title: MULTIORGAN A 92 Brain GluMspI


title: MOUSE FRONTALCTX FC14 MspI


title: BA10 CTRL 1107 MspI


title: MULTIORGAN A 91 Brain GluMspI


title: MULTIORGAN A 75 Kidney GluMspI

source_name: Kidney

value: Kidney


title: MULTIORGAN A 72 Heart GluMspI

source_name: Heart

value: Heart


title: MULTIORGAN A 73 Liver GluMspI

value: Liver


title: MULTIORGAN A 71 Brain GluMspI


title: MULTIORGAN A 61 Liver GluMspI


title: MULTIORGAN A 63 Liver GluMspI


title: MULTIORGAN A 55 Kidney GluMspI


title: MULTIORGAN A 53 Liver GluMspI


title: MULTIORGAN A 51 Brain GluMspI


title: MULTIORGAN A 74 Pancreas GluMspI

source_name: Pancreas

value: Pancreas


title: MULTIORGAN A 62 Liver GluMspI

value: 8 weeks


title: MULTIORGAN A 54 Pancreas GluMspI


title: MULTIORGAN A 3 Heart GluMspI


title: MULTIORGAN A 52 Heart GluMspI


title: MULTIORGAN A 1 Heart GluMspI


title: MULTIORGAN A 2 Heart GluMspI


title: MULTIORGAN A 31 Kidney GluMspI


title: MULTIORGAN A 33 Kidney GluMspI


title: MULTIORGAN A 123 Pancreas GluMspI


title: MULTIORGAN A 32 Kidney GluMspI


title: MULTIORGAN A 122 Pancreas GluMspI


title: MULTIORGAN A 93 Brain HpaII


title: MULTIORGAN A 91 Brain HpaII


title: MULTIORGAN A 74 Pancreas HpaII


title: MULTIORGAN A 75 Kidney HpaII


title: MULTIORGAN A 92 Brain HpaII


title: MULTIORGAN A 72 Heart HpaII


title: MULTIORGAN A 73 Liver HpaII


title: MULTIORGAN A 63 Liver HpaII


title: MULTIORGAN A 71 Brain HpaII


title: MULTIORGAN A 62 Liver HpaII


title: MULTIORGAN A 55 Kidney HpaII


title: MULTIORGAN A 54 Pancreas HpaII


title: MULTIORGAN A 53 Liver HpaII


title: MULTIORGAN A 52 Heart HpaII


title: MULTIORGAN A 51 Brain HpaII


title: MULTIORGAN A 3 Heart HpaII


title: MULTIORGAN A 33 Kidney HpaII


title: MULTIORGAN A 123 Pancreas HpaII


title: MULTIORGAN A 122 Pancreas HpaII


title: MULTIORGAN A 121 Pancreas HpaII


title: MULTIORGAN G 1 Heart GluMspI


title: MULTIORGAN A 93 Brain MspI


title: MULTIORGAN G 140 kidney GluMspI

value: 24 months


title: MULTIORGAN A 61 Liver HpaII


title: MULTIORGAN A 91 Brain MspI


title: MULTIORGAN A 32 Kidney HpaII


title: MULTIORGAN G 138 Liver GluMspI


title: MULTIORGAN A 2 Heart HpaII


title: MULTIORGAN A 1 Heart HpaII


title: MULTIORGAN A 121 Pancreas GluMspI


title: irCD1

city: Shinjuku-ku

first: Isao

last: Kobayashi

state: Tokyo

address: 35 Shinanoma-chi

department: Cell Differentiation

country: Japan

institute: Keio University

description: Zebrafish renal collecting ducts isolated from Tg(jam1a:EGFP).

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were calculated by RMA algorithm using the affy package of Bioconductor (http://www.bioconductor.org/).

label: Biotin

organism: Danio rerio

source_name: Adult zebrafish kidney

label_protocol: Biotinylated cRNAs were generated from total RNAs using GeneChip 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen) and purified on RNeasy Mini kit (Qiagen).

tag: genotype/variation

value: renal collecting ducts


title: MULTIORGAN A 74 Pancreas MspI


title: MULTIORGAN A 92 Brain MspI


title: CD1


title: MULTIORGAN G 137 Heart GluMspI


title: CD2


title: MULTIORGAN A 73 Liver MspI


title: Kidney1

description: Adult kidney tissue isolated from Tg(jam1a:EGFP) zebrafish

value: whole kidney tissue


title: MULTIORGAN G 136 Brain GluMspI


title: MULTIORGAN G 139 Pancreas GluMspI


title: Prostate_cancer_vs._benign_6082-34

value: male

value: prostate needle biopsy tissue frozen in OCT blocks


title: Kidney2


title: irCD2


title: MULTIORGAN A 75 Kidney MspI


title: Prostate_cancer_vs._benign_UW-03


title: MULTIORGAN A 72 Heart MspI


title: Prostate_cancer_vs._benign_UW-10


title: Prostate_cancer_vs._benign_UW-11


title: MULTIORGAN G 122 Pancreas GluMspI

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: Prostate_cancer_vs._benign_6082-32


title: Prostate_cancer_vs._benign_6082-25


title: MULTIORGAN A 71 Brain MspI

value: M


title: MULTIORGAN G 121 Pancreas GluMspI


title: Prostate_cancer_vs._benign_6082-24


title: Prostate_cancer_vs._benign_6082-31


title: Prostate_cancer_vs._benign_6082-16


title: Prostate_cancer_vs._benign_6082-28


title: MULTIORGAN A 63 Liver MspI


title: MULTIORGAN G 121 Brain GluMspI

value: 18 months


title: Prostate_cancer_vs._benign_6082-23


title: Prostate_cancer_vs._benign_6082-22


title: MULTIORGAN A 62 Liver MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: Prostate_cancer_vs._benign_6082-15


title: MULTIORGAN A 61 Liver MspI


title: MULTIORGAN G 92 Brain HpaII

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: CELL LINE sr5 GluMspI

description: DNA was extracted from S cell cycle stage cells of murine neuronal cell line (mHypoA-2/24).

source_name: Hypothalamic neurons (mHypoA-2/24 cell line)

tag: cell cycle stage

value: S


title: MULTIORGAN A 55 Kidney MspI


title: MULTIORGAN A 31 Kidney HpaII


title: MULTIORGAN G 91 Brain HpaII

value: Brain


title: Prostate_cancer_vs._benign_6082-13


title: CELL LINE sr4 GluMspI

value: Hypothalamic neurons (mHypoA-2/24 cell line)


title: CELL LINE sr6 GluMspI


title: CELL LINE sr3 GluMspI


title: MULTIORGAN A 54 Pancreas MspI


title: Prostate_cancer_vs._benign_6082-19


title: Prostate_cancer_vs._benign_6082-14


title: Prostate_cancer_vs._benign_6082-07


title: MULTIORGAN G 75 Kidney HpaII

value: Kidney


title: MULTIORGAN G 74 Pancreas HpaII


title: CELL LINE sr2 GluMspI


title: CELL LINE sr1 GluMspI


title: MULTIORGAN A 52 Heart MspI

value: Heart


title: MULTIORGAN A 53 Liver MspI

value: Liver


title: MULTIORGAN A 51 Brain MspI

value: 8 weeks


title: Prostate_cancer_vs._benign_UW-05


title: MULTIORGAN G 73 Liver HpaII


title: CELL LINE g2mr6 GluMspI

description: DNA was extracted from G2 cell cycle stage cells of murine neuronal cell line (mHypoA-2/24).


title: Prostate_cancer_vs._benign_6082-10


title: MULTIORGAN G 72 Heart HpaII


title: MULTIORGAN A 3 Heart MspI


title: CELL LINE g2mr5 GluMspI


title: MULTIORGAN A 33 Kidney MspI


title: CELL LINE g2mr4 GluMspI


title: MULTIORGAN G 62 Liver HpaII


title: MULTIORGAN A 32 Kidney MspI


title: MULTIORGAN G 32 Kidney HpaII


title: MULTIORGAN A 31 Kidney MspI


title: MULTIORGAN G 61 Liver HpaII


title: CELL LINE g2mr2 GluMspI


title: Prostate_cancer_vs._benign_6082-08


title: CELL LINE g2mr1 GluMspI


title: MULTIORGAN G 31 Kidney HpaII


title: MULTIORGAN A 2 Heart MspI


title: MULTIORGAN G 2 Heart HpaII


title: MULTIORGAN A 1 Heart MspI


title: MULTIORGAN G 1 Heart HpaII


title: CELL LINE g1r5 GluMspI

description: DNA was extracted from G1 cell cycle stage cells of murine neuronal cell line (mHypoA-2/24).


title: MULTIORGAN G 71 Brain HpaII


title: MULTIORGAN A 122 Pancreas MspI

value: Pancreas


title: CELL LINE g1r4 GluMspI


title: MULTIORGAN G 140 Kidney HpaII

value: 24 months


title: CELL LINE g2mr3 GluMspI


title: MULTIORGAN A 121 Pancreas MspI


title: MULTIORGAN G 139 Pancreas HpaII


title: mouse thymus tg B-IgM- 23

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

description: gene expression analysis of SuperAmplified™ polyA RNA

hyb_protocol: 0.5 μg Cy3 labeled and purified (CyScribe GFX Purification Kit, GE Healthcare) cDNAs in hybridization buffer were hybridized overnight (17 hours, 65°C) to 8x60K Agilent Whole Mouse Genome Oligo Microarrays using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated (37°C) Agilent Gene Expression Wash Buffer 2 containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES, v.10.7.3.1) was used to read out and process the microarray image files.

data_processing: FES derived output data files were further analyzed using GeneSpring GX (v11.5.1).

molecule: polyA RNA

source_name: transgenic mouse thymus

label_protocol: 250 ng of the purified PCR product (NucleoSpin® Extract II Kit, Macherey & Nagel) was labeled with Cy3-dCTP (GE Healthcare) in a Klenow Fragment reaction.

growth_protocol: Cells were directly isolated from indicated tissue sources by flow cytometry

extract_protocol: Cell samples were lysed using SuperAmp™ Lysis Buffer following manufacturer’s instructions and stored at -80°C. DNA microarray analysis of gene expression was performed at Miltenyi Biotec´s Genomics Service facility (Bergisch Gladbach, Germany), using Agilent technology (Agilent Technologies, Inc.). SuperAmplification was performed according to manufacturer’s instruction. Briefly, cell samples were collected in 6.4 μl lysis buffer (including detergent, tRNA and Protease), the mRNA extracted using magnetic beads and transcribed into cDNA using tagged random and oligo(dT) primer. First strand cDNA was 5’ tagged using terminal deoxynucleotidyl transferase (Fermentas). Tagged cDNA was globally amplified (Expand Long Template PCR System DNA Pol Mix, Roche) using primers complementary to the tag sequence. Amplified cDNAs were quantified using ND-1000 Spectrophotometer (NanoDrop Technologies, Inc). Integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies, Inc.)

treatment_protocol: Cells were directly lysed for RNA isolation

tag: sample group

value: B IgM- -/-

tag: genotype

value: -/-, Foxn1-deficient

tag: cell type

value: B IgM-, IgM surface negative B cells


title: mouse fetal-liver wt B-IgM+ 21

source_name: wild-type fetal mouse liver

value: B IgM+

value: B IgM+, IgM surface positive B cells


title: CELL LINE g1r3 GluMspI

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: MULTIORGAN G 138 Liver HpaII

value: M


title: CELL LINE g1r2 GluMspI


title: mouse thymus tg B-IgM- 22


title: mouse fetal-liver wt B-IgM+ 20


title: MULTIORGAN A 123 Pancreas MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: CELL LINE g1r6 GluMspI


title: CELL LINE g1r1 GluMspI


title: MULTIORGAN G 137 Heart HpaII

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: MULTIORGAN G 136 Brain HpaII

value: Brain


title: CELL LINE sr6 HpaII

value: Hypothalamic neurons (mHypoA-2/24 cell line)

value: S


title: MULTIORGAN G 122 Pancreas HpaII


title: CELL LINE sr5 HpaII


title: CELL LINE sr4 HpaII


title: MULTIORGAN G 121 Pancreas HpaII


title: mouse fetal-liver wt B-IgM- 18

value: B IgM-


title: CELL LINE sr3 HpaII


title: MULTIORGAN G 121 Brain HpaII

value: 18 months


title: mouse fetal-liver wt B-IgM+ 19


title: MULTIORGAN G 95 Brain MspI

value: 8 weeks


title: mouse fetal-liver wt B-IgM- 17


title: PANIC HyG-2

city: Dallas

first: Thomas

middle: Nathan

last: Person

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern

description: Sample name: 4466975071_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All data processing was performed with Genomestudio 2011.1.

source_name: Mammary tissues

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp 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.

value: Female

tag: strain

value: FVB (pure)

value: 10 weeks old

value: PANIC-ATTAC

value: mammary


title: MULTIORGAN G 95 Brain HpaII

tag: age (y)


title: mouse thymus wt SP8 15

source_name: wild-type mouse thymus

value: +/-, Foxn1 heterozygous

value: SP8, CD8 single-positive thymocytes


title: mouse fetal-liver wt B-IgM- 16

value: B IgM-, IgM surface negative B cells


title: CELL LINE sr1 HpaII

tag: Sex


title: mouse thymus wt SP8 14


title: mouse thymus wt SP8 13


title: MULTIORGAN G 92 Brain MspI

value: M

tag: post-mortem interval


title: mouse thymus wt SP4 12

value: SP4, CD4 single-positive thymocytes; SP8, CD8 single-positive thymocytes


title: WT control-2

description: Sample name: 4466975071_B

value: WT (control)

tag: tissue


title: PANIC HyG-1

description: Sample name: 4466975071_D


title: WT control-3

description: Sample name: 4466975071_C


title: PANIC HyG-3

description: Sample name: 4466975071_F


title: CELL LINE g2mr6 HpaII

tag: enzymatic digestion

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: mouse thymus wt SP4 11


title: MULTIORGAN G 91 Brain MspI

value: Brain

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: mouse thymus wt SP4 10


title: MULTIORGAN G 75 Kidney MspI

value: Kidney


title: CELL LINE g2mr5 HpaII

value: Hypothalamic neurons (mHypoA-2/24 cell line)


title: MULTIORGAN G 74 Pancreas MspI

value: 8 weeks

value: Pancreas


title: CELL LINE sr2 HpaII

value: S


title: PyMT/PANIC HyG-2

description: Sample name: 4466975070_E

source_name: Tumor tissues

value: Female

value: FVB (pure)

value: 10 weeks old

value: PyMT/PANIC

value: tumor


title: MULTIORGAN G 72 Heart MspI

value: Heart


title: CELL LINE g2mr1 HpaII


title: CELL LINE g2mr2 HpaII


title: MULTIORGAN G 71 Brain MspI

value: M


title: mouse thymus wt DN3 9

value: +/-, Foxn1 heterozygous

value: DN3, CD4/CD8-negative stage 3 thymocytes


title: MULTIORGAN G 62 Liver MspI

source_name: Liver

value: Liver


title: CELL LINE g2mr4 HpaII

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: CELL LINE g1r6 HpaII


title: PyMT/PANIC HyG-1

description: Sample name: 4466975070_D


title: PyMT control-3

description: Sample name: 4466975070_C

value: PyMT (control)


title: mouse thymus wt DN3 8


title: CELL LINE g2mr3 HpaII


title: CELL LINE g1r5 HpaII


title: MULTIORGAN G 73 Liver MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: MULTIORGAN G 61 Liver MspI


title: PyMT/PANIC HyG-3

description: Sample name: 4466975070_F


title: WT control-1

description: Sample name: 4466975071_A

value: WT (control)

value: mammary


title: mouse thymus tg DP 6A

value: -/-, Foxn1-deficient

value: DP, CD4/CD8 double-positive thymocytes


title: mouse thymus tg DP 6B


title: mouse thymus tg DP 4


title: PyMT control-1

description: Sample name: 4466975070_A

value: Female


title: mouse thymus wt DN3 7


title: PyMT control-2

description: Sample name: 4466975070_B

value: FVB (pure)


title: mouse thymus tg DP 6


title: CELL LINE g1r4 HpaII

value: Hypothalamic neurons (mHypoA-2/24 cell line)


title: CELL LINE g1r3 HpaII


title: MULTIORGAN G 31 Kidney MspI

value: 8 weeks

value: Kidney


title: CELL LINE g1r2 HpaII


title: CELL LINE g1r1 HpaII


title: CELL LINE sr6 MspI

value: S


title: MULTIORGAN G 1 Heart MspI

value: M

value: Heart


title: mouse thymus wt DP 2

value: +/-, Foxn1 heterozygous


title: MULTIORGAN G 32 Kidney MspI


title: MULTIORGAN G 140 Kidney MspI

value: 24 months


title: control #3

city: Saint Louis

first: laura

last: schuettpelz

state: MO

address: 660 S. Euclid

institute: washington university

hyb_protocol: Hybridization to Affymetrix Mouse Gene 1.0 ST array following manufacturer's recommendations

scan_protocol: Affymetrix software/protocol

data_processing: Data normalization using the Robust Multichip Average (RMA) algorithm and detection p-values were made using Affymetrix Expression Console software.

source_name: KLS cells

label_protocol: RNA was amplified using the NuGen Ovation System.

extract_protocol: KLS cells were sorted and RNA prepped used RNA XS columns (Machery-Nagel).

treatment_protocol: c-Kit+ cells were transduced with lentiviurs expressing KLF7 or control virus. 72 hrs post-transduction, KLS cells were sorted and RNA prepared.

value: bone marrow

value: Lin- c-Kit+ Sca-1+

tag: transduction

value: control


title: control #4


title: CELL LINE sr5 MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: control #2


title: KLF7 #4


title: MULTIORGAN G 139 Pancreas MspI

value: Pancreas


title: control #1


title: mouse thymus wt DP 3


title: MULTIORGAN G 138 Liver MspI

value: Liver


title: CELL LINE sr4 MspI


title: MULTIORGAN G 2 Heart MspI


title: MULTIORGAN G 137 Heart MspI


title: CELL LINE sr3 MspI


title: MULTIORGAN G 122 Pancreas MspI


title: MULTIORGAN G 136 Brain MspI

value: Brain


title: MULTIORGAN G 121 Pancreas MspI


title: CELL LINE sr1 MspI


title: CELL LINE g2mr6 MspI


title: CELL LINE g2mr5 MspI


title: MULTIORGAN G 121 Brain MspI

value: 18 months


title: CELL LINE g2mr4 MspI


title: MULTIORGAN G 95 Brain GluMspI

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: CELL LINE g2mr3 MspI

value: Hypothalamic neurons (mHypoA-2/24 cell line)


title: CELL LINE sr2 MspI


title: MULTIORGAN G 92 Brain GluMspI

value: 8 weeks


title: KLF7 #1


title: MULTIORGAN G 91 Brain GluMspI


title: MULTIORGAN G 75 kidney GluMspI

value: Kidney


title: CELL LINE g2mr1 MspI


title: CELL LINE g1r6 MspI


title: CELL LINE g2mr2 MspI


title: MULTIORGAN G 74 Pancreas GluMspI


title: MULTIORGAN G 73 Liver GluMspI


title: CELL LINE g1r5 MspI


title: CELL LINE g1r4 MspI


title: MULTIORGAN G 72 Heart GluMspI


title: CELL LINE g1r3 MspI


title: MULTIORGAN G 71 Brain GluMspI


title: KLF7 #2


title: CELL LINE g1r2 MspI


title: MULTIORGAN G 62 Liver GluMspI


title: CELL LINE g1r1 MspI


title: MULTIORGAN G 61 Liver GluMspI


title: mouse thymus wt DP 3A

value: DP, CD4/CD8 double-positive thymocytes


title: Pediatric Astrocytoma IV (glioblastoma)  A4-7124

city: San Francisco

first: Jane

last: Engler

state: CA

address: 1450 3rd Street

institute: UCSF

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Cy3 median signal intensities were recovered from Agilent Feature Extraction software output, converted to Log2 scale and quantile normalized between arrays, and duplicated probe signals were merged by taking their median values (see series normalized data file).

source_name: Pediatric Astrocytoma Tumor Sample 24

label_protocol: standard Agilent protocol

extract_protocol: Total RNA was extracted from flash-frozen pediatric astrocytoma samples. Total cellular RNA was extracted using Qiagen's RNA isolation kit according to manufacturer's protocol, and genomic DNA contamination was removed by an on-column Dnase digestion step. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

tag: tumor grade

value: IV (glioblastoma)

value: Pediatric Astrocytoma Tumor


title: Pediatric Astrocytoma IV (glioblastoma)  A4-4761

source_name: Pediatric Astrocytoma Tumor Sample 20


title: rsmA(40h)-wt replicate 3

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

country: Finland

institute: University of Helsinki

hyb_protocol: 200 ng of each labelled aRNA samples (one sample per dye and biological triplicate) were hybridized to the array according to the manufacturer's (Agilent Technologies) instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, page 31 onwards).

scan_protocol: The microarray slide was washed after hybridization according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5). The microarray slide was scanned using a Genepix 4110AL scanner (Axon Instruments). Using red dye channel for Cy5 labelled samples, green dye channel for Cy3 labelled samples and blue dye channel for Alexa488 labelled samples, using 100% PMT and a resolution of 5 um.

data_processing: The resulting images were analyzed with Agilent Genepix pro 6.1. Data generated from the scanning was then analyzed using Bioconductor with the limma software package for the R programming language. Normalization was achieved using quantile normalization, and empirical Bayesian variance shrinkage for statistical analysis, combining data from all probes for each gene. A false discovery rate (fdr) value of 0.05 was used as cut-off for significance in statistical analysis.

organism: Pectobacterium wasabiae

source_name: Bacterial colonies grown on culture medium supplemented with 10% potato extract

label_protocol: Aminoallyl-UTP containing aRNA was then hybridized to HyPer-5 (Cy5, Amersham), Cy3 (Amersham) or Alexa488 (Invitrogen) one dye per biological replicate. 5 µg of aRNA of each biological replicate of a sample was dried in a vacuum centrifuge, then resuspended in 7 µl sterile MQ water and 9 µl Na2CO3 buffer at pH 9.3, then 4 µl of dye was added. The samples were subsequently incubated at RT in darkness for 1 hour, then 4.5 µl 4M hydroxylamine was added and the samples were left to incubate at RT in darkness for an additional 15 minutes. Finally the samples were purified using the PureLink PCR purification kit (Invitrogen).

growth_protocol: Bacteria colonies were grown on M9 minimal medium (supplemented with 10% potato extract) agar plates. Wildtype was grown for 24 hours, while SCC3193 rsmA mutant were grown for 40 and 48 hours respectively.

extract_protocol: Total RNA from the SCC3193 strain was isolated following an Trizol reagent protocol supplied by the manufacturer (Invitrogen). The RNA was further treated with Dnase I (supplier: Fermentas) to remove genomic DNA traces according to the suppliers instructions. The RNA quality and quantity was checked using a NanoDrop and a Agilent BioAnalyzer (RNA Nano 6000 chip). Subsequently, 16S and 23S rRNA were removed from the samples, leaving mainly bacterial mRNA, using the Ambion MICROBExpress kit according to the manufacturer's protocol. Quality and quantity were checked after this step using Agilent BioAnalyzer and NonDrop. After this, the sampels were treated with the Ambion MessageAmp(TM) II Bacteria RNA Amplification kit, supplemented with 5-(3-aminoallyl)-UTP, according to the manufacturer's instructions to synthesize antisense RNA (aRNA) from the original RNA samples.

value: rsmA inactivation mutant cells

tag: growth protocol

value: grown 40 hours

value: wildtype cells

value: grown 24 hours


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-2390

source_name: Pediatric Astrocytoma Tumor Sample 8

value: III (anaplastic astrocytoma)


title: Pediatric Astrocytoma IV (glioblastoma)  A4-1983

source_name: Pediatric Astrocytoma Tumor Sample 13


title: Klf7-/- #1

label_protocol: RNA was amplified using the NuGen Ovation System

extract_protocol: KLS cells were sorted and RNA prepped used RNA XS columns (Machery-Nagel)

value: bone marrow

value: KLF7 KO

value: Lin- c-Kit+ Sca-1+


title: wild-type #3

description: KLS SLAM cells

hyb_protocol: Hybridization to Affymetrix Mouse Gene 1.0 ST array following manufacturer's recommendations.

source_name: KLS SLAM cells

extract_protocol: KLS SLAM cells were sorted and RNA prepped used RNA XS columns (Machery-Nagel).

value: wild-type

value: Lin- c-Kit+ Sca-1+ CD150+ CD48- CD41- cells


title: Klf7+/+ #2

value: wild type


title: Pediatric Astrocytoma IV (glioblastoma)  A4-4212

source_name: Pediatric Astrocytoma Tumor Sample 17


title: Pediatric Astrocytoma IV (glioblastoma)  A4-6906

source_name: Pediatric Astrocytoma Tumor Sample 23


title: Klf7+/+ #1


title: KLF7 #3


title: rsmA(48h)-wt replicate 3

value: grown 48 hours


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-3396

source_name: Pediatric Astrocytoma Tumor Sample 10


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-7432

source_name: Pediatric Astrocytoma Tumor Sample 12


title: wild-type #1

description: KLS SLAM cells


title: MULTIORGAN G 32 Kidney GluMspI

source_name: Kidney

value: 8 weeks

value: M

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: wild-type #2

description: KLS SLAM cells


title: Pediatric Astrocytoma IV (glioblastoma)  A4-4870

source_name: Pediatric Astrocytoma Tumor Sample 21

value: IV (glioblastoma)


title: Pediatric Astrocytoma IV (glioblastoma)  A4-3343

source_name: Pediatric Astrocytoma Tumor Sample 15

value: Pediatric Astrocytoma Tumor


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-7269

source_name: Pediatric Astrocytoma Tumor Sample 11


title: Pediatric Astrocytoma IV (glioblastoma)  A4-4532

source_name: Pediatric Astrocytoma Tumor Sample 18


title: MULTIORGAN G 31 Kidney GluMspI

value: Kidney


title: Pediatric Astrocytoma IV (glioblastoma)  A4-2975

source_name: Pediatric Astrocytoma Tumor Sample 14


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-1752

source_name: Pediatric Astrocytoma Tumor Sample 6


title: MULTIORGAN G 2 Heart GluMspI

source_name: Heart

value: Heart


title: Klf7-/- #2

source_name: KLS cells


title: Pediatric Astrocytoma IV (glioblastoma)  A4-6751

source_name: Pediatric Astrocytoma Tumor Sample 22


title: rsmA(40h)-wt replicate 2

source_name: Bacterial colonies grown on culture medium supplemented with 10% potato extract

value: rsmA inactivation mutant cells

value: grown 40 hours

value: wildtype cells


title: rsmA(48h)-wt replicate 2

value: grown 24 hours


title: Pediatric Astrocytoma IV (glioblastoma)  A4-3626

source_name: Pediatric Astrocytoma Tumor Sample 16


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-1762

source_name: Pediatric Astrocytoma Tumor Sample 7

value: III (anaplastic astrocytoma)


title: Pediatric Astrocytoma IV (glioblastoma)  A4-4635

source_name: Pediatric Astrocytoma Tumor Sample 19


title: Pediatric Astrocytoma II (diffuse low grade astrocytoma)  A2-3310

source_name: Pediatric Astrocytoma Tumor Sample 2

value: II (diffuse low grade astrocytoma)


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-1692

source_name: Pediatric Astrocytoma Tumor Sample 5


title: rsmA(40h)-wt replicate 1


title: Pediatric Astrocytoma II (diffuse low grade astrocytoma)  A2-4825

source_name: Pediatric Astrocytoma Tumor Sample 4


title: rsmA(48h)-wt replicate 1


title: Pediatric Astrocytoma II (diffuse low grade astrocytoma)  A2-4762

source_name: Pediatric Astrocytoma Tumor Sample 3


title: Pediatric Astrocytoma III (anaplastic astrocytoma)  A3-2570

source_name: Pediatric Astrocytoma Tumor Sample 9


title: Pediatric Astrocytoma II (diffuse low grade astrocytoma)  A2-3094

source_name: Pediatric Astrocytoma Tumor Sample 1


title: Ex vivo sorted T cell from spleen (3 days post adoptive transfer), replicate 1, Rat230_array-B

status: Public on Aug 23 2012

city: Göttingen

first: alexander

last: flügel

address: waldweg 33

department: Department of Neuroimmunology

institute: Institute for Multiple Sclerosis Research

description: CD4+ myelin specific T cells

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

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

data_processing: Gene expression profiles were background corrected and normalized on probe level using the variance stabilization method by Huber et al (Bioinformatics 2002;18:S96–104). Normalized probe intensities were summarized into gene expression levels using the additive model described in Irizarry et al (Nucleic Acids Res 2003;31:15)

organism: Rattus norvegicus

source_name: Spleen day 3

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

extract_protocol: RNA was isolated  using the Qiagen RNeasy mini kit according to the manufactor instruction

value: sorted T cell from spleen

value: Lewis rat

tag: age

value: 6-8 weeks

tag: gender

value: female

value: spleen


title: Ex vivo sorted T cell from spleen (3 days post adoptive transfer), replicate 2, Rat230_array-B

description: CD4+ myelin specific T cells


title: Resting T cell (7 days post invitro activation), replicate 3, Rat230_array-B

description: CD4+ myelin specific T cells

source_name: in vitro T cells day 7

value: CD4+ myelin specific T cells

tag: state

value: resting

tag: days after antigen challenge


title: 014465

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
RIV vs HT-29
Date:2007/03/15

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: RIV

label_protocol: Ambion

extract_protocol: Qiagen

tag: label

value: RIV

tag: extract

tag: sample

tag: subject

tag: cell line

tag: origin

value: Colon carcinoma


title: Resting T cell (7 days post invitro activation), replicate 4, Rat230_array-B

description: CD4+ myelin specific T cells

tag: cell type

tag: strain


title: 014464

description:
HT-29 vs RIV
Date:2007/03/15


title: Resting T cell (7 days post invitro activation), replicate 1, Rat230_array-B

description: CD4+ myelin specific T cells


title: Resting T cell (7 days post invitro activation), replicate 2, Rat230_array-B

description: CD4+ myelin specific T cells


title: PC 88N

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81111.gif

hyb_protocol: not provided

scan_protocol: After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: PC 88N2

growth_protocol:
All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.

tag: individual

value: PC 88N

tag: disease state

value: Normal

tag: tissue

value: prostate


title: PC 540N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81073.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 540N


title: Activated T cell blasts (2 days post invitro activation), replicate 2, Rat230_array-B

description: CD4+ myelin specific T cells

source_name: in vitro T cells day 2

value: blast


title: Activated T cell blasts (2 days post invitro activation), replicate 5, Rat230_array-B

description: CD4+ myelin specific T cells


title: Activated T cell blasts (2 days post invitro activation), replicate 4, Rat230_array-B

description: CD4+ myelin specific T cells


title: PC 537N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81132.gif

value: PC 537N


title: PC 343T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81114.gif

tag: ethnicity

value: Caucasian

tag: pre-operation treatment

value: PC 83T

tag: disease free survival


title: PC 188N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81104.gif

value: PC 188N


title: PC 563N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81162.gif

value: PC 563N


title: PC 375T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81116.gif

tag: age

value: PC 648T


title: PC 636T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81153.gif

value: PC 393T


title: PC 646N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81138.gif

value: PC 646N


title: PC 636N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81155.gif

value: PC 636N


title: PC 188T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81106.gif

value: PC 405T


title: PC 621T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81149.gif

value: PC 166T

value: Tumor


title: Activated T cell blasts (2 days post invitro activation), replicate 3, Rat230_array-B

description: CD4+ myelin specific T cells

value: CD4+ myelin specific T cells

tag: state

tag: days after antigen challenge

value: Lewis rat


title: PC 616T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81167.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 159T

value: prostate


title: PC 551N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81124.gif

value: PC 551N

value: Normal


title: Activated T cell blasts (2 days post invitro activation), replicate 1, Rat230_array-B

description: CD4+ myelin specific T cells

value: blast


title: PC 15T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81097.gif

source_name: PC 15T2

value: Caucasian

value: PC 97T


title: PC 343N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81115.gif

value: PC 343N


title: PC 579T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80847.gif

source_name: Human Reference RNA

source_name: PC 579T RNA

value: PC 621T


title: PC 97N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81120.gif

source_name: PC 97N2

value: PC 97N


title: PC 604N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81150.gif

value: PC 604N


title: PC 86T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81118.gif

source_name: PC 86T2

value: PC 643T


title: Resting T cell (7 days post invitro activation), replicate 4, Rat230_array-A

description: CD4+ myelin specific T cells

value: resting


title: PC 619T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81075.gif

value: PC 163T


title: Ex vivo sorted T cell from spleen (3 days post adoptive transfer), replicate 1, Rat230_array-A

description: CD4+ myelin specific T cells

value: sorted T cell from spleen

value: 6-8 weeks

tag: gender

value: female

value: spleen


title: Resting T cell (7 days post invitro activation), replicate 2, Rat230_array-A

description: CD4+ myelin specific T cells

value: CD4+ myelin specific T cells

value: Lewis rat


title: PC 370T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80897.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PC 370T

value: PC 184T

value: prostate


title: Resting T cell (7 days post invitro activation), replicate 3, Rat230_array-A

description: CD4+ myelin specific T cells


title: Activated T cell blasts (2 days post invitro activation), replicate 4, Rat230_array-A

description: CD4+ myelin specific T cells

value: blast


title: Activated T cell blasts (2 days post invitro activation), replicate 5, Rat230_array-A

description: CD4+ myelin specific T cells


title: Activated T cell blasts (2 days post invitro activation), replicate 3, Rat230_array-A

description: CD4+ myelin specific T cells


title: Resting T cell (7 days post invitro activation), replicate 1, Rat230_array-A

description: CD4+ myelin specific T cells


title: PC 2364T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81788.gif

source_name: REFERENCE RNA

value: Tumor


title: Activated T cell blasts (2 days post invitro activation), replicate 1, Rat230_array-A

description: CD4+ myelin specific T cells


title: Activated T cell blasts (2 days post invitro activation), replicate 2, Rat230_array-A

description: CD4+ myelin specific T cells


title: PC 370N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81134.gif

value: PC 370N

value: Normal


title: Ex vivo sorted T cell from spleen (3 days post adoptive transfer), replicate 2, Rat230_array-A

description: CD4+ myelin specific T cells


title: PC 205T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81786.gif

value: Caucasian

value: PC 452T


title: TB 2682T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81141.gif


title: Telencephalon cKO 3

city: Kyoto

first: Siok Lay

last: Tan

address: Sakyo-Ku, Shogoin Kawahara

institute: Kyoto University

description: Gene expression data from embryos at E14.5

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

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

data_processing: The data were analyzed with Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in SPF conditions.

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

treatment_protocol: Dorsal Telencephalon of WT or cKO (Emx2Cre) E14.5 embryos were dissected and dissolved in Trizol immediately until RNA extraction is performed.

value: male

value: dorsal telencephalon

tag: genotype

value: histone methyltransferase ESET KO

tag: genetic background


title: Telencephalon cKO 2


title: PC 252T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81101.gif

value: PC 248T


title: Telencephalon WT 3

value: wt


title: Telencephalon cKO 1


title: PC 599N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81158.gif

value: PC 599N


title: PC 233T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81787.gif

value: PC 223T


title: PC 645N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81081.gif

value: PC 645N


title: Telencephalon WT 2


title: PC 83T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81785.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PT 83

value: PC 601T


title: PC 629N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81071.gif

value: PC 629N

value: prostate


title: Telencephalon WT 1


title: PC 186T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81781.gif

value: PC 186T

value: Tumor


title: PC 237N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81109.gif

value: PC 237N

value: Normal


title: PC 646T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81136.gif

value: Caucasian

value: PC 488T


title: PC 335T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81790.gif

value: PC 21T


title: DRG_wildtype_L5_P0_TrkC-_rep3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description: WT P0 L5 TrkC- 3

hyb_protocol: The fragmented cRNA (15 µg) was used in a hybridization cocktail containing spiked controls (Affymetrix). A total of 200 µl of this hybridization cocktail was hybridized at 45°C for 16 hours to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: Following hybridization, the arrays were processed using a GeneChip Fluidics Station 400 according to recommended protocols (FS450_0001, Affymetrix). Fluorescent images of arrays were captured using the GeneChip Scanner 3000 7G (Affymetrix), and image data were acquired and analyzed using the Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: Raw data from CEL files was loaded into R using the R (v2.9) / Bioconductor (v1.6) package affy. Data was normalized with the rma function and present/absent calls were calculated using MAS5 normalization as implemented in the affy package.

source_name: DRG_wildtype_level specific_P0

label_protocol: Preparation of in vitro transcription (IVT) products was performed according to Affymetrix protocols (GeneChip Expression Analysis Technical manual, Rev. 5), with minor modifications.

extract_protocol: RNA extraction from isolated cells (Pico Pure RNA Isolation kit, KIT0204, Life Technologies)

treatment_protocol: DRG were exposed through dissection by ventral laminectomy and isolated in ice cold HBSS by pooling DRG from L1-L6 or separately by segmental level where needed (L1, L5). Isolated DRG were transferred to FCS-coated tubes using siliconized transfer pipettes, prior to dissociation in 0.25% trypsin/0.1% Collagenase H solution for 10 minutes at 37°C. HBSS was added to terminate enzymatic reaction, DRG pelleted by centrifugation (7 minutes, 800rpm), and resuspended in 1ml ice cold HBSS. Cells were dissociated by trituration using fire polished Pasteur pipettes to generate single cell suspension, and passed through 40 um gauze filters. For Fluorescent Activated Cell Sorting (FACS), a MoFlo (DAKO) high-speed 4-way cell sorter with a 3-laser setup (two water-cooled Coherent Enterprise II lasers; Model610 emitting at 488nm and Model653 allowing UV excitation; and one air-cooled Spectra Physics Helium-Neon laser emitting at 633nm) was used to separate GFPon from GFPoff cells.  To sort DRG sensory neurons, a 100μm nozzle was used at 20psi and sorted cells were collected in 1 ml Eppendorf tubes filled with 50μl Trizol to allow for subsequent RNA isolation. Average cell number used per data point was 350 for all experiments, except for L1/L5 p0 data sets, for which 100 cells were collected per sample.

tag: strain background

tag: genotype/variation

value: TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

tag: lumber/segmental level

value: FACS sorted DRG subpopulation


title: PC 21T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81789.gif

source_name: PT 21

value: PC 485T


title: PC 111T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81783.gif

value: PC 37T


title: PC 634N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80845.gif

source_name: PC 634N RNA

value: PC 634N


title: PC 180T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81780.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 180T


title: MIG#8

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner.

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Lymph node, CD4+ Tconv, pMIG empty vector

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: TRIzol.

value: 8 weeks

tag: Sex

value: female

value: lymph node

tag: cell type

value: conventional T cells (Tconv)

tag: transduced factors

tag: phenotype markers

tag: exclusion markers

tag: separation method

value: MoFlo Sorter


title: PC 555T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81085.gif

tag: reference

tag: ethnicity

tag: pre-operation treatment

tag: individual

value: PC 616T

tag: tissue

value: prostate


title: DRG_wildtype_L5_P0_TrkC+_rep3

description: WT P0 L5 TrkC+ 3

tag: age


title: PC 37T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81782.gif

source_name: PT 37

value: Caucasian

value: PC 188T

tag: disease free survival


title: PC 551T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81122.gif

value: PC 599T


title: MIG#9

tag: genetic background


title: PC 362T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81249.gif

value: PC 111T


title: DRG_wildtype_L1_P0_TrkC+_rep2

description: WT P0 L1 TrkC+ 2

tag: strain background

value: TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

value: FACS sorted DRG subpopulation


title: PC 593N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81147.gif

value: PC 593N

tag: disease state

value: Normal


title: PC 22T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81255.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PC 22T2

value: PC 26T


title: PC 563T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81160.gif

source_name: reference RNA

value: PC 619T


title: PC 582T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81164.gif

value: PC 625T


title: PC 564N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81201.gif

value: PC 564N


title: PC 92T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81784.gif

source_name: PT 92

value: PC 233T


title: GATA1+SATB1#3

source_name: Lymph node, CD4+ Tconv, GATA1+SATB1

value: 8 weeks

value: female

value: lymph node

value: conventional T cells (Tconv)

value: MoFlo Sorter


title: PC 229T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81779.gif

value: Caucasian

value: PC 636T

value: prostate


title: PC 103T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81778.gif

value: Tumor

value: PC 19T


title: DRG_wildtype_L1_P0_TrkC-_rep2

description: WT P0 L1 TrkC- 2

tag: genotype/variation

value: TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

tag: lumber/segmental level

value: FACS sorted DRG subpopulation


title: PC 527T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81293.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 527T


title: PC 540T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80822.gif

source_name: hoaa 012 RNA

value: PC 579T


title: PC 21T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81245.gif

value: PC 26T


title: DRG_wildtype_L5_P0_TrkC+_rep2

description: WT P0 L5 TrkC+ 2

tag: cell type


title: PC 411N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81202.gif

value: PC 411N

value: Normal


title: PC 527T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77939.gif

source_name: Reference RNA

source_name: PC 527T


title: EOS+LEF1#3

source_name: Lymph node, CD4+ Tconv, EOS+LEF1

value: 8 weeks

tag: Sex

value: female

value: lymph node

tag: transduced factors


title: EOS+LEF1#2

value: conventional T cells (Tconv)

tag: phenotype markers

tag: exclusion markers

value: MoFlo Sorter


title: PC 265T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81080.gif

tag: reference

value: African American

value: Hormonal

value: PC 366T

value: prostate


title: DRG_wildtype_L1_P0_TrkC-_rep3

description: WT P0 L1 TrkC- 3

value: TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)


title: DRG_wildtype_L5_P0_TrkC-_rep2

description: WT P0 L5 TrkC- 2

value: FACS sorted DRG subpopulation


title: PC 629T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81072.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: ethnicity

value: Caucasian

value: PC 361T


title: DRG_wildtype_L1_P0_TrkC-_rep1

description: WT P0 L1 TrkC- 1


title: GATA1+SATB1#1

tag: separation method


title: MIG#4

hyb_protocol: Affymetrix WT Sense Target Labeling Kit.

source_name: Lymph node, CD4+ T cells, pMIG empty vector

value: T cells


title: DRG_wildtype_L5_P0_TrkC-_rep1

description: WT P0 L5 TrkC- 1


title: EOS+LEF1#1


title: DRG_wildtype_L1_P0_TrkC+_rep1

description: WT P0 L1 TrkC+ 1


title: PC 22N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81305.gif

source_name: PC 22N2

tag: individual

value: PC 22N

value: Normal


title: DRG_wildtype_L5_EEadult_TrkC-_rep3

description: EE adult L5 3

value: wild type

tag: tissue

value: adult

tag: physical exercise

value: 5 weeks in a voluntary running wheel


title: DRG_wildtype_L5_P0_TrkC+_rep1

description: WT P0 L5 TrkC+ 1

tag: age


title: GATA1+SATB1#2

tag: genetic background

value: 8 weeks

value: female

value: lymph node

value: conventional T cells (Tconv)

value: MoFlo Sorter


title: PC 593T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81145.gif

tag: pre-operation treatment

value: PC 626T

tag: disease free survival

value: prostate


title: PC 393N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81243.gif

value: PC 393N

tag: disease state


title: PC 45T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81123.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PC 45T2

value: PC 455T


title: FITME

source_name: Lymph node, CD4+ T cells, FOXP3, intermediate FOXP3 expression

tag: foxp3 expression

value: intermediate level


title: PC 19T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81244.gif

value: Caucasian

value: PC 19T


title: FITLO

source_name: Lymph node, CD4+ T cells, FOXP3, low FOXP3 expression

tag: cell type

value: T cells

value: low level


title: PC 463T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81198.gif

value: PC 457T


title: DRG_wildtype_L5_EEadult_TrkC-_rep2

description: EE adult L5 2

tag: strain background

tag: genotype/variation

value: wild type

value: dorsal root ganglion (DRG)

value: adult

value: 5 weeks in a voluntary running wheel


title: DRG_wildtype_L1_EEadult_TrkC+_rep3

description: EE adult L1 3


title: PC 625N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81154.gif

value: PC 625N

value: Normal


title: FGME

source_name: Lymph node, CD4+ T cells, FOXP3+GATA1, intermediate FOXP3 expression

value: 8 weeks

tag: Sex

value: female

value: lymph node

tag: transduced factors

tag: phenotype markers

value: MoFlo Sorter


title: FITHI

source_name: Lymph node, CD4+ T cells, FOXP3, high FOXP3 expression

value: high level

tag: exclusion markers


title: DRG_wildtype_L5_EEadult_TrkC-_rep1

description: EE adult L5 1


title: PC 643T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81094.gif

tag: reference

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: ethnicity

value: Asian

value: PC 463T

value: prostate


title: FGLO

source_name: Lymph node, CD4+ T cells, FOXP3+GATA1, low FOXP3 expression

tag: tissue

value: T cells

value: low level

tag: separation method


title: DRG_wildtype_L1_EEadult_TrkC+_rep2

description: EE adult L1 2

value: wild type

tag: age

tag: physical exercise


title: PC 157N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81248.gif

tag: individual

value: PC 157N


title: PC 184N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81105.gif

value: PC 184N


title: FGHI

source_name: Lymph node, CD4+ T cells, FOXP3+GATA1, high FOXP3 expression

tag: genetic background


title: DRG_wildtype_L1_EEadult_TrkC+_rep1

description: EE adult L1 1

value: dorsal root ganglion (DRG)

value: adult

value: 5 weeks in a voluntary running wheel


title: PC 252N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81100.gif

value: PC 252N

tag: disease state

value: Normal


title: Xbp1#2

source_name: Lymph node, CD4+ Tconv, XBP1

value: 8 weeks

value: female

value: lymph node

value: conventional T cells (Tconv)


title: PC 621N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81151.gif

source_name: reference RNA

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 621N


title: DRG_wildtype_L5_adult_TrkC-_rep3

description: WT adult L5 3

source_name: DRG_wildtype_level specific_adult


title: PC 351T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81203.gif

value: Caucasian

tag: pre-operation treatment

value: PC 92T

tag: disease free survival

value: prostate


title: DRG_wildtype_L5_adult_TrkC-_rep2

description: WT adult L5 2

tag: strain background

value: wild type


title: Xbp1#3

tag: cell type

value: MoFlo Sorter


title: PC 99T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81077.gif

source_name: PC 99T2

value: PC 85T


title: X+F#3

source_name: Lymph node, CD4+ Tconv, XBP1+FOXP3

tag: Sex


title: PC 544T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81205.gif

value: PC 582T


title: PC 610T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81299.gif

value: PC 22T


title: DRG_wildtype_L5_adult_TrkC-_rep1

description: WT adult L5 1

tag: genotype/variation

value: dorsal root ganglion (DRG)

value: adult


title: X+F#2

tag: transduced factors

tag: phenotype markers


title: PC 167T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81246.gif

tag: reference

value: African American

value: PC 265T


title: Satb1#3

source_name: Lymph node, CD4+ Tconv, SATB1

value: 8 weeks

value: female

tag: exclusion markers


title: PC 582N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81112.gif

value: PC 582N

value: Normal

tag: tissue


title: PC 19T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81103.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PC 19T2

tag: ethnicity

value: PC 448T


title: PC 450N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81241.gif

value: PC 450N


title: PC 351T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81239.gif

value: Caucasian

tag: age

value: PC 351T

value: prostate


title: Satb1#2

value: lymph node

value: conventional T cells (Tconv)

tag: separation method

value: MoFlo Sorter


title: PC 45N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81125.gif

source_name: PC 45N2

tag: individual

value: PC 45N


title: PC 163T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81278.gif

value: PC 103T


title: PC 526T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81296.gif

value: PC 526T

value: Tumor


title: DRG_wildtype_L1_adult_TrkC+_rep2

description: WT adult L1 2

value: wild type

value: dorsal root ganglion (DRG)

value: adult

tag: physical exercise


title: DRG_mlcNT3_P0_TrkC-_rep2

description: mlcNT3 P0 TrkC- 2

value: MlcNT3 (Taylor et al., 2001)::TrkCGFP (Gong et al., 2010)

tag: lumber/segmental level

value: pooled (L1-L6)

value: FACS sorted DRG subpopulation


title: PC 574T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81144.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

value: PC 574T

tag: disease state


title: PC 389T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81287.gif

value: Hispanic

tag: pre-operation treatment

value: PC 205T

tag: disease free survival


title: PC 538T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81161.gif

value: Caucasian

value: PC 563T

value: prostate


title: PC 488T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81284.gif

value: PC 501T


title: PC 184T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81107.gif

value: PC 370T


title: S+F#3

source_name: Lymph node, CD4+ Tconv, SATB1+FOXP3

tag: genetic background

value: 8 weeks

value: female

value: lymph node

tag: cell type

value: conventional T cells (Tconv)

value: MoFlo Sorter


title: DRG_wildtype_L1_adult_TrkC+_rep1

description: WT adult L1 1

tag: strain background

tag: genotype/variation

value: wild type

value: dorsal root ganglion (DRG)

value: adult


title: DRG_wildtype_L1_adult_TrkC+_rep3

description: WT adult L1 3


title: PC 86N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81121.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

source_name: PC 86N2

value: PC 86N

value: Normal


title: PC 367N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81082.gif

value: PC 367N


title: DRG_mlcNT3_P0_TrkC+_rep1

description: mlcNT3 P0 TrkC+ 1

value: MlcNT3 (Taylor et al., 2001)::TrkCGFP (Gong et al., 2010)

value: pooled (L1-L6)

value: FACS sorted DRG subpopulation


title: MIG#2

source_name: Lymph node, CD4+ Tconv, pMIG empty vector

tag: Sex

tag: transduced factors

tag: phenotype markers


title: PC 601T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81290.gif

tag: reference

value: Caucasian

value: PC 646T

tag: tissue

value: prostate


title: DRG_mlcNT3_P0_TrkC+_rep2

description: mlcNT3 P0 TrkC+ 2

tag: age


title: MIG#3

value: 8 weeks

value: female

tag: exclusion markers

tag: separation method


title: PC 599T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81156.gif

tag: ethnicity

tag: individual

value: PC 634T


title: PC 366T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81108.gif

value: PC 167T


title: DRG_mlcNT3_P0_TrkC-_rep1

description: mlcNT3 P0 TrkC- 1

tag: lumber/segmental level


title: PC 19N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81098.gif

source_name: PC 19N2

value: PC 19N

tag: disease state


title: Lef1#4

source_name: Lymph node, CD4+ Tconv, LEF1

value: lymph node

value: conventional T cells (Tconv)

value: MoFlo Sorter


title: PC 223T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81199.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: pre-operation treatment

value: PC 538T

tag: disease free survival


title: PC 450N2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81302.gif

value: PC 450N

value: Normal


title: LEF1#3

tag: genetic background

tag: cell type


title: PC 648T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81143.gif

value: Asian

value: PC 544T


title: DRG_wildtype_P0_TrkC+_rep2

description: WT P0 TrkC+ 2

tag: strain background

tag: genotype/variation

value: TrkCGFP (Gong et al., 2010)

value: dorsal root ganglion (DRG)

value: pooled (L1-L6)

value: FACS sorted DRG subpopulation


title: PC 99N

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81079.gif

source_name: PC 99N2

value: PC 99N

value: prostate


title: L+F#3

source_name: Lymph node, CD4+ Tconv, LEF1+FOXP3

value: 8 weeks

tag: Sex

value: female

tag: transduced factors


title: PC 336T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81275.gif

tag: reference

value: Caucasian

value: PC 45T


title: S+F#2

tag: tissue

value: lymph node

value: conventional T cells (Tconv)

tag: phenotype markers

value: MoFlo Sorter


title: L+F#2

tag: age

tag: exclusion markers


title: DRG_wildtype_P0_TrkC+_rep1

description: WT P0 TrkC+ 1


title: PC 21T4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81263.gif

value: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines

tag: ethnicity

value: PC 26T


title: PC 625T

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81152.gif

tag: individual

value: PC 336T