title: Case/control experiment: P.6.01427.248.QwM58.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1427


title: Case/control experiment: P.7.01453.151.QwM78.y.AC

status: Public on Dec 01 2009

type: RNA

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

description:
CPT purified PBMC
Case/control experiment
NSCLC.1453

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: Class

value: NSCLC

tag: Smoking

value: Q

tag: Race

value: w

tag: Gender

value: M

tag: Age

tag: COPD

value: y

tag: Dx

value: AC

tag: Stage


title: Case/control experiment: P.6.01431.255.QwF64.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1431

value: F


title: Case/control experiment: P.8.01437.137.QbF73.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1437

value: b

value: LSCC


title: Case/control experiment: P.9.01444.128.QwM73.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1444


title: Case/control experiment: P.6.01415.256.QwM59.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1415


title: Case/control experiment: P.4.01439.005.NwM52.n.BAC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1439

value: N

value: n

value: BAC


title: Case/control experiment: P.9.01403.127.QwM67.u.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1403

value: u


title: Case/control experiment: P.8.01400.268.QwM80.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1400


title: Case/control experiment: P.8.01413.279.QwM77.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1413


title: Case/control experiment: P.9.01402.125.SwM41.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1402

value: S


title: Case/control experiment: P.9.01423.276.SwF76.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1423


title: Case/control experiment: P.8.01390.272.QwM80.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1390


title: Case/control experiment: P.10.01397.318.SwM67.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1397


title: Case/control experiment: P.9.01387.115.NwF53.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1387


title: AML_116_R_Hind

type: genomic

city: Ulm

first: Jan

last: Kroenke

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine III

country: Germany

institute: University Hospital of Ulm

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

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

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

data_processing: 1) CEL files and CHP files (generated by Affymetrix GTYPE) were processed by Copy Number Analyzer for GeneChip (CNAG) version 2.0 software or 2)CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. Normalization was performed against bone marrow or peripheral blood samples at remission from the same patient (paired analysis).

label: Biotin

molecule: genomic DNA

source_name: bone marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cells preparations obtained from peripheral blood using using the Qiagen ALL-Prep DNA/RNA Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: sample

value: Remission sample

tag: cell type

value: mononuclear cells

tag: disease state

value: Remission


title: AML_117_R_Hind


title: AML_119_R_Hind


title: Case/control experiment: P.4.01388.004.SwF48.n.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1388

value: NSCLC


title: Case/control experiment: P.9.01386.291.QwF45.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1386

value: Q


title: AML_114_R_Hind

source_name: peripheral blood


title: AML_115_R_Hind


title: AML_118_R_Hind


title: Case/control experiment: P.9.01362.110.QwM70.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1362

value: w


title: Case/control experiment: P.9.01373.287.QwF57.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1373


title: Case/control experiment: P.3.01375.034.QwM75.y.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1375

value: M


title: Case/control experiment: P.6.01346.249.QwF83.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1346

value: y


title: Case/control experiment: P.6.01368.236.QwF56.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1368

value: AC


title: Case/control experiment: P.6.01344.243.QwM68.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1344


title: Case/control experiment: P.9.01369.290.QwF73.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1369

value: F


title: AML_113_R_Hind


title: Case/control experiment: P.6.01340.230.QwM66.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1340


title: Case/control experiment: P.4.01352.003.QwF72.u.BAC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1352


title: Case/control experiment: P.6.01337.235.SbF65.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1337

value: b


title: Case/control experiment: P.8.01343.114.QwM62.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1343


title: AML_112_R_Hind


title: AML_111_R_Hind


title: Case/control experiment: P.4.01325.002.QwF67.y.NSCLC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1325


title: Case/control experiment: P.10.01323.321.QwF53.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1323


title: Case/control experiment: P.6.01316.239.QwF60.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1316


title: Case/control experiment: P.9.01339.146.QwF63.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1339

value: LSCC


title: AML_107_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: AML_110_R_Hind


title: Case/control experiment: P.10.01307.319.QwM69.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1307


title: Case/control experiment: P.10.01312.318.QwM74.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1312


title: Case/control experiment: P.10.01292.309.QwF79.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1292


title: Case/control experiment: P.8.01303.271.QwM62.u.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1303


title: AML_109_R_Hind


title: Case/control experiment: P.10.01287.308.QwF52.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1287


title: AML_106_R_Hind


title: Case/control experiment: P.9.01282.109.QwF72.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1282


title: Case/control experiment: P.10.01286.311.QwM50.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1286


title: Case/control experiment: P.9.01284.288.QwF73.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1284


title: Case/control experiment: P.10.01269.316.QwM68.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1269


title: AML_105_R_Hind


title: AML_102_R_Hind


title: AML_104_R_Hind


title: AML_103_R_Hind


title: Case/control experiment: P.8.01264.130.SwF78.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1264


title: Case/control experiment: P.10.01262.303.NwF63.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1262

value: N


title: AML_101_R_Hind


title: Case/control experiment: P.9.01233.280.QwM61.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1233

value: n


title: Case/control experiment: P.9.01254.292.SwF77.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1254


title: Case/control experiment: Pm.10.01227.304.QwM64.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1227


title: AML_099_R_Hind


title: AML_100_R_Hind


title: Case/control experiment: P.9.01221.105.QwM61.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1221


title: Case/control experiment: P.7.01216.238.SwF69.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1216


title: Case/control experiment: P.6.01222.231.QwM74.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1222


title: Case/control experiment: P.7.01224.229.SwF45.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1224


title: Case/control experiment: P.8.01200.113.QwF74.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1200


title: Case/control experiment: P.7.01211.232.SwF69.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1211


title: Case/control experiment: P.10.01202.315.QwF68.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1202


title: Case/control experiment: P.10.01204.310.QwM62.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1204


title: AML_098_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: Case/control experiment: P.10.01214.282.QwM61.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1214


title: AML_097_R_Hind


title: Case/control experiment: P.9.01280.133.QwF72.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1280


title: Case/control experiment: P.9.01196.278.QwF75.n.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1196


title: AML_096_R_Hind


title: AML_095_R_Hind


title: AML_093_R_Hind


title: Case/control experiment: P.10.01194.313.QwF55.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1194


title: AML_094_R_Hind


title: AML_092_R_Hind


title: Case/control experiment: P.10.01193.314.QwF70.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1193


title: Case/control experiment: P.6.01311.245.QwF75.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1311


title: Case/control experiment: P.8.01192.270.SwF57.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1192


title: Case/control experiment: P.8.01189.136.QwM74.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1189


title: Case/control experiment: P.6.01175.234.QwM68.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1175


title: Case/control experiment: P.10.01183.307.QwM79.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1183


title: Case/control experiment: P.6.01177.226.QwF67.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1177


title: Case/control experiment: P.9.01178.132.SwF75.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1178


title: AML_091_R_Hind


title: Case/control experiment: P.8.01171.277.QwM75.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1171


title: Case/control experiment: P.6.01166.224.QwF48.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1166


title: Case/control experiment: P.8.01155.112.QwF72.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1155


title: Case/control experiment: P.7.01167.237.SbF73.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1167


title: Case/control experiment: Pm.7.01153.227.SbM60.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1153


title: Case/control experiment: P.6.01143.233.QwM76.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1143


title: Case/control experiment: P.8.01154.111.QwM77.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1154


title: AML_088_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: AML_089_R_Hind


title: AML_086_R_Hind


title: Case/control experiment: P.10.01158.312.SwF59.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1158


title: AML_090_R_Hind


title: AML_087_R_Hind


title: AML_085_R_Hind


title: Case/control experiment: P.9.01138.131.QwM70.y.LSCC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1138


title: Case/control experiment: P.9.01140.126.QbM39.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1140


title: Case/control experiment: P.6.01141.240.QwF46.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1141


title: Case/control experiment: P.10.01137.306.QwM81.n.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1137


title: AML_084_R_Hind


title: Case/control experiment: P.10.01136.305.SwF62.y.AC

description:
CPT purified PBMC
Case/control experiment
NSCLC.1136


title: AML_083_R_Hind


title: Case/control experiment: C.2.01697.074.QbF68.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1697

value: NHC

value: GI

tag: Stage:


title: AML_082_R_Hind


title: Case/control experiment: C.2.01628.043.QwM72.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1628


title: Case/control experiment: C.5.01677.072.QwM88.u.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1677

value: u


title: Case/control experiment: C.2.01594.039.QwF70.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1594


title: Case/control experiment: C.5.01657.070.NwM46.n.SARC

description:
CPT purified PBMC
Case/control experiment
NHC.1657

value: SARC


title: Case/control experiment: C.5.01618.041.NwM58.u.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1618


title: Case/control experiment: C.16.01619.052.QwM73.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1619


title: Patient 2

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: blood, Patient 2

hyb_protocol: After fragmentation and quality confirmation with the Affymetrix Test-3 Array, 15 g of the biotinylated cRNA was hybridized to Affymetrix Human Genome U95A GeneChips (12,000 probe sets) (Affymetrix Inc., Santa Clara, CA)

scan_protocol: HP GeneArray Scanner, Hewlett-Packard Company, Palo Alto, CA

data_processing: The data were normalized using gcrma package in R.

source_name: blood

label_protocol: mRNA was isolated and converted to double-strand cDNA and then to biotinylated cRNA (BioArray High Yield RNA Transcription Labeling Kit, Enzo Biochem Inc., Farmingdale, NY)

growth_protocol: Peripheral blood draws were taken before alefacept administration. PBMCs were isolated and stored at -80°C, until required

extract_protocol: Total RNA was extracted from tissues frozen in liquid nitrogen using the RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Patients with moderate-to-severe psoriasis were treated with alefacept (7.5mg weekly i.v. x12 weeks)

tag: tissue type

value: blood

tag: patient id

tag: age

tag: gender

tag: histological response

value: R

tag: pasi (baseline)

tag: pasi (after)


title: Case/control experiment: C.5.01588.038.QwM51.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1588

tag: Class

tag: Smoking

tag: Race


title: Case/control experiment: C.16.01616.051.NwF67.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1616

tag: Gender

tag: Age

tag: COPD

value: NM


title: AML_081_R_Hind

tag: sample

value: Remission sample

value: mononuclear cells

value: Remission


title: Case/control experiment: C.5.01575.037.QwF54.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1575

value: Q

value: w

tag: Dx


title: AML_080_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

tag: cell type

tag: disease state


title: Case/control experiment: C.2.01562.036.QwF46.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1562

value: F

value: y

tag: Stage:


title: AML_077_R_Hind


title: AML_076_R_Hind


title: AML_079_R_Hind


title: AML_078_R_Hind


title: Patient 14

description: blood, Patient 14

tag: tissue type

tag: patient id

value: M


title: Patient 5

description: blood, Patient 5

tag: age

tag: gender

value: NR


title: Patient 6

description: blood, Patient 6

tag: histological response

tag: pasi (baseline)


title: Case/control experiment: C.7.01450.221.SwF58.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1450

tag: Class

value: S


title: Case/control experiment: C.9.01522.283.SwM38.u.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1522

value: NHC

tag: Smoking


title: AML_075_R_Hind


title: Case/control experiment: C.5.01554.035.NwF60.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1554

value: N

tag: Race

value: n


title: Case/control experiment: C.8.01442.220.QwM53.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1442

tag: Gender


title: Case/control experiment: C.8.01438.207.QwM64.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1438

tag: Age


title: Case/control experiment: C.9.01490.197.NwM74.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1490

tag: COPD


title: Patient 17

description: blood, Patient 17

tag: pasi (after)


title: Case/control experiment: C.7.01474.216.QwM69.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1474

tag: Dx


title: Patient 13

description: blood, Patient 13


title: Case/control experiment: C.7.01488.213.QwM77.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1488

value: GI


title: Case/control experiment: C.7.01424.196.QwM65.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1424


title: AML_074_R_Hind

tag: sample

tag: cell type


title: Case/control experiment: C.7.01399.211.SwM58.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1399

tag: Stage:


title: Case/control experiment: C.7.01361.208.QwM54.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1361


title: Case/control experiment: C.16.01342.161.QwF74.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1342


title: AML_072_R_Hind

tag: disease state


title: Case/control experiment: C.16.01314.160.NaF67.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1314

value: a


title: Case/control experiment: C.9.01328.192.NwM54.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1328


title: Patient 19

description: blood, Patient 19

tag: tissue type

value: blood

tag: patient id


title: AML_073_R_Hind


title: Patient 1

description: blood, Patient 1

tag: age

tag: gender


title: Patient 11

description: blood, Patient 11

tag: histological response

value: R

tag: pasi (baseline)


title: Case/control experiment: C.10.01263.302.QwM72.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1263

tag: Class

tag: Smoking

value: NM


title: Patient 21

description: blood, Patient 21


title: Case/control experiment: C.6.01289.193.QwM52.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1289

tag: Race

tag: Gender


title: Case/control experiment: C.15.01267.157.NwF61.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1267

tag: Age

tag: COPD


title: AML_070_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

value: Remission sample

value: mononuclear cells


title: AML_069_R_Hind

value: Remission


title: Case/control experiment: C.15.01309.159.QwF57.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1309

value: Q

value: w

tag: Dx


title: Patient 3

description: blood, Patient 3

tag: pasi (after)


title: Case/control experiment: C.10.01260.296.QwM53.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1260

value: y


title: Case/control experiment: Cm.9.01251.184.NbF52.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1251

value: b

value: F


title: Case/control experiment: C.7.01305.218.QwF57.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1305


title: Patient 20

description: blood, Patient 20

value: M


title: AML_067_R_Hind

tag: sample

tag: cell type


title: Case/control experiment: Cm.4.01250.156.QwF58.u.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1250

value: NHC

value: u

tag: Stage:


title: Patient 16

description: blood, Patient 16

tag: tissue type

value: NR


title: Patient 7

description: blood, Patient 7

tag: patient id


title: Case/control experiment: C.10.01191.298.QwM75.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1191

value: n


title: Patient 18

description: blood, Patient 18

tag: age


title: AML_066_R_Hind

tag: disease state


title: Patient 9

description: blood, Patient 9

tag: gender

tag: histological response


title: Case/control experiment: C.6.01242.188.QwM72.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1242

tag: Class


title: Case/control experiment: C.15.01186.155.QwF58.n.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1186

tag: Smoking


title: AML_064_R_Hind


title: Case/control experiment: C.10.01218.301.NwM59.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1218

value: N

tag: Race

value: GI


title: AML_065_R_Hind


title: Case/control experiment: C.7.01184.199.QwM56.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1184

tag: Gender


title: Case/control experiment: C.7.01185.210.QwM47.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1185

tag: Age


title: Case/control experiment: C.9.01182.203.QwM50.y.PN

description:
CPT purified PBMC
Case/control experiment
NHC.1182

tag: COPD

value: PN


title: Case/control experiment: C.9.01148.217.NbM71.n.GI

description:
CPT purified PBMC
Case/control experiment
NHC.1148

tag: Dx


title: AML_062_R_Hind


title: Case/control experiment: C.10.01146.295.SwM53.y.HAM

description:
CPT purified PBMC
Case/control experiment
NHC.1146

value: S

value: HAM


title: AML_063_R_Hind

value: Remission sample

value: mononuclear cells


title: AML_061_R_Hind

value: Remission


title: Case/control experiment: C.3.10063.047.QwM79.n.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10063

value: Q

value: w

value: COPD


title: Case/control experiment: C.2.10064.048.QbM54.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10064

value: b

value: y


title: Case/control experiment: C.15.01277.158.QwF68.y.NM

description:
CPT purified PBMC
Case/control experiment
NHC.1277

value: NHC

value: F

value: NM


title: Case/control experiment: Cm.6.10059.183.QwM79.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10059

value: M


title: AML_071_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: Case/control experiment: C.16.10057.175.QwM70.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10057


title: AML_059_R_Hind


title: Case/control experiment: C.2.10062.046.QwM68.y.COPDx

description:
CPT purified PBMC
Case/control experiment
NHC.10062


title: AML_060_R_Hind


title: Case/control experiment: C.2.10061.045.QwF57.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10061


title: Case/control experiment: C.6.10056.219.QwF70.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10056


title: Case/control experiment: C.6.10051.215.QwM75.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10051


title: Case/control experiment: C.11.10052.173.QwF56.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10052


title: Case/control experiment: C.6.10050.186.QbM66.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10050


title: Case/control experiment: Cm.4.10054.174.QwM70.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10054


title: Case/control experiment: C.6.10055.206.QoF63.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10055

value: o


title: Case/control experiment: C.6.10053.204.QwM61.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10053


title: Case/control experiment: C.11.10047.172.QwM68.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10047


title: Case/control experiment: C.6.10049.205.QwM57.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10049


title: AML_055_R_Hind


title: AML_057_R_Hind


title: AML_054_R_Hind


title: AML_053_R_Hind


title: Case/control experiment: C.10.10044.297.SbF53.y.SARC

description:
CPT purified PBMC
Case/control experiment
NHC.10044

value: SARC


title: Case/control experiment: Cm.4.10043.170.QwM68.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10043


title: Case/control experiment: C.16.10042.169.QwM84.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10042


title: AML_050_R_Hind


title: AML_052_R_Hind


title: Case/control experiment: C.6.10046.209.QwM63.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10046


title: Case/control experiment: C.6.10041.182.QwM71.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10041


title: Case/control experiment: C.6.10048.212.QbM67.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10048


title: AML_058_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: Case/control experiment: C.5.10040.001.QwF56.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10040


title: AML_049_R_Hind


title: AML_056_R_Hind


title: Case/control experiment: C.11.10058.176.QwF81.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10058


title: Case/control experiment: C.6.10037.264.QwM60.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10037


title: Case/control experiment: C.6.10038.265.QwF69.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10038


title: Case/control experiment: C.6.10039.266.QwF62.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10039


title: Case/control experiment: Cm.4.10036.168.NwM67.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10036

value: N


title: Case/control experiment: C.5.10034.166.QwM79.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10034


title: Case/control experiment: C.16.10035.167.NwM76.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10035


title: Case/control experiment: C.6.10033.263.QwM65.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10033


title: Case/control experiment: C.6.10031.262.QwM78.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10031


title: Case/control experiment: C.6.10032.195.QwM49.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10032


title: Case/control experiment: C.16.10030.165.NwF48.n.SARC

description:
CPT purified PBMC
Case/control experiment
NHC.10030

value: n


title: Case/control experiment: Cm.9.10023.185.SwM49.u.CR

description:
CPT purified PBMC
Case/control experiment
NHC.10023

value: S

value: u

value: CR


title: Case/control experiment: C.10.10027.294.SwM38.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10027


title: Case/control experiment: C.6.10028.180.QwF68.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10028


title: AML_047_R_Hind

value: Remission sample

value: mononuclear cells

value: Remission


title: AML_048_R_Hind


title: AML_045_R_Hind


title: Case/control experiment: C.6.10029.261.QwM61.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10029

value: Q

value: w

value: COPD


title: AML_046_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: Case/control experiment: C.6.10022.179.QwF65.u.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10022

value: NHC

value: y


title: Case/control experiment: C.9.10019.202.NwM44.n.NHC

description:
CPT purified PBMC
Case/control experiment
NHC.10019


title: AML_044_R_Hind


title: AML_043_R_Hind


title: 943

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: Bladder tumor sample against normal reference DNA.

hyb_protocol: We combined and precipitated 50 ml Cy3 labeled test DNA, 50 ml Cy5 labeled reference DNA and 100 mg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2 volumes of ice-cold ethanol. We collected the precipitate by centrifugation and dissolved the pellet in a final hybridization mixture containing 50% formamide, 2xSSC and 4% SDS. We denatured the hybridization mixture at 75¬∞C for 10-15 min and then incubated the samples at 37¬∞C for 1 hour to block repetitive DNA sequences. We applied a ring of rubber cement closely around the array to form a well, into which we added 50 ml of a pre-incubation solution containing 250 mg salmon sperm DNA, 50% formamide, 2xSSC and 4% SDS.  After a 30 min incubation at room temperature, we removed ~30 ml of the pre-incubation solution and added the denatured and re-annealed hybridization mixture.  We placed a silicone gasket around each hybridization area, placed a microscope slide on top of the gasket, which was thick enough to prevent the microscope slide from contacting the hybridization solution and clamped the whole unit together using binder clips to create an air tight environment.  We carried out the hybridization to the arrays for ~48 hrs on a slowly rocking table at 37¬∞C.  After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45¬∞C and finally in PN buffer at room temperature for 15 min.  Subsequently, we removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system. We used SPOT2.0 software to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot

data_processing: SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.  We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.

source_name: Bladder tumor

label_protocol: We labeled genomic DNA by random priming in a 50 ul reaction by combining 300 ng genomic DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1x dNTP solution (0.2 mM each of dATP, dTTP, dGTP, 0.05 mM dCTP, 1 mM Tris base (pH 7.6), 0.1 mM EDTA), 40 mM Cy3 or Cy5-dCTP (Amersham) and 40 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL).  We incubated the DNA and the random primers in a volume of 42 ul at 100°C for 10-15 min, placed the reaction on ice and added the dNTP solution, labeled nucleotides and Klenow fragment. We incubated the random priming reaction overnight at 37°C. We removed unincorporated nucleotides using a Sephadex spin-column.

extract_protocol: Flash-frozen tissue samples were stored at –80 °C immediately after transurethral resection or cystectomy. DNA was extracted by cesium chloride density centrifugation.

tag: origin

value: bladder tumor

source_name: Normal reference genomic DNA.

value: Reference normal DNA from blood


title: Case/control experiment: C.6.10012.259.QwF59.y.COPDx

description:
CPT purified PBMC
Case/control experiment
NHC.10012

value: F


title: 924-1


title: AML_041_R_Hind

tag: sample


title: AML_040_R_Hind

tag: cell type


title: AML_039_R_Hind


title: AML_038_R_Hind


title: AML_042_R_Hind


title: Case/control experiment: C.6.10018.260.QwM66.y.COPD

description:
CPT purified PBMC
Case/control experiment
NHC.10018

value: M

tag: Stage:


title: 908


title: Case/control experiment: C.9.10004.194.QwM54.u.PS

description:
CPT purified PBMC
Case/control experiment
NHC.10004

value: PS


title: Case/control experiment: C.6.10013.267.QwF68.y.COPDx

description:
CPT purified PBMC
Case/control experiment
NHC.10013


title: AML_037_R_Hind


title: Case/control experiment: C.9.10001.187.QbF83.u.HTN

description:
CPT purified PBMC
Case/control experiment
NHC.10001

value: b

value: HTN


title: Case/control experiment: C.9.10005.214.QbF67.y.CR

description:
CPT purified PBMC
Case/control experiment
NHC.10005


title: 877


title: Case/control experiment: Cm.2.10008.163.QwF73.y.GI

description:
CPT purified PBMC
Case/control experiment
NHC.10008

value: GI


title: 848


title: Case/control experiment: C.5.10010.044.QbF64.u.HTN

description:
CPT purified PBMC
Case/control experiment
NHC.10010

value: u


title: AML_036_R_Hind

value: Remission sample


title: AML_035_R_Hind

value: mononuclear cells


title: 506


title: 448


title: 813-1


title: Case/control experiment: Cm.9.10003.201.SbF43.u.HTN

description:
CPT purified PBMC
Case/control experiment
NHC.10003

value: S


title: 447B


title: 413


title: 338


title: AML_033_R_Hind

value: Remission


title: 407


title: 3395


title: 3554


title: 910


title: AML_034_R_Hind


title: AML_030_R_Hind


title: 3161


title: AML_032_R_Hind


title: AML_031_R_Hind


title: AML_029_R_Hind


title: AML_026_R_Hind


title: 3046


title: AML_027_R_Hind


title: AML_025_R_Hind


title: 2816


title: 2691


title: 2817


title: 2821


title: 3031


title: 2571-2


title: AML_024_R_Hind


title: AML_023_R_Hind


title: 259


title: AML_021_R_Hind


title: AML_022_R_Hind


title: 2542


title: AML_019_R_Hind


title: AML_016_R_Hind


title: AML_015_R_Hind


title: AML_014_R_Hind


title: AML_020_R_Hind


title: 2335


title: AML_028_R_Hind


title: 2505


title: 2307


title: 2380


title: 2541-1


title: AML_018_R_Hind


title: 2297


title: 2259-1


title: AML_008_R_Hind


title: AML_010_R_Hind


title: AML_017_R_Hind


title: AML_009_R_Hind


title: 195


title: AML_013_R_Hind


title: 1541-4


title: AML_011_R_Hind


title: AML_007_R_Hind


title: 1528-7


title: 1512-6


title: AML_006_R_Hind


title: 1498


title: AML_005_R_Hind


title: AML_012_R_Hind


title: 1484


title: AML_003_R_Hind


title: AML_001_R_Hind


title: 1448-2


title: AML_002_R_Hind


title: AML_159_R_Nsp

description:
Hybridized to 250K_Nsp
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: 1413


title: AML_155_R_Nsp


title: AML_157_R_Nsp


title: AML_118_D_Hind

value: Acute myeloid leukemia diagnosis sample

value: Acute myeloid leukemia


title: 1412


title: AML_119_D_Hind


title: AML_158_R_Nsp


title: AML_153_R_Nsp


title: 1382-2


title: AML_151_R_Nsp


title: 1379


title: AML_156_R_Nsp


title: AML_148_R_Nsp


title: AML_149_R_Nsp


title: AML_117_D_Hind


title: AML_154_R_Nsp


title: 1352-1


title: AML_116_D_Hind


title: 1333-4


title: AML_114_D_Hind


title: 1211-2


title: AML_115_D_Hind


title: 1212


title: AML_150_R_Nsp


title: 1210


title: AML_146_R_Nsp


title: AML_112_D_Hind


title: AML_110_D_Hind


title: 1087-1


title: AML_145_R_Nsp


title: AML_111_D_Hind


title: 1033


title: AML_143_R_Nsp


title: S3_D


title: S3_C


title: AML_109_D_Hind


title: S3_B


title: AML_106_D_Hind


title: AML_113_D_Hind


title: AML_144_R_Nsp


title: AML_141_R_Nsp


title: AML_142_R_Nsp


title: AML_107_D_Hind


title: S3_A


title: 13970000 - Col0 T0h 2leaf vs wat1 T0h 2leaf

status: Public on Aug 01 2010

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

description: identification of the role of the plant cell wall in the interactions between plants and pathogenic agents

hyb_protocol: wat1 T0h 2leaf Cy5 / Col0 T0h 2leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: wat1 T0h 2leaf

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

growth_protocol: leaf - day 16h/22°C night 8h/20°C relative humidity 70%

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T0h 2leaf:32.2ug.

treatment_protocol: Name:H20 - control - control,h2o:.

tag: ecotype

tag: genotype/variation

value: mutant (wat1-)

tag: agent

value: H2O, control

source_name: Col0 T0h 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T0h 2leaf:36.5ug.

value: wild-type


title: AML_104_D_Hind

tag: disease state


title: AML_147_R_Nsp


title: AML_152_R_Nsp


title: AML_137_R_Nsp


title: AML_139_R_Nsp


title: AML_103_D_Hind


title: AML_140_R_Nsp


title: S2_B

value: bladder tumor

value: Reference normal DNA from blood


title: S2_A


title: S1_B


title: AML_101_D_Hind


title: AML_136_R_Nsp


title: AML_138_R_Nsp


title: S1_A


title: AML_100_D_Hind


title: AML_099_D_Hind


title: AML_133_R_Nsp


title: AML_134_R_Nsp


title: AML_105_D_Hind


title: AML_135_R_Nsp


title: AML_132_R_Nsp


title: AML_130_R_Nsp


title: AML_102_D_Hind


title: AML_131_R_Nsp


title: AML_097_D_Hind


title: AML_096_D_Hind


title: AML_095_D_Hind


title: AML_129_R_Nsp


title: AML_091_D_Hind


title: AML_128_R_Nsp


title: AML_093_D_Hind


title: AML_094_D_Hind


title: AML_098_D_Hind


title: AML_090_D_Hind


title: AML_127_R_Nsp


title: AML_092_D_Hind


title: AML_089_D_Hind


title: AML_087_D_Hind


title: AML_088_D_Hind


title: AML_085_D_Hind


title: AML_084_D_Hind


title: AML_120_R_Nsp


title: AML_086_D_Hind


title: AML_083_D_Hind


title: AML_082_D_Hind


title: AML_122_R_Nsp


title: AML_124_R_Nsp


title: AML_117_R_Nsp


title: AML_123_R_Nsp


title: AB31_WT_MMara_0h_1

status: Public on Jun 01 2010

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description: 0h time point of crg1P controlled bE1/bW2 gene induction

hyb_protocol: EukGE-WS2 protocol on a GeneChip Fluidics Station 400

scan_protocol: Agilent G2500A

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: U. maydis strain AB31 grown for 0h in array medium/arabinose

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labelling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: Strain AB31 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE1 and bW2 genes were induced for 0 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer's instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

tag: time

value: 0h in array medium/arabinose

tag: strain

value: AB31 is a FB2 (a2 b2) derivative in which the induction of the bE1 and bW2 genes is under control of the arabinose-inducible crg1 promoter.


title: AML_110_R_Nsp


title: AML_126_R_Nsp


title: AML_121_R_Nsp


title: AML_125_R_Nsp


title: AB32_WT_MMara_5h_1

description: 5h time point of crg1P controlled bE2/bW2 gene induction

source_name: U. maydis strain AB32 grown for 5h in array medium/arabinose

growth_protocol: Strain AB32 was grown on a rotary shaker (200 rpm) to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25 % (w/v) salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). bE2 and bW2 genes were induced for 5 hours in liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source.

value: 5h in array medium/arabinose


title: AML_080_D_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: AML_107_R_Nsp


title: AML_079_D_Hind


title: AML_095_R_Nsp


title: AML_081_D_Hind


title: AML_078_D_Hind


title: AML_094_R_Nsp


title: AML_077_D_Hind


title: AML_076_D_Hind


title: AML_083_R_Nsp


title: AML_079_R_Nsp


title: AML_089_R_Nsp


title: AML_087_R_Nsp


title: AML_080_R_Nsp


title: AML_071_R_Nsp


title: AML_072_R_Nsp


title: AML_073_D_Hind


title: AML_075_D_Hind


title: AML_074_D_Hind


title: AML_072_D_Hind


title: AML_158_R_Sty

description:
Hybridized to 250K_Sty
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: AML_070_D_Hind


title: AML_071_D_Hind


title: AML_052_R_Nsp


title: AML_069_R_Nsp


title: AML_157_R_Sty


title: AML_060_R_Nsp


title: AML_061_R_Nsp


title: AML_155_R_Sty


title: AML_159_R_Sty


title: AML_068_D_Hind


title: AML_153_R_Sty


title: AML_037_R_Nsp


title: AML_154_R_Sty


title: AML_067_D_Hind


title: AML_066_D_Hind


title: AML_065_D_Hind


title: AML_151_R_Sty


title: AML_152_R_Sty


title: AML_035_R_Nsp


title: AML_025_R_Nsp


title: AML_034_R_Nsp


title: AML_017_R_Nsp


title: AML_150_R_Sty


title: AML_064_D_Hind


title: AML_063_D_Hind


title: AML_148_R_Sty


title: AML_149_R_Sty


title: AML_062_D_Hind


title: AML_147_R_Sty


title: AML_061_D_Hind


title: AML_011_R_Nsp


title: AML_010_R_Nsp


title: AML_146_R_Sty


title: AML_059_D_Hind


title: AML_069_D_Hind


title: AML_145_R_Sty


title: AML_058_D_Hind


title: AML_005_R_Nsp


title: AML_056_D_Hind


title: AML_143_R_Sty


title: AML_004_R_Nsp


title: AML_144_R_Sty


title: AML_141_R_Sty


title: AML_057_D_Hind


title: AML_158_D_Nsp


title: AML_159_D_Nsp


title: AML_142_R_Sty


title: AML_156_D_Nsp


title: AML_156_R_Sty


title: AML_050_R_Nsp


title: AML_140_R_Sty


title: AML_157_D_Nsp


title: AML_047_R_Nsp


title: AML_052_D_Hind


title: AML_053_D_Hind


title: AML_054_D_Hind


title: AML_155_D_Nsp


title: AML_154_D_Nsp


title: AML_055_D_Hind


title: AML_139_R_Sty


title: AML_138_R_Sty


title: AML_023_R_Nsp


title: AML_050_D_Hind


title: AML_008_R_Nsp


title: AML_152_D_Nsp


title: AML_153_D_Nsp


title: AML_049_D_Hind


title: AML_048_D_Hind


title: AML_136_R_Sty


title: AML_046_D_Hind


title: AML_135_R_Sty


title: AML_150_D_Nsp


title: AML_151_D_Nsp


title: AML_044_D_Hind


title: AML_045_D_Hind


title: AML_134_R_Sty


title: AML_042_D_Hind


title: AML_148_D_Nsp


title: AML_137_R_Sty


title: AML_133_R_Sty


title: AML_149_D_Nsp


title: AML_040_D_Hind


title: AML_041_D_Hind


title: AML_043_D_Hind


title: AML_039_D_Hind


title: AML_147_D_Nsp


title: AML_131_R_Sty


title: AML_128_R_Sty


title: AML_142_D_Nsp


title: AML_038_D_Hind


title: AML_037_D_Hind


title: AML_144_D_Nsp


title: AML_125_R_Sty


title: AML_126_R_Sty


title: AML_127_R_Sty


title: AML_143_D_Nsp


title: AML_130_R_Sty


title: AML_129_R_Sty


title: AML_036_D_Hind


title: AML_146_D_Nsp


title: AML_035_D_Hind


title: AML_141_D_Nsp


title: AML_132_R_Sty


title: AML_145_D_Nsp


title: AML_139_D_Nsp


title: AML_140_D_Nsp


title: AML_034_D_Hind


title: AML_123_R_Sty


title: AML_032_D_Hind


title: I86M193

city: Raleigh

first: Youssef

last: Idaghdour

state: NC

address: South Gardner Hall

department: Genetics

institute: NCSU

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and BeadStudio (Gene expression Module)

data_processing: Raw data was log2 transformed and median-centered using JMP Genomics (SAS, Cary NC).

source_name: Leukocytes, Ighrem, Rural

label_protocol: cDNA and cRNA labeling and amplification were all performed using a single kit: Ambion's Illumina TotalPrep RNA Amplification kit.

extract_protocol: Total RNA was extrated from leukocyte samples using Ambion's Leukolocks kit. Quality control was performed using Agilent's Bioanalyzer.

tag: geographic location

value: Ighrem

tag: lifestyle

value: rural

tag: gender

value: male

tag: tissue

value: peripheral blood

value: leukocytes


title: I88M194


title: AML_122_R_Sty

value: Remission sample

value: mononuclear cells


title: AML_121_R_Sty

value: Remission


title: AML_033_D_Hind

value: Acute myeloid leukemia diagnosis sample

value: Acute myeloid leukemia


title: AML_124_R_Sty


title: AML_031_D_Hind


title: AML_136_D_Nsp


title: AML_138_D_Nsp


title: AML_120_R_Sty


title: AML_030_D_Hind


title: AML_135_D_Nsp


title: I84F192

value: female


title: AML_029_D_Hind


title: I81F191


title: AML_110_R_Sty


title: AML_107_R_Sty


title: AML_137_D_Nsp


title: AML_095_R_Sty


title: AML_133_D_Nsp


title: AML_134_D_Nsp


title: AML_117_R_Sty


title: I79F190


title: AML_026_D_Hind


title: AML_132_D_Nsp


title: AML_027_D_Hind


title: I66F188


title: I77F189


title: AML_094_R_Sty


title: AML_131_D_Nsp


title: AML_087_R_Sty


title: I65F187


title: AML_130_D_Nsp


title: AML_028_D_Hind


title: AML_025_D_Hind


title: AML_023_D_Hind


title: AML_089_R_Sty


title: AML_024_D_Hind


title: AML_083_R_Sty


title: I57M184


title: I59F185


title: AML_127_D_Nsp


title: I62F186


title: AML_128_D_Nsp


title: AML_072_R_Sty


title: AML_021_D_Hind


title: AML_126_D_Nsp


title: AML_129_D_Nsp


title: AML_079_R_Sty


title: AML_019_D_Hind


title: AML_125_D_Nsp


title: AML_022_D_Hind


title: AML_071_R_Sty


title: AML_020_D_Hind


title: AML_069_R_Sty


title: I54F181


title: I53F180


title: AML_123_D_Nsp


title: AML_080_R_Sty


title: I52F179


title: AML_017_D_Hind


title: AML_124_D_Nsp


title: AML_121_D_Nsp


title: AML_016_D_Hind


title: AML_120_D_Nsp


title: I51F178


title: AML_122_D_Nsp


title: I55M182


title: AML_052_R_Sty


title: AML_061_R_Sty


title: AML_117_D_Nsp


title: AML_018_D_Hind


title: I50F177


title: AML_050_R_Sty


title: I56M183


title: I49F176


title: AML_014_D_Hind


title: AML_110_D_Nsp


title: I48F175


title: AML_015_D_Hind


title: AML_047_R_Sty


title: AML_107_D_Nsp


title: AML_013_D_Hind


title: I46M173


title: AML_060_R_Sty


title: I47F174


title: AML_011_D_Hind


title: AML_037_R_Sty


title: AML_010_D_Hind


title: AML_009_D_Hind


title: AML_034_R_Sty


title: AML_035_R_Sty


title: AML_012_D_Hind


title: AML_025_R_Sty


title: AML_017_R_Sty


title: AML_089_D_Nsp


title: I44M171


title: AML_095_D_Nsp


title: AML_083_D_Nsp


title: I39F170


title: AML_007_D_Hind


title: I45F172


title: AML_080_D_Nsp


title: AML_008_D_Hind


title: AML_094_D_Nsp


title: I38F169


title: AML_006_D_Hind


title: Follicular lymphoma_FL.E.23

status: Public on Feb 01 2010

first: Katia

last: Basso

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description: Gene expression data from follicular lymphoma

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Follicular lymphoma bioptic tissue

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: Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's indications.

treatment_protocol: The frozen tissue was homogeneized in Trizol reagent.

value: Follicular lymphoma biopsy


title: AML_023_R_Sty


title: AML_087_D_Nsp


title: AML_005_D_Hind


title: AML_010_R_Sty


title: AML_079_D_Nsp


title: I35F167


title: AML_072_D_Nsp


title: I37F168


title: AML_004_D_Hind


title: I34F166


title: I33F165


title: AML_005_R_Sty


title: AML_071_D_Nsp


title: AML_002_D_Hind


title: I30F163


title: AML_001_D_Hind


title: AML_003_D_Hind


title: AML_008_R_Sty


title: AML_004_R_Sty


title: AML_061_D_Nsp


title: AML_060_D_Nsp


title: Clone RM5_Root_W_90h_rep1

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0467

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

organism: Populus fremontii x Populus angustifolia

source_name: Root tip, wounded, 90 hr

label_protocol: Standard Affymetrix protocol.

growth_protocol: Rooted cuttings, 10-15 cm in height, were transferred into aerated nutrient solution.  Distilled water was added daily as needed to maintain a constant nutrient volume.  Nutrient solution was replaced weekly, and a pH of 5.8±0.3 was maintained by daily additions of 2N KOH or 2N HCl.

extract_protocol: CTAB protocol.

treatment_protocol: Plants  ~1 m height were distributed into separate ebb and flow hydroponic tubs for wounding (one tub) and non-wound control treatments (a second tub).  The tubs were separated by 3 meters.  Plants were harvested and RNA analyzed from wounded plants that exhibited a chemical signal indicative of a wound response, and from control plants that did not exhibit that response.

tag: clone

value: root tip

tag: treatment

value: wounded

tag: post-treatment time

value: 90 hours


title: AML_159_D_Sty


title: AML_069_D_Nsp


title: I31F164


title: I28F161


title: Clone RM5_Root_W_90h_rep2

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0468


title: AML_052_D_Nsp


title: AML_050_D_Nsp


title: I29F162


title: I27F160


title: Clone RM5_Root_C_90h_rep2

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0464

source_name: Root tip, unwounded control, 90 hr

value: unwounded


title: AML_156_D_Sty


title: AML_037_D_Nsp


title: I22F158


title: I25M159


title: Clone RM5_LPI5_W_90h_rep1

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0460

source_name: LPI5, wounded, 90 hr

value: leaf

tag: age

value: mature


title: AML_155_D_Sty

tag: sample


title: AML_158_D_Sty

tag: cell type


title: AML_153_D_Sty


title: AML_154_D_Sty


title: Clone RM5_LPI5_C_90h_rep2

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0459

source_name: LPI5, unwounded control, 90 hr


title: Clone RM5_Root_C_90h_rep1

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0463


title: AML_035_D_Nsp


title: Clone RM5_LPI5_W_90h_rep2

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0462


title: AML_047_D_Nsp


title: AML_152_D_Sty


title: AML_157_D_Sty


title: I19M156

value: Ighrem

value: rural


title: AML_034_D_Nsp


title: I21F157

value: peripheral blood


title: Clone RM5_LPI1_W_1wk_rep2

description:
Gene expression data from a one-week leaf wounding experiment.
bot0799

source_name: LPI0-1, wounded, 1wk

value: young

value: 1 week


title: AML_011_R_Sty

value: Remission sample

value: mononuclear cells


title: Clone RM5_LPI5_C_90h_rep1

description:
Gene expression data from a 90-hr leaf wounding experiment.
bot0457


title: I14F154

value: leukocytes


title: Clone RM5_LPI1_W_1wk_rep1

description:
Gene expression data from a one-week leaf wounding experiment.
bot0798


title: Ring1B/Eed double deficient ES cells, biological replicate 3

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

hyb_protocol: labeling, hybridization, and primary data processing were performend by Atlas Biolabs, Berlin

organism: Mus musculus

source_name: mouse embryonic stem (ES) cells

growth_protocol: ES cells were cultured as described in the corresponding Materials and Methods section

extract_protocol: Trizol

tag: genotype

value: Ring1B/Eed double mutant ES cell line generated by gene targeting of Ring1B in Eed deficient ES cells

tag: cell line

value: ES


title: AML_011_D_Nsp

description:
Hybridized to 250K_Nsp
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: bone marrow

value: Acute myeloid leukemia diagnosis sample

value: Acute myeloid leukemia


title: Control5

status: Public on Jan 30 2010

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
4256337010_E
Replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Un-treated retina

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

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

value: control


title: Clone RM5_LPI1_C_1wk_rep2

description:
Gene expression data from a one-week leaf wounding experiment.
bot0793

source_name: LPI0-1, unwounded control, 1wk


title: Ring1B/Eed double deficient ES cells, biological replicate 2

scan_protocol: labeling, hybridization, and primary data processing were performend by Atlas Biolabs, Berlin


title: I11M152

value: male


title: AML_017_D_Nsp

source_name: peripheral blood


title: Clone RM5_LPI5_W_1wk_rep2

description:
Gene expression data from a one-week leaf wounding experiment.
bot0690

source_name: LPI5, wounded, 1wk

value: wounded


title: Clone RM5_LPI1_C_1wk_rep1

description:
Gene expression data from a one-week leaf wounding experiment.
bot0792

value: leaf

value: unwounded


title: Ring1B/Eed double deficient ES cells, biological replicate 1

label_protocol: labeling, hybridization, and primary data processing were performend by Atlas Biolabs, Berlin


title: AML_150_D_Sty


title: I15F155

value: Ighrem

value: female


title: I09F151

value: rural

value: peripheral blood


title: AML_025_D_Nsp


title: I08F150


title: AML_148_D_Sty


title: I07F149


title: Clone RM5_LPI5_W_1wk_rep1

description:
Gene expression data from a one-week leaf wounding experiment.
bot0689

value: mature

value: 1 week


title: Eed deficient ES cells, biological replicate 3

value: Eed mutant generated by gene targeting (Schoeftner et al., 2006)


title: AML_151_D_Sty

description:
Hybridized to 250K_Sty
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

value: mononuclear cells


title: AML_146_D_Sty


title: I06F148

value: leukocytes


title: Clone RM5_LPI5_C_1wk_rep2

description:
Gene expression data from a one-week leaf wounding experiment.
bot0683

source_name: LPI5, unwounded control, 1wk


title: AML_008_D_Nsp


title: Eed deficient ES cells, biological replicate 1

value: ES


title: AML_145_D_Sty

value: Acute myeloid leukemia diagnosis sample


title: Clone RM5_LPI5_C_1wk_rep1

description:
Gene expression data from a one-week leaf wounding experiment.
bot0687


title: Eed deficient ES cells, biological replicate 2


title: I12M153


title: AML_149_D_Sty

value: Acute myeloid leukemia


title: AML_004_D_Nsp


title: MJ_48hr_r2

description:
Gene expression data from a cell culture feeding experiment.
bot0730

hyb_protocol: Standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocols.

organism: Populus tremuloides

source_name: cell culture, MJ-fed, 48 hr

label_protocol: Standard Affymetrix protocols.

growth_protocol: Cell cultures derived from Populus tremuloides clone L4 were maintained in WPM media supplemented with 3% sucrose and 2.2 mg/L 2.4-D.  Cells were subcultured at 11-day intervals by inoculating 5 mL of cultures to 30 mL of fresh media.

treatment_protocol: Cell cultures were fed with 25 μM of MJ diluted in DMSO or with DMSO (10.5 μL) 6 days after subculturing.  Cells were harvested for RNA extraction 48 hours after the feeding.

value: methyl jasmonate


title: Ring1B deficient ES cells, biological replicate 2

value: Ring1B mutant generated by gene targeting (Leeb et al., 2007)


title: wild type ES cells, biological replicate 3

value: wild type (Wutz et al., 2000)


title: Ring1B deficient ES cells, biological replicate 1


title: I04M147

value: male


title: I02M145


title: Ring1B deficient ES cells, biological replicate 3


title: AML_141_D_Sty


title: MJ_48hr_r1

description:
Gene expression data from a cell culture feeding experiment.
bot0729


title: I03M146


title: C_48hr_r1

description:
Gene expression data from a cell culture feeding experiment.
bot0725

source_name: cell culture, control

value: DMSO


title: AML_143_D_Sty


title: C_48hr_r2

description:
Gene expression data from a cell culture feeding experiment.
bot0726


title: AML_010_D_Nsp


title: wild type ES cells, biological replicate 2


title: D95F143

source_name: Leukocytes, Agadir, Urban

value: Agadir

value: urban


title: AML_005_D_Nsp


title: I01M144

source_name: Leukocytes, Ighrem, Rural

value: Ighrem

value: rural


title: AML_144_D_Sty


title: wild type ES cells, biological replicate 1


title: AML_142_D_Sty


title: D92M141

value: peripheral blood


title: D72F139

value: female


title: D94F142


title: D88M140


title: AML_147_D_Sty


title: AML_023_D_Nsp


title: MC 38 met 3

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label_protocol: standard Affymetrix protocol

extract_protocol: Qiagen Rneasy

tag: cancer cell type

value: metastatic


title: AML_139_D_Sty

value: mononuclear cells


title: MC 38 met 1


title: MC 38 parental 2

value: parental


title: D66F138

value: leukocytes


title: MC 38 met 2


title: D44F136


title: D61F137


title: MC 38 parental 3


title: D43M135


title: MC 38 parental 1


title: D42M134


title: D24F132


title: D37M133


title: AML_134_D_Sty

value: Acute myeloid leukemia diagnosis sample


title: D21F131


title: AML_138_D_Sty

value: Acute myeloid leukemia


title: AML_137_D_Sty


title: D17F129


title: D15F128


title: AML_136_D_Sty


title: D157F127


title: D156M126


title: AML_140_D_Sty


title: AML_132_D_Sty


title: D153M125


title: AML_128_D_Sty


title: AML_135_D_Sty


title: AML_131_D_Sty


title: D19F130


title: D152M124


title: AML_129_D_Sty


title: AML_133_D_Sty


title: AML_130_D_Sty


title: AML_126_D_Sty


title: D14F122


title: AML_125_D_Sty


title: D13F119


title: AML_123_D_Sty


title: AML_122_D_Sty


title: D132M117


title: AML_107_D_Sty


title: AML_121_D_Sty


title: D128M115


title: AML_117_D_Sty


title: D137M118


title: AML_095_D_Sty


title: D125M114


title: D12F116


title: D120M113


title: D141M120


title: D151F123


title: D111M111


title: D114M112


title: D143M121


title: AML_124_D_Sty


title: D10M110


title: AML_110_D_Sty


title: AML_127_D_Sty


title: AML_080_D_Sty


title: AML_072_D_Sty


title: AML_120_D_Sty


title: AML_087_D_Sty


title: AML_069_D_Sty


title: AML_061_D_Sty


title: D08F108


title: AML_079_D_Sty


title: AML_083_D_Sty


title: D107M109


title: D05F105


title: AML_089_D_Sty


title: AML_071_D_Sty


title: AML_052_D_Sty


title: AML_060_D_Sty


title: D07F107


title: AML_050_D_Sty


title: D06F106


title: AML_094_D_Sty


title: D01F104


title: B52M101

source_name: Leukocytes, Boutroch, Rural

value: Boutroch


title: B54M103


title: B45M99


title: B53M102


title: B51M100


title: B37F96


title: B40F98


title: B35M94


title: B39M97


title: B33F92


title: B32F91


title: B34M93


title: B30F89


title: B29F88


title: B31F90


title: B28F87


title: B36F95


title: AML_035_D_Sty


title: B23F84


title: AML_047_D_Sty


title: B26F85


title: B27F86


title: B19F82


title: B18F81


title: B16F80


title: B14F79


title: B11F76


title: AML_068_R_Hind

description:
Hybridized to 50K_Hind
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

value: Remission sample

value: Remission


title: B08F73


title: B10M75

value: male


title: B07M72


title: B05F70


title: B09M74


title: B12F77


title: AML_037_D_Sty


title: B03F68


title: AML_011_D_Sty


title: A96F65


title: B13F78


title: B04F69


title: B06F71


title: AML_004_D_Sty


title: AML_034_D_Sty


title: B01F66


title: B02F67


title: A80F60


title: A89M63


title: A79F59


title: AML_008_D_Sty


title: AML_005_D_Sty


title: A87M62


title: AML_023_D_Sty


title: AML_010_D_Sty


title: AML_017_D_Sty


title: A58F49


title: A56F47


title: A55F46


title: AML_025_D_Sty


title: A65F54


title: A63F52


title: A60F51


title: A71F55


title: A64M53


title: A53F44


title: A82M61


title: A74F56


title: A59F50


title: A77M57


title: A52F43


title: A51F42


title: A50F41


title: A78M58


title: A54M45


title: A49F40


title: A91F64


title: A48F39


title: A47F38


title: A45F36


title: A41F35


title: A39F33


title: A46M37


title: A40F34


title: A32M30


title: A35F32


title: A34F31


title: A27F27


title: A30F28


title: A25F25


title: A31F29


title: A26F26


title: A20M24


title: AML_004_R_Hind


title: A150M22


title: A18F23


title: A147M21


title: A142M19


title: A139M18


title: A145M20


title: A135M15


title: A122M12


title: A134M14


title: A136M16


title: A127M13


title: A138M17


title: A117M10


title: A112M9


title: A108M6


title: A109F7


title: A105M4


title: A110M8


title: A106M5


title: A103M3


title: A09M2


title: A119M11


title: Mouse Mammary Epithelial Cells_Knockout_rep2

city: Madison

first: Caroline

last: Alexander

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

description:
This sample is a pool of mammary epithelial cells isolated from 5 Lrp5 knockout mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
6777202

hyb_protocol: Hybridization was performed by Roche Nimblegen Systems Inc., following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche Nimblegen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 ( Roche Nimblegen, Inc.).

source_name: mammary epithelial cells, Lrp5 knockout

label_protocol: cDNA was generated and labelled with Cy3 by the Gene Expression Center, University of Wisconsin-Madison, following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) according to manufacturer's protocol. The isolated RNA was submitted to the Gene Expression Center, University of Wisconsin-Madison where quality control tests were performed.

treatment_protocol: Mammary glands (#4 and #5) were isolated from 12-16 week old virgin mice. Glands were minced and digested using reagents from Stem Cell Technologies according to manufacturer's protocol.

value: 12-16 weeks

value: virgin female

value: mammary gland

value: epithelial


title: Mouse Mammary Epithelial Cells_Wild Type_rep5

description:
This sample is a pool of mammary epithelial cells isolated from 5 wild type mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
12139602

source_name: mammary epithelial cells, wild type


title: Bladder tumor REF15

description: Genomic DNA extracted from bladder tumors was genotyped using HumanCNV370-Quadv3 Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

source_name: Bladder tumor

label_protocol: standard Illumina protocol

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction

tag: sex

value: Male

tag: stage

tag: grade


title: Mouse Mammary Epithelial Cells_Knockout_rep1

description:
This sample is a pool of mammary epithelial cells isolated from 5 Lrp5 knockout mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
6708302

tag: strain


title: A03F1

tag: geographic location

value: Agadir

value: urban

value: peripheral blood


title: Bladder tumor REF14


title: Bladder tumor REF11


title: Mouse Mammary Epithelial Cells_Wild Type_rep3

description:
This sample is a pool of mammary epithelial cells isolated from 5 wild type mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
6750502


title: Bladder tumor REF3


title: Mouse Mammary Epithelial Cells_Wild Type_rep4

description:
This sample is a pool of mammary epithelial cells isolated from 5 wild type mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
12138602


title: Mouse Mammary Epithelial Cells_Knockout_rep3

description:
This sample is a pool of mammary epithelial cells isolated from 5 Lrp5 knockout mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
6834302


title: Mouse Mammary Epithelial Cells_Wild Type_rep6

description:
This sample is a pool of mammary epithelial cells isolated from 5 wild type mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
12319702


title: Bladder tumor REF10


title: Bladder tumor REF8


title: Bladder tumor REF9


title: Mouse Mammary Epithelial Cells_Wild Type_rep2

description:
This sample is a pool of mammary epithelial cells isolated from 5 wild type mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
7452202


title: CysNO-treated yeast protein microarray - 2

type: other

city: Durham

first: Matthew

last: Foster

address: Box 2612 Research Dr.

department: Medicine

institute: Duke University

description: An analysis of protein S-nitrosylation on protein microarrays using a modified biotin switch technique.

hyb_protocol: Following the biotinylation step, slides were washed liberally with PBS containing 0.05% Tween-20 (PBST) and further blocked with 1% BSA in PBST for 2 h at 4 °C. Slides were incubated with 1:500 anti-biotin-M antibody (Vector) in PBST overnight at 4 °C. After washing PBST (3 x 10 min), slides were incubated with 1:1000 Alexa Fluor 647-labelled goat anti-mouse secondary antibody (Molecular Probes) in PBST for 1 h at room temp. Finally, slides were washed with PBST (3 x 10 min) and once with PBS. Slides were placed in 50 ml conical flasks and dried by centrifugation in a swinging bucket rotor at 700 x g for 5 min.

scan_protocol: Axon Genepix 4000B GenepixPro Single wavelength=635 nm PMTGain=600 ScanPower=100 LaserPower=3.49

data_processing: Processed using GenePixPro

label: Alexafluor 647

molecule: other

organism: Saccharomyces cerevisiae

source_name: Yeast protoarray treated with CysNO for 30 min and analyzed by modified BST

label_protocol: Incubations were performed in slide chambers unless otherwise noted. Buffers were filtered (0.22 um) before use. Invitrogen Protoarrays® for either kinase substrate identification (KSI) were first blocked by rocking with 10 mM lysine in PBS for 4 h at 4 degC. After several washes with PBS, where noted, proteins were reduced with 5 mM DTT in PBS for 30 min at 4 degC. Pretreatment with DTT did not substantially alter the pattern of S-nitrosylation, indicating that neither adventitious oxidation nor endogenous protein disulfides are major limitations. Slides were washed with PBS to remove DTT and finally with 250 mM Hepes, 1 mM EDTA, 0.1 mM neocuproine, pH 7.4 (HEN 7.4). After removal of excess buffer, 300 µl HEN 7.4 (with or without nitrosothiols) was pipetted onto the slides. A Hybrislip (60 mm x 22 mm; Molecular Probes) was placed on top of the solution, and slides were incubated in the dark for 30 min. Next, slides were washed once with HEN buffer (pH 7.7) and placed in a slide chamber with the same buffer containing 20 mM methyl methanethiosulfonate (MMTS) and 1% SDS. Slide chambers were incubated, vertically, in the dark for 20 min in a 50 ºC water bath for blocking of free thiols. To remove excess MMTS, slides were washed 4 times with a 10-fold dilution of HEN buffer and finally with HEN buffer. Finally, proteins were biotinylated by incubating slides for 1 h in the dark with HEN buffer containing 5 or 50 mM ascorbate, 0.4 mM biotin-HPDP, and 1% SDS using a Hybrislip as described above.

tag: sample type

value: Microarray treated with 50 micromolar S-nitrosocysteine for 30 min.


title: Buffer-treated yeast protein microarray - 1

scan_protocol: Axon Genepix 4000B GenepixPro Single wavelength=635 nm PMTGain=590 ScanPower=100 LaserPower=3.49

source_name: Yeast protoarray treated with buffer for 30 min and analyzed by modified BST

value: Microarray treated with buffer for 30 min.


title: GSNO-treated yeast protein microarray - 2

scan_protocol: Axon Genepix 4000B GenepixPro Single wavelength=635 nm PMTGain=750 ScanPower=100 LaserPower=3.49

source_name: Yeast protoarray treated with GSNO for 30 min and analyzed by modified BST

value: Microarray treated with 50 micromolar S-nitrosoglutathione for 30 min.


title: Bladder tumor REF13


title: Bladder tumor REF12

value: Female


title: Mouse Mammary Epithelial Cells_Wild Type_rep1

description:
This sample is a pool of mammary epithelial cells isolated from 5 wild type mice. Estrous stagin was performed and mice belonging to different stages of the cycle were assigned to each group randomly.
6748302

tag: gender


title: novobiocin T = 30 minutes experiment 2

status: Public on Nov 30 2009

city: Cambridge

first: Vikram

last: Vijayan

state: MA

address: 52 Oxford Street, Room 440

institute: Harvard University

description: no additional information

hyb_protocol: Each array was hybridized with 150 to 300 ng Cy3 and 150 to 300 ng Cy5 labeled cDNA and rotated (5 rotations min-1) at 60º C for 17 hours in SureHyb chambers (Agilent). Arrays were subsequently washed in 6.7X SSPE and 0.005% N-lauryl sarcosine buffer for at least 1 minute, 0.67X SSPE and 0.005% N-lauryl sarcosine buffer for 1 minute, and then Agilent drying and ozone protection wash for 30 seconds at room temperature (1X SSPE = 0.15 M NaCl, 10 μM sodium phosphate, 1 mM EDTA, pH 7.4).

scan_protocol: The arrays were immediately scanned using an Axon 4000B scanner at 5 μm resolution.

data_processing: The average intensity of the Cy3 and Cy5 florescence at each spot was extracted using the GenePix software (Molecular Devices) and loaded into MATLAB (Mathworks). Loess and quantile normalization were performed using the MATLAB bioinformatics toolbox.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: novobiocin T = 30 minutes

label_protocol: cDNA was prepared for each individual time-point (foreground channel) as well as for a pool of all time-points (background channel). Spike-in RNA was introduced at different concentrations and ratios to the foreground and background channels prior to reverse transcription in order to ensure proper ratio detection in a wide dynamic range. 5 μg total RNA (plus spike-ins) was reverse-transcribed with random 15-mer primers (Operon) and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma) using SuperScript III reverse-transcriptase (Invitrogen) without amplification. RNA was hydrolyzed and cDNA was purified using Microcon 30 spin column (Millipore).   cDNA was labeled with N-Hydroxysuccinimide-ester Cyanine 3 (Cy3, foreground) or Cyanine 5 (Cy5, background) (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 6 hours. Labeled cDNA was purified (Microcon 30, Millipore) in preparation for hybridization.

growth_protocol: A continuous culture apparatus was developed to keep cells in constant conditions and provide real-time bioluminescence readings. S. elongatus (strain AMC 408) was grown in a 6 liter cylindrical spinner flask (Corning) at a volume of 4.5 liters. Cells were grown in modified BG-11 medium with the following modifications: 0.0010 g/liter of FeNH4 citrate was used instead of 0.0012 g/liter of FeNH4 citrate and citric acid was supplemented at 0.00066 g/liter. Cells were initially inoculated in the presence of antibiotics (5 µg/ml spectinomycin and 5 µg/ml chloramphenicol), and subsequently diluted with modified BG-11 only. Cells were exposed to surface flux of ~25 µmol photons m-2 s-1 white light, bubbled with 500 ml min-1 1% CO2 in air, maintained at 30º C, and stirred at 1 rotation per second. Constant optical density (OD750 0.15) and volume are achieved via a two state controller. OD does not fluctuate more than 8% during an experiment.

extract_protocol: RNA was extracted from frozen cells in two steps. First, cells were lysed in 65° C phenol/SDS (sodium dodecyl sulfate) by vortexing and the total RNA was purified by phenol/chloroform extraction. Second, total RNA was subjected to DNase I (Promega) treatment followed by a second phenol/chloroform extraction. Total RNA was analyzed on agarose gel and Agilent Bioanalyzer for integrity.

treatment_protocol: For all experiments, cells are exposed to two light/dark cycles for entrainment prior to release into continuous light, collected at designated times by vacuum filtration, snap frozen in liquid nitrogen, and stored in -80º C. For novobiocin treatment experiment, cells were sampled at T = 56 and T = 64 hours into the circadian cycle. At T = 64 hours, cells were treated with novobiocin sodium salt at concentration 0.1 ug/ml. Cells were then sampled at 5, 10, 30, 90, and 150 minutes using protocol mentioned above.

tag: experiment

value: AMC 408

source_name: average of samples 17 to 23

tag: reference

value: average of samples in experiment 2


title: novobiocin T = 10 minutes experiment 2

description: no additional information

source_name: novobiocin T = 10 minutes


title: Bladder tumor REF1


title: novobiocin T = 5 minutes experiment 2

description: no additional information

source_name: novobiocin T = 5 minutes


title: Bladder tumor REF5


title: Bladder tumor S5_C


title: novobiocin T = 64 hours experiment 2

description: no additional information

source_name: novobiocin T = 64 hours


title: novobiocin T = 56 hours experiment 2

description: no additional information

source_name: novobiocin T = 56 hours


title: continuous light T = 84 hours experiment 1

description: no additional information

source_name: continuous light T = 84 hours

source_name: average of samples 1 to 16

value: average of samples in experiment 1


title: continuous light T = 80 hours experiment 1

description: no additional information

source_name: continuous light T = 80 hours


title: Bladder tumor REF2


title: Gp40 252175910003-6

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
gDNA Gp40
Date:2009/01/23

hyb_protocol: CGH-Agilent-10rpm : 500.0 ng at 65 degree_C during 20 hours

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

data_processing: No normalization performed

organism: Ehrlichia ruminantium

source_name: gDNA Gp40

label_protocol: CGH Agilent/bioprime

extract_protocol: Whole bacterial DNA was obtained using QIAamp extraction kit

value: Gardel


title: continuous light T = 76 hours experiment 1

description: no additional information

source_name: continuous light T = 76 hours


title: continuous light T = 72 hours experiment 1

description: no additional information

source_name: continuous light T = 72 hours


title: continuous light T = 68 hours experiment 1

description: no additional information

source_name: continuous light T = 68 hours


title: continuous light T = 64 hours experiment 1

description: no additional information

source_name: continuous light T = 64 hours


title: continuous light T = 60 hours experiment 1

description: no additional information

source_name: continuous light T = 60 hours


title: Bladder tumor S4_B

source_name: Bladder tumor


title: Bladder tumor S5_B

value: Ta


title: Bladder tumor S4_A


title: continuous light T = 56 hours experiment 1

description: no additional information

source_name: continuous light T = 56 hours


title: Bladder tumor REF6


title: Bladder tumor S5_A


title: Bladder tumor REF4


title: Bladder tumor REF7


title: continuous light T = 48 hours experiment 1

description: no additional information

source_name: continuous light T = 48 hours


title: continuous light T = 40 hours experiment 1

description: no additional information

source_name: continuous light T = 40 hours


title: CysNO-treated yeast protein microarray - 1

data_processing: Proccessed using GenePixPro

source_name: Yeast protoarray treated with CysNO for 30 min and analyzed by modified BST


title: Wp11 252063110001-3

description:
gDNA Wp11
Date:2008/09/26

source_name: gDNA Wp11

value: Welegevonden


title: novobiocin T = 150 minutes experiment 2

description: no additional information

source_name: novobiocin T = 150 minutes

source_name: average of samples 17 to 23


title: continuous light T = 52 hours experiment 1

description: no additional information

source_name: continuous light T = 52 hours


title: continuous light T = 44 hours experiment 1

description: no additional information

source_name: continuous light T = 44 hours

source_name: average of samples 1 to 16


title: continuous light T = 28 hours experiment 1

description: no additional information

source_name: continuous light T = 28 hours


title: continuous light T = 32 hours experiment 1

description: no additional information

source_name: continuous light T = 32 hours


title: continuous light T = 36 hours experiment 1

description: no additional information

source_name: continuous light T = 36 hours


title: continuous light T = 24 hours experiment 1

description: no additional information

source_name: continuous light T = 24 hours


title: Sh53.3 (168FARN cells expressing a KLF17 shRNA)

description: Mouse cell lines 168FARN expressing a KLF17 shRNA

hyb_protocol: Illumina Hyb protocol

scan_protocol: Illumina scan protocol

data_processing:
Illumina BeadStudio data on
1. The raw data of the spot density was extracted from Illumina BeadStudio software.
2. Check samples outlier.
3. The raw data filtering by the p-value 0.05 of each spot. If no one below p-value 0.05, the spot would be filtered out.
4. Quantile normalization for the filtering data.
5. Apply one-way ANOVA on the quantile normalization data to find out the significant gene data.

label_protocol: Pipette 2 mL Block E1 buffer + streptavidin-Cy3 into fresh Wash Tray(s). Transfer the BeadChip, face up into Wash Tray(s) on rocker. Place cover on tray and rock at medium speed for 10 minutes.

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol (Invitrogen).

tag: vector

value: expressing a KLF17 shRNA


title: Retina homozygous KO 42 days 2

city: Tuebingen

first: Marita

middle: Pauline

last: Feldkaemper

address: Calwerstrasse 7/1

department: Section of Neurobiology of the Eye

institute: University Eye Hospital Tuebingen, Institute for Ophthalmic Research

description: RNA sample consists of three separate retinal samples that were pooled

hyb_protocol: see manufacturer's website

scan_protocol: Scanning and analysis were carried out using the Affymetrix Microarray Suite Software (version 5.0)

data_processing: Signal intensities were analyzed using ArrayAssist 4.0 (Stratagene, La Jolla, CA). Transformation algorithm: GC-RMA.

source_name: Retina, 42 days old homozygous Egr-1 knock-out mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (see manufacturer´s website: Expression Analysis Technical Manual, One-Cycle Target Labeling Assay, Affymetrix).

growth_protocol: Animals were housed in standard cages with their littermates under a 12 hours light/dark cycle with unrestricted access to water and food pellets. Illumination was provided by standard fluorescent lamps and was approximately 200 lux.

extract_protocol: Three single retinas from different mice were pooled to obtain 4 samples per group (wt30, wt42, hm30, hm42), and RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The quality of total RNA was monitored by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions.

treatment_protocol: Mice were killed by an overdose of diethylether at the mean age of 30 days (p29-p31) or 42 days (p41-p43). Afterwards, the eyes were enucleated, the retinas were prepared and immediately snap-frozen in liquid nitrogen. The retinas of 12 homozygous Egr-1 knock-out mice (hm) and 12 wildtype mice (wt) of the same strain were prepared for both time points (48 animals in total).

value: male

value: Egr-1 knock-out

value: 42 days

tag: tissue

value: retina


title: 168.3 (168FARN cells expressing control vector)

first: Louise

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

description: 168FARN cells expressing a control vector

source_name: Mouse cell lines 168FARN expressing a control vector

value: expressing a control vector


title: Retina wildtype 42 days 3

source_name: Retina, 42 days old wildtype mice

value: Egr-1 wildtype

tag: age


title: 168.1 (168FARN cells expressing control vector

value: control vector


title: cDNA.3 (168FARN cells expressing a KLF17 cDNA)

description: Mouse cell lines 168FARN expressing a KLF17 cDNA

value: expressing a KLF17 cDNA


title: cDNA.1 (168FARN cells expressing a KLF17 cDNA)

source_name: Mouse cell lines 168FARN expressing a KLF17 cDNA


title: Retina homozygous KO 42 days 3


title: Sh53.1 (168FARN cells expressing a KLF17 shRNA)

source_name: Mouse cell lines 168FARN expressing a KLF17 shRNA


title: Retina homozygous KO 42 days 1


title: cDNA.2 (168FARN cells expressing a KLF17 cDNA)


title: 168.2 (168FARN cells expressing control vector)


title: Sh53.2 (168FARN cells expressing a KLF17 shRNA)


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM8

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

description: We used the default settings of GCOS software to scan the chips

hyb_protocol: Affymetrix GeneChips Human Genome U133 Array Set HG-U133A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions

data_processing: We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.

source_name: PBMC NORM8

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

growth_protocol: Before RNA extraction, cells were thaw, counted and their viability determined by Trypan Blue exclusion (>90% PBMC were viable). A minimum of 5 milion cryopreserved PBMC were centrifuged, and immediately lysed for RNA extraction.

extract_protocol: Total RNA was extracted by RNeasy mini kit (QIAGEN Inc., Valencia, CA) according to the manufacturer’s instructions and resuspended in DEPC-treated Rnase-free distilled water. RNA concentration was determined by NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and its integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: The biological material was obtained at the beginning of the second hemodialysis session of the week. PBMC were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Isolated cells were stored at –80°C in FBS+10% DMSO until use.

tag: healthy subject

tag: group

value: Training


title: Retina homozygous KO 42 days 4

tag: genotype


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM7

scan_protocol: We used the default settings of GCOS software to scan the chips

source_name: PBMC NORM7


title: Retina wildtype 42 days 1


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM6

source_name: PBMC NORM6

treatment_protocol: PBMC were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Isolated cells were stored at –80°C in FBS+10% DMSO until use.


title: Retina homozygous KO 30 days 4

source_name: Retina, 30 days old homozygous Egr-1 knock-out mice

value: 30 days


title: Retina wildtype 42 days 2


title: novobiocin T = 90 minutes experiment 2

description: no additional information

source_name: novobiocin T = 90 minutes

value: AMC 408

source_name: average of samples 17 to 23


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM4

source_name: PBMC NORM4


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM5

source_name: PBMC NORM5


title: Retina homozygous KO 30 days 2


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM2

source_name: PBMC NORM2


title: Retina homozygous KO 30 days 3


title: Retina wildtype 42 days 4


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD4

source_name: PBMC CKD4

tag: patient

tag: disease

value: chronic kidney disease in stage II-III

tag: treatment

value: conservative


title: Retina homozygous KO 30 days 1


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD7

source_name: PBMC CKD7


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM3

source_name: PBMC NORM3


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD9

source_name: PBMC CKD9


title: Retina wildtype 30 days 3

source_name: Retina, 30 days old wildtype mice


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD8

source_name: PBMC CKD8


title: Retina wildtype 30 days 1


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD5

source_name: PBMC CKD5


title: Retina wildtype 30 days 4


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD6

source_name: PBMC CKD6


title: Retina wildtype 30 days 2


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD2

source_name: PBMC CKD2

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD3

source_name: PBMC CKD3


title: Peripheral blood mononuclear cells (PBMC)- Healthy subject NORM1

source_name: PBMC NORM1


title: Peripheral blood mononuclear cells (PBMC)-Patient CKD1

source_name: PBMC CKD1


title: Peripheral blood mononuclear cells (PBMC)-Patient HD16

source_name: PBMC HD16

value: chronic kidney disease

value: undergoing hemodialysis


title: Peripheral blood mononuclear cells (PBMC)-Patient  HD12

source_name: PBMC HD12


title: Peripheral blood mononuclear cells (PBMC)-Patient HD13

source_name: PBMC HD13


title: Peripheral blood mononuclear cells (PBMC)-Patient HD17

source_name: PBMC HD17


title: ahg2-1abi1-1 rep1

status: Public on Nov 27 2009

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

country: Japan

institute: Okayama University

description: Gene expression data of ahg2-1 and abi1-1 double mutant geminating seedlings under normal conditions.

hyb_protocol: 30 ug cRNA was used. ATH1 GeneChip was used.

scan_protocol: Scanned using a GSC3000 scanner according to the manufacturer’s recommendations.

data_processing: RMA normalized using Cel file with affllmGUI.

source_name: three week old plants

label_protocol: First-strand cDNA was synthesized using 15 µg of total RNA and SuperScript Double-stranded cDNA Synthesis kit (Invitrogen). The labeled cRNA was synthesized using BioArray RNA Transcripts Labeling Kit (T7) (ENZO Life Sciences inc.). After labeling, the cRNA was digested partially by incubating in 40 mM Tris-acetate, pH8.0, 100 mM KOAc, 30 mM MgOAc, at 94°C for 35 min. Then 30 µg cRNA was used for microarrary hybridization.

growth_protocol: The plates were kept in a growth chamber under the following conditions: 23°C, 16 hr light and 8 hr dark cycles.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent (Invitrogen) and purified using the RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Plants were grown on MS-2% sucrose plate for three weeks.

value: ahg2-1 and abi1-1 double mutant


title: Peripheral blood mononuclear cells (PBMC)-Patient HD11

source_name: PBMC HD11


title: Peripheral blood mononuclear cells (PBMC)-Patient HD8

source_name: PBMC HD8


title: ahg2-1 rep2

description: Gene expression data of ABA hypersensitive germination2-1 geminating seedlings under normal conditions.

value: ABA hypersensitive germination2-1


city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from suspension cells of E. coli K-12 BW25113/pCA24N-mqsR after OD600=0.5 of growth, then 2 mM IPTG for 15 min short time in LB at 37oC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45oC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: E. coli K-12 BW25113/pCA24N-mqsR at OD600=0.5 LB 37C then 2 mM IPTG for 15 min short time suspension cell

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.5 at 37oC under 2 mM IPTG with shaking (250 rpm), the planktonic cells were quickly removed and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: Peripheral blood mononuclear cells (PBMC)-Patient HD15

source_name: PBMC HD15


title: ahg2-1sid2-2 rep2

description: Gene expression data of ahg2-1 and sid2-2 double mutant geminating seedlings under normal conditions.

value: ahg2-1 and sid2-2 double mutant


title: Peripheral blood mononuclear cells (PBMC)-Patient HD9

source_name: PBMC HD9


title: Peripheral blood mononuclear cells (PBMC)-Patient HD14

source_name: PBMC HD14


title: Peripheral blood mononuclear cells (PBMC)-Patient HD6

source_name: PBMC HD6


description: RNA extracted from suspension cells of E. coli K-12 BW25113 mqsR deleted mutant after OD600=0.5 of growth in LB at 37oC

source_name: E. coli K-12 BW25113 mqsR mutant at OD600=0.5 LB 37C suspension cell

extract_protocol: The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.5 at 37oC with shaking (250 rpm), the planktonic cells were quickly removed and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


description: RNA extracted from suspension cells of E. coli K-12 BW25113/pCA24N (empty vector) after OD600=0.5 of growth, then 2 mM IPTG for 15 min short time in LB at 37oC

source_name: E. coli K-12 BW25113/pCA24N at OD600=0.5 LB 37C then 2 mM IPTG for 15 min short time suspension cell