title: Normal-3 [miRNA]

status: Public on Dec 31 2013

type: RNA

city: seoul

first: minhee

last: park

address: shinchondong

country: South Korea

institute: student

hyb_protocol: Human microRNA Microarray Kit (Agilent Technologies) according to manufacture’s protocol. (http://www.chem.agilent.com/en-US/Pages/Homepage.aspx)

scan_protocol: Scanned on an Agilent C scanner.   Images were quantified using Agilent Feature Extraction Software ( v 10.10.1.1).

data_processing: Raw data were extracted using the Agilent Feature Extraction Software (v 10.7.1.1) and then processed as published previously <Processing of Agilent microRNA array data, BMC RES NOTES,2010>

molecule: total RNA

organism: Homo sapiens

source_name: non-neoplastic pancreas

label_protocol: 100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0

extract_protocol: Total RNA was obtained from each independent tissue of patient and extracted using TRIzol Reagent (Invitrogen).

tag: tissue

value: non-neoplastic pancreas


title: Normal-5 [miRNA]


title: PCA-5 [miRNA]

source_name: ductal adenocarcinoma

tag: gender

value: male

tag: age

value: ductal adenocarcinoma (PCA)


title: Normal-4 [miRNA]


title: Normal-2 [miRNA]


title: PCA-1 [miRNA]

value: female


title: PCA-4 [miRNA]


title: Normal-1 [miRNA]


title: NET-5 [miRNA]

source_name: neuroendocrine tumor

value: neuroendocrine tumor (NET)


title: NET-6 [miRNA]


title: NET-2 [miRNA]


title: NET-3 [miRNA]


title: PCA-3 [miRNA]


title: SPN-12 [miRNA]

source_name: solid-pseudopapillary neoplasm

value: Solid-pseudopapillary neoplasm of pancreas (SPN)


title: NET-4 [miRNA]


title: SPN-13 [miRNA]


title: PCA-6 [miRNA]


title: SPN-14 [miRNA]


title: SPN-10 [miRNA]


title: NET-1 [miRNA]


title: SPN-11 [miRNA]


title: PCA-2 [miRNA]


title: SPN-8 [miRNA]


title: SPN-5 [miRNA]


title: H3K9Ac Monocytes EDIC Participant ID 1538

type: genomic

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

country: USA

institute: City of Hope

description: ChIP-chip Monocyte H3K9Ac from DCCT/EDIC patient

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: mean-centered log2(Cy5/Cy3) in gff format. The gff files are combined to generate matrix dataset in R.

molecule: genomic DNA

source_name: Monocyte H3K9Ac ChIP DNA

label_protocol: According to standard NimbleGen Protocol

growth_protocol: RPMI 1640 medium

extract_protocol: Primary monocytes were crosslinked in 1% formaldehyde, sonicated to shear DNA, and IPs performed with antibodies. IP with no antibody was used as the Input control.

treatment_protocol: No Treatment

tag: cell type

value: Monocyte

source_name: Monocyte no antibody control


title: H3K9Ac Monocytes EDIC Participant ID 1533


title: H3K9Ac Monocytes EDIC Participant ID 1540


title: SPN-9 [miRNA]


title: SPN-4 [miRNA]


title: SPN-7 [miRNA]


title: SPN-2 [miRNA]


title: SPN-1 [miRNA]


title: H3K9Ac Monocytes EDIC Participant ID 1529


title: H3K9Ac Monocytes EDIC Participant ID 1521


title: H3K9Ac Monocytes EDIC Participant ID 1528


title: H3K9Ac Monocytes EDIC Participant ID 1526


title: H3K9Ac Monocytes EDIC Participant ID 1519


title: H3K9Ac Monocytes EDIC Participant ID 1527


title: H3K9Ac Monocytes EDIC Participant ID 1524


title: H3K9Ac Monocytes EDIC Participant ID 1535


title: H3K9Ac Monocytes EDIC Participant ID 1539


title: H3K9Ac Monocytes EDIC Participant ID 1518


title: H3K9Ac Monocytes EDIC Participant ID 1512


title: H3K9Ac Monocytes EDIC Participant ID 1507


title: H3K9Ac Monocytes EDIC Participant ID 1516


title: H3K9Ac Monocytes EDIC Participant ID 1513


title: SPN-3 [miRNA]


title: H3K9Ac Monocytes EDIC Participant ID 1505


title: H3K9Ac Monocytes EDIC Participant ID 1506


title: SPN-6 [miRNA]


title: H3K9Ac Monocytes EDIC Participant ID 1509


title: 389584

city: Houston

first: Anne

middle: Chinenye

last: Katchy

state: Texas

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

institute: University of Houston

hyb_protocol: Hybridization was performed at 42 °C for at least 40 hours after pooling of samples for each array. Subsequent to hybridization the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.

scan_protocol: Slides were scanned using an Axon GenePix 4400A (MDS Analytical Technologies) to obtain TIFF files.

data_processing: Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis. Cut-offs set as described in article.

label_protocol: Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester dured 30 min.

extract_protocol: RNA extraction was performed with TRIzol reagent (Invitrogen Carlsbad, CA) and chloroform extraction according to the manufacturer’s protocol.

tag: cell line

tag: agent

value: Vehicle

value: Soy Formula Extract (SF)


title: H3K9Ac Monocytes EDIC Participant ID 1501


title: 388822

value: Genistein (Gen)


title: H3K9Ac Monocytes EDIC Participant ID 1502


title: 354103

value: Bisphenol A (BPA)


title: H3K9Ac Monocytes EDIC Participant ID 1491


title: H3K9Ac Monocytes EDIC Participant ID 1492


title: H3K9Ac Monocytes EDIC Participant ID 1489


title: H3K9Ac Monocytes EDIC Participant ID 1497


title: H3K9Ac Monocytes EDIC Participant ID 1504


title: H3K9Ac Monocytes EDIC Participant ID 1481


title: H3K9Ac Monocytes EDIC Participant ID 1488


title: H3K9Ac Monocytes EDIC Participant ID 1483


title: H3K9Ac Monocytes EDIC Participant ID 1485


title: H3K9Ac Monocytes EDIC Participant ID 1496


title: H3K9Ac Monocytes EDIC Participant ID 1495


title: 389585


title: 388827


title: H3K9Ac Monocytes EDIC Participant ID 1476


title: H3K9Ac Monocytes EDIC Participant ID 1494


title: H3K9Ac Monocytes EDIC Participant ID 1473


title: H3K9Ac Monocytes EDIC Participant ID 1490


title: 354102


title: H3K9Ac Monocytes EDIC Participant ID 1467


title: H3K9Ac Monocytes EDIC Participant ID 1487


title: H3K9Ac Monocytes EDIC Participant ID 1511


title: H3K9Ac Monocytes EDIC Participant ID 1466


title: H3K9Ac Monocytes EDIC Participant ID 1482


title: H3K9Ac Monocytes EDIC Participant ID 1460


title: H3K9Ac Monocytes EDIC Participant ID 1458


title: H3K9Ac Monocytes EDIC Participant ID 1480


title: H3K9Ac Monocytes EDIC Participant ID 1477


title: H3K9Ac Monocytes EDIC Participant ID 1475


title: H3K9Ac Monocytes EDIC Participant ID 1470


title: H3K9Ac Monocytes EDIC Participant ID 1452


title: H3K9Ac Monocytes EDIC Participant ID 1455


title: H3K9Ac Monocytes EDIC Participant ID 1451


title: H3K9Ac Monocytes EDIC Participant ID 1454


title: H3K9Ac Monocytes EDIC Participant ID 1468


title: H3K9Ac Monocytes EDIC Participant ID 1479


title: H3K4Me3 Monocytes EDIC Participant ID 1535

description: ChIP-chip Monocyte H3K4Me3 from DCCT/EDIC patient

source_name: Monocyte H3K4Me3 ChIP DNA


title: H3K4Me3 Monocytes EDIC Participant ID 1538


title: H3K4Me3 Monocytes EDIC Participant ID 1533


title: H3K4Me3 Monocytes EDIC Participant ID 1529


title: H3K4Me3 Monocytes EDIC Participant ID 1528


title: H3K4Me3 Monocytes EDIC Participant ID 1526


title: H3K4Me3 Monocytes EDIC Participant ID 1524


title: H3K9Ac Monocytes EDIC Participant ID 1459


title: H3K4Me3 Monocytes EDIC Participant ID 1521


title: H3K4Me3 Monocytes EDIC Participant ID 1513


title: H3K4Me3 Monocytes EDIC Participant ID 1518


title: H3K4Me3 Monocytes EDIC Participant ID 1516


title: H3K9Ac Monocytes EDIC Participant ID 1462


title: H3K9Ac Monocytes EDIC Participant ID 1444


title: H3K4Me3 Monocytes EDIC Participant ID 1539


title: H3K9Ac Monocytes EDIC Participant ID 1445


title: H3K9Ac Monocytes EDIC Participant ID 1446


title: H3K4Me3 Monocytes EDIC Participant ID 1509


title: H3K4Me3 Monocytes EDIC Participant ID 1504


title: H3K4Me3 Monocytes EDIC Participant ID 1506


title: H3K4Me3 Monocytes EDIC Participant ID 1511


title: H3K4Me3 Monocytes EDIC Participant ID 1502


title: H3K4Me3 Monocytes EDIC Participant ID 1497


title: H3K9Ac Monocytes EDIC Participant ID 1443


title: H3K4Me3 Monocytes EDIC Participant ID 1527


title: H3K4Me3 Monocytes EDIC Participant ID 1519


title: H3K4Me3 Monocytes EDIC Participant ID 1512


title: H3K4Me3 Monocytes EDIC Participant ID 1490


title: H3K4Me3 Monocytes EDIC Participant ID 1507


title: H3K4Me3 Monocytes EDIC Participant ID 1540


title: H3K4Me3 Monocytes EDIC Participant ID 1505


title: H3K4Me3 Monocytes EDIC Participant ID 1488


title: H3K4Me3 Monocytes EDIC Participant ID 1482


title: H3K4Me3 Monocytes EDIC Participant ID 1501


title: H3K4Me3 Monocytes EDIC Participant ID 1476


title: H3K4Me3 Monocytes EDIC Participant ID 1480


title: H3K4Me3 Monocytes EDIC Participant ID 1477


title: H3K4Me3 Monocytes EDIC Participant ID 1495


title: H3K4Me3 Monocytes EDIC Participant ID 1496


title: H3K4Me3 Monocytes EDIC Participant ID 1494


title: H3K4Me3 Monocytes EDIC Participant ID 1492


title: H3K4Me3 Monocytes EDIC Participant ID 1491


title: H3K4Me3 Monocytes EDIC Participant ID 1462


title: H3K4Me3 Monocytes EDIC Participant ID 1467


title: H3K4Me3 Monocytes EDIC Participant ID 1483


title: H3K4Me3 Monocytes EDIC Participant ID 1487


title: H3K4Me3 Monocytes EDIC Participant ID 1485


title: H3K4Me3 Monocytes EDIC Participant ID 1489


title: H3K4Me3 Monocytes EDIC Participant ID 1466


title: H3K4Me3 Monocytes EDIC Participant ID 1481


title: H3K4Me3 Monocytes EDIC Participant ID 1479


title: H3K4Me3 Monocytes EDIC Participant ID 1475


title: H3K4Me3 Monocytes EDIC Participant ID 1470


title: H3K4Me3 Monocytes EDIC Participant ID 1473


title: H3K4Me3 Monocytes EDIC Participant ID 1445


title: H3K4Me3 Monocytes EDIC Participant ID 1460


title: H3K4Me3 Monocytes EDIC Participant ID 1451


title: H3K4Me3 Monocytes EDIC Participant ID 1446


title: H3K4Me3 Monocytes EDIC Participant ID 1468


title: H3K4Me3 Monocytes EDIC Participant ID 1458


title: H3K4Me3 Monocytes EDIC Participant ID 1459


title: H3K9Me2_lympho EDIC Participant ID 1533

description: ChIP-chip lymphocyte H3K9Me2 from DCCT/EDIC patient

source_name: Lymphocyte H3K9Me2 ChIP DNA

extract_protocol: Primary lymphocytes were crosslinked in 1% formaldehyde, sonicated to shear DNA, and IPs performed with antibodies. IP with no antibody was used as the Input control.

value: Lymphocyte

source_name: Lymphocyte no antibody control


title: H3K9Me2_lympho EDIC Participant ID 1535


title: H3K9Me2_lympho EDIC Participant ID 1529


title: H3K9Me2_lympho EDIC Participant ID 1527


title: H3K4Me3 Monocytes EDIC Participant ID 1455


title: H3K4Me3 Monocytes EDIC Participant ID 1452


title: H3K4Me3 Monocytes EDIC Participant ID 1454


title: H3K9Me2_lympho EDIC Participant ID 1518


title: H3K9Me2_lympho EDIC Participant ID 1521


title: H3K9Me2_lympho EDIC Participant ID 1526


title: H3K4Me3 Monocytes EDIC Participant ID 1444


title: H3K4Me3 Monocytes EDIC Participant ID 1443

description: ####NO DATA: FAILED DURING SAMPLE PROCESSING####


title: H3K9Me2_lympho EDIC Participant ID 1540


title: H3K9Me2_lympho EDIC Participant ID 1539


title: H3K9Me2_lympho EDIC Participant ID 1516


title: H3K9Me2_lympho EDIC Participant ID 1538


title: H3K9Me2_lympho EDIC Participant ID 1524


title: H3K9Me2_lympho EDIC Participant ID 1519


title: H3K9Me2_lympho EDIC Participant ID 1528


title: H3K9Me2_lympho EDIC Participant ID 1513


title: H3K9Me2_lympho EDIC Participant ID 1501


title: H3K9Me2_lympho EDIC Participant ID 1511


title: H3K9Me2_lympho EDIC Participant ID 1502


title: H3K9Me2_lympho EDIC Participant ID 1512


title: H3K9Me2_lympho EDIC Participant ID 1504


title: H3K9Me2_lympho EDIC Participant ID 1497


title: H3K9Me2_lympho EDIC Participant ID 1505


title: H3K9Me2_lympho EDIC Participant ID 1506


title: H3K9Me2_lympho EDIC Participant ID 1507


title: H3K9Me2_lympho EDIC Participant ID 1509


title: H3K9Me2_lympho EDIC Participant ID 1491


title: H3K9Me2_lympho EDIC Participant ID 1496


title: H3K9Me2_lympho EDIC Participant ID 1494


title: H3K9Me2_lympho EDIC Participant ID 1492


title: H3K9Me2_lympho EDIC Participant ID 1489


title: H3K9Me2_lympho EDIC Participant ID 1495


title: H3K9Me2_lympho EDIC Participant ID 1488


title: H3K9Me2_lympho EDIC Participant ID 1490


title: H3K9Me2_lympho EDIC Participant ID 1487


title: H3K9Me2_lympho EDIC Participant ID 1483


title: H3K9Me2_lympho EDIC Participant ID 1480


title: GeneDialog02 TT 112

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from PBMCs isolated from whole blood

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and Affymetrix Expression Console 1.1

label: biotin

organism: Sus scrofa

source_name: PBMC, 2nd vaccination, 14d

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany), then treated with DNase and column-purified using the RNeasy Mini Kit (Qiagen).

treatment_protocol: vaccination, 1 ml (30 IU) of tetanus toxoid (Equilis Tetanus-Vaccine)

value: peripheral blood mononuclear cell (PBMC)

tag: first or second vaccination at 14 days interval

value: 2nd vaccination

tag: time after vaccination


title: H3K9Me2_lympho EDIC Participant ID 1482


title: H3K9Me2_lympho EDIC Participant ID 1477


title: H3K9Me2_lympho EDIC Participant ID 1481


title: GeneDialog02 TT 109


title: H3K9Me2_lympho EDIC Participant ID 1479


title: H3K9Me2_lympho EDIC Participant ID 1476


title: H3K9Me2_lympho EDIC Participant ID 1475


title: H3K9Me2_lympho EDIC Participant ID 1473


title: H3K9Me2_lympho EDIC Participant ID 1470


title: GeneDialog02 TT 110


title: GeneDialog02 TT 108


title: H3K9Me2_lympho EDIC Participant ID 1468


title: GeneDialog02 TT 99


title: H3K9Me2_lympho EDIC Participant ID 1467


title: GeneDialog02 TT 104


title: GeneDialog02 TT 106


title: GeneDialog02 TT 97


title: GeneDialog02 TT 98


title: GeneDialog02 TT 101


title: GeneDialog02 TT 107


title: GeneDialog02 TT 111


title: GeneDialog02 TT 102


title: GeneDialog02 TT 103


title: H3K9Me2_lympho EDIC Participant ID 1462


title: H3K9Me2_lympho EDIC Participant ID 1466


title: GeneDialog02 TT 105


title: H3K9Me2_lympho EDIC Participant ID 1460


title: GeneDialog02 TT 100


title: H3K9Me2_lympho EDIC Participant ID 1459


title: GeneDialog02 TT 96


title: H3K9Me2_lympho EDIC Participant ID 1458


title: GeneDialog02 TT 95


title: H3K9Me2_lympho EDIC Participant ID 1455


title: GeneDialog02 TT 93


title: GeneDialog02 TT 94


title: H3K9Me2_lympho EDIC Participant ID 1454


title: H3K9Me2_lympho EDIC Participant ID 1451


title: H3K9Me2_lympho EDIC Participant ID 1452


title: H3K9Me2_lympho EDIC Participant ID 1446


title: H3K9Me2_lympho EDIC Participant ID 1443


title: GeneDialog02 TT 91


title: H3K9Me2_lympho EDIC Participant ID 1445


title: GeneDialog02 TT 89


title: GeneDialog02 TT 92


title: H3K9Me2_lympho EDIC Participant ID 1444


title: GeneDialog02 TT 90


title: GeneDialog02 TT 87


title: GeneDialog02 TT 86


title: H3K9Ac_lympho EDIC Participant ID 1538

description: ChIP-chip lymphocyte H3K9Ac from DCCT/EDIC patient

source_name: Lymphocyte H3K9Ac ChIP DNA


title: GeneDialog02 TT 88


title: GeneDialog02 TT 85


title: H3K9Ac_lympho EDIC Participant ID 1540


title: H3K9Ac_lympho EDIC Participant ID 1539


title: GeneDialog02 TT 84


title: H3K9Ac_lympho EDIC Participant ID 1535


title: H3K9Ac_lympho EDIC Participant ID 1533


title: GeneDialog02 TT 83


title: GeneDialog02 TT 81


title: GeneDialog02 TT 79


title: GeneDialog02 TT 82


title: GeneDialog02 TT 77


title: GeneDialog02 TT 78


title: H3K9Ac_lympho EDIC Participant ID 1528


title: H3K9Ac_lympho EDIC Participant ID 1526


title: GeneDialog02 TT 80


title: H3K9Ac_lympho EDIC Participant ID 1529


title: H3K9Ac_lympho EDIC Participant ID 1524


title: H3K9Ac_lympho EDIC Participant ID 1527


title: H3K9Ac_lympho EDIC Participant ID 1521


title: H3K9Ac_lympho EDIC Participant ID 1513


title: H3K9Ac_lympho EDIC Participant ID 1518


title: H3K9Ac_lympho EDIC Participant ID 1516


title: H3K9Ac_lympho EDIC Participant ID 1512


title: GeneDialog02 TT 75


title: GeneDialog02 TT 76


title: H3K9Ac_lympho EDIC Participant ID 1509


title: H3K9Ac_lympho EDIC Participant ID 1519


title: H3K9Ac_lympho EDIC Participant ID 1511


title: GeneDialog02 TT 70

source_name: PBMC, 1st vaccination, 14d

value: 1st vaccination


title: GeneDialog02 TT 74


title: H3K9Ac_lympho EDIC Participant ID 1507


title: H3K9Ac_lympho EDIC Participant ID 1506


title: GeneDialog02 TT 71


title: GeneDialog02 TT 68


title: H3K9Ac_lympho EDIC Participant ID 1504


title: GeneDialog02 TT 72


title: GeneDialog02 TT 69


title: GeneDialog02 TT 73


title: H3K9Ac_lympho EDIC Participant ID 1502


title: H3K9Ac_lympho EDIC Participant ID 1501


title: H3K9Ac_lympho EDIC Participant ID 1496


title: H3K9Ac_lympho EDIC Participant ID 1497


title: GeneDialog02 TT 66


title: GeneDialog02 TT 67


title: H3K9Ac_lympho EDIC Participant ID 1505


title: H3K9Ac_lympho EDIC Participant ID 1495


title: GeneDialog02 TT 62


title: H3K9Ac_lympho EDIC Participant ID 1494


title: H3K9Ac_lympho EDIC Participant ID 1492


title: H3K9Me2_lympho EDIC Participant ID 1485


title: H3K9Ac_lympho EDIC Participant ID 1491


title: GeneDialog02 TT 60


title: GeneDialog02 TT 61


title: GeneDialog02 TT 64


title: GeneDialog02 TT 65


title: GeneDialog02 TT 58


title: GeneDialog02 TT 53


title: GeneDialog02 TT 59


title: GeneDialog02 TT 63


title: H3K9Ac_lympho EDIC Participant ID 1488


title: GeneDialog02 TT 50


title: GeneDialog02 TT 55


title: H3K9Ac_lympho EDIC Participant ID 1487


title: H3K9Ac_lympho EDIC Participant ID 1485


title: H3K9Ac_lympho EDIC Participant ID 1483


title: H3K9Ac_lympho EDIC Participant ID 1489


title: H3K9Ac_lympho EDIC Participant ID 1490


title: GeneDialog02 TT 52


title: H3K9Ac_lympho EDIC Participant ID 1481


title: GeneDialog02 TT 57


title: GeneDialog02 TT 49


title: GeneDialog02 TT 51


title: H3K9Ac_lympho EDIC Participant ID 1480


title: H3K9Ac_lympho EDIC Participant ID 1479


title: H3K9Ac_lympho EDIC Participant ID 1476


title: H3K9Ac_lympho EDIC Participant ID 1482


title: GeneDialog02 TT 54


title: H3K9Ac_lympho EDIC Participant ID 1468


title: H3K9Ac_lympho EDIC Participant ID 1473


title: H3K9Ac_lympho EDIC Participant ID 1466


title: H3K9Ac_lympho EDIC Participant ID 1467


title: GeneDialog02 TT 47


title: GeneDialog02 TT 48


title: H3K9Ac_lympho EDIC Participant ID 1477


title: H3K9Ac_lympho EDIC Participant ID 1462


title: GeneDialog02 TT 40


title: GeneDialog02 TT 42


title: GeneDialog02 TT 45


title: GeneDialog02 TT 38


title: H3K9Ac_lympho EDIC Participant ID 1475


title: GeneDialog02 TT 41


title: GeneDialog02 TT 46


title: H3K9Ac_lympho EDIC Participant ID 1460


title: GeneDialog02 TT 37


title: GeneDialog02 TT 43


title: GeneDialog02 TT 33


title: GeneDialog02 TT 35


title: GeneDialog02 TT 36


title: H3K9Ac_lympho EDIC Participant ID 1470


title: H3K9Ac_lympho EDIC Participant ID 1459


title: H3K9Ac_lympho EDIC Participant ID 1458


title: H3K9Ac_lympho EDIC Participant ID 1452


title: H3K9Ac_lympho EDIC Participant ID 1454


title: GeneDialog02 TT 30

source_name: PBMC, 1st vaccination, 0h


title: GeneDialog02 TT 31


title: GeneDialog02 TT 29


title: GeneDialog02 TT 32


title: GeneDialog02 TT 26


title: GeneDialog02 TT 28


title: H3K9Ac_lympho EDIC Participant ID 1455


title: GeneDialog02 TT 27


title: H3K9Ac_lympho EDIC Participant ID 1445


title: H3K9Ac_lympho EDIC Participant ID 1443


title: H3K9Ac_lympho EDIC Participant ID 1444


title: H3K4Me3_lympho EDIC Participant ID 1540

description: ChIP-chip lymphocyte H3K4Me3 from DCCT/EDIC patient

source_name: Lymphocyte H3K4Me3 ChIP DNA


title: H3K9Ac_lympho EDIC Participant ID 1446


title: H3K4Me3_lympho EDIC Participant ID 1539


title: GeneDialog02 TT 25


title: H3K4Me3_lympho EDIC Participant ID 1535


title: H3K9Ac_lympho EDIC Participant ID 1451


title: GeneDialog02 TT 23


title: H3K4Me3_lympho EDIC Participant ID 1538


title: H3K4Me3_lympho EDIC Participant ID 1533


title: GeneDialog02 TT 24


title: GeneDialog02 TT 17


title: GeneDialog02 TT 19


title: GeneDialog02 TT 22


title: GeneDialog02 TT 44


title: GeneDialog02 TT 20


title: H3K4Me3_lympho EDIC Participant ID 1529


title: H3K4Me3_lympho EDIC Participant ID 1527


title: GeneDialog02 TT 21


title: H3K4Me3_lympho EDIC Participant ID 1528


title: H3K4Me3_lympho EDIC Participant ID 1526


title: GeneDialog02 TT 18


title: GeneDialog02 TT 16


title: H3K4Me3_lympho EDIC Participant ID 1519


title: H3K4Me3_lympho EDIC Participant ID 1524


title: H3K4Me3_lympho EDIC Participant ID 1521


title: GeneDialog02 TT 56


title: H3K4Me3_lympho EDIC Participant ID 1518


title: GeneDialog02 TT 14


title: GeneDialog02 TT 12


title: H3K4Me3_lympho EDIC Participant ID 1516


title: GeneDialog02 TT 09


title: GeneDialog02 TT 15


title: GeneDialog02 TT 13


title: GeneDialog02 TT 10


title: GeneDialog02 TT 11


title: H3K4Me3_lympho EDIC Participant ID 1512


title: GeneDialog02 TT 08


title: H3K4Me3_lympho EDIC Participant ID 1511


title: H3K4Me3_lympho EDIC Participant ID 1513


title: H3K4Me3_lympho EDIC Participant ID 1509


title: H3K4Me3_lympho EDIC Participant ID 1507


title: H3K4Me3_lympho EDIC Participant ID 1502


title: H3K4Me3_lympho EDIC Participant ID 1505


title: H3K4Me3_lympho EDIC Participant ID 1506


title: H3K4Me3_lympho EDIC Participant ID 1504


title: H3K4Me3_lympho EDIC Participant ID 1501


title: H3K4Me3_lympho EDIC Participant ID 1497


title: GeneDialog02 TT 06


title: GeneDialog02 TT 07


title: GeneDialog02 TT 04


title: GeneDialog02 TT 05


title: H3K4Me3_lympho EDIC Participant ID 1495


title: H3K4Me3_lympho EDIC Participant ID 1494


title: H3K4Me3_lympho EDIC Participant ID 1491


title: GeneDialog02 TT 02


title: H3K4Me3_lympho EDIC Participant ID 1490


title: H3K4Me3_lympho EDIC Participant ID 1489


title: H3K4Me3_lympho EDIC Participant ID 1492


title: H3K4Me3_lympho EDIC Participant ID 1496


title: H3K4Me3_lympho EDIC Participant ID 1488


title: GeneDialog02 TT 01


title: GeneDialog02 TT 03


title: Colorectal mucosa #13

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
exprs.13N
Colon mucosa tissue, patient #13

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 2.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

label: Biotin

source_name: Colorectal mucosa tissue, patient #13

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

growth_protocol: Human tissue samples.

extract_protocol: Total RNA from patient samples was purified by using the mirVana kit (Ambion, Life Technologies).

tag: disease status

value: colorectal cancer

tag: duke's stage

value: II

value: matching normal colon mucosa

tag: patient identifier


title: Colorectal tumor #12

description:
exprs.12T
Colon tumor, patient#12

source_name: Colorectal tumor, patient #12

value: colon tumor


title: H3K4Me3_lympho EDIC Participant ID 1487


title: Colorectal mucosa #12

description:
exprs.12N
Colon mucosa tissue, patient #12

source_name: Colorectal mucosa tissue, patient #12


title: Colorectal mucosa #8

description:
exprs.8N
Colon mucosa tissue, patient #8

source_name: Colorectal mucosa tissue, patient #8


title: Colorectal tumor #8

description:
exprs.8T
Colon tumor, patient#8

source_name: Colorectal tumor, patient #8


title: Colorectal tumor #6

description:
exprs.6T
Colon tumor, patient#6

source_name: Colorectal tumor, patient #6


title: Colorectal mucosa #6

description:
exprs.6N
Colon mucosa tissue, patient #6

source_name: Colorectal mucosa tissue, patient #6


title: H3K4Me3_lympho EDIC Participant ID 1485


title: H3K4Me3_lympho EDIC Participant ID 1483


title: H3K4Me3_lympho EDIC Participant ID 1481


title: H3K4Me3_lympho EDIC Participant ID 1482


title: Tomato planta macho viroid

city: Beijing

first: Yongjiang

last: Zhang

country: China

institute: Chinese Academy of Inspection and Quarantine

hyb_protocol: Cy3-labeled DNA fragments, pre-heated for 10 min at 80 oC, were added to the microarray for hybridization for 16 hr at 42 oC. Slides were washed for 4 min at 42 oC with 2x SSC, 0.2% SDS and then washed for 4 min at 42 oC with 0.2x SSC.

scan_protocol: The microarrays were scanned with LuxScan 3.0 (CapitalBio, China). Microarray images acquisition and signal analysis were performed using LuxScan 3.0 software.

data_processing: The signal intensity of the probes was corrected by subtracting background intensity from the feature intensity. The value in the sample table is the mean signal intensity of the replicated spots.

organism: Tomato planta macho viroid

source_name: Tomato planta macho viroid

label_protocol: First-strand reverse transcription to cDNA was initiated with a nonamer random primer. The amplified cDNA product was purified with the NucleotideSpin Extract II (MN, Germany). Cy3-dCTP was incorporated into the purified cDNA product with nonamer random primer using the Klenow fragment of DNA polymerase I.

extract_protocol: Total RNA was extracted from plant samples using TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's protocols. RNA was purified using the NucleotideSpin® RNA clean-up (MN, Duren, Germany).

tag: genus

value: Pospiviroid


title: Potato spindle tuber viroid

organism: Potato spindle tuber viroid

source_name: Potato spindle tuber viroid


title: Columnea latent viroid

organism: Columnea latent viroid

source_name: Columnea latent viroid


title: H3K4Me3_lympho EDIC Participant ID 1480


title: Citrus exocortis viroid

organism: Citrus exocortis viroid

source_name: Citrus exocortis viroid


title: H3K4Me3_lympho EDIC Participant ID 1479

source_name: Lymphocyte no antibody control


title: Tomato apical stunt viroid

organism: Tomato apical stunt viroid

source_name: Tomato apical stunt viroid


title: GeneDialog02 TT 39


title: H3K4Me3_lympho EDIC Participant ID 1477


title: Chrysanthemum stunt viroid

organism: Chrysanthemum stunt viroid

source_name: Chrysanthemum stunt viroid


title: Chrysanthemum chlorotic mottle viroid

organism: Chrysanthemum chlorotic mottle viroid

source_name: Chrysanthemum chlorotic mottle viroid

value: Pelamoviroid


title: H3K4Me3_lympho EDIC Participant ID 1476


title: Peach latent mosaic viroid

organism: Peach latent mosaic viroid

source_name: Peach latent mosaic viroid


title: Hop stunt viroid 1000x dilution

organism: Hop stunt viroid

source_name: Hop stunt viroid

value: Hostuviroid


title: GeneDialog02 TT 34

source_name: PBMC, 1st vaccination, 14d


title: H3K4Me3_lympho EDIC Participant ID 1473

source_name: Lymphocyte H3K4Me3 ChIP DNA


title: H3K4Me3_lympho EDIC Participant ID 1475


title: Hop stunt viroid 10x dilution


title: H3K4Me3_lympho EDIC Participant ID 1470


title: Hop stunt viroid 100x dilution


title: H3K4Me3_lympho EDIC Participant ID 1468


title: Hop stunt viroid


title: H3K4Me3_lympho EDIC Participant ID 1467


title: H3K4Me3_lympho EDIC Participant ID 1462


title: H3K4Me3_lympho EDIC Participant ID 1466


title: H3K4Me3_lympho EDIC Participant ID 1460


title: Coleus blumei viroid 1

organism: Coleus blumei viroid 1

source_name: Coleus blumei viroid 1

value: Coleviroid


title: Hop latent viroid

organism: Hop latent viroid

source_name: Hop latent viroid

value: Cocadviroid


title: H3K4Me3_lympho EDIC Participant ID 1458


title: Avocado sunblotch viroid

organism: Avocado sunblotch viroid

source_name: Avocado sunblotch viroid

value: Avsunviroid


title: Colorectal tumor #13

description:
exprs.13T
Colon tumor, patient#13

source_name: Colorectal tumor, patient #13


title: Citrus dwarfing viroid

organism: Citrus dwarfing viroid

source_name: Citrus dwarfing viroid

value: Apscaviroid


title: H3K4Me3_lympho EDIC Participant ID 1455


title: H3K4Me3_lympho EDIC Participant ID 1459


title: H3K4Me3_lympho EDIC Participant ID 1454


title: H3K4Me3_lympho EDIC Participant ID 1452


title: H3K4Me3_lympho EDIC Participant ID 1451


title: Colorectal cancer tissue  from  patient with lymph node metastasis 4

city: beijing

first: jie

last: ma

address: No17, panjiayuan nanli

institute: cancer hospital

description: miRNA expression

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 10.0(Agilent technologies, Santa Clara, CA, US).

source_name: tumor tissue RNA -rep1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM  PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Tissues were immediately collected after surgical removal and snap-frozen in liquid nitrogen for further use.

tag: disease state

value: colorectal cancer with lymph node metastasis

value: Female


title: H3K4Me3_lympho EDIC Participant ID 1445

value: Lymphocyte


title: Colorectal cancer tissue  from  patient without lymph node metastasis 2

description: miRNA expression

value: colorectal cancer without lymph node metastasis


title: Colorectal cancer tissue  from  patient without lymph node metastasis 3

description: miRNA expression


title: Colorectal cancer tissue  from  patient with lymph node metastasis 1

description: miRNA expression

value: Male


title: Colorectal cancer tissue  from  patient with lymph node metastasis 2

description: miRNA expression


title: Colorectal cancer tissue  from  patient with lymph node metastasis 3

description: miRNA expression


title: Apple scar skin viroid

organism: Apscaviroid cicatricimali

source_name: Apple scar skin viroid


title: H3K4Me3_lympho EDIC Participant ID 1443


title: Colorectal cancer tissue  from  patient without lymph node metastasis 1

description: miRNA expression


title: H3K4Me3_lympho EDIC Participant ID 1444


title: Colorectal cancer tissue  from  patient without lymph node metastasis 4

description: miRNA expression


title: H3K4Me3_lympho EDIC Participant ID 1446


title: ActE_Cellobiose_1

city: Madison

first: Adam

last: Book

state: WI

address: 1550 Linden Drive

department: GLBRC

institute: University of Wisconsin Madison

description: This sample is of Streptomyces sp. SirexAA-E (ActE). It is the first of three biological replicates collected from cellobiose grown cells, each from separate cultures.

hyb_protocol: Hybridization was performed by University of Wisconsin Gene Expression Center, Madison, WI USA, following their standard operating protocol using a NimbleGen 12 Bay Hybridization System.

scan_protocol: Scanning was performed by the University of Wisconsin Gene Expression Center, Madison, WI USA, following their standard operating protocol with a Nimblegen MS 200 Scanner.

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 DNASTAR ArrayStar v4.0.1.

organism: Streptomyces sp. SirexAA-E

source_name: Streptomyces sp. SirexAA-E, cellobiose medium, 7-day

label_protocol: Labeling was performed by University of Wisconsin Gene Expression Center, Madison, WI USA, following their standard operating protocol.

growth_protocol: ActE was grown in M63 minimal medium pH 6.9, where 1 L contains: 10.72 g K2HPO4; 5.24 g KH2PO4; 2 g (NH4)2SO4; 0.5 mL iron sulfate (1 mg/mL in 0.01 M HCl); 1 mL 1 M MgSO4; 1 mL thiamine solution (1 mg/mL) supplemented with glucose, cellulose ( Sigmacell-20, Sigma/Aldrich, St. Louis, MO), xylan, chitin, cellobiose, AFEX-switchgrass (AFEX pretreated at MSU), Ionic-Liquid switchgrass (IL treatment at JBEI) as the sole carbon source (0.5% w/v). Cultures were incubated for 7 days at 30 °C with shaking at 250 rpm.

extract_protocol: Total RNA was extracted using bead beating with phenol buffer, follwed by phenol:chloroform, chloroform extraction.  DNA was removed DNase digestion with the RNase-Free DNase (Promega). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the University of Wisconsin Gene Expression Center, Madison, WI USA, following their standard operating protocol.

tag: carbon source

value: cellobiose


title: ActE_AFEX-IL-SG-1

description: This sample is of Streptomyces sp. SirexAA-E (ActE). It is the first of two biological replicates collected from Ionic-Liquid treated Switchgrass grown cells, each from separate cultures.

source_name: Streptomyces sp. SirexAA-E, Ionic Liquid Switchgrass medium, 7-day

value: Ionic Liquid-Switchgrass


title: ActE_AFEX-SG

description: This sample is of Streptomyces sp. SirexAA-E (ActE). It is theonly biological replicate collected from AFEX-switchgrass grown cells

source_name: Streptomyces sp. SirexAA-E, AFEX-Switchgrass medium, 7-day

value: AFEX-Switchgrass


title: ActE_Cellobiose_2

description: This sample is of Streptomyces sp. SirexAA-E (ActE). It is the second of three biological replicates collected from cellobiose grown cells, each from separate cultures.


title: ActE_AFEX-IL-SG-2

description: This sample is of Streptomyces sp. SirexAA-E (ActE). It is the second of two biological replicates collected from Ionic-Liquid treated Switchgrass grown cells, each from separate cultures.


title: ActE_Cellobiose_3

description: This sample is of Streptomyces sp. SirexAA-E (ActE). It is the third of three biological replicates collected from cellobiose grown cells, each from separate cultures.


title: ActE_Chitin_1

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the first of three biological replicates collected from chitin grown cells, each from separate cultures.
Raw data file: ActE_Chi1_413648A01s.pair

source_name: Streptomyces sp. SirexAA-E, chitin medium, 7-day

growth_protocol: ActE was grown in M63 minimal medium pH 6.9, where 1 L contains: 10.72 g K2HPO4; 5.24 g KH2PO4; 2 g (NH4)2SO4; 0.5 mL iron sulfate (1 mg/mL in 0.01 M HCl); 1 mL 1 M MgSO4; 1 mL thiamine solution (1 mg/mL) supplemented with glucose, cellulose ( Sigmacell-20, Sigma/Aldrich, St. Louis, MO), xylan, chitin, as the sole carbon source (0.5% w/v). Cultures were incubated for 7 days at 30 °C with shaking at 250 rpm.

value: chitin


title: ActE_Chitin_2

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the second of three biological replicates collected from chitin grown cells, each from separate cultures.
Raw data file: ActE_Chi2_413684A01s.pair


title: ActE_Xylan_5

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the fifth of five biological replicates collected from xylan grown cells, each from separate cultures.
Raw data file: Xyl_2_413616A02s.pair

source_name: Streptomyces sp. SirexAA-E, xylan medium, 7-day

value: xylan


title: ActE_Sigmacell_3

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the third of three biological replicates collected from cellulose (Sigmacell-20) grown cells, each from separate cultures.
Raw data file: Sig_3_413617A02s.pair

source_name: Streptomyces sp. SirexAA-E, Sigmacell medium, 7-day

value: cellulose (sigmacell-20)


title: ActE_Xylan_3

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the third of five biological replicates collected from xylan grown cells, each from separate cultures.
Raw data file: ActE_Xyl3_jan7_413648A04S.pair


title: ActE_Glucose_2

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the second of three biological replicates collected from glucose grown cells, each from separate cultures.
Raw data file: ActE_Glu_2_413708A02.pair

source_name: Streptomyces sp. SirexAA-E, glucose medium, 7-day

value: glucose


title: ActE_Chitin_3

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the third of three biological replicates collected from chitin grown cells, each from separate cultures.
Raw data file: ActE_Chi3_413684A03s.pair


title: ActE_Glucose_3

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the third of three biological replicates collected from glucose grown cells, each from separate cultures.
Raw data file: Glu_2B_413617A01s.pair


title: ActE_Xylan_1

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the first of five biological replicates collected from xylan grown cells, each from separate cultures.
Raw data file: ActE_Xyl1_413648A03s.pair


title: ActE_Glucose_1

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the first of three biological replicates collected from glucose grown cells, each from separate cultures.
Raw data file: ActE_Glu_1_413708A01.pair


title: ActE_Xylan_2

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the second of five biological replicates collected from xylan grown cells, each from separate cultures.
Raw data file: ActE_Xyl3_jan5_413684A04s.pair


title: ActE_Xylan_4

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the fourth of five biological replicates collected from xylan grown cells, each from separate cultures.
Raw data file: Xyl_1_413616A01s.pair


title: ActE_Sigmacell_1

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the first of three biological replicates collected from cellulose (Sigmacell-20) grown cells, each from separate cultures.
Raw data file: ActE_Sig_1_413708A03.pair


title: 8d-shock rep1

city: Guangzhou

first: SH

last: Shi

address: 135 Xin Gang Xi

institute: Sun Yat-Sen University

description: biological replicate 1 of 3, shocked for 192 hours

hyb_protocol: Hybridizations were performed at 42℃ for 16h in a sealed hybridization cassette with 1×PBS. After hybridization, the slides were removed and placed in a slide rack submerged in washing solution Ⅰ(1×SSC , 0.2% SDS) with the array face of the slide tilted down so that when the cover slip dropped off it did not scratch the array surface. After the cover slip came off, the slide racks were plunged up and down three times in washing solutionⅠand transferred to washing solutionⅡ( 0.1 × SSC ) carefully to minimize the transfer of washing solutionⅠ to the second chamber. The slide chamber was rocked gently for about 10 min. The slide racks were transferred to washing solutionⅢ (0.01 × SSC) and rinsed gently for 5 min. The slides were dried by brief centrifugation (1500rpm, 5min).

scan_protocol: The slides were scanned using the DNA microarray scanner (Agilent Technologies). Separate images were acquired for each fluor at a resolution of 10 μm per pixel. The images were analyzed using ImaGene 4.1 software (Biodiscovery).

data_processing: Intensity-dependent (LOWESS) normalization was performed using the GeneSpring software (Agilent Technologies). The intensity values of duplicated probe were averaged for Cy3 and Cy5, respectively, to calculate the Cy3/Cy5 ratio of a given cDNA probe. Relative transcript abundance of a given cDNA probe at a specific time point were represented by the averaged Cy3/Cy5 ratio of 3 biological replicates. Averaged ratios are provided in a supplementary file on the Series record.

organism: Ceriops tagal

source_name: 8d-shocked root

label_protocol: Total RNA was linearly amplified  using the Ambion® MessageAmp™ aRNA Kit (Ambion). The resulting aRNA was then reverse-transcribed in the presence of Cy3-dCTP or Cy5-dCTP (Amersham) to generate labeled cDNA probes.Fluorscent labeled cDNA were purified with a QIAquick Nucleotide Removal Kit (Qiagen) and then collected by centrifugation after addition of 0.1 volume of 3 M sodium acetate (pH 5.2) and 1 volume of isopropanol. The dried pellets were reconstituted in 20 μl 5×SSC, 0.1% SDS and 50% formamide and denatured (95℃) before use in the hybridization.

growth_protocol: Propagules of C. tagal were collected from Dongzhaigang Mangrove Reserve in Hainan Island of China, and planted in culture pots which contained a mixture of water-washed sands and nutritive soils. Seedlings were grown under a natural photoperiod until the main roots were 1.0~1.5 cm in length.

extract_protocol: Total RNA was extracted from young roots using a CATB-based method (Fu et al.,Plant Mol Biol Rep, 2004, 22: 197a-197e).

treatment_protocol: Then the seedlings were transferred to another pot and stressed with 500 mM NaCl for 2, 5, 10, 24 and 196 hours (8 days), respectively, for collecting stressed samples. Control samples were collected in parallel from seedlings treated with fresh water at the same time.

tag: treatment

value: 500 mM NaCl

tag: time

value: main root

source_name: 8d-unshocked root

value: fresh water


title: 8d-shock rep3

description: biological replicate 3 of 3, shocked for 192 hours


title: 24h-shock rep3

description: biological replicate 3 of 3, shocked for 24 hours

source_name: 24h-shocked root

source_name: 24h-unshocked root


title: 24h-shock rep2

description: biological replicate 2 of 3, shocked for 24 hours


title: 24h-shock rep1

description: biological replicate 1 of 3, shocked for 24 hours


title: 8d-shock rep2

description: biological replicate 2 of 3, shocked for 192 hours


title: 10h-shock rep3

description: biological replicate 3 of 3, shocked for 10 hours

source_name: 10h-shocked root

source_name: 10h-unshocked root


title: ActE_Sigmacell_2

description:
This sample is of Streptomyces sp. SirexAA-E (ActE). It is the second of three biological replicates collected from cellulose (Sigmacell-20) grown cells, each from separate cultures.
Raw data file: ActE_Sig_2_413708A04.pair


title: Hop stunt viroid from infected citrus field sample

source_name: Hop stunt viroid

value: Hostuviroid


title: 10h-shock rep2

description: biological replicate 2 of 3, shocked for 10 hours


title: 2h-shock rep1

description: biological replicate 1 of 3, shocked for 2 hours

source_name: 2h-shocked root

source_name: 2h-unshocked root


title: 5h-shock rep3

description: biological replicate 3 of 3, shocked for 5 hours

source_name: 5h-shocked root

source_name: 5h-unshocked root


title: 5h-shock rep2

description: biological replicate 2 of 3, shocked for 5 hours


title: 10h-shock rep1

description: biological replicate 1 of 3, shocked for 10 hours


title: 5h-shock rep1

description: biological replicate 1 of 3, shocked for 5 hours


title: 2h-shock rep3

description: biological replicate 3 of 3, shocked for 2 hours


title: 2h-shock rep2

description: biological replicate 2 of 3, shocked for 2 hours


title: Stage IV 2010 replicate 2

city: Charlottetown

first: Dan

last: Hines

state: PE

address: 550 University Ave

country: Canada

institute: AVCLSC

description:
14337 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool

hyb_protocol: 140 ng labeled sample cDNA was hybridized with 100 pmol of dye labelled aRNA reference, with 50 µL of Hybridization buffer #3 (Ambion) and 1 µL of LNA blocker (Ambion). Hybridization performed using Tecan HS PRO 400, with dual area chambers. Hyb protocol was identical to GPL16521.

scan_protocol: Arrays scanned with Axon GenePix 4000B Microarray Scanner using the Auto Photomultiplier Tube setting to balance fluorescent channels.

data_processing: Results were extracted and features were flagged using SpotReader software v 1.3.1 (Niles Scientific), LOWESS normalization was performed with Acuity 4.0 (Molecular Devices). Flagged spots were removed. Features with > 4 missing features per stage were removed from dataset. All features were then normalized to the average Log2 ratio of stage 1.

label: Alexafluor 555

organism: Homarus americanus

source_name: whole animal homogenate_stage IV

label_protocol: Ch1: RT and labeling reactions performed with Invitrogen Superscript™ Indirect cDNA Labeling System. Total RNA yield from each extraction was primed with 2 µL of 2.5 µg/µL anchored oligo dT primer at 70 °C for 5 min, then reverse transcribed at 48 °C for 180 min using 2µL of 400 U/µL Supersctipt III RT(Invitrogen), 6 µL of 5X First Strand Buffer, 1.5 µL of 0.1 M DTT, 1.5 µL of dNTP mix (including aminoallyl modified nucleotides), and 1 µL of 40 U/µL  RNase OUT. After RT, RNA was hydrolized with 15 µL of 1N NaOH at 70 °C for 10 min, then neutralized with 15 µL of 1 N HCL and 20 µL of 3M sodium acetate pH 5.2. cDNA purified according to manufacturers instructions. Total cDNA yeild was adjusted to 3 µL volume using a MiVac DNA concentrator (Gene Vac). Dye Coupling was performed using 5 µL of 2X coupling buffer, 60 µg Alexafluor 555 reconsitituted in 2 µL ambient temperature DMSO and incubated at ambient temperature for 120 min. Labelled cDNA was purified using manufactuers instructions.

extract_protocol: Total RNA isolated from whole animal homogenates in phenol chloroform solution, using Qiagen Rneasy kit according to manufacturers instructions

tag: Stage

value: IV

tag: sampling year

value: whole animal homogenate

label: Alexafluor 647

source_name: Reference Pool RNA, generated from whole animal homogenates of 16 animals

label_protocol: Ch2: RT and labelling reactions were performed using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion). 5 µg total RNA (312.5 ng/individual, n=16) was reverse transcribed with 1 µL T7 oligo dT primer, 2 µL of 10 X first strand buffer, 4 µL dNTPs, 1 µL Rnase inhibitor, 1 µL ArrayScript (RT) for 120 min at 42 °C. Second strand cDNA was synthesized by adding 63 µL Nuclease Free H2O, 10 µL of 10X second strand buffer, 4 µL dNTPs, 2 µL of DNA polymerase, 1 µL of RNase H to the first strand reaction mix, and incubated for 120 min at 16 °C. cDNA was purified from reaction componants using manufactuers instructions. Second strand cDNA was amplified with 3 µL of 50 mM aminoallyl-UTP, 12 µL of ATP/CTP/GTP mix, 3 µL of 50 mM UTP, 4 µL of T7 10X reaction buffer, 4 µL Enzyme Mix for 14 h at 37 °C. Amplification was terminated with 58 µL nuclease free H2O, and purified accoding to manufactures instructions. aRNA was aliquoted and stored at -80 °C, and used as reference for all arrays. aRNA was fluorescently labelled by drying aRNA in a MiVac DNA concentrator (Gene Vac). aRNA was labeled by combining it with 9 µL of coupling buffer and 11 µL of 60 µg Alexafluor 647 dye suspended in DMSO for 120 min at ambient temperature. Uncoupled dye was quenched with 4.5 µL of 4 M hydroylamine for 15 min at ambient temperature. Labelled aRNA was purified according to manufactuers instructions.

value: I - IV

tag: individuals/year/stage


title: Stage IV 2009 replicate 4

description:
14301 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool

tag: tissue


title: Stage IV 2010 replicate 4

description:
14329 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage IV 2009 replicate 1

description:
14300 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2010 replicate 5

description:
14335 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool

source_name: whole animal homogenate_stage III

value: III


title: Stage IV 2009 replicate 2

description:
14316 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage IV 2010 replicate 5

description:
14299 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2009 replicate 4

description:
14294 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage IV 2009 replicate 3

description:
14326 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2010 replicate 3

description:
14330 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage IV 2010 replicate 1

description:
14334 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage IV 2010 replicate 3

description:
14321 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2009 replicate 5

description:
14297 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2010 replicate 4

description:
14329 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2009 replicate 2

description:
14316 Top_4 HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2010 replicate 1

description:
14334 Top_2 HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage IV 2009 replicate 5

description:
14297 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2009 replicate 3

description:
14326 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2009 replicate 1

description:
14300 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage III 2010 replicate 2

description:
14337 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2010 replicate 5

description:
14335 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool

source_name: whole animal homogenate_stage II

value: II


title: Stage II 2010 replicate 4

description:
14325 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2010 replicate 3

description:
14330 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2009 replicate 5

description:
14320 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2010 replicate 1

description:
14323 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2010 replicate 2

description:
14328 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2009 replicate 4

description:
14294 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2009 replicate 3

description:
14293 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2009 replicate 2

description:
14331 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2010 replicate 2

description:
14328 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool

source_name: whole animal homogenate_stage I

value: I


title: Stage I 2009 replicate 5

description:
14320 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2010 replicate 4

description:
14325 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2009 replicate 4

description:
14321 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2009 replicate 2

description:
14331 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2010 replicate 5

description:
14299 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage II 2009 replicate 1

description:
14315 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2010 replicate 1

description:
14323 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Stage I 2009 replicate 3

description:
14293 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Satellite_cells_WTBmi1_mice_biological_replicate_2 [Set 4]

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

hyb_protocol: After fragmentation, 600 ng of labeled cDNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Mus musculus

source_name: Satellite cells_WTBmi1 mice muscle

label_protocol: Total cDNA from each sample was labeled with Cy3-UTP and purified using the SureTag Complete DNA Labeling Kit (Agilent).

extract_protocol: FACS sorted satellite cells were collected in lysis buffer and RNA extraction and WTA amplification were performed at the Genomic Facility of the IRB (Barcelona, Spain), following a protocol described in Gonzalez_Roca et al. 2009 Accurate Expression Profiling of Very Small Cell Populations. PLOS One.

tag: strain background

value: FVB

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 2 months

value: Skeletal muscle

tag: cell type

value: muscle stem cells (satellite cells)


title: Satellite_cells_KOBmi1_mice_biological_replicate_4 [Set 4]

source_name: Satellite cells_KOBmi1 mice muscle


title: Satellite_cells_KOBmi1_mice_biological_replicate_2 [Set 4]


title: Satellite_cells_KOBmi1_mice_biological_replicate_5 [Set 4]


title: Satellite_cells_KOBmi1_mice_biological_replicate_6 [Set 4]


title: Satellite_cells_Adult_mice_biological_replicate_2 [Set 3]

source_name: Satellite cells_Adult mice muscle

tag: strain

value: 6 months


title: Satellite_cells_Adult_mice_biological_replicate_3 [Set 3]


title: Satellite_cells_Young_mice_biological_replicate_3 [Set 3]

source_name: Satellite cells_Young mice muscle

value: 3 months


title: Satellite_cells_KOBmi1_mice_biological_replicate_1 [Set 4]


title: Satellite_cells_Young_mice_biological_replicate_2 [Set 3]


title: Stage I 2010 replicate 3

description:
14301 Bottom HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Satellite_cells_Adult_mice_biological_replicate_1 [Set 3]


title: Satellite_cells_KOBmi1_mice_biological_replicate_3 [Set 4]


title: Stage I 2009 replicate 1

description:
14315 Top HAZ
cDNA prepared from ch1 total RNA, hybridized with amplified RNA generated from ch2 reference RNA pool


title: Satellite_cells_SAMP8_mice_biological_replicate_3 [Set 2]

source_name: Satellite cells_SAMP8 mice muscle

value: 12 months


title: Satellite_cells_WTBmi1_mice_biological_replicate_3 [Set 4]


title: Satellite_cells_SAMP8_mice_biological_replicate_2 [Set 2]


title: Satellite_cells_Geriatric_mice_biological_replicate_3 [Set 2]

source_name: Satellite cells_Geriatric mice muscle

value: 29 months


title: Satellite_cells_SAMR1_mice_biological_replicate_1 [Set 2]

source_name: Satellite cells_SAMR1 mice muscle


title: leaf_38_Fremont

city: Chicago

first: Nadia

last: Shakoor

state: Illinois

address: 10 South LaSalle Street, Suite 2100

institute: Chromatin, Inc.

hyb_protocol: Synthesis of cDNA, probe labeling and hybridization was performed by Precision Biomarker (Precision Biomarker Resources, Inc. Evanston, Illinois). A hybridization cocktail was made with the labeled sample, loaded onto the arrays, and hybridized at 45°C for 17 h.  The arrays were washed with stringent and non-stringent buffers and stained with streptavidin-phycoerythrin (SAPE).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Background correction and normalization were performed using a robust multi-chip average(RMA) algorithm in the Bioconductor Affy package in R

organism: Sorghum bicolor

label_protocol: Synthesis of cDNA, probe labeling and hybridization was performed by Precision Biomarker (Precision Biomarker Resources, Inc. Evanston, Illinois).  Briefly, 150 ng of total RNA was used as starting material with diluted Poly-A control and taken through the first and second strand cDNA synthesis reactions followed by a 16-h in vitro transcription reaction resulting in amplified cRNA. The cRNA was then cleaned up using nucleic acid binding beads and quantified for concentration and yield.  10 μg of the amplified cRNA was then subject to a second-round cDNA reaction that generated the sense target cDNA. The resulting single-stranded cDNA was again cleaned with NA binding beads and quantified.  5.5 μg of the sense target sscDNA was fragmented to between 40-70 bp and end-labeled with biotin.

growth_protocol: See samples for specific growth protocols

extract_protocol: Total RNA from all tissue types was extracted using a NucleoSpin RNA Plant Kit (Maxherey-Nagel, Germany). RNA integrity, as indicated by the detection of discrete ribosomal subunits, was verified electrophoretically.  The RNA quality and quantity was further validated with a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Prior to hybridization, the total RNA profile was also analyzed with Agilent 2100 Bioanalyzer (Agilent technologies, Waldbronn, Germany).

treatment_protocol: Not applicable

tag: major tissue

value: leaf

tag: tissue location

tag: tissue subsection

value: all

tag: replicate

tag: days after planting

tag: genotype

value: Fremont

tag: ideotype

value: sweet


title: HDF_SAHA_rep1

city: Kyoto

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

country: Japan

institute: Kyoto University

description: Gene expression in HDFs after 48hr treatment with SAHA

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 20 hr at 48°C on Human Gene ST Array Strip. Strip was washed and stained in the Fluidics Station of GeneAtlas System.

scan_protocol: Strip was scanned using the Imaging Station.

data_processing: The data were analyzed with Expression Console 1.3.1 and Transcriptome Analysis Console 1.0 using iterPLIER.

organism: Homo sapiens

source_name: Human Dermal Fibroblasts, SAHA

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: 54-year-old female Caucasian HDFs were maintained in Dulbecco's modified eagle medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Japan Serum).

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HDFs within the passage P6 were trypsinized for 5 min at 37 °C, and were resuspended in the fresh medium to a concentration of 1.5 x 10^5 cells/2ml in a 35 mm plate and were grown for 24 hours. The medium was then removed and replaced with 2 ml of fresh medium supplimented with DMSO solusion of SAHA, SAHA-PIP9 (final concentration: 1 μM). The cultures were incubated for 48 hours.

tag: cell source

value: human dermal fibroblasts derived from normal human breast skin

value: female

tag: treatment

value: 48hr treatment with SAHA


title: Satellite_cells_Old_mice_biological_replicate_3 [Set 2]

source_name: Satellite cells_Old mice muscle

value: 24 months


title: HDF_DMSO_rep1

description: Gene expression in HDFs after 48hr treatment with DMSO

source_name: Human Dermal Fibroblasts, DMSO

value: 48hr treatment with DMSO


title: Satellite_cells_SAMP8_mice_biological_replicate_1 [Set 2]

value: male


title: seedling_root_Fremont_1

value: seedling

value: root


title: Satellite_cells_SAMR1_mice_biological_replicate_3 [Set 2]

value: Skeletal muscle

value: muscle stem cells (satellite cells)


title: HDF_SAHA-PIP9_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP9 (SAHA-PIP I)

source_name: Human Dermal Fibroblasts, SAHA-PIP9(SAHA-PIP I)


title: internode_61DAP_Fremont_B

value: stem

value: internode

value: bottom


title: Satellite_cells_SAMR1_mice_biological_replicate_2 [Set 2]

value: 12 months


title: seedling_shoot_Fremont_2

value: shoot

value: all


title: internode_70DAP_Fremont_M

value: middle

value: Fremont

value: sweet


title: shoot_tip_38_Fremont


title: Satellite_cells_Old_mice_biological_replicate_1 [Set 2]

value: 22 months


title: Satellite_cells_Geriatric_mice_biological_replicate_1 [Set 2]

value: 30 months


title: internode_61DAP_Fremont_T

value: top


title: Satellite_cells_Old_mice_biological_replicate_2 [Set 2]

value: 23 months

value: male


title: Satellite_cells_WTBmi1_mice_biological_replicate_1 [Set 4]

value: FVB

value: wild type

value: 2 months


title: seedling_root_AR2400_2

value: seedling

value: root

value: BTU


title: Satellite_cells_Young_mice_biological_replicate_2 [Set 2]

value: Skeletal muscle

value: muscle stem cells (satellite cells)


title: Satellite_cells_Young_mice_biological_replicate_1 [Set 2]


title: Satellite_cells_Young_mice_biological_replicate_3 [Set 2]

value: 3 months


title: shoot_tip_38_AR2400

value: shoot

value: all


title: Satellite_cells_Young_mice_biological_replicate_1 [Set 3]


title: leaf_38_AR2400

value: leaf


title: seedling_root_AR2400_1


title: Satellite_cells_Geriatric_mice_biological_replicate_3 [Set 1]

value: 29 months


title: seedling_shoot_AR2400_2


title: Satellite_cells_Geriatric_mice_biological_replicate_1 [Set 1]

value: 28 months


title: Satellite_cells_Young_mice_biological_replicate_3 [Set 1]


title: Satellite_cells_Young_mice_biological_replicate_2 [Set 1]


title: Satellite_cells_Geriatric_mice_biological_replicate_2 [Set 1]


title: internode_61DAP_AR2400_B

value: stem

value: internode

value: bottom


title: Satellite_cells_Geriatric_mice_biological_replicate_4 [Set 1]

value: male

value: 30 months


title: seedling_shoot_PI152611_2

value: forage


title: internode_70DAP_AR2400_M

value: middle


title: shoot_tip_38_PI152611


title: internode_61DAP_AR2400_T

value: top


title: seedling_shoot_AR2400_1

value: seedling

value: BTU


title: seedling_root_PI152611

value: root


title: leaf_38_PI152611


title: internode_61DAP_PI152611_B


title: pith_60DAP_Atlas_3

value: pith

value: Atlas

value: sweet


title: rind_60DAP_Atlas_3

value: rind

value: all


title: pith_60DAP_Atlas_1


title: internode_70DAP_PI152611_M


title: Satellite_cells_Young_mice_biological_replicate_1 [Set 1]

value: 2 months

value: Skeletal muscle

value: muscle stem cells (satellite cells)


title: rind_60DAP_Atlas_2

value: stem


title: seedling_shoot_PI152611_1

value: shoot


title: pith_60DAP_Atlas_2


title: rind_60DAP_Atlas_1


title: rind_70DAP_Atlas_M


title: rind_70DAP_Atlas_B

value: bottom


title: pith_70DAP_Atlas_M


title: pith_70DAP_Atlas_B


title: pith_70DAP_Atlas_T


title: rind_70DAP_Atlas_T


title: shoot_tip_38_Atlas


title: leaf_38_Atlas

value: leaf


title: seedling_shoot_Atlas_2


title: fos_nih 3t3_day7_rep1 [Cy5/Cy3]

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

institute: University of Montreal

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of fos

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol except that 3ug of each of the test and control samples were hybed, rather than 6ug of the test. See www.nimblegen.com.

scan_protocol: Scanning was performed on an Axon 4000b scanner in two channels  as per the guidelines by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 data extraction.  Values for each channel were divided to compute a ratio (overexpressed factor vs. control).

source_name: RNA from cells with empty vector

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: cells were tranduced with lentiviral expression vector containing cDNA for test protein and grown for 3 or 7 days

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: 10 µg of total RNA was isolated from Trizol (Invitrogen, Burlington, ON, Canada) samples of either NIH 3T3 cells or GP+E86 cells 3-7 days after transfection with either empty vector or vectors overexpressing individual factors.

tag: time point

value: NIH 3T3

tag: protocol

value: transduced with empty vector (control)

source_name: RNA from cells over-expressing factor

value: transfected with fos


title: internode_61DAP_Atlas_B

value: internode


title: seedling_root_Fremont_2

value: seedling

value: root

value: Fremont


title: internode_61DAP_PI152611_T

value: top

value: forage


title: seedling_shoot_Fremont_1

value: all

value: sweet


title: tcfec_nih 3t3_day7_rep1 [Cy5/Cy3]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of tcfec

value: transfected with tcfec


title: seedling_root_Atlas

value: Atlas


title: internode_70DAP_Atlas_M

value: stem

value: middle


title: fos_nih 3t3_day7_rep2 [Cy5/Cy3]


title: seedling_shoot_Atlas_1

value: shoot


title: rind_60DAP_R159

value: rind

value: grain


title: prdm16_GPE_day3_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of prdm16

value: transfected with prdm16

value: GPE

value: transduced with empty vector (control)


title: pith_70DAP_R159_B

value: pith

value: bottom


title: klf10_GPE_day7_rep3 [Cy5/Cy3]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of klf10

value: transfected with klf10


title: rind_70DAP_R159_B


title: pith_60DAP_R159


title: pu.1_nih 3t3_day7_rep1 [Cy5/Cy3]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of pu.1

value: NIH 3T3

value: transfected with pu.1


title: internode_61DAP_Atlas_T

value: internode

value: top


title: klf10_GPE_day7_rep4 [Cy5/Cy3]


title: internode_61DAP_R159_B


title: rind_60DAP_PI455230_3

value: all

value: BTU


title: rind_60DAP_PI455230_2

value: stem


title: rind_60DAP_PI455230_1


title: klf10_nih 3t3_day7_rep1 [Cy5/Cy3]


title: trim27_GPE_day7_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of trim27

value: transfected with trim27


title: pith_60DAP_PI455230_1


title: klf10_GPE_day3_rep2 [Cy3/Cy5]


title: pith_60DAP_PI455230_3


title: trim27_GPE_day3_rep1 [Cy3/Cy5]


title: rind_70DAP_PI455230_B


title: prdm16_GPE_day7_rep1 [Cy3/Cy5]


title: sox4_GPE_day7_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of sox4

value: transfected with sox4


title: pith_60DAP_PI455230_2


title: smarcc1_GPE_day3_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of smarcc1

value: transfected with smarcc1


title: smarcc1_GPE_day7_rep1 [Cy3/Cy5]


title: erdr1_GPE_day7_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of erdr1

value: transfected with erdr1


title: vps72_GPE_day7_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of vps72

value: transfected with vps72


title: pith_70DAP_PI455230_B


title: sox4_GPE_day3_rep1 [Cy3/Cy5]

value: GPE


title: vps72_GPE_day3_rep1 [Cy3/Cy5]

value: transduced with empty vector (control)


title: rind_70DAP_PI455230_M

value: rind

value: middle


title: erdr1_GPE_day3_rep1 [Cy3/Cy5]


title: fos_GPE_day3_rep2 [Cy3/Cy5]

value: transfected with fos


title: pith_70DAP_PI455230_M

value: pith


title: hmgb1_GPE_day3_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of hmgb1

value: transfected with hmgb1


title: internode_70DAP_PI455230_M

value: internode


title: vps72_GPE_day3_rep2 [Cy3/Cy5]


title: ski1_GPE_day3_rep2 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of ski1

value: transfected with ski1


title: shoot_tip_38DAP_ R159

source_name: shoot_tip_38DAP_ R159

value: shoot

value: all

value: grain


title: rind_70DAP_R159_T

value: stem

value: top


title: seedling_root_R159

value: seedling

value: root


title: internode_61DAP_R159_T


title: internode_61DAP_PI455230_B

value: bottom

value: BTU


title: seedling_shoot_R159_2


title: pith_70DAP_R159_T


title: klf10_nih 3t3_day7_rep2 [Cy5/Cy3]

value: NIH 3T3

value: transduced with empty vector (control)

value: transfected with klf10


title: fos_GPE_day3_rep1 [Cy3/Cy5]

value: transfected with fos

value: GPE


title: pu.1_GPE_day7_rep2 [Cy3/Cy5]

value: transfected with pu.1


title: leaf_38DAP_ R159

source_name: leaf_38DAP_ R159

value: leaf


title: fos_GPE_day7_rep2 [Cy3/Cy5]


title: seedling_shoot_R159_1


title: ski1_GPE_day3_rep1 [Cy3/Cy5]

value: transfected with ski1


title: pu.1_GPE_day7_rep1 [Cy3/Cy5]


title: tcfec_GPE_day3_rep2 [Cy3/Cy5]

value: transfected with tcfec


title: seedling_root_PI455230

value: all


title: internode_61DAP_PI455230

value: internode


title: leaf_38DAP_ PI455230


title: rind_70DAP_PI455230_T

value: stem

value: rind


title: seedling_shoot_PI455230_2

value: seedling

value: shoot


title: TOX_16h_Exp2

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

description: Gene expression after 16h incubated with SBTX,experiment2

hyb_protocol: The hybridisations were performed for 17 h at 10 rpm and 65°C in the Hybridisation Oven G2545A (Agilent Technologies, Waldbronn, Germany). Washing and staining of the arrays were performed according to the manufacturer’s instructions.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA Microarray Scanner (G2505B) (Agilent Technologies, Waldbronn, Germany) at 5-micron resolution. Scanned image files were visually inspected for artefacts and then analysed.

data_processing: Intensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1). A quality control based on internal controls using Agilent’s protocol GE1_107_Sep09 was included. All chips passed the quality control.

organism: Candida albicans

source_name: Candida albicans

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cells (1×104 cells per 1.0 mL of 0.15 M NaCl) were incubated at 30°C resting in 200 μL microplate wells in the presence or absence of SBTX at a final concentration of  200 µg∙mL-1 in SDB/4

extract_protocol: RNA was extracted with an RNeasy Mini Kit (Qiagen, Düsseldorf, Germany) according to the manufacturer’s instructions.

tag: timepoint

value: Soybean toxin


title: CTRL_18h_Exp2

description: Gene expression after 18h control, experiment2


title: pu.1_GPE_day3_rep2 [Cy3/Cy5]


title: TOX_18h_Exp1

description: Gene expression after 18h incubated with SBTX,experiment1


title: TOX_16h_Exp1

description: Gene expression after 16h incubated with SBTX, experiment1


title: CTRL_16h_Exp2

description: Gene expression after 16h control, experiment2


title: seedling_shoot_PI455230_1

value: BTU


title: TOX_18h_Exp2

description: Gene expression after 18h incubated with SBTX,experiment2


title: tcfec_GPE_day7_rep2 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of tcfec


title: hmgb1_GPE_day7_rep1 [Cy3/Cy5]

value: transfected with hmgb1


title: klf10_GPE_day3_rep1 [Cy3/Cy5]

value: transduced with empty vector (control)


title: shoot_tip_38DAP_ PI455230

source_name: shoot_tip_38DAP_ PI455230


title: tcfec_GPE_day7_rep1 [Cy3/Cy5]


title: FliC2-WT2_Vivo

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Biological replicate 3 of 3.
raw data file: F_FliC-02_cy3-400_cy5-350.gpr

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BY [statistical results provided as Series Supplementary file].

organism: Clostridioides difficile

source_name: FliC mutant grown 14h in vivo

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strains R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in Vivo

extract_protocol: Total RNA extracted using RNAPro Blue (FastPrep) and following Qbiogen manufacturer's instructions

tag: strain background

tag: genotype/variation

value: fliC::erm (fliC mutant)

source_name: R20291 grown 14h in PY (reference)

value: wild type


title: FliC1-WT1_Vivo

description:
Biological replicate 2 of 3.
raw data file: E_FliC-01_cy3-400_cy5-350.gpr


title: klf10_GPE_day7_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of klf10

value: transfected with klf10

value: GPE


title: CTRL_18h_Exp1

description: Gene expression after 18h control, experiment1


title: FliC3-Comp3-WT3

description:
Biological replicate 3 of 4.
raw data file: FliC-Comp3-cy3-390_WT3-cy5-490.gpr

source_name: complemented FliC mutant grown 14H in PY

value: fliC::erm + pMTL84151 fliC (fliC mutant complemented)


title: ski1_GPE_day7_rep1 [Cy3/Cy5]

value: transfected with ski1


title: FliC1-Comp1-WT1

description:
Biological replicate 1 of 4.
raw data file: FliC-Comp1-cy5-490_WT1-cy3-420.gpr


title: FliC4-Comp4-WT4

description:
Biological replicate 4 of 4.
raw data file: FliC-Comp4-cy3-390_WT4-cy5-500.gpr


title: FliC2-Comp2-WT2

description:
Biological replicate 2 of 4.
raw data file: FliC-Comp2-cy5-490_WT2-cy3-430.gpr


title: CTRL_16h_Exp1

description: Gene expression after 16h control, experiment1


title: tcfec_GPE_day3_rep1 [Cy3/Cy5]

value: transfected with tcfec


title: FliC4-WT4

description:
Biological replicate 4 of 4.
raw data file: FliC4-cy3-430_WT4-cy5-490.gpr

source_name: FliC mutant grown 14H in PY


title: FliC3-WT3

description:
Biological replicate 3 of 4.
raw data file: FliC3-cy3-430_WT3-cy5-490.gpr


title: FliC2-WT2

description:
Biological replicate 2 of 4.
raw data file: FliC2-cy5-490_WT2-cy3-360.gpr


title: pu.1_GPE_day3_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of pu.1

value: transfected with pu.1


title: fos_GPE_day7_rep1 [Cy3/Cy5]

description:
Ratio of signal of overexpressed experimental factor compared to empty vector
overexpression of fos

value: transfected with fos


title: FliC6-WT6_Vivo

description:
Biological replicate 1 of 3.
raw data file: H_FliC-06_cy3-290_cy5-420.gpr


title: MPI-903_tissue

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

hyb_protocol: Affymetrix hybridization was carried out on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter. Hybridization was performed overnight (16 hours, 45° C).

scan_protocol: After hybridization, the hybridization mixture was removed from the GeneChip, and washing and staining of the GeneChips were performed in a fluidics station (Affymetrix). The detection of the biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500).

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260).

source_name: tumor

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the Invitrogen SuperScript kit. After removal of small molecular components (Affymetrix Clean-up Module), biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop), and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (QIAGEN), and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent).

tag: gender

value: male

tag: age

tag: tissue

value: non-Burkitt diffuse large B-cell lymphoma

value: GCB

value: non-mBL

value: pos

value: neg

value: IG-MYC

value: double


title: 14h-05_Vivo

description:
Biological replicate 2 of 3.
raw data file: C_14h-05_cy3-290_cy5-420.gpr

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

data_processing: Background correction: backgroundCorrect 'normexp', Normalization: normalizeWithinArrays 'loess', Correlation of spot duplicat: duplicateCorrelation, Adjust to linear method: lmFit, Statistical analysis: eBayes, decideTests 'global' 'BY'[statistical results provided as Series Supplementary file].

source_name: R20291 extracted after 14h in vivo growth

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark. DNA samples were labelled using the Bioprime plus array CGH indirect genomic labeling system (invitrogen)

growth_protocol: We did a 9 hours preculture of Clostridium difficile R20291 in Tryptone yeast extract (TY), we centrifuged and resuspended in PBS. Then we gave 5ml of this preparation to 6 mouses  per time point (C. difficile monoxenic mouse model). Finally mouse were sacrificed, according European rules, at different time 4, 6, 8, 14 and 38 hours after infection to collect the luminal and mucosa associated bacteria in the caeca.

source_name: R20291 grown 14H in PY (reference)


title: MPI-721_tissue

value: intermediate


title: MPI-701_tissue

value: female


title: 14h-06_Vivo

description:
Biological replicate 3 of 3.
raw data file: D_14h-06_cy3-290_cy5-420.gpr

value: wild type


title: MPI-884_tissue

value: non-IG-MYC

value: triple


title: MPI-662_tissue


title: 14h-02_Vivo

description:
Biological replicate 1 of 3.
raw data file: B_14h-02_cy3-350_cy5-400.gpr


title: MPI-687_tissue

value: unclassified


title: MPI-866_tissue


title: MPI-893_tissue

value: single


title: MPI-870_tissue


title: MPI-645_tissue


title: MPI-690_tissue


title: MPI-549_tissue


title: MPI-565_tissue


title: MPI-396_tissue


title: MPI-510_tissue


title: MPI-275_tissue


title: MPI-387_tissue


title: MPI-507_tissue


title: MPI-266_tissue


title: MPI-102_tissue


title: MPI-322_tissue


title: MPI-214_tissue


title: MPI-020_tissue


title: MPI-058_tissue


title: MPI-447_tissue


title: MPI-642_tissue


title: MPI-517_tissue


title: MPI-333_tissue

value: ABC


title: 9a5ccy5 x Coffee23cy3 replica2

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description:
Total DNA from Xylella fastidiosa grown on solid PW medium.
This hybridization is part of an experiment aimed at performing comparative genomic analyses among different isolates of Xylella fastidiosa

hyb_protocol: Labelled DNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardts solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS´and 50% formamide. Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GenePix 4000B Array Scanner.Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

data_processing: Hybridized arrays were scanned in an GenePix 4000B Array Scanner and images were analyzed with Affymetrix Jaguar v 2.0. Quality control of the hybridized spots was automatically performed by the software, based on spot morphology and local signal-to-background ratio, using the Easy Threshold and Variable Circle Size Algorithms. In all experiments, reliable hybridization signals could be obtained for more than 90% of the arrayed probes. Normalization between the intensities in the two channels was achieved with the Jaguar Control Spots option, using a list of 30 control ORFs that shared sequence identity in the genomes of strains 9a5c and Temecula-1.

organism: Xylella fastidiosa

source_name: Xylella fastidiosa 23 cells grown in PW medium

label_protocol: DNA labelling was performed as described by: Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S. and Small, P.M. (1999) Comparative genomics of BCG vaccines by whole-genome DNA Microarray. Science 284, 1520-1523.

growth_protocol: Bacteria have been recovered from -70oC glycerol stocks and inoculated onto PW agar plates. Plates were maintained for 10 days at 28oC. The colonies were transferred once to new plates containing the same medium, grown for 20 days and harvested for DNA extraction

extract_protocol: Total genomic DNA was extracted according to : Dungan, D. (1989) in: Current Protocols in Molecular Biology (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K., Eds.), pp. 241-242. John Wiley and Sons, New York.

tag: isolate

source_name: Xylella fastidiosa 9a5c cells grown in PW medium


title: 9a5ccy5 x Coffee23cy3 replica1

treatment_protocol: Bacteria have been recovered from -70oC glycerol stocks and inoculated onto PW agar plates. Plates were maintained for 10 days at 28oC. The colonies were transferred once to new plates containing the same medium, grown for 20 days and harvested for DNA extraction


title: 9a5ccy3 x Coffee23cy5 replica1


title: MPI-569_tissue


title: 9a5ccy3 x Coffee 9ccy5 replica2

source_name: Xylella fastidiosa 9c cells grown in PW medium


title: 9a5ccy5 x Coffee 9ccy3 replica2


title: 9a5ccy3 x Coffee23cy5 replica2


title: 9a5ccy3 x Coffee 08cy5 replica2

source_name: Xylella fastidiosa 08 cells grown in PW medium


title: 9a5ccy3 x Coffee 9ccy5 replica1


title: 9a5ccy3 x Coffee 08cy5 replica1


title: 9a5ccy5 x Coffee 9ccy3 replica1


title: 9a5ccy5 x Coffee 08cy3 replica2


title: 9a5ccy5 x Coffee 08cy3 replica1


title: FliC1-WT1

description:
Biological replicate 1 of 4.
raw data file: FliC1-cy5-490_WT1-cy3-360.gpr

value: fliC::erm (fliC mutant)


title: 9a5ccy3 x Coffee 33cy5 replica1

source_name: Xylella fastidiosa 33 cells grown in PW medium


title: 9a5ccy3 x Coffee 6ccy5 replica2

scan_protocol: Slides were subjected to fluorescent detection with a GenePix 4000B Scanner. Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

source_name: Xylella fastidiosa 6c cells grown in PW medium


title: 9a5ccy3 x Coffee 33cy5 replica2


title: 9a5ccy3 x Coffee48cy5 replica1

source_name: Xylella fastidiosa 48 cells grown in PW medium


title: 9a5ccy3 x Coffee48cy5 replica2


title: 9a5ccy3 x Coffee 32cy5 replica1

source_name: Xylella fastidiosa 32 cells grown in PW medium


title: 9a5ccy3 x Coffee 6ccy5 replica1


title: 9a5ccy5 x Coffee 6ccy3 replica1


title: 9a5ccy5 x Coffee 6ccy3 replica2


title: 9a5ccy5 x Coffee48cy3 replica1


title: 9a5ccy5 x Coffee 32cy3 replica2


title: 9a5ccy5 x Coffee 32cy3 replica1


title: 9a5ccy5 x Coffee48cy3 replica2


title: 9a5ccy3 x Coffee 32cy5 replica2


title: 9a5ccy5 x Coffee 33cy3 replica2


title: 9a5ccy3 x Coffee9ciso32cy5 replica1

scan_protocol: Slides were subjected to fluorescent detection with a GenePix 4000B Array Scanner. Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

source_name: Xylella fastidiosa 9c iso 32 cells grown in PW medium

label_protocol: DNA labelling was performed as described by: Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S. and Small, P.M. (1999) Comparative genomics of BCG vaccines by whole-genome DNA Microarray. Science 284, 1520-1523

value: 9c iso 32


title: 9a5ccy3 x Coffee9ciso32cy5 replica2


title: 9a5ccy5 x Coffee9ciso32cy3 replica2

scan_protocol: Slides were subjected to fluorescent detection with a GenePix 4000B Array Scanner. Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

data_processing: Hybridized arrays were scanned in an GenePix 4000B Array Scanner and images were analyzed with Affymetrix Jaguar v 2.0. Quality control of the hybridized spots was automatically performed by the software, based on spot morphology and local signal-to-background ratio, using the Easy Threshold and Variable Circle Size Algorithms. In all experiments, reliable hybridization signals could be obtained for more than 90% of the arrayed probes. Normalization between the intensities in the two channels was achieved with the Jaguar Control Spots option, using a list of 30 control ORFs that shared sequence identity in the genomes of strains 9a5c and Temecula-1


title: 9a5ccy5 x Coffee 33cy3 replica1


title: Rice seedlings, SA treatment, rep1

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Gene expression data from SA-treated rice seedlings

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 h at 45 degree C on the rice Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip were scanned using Affymetrix scanner

data_processing: CEL files were imported into Genespring software and probe summarization and normalization was performed using GCRMA algorithm

organism: Oryza sativa

source_name: SA-treated rice seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Rice seedlings were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark

extract_protocol: Total RNA was extracted using TRI reagent according to the manufacturer's instructions

treatment_protocol: Seedlings were incubated in water (control) or 50 µM solution of indole-3-acetic acid (auxin, IAA) and benzyl aminopurine (cytokinin, BAP) and 100 µM solution of abscisic acid (ABA), 1-aminocyclopropane-1-carboxylic acid (ethylene derivative, ACC), salicylic acid (SA) and jasmonic acid (JA) for 3h

tag: subspecies

value: indica

tag: variety

value: Seedlings

tag: Stage


title: 9a5ccy5 x Coffee9ciso32cy3 replica1

scan_protocol: Slides were subjected to fluorescent detection with a GenePix 4000B Array Scanner.Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain


title: Rice seedlings, JA treatment, rep1

description: Gene expression data from JA-treated rice seedlings

source_name: JA-treated rice seedlings


title: Rice seedlings, SA treatment, rep2


title: Rice seedlings, ACC treatment, rep2

description: Gene expression data from ACC-treated rice seedlings

source_name: ACC-treated rice seedlings


title: Rice seedlings, ACC treatment, rep1


title: Mock

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

description: Mock cells

hyb_protocol: Ten mg of labelled cRNA was hybridized to each pre-hybed microarray at 55℃ for 16 hours.

scan_protocol: After Chemiluminescence detection using Applied Biosystems Chemiluminescence Detection Kit, images were collected by the AB1700 Chemiluminescent Microarray Aanalyzer.

data_processing:
Quantile was used background correction and normalization.
GeneSpring GX 12.5 software computed normalized signal intensity (log2).

label: digoxigenin

source_name: oral squamous cell carcinoma cell lines

label_protocol: Digoxigenin-UTP-labelled cRNA was generated and amplified from 1 mg of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labelling Kit.

extract_protocol: Total RNA was extracted by ISOGEN (NipponGene, Toyama, Japan).

tag: cell type

value: human oral squamous cell carcinoma cell line

tag: cell line

value: mock


title: Rice seedlings, IAA treatment, rep2

description: Gene expression data from IAA-treated rice seedlings

source_name: IAA-treated rice seedlings


title: Rice seedlings, JA treatment, rep2


title: OsPE mutant replicate 2

city: Roorkee

first: Anjali

last: Awasthi

state: Uttarakhand

address: Department of Biotechnology

department: Biotechnology

institute: Indian Institute of Technology Roorkee

description:
Gene expression profile of mutant OsPE.
OsPE_mutant_B

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

organism: Oryza sativa Indica Group

source_name: T-DNA insertional mutant; seedling 15 days after germination

label_protocol: standard Affymetrix procedures

growth_protocol: Grown under optimal rice growing conditions

extract_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

value: mutant OsPE


title: SDF-1

description: SDF-1 stable transfectant

value: SDF-1 transfection


title: Rice seedlings, BAP treatment, rep2

description: Gene expression data from BAP-treated rice seedlings

source_name: BAP-treated rice seedlings


title: Ossl mutant replicate 2

description:
Gene expression profile of mutant Ossl.
Ossl_mutant_B

value: mutant Ossl


title: Osoc mutant replicate 2

description:
Gene expression profile of mutant Osoc.
Osoc_mutant_B

value: mutant Osoc


title: Rice seedlings, ABA treatment, rep2

description: Gene expression data from ABA-treated rice seedlings

source_name: ABA-treated rice seedlings


title: Osoc mutant replicate 1

description:
Gene expression profile of mutant Osoc.
Osoc_mutant_A


title: Rice seedlings, BAP treatment, rep1


title: Rice seedlings, ABA treatment, rep1


title: Rice seedlings, control1, rep2

description: Gene expression data from control rice seedlings

source_name: control rice seedlings


title: Rice seedlings, control2, rep2


title: Rice seedlings, IAA treatment, rep1


title: Ossl mutant replicate 1

description:
Gene expression profile of mutant Ossl.
Ossl_mutant_A


title: Rice seedlings, control2, rep1


title: OsPE mutant replicate 1

description:
Gene expression profile of mutant OsPE.
OsPE_mutant_A


title: OsAPC6 mutant replicate 1

description: Gene expression profile of mutant OsAPC6.

source_name: Seedling 15 days after germination

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

tag: cultivar

value: Basmati 370

value: T-DNA insertional mutant OsAPC6


title: B370 wild replicate 1

description: Gene expression profile of wild B370.

value: Wild type