title: BJ, RF-tf

description: replicate 1

source_name: BJ, RF-transfected

value: BJ (purchased from ATCC)

value: reprogramming factor (RF)-transfected

value: neonatal foreskin fibroblasts


title: cervix_tumour_cs2_scc_4

status: Public on Jul 04 2012

type: RNA

city: Manchester

first: Jan

last: Taylor

address: Wilmslow Road

department: Bioinformatics

country: United Kingdom

institute: Paterson Institute for Cancer Research

hyb_protocol: GeneChip Eukaryotic Hybridization Control Kit - Genisphere standard protocol

scan_protocol: Affymetrix GeneChip scanner 3000 running GCOS software

data_processing:
Background adjustment and quantile normalisation using Affymetrix miRNA QC Tool (v.1.1.1.0)
probe group file: miRNA-2_0_v2.pgf

label: FlashTag-Biotin-HSR

molecule: total RNA

organism: Homo sapiens

source_name: cervix tumour FFPE series 2 scc

label_protocol: Genisphere FlashTag Biotin HSR RNA labelling Kit

growth_protocol: Cell lines were grown in DMEM + 10% FCS. Cell lines were classified as SCC or AC according to P63 protein expression

extract_protocol: RNA was extracted and Dnase treated using RecoverAll Total Nucleic Acid Isolation kit (Ambion).

tag: tissue source

value: clinical cervical tumour sample

tag: tissue type

value: tumour

tag: storage

value: formalin-fixed paraffin-embedded (FFPE)

tag: classification

value: squamous cell carcinoma (SCC)

tag: data series

tag: ffpe block storage duration time (yrs)


title: Tkv expression L3_1

city: Seattle

first: Laura

last: Buttitta

state: WA

address: 1100 Fairview Ave. N.

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Hybridization was performed by the FHCRC microarray facility, follwing Nimblegen standard hybridization protocol (see www.nimblegen.com)

scan_protocol: Scanning was performed by the FHCRC microarray facility, follwing Nimblegen standard scanning protocol (see www.nimblegen.com)

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

organism: Drosophila melanogaster

source_name: dissected wing

label_protocol: Labeling was performed by the FHCRC microarray facility, follwing Nimblegen standard operating protocol (see www.nimblegen.com)

growth_protocol: Drosophila were grown on standard cornmeal, molasses media at 18oC until transgene induction

extract_protocol: 10 wings of the indicated stages were dissected and total RNA was extracted using a Qiagen RNAeasy kit.

treatment_protocol: Gal4/UAS transgene expression (or mock controls) were shifted to 28oC, permissive for Gal4/UAS driven expression without excessive cell death, for 10 hours before dissection. For pupal stages, all animals were staged from white-prepupae collected at 0hr APF.

tag: tissue

value: dissected wing

tag: developmental stage

value: wandering 3rd larval instar

tag: transgene

value: Tkv


title: Tkv expression L3_2


title: cervix_tumour_cs2_ac_1

source_name: cervix tumour FFPE series 2 ac

value: adenocarcinoma (AC)


title: cervix_tumour_cs1_1

hyb_protocol: RNA was quantified using a Bioanalyser (Agilent Technologies) and 100 ng amplified using NuGEN WT-Ovation FFPE v2 kit. The WT-Ovation Exon Module V1.0 was used to generate ST-cDNA and 4 µg was hybridised to Affymetrix Human Exon 1.0 ST arrays.

data_processing:
Background adjustment, quantile normalisation and summarisation of probe-level intensity were performed with the Robust Multi-array Average (RMA) algorithm, using R and the Affymetrix Power Tools
probe group file: HuEx-1_0-st-v2.r2.pgf

label: biotin

source_name: cervix tumour FFPE series 1

label_protocol: The RNA was amplified using the WT-Ovation Pico RNA Amplification System, converted using the WT-Ovation Exon Module, and fragmented and labelled using the NuGEN FL-Ovation cDNA Biotin Module v2

extract_protocol: RNA was extracted and Dnase treated using RecoverAll Total Nucleic Acid Isolation kit (Ambion)

tag: organ

value: cervix

tag: histology

tag: ffpe block storage duration (yrs)


title: cervix_tumour_cs2_scc_2


title: HFF1, RF-tf

city: Berlin

first: Katharina

last: Drews

address: Ihnestr. 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation after background subtraction using the Gene Expression Module 1.8.0 of GenomeStudio V2010.3 (Illumina).

source_name: HFF1, RF-transfected

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using the RNeasy Mini Kit (Qiagen), including RNase-free Dnase (Qiagen) digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

tag: cell line

value: HFF1 (purchased from ATCC)

tag: treatment

tag: passage


title: D425-shOTX2_2, t=0

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
NB161
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Cells were cultured in MEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.

value: Medulloblastoma cell line D425

tag: protocol

value: doxycyline inducible shRNA against OTX2

tag: time

value: 0 hrs

tag: time course


title: Tkv expression L3_4


title: cervix_tumour_cs2_scc_1

tag: tissue source

tag: tissue type


title: D425-shOTX2_1, t=48

description:
NB129
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 48 hrs


title: HFF1, mock

description: replicate 1

source_name: HFF1, mock-transfected


title: D425-shOTX2_1, t=96

description:
NB130
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 96 hrs


title: control L3_5


title: cervix_tumour_cs1_2

tag: storage


title: control L3_4


title: D425-shOTX2_1, t=16

description:
NB127
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 16 hrs


title: BJ-a

description: replicate 1

source_name: BJ, un-treated

value: BJ (purchased from ATCC)

value: neonatal foreskin fibroblasts


title: BJ, mock

description: replicate 1

source_name: BJ, mock-transfected


title: D425-shOTX2_1, t=24

description:
NB128
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 24 hrs


title: cervix cell line HeLa

source_name: cervix cell line HeLa

value: cervix cell line

value: fresh

tag: classification

tag: data series

value: cell line


title: control L3_3

tag: tissue

value: dissected wing

value: wandering 3rd larval instar


title: D425-shOTX2_1, t=8

description:
NB126
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

value: 8 hrs


title: BJ-b

description: replicate 2


title: HFF1-b

description: replicate 2

source_name: HFF1, un-treated


title: control L3_1

tag: developmental stage


title: cervix cell line Me180

source_name: cervix cell line Me180

value: squamous cell carcinoma (SCC)

tag: ffpe block storage duration time (yrs)


title: control L3_2

tag: transgene


title: D425-shOTX2_1, t=0

description:
NB125
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.


title: HFF1-a

description: replicate 1

value: HFF1 (purchased from ATCC)


title: H_TAX_2

status: Public on Jul 03 2012

city: Namur

first: Bertrand

last: De Meulder

state: Namur

address: Rue de Bruxelles, 61

department: Biology

country: Belgium

institute: FUNDP

description: Gene expression data from MDA-MB-231 cells

hyb_protocol: Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.

scan_protocol: GeneChip® Scanner 3000

data_processing: Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.

source_name: Cells + paclitaxel 50 uM in hypoxia

label_protocol: Affymetrix protocol

growth_protocol: MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum

extract_protocol: Trizol extraction kit (Invitrogen)

treatment_protocol: 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)


title: H_CTL_2

source_name: Control cells in hypoxia


title: H_CTL_3

source_name: Cells + epirubicin 10 uM in hypoxia


title: N_TAX_1

source_name: Cells + paclitaxel 50 uM in normoxia


title: N_TAX_3

source_name: Control cells in normoxia


title: N_EPI_3


title: H_EPI_3


title: H_TAX_3


title: N_TAX_2


title: N_CTL_1


title: N_EPI_2

source_name: Cells + epirubicin 10 uM in normoxia


title: N_CTL_3


title: N_CTL_2


title: N_EPI_1


title: Sox10 KD 96h rep2

city: Zurich

first: Michal

middle: J

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

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

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

data_processing: The data were analyzed using default analysis settings of the RMA algorithm as implemented in the affy package of Bioconductor.

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

extract_protocol: RNA extraction was performed using RNAeasy kit (QIAGEN) according to manufacturer's instructions.

value: Sox10 KD


title: control 48h rep2

value: control


title: H_CTL_1


title: H_EPI_2


title: H_TAX_1


title: Sox10 KD 96h rep1


title: Sox10 KD 48h rep1


title: H_EPI_1


title: Sox10 KD 48h rep2


title: control 96h rep1


title: control 96h rep2


title: BMD DNA 569

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at 48oC. Single-base extension and allele-specific staining were performed by hand.

scan_protocol: After allele-specific staining, BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: whole blood, case

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using either Proteinase K and phenol/chloroform with standard protocols (NIH and University of Utrecht) or the Nucleon BACC Genomic DNA extraction kit (University of Rennes).

tag: breed

value: Bernese Mountain Dog (BMD)

tag: phenotype

value: histiocytic sarcoma (HS)

tag: origin

value: The Netherlands

value: whole blood


title: BMD DNA 574

source_name: whole blood, control

value: unaffected


title: control 48h rep1

tag: cell line

tag: treatment


title: BMD DNA 573


title: BMD DNA 564


title: BMD DNA 570


title: BMD DNA 568


title: BMD DNA 562


title: BMD DNA 572


title: BMD DNA 563


title: BMD DNA 565


title: BMD DNA 558


title: BMD DNA 566


title: BMD DNA 571


title: BMD DNA 567


title: BMD DNA 557


title: BMD DNA 561


title: BMD DNA 559


title: BMD DNA 556


title: BMD DNA 554


title: BMD DNA 555


title: BMD DNA 553


title: BMD DNA 552


title: BMD DNA 560


title: BMD DNA 551


title: BMD DNA 550


title: BMD DNA 548


title: BMD DNA 549


title: BMD DNA 545


title: BMD DNA 543


title: BMD DNA 544


title: BMD DNA 547


title: BMD DNA 546


title: BMD DNA 542


title: BMD DNA 540


title: BMD DNA 541


title: BMD DNA 539


title: BMD DNA 538


title: BMD DNA 536


title: BMD DNA 532


title: BMD DNA 534


title: BMD DNA 535


title: BMD DNA 529


title: BMD DNA 537


title: BMD DNA 530


title: BMD DNA 528


title: BMD DNA 527

value: France


title: BMD DNA 533


title: BMD DNA 526


title: BMD DNA 525


title: BMD DNA 531


title: BMD DNA 519


title: BMD DNA 523


title: BMD DNA 514


title: BMD DNA 522


title: BMD DNA 521


title: BMD DNA 515


title: BMD DNA 518


title: BMD DNA 513


title: BMD DNA 512


title: BMD DNA 520


title: BMD DNA 510


title: BMD DNA 508


title: BMD DNA 509


title: BMD DNA 517


title: BMD DNA 507


title: BMD DNA 511


title: BMD DNA 505


title: BMD DNA 503


title: BMD DNA 504


title: BMD DNA 502


title: BMD DNA 498


title: BMD DNA 490


title: BMD DNA 524


title: BMD DNA 500


title: BMD DNA 501


title: BMD DNA 494


title: BMD DNA 492


title: BMD DNA 499


title: BMD DNA 486


title: BMD DNA 493


title: BMD DNA 496


title: BMD DNA 495


title: BMD DNA 488


title: BMD DNA 484


title: BMD DNA 506


title: BMD DNA 487


title: BMD DNA 491


title: BMD DNA 483


title: BMD DNA 489


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 1, normal [Affymetrix]

city: Lund

first: Henrik

last: Lilljebjörn

address: Lund University Hospital

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Hybridized to Cytogenetics Whole-Genome 2.7M Array

hyb_protocol: The protocol provided by the manufacturer (Affymetrix) was used

scan_protocol: The chips were washed and stained according to the manufacturer's instructions and scanned using a GeneChip Scanner 3000

data_processing: CEL files containing raw signal intensities were exported from the GeneChip Operating Software. The CEL files were imported into Chromosome Analysis Suite to produce copy number estimates (CYCHP-files).

label: Biotin

extract_protocol: Genomic DNA was extracted from leukemic bone marrow at diagnosis or normal blood using standard methods. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: Normal Blood


title: BMD DNA 497


title: BMD DNA 485


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 1, leukemia [Affymetrix]

label_protocol: The protocol provided by the manufacturer (Affymetrix) was used

value: Acute lymphoblastic leukemia


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 2, normal [Affymetrix]


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 2, leukemia [Affymetrix]


title: BMD DNA 481


title: BMD DNA 468

value: Italy


title: BMD DNA 482


title: BMD DNA 479


title: BMD DNA 477


title: BMD DNA 464


title: BMD DNA 459


title: BMD DNA 475


title: BMD DNA 463


title: BMD DNA 470


title: BMD DNA 473


title: BMD DNA 460


title: BMD DNA 455


title: BMD DNA 456


title: BMD DNA 471


title: BMD DNA 457


title: BMD DNA 480


title: BMD DNA 461


title: BMD DNA 474


title: BMD DNA 467


title: BMD DNA 466


title: BMD DNA 458


title: BMD DNA 465


title: BMD DNA 476


title: BMD DNA 478


title: BMD DNA 462


title: BMD DNA 454


title: BMD DNA 469


title: BMD DNA 451


title: BMD DNA 444

value: Denmark


title: BMD DNA 449


title: BMD DNA 445


title: BMD DNA 450


title: BMD DNA 443


title: BMD DNA 439


title: BMD DNA 516


title: BMD DNA 448


title: BMD DNA 435


title: BMD DNA 446


title: BMD DNA 441


title: BMD DNA 434


title: BMD DNA 433


title: BMD DNA 428


title: BMD DNA 429


title: BMD DNA 452


title: BMD DNA 430


title: BMD DNA 442


title: BMD DNA 431


title: BMD DNA 436


title: BMD DNA 447


title: BMD DNA 440


title: BMD DNA 437


title: BMD DNA 432


title: BMD DNA 426


title: BMD DNA 425


title: BMD DNA 427


title: BMD DNA 419


title: BMD DNA 412


title: BMD DNA 417


title: BMD DNA 420


title: BMD DNA 414


title: BMD DNA 416


title: BMD DNA 411


title: BMD DNA 415


title: BMD DNA 421


title: BMD DNA 413


title: BMD DNA 423


title: BMD DNA 405


title: BMD DNA 418


title: BMD DNA 409


title: BMD DNA 408


title: BMD DNA 402


title: BMD DNA 401


title: BMD DNA 404


title: BMD DNA 403


title: BMD DNA 424


title: BMD DNA 410


title: BMD DNA 407


title: BMD DNA 398


title: BMD DNA 472


title: BMD DNA 406


title: BMD DNA 400


title: BMD DNA 395


title: BMD DNA 391


title: BMD DNA 394


title: BMD DNA 392


title: BMD DNA 390


title: BMD DNA 389


title: BMD DNA 396


title: BMD DNA 387


title: BMD DNA 388


title: BMD DNA 375


title: BMD DNA 377


title: BMD DNA 383


title: BMD DNA 378


title: BMD DNA 381


title: BMD DNA 397


title: BMD DNA 422


title: BMD DNA 376


title: BMD DNA 380


title: BMD DNA 373


title: BMD DNA 393


title: BMD DNA 379


title: BMD DNA 374


title: BMD DNA 384


title: BMD DNA 386


title: BMD DNA 382


title: BMD DNA 385


title: BMD DNA 372


title: BMD DNA 370


title: BMD DNA 369


title: BMD DNA 371


title: BMD DNA 363


title: BMD DNA 368


title: BMD DNA 360


title: BMD DNA 361


title: BMD DNA 364


title: BMD DNA 366


title: BMD DNA 438


title: BMD DNA 367


title: BMD DNA 359


title: BMD DNA 365


title: BMD DNA 362


title: BMD DNA 357


title: BMD DNA 399


title: BMD DNA 355


title: BMD DNA 352


title: BMD DNA 356


title: BMD DNA 354


title: BMD DNA 353


title: BMD DNA 358


title: BMD DNA 453


title: BMD DNA 351


title: BMD DNA 350


title: BMD DNA 349


title: BMD DNA 348


title: BMD DNA 347


title: BMD DNA 345


title: BMD DNA 346


title: DLBCL patient 08-379

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

description: DLBCL patient

hyb_protocol: standard Affymetrix procedures using Fluidics Station

scan_protocol: standard Affymetrix procedures using GeneChip Scanner 3000

data_processing:
Affymetrix GeneChip GCOS 1.4, GTYPE 4.1. The data matrix contains CN data as Log2Ratio from mBPCR (Rancoita, BMC Bioinformatics, 2009), and LOH as computed by dCHIP. Female HapMap were used as reference.
signal = log2ratio; loh = 0 or 1

source_name: DLBCL patient

label_protocol: standard Affymetrix protocol starting from 250 ng of DNA.

extract_protocol: All clinical specimens were derived from involved sites and obtained in the course of routine diagnostic procedures before therapy initiation. Cases were selected based upon the availability of frozen material with a fraction of neoplastic cells in the specimen representing >70% of overall cellularity as determined by morphologic and/or immunophenotypic studies.

value: human DLBCL clinical sample

tag: age

tag: Sex

value: F

tag: ipiscore

value: II


title: BMD DNA 344


title: BMD DNA 342


title: BMD DNA 341


title: BMD DNA 343


title: BMD DNA 340


title: DLBCL patient 08-381

description: DLBCL patient

value: M


title: DLBCL patient 08-382

description: DLBCL patient


title: DLBCL patient 08-383

description: DLBCL patient


title: DLBCL patient 08-380

description: DLBCL patient


title: DLBCL patient 08-378

description: DLBCL patient

value: III


title: DLBCL patient 08-377

description: DLBCL patient

value: I


title: BMD DNA 339


title: DLBCL patient 08-374

description: DLBCL patient


title: DLBCL patient 08-376

description: DLBCL patient


title: BMD DNA 337

value: North America


title: DLBCL patient 08-375

description: DLBCL patient


title: BMD DNA 336

value: Bernese Mountain Dog (BMD)


title: DLBCL patient 08-384

description: DLBCL patient


title: BMD DNA 332

value: histiocytic sarcoma (HS)


title: BMD DNA 338

value: The Netherlands


title: DLBCL patient 08-370

description: DLBCL patient


title: BMD DNA 334

value: whole blood


title: DLBCL patient 08-371

description: DLBCL patient


title: DLBCL patient 08-357

description: DLBCL patient


title: BMD DNA 333

value: unaffected


title: BMD DNA 335


title: DLBCL patient 08-373

description: DLBCL patient

value: IV


title: DLBCL patient 08-356

description: DLBCL patient


title: BMD DNA 330


title: DLBCL patient 08-372

description: DLBCL patient


title: BMD DNA 329


title: DLBCL patient 08-355

description: DLBCL patient


title: BMD DNA 328


title: BMD DNA 326


title: BMD DNA 325


title: DLBCL patient 08-353

description: DLBCL patient


title: BMD DNA 322


title: DLBCL patient 08-348

description: DLBCL patient


title: DLBCL patient 08-347

description: DLBCL patient


title: DLBCL patient 08-336

description: DLBCL patient


title: DLBCL patient 08-354

description: DLBCL patient


title: DLBCL patient 08-349

description: DLBCL patient


title: BMD DNA 323


title: BMD DNA 324


title: BMD DNA 321


title: DLBCL patient 08-325

description: DLBCL patient


title: DLBCL patient 08-335

description: DLBCL patient


title: BMD DNA 327


title: DLBCL patient 08-326

description: DLBCL patient


title: DLBCL patient 08-327

description: DLBCL patient


title: DLBCL patient 08-324

description: DLBCL patient


title: DLBCL patient 08-321

description: DLBCL patient


title: BMD DNA 320


title: DLBCL patient 08-317

description: DLBCL patient


title: BMD DNA 319


title: BMD DNA 331


title: BMD DNA 318


title: BMD DNA 317


title: BMD DNA 316


title: BMD DNA 315


title: DLBCL patient 08-319

description: DLBCL patient


title: DLBCL patient 08-314

description: DLBCL patient


title: DLBCL patient 08-318

description: DLBCL patient


title: DLBCL patient 08-323

description: DLBCL patient


title: DLBCL patient 08-315

description: DLBCL patient


title: BMD DNA 313


title: DLBCL patient 08-320

description: DLBCL patient


title: DLBCL patient 08-316

description: DLBCL patient


title: BMD DNA 312


title: BMD DNA 310


title: BMD DNA 308


title: DLBCL patient 08-313

description: DLBCL patient


title: BMD DNA 306


title: DLBCL patient 08-311

description: DLBCL patient


title: BMD DNA 307


title: BMD DNA 311


title: BMD DNA 305


title: DLBCL patient 08-312

description: DLBCL patient


title: BMD DNA 309


title: DLBCL patient 08-308

description: DLBCL patient


title: BMD DNA 304


title: DLBCL patient 08-293

description: DLBCL patient


title: DLBCL patient 08-288

description: DLBCL patient


title: DLBCL patient 08-309

description: DLBCL patient


title: DLBCL patient 08-310

description: DLBCL patient


title: BMD DNA 314


title: BMD DNA 303


title: BMD DNA 299


title: DLBCL patient 08-276

description: DLBCL patient


title: DLBCL patient 08-277

description: DLBCL patient


title: BMD DNA 302


title: BMD DNA 298


title: BMD DNA 301


title: BMD DNA 300


title: DLBCL patient 08-270

description: DLBCL patient


title: DLBCL patient 08-274

description: DLBCL patient


title: DLBCL patient 08-275

description: DLBCL patient


title: BMD DNA 297


title: DLBCL patient 08-272

description: DLBCL patient


title: BMD DNA 295


title: BMD DNA 296


title: BMD DNA 293


title: BMD DNA 294


title: BMD DNA 291


title: DLBCL patient 08-268

description: DLBCL patient


title: DLBCL patient 08-267

description: DLBCL patient


title: DLBCL patient 08-269

description: DLBCL patient


title: BMD DNA 290


title: DLBCL patient 08-264

description: DLBCL patient


title: BMD DNA 288


title: BMD DNA 292


title: DLBCL patient 08-266

description: DLBCL patient


title: BMD DNA 287


title: DLBCL patient 08-263

description: DLBCL patient


title: BMD DNA 289


title: BMD DNA 285


title: DLBCL patient 08-265

description: DLBCL patient


title: DLBCL patient 08-047

description: DLBCL patient


title: DLBCL patient 08-260

description: DLBCL patient


title: DLBCL patient 08-048

description: DLBCL patient


title: BMD DNA 284


title: DLBCL patient 08-262

description: DLBCL patient


title: BMD DNA 286


title: DLBCL patient 08-271

description: DLBCL patient


title: BMD DNA 281


title: DLBCL patient 08-261

description: DLBCL patient


title: BMD DNA 282


title: DLBCL patient 08-045

description: DLBCL patient


title: BMD DNA 279


title: BMD DNA 283


title: BMD DNA 280


title: BMD DNA 274


title: DLBCL patient 08-044

description: DLBCL patient


title: DLBCL patient 08-046

description: DLBCL patient


title: BMD DNA 277


title: DLBCL patient 08-040

description: DLBCL patient


title: BMD DNA 276


title: DLBCL patient 08-043

description: DLBCL patient


title: DLBCL patient 08-041

description: DLBCL patient


title: DLBCL patient 08-042

description: DLBCL patient


title: DLBCL patient 08-014

description: DLBCL patient


title: BMD DNA 275


title: DLBCL patient 08-013

description: DLBCL patient


title: DLBCL patient 08-039

description: DLBCL patient


title: DLBCL patient 08-012

description: DLBCL patient


title: DLBCL patient 08-010

description: DLBCL patient


title: DLBCL patient 08-007

description: DLBCL patient


title: BMD DNA 272


title: DLBCL patient 08-008

description: DLBCL patient


title: BMD DNA 273


title: BMD DNA 270


title: BMD DNA 271


title: DLBCL patient 08-011

description: DLBCL patient


title: DLBCL patient 07-511

description: DLBCL patient


title: DLBCL patient 07-513

description: DLBCL patient


title: BMD DNA 269


title: BMD DNA 267


title: BMD DNA 265


title: BMD DNA 268


title: BMD DNA 266


title: BMD DNA 264


title: BMD DNA 278


title: DLBCL patient 08-006

description: DLBCL patient


title: DLBCL patient 07-509

description: DLBCL patient


title: BMD DNA 263


title: DLBCL patient 07-510

description: DLBCL patient


title: BMD DNA 260


title: BMD DNA 262


title: BMD DNA 261


title: DLBCL patient 07-508

description: DLBCL patient


title: BMD DNA 259


title: BMD DNA 258


title: DLBCL patient 07-503

description: DLBCL patient


title: BMD DNA 257


title: DLBCL patient 07-504

description: DLBCL patient


title: BMD DNA 256


title: BMD DNA 255


title: DLBCL patient 07-501

description: DLBCL patient


title: DLBCL patient 07-507

description: DLBCL patient


title: DLBCL patient 07-506

description: DLBCL patient


title: DLBCL patient 07-502

description: DLBCL patient


title: DLBCL patient 07-505

description: DLBCL patient


title: DLBCL patient 07-499

description: DLBCL patient


title: BMD DNA 253


title: DLBCL patient 07-497

description: DLBCL patient


title: DLBCL patient 07-496

description: DLBCL patient


title: BMD DNA 254


title: BMD DNA 251


title: BMD DNA 252


title: BMD DNA 250


title: BMD DNA 249


title: DLBCL patient 08-009

description: DLBCL patient


title: DLBCL patient 07-498

description: DLBCL patient


title: DLBCL patient 07-493

description: DLBCL patient


title: DLBCL patient 07-492

description: DLBCL patient


title: BMD DNA 247


title: BMD DNA 246


title: BMD DNA 248


title: BMD DNA 243


title: BMD DNA 245


title: DLBCL patient 07-490

description: DLBCL patient


title: BMD DNA 244


title: BMD DNA 242


title: DLBCL patient 07-494

description: DLBCL patient


title: DLBCL patient 07-487

description: DLBCL patient


title: DLBCL patient 07-488

description: DLBCL patient


title: DLBCL patient 07-439

description: DLBCL patient


title: DLBCL patient 07-491

description: DLBCL patient


title: DLBCL patient 07-489

description: DLBCL patient


title: DLBCL patient 07-440

description: DLBCL patient


title: BMD DNA 240


title: BMD DNA 236


title: DLBCL patient 07-437

description: DLBCL patient


title: DLBCL patient 07-436

description: DLBCL patient


title: BMD DNA 235


title: BMD DNA 241


title: DLBCL patient 07-433

description: DLBCL patient


title: BMD DNA 239


title: BMD DNA 234


title: DLBCL patient 07-485

description: DLBCL patient


title: BMD DNA 238


title: DLBCL patient 07-435

description: DLBCL patient


title: DLBCL patient 07-432

description: DLBCL patient


title: DLBCL patient 07-431

description: DLBCL patient


title: DLBCL patient 07-438

description: DLBCL patient


title: BMD DNA 233


title: BMD DNA 231


title: BMD DNA 232


title: BMD DNA 230


title: BMD DNA 227


title: BMD DNA 237


title: BMD DNA 226


title: DLBCL patient 07-429

description: DLBCL patient


title: DLBCL patient 07-413

description: DLBCL patient

value: m


title: BMD DNA 228


title: DLBCL patient 07-414

description: DLBCL patient

value: f


title: DLBCL patient 07-395

description: DLBCL patient


title: BMD DNA 229


title: BMD DNA 223


title: BMD DNA 225


title: DLBCL patient 07-394

description: DLBCL patient


title: DLBCL patient 07-392

description: DLBCL patient


title: DLBCL patient 07-391

description: DLBCL patient


title: BMD DNA 221


title: DLBCL patient 07-389

description: DLBCL patient


title: DLBCL patient 07-390

description: DLBCL patient


title: DLBCL patient 07-388

description: DLBCL patient


title: DLBCL patient 07-382

description: DLBCL patient


title: DLBCL patient 07-387

description: DLBCL patient


title: DLBCL patient 07-386

description: DLBCL patient


title: DLBCL patient 07-486

description: DLBCL patient


title: DLBCL patient 07-383

description: DLBCL patient


title: BMD DNA 216


title: BMD DNA 217


title: DLBCL patient 07-380

description: DLBCL patient


title: BMD DNA 220


title: DLBCL patient 07-385

description: DLBCL patient


title: DLBCL patient 07-384

description: DLBCL patient


title: BMD DNA 215


title: BMD DNA 224


title: BMD DNA 214


title: BMD DNA 218


title: BMD DNA 222


title: BMD DNA 213


title: BMD DNA 211


title: DLBCL patient 07-369

description: DLBCL patient


title: BMD DNA 212


title: DLBCL patient 07-370

description: DLBCL patient


title: DLBCL patient 07-367

description: DLBCL patient


title: BMD DNA 210


title: BMD DNA 208


title: DLBCL patient 07-361

description: DLBCL patient


title: DLBCL patient 07-363

description: DLBCL patient


title: DLBCL patient 07-213

description: DLBCL patient


title: BMD DNA 205


title: BMD DNA 204


title: BMD DNA 209


title: BMD DNA 206


title: DLBCL patient 07-365

description: DLBCL patient


title: BMD DNA 207


title: BMD DNA 219


title: DLBCL patient 07-368

description: DLBCL patient


title: DLBCL patient 07-211

description: DLBCL patient


title: DLBCL patient 07-364

description: DLBCL patient


title: DLBCL patient 07-362

description: DLBCL patient


title: BMD DNA 203


title: day 10 Tumor No.312

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

country: Japan

institute: Kanazawa University

hyb_protocol: The 825 ng of cRNA was fragmented and hybiridized to Whole Mouse Genome 4x44K Array (Agilent) oligo DNA chip using hybridization buffer (Agilent Gene Expression Hybridization Kit) at 60 celcius degree for 17 hours.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (version 9.1.3.1) was used for background subtraction and normalization.

organism: Mus musculus

source_name: tumor

label_protocol: cRNA was amplified and labaled with each labeling fluorescence using QuickAmp Labeling Kit (Agilent Techologies, Santa Clara, CA).

growth_protocol: Hepa1-6 was culture in Dulbecco's modified eagle medium supplemented with 10% of heat-inactivated fetus bovine serum

extract_protocol: Total RNA was isolated using RNeasy Minit Kit (QIAGEN) in accordance with the manufacturer's protocol.

treatment_protocol: Ten million Hepa1-6 cells were subcutaneously inoculated to C57Bl/6 mice. Tumor tissues were obtained 10 days or 15 days after inoculation. The obtained tissue samples were immediately put into RNAlater solution.

value: tumor

tag: strain

tag: gender

value: female

source_name: Total RNA from blood of C57Bl/6 mouse without any treatment

value: blood


title: BMD DNA 200


title: BMD DNA 197


title: DLBCL patient 07-206

description: DLBCL patient

value: human DLBCL clinical sample


title: DLBCL patient 03-131

description: DLBCL patient


title: day 15 Tumor No.313


title: BMD DNA 198


title: day 15 Tumor No.303


title: BMD DNA 199


title: BMD DNA 196


title: DLBCL patient 07-207

description: DLBCL patient

value: F


title: day 10 Tumor No.307


title: DLBCL patient 03-136

description: DLBCL patient

value: M


title: day 25 Blood No.320

source_name: blood

extract_protocol: Total RNA was isolated using Mouse RiboPure-Blood RNA Isolation Kit (Ambion) in accordance with the manufacturer's protocol.

treatment_protocol: Ten million Hepa1-6 cells were subcutaneously inoculated to C57Bl/6 mice. Blood was obtained before inoculatoin. After 10 days, blood was also collected every 5 days. The obtained blood samples were immediately put into RNAlater solution.

value: blood with Hepa1-6 cells

tag: sample time

value: day 25


title: DLBCL patient 07-185

description: DLBCL patient

value: I


title: DLBCL patient 07-209

description: DLBCL patient

value: II


title: day 10 Tumor No.302


title: DLBCL patient 07-183

description: DLBCL patient


title: BMD DNA 194

value: Bernese Mountain Dog (BMD)

value: North America


title: BMD DNA 195

value: histiocytic sarcoma (HS)

value: whole blood


title: day 25 Blood No.315


title: DLBCL patient 07-184

description: DLBCL patient

value: III


title: DLBCL patient 03-126

description: DLBCL patient


title: BMD DNA 193

value: unaffected


title: BMD DNA 190


title: BMD DNA 202


title: day 25 Blood No.305


title: BMD DNA 191


title: BMD DNA 188


title: day 20 Blood No.315

value: day 20


title: day 20 Blood No.320


title: day 20 Blood No.310


title: BMD DNA 192


title: day 25 Blood No.310


title: BMD DNA 189


title: day 15 Blood No.320

value: day 15


title: BMD DNA 187


title: day 15 Blood No.305

value: female


title: BMD DNA 186


title: day 15 Blood No.310

value: blood


title: day 10 Blood No.320

value: day 10


title: day 10 Blood No.315


title: day 10 Blood No.310


title: day 20 Blood No.305


title: BMD DNA 185


title: BMD DNA 182


title: BMD DNA 184


title: day 15 Blood No.315


title: BMD DNA 181


title: BMD DNA 183


title: day 15 Tumor No.318

value: tumor


title: BMD DNA 201


title: BMD DNA 180


title: DLBCL patient 07-205

description: DLBCL patient

value: human DLBCL clinical sample

value: F


title: BMD DNA 179


title: BMD DNA 178


title: day 0 Blood No.305

value: blood with Hepa1-6 cells

value: day 0


title: day 0 Blood No.320


title: BMD DNA 177


title: BMD DNA 176


title: TIC No.897

source_name: enriched fraction of infiltrating inflammatory cells of tumors

growth_protocol: Hepa1-6 was culture in Dulbecco's modified eagle medium supplemented with 10% of heat-inactivated fetus bovine serum.

extract_protocol: RNA was extracted from the enriched fraction of tumor-infiltrating inflammatory cells using MicroRNA isolation kit (Stratagene). Total RNA from blood was isolated using Mouse RiboPure-Blood RNA Isolation Kit (Ambion) in accordance with the manufacturer's protocol.

treatment_protocol: Ten million Hepa1-6 cells were subcutaneously inoculated to C57Bl/6 athymic mice. Ten days later, blood and tumors were obtained. The obtained blood samples were immediately put into RNAlater solution. The obtained tissues samples were mashed and the fraction eniched with tumor-infiltraing inflammatory cells were obtained by density gradient centrifugation.

value: tumor infiltrating cells


title: BMD DNA 175

value: Bernese Mountain Dog (BMD)


title: day 0 Blood No.310


title: day 10 Blood No.305


title: BMD DNA 173

value: North America


title: day 0 Blood No.315


title: TIC No.898


title: TIC No.896


title: BMD DNA 174

value: histiocytic sarcoma (HS)


title: TIC No.894


title: BMD DNA 172

value: whole blood


title: BMD DNA 171


title: TIC No.893


title: BMD DNA 169


title: BMD DNA 170


title: TIC No.891


title: TIC No.890


title: TIC No.889


title: BMD DNA 167


title: Blood No.898


title: BMD DNA 168


title: Blood No.897


title: #144

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

hyb_protocol: Illumina Infinium Beadarrays hyb protocol

scan_protocol: Standard Beadarray 500 Scanner parameter

data_processing: Illumina Genotyping Processing with GenomeStudio and the provided Illumina Cluster-File

source_name: liver

label_protocol: Illumina Infinium labeling protocol with C-Bio and A-DNP for Human HAPMAP SNP 300v2

extract_protocol: QIAamp DNA isolation procedure for blood or tissue (Qiagen)

treatment_protocol: no treatment

value: male

tag: presurgical medication

value: yes

tag: smoking

value: non-smoker

tag: alcohol intake

value: no


title: #141

value: female


title: #147

value: smoker


title: #143


title: #142


title: BMD DNA 166

value: unaffected

tag: tissue


title: Blood No.896

value: blood


title: #137


title: #148


title: #139


title: #145


title: #138


title: BMD DNA 165


title: #140


title: #130


title: Blood No.894


title: #134


title: BMD DNA 164


title: BMD DNA 163


title: #136


title: #135


title: #131


title: Blood No.893


title: Blood No.891


title: BMD DNA 162


title: #132


title: #133


title: #125


title: BMD DNA 160


title: #127


title: #124


title: Blood No.889


title: #129


title: day 10 TIC No.834

extract_protocol: Tumor tisseus were grinded and the enriched fraction of tumor-infiltrating inflammatory cells(TICs) were obtained followed by RNA extraction using MicroRNA isolation kit (Stratagene). Total RNA from blood was isolated using Mouse RiboPure-Blood RNA Isolation Kit (Ambion) in accordance with the manufacturer's protocol.

treatment_protocol: Ten million Hepa1-6 cells were subcutaneously inoculated to Balb/c athymic mice. Blood was obtained before as well as 10 days after Hepa1-6 cells inoculation. The tumor tissues were obtained 10 days after Hepa1-6 cells inoculation. The obtained samples were immediately put into RNAlater solution.

value: day 10

value: Balb/c atymic


title: #149


title: #146


title: #126


title: #123


title: #128


title: day 10 TIC No.833


title: BMD DNA 159


title: #122


title: Blood No.890


title: BMD DNA 161


title: BMD DNA 158


title: #121


title: day 10 TIC No.832


title: day 10 Blood No.834


title: BMD DNA 157


title: #117


title: day 10 Blood No.833


title: BMD DNA 155


title: day 10 Blood No.832


title: BMD DNA 154


title: BMD DNA 156


title: #116


title: #118


title: #119


title: #114


title: day 0 Blood No.834


title: #120


title: #112


title: #113


title: #115


title: #108


title: BMD DNA 153


title: #111


title: day 0 Blood No.832


title: day 0 Blood No.833


title: #110


title: BMD DNA 152


title: Knock out + rescue

city: Boston

first: Endre

last: Anderssen

state: Massachusetts

address: 185 Cambridge Street

department: Cancer center

institute: MGH

description: ES cells L3mbtl2-/- + Lentiviral L3mbtl2

hyb_protocol: For each sample 1.65 micrograms of Cy-3 labeled cRNA was fragmented and hybridized on an individual subarray of a Agilent 4x44k Mouse microarray (G4122F) for 17 hours in a rotation hybridization oven.

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

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.1). 1 - color defaults were used on all settings. For analysis the green median signal was transformed to log(2) scale.

source_name: Embryonic stem cells

label_protocol: Starting with 500 ng of RNA from each sample, Cy3 labeled cRNA was produced using the Agilent-1 color microarray based gene expression protocol. Quantity and Cy-dye incorporation rates were assessed using a NanoDrop ND-100.

extract_protocol: Total RNA was harvested from cells using Trizol (Invitrogen)

tag: genotype/variation

value: L3mbtl2-/- + Lentiviral L3mbtl2


title: BMD DNA 151


title: #109


title: #107


title: #105


title: BMD DNA 150


title: #106


title: BMD DNA 149


title: Knock out + Empty vector

description: ES cells L3mbtl2-/- + empty vector

value: L3mbtl2-/- + empty vector


title: BMD DNA 148


title: #102


title: BMD DNA 147

value: Denmark


title: Hmhi-MYC-TA + EGF

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: Melan-a Hmhi-MYC-TA + 14 days 100 ng/ml EGF

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and quantile-quantile as normalization method

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: Cells were kept on 10 cm Petri dishes (Falcon) in DMEM containing 10% FCS, 200 nM TPA, 12 nM cholera toxin,  400 U/ml penicillin, 50 µg/ml streptomycin

extract_protocol: RNA was extracted with the miRNeasy kit (Qiagen) according to the manufacturer`s instructions

treatment_protocol: Cells were starved in DMEM containing 10% dialyzed FCS, 400 U/ml penicillin, 50 µg/ml streptomycin and, where indicated, were treated with 100 ng/ml EGF for 14 days

tag: cell type

value: Melan-a Hmhi-MYC-TA cells


title: #104


title: Hmhi-Miz1 kd + EGF

description: Melan-a Hmhi-pS-Miz1 + 14 days 100 ng/ml EGF

value: Melan-a Hmhi-Miz1 kd cells


title: #103


title: Wild type

description: ES cells wild type

value: wild type


title: #098


title: BMD DNA 146

tag: breed

value: Bernese Mountain Dog (BMD)

value: histiocytic sarcoma (HS)

value: North America

value: whole blood


title: #100

value: yes

value: non-smoker

value: no


title: Knock out

description: ES cells L3mbtl2-/-


title: #101

value: female


title: BMD DNA 145

tag: phenotype


title: #099

value: male


title: #096

value: smoker


title: BMD DNA 144

tag: origin


title: Hmhi + EGF

description: Melan-a Hmhi + 14 days 100 ng/ml EGF

source_name: Melan-a Hmhi + 14 days 100 ng/ml EGF

value: Melan-a Hmhi cells


title: #094


title: #095


title: BMD DNA 143


title: #091


title: Hmhi

description: Melan-a Hmhi cells starved for 14 days

source_name: Melan-a Hmhi cells starved for 14 days


title: #092


title: #090


title: #097


title: BMD DNA 141

value: unaffected


title: BMD DNA 139


title: #084


title: BMD DNA 140


title: BMD DNA 142

value: Switzerland


title: #085


title: #082


title: #086


title: 924_Tumor

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

data_processing: Illumina BeadStudio Methylation software was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: = (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations

source_name: Tumor

label_protocol: sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).

extract_protocol: DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)

tag: disease state

value: Non-small-cell lung tumor

tag: tissue type

value: lung


title: BMD DNA 138


title: #083

tag: age


title: BMD DNA 137


title: #087


title: #089


title: #081


title: #088


title: 900_Tumor

scan_protocol: Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.


title: 889_Tumor


title: BMD DNA 136


title: #080


title: #079


title: 778_Tumor


title: #093


title: 759_Tumor


title: #077


title: #078


title: BMD DNA 134


title: BMD DNA 135

value: Germany


title: #076


title: 723_Tumor


title: #075


title: 986_Tumor


title: 622_Tumor


title: #069


title: #067


title: #070


title: #071


title: BMD DNA 132


title: #072


title: 621_Tumor


title: BMD DNA 130


title: 615_Tumor


title: #073


title: 587_Tumor


title: BMD DNA 129


title: #065


title: BMD DNA 133


title: 554_Tumor


title: BMD DNA 128


title: 528_Tumor


title: #064


title: BMD DNA 127


title: BMD DNA 131


title: #063


title: BMD DNA 126


title: #058


title: #061


title: #062


title: #056


title: #074


title: 307_Tumor


title: 286_Tumor


title: BMD DNA 125


title: 268_Tumor


title: #068


title: #057


title: BMD DNA 124


title: #048


title: #059


title: #060


title: 245_Tumor


title: #055


title: #050


title: #054


title: 234_Tumor


title: BMD DNA 123


title: BMD DNA 122


title: #053


title: #049


title: #052


title: #051


title: BMD DNA 121


title: #066


title: 233_Tumor


title: #046


title: 226_Tumor


title: #047


title: #042


title: BMD DNA 119


title: BMD DNA 120


title: 224_Tumor


title: BMD DNA 118


title: BMD DNA 117


title: #043


title: 244_Tumor


title: 211_Tumor


title: #044


title: #041


title: #039


title: #045


title: #038


title: BMD DNA 116


title: 202_Tumor


title: 205_Tumor


title: #037


title: #040


title: #036


title: 146_Tumor


title: BMD DNA 115


title: 204_Tumor


title: #032


title: 145_Tumor


title: BMD DNA 113


title: #034


title: BMD DNA 114


title: #035


title: BMD DNA 112


title: 141_Tumor


title: 140_Tumor


title: BMD DNA 111


title: #028


title: #030


title: #031


title: #033


title: BMD DNA 110


title: #029


title: BMD DNA 109


title: 127_Tumor


title: 119_Tumor


title: #025


title: 116_Tumor


title: #023


title: BMD DNA 107


title: BMD DNA 106


title: BMD DNA 108


title: #024


title: #026


title: #027


title: #018


title: 115_Tumor


title: #022


title: 113_Tumor


title: #013


title: #016


title: #020


title: Ckit-positive (Ckit+) cells at time T0, biological rep3

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description:
T0p_R3
Gene expression data from total RNA of Ckit+ cells from AGM regions obtained from E11.5 embryos by dissection.

hyb_protocol: Biotinylated cDNA was hybridized to Affymetrix GeneChip® Mouse Gene 1.0 ST arrays.

scan_protocol: GeneChips were scanned using the GCS3000 Affymetrix Platform.

data_processing: Affymetrix CEL files were background corrected and normalized using Bioconductor package “affy” by RMA normalization.

source_name: Ckti+ CD31+ CD45- cells from AGM regions obtained from E11.5 mouse embryos

label_protocol: 5ng of total RNA from each sample was amplified using the Ovation™  Pico WTA System (NuGEN Technologies, San Carlos, CA) and sense transcript cDNA (ST-cDNA) was generated using the WT-Ovation™ Exon Module (NuGEN Technologies). After, ST-cDNA was fragmented and labelled with the FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technologies).

extract_protocol: Total RNA from the different populations was extracted using the Qiagen RNeasy Midi C-kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: AGM regions were obtained from E11.5 embryos by dissection and digested with 0.1% collagenase. Cells were stained with anti-CD31, anti-ckit, anti-CD45 and anti-Ter119 antibodies. Sorting of the CD31+CD45-Ter119- population was performed, and cells were separated into c-kit+ and c-kit-.

value: aorta/gonad/mesonephros (AGM) region

value: Ckti+ CD31+ CD45- cells


title: BMD DNA 105

value: Bernese Mountain Dog (BMD)


title: Ckit-positive (Ckit+) cells at time T0, biological rep2

description:
T0p_R2
Gene expression data from total RNA of Ckit+ cells from AGM regions obtained from E11.5 embryos by dissection.


title: #017


title: #015


title: 100_Tumor


title: Ckit-positive (Ckit+) cells at time T0, biological rep1

description:
T0p_R1
Gene expression data from total RNA of Ckit+ cells from AGM regions obtained from E11.5 embryos by dissection.


title: Ckit-negative (Ckit-) cells at time T0, biological rep2

description:
T0n_R2
Gene expression data from total RNA of Ckit- cells from AGM regions obtained from E11.5 embryos by dissection.

source_name: Ckit- CD31+ CD45- cell population from AGM regions obtained from E11.5 mouse embryos

value: Ckit- CD31+ CD45- cells


title: BMD DNA 104

value: histiocytic sarcoma (HS)

value: North America

value: whole blood


title: #009

value: yes

value: non-smoker


title: BMD DNA 103


title: 77_Tumor


title: 71_Tumor


title: 68_Tumor


title: Ckit-negative (Ckit-) cells at time T0, biological rep1

description:
T0n_R1
Gene expression data from total RNA of Ckit- cells from AGM regions obtained from E11.5 embryos by dissection.


title: 1316-T1_mRNA

first: Mei

last: Xu

address: 1959 NE Pacific ave N

institute: University of Washington

hyb_protocol: Illumina hybridization protocol

scan_protocol: Illumina Beadscan

data_processing: Arrays were processed by the Fred Hutchinson Cancer Research Center's Genomics Shared Resource (Seattle, WA) using Illumina BeadScan and GenomeStudio software packages.  The summarized data was imported into BioConductor package 'Lumi' for background adjustment and quantile normalization.  The 75th percentile of negative controls was calculated for each array and used as a minimum signal intensity threshold value, followed by signal intensity and variance filters. Normalized signal intensity is in Log2 scale, and non-normalized signal intensity is linear scaled.

source_name: Liver tumor 1306-T1

label_protocol: Illumina labeling protocol

growth_protocol: Fresh liver tumor and control tissues were excised and frozen directly

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit from Qiagen.

treatment_protocol: 3E10 AAV-Rian-CMV vector particles were injected into the superficial temporal vein at the day after birth.  Six months later, liver tumors and their adjacent normal tissue were dissected out for analysis.

value: 6 months

tag: injected with

value: 3E10 AAV-Rian-CMV vector particles


title: #010

value: male

value: no


title: #011


title: 1316-L1_mRNA

source_name: Adjacent tissue to liver tumor 1316-T1


title: #014

value: female

value: smoker


title: 1316-T1_miRNA

hyb_protocol: Agilent hybridization protocol

scan_protocol: Scan with the Agilent 'C' Microarray Scanner

data_processing: Use the Bioconductor package “AgiMicroRNA” for RMA processing, without background subtraction.  Bioconductor package “limma” was used for a moderated, sample source paired t-test.

label_protocol: Agilent miRNA Complete labeling protocol

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit from Qiagen

treatment_protocol: 3E10 AAV-Rian-CMV vector particles were injected into the superficial temporal vein at the day after birth.  Six months later, liver tumors and their adjacent normal tissue were used for analysis.

value: Liver tumor


title: #007


title: 1309-T5_mRMA

source_name: Liver tumor 1309-T5


title: 56_Tumor

value: Non-small-cell lung tumor

value: lung


title: #019


title: #012


title: 1293-T1_mRNA

source_name: Liver tumor 1293-T1


title: #021


title: 46_Tumor


title: 1293-L1_mRNA

source_name: Adjacent tissue to liver tumor 1293-T1


title: 1309-T5_miRNA


title: #001


title: #008


title: 1293-T1_miRNA


title: 1309-L5_miRNA

source_name: Adjacent tissue to liver tumor 1309-T5

value: Adjacent tissue to liver tumor


title: 1316-L1_miRNA


title: #004


title: 1293-L1_miRNA


title: 21_Tumor


title: 24_Tumor


title: 44_Tumor


title: 23_Tumor


title: #002


title: 15_Tumor


city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description:
mid-log, cellobiose minimal media, biological replicate 2
cellobiose_2

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.).

organism: Thermotoga maritima MSB8

source_name: T. maritima MSB8 (ATCC: 43589) wild type

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

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown in an 500 mL serum bottles containing 200 mL of anoxic minimal media{Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85} with 10 mM maltose, cellobiose, or L-arabinose as the sole carbon source at 80˚ C.  All samples were collected during log-phase growth.

extract_protocol: RNA isolation was performed using a typical RNAeasy mini kit (Qiagen) protocol with DNaseI treatment. Total RNA yields were measured by using a NanoDrop (Thermo) at wavelength of 260 nm and quality was checked by measuring the sample A260/A280 ratio (>1.8).  cDNA synthesis was conducted as described in {Qiu et al., 2010, Genome Res, 20, 1304-11}, in short: 10 μg of purified total RNA sample was reversed transcribed to cDNA with amino-allyl dUTP. The amino-allyl labeled cDNA samples were then coupled with Cy3 Monoreactive dyes (Amersham). Cy3 labeled cDNA samples were fragmented to 5-0-300 bp range with DNase I (Epicentre). High-density four-plex oligonucleotide tilling arrays consisting of 4 x 71,548 probes of variable length spaced across the whole Thermotoga maritima genome were used (Roche Nimblegen). Hybridization, wash and scan were performed according to the manufacturer’s instructions.

tag: genotype

value: wild-type

tag: minimal sugar medium

value: cellobiose


title: #006

tag: gender


title: 13_Tumor


title: #005


title: mid-log, L-arabinose minimal media, biological replicate 2

description:
mid-log, arabinose minimal media, biological replicate 2
arabinose_2

value: arabinose


title: BMD DNA 101

source_name: whole blood, case

value: Bernese Mountain Dog (BMD)

value: histiocytic sarcoma (HS)

value: North America


description:
mid-log, maltose minimal media, biological replicate 3
maltose_3

value: maltose


title: U266_3

status: Public on Jul 02 2012

city: St. Louis

first: Mack

last: Su

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St. Louis School of Medicine

hyb_protocol: Hybridization was performed with the NimbleGen Hybridization System, NimbleGen Systems Inc., Madison, WI, USA

scan_protocol: Scanning was performed according to NimbleGen's standard operating protocol, NimbleGen Systems Inc., Madison, WI USA

data_processing: The raw data were analyzed with Partek Genomic Suite (St. Louis, MO). The overall expression profile of the region of interest was generated from the median values of the raw expression values of the quadruplicate tiling probes. The grand mean of each sample was shifted to 1000.

label_protocol: Using 5ug of total cellular RNA, the RNAs were polyadenylated using Genisphere's Plus Module 10 Assay (Cat# P10PLUS), according to manufacturer's protocol.  Using oligo-dT priming in the initial 1st-strand synthesis step, we created double-stranded cDNA using the Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit (Cat# 11917-010). cDNA was then labeled with NimbleGen's DNA Labeling Kit, NimbleGen Systems Inc., Madison, WI, USA

growth_protocol: Hela cells were grown in Dulbecco's modified Eagle's medium (Lonza) containing 10% fetal bovine serum (FBS, Thermo) and 1× penicillin-streptomycin (Pen/Strep). LP-1 cells were grown in Roswell Park Memorial Institute medium 1640 (RPMI 1640, Lonza) containing 10% FBS and 1× Pen/Strep. U266 and H929 cells were grown in RPMI 1640 (ATCC) containing 10% FBS, 1× Pen/Strep and 0.05 mM 2- mercaptoethanol (Sigma, H929 only).

extract_protocol: Cell line RNA samples were extracted using TRIzol (Invitrogen). Patient RNA samples were obtained anonymously from the Tissue Procurement Core Facility and Tumor Bank of Washington University in St. Louis.

value: Malignant

tag: translocation

value: No


title: LP-1_3

value: Yes


description:
mid-log, cellobiose minimal media, biological replicate 1
cellobiose_1


title: mid-log, L-arabinose minimal media, biological replicate 1

description:
mid-log, arabinose minimal media, biological replicate 1
arabinose_1


title: Ckit-negative (Ckit-) cells at time T0, biological rep3

description:
T0n_R3
Gene expression data from total RNA of Ckit- cells from AGM regions obtained from E11.5 embryos by dissection.

tag: strain

value: aorta/gonad/mesonephros (AGM) region

value: Ckit- CD31+ CD45- cells


description:
mid-log, maltose minimal media, biological replicate 2
maltose_2


title: Hela_2

source_name: Hela


title: H929_2


title: LP-1_2


description:
mid-log, maltose minimal media, biological replicate 4
maltose_4


description:
mid-log, maltose minimal media, biological replicate 1
maltose_1


title: U266_2


title: H929_1


title: Hela_3


title: U266_1


title: LP-1_1


title: Hela_1


title: BMD DNA 102

source_name: whole blood, control

value: unaffected

value: whole blood


title: Esophagus_normal_2

value: Normal

value: Not Applicable


title: Esophagus_malignant_6


title: Testis_normal_1


title: Esophagus_malignant_3


title: Esophagus_malignant_4


title: Esophagus_normal_1


title: Esophagus_malignant_2


title: #003

source_name: liver

value: male

tag: presurgical medication

value: yes

tag: smoking

value: non-smoker


title: Bladder_normal_1


title: 1309-L5_mRNA

value: 6 months

value: 3E10 AAV-Rian-CMV vector particles


title: Colon_normal_1


title: Colon_malignant_3


title: Colon_malignant_4


title: Colon_malignant_5


title: Esophagus_malignant_1


title: Colon_malignant_6


title: Colon_malignant_7


title: MM_nont414_12


title: MM_nont414_10


title: MM_nont414_11


title: MM_nont414_5


title: Bladder_malignant_5


title: Colon_malignant_2


title: Bladder_malignant_6


title: MM_nont414_9


title: MM_nont414_6


title: Colon_malignant_1


title: Bladder_malignant_4


title: MM_t414_4


title: MM_nont414_8


title: MM_nont414_4


title: Bladder_malignant_3


title: MM_nont414_7


title: Bladder_malignant_2


title: Esophagus_malignant_5


title: Bladder_malignant_1


title: Control_4

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: testis explants, 12 hour incubation with chemicals

hyb_protocol: FHM 8 x 15K microarrays were manufactured with Agilent Sure Print Technology in Fall 2010.  RNA labeling, microarray hybridization, and microarray analysis were performed according to Agilent’s One-Color Microarray-Gene Based Expression Analysis protocol (May 2010) using an Agilent kit (Agilent, Mississauga, ON, CAN).  After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

data_processing: Normalized signal intensity provided here is LOESS Normalization

organism: Pimephales promelas

label_protocol: Agilent one color protocol for Cy3

extract_protocol: RNA was extracted from gonad explants according to RNA isolation protocol (TRIzol® Reagent, Invitrogen, Burlington, ON, CAN).  After extraction using 1 ml TRIzol®, nucleic acid pellets were reconstituted in 20-25 µl RNA Secure™ (Ambion, Austin, TX, USA) in order to protect RNA integrity as per manufacturer’s protocol.  RNA quantity was measured using the NanoDrop ND2000 (Thermo Scientific) prior to DNase treatment for real-time PCR and RNA integrity was evaluated according to Agilent 2100 Bioanalyzer protocol (Agilent, Mississauga, ON, CAN).

treatment_protocol: testis explants were treated with 10^-6M progesterone for 12 hours; 6 control and 4 treatment samples

tag: agent

value: control

tag: tissue

value: testis


title: MM_t414_2


title: MM_nont414_3


title: MM_nont414_1


title: MM_t414_3


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 2, normal [Illumina]

description: Hybridized to HumanCNV370-QuadV3 DNA Analysis BeadChip arrays

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Genotyping was performed using Illumina Genome Studio software. Genotypes and raw signal values were exported from this software.

label_protocol: standard Illumina protocol

value: Normal Blood


title: MM_nont414_2

value: Malignant


title: Control_7

scan_protocol: After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.


title: Control_5


title: Control_2


title: MM_t414_1


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 2, leukemia [Illumina]

value: Acute lymphoblastic leukemia


title: P4_7

value: 10^-6M progesterone


title: Control_10


title: P4_4


title: FLU6

description: ovary explants, 12 hour incubation with chemicals

extract_protocol: RNA was extracted from gonad explants according to RNA isolation protocol (TRIzol® Reagent, Invitrogen, Burlington, ON, CAN).  After extraction using 1 ml TRIzol®, nucleic acid pellets were reconstituted in 20-25 µl RNA Secure™ (Ambion, Austin, TX, USA) in order to protect RNA integrity as per manufacturer’s protocol.  RNA quantity was measured using the NanoDrop ND2000 (Thermo Scientific) prior to DNase treatment for real-time PCR and RNA integrity was evaluated according to Agilent 2100 Bioanalyzer protocol (Agilent, Mississauga, ON, CAN).  RNA integrity values were generated and ranged from 6.5-8.3 (RIN average ± SD = 7.45 ± 0.55) for ovary explants.  To clean-up RNA, samples that had RIN numbers below 7.5 were purified using QIAGEN RNeasy® Kit (Toronto, ON) according to the Qiagen RNeasy® Kit protocol.  After purification, only samples with RIN values greater than 7.5 were used for microarray and qPCR analyses.

treatment_protocol: Ovary explants were incubated with 10^-6M of DHT, FLUY, and LIN for 12 hours

value: Flutamide

value: ovary

value: female


title: Sus rep2

middle: C

last: Krolewski

state: MA

address: 136 Harrison Ave

department: Anatomy and Cellular Biology

institute: Tufts University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol (performed by Keck Foundation Biotechnology Reseource Lab at Yale University)

scan_protocol: Standard Illumina scanning protocol (performed by Keck Foundation Biotechnology Resource Lab at Yale University)

data_processing: The data were background corrected and normalized using quantile normalization with Illumina Genome Studio

source_name: Sox2-eGFP heterozygotes

label_protocol: Amplified, Biotinylated cRNA were prepared with the Illumina TotalPrep Kit for Illumina arrays (performed by Keck Foundation Biotechnology Resource Lab at Yale University)

extract_protocol: FACS purified cell pellets were resuspended in Buffer ZR (Zymo Research Quick RNA Microprep Cat#R1050) and RNA was isolated according to the manufacturers instructions.  RNA was further purified using the DNA-free RNA kit from Zymo Research (Cat#R1013).

value: olfactory mucosa

tag: genotype/variation

value: normal transgenic

value: adult

value: heterozygous offspring of ∆Sox2-GFP x FVB/NJ

value: 8-12 weeks old

tag: facs gating

value: GFP(+high), PI(–), CD54(–)


title: P4_8

value: male


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 1, normal [Illumina]

extract_protocol: Genomic DNA was extracted from leukemic bone marrow at diagnosis or normal blood using standard methods. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.


title: P4_5


title: OMP-OBX rep3

source_name: OMP-GFP heterozygotes 3 weeks after bulbectomy

value: olfactory mucosa ipsilateral to unilateral removal of the olfactory bulb, 3 weeks after surgery

value: heterozygous offspring of ∆OMP-GFP x CD-1

value: GFP(+), PI(–), FSC/SSC low


title: mouse reference RNA rep3

source_name: Pooled total RNA from 11 mouse cell lines (Stratagene Catolog #740100)

tag: cell line

value: multiple cell lines

tag: cell type

value: pooled RNA from cultured cells (embryo, embryo, fibroblast, kidney, liver hepatocyte, lung alveolar macrophage, B-lymphocyte, T-lymphocyte, mammary gland, muscle myoblast, skin, testis)

value: various strains

value: cultured cells


title: CON6

value: control


title: mouse reference RNA rep2


title: Control_8

value: testis


title: LIN5

value: LIN

value: ovary

value: female


title: LIN6


title: OMP rep1

source_name: OMP-GFP heterozygotes

value: olfactory mucosa

value: normal transgenic

value: adult


title: DHT6

value: DHT


title: Sus rep1

value: heterozygous offspring of ∆Sox2-GFP x FVB/NJ

value: 8-12 weeks old

value: GFP(+high), PI(–), CD54(–)


title: mouse reference RNA rep1


title: DHT5


title: Sus rep3


title: OMP rep3

value: heterozygous offspring of ∆OMP-GFP x CD-1

value: GFP(+), PI(–), FSC/SSC low


title: OMP rep2


title: Neurog1-OBX rep2

source_name: Neurog1-eGFP heterozygotes 3 weeks after bulbectomy

value: olfactory mucosa ipsilateral to unilateral removal of the olfactory bulb, 3 weeks after surgery

value: heterozygous offspring of Neurog1-GFP x FVB/NJ


title: Neurog1-OBX rep3


title: OMP-OBX rep1


title: Neurog1-OBX rep1


title: ETV6/RUNX1-positive acute lymphoblastic leukemia, sample 1, leukemia [Illumina]

value: Acute lymphoblastic leukemia


title: OMP-OBX rep2


title: Neurog1-Ctrl rep3

source_name: Neurog1-eGFP heterozygotes


title: CON4

value: control


title: Neurog1-Ctrl rep2


title: LIN4


title: FLU5

value: Flutamide


title: CON3


title: DHT4


title: FLU2


title: Sox2GBC rep1

value: GFP(+low), Ecad/CD54(–), PI(–), FSC/SSC low


title: Sox2GBC rep3


title: PhoR(TV) M5G vs. WT M5G (biological rep)

city: Cambridge

first: Emily

last: Capra

address: 31 Ames Street, 68-570

institute: Massachusetts Institute of Technology

hyb_protocol: RNA was hybridized to the arrays following the manufacturer's protocol

scan_protocol: Arrays were scanned using Agilent Technologies Scanner G2505C

data_processing: Data was retreived using Agilent Feature Extractor 10.6

organism: Caulobacter vibrioides NA1000

source_name: PhoR(TV) grown in M5G

label_protocol: RNA was reverse transcribed into cDNA as described previously (Laub et al. 2000)

growth_protocol: Integration vectors were used to create either tetracylcline marked deletions or allelic replacements.

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

treatment_protocol: Cells were grown into log-phase in M2G media, before being diluted to an OD600 of ~.01 and resuspended in either M2G or M5G media. Cells were then allowed to grow for 10 hours before samples were taken for RNA preparation

value: PhoR(TV)

tag: media

value: phosphate limited

source_name: WT grown in M5G

value: wild type


title: LIN3

value: LIN

value: ovary

value: female


title: Normal olfactory mucosa rep1

first: Richard

source_name: control olfactory mucosa

value: olfactory mucosa

value: normal, wildtype

value: adult

value: F1 (129S1/SvImJ x C57BL/6J)

value: PI(–)


title: Neurog1-Ctrl rep1

value: normal transgenic

value: 8-12 weeks old

value: GFP(+), PI(–), FSC/SSC low


title: Normal olfactory mucosa rep2

value: wild type F1 (129S1/SvImJ x C57BL/6J)


title: DPhoR M5G vs. WT-M5G (biological rep)

source_name: DPhoR grown in M5G

value: DPhoR


title: PhoR(TV) M5G vs. WT M5G


title: FLU3

value: Flutamide


title: Normal olfactory mucosa rep3


title: DPhoR M5G vs. WT-M5G


title: DNtrX M2G vs. WT-M2G

source_name: DNtrX grown in M2G

value: DNtrX

value: phosphate replete

source_name: WT grown in M2G


title: Sox2GBC rep2

value: heterozygous offspring of ∆Sox2-GFP x FVB/NJ

value: GFP(+low), Ecad/CD54(–), PI(–), FSC/SSC low


title: DHT1

value: DHT

value: ovary


title: DPhoR M2G vs. WT-M2G

source_name: DPhoR grown in M2G

value: wild type


title: CON1

value: control

value: female


title: WT v. Complemented Cj1501 knockout, array 3

city: Norwich

first: Bruce

middle: MacKenzie

last: Pearson

state: Norfolk

address: Colney Lane

department: Food Safety

institute: Institute of Food Research

hyb_protocol: Standard Agilent hybridization was carried out overnight at 62 °C. Both hybridization and washing steps were performed per manufacturer's instructions.

scan_protocol: Microarrays were scanned at 5um resolution using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon).

data_processing: Data was block median normalized prior to analysis.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Batch cultured control sample, WT

label_protocol: Sample was labelled with Cy5-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences) and made to 12.4 µl total volume with water and supplemented on ice with 3 µl 10x RT buffer (Invitrogen), 0.6 µl 50x dNTPs mixture (25 mM each dCTP, dATP, dGTP and 10 mM dTTP), 3 µl 0.1 M DTT, 2 µl 1mM Cy5-dUTP (Perkin Elmer), and 200U Superscript II RNase H reverse transcriptase (Invitrogen). Incubation was at 37 °C overnight. Labelled cDNA was purified using a Qiaquick purification kit (Qiagen) and dried.

growth_protocol: Batch cultures of C. jejuni strains were grown in 50 ml volumes of Brucella broth in tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 ºC.

extract_protocol: 50 ml samples were mixed immediately on ice with 5 ml 95% ethanol and 5% phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier.

value: WT

source_name: Batch cultured test sample, complemented Cj1501 knockout mutant

label_protocol: Sample was labelled with Cy3-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences) and made to 12.4 µl total volume with water and supplemented on ice with 3 µl 10x RT buffer (Invitrogen), 0.6 µl 50x dNTPs mixture (25 mM each dCTP, dATP, dGTP and 10 mM dTTP), 3 µl 0.1 M DTT, 2 µl 1mM Cy3-dUTP (Perkin Elmer), and 200U Superscript II RNase H reverse transcriptase (Invitrogen). Incubation was at 37 °C overnight. Labelled cDNA was purified using a Qiaquick purification kit (Qiagen) and dried.

value: Complemented Cj1501 knockout mutant


title: WT v. Complemented Cj1501 knockout, array 2


title: WT v. WT over-expressing Cj1501, array 3

source_name: Batch cultured test sample, WT over-expressing Cj1501

value: WT over-expressing Cj1501


title: WT v. Cj1501 knockout, array 3

source_name: Batch cultured test sample, Cj1501 knockout mutant

value: Cj1501 knockout mutant


title: WT v. WT over-expressing Cj1501, array 1


title: WT v. Cj1501 knockout, array 2


title: WT v. Complemented Cj1501 knockout, array 1


title: seedlings sps1 rep 3

status: Public on Jul 01 2012

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Applied Science

institute: University of Arkansas at Little Rock

description: Gene expression data from 10-days old Arabidopsis seedlings

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Arabidopsis thaliana

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix IVT Express Kit as specified in the GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol: Arabidopsis seeds were germinated on Petri plates in dark and harvested after 10 days of cultivation.

extract_protocol: Total 10-days old dark-grown Arabidopsis seedlings were immediately frozen in liquid nitrogen. The seedlings were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No special tretments before harvesting were carried out.

tag: sample type

value: 10-days old dark grown seedlings of Arabidopsis sps1 line

value: seedling

tag: genetic background


title: seedlings sps1 rep 2

tag: age


title: seedlings wild type rep 2

source_name: wild type

value: 10-days old dark grown seedlings of Arabidopsis wild type (Col-0).

tag: genotype


title: seedlings wild type rep 3


title: seedlings sps1 rep 1


title: seedlings L17 rep 1

source_name: L17 phyA' line

value: 10-days old dark grown seedlings of Arabidopsis L17 line

value: L17 phyA' line


title: PhoR(TV) M2G vs. WT M2G

source_name: PhoR(TV) grown in M2G

value: PhoR(TV)

value: phosphate replete


title: seedlings L17 rep 3


title: seedlings wild type rep 1


title: seedlings L17 rep 2


title: WT v. Cj1501 knockout, array 1


title: lky-b-2_(Poplar)

city: Haidian

first: Dong-hui

last: YAN

state: Beijing

address: 1#, Dong Xiao Fu

country: China

institute: Chinese Academy of Forestry

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

scan_protocol: GeneChips were scanned using GeneChip TM scanner 3000 7G 4C

data_processing: The data were analyzed with Flexarray software package using RMA for normalization and SAM for differently expression genes.

organism: Populus deltoides

source_name: 2 day after innoculation  with Marssonina brunneain

label_protocol: Biotinylated cRNA were labeled according to GeneChip IVT Labeling Kit

growth_protocol: The seedlings of Populus deltoides were grown under a natural photoperiod, humidity and temperaturein in a rain-shelter field in Beijing

extract_protocol: TRIzol kit was used to extract total RNA.

treatment_protocol: spraying spore suspension at concentration of 3×105 /mL onto leaves, maitaining moisture for 48 h, spraying water as control.

tag: dev stage

value: leaves


title: lky-c-1_(Poplar)

source_name: 7 day after innoculation with Marssonina brunneain


title: lky-a-2_(Poplar)

source_name: 0 day after innoculation with Marssonina brunneain


title: lky-c-2_(Poplar)


title: watering 20% of daily evapotranspiration regime 3-2

scan_protocol: GeneChips were scanned using GeneChip TM scanner 3000.

organism: Populus euphratica

source_name: Poplar  seedlings

growth_protocol: The seedlings of Populus euphratica were grown under a natural photoperiod, humidity and temperaturein 5L (30 cm deep) pots with a mixture composed of sand, loamy soil, peat (1:1:1, v/v) in a rain-shelter field in Beijing

extract_protocol: All of the fifth and sixth leaves of a single poplar in each treatment were collected as its RNA sample pool. Total RNA were prepared mainly using CTAB extraction procedure(Chang et al. 1993)

treatment_protocol: Water stresses on poplars under regime 1, regime 2, regime 3 and regime 4 were imposed by watering 70%, 50%, 20%, and 5% of daily evapotranspiration back into the selected pots, respectively, for up to seven weeks, watering 100%, assigned as regime 0, of daily evapotranspiration were taken as control for the stress treatment. The amount of daily evapotranspiration of each pot was determined by its average daily mass loss in 10 consecutive days before executing the regimes.

value: leaf

tag: treatment


title: watering 20% of daily evapotranspiration regime 3-1


title: watering 5% of daily evapotranspiration regime 4-1

value: watering 5% of daily evapotranspiration


title: AND.Rag1-/-H-2d DP thymocytes_MCC/I-Ek stimulation_rep2

city: Saint Louis

first: Wan-Lin

last: Lo

address: 425 S Euclid Ave, campus box 8118

institute: Washington University in St Louis

description:
Gene expression data of pre-selected DP thymocytes from MCC/I-Ek stimulation (negative selection signals)
SAMPLE 4

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalized and modeled using dChip software.

source_name: Pre-selected DP thymocytes from AND.Rag1-/-H-2d mouse

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

growth_protocol: Pre-selected thymocytes were cultured in Iscove's DMEM containing 10% FCS, 1x nonessential amino acid, 2 mM GlutaMax, 1 mM sodium pyruvate, 0.05% gentamicin, 50 µM 2-mercaptoethanol

extract_protocol: Total RNA was isolated using Rneasy kits (Qiagene) according to the manufacturer's instructions

treatment_protocol: 1x106 thymocytes were stimulated with plate bound peptide loaded I-Ek Ig dimers for seven hours

value: Pre-selected DP thymocyte

value: MCC/I-Ek

tag: protocol

value: negative selection signals


title: watering 50% of daily evapotranspiration regime 2-1


title: 5388876097_H

city: La Jolla

first: Chiungfang

last: Chang

state: CA

address: 9500 Gilman Drive

department: Biological Science

institute: University of California, San Diego

description: KO d1 Th0+ 3hr TGF

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Erk2 deficient d1 Th0+3hr TGF

growth_protocol: CD4 T cells were cultured under TH0-, Th1-, or iTreg-inducing conditions

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

tag: strain

value: CD4 T cells

value: Erk2 KO

tag: culture conditions

value: Th0+ 3hr TGF

tag: time

value: d1 Th0+ 3hr TGF


title: 5388876097_C

description: WT d1 iTreg

source_name: WT d1 iTreg

value: WT

value: iTreg


title: 5388876097_E

description: WT d1 Th0+ 1hr TGF

source_name: WT d1 TH0+1hr TGF

value: Th0+ 1hr TGF

value: d1 Th0+ 1hr TGF


title: AND.Rag1-/-H-2d DP thymocytes_Hb/I-Ek stimulation_rep2

description:
Gene expression data of pre-selected DP thymocyts from Hb/I-Ek stimulation (non-selecting signals)
SAMPLE 6

tag: agent

value: Hb/I-Ek

value: non-selecting signals


title: AND.Rag1-/-H-2d DP thymocytes_Hb/I-Ek stimulation_rep1

description:
Gene expression data of pre-selected DP thymocyts from Hb/I-Ek stimulation (non-selecting signals)
SAMPLE 3


title: 5388876097_A

description: WT d1 Th1

source_name: WT d1 Th1


title: 5388876097_G

description: WT d1 Th0+ 3hr TGF

source_name: WT d1 Th0+3hr TGF


title: watering 70% of daily evapotranspiration regime 1-2

tag: tissue


title: 5388876097_B

description: KO d1 Th1

source_name: Erk2 deficient d1 Th1

tag: genotype/variation


title: 5388876097_F

description: KO d1 Th0+ 1hr TGF

source_name: Erk2 deficient d1 Th0+1hr TGF


title: AND.Rag1-/-H-2d DP thymocytes_MCC/I-Ek stimulation_rep1

description:
Gene expression data of pre-selected DP thymocytes from MCC/I-Ek stimulation (negative selection signals)
SAMPLE 1


title: watering 100% of daily evapotranspiration regime 0-2


title: watering 5% of daily evapotranspiration regime 4-2


title: watering 50% of daily evapotranspiration regime 2-2


title: lky-b-1_(Poplar)

value: seedling


title: watering 70% of daily evapotranspiration regime 1-1


title: watering 100% of daily evapotranspiration regime 0-1


title: lky-a-1_(Poplar)

value: leaves


title: AND.Rag1-/-H-2d DP thymocytes_gp250/I-Ek stimulation_rep1

description:
Gene expression data from pre-selected DP cells from gp250/I-Ek stimulation (positive selection signals)
SAMPLE 2

value: positive selection signals


title: AND.Rag1-/-H-2d DP thymocytes_gp250/I-Ek stimulation_rep2

description:
Gene expression data from pre-selected DP cells from gp250/I-Ek stimulation (positive selection signals)
SAMPLE 5


title: 5388876097_D

description: KO d1 iTreg

source_name: Erk2 deficient d1 iTreg


title: 5388876092_D

description: KO 3hr Th0

source_name: Erk2 deficient 3hr Th0


title: 5388876092_C

description: WT 3hr Th0

source_name: WT 3hr Th0


title: 5388876092_F

description: KO 3hr iTreg

source_name: Erk2 deficient 3hr iTreg


title: 5388876092_E

description: WT 3hr iTreg

source_name: WT 3hr iTreg


title: 5388876092_A

description: WT d0

source_name: WT d0

value: control


title: Testis_F3-Control_biological rep2

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Testis  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Testis_F3-Con2-100610-62.CEL

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 450.

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

data_processing:
The data for each of the 11 male and female tissues were pre-processed and analyzed as a separate group (11 groups, 6 chips per group) with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) in October, 2010, using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.
Scan  date batch effect was removed if applicable.

organism: Rattus norvegicus

source_name: Testis from F3-generation control lineage (vehicle) rat male

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: F0 - F3 generations rats were grown in standard vivarium conditions.  Male and female rats of the F3 generation of Vinclozolin and Control lineages were selected out of litters from corresponding F2 generation and sacrifised at age of 4 months.

extract_protocol: RNA was isolated from tissue homogenates in 1 ml Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.  Equal amount of RNA from 2 randomly chosen individuals within the same tissue/treatment group were pooled together for one RNA microarray sample (one microarray biological replica).   The same  pairs of animals were used for each pool of tissue microarray samples.  For microarray analysis, 3 biological replicas were prepared as above for each tissue/treatment group.

treatment_protocol: Gestating outbred Sprague-Dawley mother rats (F0 generation) were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation  [Cupp AS, et al., 2003] which at proper time gave birth of F1 generation rats.  Male and female rats of the subsequent F3 generation of Vinclozolin and Control lineages were selected out of litters from corresponding F2 generations and sacrifised at age of 4 months.

tag: rna prep date

tag: scan date

value: Sprague-Dawley

tag: f3-generation of

value: control lineage (vehicle)

tag: gender

value: Male

value: Testis

tag: developmental stage

value: PND 120


title: Testis_F3-Vinclozolin_biological rep1

description:
Testis  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Testis_F3-Vin1-100610-64.CEL

source_name: Testis from F3-generation Vinclozolin lineage rat male

value: Vinclozolin lineage


title: 5388876092_G

description: WTd1 Th0

source_name: WT d1 Th0

tag: cell type

value: CD4 T cells


title: Testis_F3-Control_biological rep3

description:
Testis  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Testis_F3-Con3-100610-63.CEL


title: Testis_F3-Vinclozolin_biological rep3

description:
Testis  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Testis_F3-Vin3-100610-66.CEL


title: Seminal vesicle_F3-Vinclozolin_biological rep2

description:
Seminal vesicle  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-SV_F3-Vin2-100610-59.CEL

source_name: Seminal vesicle from F3-generation Vinclozolin lineage rat male

value: Seminal vesicle


title: Seminal vesicle_F3-Control_biological rep3

description:
Seminal vesicle  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-SV_F3-Con3-100610-57.CEL

source_name: Seminal vesicle from F3-generation control lineage (vehicle) rat male


title: Prostate_F3-Control_biological rep3

description:
Prostate  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Prostate_F3-Con3-100510-51.CEL

source_name: Prostate from F3-generation control lineage (vehicle) rat male

value: Prostate


title: Male liver_F3-Vinclozolin_biological rep2

description:
Liver  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Liver_F3-Vin2-091510-35.CEL

source_name: Liver from F3-generation Vinclozolin lineage rat male

value: Liver


title: Testis_F3-Vinclozolin_biological rep2

description:
Testis  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Testis_F3-Vin2-100610-65.CEL


title: 5388876092_H

description: KO d1 Th0

source_name: Erk2 deficient d1 Th0

value: Erk2 KO


title: Prostate_F3-Vinclozolin_biological rep3

description:
Prostate  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Prostate_F3-Vin3-100510-54.CEL

source_name: Prostate from F3-generation Vinclozolin lineage rat male


title: Seminal vesicle_F3-Control_biological rep2

description:
Seminal vesicle  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-SV_F3-Con2-100610-56.CEL


title: Prostate_F3-Control_biological rep2

description:
Prostate  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Prostate_F3-Con2-100510-50.CEL


title: Prostate_F3-Control_biological rep1

description:
Prostate  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Prostate_F3-Con1-100510-49.CEL


title: Male liver_F3-Vinclozolin_biological rep3

description:
Liver  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Liver_F3-Vin3-091510-36.CEL


title: Seminal vesicle_F3-Vinclozolin_biological rep1

description:
Seminal vesicle  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-SV_F3-Vin1-100610-58.CEL


title: Seminal vesicle_F3-Control_biological rep1

description:
Seminal vesicle  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-SV_F3-Con1-100610-55.CEL


title: Prostate_F3-Vinclozolin_biological rep1

description:
Prostate  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Prostate_F3-Vin1-100510-52.CEL


title: Testis_F3-Control_biological rep1

description:
Testis  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Testis_F3-Con1-100610-61.CEL


title: Male liver_F3-Vinclozolin_biological rep1

description:
Liver  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Liver_F3-Vin1-091510-34.CEL


title: 5388876092_B

description: KO d0

source_name: Erk2 deficient d0


title: Seminal vesicle_F3-Vinclozolin_biological rep3

description:
Seminal vesicle  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-SV_F3-Vin3-100610-60.CEL


title: Male kidney_F3-Vinclozolin_biological rep3

description:
Kidney  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Kidn_F3-Vin3-071910-24.CEL

source_name: Kidney from F3-generation Vinclozolin lineage rat male

value: Kidney


title: Male kidney_F3-Vinclozolin_biological rep2

description:
Kidney  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Kidn_F3-Vin2-071910-23.CEL


title: Male kidney_F3-Vinclozolin_biological rep1

description:
Kidney  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Kidn_F3-Vin1-071910-22.CEL


title: Prostate_F3-Vinclozolin_biological rep2

description:
Prostate  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Prostate_F3-Vin2-100510-53.CEL


title: Male liver_F3-Control_biological rep3

description:
Liver  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Liver_F3-Con3-091510-33.CEL

source_name: Liver from F3-generation control lineage (vehicle) rat male


title: Male liver_F3-Control_biological rep2

description:
Liver  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Liver_F3-Con2-091510-32.CEL


title: Male kidney_F3-Control_biological rep2

description:
Kidney  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Kidn_F3-Con2-071910-20.CEL

source_name: Kidney from F3-generation control lineage (vehicle) rat male


title: Male kidney_F3-Control_biological rep3

description:
Kidney  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Kidn_F3-Con3-071910-21.CEL


title: Male heart_F3-Vinclozolin_biological rep1

description:
Heart  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Hrt_F3-Vin1-061610-10.CEL

source_name: Heart from F3-generation Vinclozolin lineage rat male

value: Heart


title: Male liver_F3-Control_biological rep1

description:
Liver  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Liver_F3-Con1-091510-31.CEL


title: Male kidney_F3-Control_biological rep1

description:
Kidney  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Kidn_F3-Con1-071910-19.CEL


title: Male heart_F3-Vinclozolin_biological rep3

description:
Heart  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Hrt_F3-Vin3-061610-12.CEL


title: Male heart_F3-Control_biological rep2

description:
Heart  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Hrt_F3-Con2-061610-8.CEL

source_name: Heart from F3-generation control lineage (vehicle) rat male


title: Male heart_F3-Control_biological rep3

description:
Heart  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Hrt_F3-Con3-061610-9.CEL


title: Male heart_F3-Control_biological rep1

description:
Heart  from 120 days old F3-generation control (vehicle) lineage male rat
Marina-Male-Hrt_F3-Con1-061610-7.CEL


title: Male heart_F3-Vinclozolin_biological rep2

description:
Heart  from 120 days old F3-generation Vinclozolinlineage male rat
Marina-Male-Hrt_F3-Vin2-061610-11.CEL


title: Uterus_F3-Vinclozolin_biological rep3

description:
Uterus  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-Uterus_F3-Vin3-100110-48.CEL

source_name: Uterus from F3-generation Vinclozolin lineage rat female

value: Female

value: Uterus


title: Ovary_F3-Vinclozolin_biological rep2

description:
Ovary  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-Ovary_F3-Vin2-100110-41.CEL

source_name: Ovary from F3-generation Vinclozolin lineage rat female

value: Ovary


title: Uterus_F3-Control_biological rep3

description:
Uterus  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-Uterus_F3-Con3-100110-45.CEL

source_name: Uterus from F3-generation control lineage (vehicle) rat female


title: Uterus_F3-Vinclozolin_biological rep1

description:
Uterus  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-Uterus_F3-Vin1-100110-46.CEL


title: Uterus_F3-Vinclozolin_biological rep2

description:
Uterus  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-Uterus_F3-Vin2-100110-47.CEL


title: Uterus_F3-Control_biological rep2

description:
Uterus  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-Uterus_F3-Con2-100110-44.CEL


title: Uterus_F3-Control_biological rep1

description:
Uterus  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-Uterus_F3-Con1-100110-43.CEL


title: Ovary_F3-Vinclozolin_biological rep1

description:
Ovary  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-Ovary_F3-Vin1-100110-40.CEL


title: Female liver_F3-Vinclozolin_biological rep1

description:
Liver  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-FM-Liver_F3-Vin1-091510-28.CEL

source_name: Liver from F3-generation Vinclozolin lineage rat female


title: Female liver_F3-Control_biological rep3

description:
Liver  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-FM-Liver_F3-Con3-091510-27.CEL

source_name: Liver from F3-generation control lineage (vehicle) rat female


title: Ovary_F3-Control_biological rep1

description:
Ovary  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-Ovary_F3-Con1-100110-37.CEL

source_name: Ovary from F3-generation control lineage (vehicle) rat female


title: Ovary_F3-Control_biological rep3

description:
Ovary  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-Ovary_F3-Con3-100110-39.CEL


title: Female liver_F3-Vinclozolin_biological rep3

description:
Liver  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-FM-Liver_F3-Vin3-091510-30.CEL


title: Ovary_F3-Vinclozolin_biological rep3

description:
Ovary  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-Ovary_F3-Vin3-100110-42.CEL


title: Female liver_F3-Control_biological rep2

description:
Liver  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-FM-Liver_F3-Con1-091510-25.CEL


title: Female kidney_F3-Vinclozolin_biological rep3

description:
Kidney  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-FM-Kidn_F3-Vin3-071910-18.CEL

source_name: Kidney from F3-generation Vinclozolin lineage rat female


title: Ovary_F3-Control_biological rep2

description:
Ovary  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-Ovary_F3-Con2-100110-38.CEL


title: Female liver_F3-Vinclozolin_biological rep2

description:
Liver  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-FM-Liver_F3-Vin2-091510-29.CEL


title: Female kidney_F3-Vinclozolin_biological rep2

description:
Kidney  from 120 days old F3-generation Vinclozolinlineage female rat
Marina-FM-Kidn_F3-Vin2-071910-17.CEL


title: Female kidney_F3-Control_biological rep3

description:
Kidney  from 120 days old F3-generation control (vehicle) lineage female rat
Marina-FM-Kidn_F3-Con3-071910-15.CEL

source_name: Kidney from F3-generation control lineage (vehicle) rat female