title: 495_liver


title: 542_liver

status: Public on Jan 08 2015

type: RNA

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 16 week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

tag: tissue

value: liver

tag: gender

value: male

tag: age

value: 16 weeks

tag: strain


title: 517_liver


title: 502_liver


title: 528_liver

value: SEA/GnJ


title: 526_liver

value: female


title: 471_liver


title: 487_liver


title: 486_liver


title: 490_liver


title: 457_liver


title: 494_liver


title: 455_liver


title: 529_liver


title: 460_liver


title: 450_liver


title: 461_liver


title: 463_liver

value: RIIIS/J


title: 452_liver


title: 470_liver


title: 439_liver


title: 446_liver


title: 491_liver


title: 464_liver


title: 447_liver


title: 468_liver


title: 469_liver


title: 441_liver


title: 449_liver


title: 436_liver


title: 458_liver


title: 440_liver


title: 432_liver


title: 435_liver


title: 438_liver


title: 418_liver


title: 429_liver


title: 430_liver


title: 393_liver


title: 431_liver


title: 404_liver


title: 397_liver

value: BUB/BnJ


title: 422_liver


title: 400_liver


title: 382_liver


title: 403_liver


title: 387_liver


title: 377_liver


title: 360_liver


title: 384_liver


title: 388_liver


title: 361_liver


title: 398_liver


title: 368_liver


title: 392_liver


title: 386_liver


title: 417_liver


title: 369_liver


title: 373_liver


title: 374_liver


title: 365_liver


title: 421_liver


title: 381_liver


title: 401_liver


title: 357_liver


title: 355_liver


title: 358_liver


title: 354_liver


title: 556_liver


title: 347_liver


title: 328_liver


title: 298_liver


title: 337_liver


title: 340_liver


title: 336_liver


title: 343_liver


title: 311_liver


title: 310_liver


title: 332_liver


title: 318_liver

value: LG/J


title: 316_liver


title: 297_liver


title: 285_liver


title: 329_liver


title: 303_liver


title: 346_liver


title: 339_liver


title: 296_liver


title: 344_liver


title: 288_liver


title: 287_liver


title: 302_liver


title: 321_liver


title: 284_liver


title: 295_liver


title: 279_liver


title: 276_liver


title: 278_liver


title: 275_liver


title: 256_liver

value: MA/MyJ


title: 265_liver


title: 248_liver


title: 264_liver


title: 236_liver


title: 242_liver


title: 225_liver


title: 254_liver


title: 272_liver


title: 217_liver


title: 240_liver


title: 252_liver


title: 247_liver


title: 233_liver


title: 251_liver


title: 220_liver


title: 243_liver


title: 213_liver


title: 234_liver


title: 235_liver


title: 216_liver


title: 224_liver


title: 221_liver


title: 214_liver


title: 210_liver


title: 209_liver


title: 206_liver


title: 201_liver


title: 205_liver


title: 200_liver


title: 194_liver


title: 193_liver


title: 181_liver


title: 185_liver


title: 184_liver


title: 171_liver

value: SWR/J


title: 188_liver


title: 180_liver


title: 160_liver

value: BALB/cJ


title: 150_liver


title: 189_liver


title: 168_liver


title: 143_liver

value: PL/J


title: 146_liver


title: 149_liver


title: 179_liver


title: 167_liver


title: 174_liver


title: 142_liver


title: 159_liver


title: 170_liver


title: 144_liver


title: 139_liver


title: 177_liver


title: 138_liver


title: 137_liver


title: 134_liver


title: 133_liver


title: 131_liver


title: 94_liver


title: 92_liver


title: 90_liver


title: 80_liver

value: NON/SHiLtJ


title: 72_liver


title: 79_liver


title: 91_liver


title: 111_liver

value: KK/HlJ


title: 60_liver


title: 65_liver


title: 85_liver


title: 64_liver


title: 71_liver


title: 110_liver


title: 83_liver


title: 58_liver

value: FVB/NJ


title: 57_liver


title: 47_liver

value: AKR/J


title: 28_liver

value: A/J


title: 42_liver

value: liver

value: SJL/J


title: 46_liver

value: male

value: 16 weeks


title: 26_liver

value: female


title: 62_liver


title: 1500_adipose

source_name: gonadal adipose tissue

value: gonadal adipose


title: 1494_adipose

value: NZB/BlNJ


title: 1493_adipose


title: 43_liver


title: 1495_adipose


title: 1485_adipose


title: 1492_adipose


title: 1484_adipose


title: 1488_adipose


title: 1499_adipose


title: 1463_adipose


title: 1466_adipose


title: 1465_adipose


title: 1451_adipose

value: I/LnJ


title: 1455_adipose


title: 1462_adipose


title: 1452_adipose


title: 1453_adipose


title: 1448_adipose


title: 1489_adipose


title: 1437_adipose


title: 1439_adipose


title: 1436_adipose


title: 1430_adipose


title: 1432_adipose


title: 1449_adipose


title: 1365_adipose


title: 1435_adipose


title: 1416_adipose

value: CE/J


title: 1395_adipose


title: 1325_adipose


title: 1340_adipose


title: 1406_adipose


title: 1350_adipose

value: SM/J


title: 1347_adipose


title: 1352_adipose


title: 1355_adipose


title: 1359_adipose


title: 1357_adipose


title: 1358_adipose


title: 1393_adipose


title: 1364_adipose


title: 1307_adipose


title: 1354_adipose


title: 1312_adipose


title: 1276_adipose


title: 1278_adipose


title: 173_liver


title: 1270_adipose

value: NZW/LacJ


title: 1272_adipose


title: 1275_adipose


title: 1271_adipose


title: 1268_adipose

value: LP/J


title: 1257_adipose


title: 1241_adipose


title: 1259_adipose


title: 1246_adipose


title: 1253_adipose


title: 1237_adipose


title: 1236_adipose


title: 1230_adipose


title: 1222_adipose


title: 1233_adipose


title: 1191_adipose


title: 1192_adipose


title: 1210_adipose


title: 1221_adipose


title: 1245_adipose


title: 1208_adipose


title: 1254_adipose


title: 1265_adipose


title: 1239_adipose


title: 1209_adipose


title: 1235_adipose


title: 1182_adipose


title: 1188_adipose


title: 1181_adipose


title: 1211_adipose


title: 1242_adipose


title: 1187_adipose


title: 1160_adipose


title: 1150_adipose


title: 1151_adipose


title: 1148_adipose


title: 1133_adipose


title: 1149_adipose


title: 1082_adipose


title: 1073_adipose


title: 1075_adipose


title: 1110_adipose


title: 1079_adipose


title: 1162_adipose


title: 1076_adipose


title: 1132_adipose


title: 1071_adipose


title: 1078_adipose


title: 1070_adipose


title: 1081_adipose


title: 1064_adipose


title: 1059_adipose


title: 1063_adipose


title: 1060_adipose


title: 1050_adipose


title: 1048_adipose


title: 1111_adipose


title: 1069_adipose


title: 1004_adipose


title: 1010_adipose


title: 1006_adipose


title: 995_adipose


title: 1047_adipose


title: 998_adipose


title: 1012_adipose


title: 1002_adipose


title: 994_adipose


title: 983_adipose


title: 1007_adipose


title: 986_adipose

value: NOD/ShiLtJ


title: 1052_adipose


title: 991_adipose


title: 985_adipose


title: 1003_adipose


title: 981_adipose


title: 976_adipose


title: 972_adipose


title: 1000_adipose


title: 978_adipose


title: 964_adipose


title: 965_adipose


title: 969_adipose


title: 961_adipose


title: 937_adipose


title: 914_adipose


title: 916_adipose


title: 960_adipose


title: 936_adipose


title: 897_adipose


title: 917_adipose


title: 973_adipose


title: 895_adipose


title: 915_adipose


title: 905_adipose


title: 887_adipose


title: 903_adipose


title: 890_adipose


title: 885_adipose


title: 894_adipose


title: 884_adipose


title: 891_adipose


title: 879_adipose


title: 874_adipose


title: 880_adipose


title: 886_adipose


title: 873_adipose


title: 872_adipose


title: 867_adipose


title: 866_adipose


title: 883_adipose


title: 881_adipose


title: 898_adipose


title: 861_adipose


title: 848_adipose


title: 889_adipose


title: 863_adipose


title: 869_adipose


title: 811_adipose

value: BTBR T<+> tf/J


title: 831_adipose


title: 847_adipose


title: 799_adipose


title: 837_adipose


title: 857_adipose


title: 862_adipose


title: 808_adipose


title: 800_adipose


title: 788_adipose


title: 865_adipose


title: 791_adipose


title: 792_adipose


title: 767_adipose


title: 765_adipose


title: 762_adipose


title: 743_adipose


title: 763_adipose


title: 766_adipose


title: 744_adipose


title: 738_adipose


title: 733_adipose


title: 728_adipose


title: 707_adipose


title: 717_adipose


title: 764_adipose


title: 732_adipose


title: 714_adipose


title: 706_adipose


title: 735_adipose


title: 715_adipose


title: 698_adipose


title: 696_adipose


title: 699_adipose


title: 700_adipose


title: 691_adipose

value: CBA/J


title: 719_adipose


title: 690_adipose


title: 786_adipose


title: 697_adipose


title: 695_adipose


title: 686_adipose


title: 688_adipose


title: 666_adipose


title: 646_adipose


title: 651_adipose

value: FVB/NJ


title: 671_adipose


title: 659_adipose


title: 642_adipose


title: 648_adipose


title: 640_adipose


title: 643_adipose


title: 647_adipose


title: 665_adipose


title: 608_adipose


title: 631_adipose

value: MA/MyJ


title: 669_adipose


title: 606_adipose


title: 591_adipose

value: BALB/cJ


title: 599_adipose


title: 584_adipose


title: 600_adipose


title: 592_adipose


title: 632_adipose


title: 579_adipose


title: 578_adipose


title: 582_adipose


title: 577_adipose


title: 639_adipose


title: 576_adipose


title: Brain_Male_A20

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

hyb_protocol: Equal amounts of labeled target sample cRNA (600 ng) samples were hybridized to each individual array. Microarray hybridization conditions and washing procedures were performed as described in Agilent Gene Analysis protocols (One Color Microarray-Based Gene Expression Analysis, Version 6.5).

scan_protocol: Microarray slides were scanned using Profile AgilentG3_GX_1Color and the scan data were extracted using Agilent Feature Extraction Software.

data_processing: Partek® Genomic Suite (v6.6) was used to generate the matrix table. gProcessedSignal data were quantile normalized and log2 transformed.

organism: Lates calcarifer

source_name: Brain from adult male with M3-stage testis

label_protocol: All microarray was carried out on Agilent SurePrint G3 custom gene expression 8X60K oligonucleotide array (Cat No. G4102A).Total RNA (100 ng) was reverse transcribed and labeled using Agilent Low Input Quick Amp One Color labeling kit (Cat No. 5190-2305) according to the manufacturer’s instructions. cRNA samples were labeled with cyanine 3-CTP and the amount of cyanine 3-labeled cRNA was determined using NanoDrop. Only labeled cRNA samples with cRNA yields > 0.825 µg and specific activity > 6 pmol Cy3 per µg cRNA were selected for hybridization.

growth_protocol: None.

extract_protocol: The whole brain, including pituitary, was homogenized using a sterile scapel and a small quantity of the homogenized sample was used for total RNA extraction using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quantity and quality was determined using spectrophotometer (NanoDrop) and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively. Only RNA samples with RIN number >8 were used for microarray analysis.

treatment_protocol: None.

value: Brain

tag: Sex

value: Male

value: Adult; 5 years old


title: 572_adipose

value: male

value: 16 weeks


title: 561_adipose

value: gonadal adipose


title: 573_adipose


title: Brain_Female_A22

source_name: Brain from adult female with F3-stage ovary

value: Female


title: Brain_Male_A19


title: Brain_Female_A15


title: 547_adipose


title: 570_adipose

value: female


title: 557_adipose


title: 546_adipose


title: 542_adipose


title: Brain_Male_A18


title: Brain_Male_A17


title: Gonad_Undifferentiated_B1

source_name: Undifferentiated Gonads; 4.5 months old fish

extract_protocol: Total RNA was extracted from the gonads using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quantity and quality was determined using spectrophotometer (NanoDrop) and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively. Only RNA samples with RIN number >8 were used for microarray analysis.

value: Gonads (Undifferentiated)

value: Juvenile; 4.5 months old


title: Brain_Female_A14


title: 562_adipose


title: 556_adipose


title: 537_adipose


title: Gonad_Undifferentiated_B3


title: Brain_Female_A25


title: Gonad_Undifferentiated_B4


title: Gonad_Undifferentiated_B2


title: Gonad_Late Transforming_PSB18

source_name: Late Transforming Gonad (T3/T4-stage); >2 years old fish

value: Gonads (Transiting, T3/T4)

value: Adult; >2 years old


title: 538_adipose


title: 540_adipose


title: Gonad_Late Transforming_PSB04


title: Gonad_Late Transforming_PSB16


title: 528_adipose

value: SEA/GnJ


title: Gonad_Early Transforming_TSB11

source_name: Early Transforming Gonad (T1/T2-stage); >2 years old fish

value: Gonads (Transiting, T1/T2)


title: 534_adipose


title: Gonad_Early Transforming_PSB08


title: Gonad_Late Transforming_PSB01


title: 523_adipose


title: 522_adipose


title: 529_adipose


title: Gonad_Early Transforming_PSB02


title: 526_adipose


title: 521_adipose


title: Gonad_Early Testis_E1

source_name: Early Testis (M3-stage); 8 months old fish

value: Gonads (M3 Testis-like)

value: Juvenile; 8 months old


title: Gonad_Early Testis_E2


title: 524_adipose


title: Gonad_Early Testis_9MSB1

source_name: Early Testis (M3-stage); 9 months old fish

value: Juvenile; 9 months old


title: 525_adipose


title: Gonad_Adult Testis_A3

source_name: Adult Testis (M3-stage); 5 years old fish

value: Gonads (Testis, M3)


title: 727_adipose


title: Gonad_Adult Testis_A19


title: 514_adipose


title: Gonad_Adult Ovary_A25

source_name: Adult Ovary (F3-stage); 5 years old fish

value: Gonads (Ovary, F3)


title: 516_adipose


title: Gonad_Adult Testis_A18.2

value: Adult; 5 years old


title: Gonad_Adult Ovary_A22


title: 517_adipose

value: male


title: 490_adipose

value: 16 weeks


title: 536_adipose

value: gonadal adipose


title: 495_adipose


title: 491_adipose


title: 513_adipose


title: 494_adipose


title: 502_adipose


title: Gonad_Adult Ovary_A15


title: Gonad_Adult Ovary_A14


title: 501_adipose


title: 486_adipose


title: 469_adipose

value: RIIIS/J


title: 467_adipose

value: female


title: 487_adipose


title: 466_adipose


title: 461_adipose


title: 464_adipose


title: 463_adipose


title: 460_adipose


title: 455_adipose


title: 457_adipose


title: 452_adipose


title: 450_adipose


title: 458_adipose


title: 447_adipose


title: 440_adipose


title: 449_adipose


title: 441_adipose


title: 446_adipose


title: 439_adipose


title: 432_adipose


title: 431_adipose


title: 426_adipose


title: 435_adipose


title: 436_adipose


title: 429_adipose


title: 418_adipose


title: 438_adipose


title: 430_adipose


title: 404_adipose


title: 400_adipose

value: BUB/BnJ


title: 401_adipose


title: 422_adipose


title: 421_adipose


title: 397_adipose


title: 392_adipose


title: 388_adipose


title: 393_adipose


title: 417_adipose


title: 403_adipose


title: 382_adipose


title: 365_adipose


title: 387_adipose


title: 386_adipose


title: 369_adipose


title: 360_adipose


title: 368_adipose


title: 359_adipose


title: 384_adipose


title: 361_adipose


title: 377_adipose


title: 367_adipose


title: 374_adipose


title: 363_adipose


title: 362_adipose


title: 357_adipose


title: 378_adipose


title: 347_adipose


title: 344_adipose


title: 373_adipose


title: 337_adipose


title: 339_adipose


title: 354_adipose


title: 342_adipose


title: 340_adipose


title: 355_adipose


title: 346_adipose


title: 398_adipose


title: 329_adipose


title: 336_adipose


title: 321_adipose


title: 314_adipose


title: 310_adipose


title: 316_adipose

value: LG/J


title: 295_adipose


title: 312_adipose


title: 328_adipose


title: 318_adipose


title: 302_adipose


title: 296_adipose


title: 298_adipose


title: 276_adipose


title: 285_adipose


title: 284_adipose


title: 287_adipose


title: 297_adipose


title: 288_adipose


title: 311_adipose


title: 275_adipose


title: 279_adipose


title: 303_adipose


title: 271_adipose


title: Gonad_Adult Testis_A20


title: 263_adipose


title: 278_adipose


title: 256_adipose

value: MA/MyJ


title: 254_adipose


title: 243_adipose


title: 242_adipose


title: 246_adipose


title: 244_adipose


title: 236_adipose


title: 224_adipose


title: Whole Hippocampus TBI+E33 drug rep2

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: Gene expression of whole hippocampus 24hr post-injury

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: Whole hippocampus, fluid percussion injury, E33 drug treatment, rep2

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using Arcturus RiboAmp HS reagents (Molecular Devices, Sunnyvale, CA).  Alternatively, MessageAMP II (Applied Biosystems, Foster City, CA) was used.  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Rats were subjected to experimental severe fluid percussion brain injury,  with and without drug treatment, sham injury or were sacrificed with no treatment (naïve) and brains were removed 24 hours later, hippocampi microdissected and stored in RNA later. JM6 and PMI were administered by oral gavage and E33 administered subcutaneously.

value: Sprague-Dawley

value: hippocampus


title: 239_adipose


title: Whole Hippocampus TBI+JM6 drug rep2

source_name: Whole hippocampus, fluid percussion injury, JM6 drug treatment, rep2


title: 247_adipose


title: Whole Hippocampus TBI+E33 drug rep1

source_name: Whole hippocampus, fluid percussion injury, E33 drug treatment, rep1


title: 221_adipose


title: 235_adipose


title: Whole Hippocampus TBI+PMI drug rep1

source_name: Whole hippocampus, fluid percussion injury, PMI drug treatment, rep1


title: 220_adipose


title: Whole Hippocampus TBI+PMI drug rep3

source_name: Whole hippocampus, fluid percussion injury, PMI drug treatment, rep3


title: Whole Hippocampus Traumatic Brain Injury rep3

source_name: Whole hippocampus, fluid percussion injury, rep3


title: Whole Hippocampus TBI+PMI drug rep2

source_name: Whole hippocampus, fluid percussion injury, PMI drug treatment, rep2


title: Whole Hippocampus TBI+JM6 drug rep1

source_name: Whole hippocampus, fluid percussion injury, JM6 drug treatment, rep1


title: 216_adipose

source_name: gonadal adipose tissue


title: Whole Hippocampus TBI+JM6 drug rep3

source_name: Whole hippocampus, fluid percussion injury, JM6 drug treatment, rep3


title: 265_adipose


title: 272_adipose


title: Whole Hippocampus Traumatic Brain Injury rep2

source_name: Whole hippocampus, fluid percussion injury, rep2


title: 225_adipose


title: 214_adipose


title: 252_adipose


title: 217_adipose


title: Whole Hippocampus Traumatic Brain Injury rep1

source_name: Whole hippocampus, fluid percussion injury, rep1


title: 201_adipose


title: Whole Hippocampus Naïve rep2

source_name: Whole hippocampus, no treatment, rep2


title: 210_adipose


title: 209_adipose


title: Whole Hippocampus Sham rep1

source_name: Whole hippocampus, Sham injury, rep1


title: 185_adipose


title: Carcinoma in situ_2 (CIS, double transgene)

city: New York

first: Feng

last: He

address: 423 E23rd Street

institute: New York University

description: gene expression data from carcinoma in situ

hyb_protocol: Prepare hybridization cocktail using the GeneChip Hybridization Wash and Stain Kit and hybridize arrays according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data was processed by importing CEL files into Partek Genomics Suite Software and RMA normalization was performed.  A 1-way ANOVA was then used to generate fold changes.

label: 3' IVT

source_name: Bladder urothelium

label_protocol: 100 ng of each sample was labeled using the Affymetrix IVT expression Kit accoring to the manufacturer's protocol. Normal aRNA yield is about 60 ug.

growth_protocol: The transgenic mice and normal mice were sacrificed at 8-month-old age, when the H-rastransgenic and p53 knockout mice had developed high-grade invasive carcinomas in the bladders.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the instructions.

treatment_protocol: The bladder tissues were treated with liquid nitrogen, embedded with OCT medium, and then cut into frozen sections. A quick H&E staining was performed before processing LCM. The dissected cells were collected for RNA extraction.

value: 8 month

value: FVB/N

tag: genotype

value: carcinoma in situ


title: 213_adipose


title: 189_adipose


title: Whole Hippocampus Naïve rep3

source_name: Whole hippocampus, no treatment, rep3


title: Invasive carcinoma_1 (tumor, double transgene)

description: gene expression data from invasive carcinomas

value: invasive carcinomas


title: Whole Hippocampus Sham rep2

source_name: Whole hippocampus, Sham injury, rep2


title: 251_adipose


title: 193_adipose


title: Invasive carcinoma_2 (tumor, double transgene)


title: 177_adipose


title: 184_adipose


title: Normal urothelium_2 (Wild-type)

description: gene expression data from normal urothelium

value: wide type

value: normal urothelium


title: 179_adipose


title: 194_adipose


title: 200_adipose


title: Whole Hippocampus Naïve rep1

source_name: Whole hippocampus, no treatment, rep1


title: 206_adipose


title: 188_adipose


title: 171_adipose

value: SWR/J


title: 173_adipose

value: male


title: 205_adipose

value: 16 weeks


title: 174_adipose

value: gonadal adipose


title: Carcinoma in situ_1 (CIS, double transgene)


title: 170_adipose


title: 168_adipose


title: 167_adipose


title: 160_adipose

value: BALB/cJ


title: Normal urothelium_1 (Wild-type)


title: 149_adipose


title: BXD98 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD98_3_H5_Exp]

city: St Louis

first: Adrianus

middle: Cornelis Maria

last: Boon

state: Missouri

address: 660 Euclid Avenue

department: Department of Medicine

institute: Washington University School of Medicine

description: Gene expression data from lungs of highly pathogenic H5N1 influenza A virus infected mice

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analysed with Affymetrix CGOS software version 1.4. The default parameters were used to generate the signal values and detection calls. Signal values were scaled to a 2% trimmed mean target value of 500.

source_name: Highly Pathogenic H5N1 Influenza A virus infected; 72 hours

label_protocol: Affymetrix eukaryotic one-cycle target-labeling protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The extracted RNA was subjected to a RNA clean-up protocol (Qiagen) according to manufacturer's instructions.

treatment_protocol: Inoculated with 10000 Egg infectious units of A/Hong Kong/213/2003 H5N1 influenza A virus for 72 hours

value: 6-8wk old

value: female


title: 144_adipose


title: 146_adipose


title: 159_adipose


title: BXD98 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD98_2_H5_Exp]


title: 111_adipose

value: KK/HlJ


title: BXD83 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD83_3_H5_Exp]


title: BXD97 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD97_1_H5_Exp]


title: 150_adipose


title: 94_adipose

value: PL/J


title: 134_adipose


title: 110_adipose


title: 139_adipose


title: 129_adipose


title: 131_adipose


title: 138_adipose


title: 143_adipose


title: BXD98 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD98_1_H5_Exp]


title: 142_adipose


title: BXD83 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD83_1_H5_Exp]


title: BXD97 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD97_3_H5_Exp]


title: 92_adipose


title: 85_adipose


title: 133_adipose


title: BXD97 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD97_2_H5_Exp]


title: 90_adipose


title: 83_adipose


title: BXD83 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD83_2_H5_Exp]


title: 91_adipose


title: BXD73 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD73_1_H5_Exp]


title: BXD73 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD73_3_H5_Exp]


title: 80_adipose

value: NON/SHiLtJ


title: 79_adipose


title: 47_adipose

value: AKR/J


title: 64_adipose


title: 72_adipose


title: BXD73 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD73_2_H5_Exp]


title: BXD68 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD68_3_H5_Exp]


title: 62_adipose


title: BXD67 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD67_2_H5_Exp]


title: 71_adipose


title: BXD68 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD68_2_H5_Exp]


title: BXD67 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD67_1_H5_Exp]


title: 65_adipose


title: 43_adipose

value: SJL/J


title: 58_adipose

value: FVB/NJ


title: 60_adipose


title: BXD68 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD68_1_H5_Exp]


title: BXD67 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD67_3_H5_Exp]


title: BXD43 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD43_2_H5_Exp]


title: BXD43 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD43_3_H5_Exp]


title: 57_adipose


title: 42_adipose


title: 46_adipose


title: Allograft undergoing chronic allograft nephropathy 9

city: San Francisco

first: Matthew

middle: James

last: Vitalone

state: CA

address: 475 Brannan st

department: BIOMARC

institute: CPMCRI

description: Renal allograft

hyb_protocol: We followed Agilent’s hybridization protocol. Equal amounts of the exposed and negative control sample (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.

scan_protocol: We followed Agilent’s scan protocol. The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies, Palo Alto, CA), and further processed using Agilent Feature Extraction Software.

data_processing: GeneSpring was used for normalization. We used a cut off for absolute value of log2red channel/green channel >0.5 for at least one array; data was processed and normalized using LOWESS method by GeneSpring GX7.3.

organism: Homo sapiens

source_name: cells from allografts with chronic injury

label_protocol: Cy5-CTP (transplant samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions

extract_protocol: The blood was drawn in the presence of sodium heparin.  PBMC were isolated by density separation over Ficoll solution. Mononuclear cells at the interface were washed twice with phosphate buffered saline (PBS). Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).

tag: sample type

value: allografts with chronic injury

value: PBMCs

source_name: pooled human cell lines (n=21)

value: cultured cell lines


title: Allograft undergoing chronic allograft nephropathy 10

description: Renal allograft


title: BXD43 Recombinant inbred mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [BXD43_1_H5_Exp]


title: Allograft undergoing chronic allograft nephropathy 4

description: Renal allograft


title: C57BL/6J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [C57_1_H5_Exp]


title: Allograft undergoing chronic allograft nephropathy 1

description: Renal allograft


title: Allograft undergoing chronic allograft nephropathy 6

description: Renal allograft


title: C57BL/6J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [C57_4_H5_Exp]


title: Allograft undergoing chronic allograft nephropathy 3

description: Renal allograft


title: non-transplant healthy donor 1

description: Non-transplant

source_name: cells from non-transplant healthy donors

value: non-transplant healthy donors


title: non-transplant healthy donor 4

description: Non-transplant


title: C57BL/6J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [C57_3_H5_Exp]


title: C57BL/6J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [C57_2_H5_Exp]


title: non-transplant healthy donor 5

description: Non-transplant


title: C57BL/6J mouse strain. Lung homogenate uninfected  [C57_6_Un_Exp]

description: Gene expression data from lungs of unfected mice

source_name: Uninfected control


title: Allograft undergoing chronic allograft nephropathy 7

description: Renal allograft


title: C57BL/6J mouse strain. Lung homogenate uninfected  [C57_5_Un_Exp]


title: Allograft undergoing chronic allograft nephropathy 5

description: Renal allograft


title: Allograft undergoing chronic allograft nephropathy 2

description: Renal allograft


title: non-transplant healthy donor 3

description: Non-transplant


title: Tolerant allograft 14

description: Renal allograft

source_name: cells from tolerant allografts

value: tolerant allografts


title: Tolerant allograft 16

description: Renal allograft


title: non-transplant healthy donor 2

description: Non-transplant


title: Tolerant allograft 13

description: Renal allograft


title: Allograft undergoing chronic allograft nephropathy 8

description: Renal allograft


title: Tolerant allograft 15

description: Renal allograft


title: DBA/2J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [DBA_4_H5_Exp]


title: Tolerant allograft 10

description: Renal allograft


title: Tolerant allograft 11

description: Renal allograft


title: C57BL/6J mouse strain. Lung homogenate uninfected  [C57_4_Un_Exp]


title: Tolerant allograft 7

description: Renal allograft


title: DBA/2J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [DBA_1_H5_Exp]


title: DBA/2J mouse strain. Lung homogenate uninfected  [DBA_6_Un_Exp]


title: Tolerant allograft 12

description: Renal allograft


title: Tolerant allograft 9

description: Renal allograft


title: Tolerant allograft 8

description: Renal allograft


title: DBA/2J mouse strain. Lung homogenate uninfected  [DBA_3_Un_Exp]


title: DBA/2J mouse strain. Lung homogenate uninfected  [DBA_7_Un_Exp]


title: DBA/2J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [DBA_2_H5_Exp]


title: DBA/2J mouse strain. Lung homogenate 72 hours post H5N1 influenza A virus infection [DBA_3_H5_Exp]


title: DBA/2J mouse strain. Lung homogenate uninfected  [DBA_4_Un_Exp]


title: NRK52E_control

city: Kyoto

first: Shunsaku

last: Nakagawa

address: Kawahara-cho

department: Department of Pharmacy

country: Japan

institute: Kyoto University Hospital

hyb_protocol: 1.0 ug of cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The assay signals were normalized with each median.

source_name: NRK52E cells, control

label_protocol: Cyanine-3-labeled complementary (c) RNA was generated with Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the Spectrophotometer.

growth_protocol: NRK-52E cells were seeded in 6-well plates and cultured in DMEM with 10% FBS to 100% confluence before being starved in DMEM with hydrogen peroxide.

extract_protocol: Total RNA was extracted from NRK-52E cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was quantified using a spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were treated with hydrogen peroxide (0, 0.003, 0.006, 0.009% in DMEM) for 1 hour. After wash with PBS, cells were incubated with non-serum DMEM for 12 hours.

tag: treatment

value: control

value: kidney

tag: cell line


title: NRK52E_0.009

source_name: NRK52E cells, hydrogen peroxide, 0.009%

value: hydrogen peroxide 0.009%


title: NRK52E_0.006

source_name: NRK52E cells, hydrogen peroxide, 0.006%

value: hydrogen peroxide 0.006%


title: Germ-free_cholic_acid_diet

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: Standard Affymetrix protocols

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA, unlogged using R

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: An approximately 5 mm2 section of frozen liver tissue was placed in a 2.0 ml tube with a steel bead and 1ml Trizol reagent (Invitrogen).  Following disruption in a Qiagen Tissuelyser 200ul of chloroform was added to the homogenate, mixed and centrifuged.  The aqueous layer containing the RNA was transferred to a tube containing 500ul of ice cold isopropanol and mixed.  This mixture was loaded onto an RNeasy spin column (Qiagen) and RNA was washed and eluted as per manufacturer’s instructions.  For microarray analysis, the integrity and concentration of RNA was determined on an Experion instrument (BioRad). Samples were pooled based on experimental condition.

treatment_protocol: Conventional and germ free mice were maintained on purified diet, cholic acid diet or deoxycholic acid diet for two weeks.  After being fasted overnight animals were anesthetized with isoflurane and liver and bile samples were collected and snap frozen for further analysis.

value: Swiss Webster

tag: genotype/variation

value: Germ-free

tag: diet


title: Germ-free_DCA_diet


title: Tolerant allograft 5

description: Renal allograft


title: Tolerant allograft 1

description: Renal allograft


title: Conventional_DCA_diet

value: Conventional


title: Tolerant allograft 4

description: Renal allograft


title: NRK52E_0.003

source_name: NRK52E cells, hydrogen peroxide, 0.003%

value: hydrogen peroxide 0.003%


title: Tolerant allograft 6

description: Renal allograft


title: Germ-free_purified_diet


title: Conventional_cholic_acid_diet


title: Tolerant allograft 3

description: Renal allograft


title: glp-4_polysomal_4

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

hyb_protocol: hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix)

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing:
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probeId_to_tr_min10probes.tab
RMA signal estimates (total and polysomal samples were quantile normalized separately)

organism: Caenorhabditis elegans

source_name: whole worm lysate of young adults

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix, fragmented and Biotin labeled using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)

growth_protocol: Worms were grown until the young adult stage, washed in cold M9, and washed and frozen in washing buffer.

extract_protocol: RNA from total and polysomal sucrose fractions was extracted using Trizol

treatment_protocol: Worm lysates were prepared in extraction buffer and subjected to sucrose density gradient ultracentrifugation; the gradients were fractionated into 12 samples

value: glp-4 (bn2) mutant


title: DBA/2J mouse strain. Lung homogenate uninfected  [DBA_5_Un_Exp]

value: 6-8wk old

value: female


title: glp-4_polysomal_2


title: glp-4_polysomal_1


title: glp-4_total_4


title: glp-4_total_2


title: glp-4_total_1


title: glp-4_polysomal_3


title: Tolerant allograft 2

description: Renal allograft


title: bbx24 in Simulated Shade, biological rep2

city: Buenos Aires

first: Carlos

middle: Daniel

last: Crocco

state: Buenos Aires

address: Av. San Martín 4453

country: Argentina

institute: University of Buenos Aires - IFEVA - CONICET

description: Gene expression data from bbx24 mutant seedlings under simulated shade conditions

hyb_protocol: Hybridized for 16 hours at 45oC on GeneChip Arabidopsis Genome Array

scan_protocol: GeneChip scanned with the Affymetrix GeneChip Scanner 3000

data_processing: Data were normalized by multiplying the value of each gene by the mean of each chip, divided by the average intensity of all mean values. Significantly differentially expressed genes were identified by performing profile analysis using Significance Analysis of Microarrays (SAM) software (Tusher et al., 2001)

organism: Arabidopsis thaliana

source_name: bbx24 seedlings grown under simulated shade

label_protocol: Biotynlated aRNA were prepared according to the standard ATH1 affymetrix protocol for 5 ug total RNA.

growth_protocol: Seedlings grown under while light or simulated shade conditions

extract_protocol: For RNA expression, 100 mg of fresh seedlings was harvested and frozen immediately in liquid nitrogen. Total RNA was extracted using an RNeasy plant mini kit (Qiagen, http://www.qiagen.com). Crude RNA preparations were treated with 10 units of RNase-free DNase I (http://www.promega.com), and the samples were purified according to the RNeasy plant mini kit protocol.

treatment_protocol: The microarray experiment consisted in a factorial design comprising two genotypes (col and bbx24-1) and two light treatments (white light and simulated shade).  RNA material was extracted from 7-day-old seedlings. Two replicates per treatment were performed using Affymetrix Arabidopsis ATH1 GeneChip® (http://www.affymetrix.com).

value: 7-d-old seedlings

value: seedling

value: shade

value: bbx24 mutant

tag: genetic background


title: Wild type in Simulated Shade, biological rep2

description: Gene expression data from wild type (col) seedlings under simulated shade conditions

source_name: col seedlings grown under simulated shade

value: wild type


title: bbx24 in With Light, biological rep2

description: Gene expression data from bbx24 mutant seedlings under white light conditions

source_name: bbx24 seedlings grown under white light

value: light


title: Wild type in simulated shade, biological rep1


title: glp-4_total_3


title: Wild type in With Light, biological rep1

description: Gene expression data from wild type (col) seedlings under white light conditions

source_name: col seedlings grown under white light


title: GIST882_basal

city: Cambridge

first: Fang

last: Li

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research, Inc.

description: Basal gene expression data from GIST882

hyb_protocol: Following fragmentation cRNA was hybridized at 45ºC for approximately 18 hours, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console 1.3 and the default analysis settings. The trimmed mean target intensity of each array was set to 150.

source_name: Human cell line harvested 20 hours after splitting

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 µg total RNA.

growth_protocol: GIST cell lines were split 20 hours prior to harvest.  Cells were harvested at 70% confluence.

extract_protocol: Total RNA was extracted using Qiagen Rneasy Plus Mini Kit according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: lineage

value: Gastrointestinal Stromal Tumor


title: bbx24 in With Light, biological rep1


title: Wild type in With Light, biological rep2


title: Ov_Tumor_Ref_Mix  vs. 1761

status: Public on Jan 07 2015

city: Santa Monica

first: Judy

last: Dering

address: 2825 Santa Monica Blvd. Suite 200

department: Medicine

institute: UCLA School of Medicine

description:
reference_mix: The reference mix contained equal amounts of 106 ovarian samples including the following histologies: adenocarcinama=1, benign=4, clear cell= 3, endothelial=5, goblet cell=1, MMMT=5, mucinous=3. normal=7, serous=67, squamous=1, transitional cell=1, unknown=7
ovarian serous tumor sample

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505B scanner.  All  experiments were scanned with extended dynamic range enabled.

data_processing:
Agilent Feature Extraction Software (v9.5.1) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.

source_name: 106 pooled ovarian samples

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

value: ovarian

source_name: ovarian tumor 1761

tag: morphology

value: Serous

tag: Stage

value: IV

tag: grade

tag: debulking

value: Optimal

value: Dead


title: Ov_Tumor_Ref_Mix  vs. 1208

tag: tissue

source_name: ovarian tumor 1208

value: III

tag: substage

value: C

value: Alive


title: Ov_Tumor_Ref_Mix  vs. 1190

source_name: ovarian tumor 1190


title: Ov_Tumor_Ref_Mix  vs. 1234

source_name: ovarian tumor 1234


title: GIST-T1_basal

description: Basal gene expression data from GIST-T1


title: Ov_Tumor_Ref_Mix  vs. 1210

source_name: ovarian tumor 1210


title: GIST430_basal

description: Basal gene expression data from GIST430


title: bbx24 in Simulated Shade, biological rep1

tag: age


title: GIST48_basal

description: Basal gene expression data from GIST48


title: Ov_Tumor_Ref_Mix  vs. 1219

source_name: ovarian tumor 1219


title: Ov_Tumor_Ref_Mix  vs. 1181

source_name: ovarian tumor 1181


title: Ov_Tumor_Ref_Mix  vs. 1226

source_name: ovarian tumor 1226


title: ASC_muse-poor_rep1

city: Tsukuba

first: Hisako

last: Ishimine

state: Japan Ibaraki

address: higashi1-1-1 Tsukuba central 4

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression of muse-poor ASCs

hyb_protocol: 0.2 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile,  then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20111107 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.

source_name: human adipose tissue resident stem cells, SSEA-3(-)

label_protocol: RNA was labeled using the ‘Agilent Quick-Amp Labeling Kit’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.

growth_protocol: Liposuction aspirates were obtained from liposuction operation of the abdomen and thighs. The aspirated fat was washed with phosphate-buffered saline (PBS) and digested on a shaker at 37℃ in PBS containing 0.075% collagenase for 30 minutes. Mature adipocytes and connective tissue were separated from pellets by centrifugation.

extract_protocol: Total RNA were isolated from each samples using ISOGEN (Nippon Gene) and purified using Rneasy mini kit (QIAGEN) according to the manufactureres’ recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Muse cells that express human SSEA-3 were collected from SVF using anti SSEA-3 antibody conjugated with PE and anti-PE microbeads by magnetic cell separation (MACS) technology. SSEA-3-negative fraction was considered ‘Muse-poor population’.

tag: cell type

value: adipose-derived MSCs

tag: cell population


title: Ov_Tumor_Ref_Mix  vs. 1206

source_name: ovarian tumor 1206

value: Sub-optimal


title: Ov_Tumor_Ref_Mix  vs. 1221

source_name: ovarian tumor 1221


title: Ov_Tumor_Ref_Mix  vs. 1693

source_name: ovarian tumor 1693

value: II


title: ASC_muse-rich_rep1

description: Gene expression of muse-rich ASCs

source_name: human adipose tissue resident stem cells, SSEA-3(+)


title: Ov_Tumor_Ref_Mix  vs. 1176

source_name: ovarian tumor 1176


title: Ov_Tumor_Ref_Mix  vs. 1180

source_name: ovarian tumor 1180


title: Ov_Tumor_Ref_Mix  vs. 1155

source_name: ovarian tumor 1155


title: Ov_Tumor_Ref_Mix  vs. 1135

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 1135


title: Ov_Tumor_Ref_Mix  vs. 1125

source_name: ovarian tumor 1125


title: Ov_Tumor_Ref_Mix  vs. 1171

source_name: ovarian tumor 1171

value: Unknown


title: Ov_Tumor_Ref_Mix  vs. 1124

source_name: ovarian tumor 1124


title: Ov_Tumor_Ref_Mix  vs. 1099

source_name: ovarian tumor 1099


title: Ov_Tumor_Ref_Mix  vs. 1103

source_name: ovarian tumor 1103


title: Ov_Tumor_Ref_Mix  vs. 1089

source_name: ovarian tumor 1089


title: Ov_Tumor_Ref_Mix  vs. 1086

source_name: ovarian tumor 1086


title: Ov_Tumor_Ref_Mix  vs. 1038

source_name: ovarian tumor 1038


title: Ov_Tumor_Ref_Mix  vs. 1076

source_name: ovarian tumor 1076


title: Ov_Tumor_Ref_Mix  vs. 1072

source_name: ovarian tumor 1072


title: Ov_Tumor_Ref_Mix  vs. 1008

source_name: ovarian tumor 1008


title: Ov_Tumor_Ref_Mix  vs. 1131

source_name: ovarian tumor 1131


title: Ov_Tumor_Ref_Mix  vs. 1004

source_name: ovarian tumor 1004


title: Ov_Tumor_Ref_Mix  vs. 1090

source_name: ovarian tumor 1090


title: Ov_Tumor_Ref_Mix  vs. 1123

source_name: ovarian tumor 1123


title: Ov_Tumor_Ref_Mix  vs. 1037

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 1037


title: Ov_Tumor_Ref_Mix  vs. 992

source_name: ovarian tumor 992


title: Ov_Tumor_Ref_Mix  vs. 999

source_name: ovarian tumor 999


title: Ov_Tumor_Ref_Mix  vs. 1002

source_name: ovarian tumor 1002

value: A


title: Ov_Tumor_Ref_Mix  vs. 983

source_name: ovarian tumor 983


title: Ov_Tumor_Ref_Mix  vs. 1039

source_name: ovarian tumor 1039


title: Ov_Tumor_Ref_Mix  vs. 1016

source_name: ovarian tumor 1016


title: Ov_Tumor_Ref_Mix  vs. 1052

source_name: ovarian tumor 1052


title: Ov_Tumor_Ref_Mix  vs. 1033

source_name: ovarian tumor 1033

value: B


title: Ov_Tumor_Ref_Mix  vs. 1058

source_name: ovarian tumor 1058


title: Ov_Tumor_Ref_Mix  vs. 988

source_name: ovarian tumor 988


title: Ov_Tumor_Ref_Mix  vs. 973

source_name: ovarian tumor 973


title: Ov_Tumor_Ref_Mix  vs. 1094

source_name: ovarian tumor 1094


title: Ov_Tumor_Ref_Mix  vs. 965

source_name: ovarian tumor 965


title: Ov_Tumor_Ref_Mix  vs. 962

source_name: ovarian tumor 962


title: Conventional_purified_diet

tag: strain

value: Swiss Webster

value: Conventional


title: Ov_Tumor_Ref_Mix  vs. 964

source_name: ovarian tumor 964


title: Ov_Tumor_Ref_Mix  vs. 953

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 953


title: Ov_Tumor_Ref_Mix  vs. 969

source_name: ovarian tumor 969


title: Ov_Tumor_Ref_Mix  vs. 944

source_name: ovarian tumor 944


title: Ov_Tumor_Ref_Mix  vs. 956

source_name: ovarian tumor 956


title: Ov_Tumor_Ref_Mix  vs. 960

source_name: ovarian tumor 960


title: Ov_Tumor_Ref_Mix  vs. 939

source_name: ovarian tumor 939


title: Ov_Tumor_Ref_Mix  vs. 926

source_name: ovarian tumor 926


title: Ov_Tumor_Ref_Mix  vs. 870

source_name: ovarian tumor 870


title: Ov_Tumor_Ref_Mix  vs. 957

source_name: ovarian tumor 957


title: Ov_Tumor_Ref_Mix  vs. 952

source_name: ovarian tumor 952


title: Ov_Tumor_Ref_Mix  vs. 824

source_name: ovarian tumor 824


title: Ov_Tumor_Ref_Mix  vs. 846

source_name: ovarian tumor 846


title: Ov_Tumor_Ref_Mix  vs. 898

source_name: ovarian tumor 898


title: Ov_Tumor_Ref_Mix  vs. 855

source_name: ovarian tumor 855


title: Ov_Tumor_Ref_Mix  vs. 869

source_name: ovarian tumor 869


title: Ov_Tumor_Ref_Mix  vs. 929

source_name: ovarian tumor 929


title: Ov_Tumor_Ref_Mix  vs. 844

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 844


title: Ov_Tumor_Ref_Mix  vs. 945

source_name: ovarian tumor 945


title: Ov_Tumor_Ref_Mix  vs. 909

source_name: ovarian tumor 909


title: Ov_Tumor_Ref_Mix  vs. 910

source_name: ovarian tumor 910


title: Ov_Tumor_Ref_Mix  vs. 815

source_name: ovarian tumor 815


title: Ov_Tumor_Ref_Mix  vs. 927

source_name: ovarian tumor 927


title: Ov_Tumor_Ref_Mix  vs. 860

source_name: ovarian tumor 860


title: Ov_Tumor_Ref_Mix  vs. 771

source_name: ovarian tumor 771


title: Ov_Tumor_Ref_Mix  vs. 748

source_name: ovarian tumor 748


title: Ov_Tumor_Ref_Mix  vs. 764

source_name: ovarian tumor 764


title: Ov_Tumor_Ref_Mix  vs. 799

source_name: ovarian tumor 799


title: Ov_Tumor_Ref_Mix  vs. 803

source_name: ovarian tumor 803


title: Ov_Tumor_Ref_Mix  vs. 793

source_name: ovarian tumor 793


title: Ov_Tumor_Ref_Mix  vs. 765

source_name: ovarian tumor 765


title: Ov_Tumor_Ref_Mix  vs. 808

source_name: ovarian tumor 808


title: Ov_Tumor_Ref_Mix  vs. 820

source_name: ovarian tumor 820


title: Ov_Tumor_Ref_Mix  vs. 741

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 741


title: Ov_Tumor_Ref_Mix  vs. 760

source_name: ovarian tumor 760


title: Ov_Tumor_Ref_Mix  vs. 812

source_name: ovarian tumor 812


title: Ov_Tumor_Ref_Mix  vs. 990

source_name: ovarian tumor 990


title: Ov_Tumor_Ref_Mix  vs. 733

source_name: ovarian tumor 733


title: Ov_Tumor_Ref_Mix  vs. 717

source_name: ovarian tumor 717


title: Ov_Tumor_Ref_Mix  vs. 656

source_name: ovarian tumor 656


title: Ov_Tumor_Ref_Mix  vs. 739

source_name: ovarian tumor 739


title: Ov_Tumor_Ref_Mix  vs. 735

source_name: ovarian tumor 735


title: Ov_Tumor_Ref_Mix  vs. 669

source_name: ovarian tumor 669


title: Ov_Tumor_Ref_Mix  vs. 724

source_name: ovarian tumor 724


title: Ov_Tumor_Ref_Mix  vs. 695

source_name: ovarian tumor 695


title: Ov_Tumor_Ref_Mix  vs. 678

source_name: ovarian tumor 678


title: Ov_Tumor_Ref_Mix  vs. 688

source_name: ovarian tumor 688


title: Ov_Tumor_Ref_Mix  vs. 638

source_name: ovarian tumor 638


title: Ov_Tumor_Ref_Mix  vs. 639

source_name: ovarian tumor 639


title: Ov_Tumor_Ref_Mix  vs. 707

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 707


title: Ov_Tumor_Ref_Mix  vs. 651

source_name: ovarian tumor 651


title: Ov_Tumor_Ref_Mix  vs. 593

source_name: ovarian tumor 593


title: Ov_Tumor_Ref_Mix  vs. 605

source_name: ovarian tumor 605


title: Ov_Tumor_Ref_Mix  vs. 575

source_name: ovarian tumor 575


title: Ov_Tumor_Ref_Mix  vs. 571

source_name: ovarian tumor 571


title: Ov_Tumor_Ref_Mix  vs. 600

source_name: ovarian tumor 600


title: Ov_Tumor_Ref_Mix  vs. 609

source_name: ovarian tumor 609


title: Ov_Tumor_Ref_Mix  vs. 589

source_name: ovarian tumor 589


title: Ov_Tumor_Ref_Mix  vs. 614

source_name: ovarian tumor 614


title: Ov_Tumor_Ref_Mix  vs. 596

source_name: ovarian tumor 596


title: Ov_Tumor_Ref_Mix  vs. 563

source_name: ovarian tumor 563


title: Ov_Tumor_Ref_Mix  vs. 652

source_name: ovarian tumor 652


title: Ov_Tumor_Ref_Mix  vs. 716

source_name: ovarian tumor 716


title: Ov_Tumor_Ref_Mix  vs. 557

source_name: ovarian tumor 557


title: Ov_Tumor_Ref_Mix  vs. 550

source_name: ovarian tumor 550


title: Ov_Tumor_Ref_Mix  vs. 582

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 582


title: Ov_Tumor_Ref_Mix  vs. 530

source_name: ovarian tumor 530


title: Ov_Tumor_Ref_Mix  vs. 554

source_name: ovarian tumor 554


title: Ov_Tumor_Ref_Mix  vs. 540

source_name: ovarian tumor 540


title: Ov_Tumor_Ref_Mix  vs. 555

source_name: ovarian tumor 555


title: Ov_Tumor_Ref_Mix  vs. 527

source_name: ovarian tumor 527


title: Ov_Tumor_Ref_Mix  vs. 502

source_name: ovarian tumor 502


title: Ov_Tumor_Ref_Mix  vs. 509

source_name: ovarian tumor 509


title: Ov_Tumor_Ref_Mix  vs. 523

source_name: ovarian tumor 523


title: Ov_Tumor_Ref_Mix  vs. 508

source_name: ovarian tumor 508


title: Ov_Tumor_Ref_Mix  vs. 501

source_name: ovarian tumor 501


title: Ov_Tumor_Ref_Mix  vs. 503

source_name: ovarian tumor 503

value: III/IV


title: Ov_Tumor_Ref_Mix  vs. 485

value: ovarian

source_name: ovarian tumor 485


title: Ov_Tumor_Ref_Mix  vs. 488

source_name: ovarian tumor 488

value: Serous


title: Ov_Tumor_Ref_Mix  vs. 478

source_name: ovarian tumor 478


title: Ov_Tumor_Ref_Mix  vs. 521

source_name: ovarian tumor 521


title: Ov_Tumor_Ref_Mix  vs. 448

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 448


title: Ov_Tumor_Ref_Mix  vs. 447

source_name: ovarian tumor 447


title: Ov_Tumor_Ref_Mix  vs. 428

source_name: ovarian tumor 428


title: Ov_Tumor_Ref_Mix  vs. 963

source_name: ovarian tumor 963


title: Ov_Tumor_Ref_Mix  vs. 405

source_name: ovarian tumor 405

value: IV


title: Ov_Tumor_Ref_Mix  vs. 427

source_name: ovarian tumor 427

value: Optimal


title: Ov_Tumor_Ref_Mix  vs. 422

source_name: ovarian tumor 422

value: Dead


title: Ov_Tumor_Ref_Mix  vs. 404

source_name: ovarian tumor 404

value: III


title: Ov_Tumor_Ref_Mix  vs. 402

source_name: ovarian tumor 402


title: Ov_Tumor_Ref_Mix  vs. 444

source_name: ovarian tumor 444

value: C


title: Ov_Tumor_Ref_Mix  vs. 474

source_name: ovarian tumor 474

value: Alive


title: Ov_Tumor_Ref_Mix  vs. 418

source_name: ovarian tumor 418


title: Ov_Tumor_Ref_Mix  vs. 472

source_name: ovarian tumor 472


title: Ov_Tumor_Ref_Mix  vs. 400

source_name: ovarian tumor 400


title: Ov_Tumor_Ref_Mix  vs. 381

source_name: ovarian tumor 381


title: Ov_Tumor_Ref_Mix  vs. 397

source_name: ovarian tumor 397


title: Ov_Tumor_Ref_Mix  vs. 396

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 396


title: Ov_Tumor_Ref_Mix  vs. 373

source_name: ovarian tumor 373


title: Ov_Tumor_Ref_Mix  vs. 385

source_name: ovarian tumor 385


title: Ov_Tumor_Ref_Mix  vs. 500

source_name: ovarian tumor 500


title: Ov_Tumor_Ref_Mix  vs. 380

source_name: ovarian tumor 380


title: Ov_Tumor_Ref_Mix  vs. 392

source_name: ovarian tumor 392


title: Ov_Tumor_Ref_Mix  vs. 390

source_name: ovarian tumor 390


title: Ov_Tumor_Ref_Mix  vs. 440

source_name: ovarian tumor 440


title: Ov_Tumor_Ref_Mix  vs. 357

source_name: ovarian tumor 357


title: Ov_Tumor_Ref_Mix  vs. 356

source_name: ovarian tumor 356


title: Ov_Tumor_Ref_Mix  vs. 352

source_name: ovarian tumor 352


title: Ov_Tumor_Ref_Mix  vs. 335

source_name: ovarian tumor 335


title: Ov_Tumor_Ref_Mix  vs. 337

source_name: ovarian tumor 337


title: Ov_Tumor_Ref_Mix  vs. 342

source_name: ovarian tumor 342


title: Ov_Tumor_Ref_Mix  vs. 336

source_name: ovarian tumor 336


title: Ov_Tumor_Ref_Mix  vs. 270

source_name: ovarian tumor 270


title: Ov_Tumor_Ref_Mix  vs. 318

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 318


title: Ov_Tumor_Ref_Mix  vs. 314

source_name: ovarian tumor 314


title: Ov_Tumor_Ref_Mix  vs. 283

source_name: ovarian tumor 283


title: Ov_Tumor_Ref_Mix  vs. 399

source_name: ovarian tumor 399


title: Ov_Tumor_Ref_Mix  vs. 339

source_name: ovarian tumor 339


title: Ov_Tumor_Ref_Mix  vs. 308

source_name: ovarian tumor 308


title: male control P1211

city: Muenster

first: Steffi

last: Werler

address: Albert-Schweitzer-Campus 1 (D11)

department: Center for Reproductive Medicine and Andrology

country: Germany

institute: University Hospital Muenster

description: gene expression data from whole blood of healthy male control

hyb_protocol: Hybridisation of the cartridge arrays was performed following the Affymetrix GeneChip User Manual for use with Affymetrix GeneChip Hybridization Wash and Stain Kit

scan_protocol: Arrays were scanned with an Affymetrix GCS3000 7G using the AGCC Scan Control software

data_processing: The data were analyzed with Partek Genomcis Suite using the GC_RMA normalization method

label: Biotin

source_name: whole blood (male)

label_protocol: The samples were processed using the Ambion WT Expression Kit and the Affymetrix GeneChip WT Terminal Labeling and Control Kit

extract_protocol: 7.5 ml of whole EDTA-Blood was diluted with 6 ml RNA/DNA Stabilization Reagent for Blood/Bone Marrow (Roche). Then RNA was isolated with the High Pure RNA isolation Kit (Roche).

value: blood

tag: gender

value: male

tag: condition

value: control


title: Ov_Tumor_Ref_Mix  vs. 323

source_name: ovarian tumor 323


title: Ov_Tumor_Ref_Mix  vs. 354

source_name: ovarian tumor 354

value: Unknown


title: Ov_Tumor_Ref_Mix  vs. 284

source_name: ovarian tumor 284


title: Ov_Tumor_Ref_Mix  vs. 332

source_name: ovarian tumor 332


title: Ov_Tumor_Ref_Mix  vs. 304

source_name: ovarian tumor 304

value: Sub-optimal


title: Ov_Tumor_Ref_Mix  vs. 315

source_name: ovarian tumor 315


title: Ov_Tumor_Ref_Mix  vs. 282

source_name: ovarian tumor 282


title: KS patient 20628

description: gene expression data from whole blood of KS patient

source_name: whole blood (KS)

value: Klinefelter Syndrome


title: KS patient 20141


title: male control P1244


title: KS patient 17739


title: Ov_Tumor_Ref_Mix  vs. 395

source_name: ovarian tumor 395

value: B


title: male control P1241


title: Ov_Tumor_Ref_Mix  vs. 305

source_name: 106 pooled ovarian samples

source_name: ovarian tumor 305


title: Ov_Tumor_Ref_Mix  vs. 266

source_name: ovarian tumor 266

value: II


title: KS patient 17646


title: KS patient 21664


title: OSCC_40T

city: Zhunan

first: Shine-Gwo

last: Shiah

state: Miaoli County

address: No. 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: oral squamous cell carcinoma

label_protocol: Cy3 labled cRNA (PCR product) were prepared with illumina GoldenGate assay

extract_protocol: Total RNA was extracted  from 40 pairs of OSCC patients using the miRNeasy Mini Kit (Qiagen, #217004) according to the manufacturer’s protocol.

value: IVA

value: oral squamous cell carcinoma


title: KS patient 15637


title: KS patient 21038


title: KS patient 19443


title: KS patient 18261


title: KS patient 14623


title: KS patient 19439


title: female control P1190

description: gene expression data from whole blood of healthy female control

source_name: whole blood (female)

value: female


title: KS patient 15708


title: KS patient 20292


title: KS patient 12538


title: OSCC_35T

description: replicate 1


title: OSCC_33T

description: replicate 1


title: OSCC_32T

description: replicate 1


title: OSCC_34T

description: replicate 1


title: OSCC_39T

description: replicate 1


title: OSCC_37T

description: replicate 1


title: female control P1239


title: KS patient 12505


title: OSCC_38T

description: replicate 1


title: KS patient 18410


title: OSCC_36T

description: replicate 1


title: KS patient 17625


title: KS patient 16539


title: OSCC_30T

description: replicate 1


title: OSCC_31T

description: replicate 1


title: OSCC_28T

description: replicate 1


title: OSCC_29T

description: replicate 1


title: KS patient 17041


title: KS patient 10358


title: female control P1157


title: female control P1235


title: male control P1188


title: female control P1236


title: KS patient 15588


title: OSCC_27T

description: replicate 1


title: KS patient 13973


title: OSCC_26T

description: replicate 1


title: OSCC_22T

description: replicate 1


title: OSCC_24T

description: replicate 1


title: OSCC_23T

description: replicate 1


title: OSCC_25T

description: replicate 1


title: male control P1230


title: female control P1233


title: OSCC_21T

description: replicate 1


title: OSCC_19T

description: replicate 1


title: OSCC_18T

description: replicate 1


title: OSCC_17T

description: replicate 1


title: OSCC_20T

description: replicate 1


title: OSCC_15T

description: replicate 1

value: I


title: KS patient P1208


title: OSCC_16T

description: replicate 1


title: OSCC_14T

description: replicate 1


title: male control P1232


title: male control P1185


title: KS patient 8845


title: female control P1199


title: KS patient 18277


title: KS patient 18771


title: female control P1184


title: OSCC_13T

description: replicate 1


title: KS patient 22264


title: OSCC_12T

description: replicate 1


title: female control P1229


title: OSCC_11T

description: replicate 1


title: OSCC_10T

description: replicate 1


title: male control P1151


title: KS patient P1225


title: male control P1231


title: OSCC_09T

description: replicate 1


title: OSCC_08T

description: replicate 1


title: male control 22080


title: OSCC_03T

description: replicate 1


title: OSCC_05T

description: replicate 1


title: OSCC_04T

description: replicate 1


title: OSCC_06T

description: replicate 1


title: OSCC_07T

description: replicate 1


title: KS patient 21278


title: OSCC_01T

description: replicate 1


title: female control P1224


title: male control P1183


title: OSCC_02T

description: replicate 1


title: KS patient 21481


title: female control P1145


title: male control P1139


title: female control P1156


title: female control P1177


title: endometrioid ovarian cancer sample 45

city: Pittsburgh

first: SungHwan

last: Kim

address: 200 Lothrop, BST W1200

institute: University of Pittsburgh

hyb_protocol: according to Nanostring instructions

scan_protocol: according to Nanostring instructions

data_processing: Used EdgeR package. Once negative binomial models were fitted and dispersion estimates were obtained, we performed testing procedures for determining differential expression using an exact test with the quantile-adjusted conditional maximum likelihood (qCML) method.

source_name: endometrioid ovarian cancer sample

label_protocol: according to Nanostring instructions

extract_protocol: The RNeasy FFPE Kit (Qiagen) was used to isolate total RNA from FFPE tissues. The nCounter® GX Human Immunology Kit (Nanostring) was used to profile 511 immune genes.

tag: sample type

value: Paraffin tissue blocks

value: Ovarian tumor

tag: tissue subtype

value: endometrioid ovarian cancer


title: non-OSCC_39N

description: replicate 1

source_name: adjacent non-tumor epithelia

value: oral epithelia


title: non-OSCC_40N

description: replicate 1


title: KS patient 16358


title: KS patient P1212


title: male control P1137

source_name: whole blood (male)


title: endometrioid ovarian cancer sample 44


title: KS patient 9516


title: high grade serous ovarian cancer sample 43

source_name: high grade serous ovarian cancer sample

value: high grade serous ovarian cancer


title: high grade serous ovarian cancer sample 42


title: high grade serous ovarian cancer sample 41


title: Geminin-KO Lineage negative fetal liver cells E15.5, rep2

city: Patras

first: Stavros

last: Taraviras

state: Achaia

address: Asklipiou 1

department: School of Medicine

country: Greece

institute: University of Patras

description: Geminin-KO hematopoietic stem/progenitor cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45°C. Washing was done in GeneChip Fluidics Station 450.

scan_protocol: Affymetrix  Scanner 3000 7G with autoloader

data_processing: The data were processed and analyzed using GeneSpring (v.12.5, Agilent). The cutoff values were set as FC>1.5 and p-value <0.05. The analysis was carried out using the genotype criterion, but non-averaged for the three biological replicates.

source_name: Geminin-KO, lin- cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse fetal livers dissected at E15.5

extract_protocol: Total RNA was extracted from FACS-sorted lineage-negative (lineage-negative for the expression of CD3, CD8a, CD19, B220, GR1, CD11b, CD11c, Ter119) fetal liver cells using the Rneasy Micro Kit (Qiagen), according to the manufacturer's instructions. RNAs were quantified with a Nanodrop 2000 spectrophotometer (Thermo Scientific) and assessed with an Aagilent 2000 Bioanalyzer.

tag: stain background

value: mixed

tag: developmental stage

tag: genotype/variation

value: Geminin-KO

value: fetal liver

value: hematopoietic stem cells


title: high grade serous ovarian cancer sample 40


title: non-OSCC_26N

description: replicate 1

value: male


title: non-OSCC_24N

description: replicate 1


title: non-OSCC_27N

description: replicate 1


title: non-OSCC_28N

description: replicate 1


title: high grade serous ovarian cancer sample 39


title: KS patient 15700

value: blood

value: Klinefelter Syndrome


title: non-OSCC_22N

description: replicate 1

value: III


title: non-OSCC_23N

description: replicate 1

value: II


title: non-OSCC_29N

description: replicate 1

value: IVA


title: high grade serous ovarian cancer sample 38


title: non-OSCC_20N

description: replicate 1


title: non-OSCC_21N

description: replicate 1


title: non-OSCC_16N

description: replicate 1


title: high grade serous ovarian cancer sample 37


title: non-OSCC_15N

description: replicate 1


title: non-OSCC_19N

description: replicate 1


title: non-OSCC_18N

description: replicate 1


title: non-OSCC_17N

description: replicate 1


title: non-OSCC_14N

description: replicate 1


title: high grade serous ovarian cancer sample 35


title: high grade serous ovarian cancer sample 34


title: high grade serous ovarian cancer sample 36


title: non-OSCC_09N

description: replicate 1


title: non-OSCC_10N

description: replicate 1


title: non-OSCC_13N

description: replicate 1


title: non-OSCC_25N

description: replicate 1


title: non-OSCC_30N

description: replicate 1


title: high grade serous ovarian cancer sample 33


title: male control P658

value: control


title: non-OSCC_12N

description: replicate 1


title: non-OSCC_11N

description: replicate 1


title: female control P1123

value: female


title: non-OSCC_08N

description: replicate 1


title: high grade serous ovarian cancer sample 32

value: Paraffin tissue blocks


title: high grade serous ovarian cancer sample 31

value: Ovarian tumor


title: female control P1122


title: non-OSCC_31N

description: replicate 1


title: high grade serous ovarian cancer sample 30


title: non-OSCC_07N

description: replicate 1


title: non-OSCC_06N

description: replicate 1


title: clear cell carcinoma sample 28

source_name: clear cell carcinoma sample

value: clear cell carcinoma


title: non-OSCC_03N

description: replicate 1

value: oral epithelia


title: non-OSCC_01N

description: replicate 1


title: non-OSCC_02N

description: replicate 1


title: non-OSCC_05N

description: replicate 1


title: non-OSCC_04N

description: replicate 1


title: Geminin-KO Lineage negative fetal liver cells E15.5, rep1


title: clear cell carcinoma sample 26


title: clear cell carcinoma sample 27


title: high grade serous ovarian cancer sample 29

value: high grade serous ovarian cancer


title: non-OSCC_33N

description: replicate 1


title: non-OSCC_32N

description: replicate 1


title: non-OSCC_34N

description: replicate 1


title: non-OSCC_35N

description: replicate 1


title: non-OSCC_36N

description: replicate 1


title: non-OSCC_37N

description: replicate 1


title: non-OSCC_38N

description: replicate 1


title: Geminin-KO Lineage negative fetal liver cells E15.5, rep3

value: mixed


title: male control P1223


title: clear cell carcinoma sample 25


title: clear cell carcinoma sample 24


title: KS patient P1218


title: WT Lineage negative fetal liver cells E15.5, rep 2

description: WT hematopoietic stem/progenitor cells

source_name: wild-type, lin- cells

value: wild type


title: clear cell carcinoma sample 23


title: 5-3 S3 K5

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

description:
Prefrontal cortex; Stress-13 days + 5 days of rest; Biol. Rep. 3, dye swap
Technical replicate of 5-3 S5 K3

hyb_protocol: cRNA was hybridized using Gene Expression Hybridization Kit (Agilent). Hybridized microarrays were washed using standard Washing Buffer kit (Agilent). All procedures were performed according to manufacturer's protocol

scan_protocol: Data were extracted using G2565CA Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (Agilent, USA) on default settings (GE2_1010_Sep10).

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

label_protocol: RNA was labeled using Two-Color Low Input Quick Amp Labeling Kits (Agilent) according to manufacturer's protocol

growth_protocol: Before experiment male mice were kept in cages with their brothers (3-6 in cage) at ambient temperature of 22±1°C and 52 ±2% humidity

extract_protocol: RNA was extracted using column-based NucleoSpin RNA II kit (Machery-Nagel) according to manufacturer protocol

treatment_protocol: Mice were subjected to chronic social stress. Social stress was performed by placing the animal into the cage belonging to group housed (4-5) male Swiss Webster mice (4 months old).

value: Prefrontal cortex

tag: stress

value: stress

tag: time point

value: 13 days + 5 days of rest

source_name: Prefrontal cortex; Control-13 days + 5 days of rest


title: WT Lineage negative fetal liver cells E15.5, rep 3

description: WT hematopoietic stem/progenitor cells

value: fetal liver

value: hematopoietic stem cells


title: clear cell carcinoma sample 22


title: clear cell carcinoma sample 21


title: 5-1 S5 K3

description: Prefrontal cortex; Stress-13 days + 5 days of rest; Biol. Rep. 1


title: 5-2 S3 K5

description:
Prefrontal cortex; Stress-13 days + 5 days of rest; Biol. Rep. 2, dye swap
Technical replicate of 5-2 S5 K3


title: clear cell carcinoma sample 20


title: clear cell carcinoma sample 19


title: 5-3 S5 K3

description:
Prefrontal cortex; Stress-13 days + 5 days of rest; Biol. Rep. 3
Technical replicate of 5-3 S3 K5


title: WT Lineage negative fetal liver cells E15.5, rep 1

description: WT hematopoietic stem/progenitor cells


title: clear cell carcinoma sample 18


title: clear cell carcinoma sample 17


title: 4-3 S5 K3

description:
Prefrontal cortex; Stress-13 days; Biol. Rep. 3
Technical replicate of 4-3 S3 K5

source_name: Prefrontal cortex; Control-13 days

value: 13 days

source_name: Prefrontal cortex; Stress-13 days


title: 4-2 S5 K3

description:
Prefrontal cortex; Stress-13 days; Biol. Rep. 2
Technical replicate of 4-2 S3 K5


title: 4-3 S3 K5

description:
Prefrontal cortex; Stress-13 days; Biol. Rep. 3, dye swap
Technical replicate of 4-3 S5 K3


title: 5-2 S5 K3

description:
Prefrontal cortex; Stress-13 days + 5 days of rest; Biol. Rep. 2
Technical replicate of 5-2 S3 K5


title: 3-3 S3 K5

description:
Prefrontal cortex; Stress-8 days; Biol. Rep. 3, dye swap
Technical replicate of 3-3 S5 K3

source_name: Prefrontal cortex; Stress-8 days

value: 8 days

source_name: Prefrontal cortex; Control-8 days


title: endometrioid ovarian cancer sample 16

value: endometrioid ovarian cancer


title: 4-1 S5 K3

description: Prefrontal cortex; Stress-13 days; Biol. Rep. 1

value: control


title: 1-2 S3 K5

description:
Prefrontal cortex; Stress-acute; Biol. Rep. 2, dye swap
Technical replicate of 1-2 S5 K3

source_name: Prefrontal cortex; Stress-acute

value: acute

source_name: Prefrontal cortex; Control-acute


title: 3-1 S5 K3

description: Prefrontal cortex; Stress-8 days; Biol. Rep. 1


title: 3-2 S5 K3

description:
Prefrontal cortex; Stress-8 days; Biol. Rep. 2
Technical replicate of 3-2 S3 K5


title: 1-3 S3 K5

description:
Prefrontal cortex; Stress-acute; Biol. Rep. 3, dye swap
Technical replicate of 1-3 S5 K3


title: 3-3 S5 K3

description:
Prefrontal cortex; Stress-8 days; Biol. Rep. 3
Technical replicate of 3-3 S3 K5


title: 1-3 S5 K3

description:
Prefrontal cortex; Stress-acute; Biol. Rep. 3
Technical replicate of 1-3 S3 K5


title: 4-2 S3 K5

description:
Prefrontal cortex; Stress-13 days; Biol. Rep. 2, dye swap
Technical replicate of 4-2 S5 K3


title: 1-1 S5 K3

description: Prefrontal cortex; Stress-acute; Biol. Rep. 1


title: endometrioid ovarian cancer sample 15

value: Paraffin tissue blocks


title: endometrioid ovarian cancer sample 14

value: Ovarian tumor


title: endometrioid ovarian cancer sample 13


title: endometrioid ovarian cancer sample 12


title: endometrioid ovarian cancer sample 11


title: endometrioid ovarian cancer sample 10


title: endometrioid ovarian cancer sample 9


title: 1-2 S5 K3

description:
Prefrontal cortex; Stress-acute; Biol. Rep. 2
Technical replicate of 1-2 S3 K5


title: 3-2 S3 K5

description:
Prefrontal cortex; Stress-8 days; Biol. Rep. 2, dye swap
Technical replicate of 3-2 S5 K3


title: endometrioid ovarian cancer sample 7


title: PANC1 10uM ICG-001 12h_replicates 1, 2, and 3

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description: replicates 1, 2 and 3

data_processing: The data was analyzed and exported from Illumina’s GenomeStudio software using quantile normalization without background subtraction

label_protocol: The Illumina TotalPrep RNA Amplification Kit was used according to the manufacturer’s instructions to amplify and label RNA samples for Illumina array hybridization

extract_protocol: RNA was extracted with Trizol reagent (Life Technologies) according to the manufacturers protocol. To confirm RNA samples were not degraded, RNA quality was checked with the Experion StdSens kit (Bio-Rad) prior to amplification and labeling.

tag: cell line

value: pancreatic ductal carcinoma cell type

tag: treatment


title: HCT116 10uM ICG-001 96h_replicates 1 and 2

description: replicates 1 and 2

value: colorectal cancer cell type


title: PANC1 0.05% DMSO 12h_replicates 1 and 2

description: replicates 1 and 2

value: DMSO control


title: PANC1 10uM C646 96h_replicates 1 and 2

description: replicates 1 and 2


title: PANC1 0.05% DMSO 96h_replicates 1 and 2

description: replicates 1 and 2


title: PANC1 10uM ICG-001 96h_replicates 1 and 2

description: replicates 1 and 2


title: HCT116 0.05% DMSO 96h_replicates 1 and 2

description: replicates 1 and 2


title: PANC1 10uM C646 12h_replicates 1 and 2

description: replicates 1 and 2


title: endometrioid ovarian cancer sample 6

tag: tissue


title: HCT116 10uM ICG-001 12h_replicates 1 and 2

description: replicates 1 and 2


title: endometrioid ovarian cancer sample 5


title: HCT116 10uM C646 96h_replicates 1 and 2

description: replicates 1 and 2


title: endometrioid ovarian cancer sample 4


title: endometrioid ovarian cancer sample 8


title: Control vs CMCAAT treated MCF-7 cells, replicate 4

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: Biological replicate 4 of 4. MCF-7 cells treated with CMCAAT, harvested after 48h treatment.

hyb_protocol: According to manufacturer's protocol.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray G2505B scanner Images were quantified using Agilent Feature Extraction Software (v 8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: MCF-7 treated with CMCAAT, replicate 4 (LL-10)

label_protocol: According to manufacturer's protocol.

growth_protocol: MCF-7 cells were grown in Dulbecco’s minimal essential medium (DMEM) supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin (Invitrogen, Carlsbad, CA) and 2.5 μg/mL fungizone (Bristol-Meyers Squibb, Brussels, Belgium)

extract_protocol: Total RNA was isolated using the Nucleospin RNA II kit (Macherey-Nagel, Düren, Germany) including DNAse I treatment.

treatment_protocol: MCF-7 cells were washed three times with serum-free DMEM supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin and 2.5 μg/mL fungizone;  afterwards MCF-7 cells were treated for 48h with control medium (DMEM/F12 + 0,5%BSA) or CMCAAT

tag: tissue type

value: breast cancer

source_name: MCF-7 control (LL1-2-4)


title: endometrioid ovarian cancer sample 3


title: endometrioid ovarian cancer sample 2


title: HCT116 0.05% DMSO 12h_replicates 1 and 2

description: replicates 1 and 2


title: endometrioid ovarian cancer sample 1


title: Control vs CMCAAT treated MCF-7 cells, replicate 2

description: Biological replicate 2 of 4. MCF-7 cells treated with CMCAAT, harvested after 48h treatment.

source_name: MCF-7 treated with CMCAAT, replicate 2 (LL-8)


title: Control vs CMCAAT treated MCF-7 cells, replicate 1

description: Biological replicate 1 of 4. MCF-7 cells treated with CMCAAT, harvested after 48h treatment.

source_name: MCF-7 treated with CMCAAT, replicate 1 (LL-6)


title: HCT116 10uM C646 12h_replicates 1 and 2

description: replicates 1 and 2


title: atypical endometriosis sample 15

source_name: atypical endometriosis sample

value: Peritoneal implant

value: atypical endometriosis


title: atypical endometriosis sample 14


title: atypical endometriosis sample 13


title: Control vs CMCAAT treated MCF-7 cells, replicate 3

description: Biological replicate 3 of 4. MCF-7 cells treated with CMCAAT, harvested after 48h treatment.

source_name: MCF-7 treated with CMCAAT, replicate 3 (LL-9)


title: atypical endometriosis sample 12


title: 3D7/cam 34-44hpi

city: Melbourne

first: Michaela

last: Petter

state: VIC

address: 792 Elizabeth Street

department: Peter Doherty Institute

country: Australia

institute: University of Melbourne

description: 3D7/cam TP4

hyb_protocol: Microarray hybridizations were carried out as described in [PMID:12929205]. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Microarrays were scanned as described in PMID: 12929205. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Lowess normalisation was applied to all arrays as implemented in the Acuity 4.0 software (Molecular Devices). The microarray data were then filtered to include only spots with at least 95% of pixels having signal intensity greater than two standard deviations above background for both Cy3 and Cy5 fluorescence intensity.

organism: Plasmodium falciparum 3D7

label_protocol: Labeling was carried out as described in [PMID: 12929205]

extract_protocol: Total RNA was extracted using Ribozol (Amresco) following manufacturer's instructions.

treatment_protocol: Pre-synchronized parasite cultures were synchronized twice 14 hours apart to achieve a ten hour growth window. Four consecutive samples were harvested for both 3D7/PfBDP1 OE and 3D7/cam during the intra-erythrocytic cell cycle at 4-14, 24-24, 24-34 and 34-44 hours post-invasion.

tag: line

value: expressing hDHFR

tag: culture conditions

value: 5μg/ml BSD-S-HCl

value: 34-44 hours post-invasion

tag: life cycle stage

value: intra-erythrocytic parasites

value: whole organism

source_name: reference pool RNA

value: cDNA reference pool consisting of time points 2, 3, 4, 5, 6


title: 3D7/cam 24-34hpi

description: 3D7/cam TP3

value: 24-34 hours post-invasion


title: cultured primary RhoA-KO in vitro biological rep1

city: Copenhagen

first: Alberto

last: Garcia Mariscal

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Gene expression data from cultured primary keratinocytes

hyb_protocol: The labeled samples were hybridized to the GeneChip Genome U133 plus 2 arrays (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® 2500 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol. Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (AGCC) (Affymetrix, Santa Clara, CA, USA).

data_processing: The arrays were normalized and scaled my the MAS5 protocol to a target intensity of 100

source_name: cultured primary RhoA-KO keratinocytes

label_protocol: RNA was amplified and labeled using the 3’ IVT Express kit (Affymetrix, Santa Clara, CA, USA) according to manufactures instructions. 250 ng total RNA was used as input

growth_protocol: In vivo samples correspond to keratinocytes freshly isolated from epidermis. In vitro samples are primary keratinocytes

extract_protocol: RNA was isolated from freshly isolated (in vivo) or cultured (in vitro) primary keratinocytes using the RNeasy kit  (Qiagen, Germany). Hybridization to GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA) was carried out at the Copenhagen University Hospital Microarray Center using standard protocols

value: skin

tag: genotype

value: RhoA fl/fl K5 cre


title: 3D7/PfBDP1 OE 24-34hpi

description: 3D7/PfBDP1 OE TP3

source_name: 3D7/PfBDP1 OE

value: 3D7/PfBDP1 OE

value: over-expressing PfBDP1-3xHA (3D7/PfBDP1 OE)


title: 3D7/PfBDP1 OE 4-14hpi

description: 3D7/PfBDP1 OE TP1

value: 4-14 hours post-invasion


title: 3D7/cam 14-24hpi

description: 3D7/cam TP2

value: 14-24 hours post-invasion


title: atypical endometriosis sample 11

value: Paraffin tissue blocks


title: 3D7/cam 4-14hpi

description: 3D7/cam TP1


title: atypical endometriosis sample 10


title: cultured primary RhoA-KO in vitro biological rep3


title: 3D7/PfBDP1 OE 34-44hpi

description: 3D7/PfBDP1 OE TP4


title: cultured primary Wildtype in vitro biological rep1

source_name: cultured primary wildtype keratinocytes

value: RhoA fl/+ K5 cre


title: freshly isolated RhoA-KO in vivo biological rep2

description: Gene expression data from freshly isolated keratinocytes

source_name: freshy isolated RhoA-KO keratinocytes


title: cultured primary RhoA-KO in vitro biological rep2


title: 3D7/PfBDP1 OE 14-24hpi

description: 3D7/PfBDP1 OE TP2


title: cultured primary Wildtype in vitro biological rep2


title: atypical endometriosis sample 8

value: Peritoneal implant


title: atypical endometriosis sample 7

value: atypical endometriosis


title: PfBDP1DD OFF Shld1 44+/-4hpi_Bio 3

hyb_protocol: Microarray hybridizations were carried out as described in [PMID: 12929205]. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Microarrays were scanned as described in [PMID: 12929205]. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

source_name: PfBDP1DD OFF Shld1 44+/-4hpi

growth_protocol: Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.5% Albumax (Gibco). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) following manufacturer's instructions

treatment_protocol: PfBDP1DD parasites grown  in the presence of 2.5 nM WR99210/500 nM Shld1 and synchronized by MACS and sorbitol treatment to an 8-hour growth window were split into two cultures at 30 hours post invasion (hpi) and Shld1 removed from one batch. This is the sample grown in the absence of Shld1.

tag: transgenic line

value: expressing an endogeneous PfBDP1-HA-DD fusion protein

value: whole organsim

treatment_protocol: RNA from highly synchronized cells was extracted at 6 time points across the IDC at 8 h intervals. Equal amount of RNA from each time point was mixed to prepare the cDNA which was used as a reference pool.

value: reference pool


title: atypical endometriosis sample 6


title: PfBDP1DD OFF Shld1 44+/-4hpi_Bio 1


title: PfBDP1DD OFF Shld1 36+/-4hpi_Bio 2

source_name: PfBDP1DD OFF Shld1 36+/-4hpi


title: atypical endometriosis sample 5


title: PfBDP1DD OFF Shld1 44+/-4hpi_Bio 2


title: freshly isolated Wildtype in vivo biological rep1

source_name: freshly isolated wildtype keratinocytes


title: atypical endometriosis sample 4


title: PfBDP1DD OFF Shld1 36+/-4hpi_Bio 3


title: PfBDP1DD OFF Shld1 28+/-4hpi_Bio 3

source_name: PfBDP1DD OFF Shld1 28+/-4hpi


title: freshly isolated RhoA-KO in vivo biological rep1

source_name: freshly isolated RhoA-KO keratinocytes


title: freshly isolated Wildtype in vivo biological rep2


title: cultured primary Wildtype in vitro biological rep3


title: atypical endometriosis sample 3


title: PfBDP1DD OFF Shld1 36+/-4hpi_Bio 1


title: atypical endometriosis sample 2


title: atypical endometriosis sample 1


title: benign endometrium sample 30

source_name: benign endometrium sample

value: benign endometrium


title: PfBDP1DD OFF Shld1 12+/-4hpi_Bio 3

source_name: PfBDP1DD OFF Shld1 12+/-4hpi


title: benign endometrium sample 29


title: PfBDP1DD OFF Shld1 20+/-4hpi_Bio 2

source_name: PfBDP1DD OFF Shld1 20+/-4hpi


title: benign endometrium sample 28


title: PfBDP1DD OFF Shld1 20+/-4hpi_Bio 1


title: Benign endometriosis sample 25

source_name: Benign endometriosis sample

value: Benign endometriosis


title: Benign endometriosis sample 26


title: PfBDP1DD OFF Shld1 12+/-4hpi_Bio 2


title: Benign endometriosis sample 24


title: PfBDP1DD OFF Shld1 12+/-4hpi_Bio 1


title: PfBDP1DD OFF Shld1 28+/-4hpi_Bio 1


title: PfBDP1DD OFF Shld1 20+/-4hpi_Bio 3


title: PfBDP1DD OFF Shld1 4+/-4hpi_Bio 2

source_name: PfBDP1DD OFF Shld1 4+/-4hpi


title: Benign endometriosis sample 23


title: PfBDP1DD OFF Shld1 4+/-4hpi_Bio 1


title: PfBDP1DD ON Shld1 44+/-4hpi_Bio 3

source_name: PfBDP1DD ON Shld1 44+/-4hpi

treatment_protocol: PfBDP1DD parasites grown  in the presence of 2.5 nM WR99210/500 nM Shld1 and synchronized by MACS and sorbitol treatment to an 8-hour growth window were split into two cultures at 30 hours post invasion (hpi) and Shld1 removed from one batch. This is the sample grown in the presence of Shld1.


title: PfBDP1DD OFF Shld1 4+/-4hpi_Bio 3


title: benign endometrium sample 27


title: Benign endometriosis sample 22


title: PfBDP1DD ON Shld1 44+/-4hpi_Bio 2


title: REP_R1881_rep2

city: Chicago

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

hyb_protocol: RNA samples are sent to Mogene company for further processing and data generation.

source_name: immortalized primary fetal human epididymis cells

growth_protocol: Cells are cultured in Primaria flasks (Falcon) in CMRL 1066 medium, containing 20% foetal calf serum (FCS) (Gibco, UK); L-glutamine (4mM); insulin (0.2 unit/ml); cholera toxin (10-10M) and hydrocortisone (1μg/ml), all from Sigma. Cultures were routinely maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol: TRIzol® (Life Technologies) used for RNA extraction.

treatment_protocol: Cells are cultured in phenol-free CMRL-1066 medium containing 10% dextran coated-charcoal (C6241, Sigma) - stripped FBS for 72h prior to stimulation with 1 nM R1881 (NLP005005MG, PerkinElmer, Waltham, MA) or vehicle for a further 16h.

tag: cell type

value: SV-40 transformed primary human fetal epididymis cells


title: REP_R1881_rep1

scan_protocol: RNA samples are sent to Mogene company for further processing and data generation.


title: PfBDP1DD ON Shld1 44+/-4hpi_Bio 1

source_name: reference pool RNA

tag: sample type


title: Benign endometriosis sample 21

tag: tissue subtype


title: PfBDP1DD ON Shld1 36+/-4hpi_Bio 3

source_name: PfBDP1DD ON Shld1 36+/-4hpi


title: Benign endometriosis sample 20


title: PfBDP1DD OFF Shld1 28+/-4hpi_Bio 2


title: Benign endometriosis sample 19


title: REP_ctr_rep1

data_processing: RNA samples are sent to Mogene company for further processing and data generation.


title: Benign endometriosis sample 18