title: BC 660


title: BC 664

status: Public on Jan 08 2016

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2. The 'complete.betas.nocurelung.txt' contains unmethylated and methylated signal intensities along with average Beta and P-val

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: disease state

value: cancer


title: BC 663


title: Breast 751

value: normal


title: BC 662


title: BC 654


title: Breast 753


title: BC 653


title: BC 659


title: BC 658


title: Breast 750


title: BC 651


title: BC 656


title: BC 650


title: BC 649


title: Breast 746


title: BC 655


title: BC 648


title: Breast 747


title: BC 652


title: Breast 745


title: BC 645


title: BC 643


title: BC 642


title: BC 665


title: BC 640


title: BC 661


title: BC 635


title: BC 646


title: BC 647


title: BC 636


title: BC 633


title: BC 630


title: BC 632


title: BC 638


title: BC 639


title: BC 629


title: BC 637


title: BC 631


title: BC 628


title: BC 644


title: BC 625


title: BC 624


title: BC 641


title: BC 634


title: BC 621


title: BC 619


title: BC 617


title: BC 622


title: BC 615


title: BC 627


title: BC 626


title: BC 613


title: BC 623


title: BC 611


title: BC 609


title: BC 610


title: BC 616


title: BC 618


title: BC 620


title: BC 614


title: BC 602


title: Colon 574

source_name: Large Intestine


title: BC 601


title: GB 339

source_name: Central Nervous System


title: BC 608


title: BC 612


title: BC 605


title: BC 607


title: GB 338


title: GB 337


title: GB 336


title: GB 335


title: GB 331


title: GB 329


title: GB 330


title: GB 328


title: GB 332


title: BC 606


title: GB 333


title: GB 326


title: BC 604


title: GB 327


title: Colon 575


title: GB 325


title: BC 603


title: GB 321


title: GB 322


title: GB 323


title: GB 324


title: GB 319


title: GB 320


title: GB 318


title: GB 317


title: GB 316


title: B_cells 296

source_name: Haematopoietic & Lymphoid


title: B_cells 295


title: White matter 293


title: White matter 292


title: B_cells 298


title: GB 334


title: White matter 291


title: B_cells 297


title: White matter 290


title: B_cells 294


title: White matter 288


title: White matter 289


title: White matter 286


title: White matter 287


title: Colon 247


title: CC 245


title: CC 242


title: CC 248


title: CC 246


title: Colon 243


title: CC 238


title: CC 244


title: Colon 241


title: CC 237


title: Colon 236


title: CC 234


title: GB 235


title: Colon 233


title: CC 229


title: CC 228


title: CC 227


title: Colon 226


title: CC 224


title: GB 225


title: GB 223


title: CC 222


title: GB 220


title: Colon 221


title: CC 219


title: CC 218


title: CC 216


title: CC 207


title: GB 206


title: CC 211


title: CC 230


title: GB 209


title: GB 214


title: Colon 210


title: CC 205


title: GB 212


title: CC 208


title: CC 204


title: CC 203


title: GB 201


title: CC 202


title: GB 199


title: CC 200


title: GB 217


title: GB 195


title: CC 198


title: GB 215


title: GB 192


title: CC 190


title: CC 191


title: CC 189


title: GB 213


title: CC 186


title: CC 185


title: Colon 183


title: CC 184


title: CC 180


title: CC 179


title: CC 178


title: CC 176


title: GB 197


title: CC 177


title: CC 175


title: CC 174


title: CC 194


title: CC 173


title: CC 172


title: CC 171


title: CC 170


title: CC 193


title: CC 181


title: CC 182


title: CC 188


title: CC 168


title: GB 166


title: CC 169


title: CC 163


title: CC 164


title: CC 187


title: CC 161


title: CC 160


title: CC 159


title: EB-differentiated-day-0

type: RNA

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

country: USA

institute: University of Cincinnati

hyb_protocol: Supported by LC Sciences. Array Part No: MRA-1002 (Version No: miRMouse_19). Chip id: 01_M19_121342 (EB0); 02_M19_121402 (EB10). 1265 of of Unique Probes. 3 of Repeats.

scan_protocol: Supported by LC Sciences. Axon GenePix 4000B Microarray Scanner

data_processing:
Supported by LC Sciences: The signal values are derived by background subtraction. Blank spaces represent signal values below detection level. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV <0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
Data were corrected by subtracting background and normalized to the statistical mean of all detectable transcripts with LC Sciences in house software.

molecule: total RNA

organism: Mus musculus

source_name: ESCs, differentiated, day-0

label_protocol: Supported by LC Sciences (Houston, TX)-Experiment: S120369; cy5 dye labling

growth_protocol: DMEM containing 15% FBS, 0.1mM nonessential amino acids, 2mM L-glutamine, 0.1mM b-mercaptoethanol

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen).

treatment_protocol: The suspended cells were transferred to ultra-low attachment dishes.

tag: strain

tag: cell type

value: Embryonic stem cells

tag: protocol

value: differentiation

tag: time

value: day 0


title: EB-differentiated-day-10

source_name: ESCs, differentiated, day-10

value: day 10


title: can_Ad_VEGF_60_Day_NT_080

city: Indianapolis

first: Jiangang

last: Liu

state: IN

address: 893 S Delaware St

department: Tailored Therapeutics

institute: Eli Lilly and Company

scan_protocol: standard Affymetrix protocol

data_processing: A summary of the image signal data, detection calls and gene annotations for every gene interrogated on the arrays was generated using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) (scaling factor = 1500) .

label: biotin

source_name: Flank tissue_Ad-VEGF-A164_day 60_No Treatment

label_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA) according to the company's standard operating procedures as described previously in detail

growth_protocol: Ten to the power 8 PFU of Ad-VEGF-A164 in 10 μl PBS/glycerol were injected intradermally into the ears of 4-6 week old female athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490). In addition, 5 x 10**8 PFU of Ad-VEGF-A164 in 50 μl PBS/glycerol were injected intradermally into the flank skin of the same mice. All studies were performed under protocols approved by the BIDMC Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was isolated with the RNeasy kit following the manufacturer’s instructions (Qiagen, CA), and cDNA was prepared using reverse transcriptase III (Invitrogen) as described

treatment_protocol: Animals were treated with various anti-VEGF Receptor antibodies via intraperitoneal injection at the doses (DC101 20 mpk or G6 10 mpk) and time points (day 0, day 5, day 20, day 60)to target all of the different populations of tumor-surrogate blood vessels, as they each develop at different time points.

tag: age

value: 4-6 week old

tag: gender

value: female

tag: injected with

tag: treated with

tag: sample status

value: Ad_VEGF_Vasculature, No Treatment

tag: tissue

value: flank


title: CC 158


title: GB 157


title: can_Ad_VEGF_60_Day_NT_078

hyb_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA)

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)


title: can_Ad_VEGF_60_Day_NT_074


title: CC 165


title: CC 156


title: can_Ad_VEGF_60_Day_NT_076


title: can_Ad_VEGF_60_Day_NT_079


title: CC 162


title: CC 155


title: can_Ad_VEGF_60_Day_G6_087

source_name: Flank tissue_Ad-VEGF-A164_day 60_G6 treated

value: G6 10 mpk at day 60

value: Ad_VEGF_Vasculature, G6 treated


title: CC 154


title: GB 153


title: can_Ad_VEGF_60_Day_NT_073


title: can_Ad_VEGF_60_Day_NT_075


title: can_Ad_VEGF_60_Day_G6_086


title: CC 152


title: can_Ad_VEGF_60_Day_G6_088


title: can_Ad_VEGF_60_Day_NT_077


title: CC 151


title: can_Ad_VEGF_60_Day_G6_085


title: CC 149


title: CC 148


title: CC 150


title: CC 147


title: CC 145


title: CC 146


title: can_Ad_VEGF_60_Day_G6_084


title: CC 144


title: CC 143


title: can_Ad_VEGF_60_Day_G6_083


title: Colon 142


title: PBMC, sorted CD3+CD4+CD8-CD57-PD1- HC082

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip HU133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA).

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

data_processing: Background adjustment, normalization and median polish summarization of .CEL files was performed using the robust multi-chip average (RMA) algorithm. Quality of hybridized chips was assessed after normalization by the distribution of their NUSE and RLE plots using the RACE tool. Downstream analyses were performed using Partek Genomics Suite software v6.5 (Partek Inc. St. Louis, MO).

source_name: HC082, PBMC, CD57-

label_protocol: RNA was amplified and labeled using the NuGen Ovation Pico system according to kit instructions.

extract_protocol: Sorted cells were placed into 350 μl of RLT buffer (QIAGEN, Valencia, CA) and total RNA was purified using RNEasy Micro kits (QIAGEN) according to manufacturer’s specifications with optional on-column DNAse digestion.

tag: array facility id

tag: subjectid

tag: population

value: T cell


title: GB 135


title: PBMC, sorted CD3+CD4+CD8-CD57+PD1- HC082

source_name: HC082, PBMC, CD57+


title: PBMC, sorted CD3+CD4+CD8-CD57-PD1- HC093

source_name: HC093, PBMC, CD57-


title: can_Ad_VEGF_60_Day_G6_081


title: can_Ad_VEGF_60_Day_G6_082


title: can_Ad_VEGF_60_Day_DC101_094

source_name: Flank tissue_Ad-VEGF-A164_day 60_DC101 treated

value: DC101 20 mpk at day 60

value: Ad_VEGF_Vasculature, DC101 treated


title: can_Ad_VEGF_60_Day_DC101_090


title: PBMC, sorted CD3+CD4+CD8-CD57+PD1- HC097

source_name: HC097, PBMC, CD57+


title: PBMC, sorted CD3+CD4+CD8-CD57-PD1- HC097

source_name: HC097, PBMC, CD57-


title: CC 133


title: can_Ad_VEGF_60_Day_DC101_091


title: PBMC, sorted CD3+CD4+CD8-CD57+PD1- HC052

source_name: HC052, PBMC, CD57+


title: GB 134


title: can_Ad_VEGF_60_Day_DC101_093


title: can_Ad_VEGF_60_Day_DC101_092


title: PBMC, sorted CD3+CD4+CD8-CD57-PD1- HC044

source_name: HC044, PBMC, CD57-


title: CC 131


title: PBMC, sorted CD3+CD4+CD8-CD57+PD1- HC044

source_name: HC044, PBMC, CD57+


title: PBMC, sorted CD3+CD4+CD8-CD57-PD1- HC052

source_name: HC052, PBMC, CD57-


title: GB 132


title: CC 130

source_name: Large Intestine


title: can_Ad_VEGF_20_Day_NT_056

source_name: Flank tissue_Ad-VEGF-A164_day 20_No Treatment


title: can_Ad_VEGF_20_Day_NT_055


title: CC 121


title: can_Ad_VEGF_60_Day_DC101_089


title: can_Ad_VEGF_20_Day_NT_053


title: can_Ad_VEGF_20_Day_NT_051


title: Glioma  patient 49

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data is log2-transformed.

source_name: Human brain tumor tissue from Glioma patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: not applicable

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

treatment_protocol: not applicable

value: glioma

value: Male

tag: age (years)

tag: kps

tag: pathological diagnosis

value: GBM

tag: who grade

tag: outcome

value: DEAD

tag: survival time (days)


title: can_Ad_VEGF_20_Day_NT_054

tag: strain


title: Glioma  patient 50

tag: disease state

value: Female


title: Glioma  patient 48


title: Glioma  patient 47

value: Anaplastic oligodendroglioma

value: ALIVE


title: GB 118

source_name: Central Nervous System

value: cancer


title: can_Ad_VEGF_20_Day_NT_050

tag: age

value: 4-6 week old

value: female


title: can_Ad_VEGF_20_Day_NT_052

tag: gender

value: Ad_VEGF_Vasculature, No Treatment

value: flank


title: Glioma  patient 45


title: CC 117


title: Glioma  patient 46

value: Anaplastic astrocytoma


title: CC 115


title: CC 116


title: can_Ad_VEGF_20_Day_NT_049

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

tag: injected with


title: Colon 114

value: normal


title: Glioma  patient 44


title: can_Ad_VEGF_20_Day_G6_064

source_name: Flank tissue_Ad-VEGF-A164_day 20_G6 treated

tag: treated with

value: G6 10 mpk at day 20

value: Ad_VEGF_Vasculature, G6 treated


title: Glioma  patient 43

value: glioma


title: CC 113


title: can_Ad_VEGF_20_Day_G6_063

tag: sample status


title: Colon 112


title: can_Ad_VEGF_20_Day_G6_061

tag: tissue


title: Glioma  patient 41


title: can_Ad_VEGF_20_Day_G6_062


title: CC 111


title: Glioma  patient 42


title: Glioma  patient 39


title: can_Ad_VEGF_20_Day_G6_060


title: CC 110


title: Glioma  patient 40

value: Anaplastic oligoastrocytoma


title: can_Ad_VEGF_20_Day_G6_059


title: PBMC, sorted CD3+CD4+CD8-CD57+PD1- HC093

source_name: HC093, PBMC, CD57+

tag: array facility id

tag: cell type

value: T cell


title: CC 109


title: Glioma  patient 36

value: GBM

value: DEAD


title: Glioma  patient 37

value: Female


title: Glioma  patient 38

value: Male

value: ALIVE


title: can_Ad_VEGF_20_Day_G6_057

value: 4-6 week old


title: CC 107

value: cancer


title: can_Ad_VEGF_20_Day_G6_058

value: female


title: can_Ad_VEGF_20_Day_DC101_072

source_name: Flank tissue_Ad-VEGF-A164_day 20_DC101 treated

value: DC101 20 mpk at day 20

value: Ad_VEGF_Vasculature, DC101 treated

value: flank


title: Glioma  patient 35


title: can_Ad_VEGF_20_Day_DC101_071

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)


title: can_Ad_VEGF_20_Day_DC101_070


title: CC 106


title: Glioma  patient 34


title: Glioma  patient 32

value: Astrocytoma


title: CC 105


title: Blood_obsessive-compulsive disorder_193

city: Tokushima

first: Hidehiro

last: Umehara

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate School

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

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

data_processing: Data processing was done using GenomeStudio (Illumina)

label: Biotin (C, G), DNP (A,T)

source_name: DNA from blood

label_protocol: 500ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using Multi-Sample Amplification Master Mix (MSM) and primer/neutralization mix (MA1 & MA2 & 0.1N NaOH). After incubation the amplified DNA was fragmented with Fragmentation solution (FMS), precipitated with isopropanol and Precipitation solution (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using the QIAamp DNA Blood Maxi Kit (Qiagen) according to the manufacturers protocol

value: blood

tag: treatment response

value: NonResponder

tag: dosage

value: Escitalopram 40mg Quetiapine 25mg


title: CC 104


title: can_Ad_VEGF_20_Day_DC101_069


title: Glioma  patient 33

value: glioma

tag: age (years)

tag: kps


title: can_Ad_VEGF_20_Day_DC101_068


title: CC 103


title: Glioma  patient 30

tag: pathological diagnosis

value: Anaplastic astrocytoma

tag: who grade


title: Glioma  patient 31

value: GBM

tag: outcome

value: DEAD

tag: survival time (days)


title: Blood_obsessive-compulsive disorder_188

value: Female

value: Responder to SSRI

value: Paroxetine 50mg


title: Blood_obsessive-compulsive disorder_189

value: Male

value: Responder to SSRI combination with antipsychotic

value: Paroxetine 60mg Olanzapine 10mg


title: CC 108

tag: disease state

value: cancer


title: can_Ad_VEGF_20_Day_DC101_066

tag: strain

tag: age

value: 4-6 week old

value: female

value: DC101 20 mpk at day 20

value: Ad_VEGF_Vasculature, DC101 treated

value: flank


title: Glioma  patient 29

tag: gender

value: Anaplastic oligodendroglioma


title: can_Ad_VEGF_20_Day_DC101_067

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

tag: injected with

tag: treated with


title: CC 98


title: Blood_obsessive-compulsive disorder_191

tag: tissue

value: blood

value: NonResponder

value: Sertraline200mg   Aripiprazole 3mg


title: CC 97


title: Blood_obsessive-compulsive disorder_190

value: Female

value: Paroxetine 40mg


title: Blood_obsessive-compulsive disorder_187

value: Paroxetine 50mg Aripiprazole 3mg


title: Colon 83

value: normal


title: Glioma  patient 28

value: glioma

value: GBM

value: DEAD


title: Blood_obsessive-compulsive disorder_183

value: Male

value: Responder to SSRI

value: Paroxetine 50mg


title: can_Ad_VEGF_5_Day_NT_007

source_name: Flank tissue_Ad-VEGF-A164_day 5_No Treatment

value: 4-6 week old

value: female

tag: sample status

value: Ad_VEGF_Vasculature, No Treatment


title: Blood_obsessive-compulsive disorder_186


title: can_Ad_VEGF_5_Day_NT_008

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: flank


title: Glioma  patient 25

value: Astrocytoma

value: ALIVE


title: Glioma  patient 26


title: Glioma  patient 27


title: CC 81

value: cancer


title: Blood_obsessive-compulsive disorder_184

value: Female

value: blood

value: Fluvoxamine 300mg


title: Blood_obsessive-compulsive disorder_182

value: Paroxetine 60mg


title: Blood_obsessive-compulsive disorder_178

value: Paroxetine 50㎎


title: can_Ad_VEGF_5_Day_NT_006


title: Glioma  patient 24

value: glioma

value: GBM

value: DEAD


title: CC 79


title: CC 84


title: White matter 77

value: normal


title: Blood_obsessive-compulsive disorder_179

value: Responder to SSRI

value: Fluvoxamine 200mg


title: Blood_obsessive-compulsive disorder_180

value: Responder to SSRI combination with antipsychotic

value: Paroxetine 40mg Risperidone 0.5mg


title: Glioma  patient 23


title: can_Ad_VEGF_5_Day_NT_004

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: 4-6 week old

value: female

value: Ad_VEGF_Vasculature, No Treatment

value: flank


title: Glioma  patient 22

value: Male


title: CC 76

value: cancer


title: Blood_obsessive-compulsive disorder_169

value: blood

value: Sertraline 200mg


title: Glioma  patient 21

value: glioma


title: Blood_obsessive-compulsive disorder_172

value: Female

value: NonResponder

value: Fluvoxamine 250mg Aripiprazole 18mg


title: can_Ad_VEGF_5_Day_NT_003


title: Blood_obsessive-compulsive disorder_176

value: Responder to SSRI

value: Sertraline 150mg


title: can_Ad_VEGF_5_Day_NT_002


title: Glioma  patient 20

value: GBM

value: DEAD


title: Colon 75

value: normal


title: Glioma  patient 19


title: can_Ad_VEGF_5_Day_NT_001

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: 4-6 week old


title: Blood_obsessive-compulsive disorder_170

value: Paroxetine 40mg


title: CC 73


title: can_Ad_VEGF_5_Day_G6_016

source_name: Flank tissue_Ad-VEGF-A164_day 5_G6 treated

value: female

value: G6 10 mpk at day 5

value: Ad_VEGF_Vasculature, G6 treated

value: flank


title: Blood_obsessive-compulsive disorder_174

value: blood

value: ParoxetineCR 50mg


title: CC 72

value: cancer


title: CC 71


title: can_Ad_VEGF_5_Day_NT_005

value: Ad_VEGF_Vasculature, No Treatment


title: Blood_obsessive-compulsive disorder_173

value: Male

value: Paroxetine 60mg


title: Blood_obsessive-compulsive disorder_163

value: NonResponder

value: Paroxetine60mg Risperidone1.5mg


title: Glioma  patient 17

value: glioma

value: Anaplastic astrocytoma

value: DEAD


title: can_Ad_VEGF_5_Day_G6_014

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: 4-6 week old


title: Glioma  patient 18

value: Female

value: GBM


title: GB 67


title: can_Ad_VEGF_5_Day_G6_015

value: female

value: G6 10 mpk at day 5

value: Ad_VEGF_Vasculature, G6 treated


title: CC 65


title: CC 74


title: Glioma  patient 15


title: Glioma  patient 16


title: can_Ad_VEGF_5_Day_G6_013

value: flank


title: Blood_obsessive-compulsive disorder_165

value: blood

value: Responder to SSRI

value: Escitalopram 20mg


title: Blood_obsessive-compulsive disorder_166

value: Paroxetine 40mg


title: Colon 64

value: normal


title: Blood_obsessive-compulsive disorder_162


title: can_Ad_VEGF_20_Day_DC101_065

value: DC101 20 mpk at day 20

value: Ad_VEGF_Vasculature, DC101 treated


title: Glioma  patient 14

value: glioma


title: CC 63

value: cancer


title: can_Ad_VEGF_5_Day_G6_011

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)


title: Glioma  patient 13

value: DEAD


title: Blood_obsessive-compulsive disorder_158

value: Male

value: Responder to SSRI combination with antipsychotic

value: Paroxetine 60mg Perospirone 4mg


title: can_Ad_VEGF_5_Day_G6_010

value: 4-6 week old

value: female

value: G6 10 mpk at day 5


title: Blood_obsessive-compulsive disorder_160

value: blood

value: NonResponder

value: Paroxetine 60mg Olanzapine 10mg


title: can_Ad_VEGF_5_Day_G6_009

value: Ad_VEGF_Vasculature, G6 treated

value: flank


title: Glioma  patient 12

value: GBM


title: Blood_obsessive-compulsive disorder_161

value: Female

value: Escitalopram 40mg Risperidone0.5mg


title: can_Ad_VEGF_5_Day_DC101_024

source_name: Flank tissue_Ad-VEGF-A164_day 5_DC101 treated

value: DC101 20 mpk at day 5

value: Ad_VEGF_Vasculature, DC101 treated


title: CC 62

value: cancer


title: CC 60


title: can_Ad_VEGF_5_Day_G6_012

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)


title: BC 4

source_name: Breast


title: can_Ad_VEGF_5_Day_DC101_023


title: Glioma  patient 10

value: glioma

value: Male

value: Anaplastic oligoastrocytoma

value: DEAD


title: can_Ad_VEGF_5_Day_DC101_022

value: 4-6 week old

value: female


title: Glioma  patient 9


title: Glioma  patient 8


title: Glioma  patient 11

value: Anaplastic astrocytoma


title: Blood_obsessive-compulsive disorder_157

value: blood

value: Responder to SSRI combination with antipsychotic

value: Fluvoxamine 300mg Aripiprazole 6mg


title: Blood_obsessive-compulsive disorder_152

value: NonResponder

value: Paroxetine 50mg Risperidone 0.5mg


title: can_Ad_VEGF_5_Day_DC101_021

value: flank


title: Blood_obsessive-compulsive disorder_148

value: Female

value: Responder to SSRI

value: Paroxetine 30mg


title: Blood_obsessive-compulsive disorder_153

value: Paroxetine 60mg


title: Blood_obsessive-compulsive disorder_147

value: Paroxetine 40mg Risperidone 2mg


title: Colon 61

value: normal


title: can_Ad_VEGF_5_Day_DC101_019

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: DC101 20 mpk at day 5

value: Ad_VEGF_Vasculature, DC101 treated


title: can_Ad_VEGF_5_Day_DC101_020

value: 4-6 week old

value: female


title: can_Ad_VEGF_5_Day_DC101_018


title: Blood_obsessive-compulsive disorder_144

value: Male

value: blood

value: Paroxetine 50mg


title: Glioma patient 4

value: glioma

value: Anaplastic oligodendroglioma

value: DEAD


title: Glioma patient 5

value: Female

value: GBM


title: Glioma patient 7

value: Astrocytoma

value: ALIVE


title: can_Ad_VEGF_Normal_102

source_name: Flank tissue_control_day 0

value: control

value: flank


title: Blood_obsessive-compulsive disorder_142

value: Responder to SSRI


title: Glioma patient 3


title: can_Ad_VEGF_5_Day_DC101_017

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: DC101 20 mpk at day 5


title: Glioma patient 6

value: Anaplastic astrocytoma


title: Blood_obsessive-compulsive disorder_146


title: Blood_obsessive-compulsive disorder_132

value: Responder to SSRI combination with antipsychotic

value: Fluvoxamine 300mg Perospirone 2mg


title: Glioma patient 2

value: Male


title: Blood_obsessive-compulsive disorder_129

value: blood

value: Paroxetine 50mg Aripiprazole 12mg


title: genomic DNA from normal nasopharyngeal epithelial tissue 22

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

description: SAMPLE 46

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina Genomestudio 2011，Methylation 1.9.0

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from  samples using Qiagen DNeasy Kit according to standard instructions

value: female

tag: tissue type

value: normal nasopharyngeal epithelial


title: genomic DNA from normal nasopharyngeal epithelial tissue 23

description: SAMPLE 47

value: male


title: ChIP-USF1 (sc)

city: Niigata

first: Tomoyuki

address: 1-757 Asahimachidori, Chuo-ku

department: Brain Research Institute

institute: Niigata University

hyb_protocol: The labeled DNAs were hybridized to Affymetrix GeneChip Mouse Promoter 1.0R Arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The obtained data were analyzed using CisGenome software to identify transcription factor-binding regions with high signals compared with those of the control.

source_name: Brain cortical lysates

label_protocol: The ChIP DNAs were amplified with sequenase and rTaq polymerase and then labeled with biotin according to the ChIP Assay Protocol (Affymetrix).

extract_protocol: Cortices were isolated from 8-week-old B6_CBA hybrid male mice, and then fixed, lyzed, sonicated, and processed for ChIP.

value: Brain cortical lysates


title: genomic DNA from normal nasopharyngeal epithelial tissue 24

description: SAMPLE 48


title: Blood_obsessive-compulsive disorder_139

value: Female

tag: treatment response

value: Fluvoxamine 300mg


title: can_Ad_VEGF_Normal_100

value: 4-6 week old

value: control


title: Glioma patient 1

value: glioma

value: GBM

value: DEAD


title: can_Ad_VEGF_Normal_101

value: athymic nude mice (Charles River Crl:NU(NCr)-Foxn1nu , Strain #490)

value: flank


title: ChIP-USF1 (C-2)


title: can_Ad_VEGF_Normal_099


title: ChIP-NF-Y (YC6-3)


title: ChIP-NF-Y (YAsc)


title: genomic DNA from normal nasopharyngeal epithelial tissue 20

description: SAMPLE 44


title: genomic DNA from normal nasopharyngeal epithelial tissue 21

description: SAMPLE 45


title: can_Ad_VEGF_Normal_098


title: can_Ad_VEGF_Normal_097


title: ChIP-NF-Y (YA2-3)


title: Blood_obsessive-compulsive disorder_122

value: Responder to SSRI

tag: dosage


title: Blood_obsessive-compulsive disorder_118

value: Male

value: Sertraline 250mg


title: Blood_obsessive-compulsive disorder_124

value: blood

value: Paroxetine 40mg


title: ChIP-Rb IgG


title: Blood_obsessive-compulsive disorder_131

value: Paroxetine 60mg


title: can_Ad_VEGF_Normal_096

value: female


title: can_Ad_VEGF_Normal_095


title: Blood_obsessive-compulsive disorder_112


title: genomic DNA from normal nasopharyngeal epithelial tissue 19

description: SAMPLE 43

value: male

value: normal nasopharyngeal epithelial


title: genomic DNA from normal nasopharyngeal epithelial tissue 18

description: SAMPLE 42


title: Blood_obsessive-compulsive disorder_97

value: Responder to SSRI combination with antipsychotic

value: Sertraline 150mg Olanzapine 20mg


title: UPEC and Mycoplasma

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

country: South Korea

institute: Chonbuk National University

description: UPEC without or with M. hominis

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing:
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).
The averages of normalized ratios were calculated by dividing the average of normalized test channel intensity by the average of normalized control channel intensity.

organism: Escherichia coli CFT073

source_name: UPEC biofilm alone

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).

growth_protocol: UPEC biofilms were formed on glass wool with or without M. hominis (10^5 ccu/ml) using overnight cultures to inoculate 250 ml of 1/5 diluted LB medium with 10 g of glass wool (Corning Glass Works).  After incubation for 24 h with shaking (250 rpm), biofilm cells were prepared by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C.

extract_protocol: After culturing UPEC CFT073 cells, bacterial cells were distrupted with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) and Rnase free-DNase I treatment (Qiagen)

treatment_protocol: For infection with M. hominis, UPEC biofilms were cultured on glass wool with or without M. hominis (10^5 ccu/ml)

tag: cultured

value: alone

source_name: UPEC biofilm with M. hominis

tag: cultured with

value: Mycoplasma hominis PG21 (10^5 ccu/ml)


title: genomic DNA from normal nasopharyngeal epithelial tissue 16

description: SAMPLE 40


title: # 2VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy3 and  # 2VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy5

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-, Hif2a-/-_logRatio
mouse number 2VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy3 labeled and mouse number_ 2VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy5 labeled.

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
Data were processed using R Bioconductor (limma). For the final analysis the gene expression levels were dye effect corrected and values for biological replicates were averaged to obtain a matrix with gene expression levels for 4 independent biological conditions (Vhlh-/-, Vhlh-/-/Hif1α-/-, Vhlh-/-/Hif2α-/- and Vhlh-/-/Hif1α-/-/Hif2α-/-).
normalized log2 ratio (Cy5/Cy3) representing values for primary kidney cells with defined alleles floxed infected either with CRE-GFP adenovirus (excision) or GFP adenovirus (control).

source_name: Animal 2. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy3

label_protocol: standard Agilent protocol

growth_protocol: Kidneys were dissected from 2-month-old floxed mice. After removing the capsule under sterile conditions, kidneys were mashed with a razor blade on ice and digested in collagenase II (Gibco) and soya trypsin inhibitor (Gibco) solution at 37°C for 30 min. The cell suspension was filtered through a 70 µm cell strainer and washed in HBSS + 5% FCS. Erythrocytes were lysed for 1 min using standard ACK buffer. Cells were resuspended in complete K-1 culture medium [Dulbecco's modified Eagle's medium (DMEM):Hams F12] (50:50), supplemented with 0.5% foetal calf serum, hormone mix [5 µg/ml insulin, 1.25 ng/ml prostaglandin E1 (PGE1), 34 pg/ml triiodothyronine, 5 µg/ml Apo-transferrin, 1.73 ng/ml sodium selenite and 18 ng/ml of hydrocortisone] and 25 ng/ml epidermal growth factor (EGF). Cells were counted and seeded at a density of 1 × 106 cells on standard 100 mm plastic tissue culture plates.

extract_protocol: Machery Nagel Nucleospin RNA II according to producer instructions.

treatment_protocol: After 5–6 days in culture, cells were infected with adenoviruses expressing GFP (Vector Biolabs, 1060) or Cre-GFP (Vector Biolabs, 1700).

tag: Sex

tag: cell type

value: primary kidney epithelial cell

value: 50 days (adult)

source_name: and Animal 2; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy5 labeled.


title: # 2VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 2VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-, Hif2a-/-_logRatio
mouse number 2VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 2VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: # 3VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy3 and  # 3VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy5

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-, Hif2a-/-_logRatio
mouse number 3VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy3 labeled and mouse number_ 3VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy5 labeled.

source_name: Animal 3. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy3

source_name: and Animal 3; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy5 labeled.


title: genomic DNA from normal nasopharyngeal epithelial tissue 17

description: SAMPLE 41


title: Blood_obsessive-compulsive disorder_95

value: Female


title: Blood_obsessive-compulsive disorder_110

value: Paroxetine 60mg Risperidone 0.5mg


title: genomic DNA from normal nasopharyngeal epithelial tissue 15

description: SAMPLE 39


title: genomic DNA from normal nasopharyngeal epithelial tissue 14

description: SAMPLE 38


title: Blood_obsessive-compulsive disorder_88

value: Responder to SSRI


title: # 2VHL/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 2VHL/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif2a-/-_logRatio
mouse number 2VHL/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 2VHL/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2; Primary kidney epithelial cells from Vhlh flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2. Primary kidney epithelial cells from Vhlh flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: genomic DNA from normal nasopharyngeal epithelial tissue 12

description: SAMPLE 36


title: # 1VHL/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy3 and  # 1VHL/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy5

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif2a-/-_logRatio
mouse number 1VHL/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy3 labeled and mouse number_ 1VHL/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy5 labeled.

source_name: Animal 1. Primary kidney epithelial cells from Vhlh flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy3

source_name: and Animal 1; Primary kidney epithelial cells from Vhlh flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy5 labeled.


title: Blood_obsessive-compulsive disorder_105

source_name: DNA from blood

value: Male


title: # 3VHL/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 3VHL/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif2a-/-_logRatio
mouse number 3VHL/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 3VHL/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 3; Primary kidney epithelial cells from Vhlh flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 3. Primary kidney epithelial cells from Vhlh flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: genomic DNA from normal nasopharyngeal epithelial tissue 11

description: SAMPLE 35


title: genomic DNA from normal nasopharyngeal epithelial tissue 13

description: SAMPLE 37


title: Blood_obsessive-compulsive disorder_61

value: Fluvoxamine 100mg


title: # 3VHL/HIF1A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 3VHL/HIF1A Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-_logRatio
mouse number 3VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 3VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 3; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 3. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: genomic DNA from normal nasopharyngeal epithelial tissue 10

description: SAMPLE 34


title: cancerous, RNAlater, Patient 33, renal biopsy

type: SRA

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

description:
TR33
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Assembly of reads and alignment of the contigs to the Human genome assembly GRCh38 was guided by Tophat and Bowtie
logcpm (counts per million) were calculated using EdgeR (R bioconductor)
features with logcpm>=15 in at least 8 samples were considered further
Raw data are being submitted to EGA.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: Eikrem_et_al_count_matrix.txt, Eikrem_et_al_logcpm_matrix_filtered.txt

molecule: polyA RNA

source_name: renal biopsy

extract_protocol:
Total RNA was extracted with miRNeasy FFPE kit for samples stored in FFPE, or miRNeasy micro kit (Qiagen) in the case of RNAlater storage.
RNA sequencing libraries were prepared using TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol.
RNA-seq exome capture

tag: individual

value: patient 33

value: ccRCC (clear cell renal cell carcinoma)

tag: storage

value: RNAlater (Qiagen)

tag: tumor stage

value: I

tag: fuhrmann degree

tag: nephroctomy type

value: Partial


title: # 1VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 1VHL/HIF1A/HIF2A Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-, Hif2a-/-_logRatio
mouse number 1VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 1VHL/HIF1A/HIF2A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 1; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

value: female

tag: age

source_name: Animal 1. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox, Hif2a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: genomic DNA from normal nasopharyngeal epithelial tissue 8

description: SAMPLE 32

tag: gender

value: male

value: normal nasopharyngeal epithelial


title: # 1VHL/HIF1A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy3 and  # 1VHL/HIF1A Vhlh fl/fl w/ Adeno-GFP. Control Cy5

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-_logRatio
mouse number 1VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy3 labeled and mouse number_ 1VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy5 labeled.

source_name: Animal 1. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy3.

source_name: Animal 1; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy5 labeled.


title: # 2VHL/HIF1A Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 2VHL/HIF1A Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for Vhlh-/-, Hif1a-/-_logRatio
mouse number 2VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 2VHL/HIF1A_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2; Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2. Primary kidney epithelial cells from Vhlh flox/flox, Hif1a flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: Blood_obsessive-compulsive disorder_57

value: blood

value: NonResponder

value: Paroxetine 50mg Perospirone 8mg


title: Blood_obsessive-compulsive disorder_58

value: Paroxetine 60mg


title: Blood_obsessive-compulsive disorder_60

value: Responder to SSRI combination with antipsychotic

value: Fluvoxamine 300mg Olanzapine 5mg


title: genomic DNA from normal nasopharyngeal epithelial tissue 6

description: SAMPLE 30


title: cancerous, FFPE, Patient 33, renal biopsy

description:
TF33
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE


title: Blood_obsessive-compulsive disorder_55

value: Female

value: Responder to SSRI

value: Paroxetine 50mg


title: non-cancerous, FFPE, Patient 33, renal biopsy

description:
NF33
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 33

value: non-cancerous


title: Blood_obsessive-compulsive disorder_54

value: Male

value: Paroxetine 40mg  Risperidone 1mg


title: Blood_obsessive-compulsive disorder_84

value: Sertraline 150mg


title: Blood_obsessive-compulsive disorder_59

value: Paroxetine 40mg


title: non-cancerous, RNAlater, Patient 33, renal biopsy

description:
NR33
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: RNAlater (Qiagen)

value: I

value: Partial

value: male


title: # 2VHL Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 2VHL Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for VHL-/- logRatio
mouse number 2VHL_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 2VHL_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 2; Primary kidney epithelial cells from Vhlh flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

value: female

value: primary kidney epithelial cell

value: 50 days (adult)

source_name: Animal 2. Primary kidney epithelial cells from Vhlh flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: genomic DNA from normal nasopharyngeal epithelial tissue 7

description: SAMPLE 31

value: normal nasopharyngeal epithelial


title: cancerous, RNAlater, Patient 32, renal biopsy

description:
TR32
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 32

value: ccRCC (clear cell renal cell carcinoma)


title: # 1VHL Vhlh fl/fl w/ Adeno-Cre-GFP  Cy3 and  # 1VHL Vhlh fl/fl w/ Adeno-GFP. Control Cy5

description:
One of the biological replicates avaraged to obtain values for VHL-/- logRatio
mouse number 1VHL_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy3 labeled and mouse number_ 1VHL_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy5 labeled.

source_name: Animal 1. Primary kidney epithelial cells from Vhlh flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy3

source_name: Animal 1; Primary kidney epithelial cells from Vhlh flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy5 labeled.


title: non-cancerous, RNAlater, Patient 32, renal biopsy

description:
NR32
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: genomic DNA from normal nasopharyngeal epithelial tissue 5

description: SAMPLE 29


title: genomic DNA from normal nasopharyngeal epithelial tissue 9

description: SAMPLE 33


title: genomic DNA from normal nasopharyngeal epithelial tissue 3

description: SAMPLE 27


title: non-cancerous, FFPE, Patient 32, renal biopsy

description:
NF32
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE


title: Blood_obsessive-compulsive disorder_52

value: Female

value: blood

value: Responder to SSRI

value: Fluvoxamine 50mg


title: genomic DNA from normal nasopharyngeal epithelial tissue 2

description: SAMPLE 26


title: genomic DNA from normal nasopharyngeal epithelial tissue 4

description: SAMPLE 28


title: cancerous, FFPE, Patient 32, renal biopsy

description:
TF32
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: Blood_obsessive-compulsive disorder_44

value: Responder to SSRI combination with antipsychotic

value: Sertraline100mg Perospirone 4mg


title: non-cancerous, RNAlater, Patient 31, renal biopsy

description:
NR31
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 31

value: non-cancerous

value: RNAlater (Qiagen)


title: genomic DNA from nasopharyngeal carcinoma tissue 24

description: SAMPLE 24

source_name: nasopharyngeal carcinoma tissue 24

value: male

value: nasopharyngeal carcinoma


title: genomic DNA from normal nasopharyngeal epithelial tissue 1

description: SAMPLE 25


title: Blood_obsessive-compulsive disorder_45

source_name: DNA from blood

value: Paroxetine 30mg


title: cancerous, FFPE, Patient 31, renal biopsy

description:
TF31
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: I

value: Partial


title: Blood_obsessive-compulsive disorder_42

value: Male

value: Paroxetine 20mg


title: Blood_obsessive-compulsive disorder_40

value: Fluvoxamine 300mg


title: Blood_obsessive-compulsive disorder_49

value: Female

value: Sertraline 200mg


title: cancerous, RNAlater, Patient 31, renal biopsy

description:
TR31
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: ccRCC (clear cell renal cell carcinoma)


title: non-cancerous, FFPE, Patient 31, renal biopsy

description:
NF31
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE


title: Blood_obsessive-compulsive disorder_39

value: blood

value: NonResponder

value: Sertraline 200mg Risperidone 1mg


title: cancerous, RNAlater, Patient 29, renal biopsy

description:
TR29
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 29

value: female


title: genomic DNA from nasopharyngeal carcinoma tissue 23

description: SAMPLE 23

source_name: nasopharyngeal carcinoma tissue 23

value: male


title: genomic DNA from nasopharyngeal carcinoma tissue 22

description: SAMPLE 22

source_name: nasopharyngeal carcinoma tissue 22

value: nasopharyngeal carcinoma


title: non-cancerous, RNAlater, Patient 29, renal biopsy

description:
NR29
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: non-cancerous

value: RNAlater (Qiagen)


title: # 3VHL Vhlh fl/fl w/ Adeno-Cre-GFP  Cy5 and  # 3VHL Vhlh fl/fl w/ Adeno-GFP. Control Cy3

description:
One of the biological replicates avaraged to obtain values for VHL-/- logRatio
mouse number 3VHL_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-Cre-GFP virus Cy5 labeled and mouse number_ 3VHL_primary kidney epithelial cells from Vhlh flox/flox infected with Adeno-GFP virus. Control cell culture Cy3 labeled.

source_name: Animal 3; Primary kidney epithelial cells from Vhlh flox/flox animal. Cells treated with Adeno-GFP virus. Control cell culture Cy3 labeled.

value: primary kidney epithelial cell

value: 50 days (adult)

source_name: Animal 3. Primary kidney epithelial cells from Vhlh flox/flox animals. Cells treated with Adeno-Cre-GFP virus labeled with Cy5.


title: cancerous, FFPE, Patient 29, renal biopsy

description:
TF29
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

source_name: renal biopsy

value: I

value: Partial


title: Blood_obsessive-compulsive disorder_47

value: Female

value: Responder to SSRI

value: Paroxetine 60mg


title: genomic DNA from nasopharyngeal carcinoma tissue 19

description: SAMPLE 19

source_name: nasopharyngeal carcinoma tissue 19


title: genomic DNA from nasopharyngeal carcinoma tissue 18

description: SAMPLE 18

source_name: nasopharyngeal carcinoma tissue 18


title: genomic DNA from nasopharyngeal carcinoma tissue 21

description: SAMPLE 21

source_name: nasopharyngeal carcinoma tissue 21


title: Blood_obsessive-compulsive disorder_41

value: Fluvoxamine 300mg Aripiprazole 24mg


title: genomic DNA from nasopharyngeal carcinoma tissue 20

description: SAMPLE 20

source_name: nasopharyngeal carcinoma tissue 20


title: non-cancerous, FFPE, Patient 29, renal biopsy

description:
NF29
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE


title: cancerous, FFPE, Patient 27, renal biopsy

description:
TF27
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 27

value: ccRCC (clear cell renal cell carcinoma)

value: II

value: Full


title: cancerous, RNAlater, Patient 27, renal biopsy

description:
TR27
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: male


title: non-cancerous, RNAlater, Patient 27, renal biopsy

description:
NR27
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: Blood_obsessive-compulsive disorder_36

value: blood

value: Responder to SSRI combination with antipsychotic

value: Paroxetine 60mg Risperidone 1mg


title: Blood_obsessive-compulsive disorder_34

value: Male

value: Paroxetine 60mg Olanzapine 2.5mg


title: non-cancerous, FFPE, Patient 27, renal biopsy

description:
NF27
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: non-cancerous


title: genomic DNA from nasopharyngeal carcinoma tissue 16

description: SAMPLE 16

source_name: nasopharyngeal carcinoma tissue 16

value: nasopharyngeal carcinoma


title: Blood_obsessive-compulsive disorder_37

value: Paroxetine 40mg


title: genomic DNA from nasopharyngeal carcinoma tissue 15

description: SAMPLE 15

source_name: nasopharyngeal carcinoma tissue 15


title: genomic DNA from nasopharyngeal carcinoma tissue 17

description: SAMPLE 17

source_name: nasopharyngeal carcinoma tissue 17


title: Blood_obsessive-compulsive disorder_33

value: Responder to SSRI


title: Blood_obsessive-compulsive disorder_35

value: Female


title: cancerous, RNAlater, Patient 24, renal biopsy

description:
TR24
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 24

value: RNAlater (Qiagen)

value: I

value: Partial


title: non-cancerous, RNAlater, Patient 24, renal biopsy

description:
NR24
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: genomic DNA from nasopharyngeal carcinoma tissue 13

description: SAMPLE 13

source_name: nasopharyngeal carcinoma tissue 13

value: female


title: Blood_obsessive-compulsive disorder_29

value: Fluvoxamine 100mg


title: genomic DNA from nasopharyngeal carcinoma tissue 14

description: SAMPLE 14

source_name: nasopharyngeal carcinoma tissue 14


title: cancerous, FFPE, Patient 24, renal biopsy

description:
TF24
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: ccRCC (clear cell renal cell carcinoma)

value: FFPE

value: male


title: genomic DNA from nasopharyngeal carcinoma tissue 11

description: SAMPLE 11

source_name: nasopharyngeal carcinoma tissue 11


title: Blood_obsessive-compulsive disorder_30

value: blood

value: Fluvoxamine 300mg


title: genomic DNA from nasopharyngeal carcinoma tissue 12

description: SAMPLE 12

source_name: nasopharyngeal carcinoma tissue 12


title: non-cancerous, FFPE, Patient 24, renal biopsy

description:
NF24
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: genomic DNA from nasopharyngeal carcinoma tissue 10

description: SAMPLE 10

source_name: nasopharyngeal carcinoma tissue 10


title: Blood_obsessive-compulsive disorder_32

source_name: DNA from blood

value: NonResponder

value: Paroxetine 60mg Olanzapine 5mg


title: non-cancerous, RNAlater, Patient 22, renal biopsy

description:
NR22
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 22

value: non-cancerous


title: genomic DNA from nasopharyngeal carcinoma tissue 8

description: SAMPLE 8

source_name: nasopharyngeal carcinoma tissue 8

value: nasopharyngeal carcinoma


title: Blood_obsessive-compulsive disorder_27

value: Male

value: Responder to SSRI combination with antipsychotic

value: Paroxetine 60mg Risperidone 0.5mg


title: Blood_obsessive-compulsive disorder_28

value: Paroxetine 30mg Olanzapine 5mg


title: genomic DNA from nasopharyngeal carcinoma tissue 9

description: SAMPLE 9

source_name: nasopharyngeal carcinoma tissue 9


title: cancerous, FFPE, Patient 22, renal biopsy

description:
TF22
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: I

value: Partial


title: non-cancerous, FFPE, Patient 22, renal biopsy

description:
NF22
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: genomic DNA from nasopharyngeal carcinoma tissue 6

description: SAMPLE 6

source_name: nasopharyngeal carcinoma tissue 6


title: cancerous, RNAlater, Patient 22, renal biopsy

description:
TR22
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

source_name: renal biopsy

value: RNAlater (Qiagen)


title: genomic DNA from nasopharyngeal carcinoma tissue 5

description: SAMPLE 5

source_name: nasopharyngeal carcinoma tissue 5


title: genomic DNA from nasopharyngeal carcinoma tissue 7

description: SAMPLE 7

source_name: nasopharyngeal carcinoma tissue 7


title: Blood_obsessive-compulsive disorder_25

value: Female

value: Responder to SSRI

value: Paroxetine 20mg


title: Blood_obsessive-compulsive disorder_26

value: blood

value: Paroxetine 40mg


title: non-cancerous, RNAlater, Patient 21, renal biopsy

description:
NR21
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 21

value: Full

value: female


title: gallbladder_rep1 [9N]

city: Shanghai

first: Huaifeng

last: Li

address: NO.1665, kongjiang road, Shanghai, China

department: general surgery

institute: Xinhua hospital affiliated to Shanghai jiaotong university, school of medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65C 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 37C 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 1x44k array slides (Scan Area 61x21.6 mm, 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 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA was extracted using TRIzol reagent(Cat.15596-026 Life technologies)and purified using QIAGEN RNeasy® Kit according to the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: tissues were cut off immediately after cholecystectomy, put into and stored in liquid nitrogen before total RNA extration

tag: subject status

value: gallbladder cancer

value: Nevin IV

value: gallbladder

tag: tissue subtype

value: paired adjacent normal gallbladder tissue after surgery


title: gallbladder_rep1 [9C]

source_name: gallbladder cancer

tag: tissue

value: gallbladder cancer tissue after surgery


title: cancerous, FFPE, Patient 21, renal biopsy

description:
TF21
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: ccRCC (clear cell renal cell carcinoma)

value: FFPE


title: Blood_obsessive-compulsive disorder_21

value: Paroxetine 60mg


title: cancerous, RNAlater, Patient 21, renal biopsy

description:
TR21
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: RNAlater (Qiagen)

value: I


title: Blood_obsessive-compulsive disorder_23

value: Female

value: NonResponder

value: Fluvoxamine 300mg  Risperidone 2mg


title: non-cancerous, FFPE, Patient 21, renal biopsy

description:
NF21
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: non-cancerous


title: Blood_obsessive-compulsive disorder_18

value: Male

value: blood

value: Responder to SSRI

value: Paroxetine 40mg


title: genomic DNA from nasopharyngeal carcinoma tissue 4

description: SAMPLE 4

source_name: nasopharyngeal carcinoma tissue 4

value: male

tag: tissue type

value: nasopharyngeal carcinoma


title: Blood_obsessive-compulsive disorder_17

tag: treatment response

value: Fluvoxamine 300mg Risperidone 1mg


title: cancerous, RNAlater, Patient 19, renal biopsy

description:
TR19
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 19

value: II

value: Full

value: female


title: genomic DNA from nasopharyngeal carcinoma tissue 2

description: SAMPLE 2

source_name: nasopharyngeal carcinoma tissue 2


title: non-cancerous, RNAlater, Patient 19, renal biopsy

description:
NR19
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: RNAlater (Qiagen)


title: gallbladder_rep1 [8C]

value: gallbladder cancer

value: Nevin I

value: gallbladder

value: gallbladder cancer tissue after surgery


title: Blood_obsessive-compulsive disorder_24

value: Responder to SSRI combination with antipsychotic

tag: dosage

value: Paroxetine 60mg Olanzapine 5mg


title: Blood_obsessive-compulsive disorder_16

value: Male

value: blood

value: NonResponder

value: Fluvoxamine 250mg Risperidone 0.5mg


title: KO_DSS_6622

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: Gene expression data from colon of Parp1-/- mice treated with 4% DSS

hyb_protocol: According to menufacturer's (Affymetrix) protocol

data_processing: The data were analyzed with GeneSpring 13.1.1, using  ExonRMA16 summarization algorithm; quantile sample normalization with baseline transformation to median of all samples

source_name: colon,Parp1-/-, DSS

growth_protocol: 6-8 week old mice housed in conventional animal facility monitored and free of common murine pathogens (MHV, MPV, MVM, TMEV, Mycoplasma pulmonis, Sendai, EDIM, MNV, and eco- and endoparasites)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by column purification (Qiagen Mini RNA kit)

treatment_protocol: Mice were assigned to control group (continous access to plain drinking water) or to colitis group [4% dextran sulfate sodium (DSS) for 7 days]. At sacrifice, whole colon was colected, washed, and flash-frozen in liquuid N2 for RNA isolation.

value: Colon

tag: genotype

tag: treatment

value: DSS


title: gallbladder_rep1 [8N]

value: paired adjacent normal gallbladder tissue after surgery


title: genomic DNA from nasopharyngeal carcinoma tissue 3

description: SAMPLE 3

source_name: nasopharyngeal carcinoma tissue 3

value: nasopharyngeal carcinoma


title: cancerous, RNAlater, Patient 18, renal biopsy

description:
TR18
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 18

value: ccRCC (clear cell renal cell carcinoma)

value: III

value: Full

value: male


title: gallbladder_rep1 [7N]

source_name: paired adjacent normal gallbladder tissue

value: gallbladder cancer

value: female

value: Nevin IV

value: gallbladder


title: KO_DSS_6623

scan_protocol: According to menufacturer's (Affymetrix) protocol


title: cancerous, FFPE, Patient 19, renal biopsy

description:
TF19
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 19

value: FFPE

value: II


title: non-cancerous, FFPE, Patient 19, renal biopsy

description:
NF19
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: non-cancerous


title: KO_H2O_6625

description: Gene expression data from colon of Parp1-/- mice treated with H2O

source_name: colon,Parp1-/-, H2O

label_protocol: According to menufacturer's (Affymetrix) protocol

value: Colon


title: Blood_obsessive-compulsive disorder_14

value: Female

value: blood

value: NonResponder

value: Fluvoxamine 300mg Risperidone 1mg


title: genomic DNA from nasopharyngeal carcinoma tissue 1

description: SAMPLE 1

source_name: nasopharyngeal carcinoma tissue 1

value: nasopharyngeal carcinoma


title: KO_H2O_6626


title: KO_H2O_6624


title: cancerous, FFPE, Patient 18, renal biopsy

description:
TF18
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 18

value: ccRCC (clear cell renal cell carcinoma)

value: III


title: gallbladder_rep1 [6N]

value: gallbladder cancer

value: paired adjacent normal gallbladder tissue after surgery


title: WT_DSS_6619

description: Gene expression data from colon of wild-type mice treated with 4% DSS

source_name: colon, wild-type, DSS

value: wild type

value: DSS


title: gallbladder_rep1 [6C]

value: female

value: Nevin IV

value: gallbladder

value: gallbladder cancer tissue after surgery


title: non-cancerous, FFPE, Patient 18, renal biopsy

description:
NF18
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: non-cancerous

value: FFPE

value: Full

value: male


title: gallbladder_rep1 [4C]

value: Nevin II


title: Blood_obsessive-compulsive disorder_19

value: Male

value: blood

value: Responder to SSRI

value: Paroxetine 40mg


title: gallbladder_rep1 [4N]

value: gallbladder cancer


title: non-cancerous, RNAlater, Patient 16, renal biopsy

description:
NR16
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 16

value: RNAlater (Qiagen)

value: IV


title: Blood_obsessive-compulsive disorder_12

value: NonResponder

value: Fluvoxamine 300mg Risperidone 1mg


title: gallbladder_rep1 [5C]

value: female

value: Nevin III

value: gallbladder


title: Blood_obsessive-compulsive disorder_15

value: Female

value: Responder to SSRI combination with antipsychotic

value: Fluvoxamine 300mg Risperidone 0.8mg


title: KO_DSS_6620

value: Colon

value: DSS


title: WT_H2O_6616

description: Gene expression data from colon of wild-type mice treated with H2O

source_name: colon, wild-type, H2O

value: wild type


title: cancerous, FFPE, Patient 16, renal biopsy

description:
TF16
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: ccRCC (clear cell renal cell carcinoma)

value: FFPE

value: Full

value: male


title: gallbladder_rep1 [5N]

value: gallbladder cancer

value: paired adjacent normal gallbladder tissue after surgery


title: WT_DSS_6617


title: cancerous, RNAlater, Patient 16, renal biopsy

description:
TR16
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 16

value: RNAlater (Qiagen)

value: IV


title: non-cancerous, RNAlater, Patient 18, renal biopsy

description:
NR18
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 18

value: non-cancerous

value: III


title: non-cancerous, FFPE, Patient 16, renal biopsy

description:
NF16
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: Blood_obsessive-compulsive disorder_11

source_name: DNA from blood

value: Female

value: blood

value: Responder to SSRI

value: Fluvoxamine 150mg


title: WT_DSS_6618

value: Colon

value: wild type

value: DSS


title: WT_H2O_6610


title: cancerous, RNAlater, Patient 15, renal biopsy

description:
TR15
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 15

value: ccRCC (clear cell renal cell carcinoma)

value: I

value: Partial


title: gallbladder_rep1 [3C]

value: gallbladder cancer

value: female

value: Nevin IV

value: gallbladder

value: gallbladder cancer tissue after surgery


title: gallbladder_rep1 [3N]

value: paired adjacent normal gallbladder tissue after surgery


title: WT_H2O_6609


title: cancerous, FFPE, Patient 15, renal biopsy

description:
TF15
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE

value: male


title: gallbladder_rep1 [7C]


title: gallbladder_rep1 [2N]

value: Nevin II


title: non-cancerous, RNAlater, Patient 15, renal biopsy

description:
NR15
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: non-cancerous

value: RNAlater (Qiagen)


title: USFKD; biological rep 3

hyb_protocol: Labeled probes were hybridized on GeneChip Mouse Gene 1.0 ST Array.

data_processing: The data were analyzed by an Agilent GeneSpring software.

source_name: neuro2a cell line

label_protocol: The obtained RNAs were then used for preparation of labeled cDNA probes by Ambion WT Expression Kit and Affymetrix WT Terminal Labeling Kit according to the manufactures protocols.

growth_protocol: Neuro2a mouse neuroblastome cells were maintained in DMED supplemented with 10% fetal bovine serum and penicillin-streptomycin in an atmosphere containing 5% CO2.

extract_protocol: The RNAs were prepared by Qiagen RNeasy kit according to the manufacture's protocol.

treatment_protocol: For knockdown, we constructed miR RNAi expression vectors for USF1 or USF2 using pcDNA6.2-GW/EmGFP-miR vector system (Invitrogen). These RNAi expression vectors were introduced into neuro2a cells using Lipofectamine 2000 regions (Invitrogen).

tag: cell line

tag: vector


title: non-cancerous, FFPE, Patient 15, renal biopsy

description:
NF15
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

tag: individual


title: Blood_obsessive-compulsive disorder_7

value: Male

value: blood

value: Responder to SSRI combination with antipsychotic

value: Fluvoxamine 200mg Risperidone 0.5mg


title: USFKD; biological rep 1


title: cancerous, RNAlater, Patient 13, renal biopsy

description:
TR13
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 13

value: ccRCC (clear cell renal cell carcinoma)

tag: storage

value: III

value: Full


title: Control; biological rep 3

value: Empty vector


title: non-cancerous, RNAlater, Patient 13, renal biopsy

description:
NR13
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

tag: tumor stage


title: gallbladder_rep1 [2C]

value: gallbladder cancer

value: female

value: gallbladder


title: gallbladder_rep1 [1N]

value: Nevin IV

value: paired adjacent normal gallbladder tissue after surgery


title: Blood_obsessive-compulsive disorder_6

value: Female

value: Paroxetine 60mg Risperidone 0.75mg


title: Blood_obsessive-compulsive disorder_10

value: Fluvoxamine 150mg Risperidone 0.2mg


title: USFKD; biological rep 2


title: cancerous, FFPE, Patient 13, renal biopsy

description:
TF13
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE

tag: fuhrmann degree

value: male


title: Blood_obsessive-compulsive disorder_13

value: Male

value: blood

value: Responder to SSRI

value: Paroxetine 40mg


title: Control; biological rep 2


title: Blood_obsessive-compulsive disorder_8

value: Paroxetine 20mg


title: gallbladder_rep1 [1C]

value: gallbladder cancer tissue after surgery


title: Blood_obsessive-compulsive disorder_5

value: NonResponder

value: Fluvoxamine 200mg Risperidone 0.25mg


title: Control; biological rep 1

value: Empty vector


title: non-cancerous, FFPE, Patient 13, renal biopsy

description:
NF13
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 13

value: non-cancerous

value: III

tag: nephroctomy type

value: Full


title: cancerous, RNAlater, Patient 11, renal biopsy

description:
TR11
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 11

value: ccRCC (clear cell renal cell carcinoma)

value: RNAlater (Qiagen)

value: I

value: Partial


title: cancerous, FFPE, Patient 11, renal biopsy

description:
TF11
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: FFPE

value: male


title: Blood_obsessive-compulsive disorder_4

value: Male

value: blood

value: Responder to SSRI combination with antipsychotic

value: Fluvoxamine 300mg Risperidone 1mg


title: non-cancerous, FFPE, Patient 11, renal biopsy

description:
NF11
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: cancerous, RNAlater, Patient 10, renal biopsy

description:
TR10
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 10


title: non-cancerous, RNAlater, Patient 11, renal biopsy

description:
NR11
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: cancerous, FFPE, Patient 10, renal biopsy

description:
TF10
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: non-cancerous, RNAlater, Patient 10, renal biopsy

description:
NR10
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: non-cancerous, FFPE, Patient 10, renal biopsy

description:
NF10
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: cancerous, RNAlater, Patient 9, renal biopsy

description:
TR9
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

value: patient 9


title: non-cancerous, RNAlater, Patient 9, renal biopsy

description:
NR9
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: cancerous, FFPE, Patient 9, renal biopsy

description:
TF9
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single


title: SKBR3_CDCP1-exp1

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

description: Sample name: 9373549087_F

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalized using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

source_name: SKBR3 cell lines overexpressing CDCP1

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent)

tag: genotype/variation

value: overexpressing CDCP1


title: SKBR3_CDCP1-exp2

description: Sample name: 9373549087_H


title: DoHH2 DMSO-2

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

source_name: DOHH2 cell lines treated with DMSO

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with ST1926-derivative ST5589.

value: DMSO


title: SKBR3_CDCP1-exp3

description: Sample name: 9373549087_J


title: SKBR3_GFP-exp2

description: Sample name: 9373549087_B

source_name: SKBR3 control cell line

value: control


title: SKBR3_GFP-exp3

description: Sample name: 9373549087_D


title: DoHH2 ST5589 300nM-2

source_name: DOHH2 cell lines treated with  ST5589 300nM


title: SKBR3_GFP-exp1

description: Sample name: 9373549087_K


title: DoHH2 DMSO-1


title: DoHH2 ST5589 300nM-3


title: DoHH2 ST5589 300nM-1


title: DoHH2 DMSO-3


title: a6-integrin+/CD34+ cells, OT14 PD/S-SCC, biological replicate 1

description: Gene expression data from CSC from PD-SCC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized

scan_protocol: GeneChips were scanned using Gene Chip Operating Software (GCOS 1.2, Affymetrix)

data_processing: The data were analyzed with Bioconductor affy package under statistical R software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale described in Irizarry et al Biostatistics (2003).

source_name: CSCs of PD-SCCs from tumour OT14

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

growth_protocol: Cells were  isolated by sorter-flow cytometer from  orthotopically implanted  skin SCC implanted at different stage of progression

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

treatment_protocol: SCCs used to cancer stem cell isolation were orthotopically engrafted in immunodeficient mice and allowed to growth. Then, tumours from different passages, corresonding a different stage ot tumour progression were excised and tumor cells were disgregated. Tumour cell suspension was depleted from hematopoietic and endothelial cell and  lineages and labelled with antibodies against CD34 and a6-integrin cell surface proteins. Cells showing possitive labelling to these markers were isolated in a AriaFluorescence-activated cell sorting (FACS).

tag: strain

tag: tumor type

value: skin SCC

tag: location

value: orthotopically implanted in nude mice

tag: stage of progression

value: poorly differentiated SCC


title: Blood_obsessive-compulsive disorder_2

tag: gender

tag: tissue

value: Paroxetine 40mg Risperidone 1mg


title: Blood_obsessive-compulsive disorder_3

tag: treatment response

value: Responder to SSRI

tag: dosage

value: Fluvoxamine 300mg


title: TMD8 ST5589 300nM-2

source_name: TMD8 cell lines treated with  ST5589 300nM

tag: treatment


title: a6-integrin+/CD34+ cells, OT14 WD-SCC, biological replicate 1

description: Gene expression data from CSC from WD-SCC

source_name: CSCs of WD-SCCs from tumour OT14

value: well differentiated SCC


title: non-cancerous, FFPE, Patient 9, renal biopsy

description:
NF9
Eikrem et al_logcpm_matrix_filtered.txt
Eikrem et al_count_matrix.txt
read length: 50
read (single or paired-end): single

source_name: renal biopsy

value: non-cancerous

value: FFPE

value: I

value: Partial

value: male


title: TMD8 ST5589 300nM-3

tag: cell line


title: TMD8 ST5589 300nM-1


title: a6-integrin+/CD34+ cells, OT7 PD/S-SCC, biological replicate 2

source_name: CSCs of PD-SCCs from tumour OT7


title: a6-integrin+/CD34+ cells, OT7 PD/S-SCC, biological replicate 1


title: Poly IC-only treatment of HT-29 cells_4

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

country: Canada

institute: Lallemand Health Solutions Inc.

description: Poly IC-only

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50oC for 18h on the whole human gene expression microarrays version 2 Agilent microaray (GE 4x44K; GPL10332).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with ImaGene® microarray analysis software.

data_processing:
Global LOWESS normalization was conducted with ImaGene® microarray analysis software. Statistical analysis (T-test) was performed with Multi-Experiment Viewer (MeV, version 4.2).

The Sample supplementary .txt file includes the quantified normalized data before data analysis (e.g., log2 fold and T-test analysis). The Sample data table includes the raw log2fold changes before statistical analysis using T-test from MeV.

source_name: Control Rep 4

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript III (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Burlington, ON, Canada) following manufacturer's protocol and with PhaseLock tubes (5 Prime, Gaithersburg, MD) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, Germantown, MD). Quality was assessed by Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). RIN over 9.0 were considered good quality RNA for reverse transcription.

treatment_protocol: HT-29 cells were incubated for 3 h with with either the single strains (R0033, R0052 or R0071), probiotic combination (PC), R0052-SLP (38µg/ml) alone or in combination with poly (I:C) at 10 µg/mL at a MOI of 100:1.

tag: cell type

value: Colonic adenocarcinoma cells

value: unchallenged HT-29 cells

source_name: Poly IC Rep 4

value: 3h incubation of HT-29 cells with poly IC


title: TMD8 DMSO-3

source_name: TMD8 cell lines treated with DMSO

value: DMSO


title: TMD8 DMSO-2


title: TMD8 DMSO-1


title: WT_eWAT

city: Tokyo

first: Kazuki

last: Hattori

address: 7-3-1, Hongo, Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

description: Gene expression under normal condition. RNA sample pool was derived from 3 individuals.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: WT, eWAT

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample pool was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). RNA quality was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies) and the samples were pooled.

tag: genotype

value: wildtype

value: eWAT

tag: age

value: 10 weeks


title: Poly IC-only treatment of HT-29 cells_2

description: Poly IC-only

source_name: Poly IC Rep 2

source_name: Control Rep 2


title: a6-integrin+/CD34+ cells, OT7 WD-SCC, biological replicate 2

source_name: CSCs of WD-SCCs from tumour OT7

value: skin SCC

value: orthotopically implanted in nude mice


title: Poly IC-only treatment of HT-29 cells_5

description: Poly IC-only

source_name: Poly IC Rep 1

source_name: Control Rep 1


title: Poly IC-only treatment of HT-29 cells_3

description: Poly IC-only

source_name: Control Rep 3

source_name: Poly IC Rep 3


title: ASK1KO_iBAT

source_name: ASK1KO, iBAT

value: iBAT


title: NP wild type, biological rep3

status: Public on Jan 07 2016

city: Greenville

first: Brett

middle: D

last: Keiper

state: NC

address: 600 Moye Blvd

department: Biochem and Mol Biol

institute: Brody School of Med at ECU

description:
N2np signal (orange)
Set 3 fraction of non-translating mRNA from wild type worms

hyb_protocol: Hybridization according to the standard protocol at UNC Functional Genomics core

scan_protocol: GeneChips were scanned at the UNC Functional Genomics core, Chapel Hill, NC.

data_processing:
Custom Excel spreadsheets were created by AJF for calculating translation ratios, relative (fold) translation changes, and statistics (provided in the 'complete_data.xls)
Comparisons:  Samples were paired (WT and ife-1) for each biological growth set.  Replicate 1 includes samples from gradients for an ife-1 set and a wild type set.  The set includes a wild type non-polysomal measurement (NPw), a wild type polysomal measurement (Pw), an ife-1 non-polysomal measurement (NPi), and an ife-1 polysomal measurement (Pi).
each set of replicate measurements, P values, present/absent calls, and subsequent calculated columns are color coded.  Green header columns are data from Replicate 1, blue are Replicate 2, and orange are Replicate 3. P and A for present/absent calls were replaced by 1 and 0, respectively, for clarity and for mathematical culling.
Data calculations:  [Pw/(NPw+Pw)]=Rw, [Pi/(NPi+Pi)]=Ri, [Rw/Ri]= Relative Fold Change in R (MFR). Summing the non-polysomal and polysomal signals (NP+P) from single replicates allowed similar calculation of mean fold change in total mRNA (MFT).
Affymetrix returned a probe signal output value for each of 22,625 genes. Each gene was tagged as being statistically “present” or “absent” for each of 4 samples (Pw, NPw, Pi, and NPi). Signals flagged as “absent” by Affymetrix in 3 or more of the 4 samples for a single replicate were removed. This analysis was performed in three biological replicates. Any mRNAs that did not pass the “present”/”absent” test in all three replicates were removed from the data set, leaving a representative group of 13,372 mRNAs.

organism: Caenorhabditis elegans

source_name: wild type_mixed worm stages

label_protocol: Labelled cRNA were prepared according to the standard protocol at UNC Functional Genomics core (www.med.unc.edu/corefacilities/functionalgenomics)

growth_protocol: Three day final passage growth at 20C on agar plates with OP50 E coli supplemented with chicken egg yolk.

extract_protocol: Trizol extraction of RNA from each sucrose fraction, pooling, re-extraction with chloroform, and reprecipitation as described in the tsaa overview sheet.

treatment_protocol: Worms were isolated, lysed and resolved on 10-45% sucrose gradients as described in detail in the tsaa overview sheet.

value: wild type, N2

tag: tissue/stage

value: mixed worm, egg, larval stages

tag: molecule subtype

value: fraction of non-translating mRNA; RNA <80S


title: a6-integrin+/CD34+ cells, OT15 WD-SCC, biological replicate 1

city: L'Hospitalet de Llobregat

first: Manel

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

institute: IDIBELL

source_name: CSCs of WD-SCC from tumour OT15

value: well differentiated SCC


title: WT_iBAT

source_name: WT, iBAT


title: ASK1KO_eWAT

source_name: ASK1KO, eWAT


title: P wild type, biological rep3

description:
N2p signal (orange)
Set 3 fraction of translating mRNA from wild type worms

value: fraction of translating mRNA; RNA >80S


title: a6-integrin+/CD34+ cells, OT7 WD-SCC, biological replicate


title: a6-integrin+/CD34+ cells, OT15 PD/S-SCC, biological replicate 1

source_name: CSCs of PD-SCC from tumour OT15

value: poorly differentiated SCC


title: P ife-1, biological rep3

description:
i1p signal (orange)
Set 3 fraction of translating mRNA from ife-1 worms

source_name: ife-1(bn127)_mixed worm stages


title: Poly IC-only treatment of HT-29 cells_1

description: Poly IC-only


title: P ife-1, biological rep2

description:
i1p signal (blue)
Set 2 fraction of translating mRNA from ife-1 worms


title: NP wild type, biological rep2

description:
N2np signal (blue)
Set 2 fraction of non-translating mRNA from wild type worms


title: NP ife-1, biological rep3

description:
i1np signal (orange)
Set 3 fraction of non-translating mRNA from ife-1 worms


title: P wild type, biological rep1

description:
N2p signal (green)
Set 1 fraction of translating mRNA from wild type worms


title: NP ife-1, biological rep2

description:
i1np signal (blue)
Set 2 fraction of non-translating mRNA from ife-1 worms


title: NP wild type, biological rep1

description:
N2np signal (green)
Set 1 fraction of non-translating mRNA from wild type worms


title: P ife-1, biological rep1

description:
i1p signal (green)
Set 1 fraction of translating mRNA from ife-1 worms


title: NP ife-1, biological rep1

description:
i1np signal (green)
Set 1 fraction of non-translating mRNA from ife-1 worms


title: P wild type, biological rep2

description:
N2p signal (blue)
Set 2 fraction of translating mRNA from wild type worms


title: Cox2 KO BMMs in vitro MCSF+RANKL 3days 12r

city: Farmington

first: Carol

last: Pilbeam

state: CT

address: 263 Farmington Avenue

department: Medicine and New England Musculoskeletal Institute

institute: UConn Health

hyb_protocol: Labeled cRNA were hybridized onto  Mouse-8 v2 Illumina BeadChips (Illumina Inc. San Diego, CA) for 16 h at 58 degrees.

scan_protocol: BeadChips were washed, stained with streptavidin-Cy3 and scanned onto the Illumina BeadArray Reader.

data_processing: Raw data were normalized and analyzed using Illumina GenomeStudio software. Quantile normalization, differential expression algorithm and Illumina custom error model were applied to compute Detection p-val and DiffScores. In brief, first, the normalized signal intensity for each sample and each Illumina probe ID were obtained (Sample data tables). And finally, the differential gene expression comparisons, defined as ratio of average signal intensity of a gene for two sample groups, were obtained (please see the comparison data on the Series record, Exp1 (A) and (B) worksheets and the comparison data, Exp 2 (A), (B) and (C) worksheets).

source_name: BMMs from bone marrow

label_protocol: cRNA were labeled with biotin-16-UTP

growth_protocol: Whole marrow from femurs and tibiae was used to isolate BMMs. Briefly, 10 million marrow cells were plated in petri-dishes with alpha-MEM medium, 10% heat inactivated serum and 100 ng/ml M-CSF for 3 days. These cells were expanded twice in 100 ng/ml M-CSF before being plated for the experiment 1and 2.

extract_protocol: Total RNA from BMMs were column purified using the RNAeasy kit (Invitrogen) and RNA quality were verified using Bioanalyzer RNA Nano Chips (Agilent Technologies, Santa Clara, CA). 350 ng of total RNA were reverse transcribed to cDNA using T7 oligo (dt) primer. Second-strand cDNA were synthesized, in vitro transcribed, and labeled with biotin -16-UTP.

treatment_protocol: For both experiments, BMMs were plated in 12 well tissue cultures dishes at 6X104 cells/well and treated as stated in the overall design.

value: Cox2 KO

value: with MCSF+RANKL for 3 days

value: Male

value: 2 month old

tag: experiment

value: Marrow from femurs and tibiae used to isolate BMMs


title: Cox2 KO BMMs in vitro MCSF+RANKL 3days 7

tag: genotype/variation


title: WT BMMs in vitro MCSF+RANKL 3days 2

value: WT

tag: strain


title: WT BMMs in vitro MCSF+RANKL+NS398 3days 18

value: with MCSF+RANKL+NS398 for 3 days


title: WT BMMs in vitro MCSF+RANKL 3days 4


title: WT BMMs in vitro MCSF+RANKL+NS398 3days 17


title: Cox2 KO BMMs in vitro MCSF+RANKL+PGE2 3days 23r

value: with MCSF+RANKL+PGE2 for 3 days


title: WT BMMs in vitro MCSF+RANKL+NS398 3days 13


title: WT BMMs in vitro MCSF+RANKL 1day 11

value: with MCSF+RANKL for 1 day


title: Cox2 KO BMMs in vitro MCSF+RANKL+PGE2 3days 21r


title: Cox2 KO BMMs in vitro MCSF+RANKL 3days 8


title: Cox2 KO BMMs in vitro MCSF+RANKL 3days 11


title: WT BMMs in vitro MCSF only 1day 6

value: with MCSF for 1 day


title: WT BMMs in vitro MCSF+RANKL 3days 3


title: WT BMMs in vitro MCSF+RANKL 3days 6


title: Cox2 KO BMMs in vitro MCSF+RANKL+PGE2 3days 20


title: WT BMMs in vitro MCSF only 1day 3


title: WT BMMs in vitro MCSF+RANKL+NS398 3days 16r


title: Cox2 KO BMMs in vitro MCSF+RANKL 1day 20


title: WT BMMs in vitro MCSF+RANKL 1day 10


title: Cox2 KO BMMs in vitro MCSF+RANKL 1day 21


title: WT BMMs in vitro MCSF only 1day 5


title: WT BMMs in vitro MCSF+RANKL 1day 12


title: Cox2 KO BMMs in vitro MCSF+RANKL 1day 19


title: WT BMMs in vitro MCSF only 1day 2


title: Cox2 KO BMMs in vitro MCSF+RANKL+PGE2 3days 24r